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	✔ A User's Guide to the Encyclopedia of DNA Elements (ENCODE) [Quick Edit] [CiTO] PLoS Biol, Vol. 9, No. 4. (19 April 2011), e1001046, doi:10.1371/journal.pbio.1001046 by The ENCODE Project Consortium posted by 62 people koyanagicl daveGerrard kmdaily provero djkt sriesenfeld aprasad pickw nailest dakelley ahsanur babakap ekrzepka dullhunk druvus lp2 songpku arjun_citeulike BergmanLab shikin gthorisson AaronArvey erschuur ccw20 xingxu akdess bertelsen nklee kshameer fsm guhjy megraw tonamswish davidliwei simonalpha buske daed mysickova absterga Edwards Lab - molecular evolution & bioinformatics cabbagesofdoom myles zhaodj qayub Yanno Jameslz jfr daisukekomura Journal picks antonkratz PollardWall sebastien_vigneau roys cisevol muratsincan tnkysr ajank golharam mespantaleon M_Hasegawa astoddard daforerog Abstract Copy My Attachments My Copy Abstract The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ...
	✔ RNA sequencing: advances, challenges and opportunities [Quick Edit] [CiTO] Nat Rev Genet, Vol. 12, No. 2. (30 February 2011), pp. 87-98, doi:10.1038/nrg2934 by Fatih Ozsolak, Patrice M. Milos posted by 79 people nailest darian arjun_citeulike scchou mikelove natstreet cdsouthan emmameaburn djkt Journal picks 01_pachinko_pagan Eduvernois bitar guhjy gpappas rsantana qayub jgalag provero zivganor dullhunk cantalapiedra sr320 sannenygaard stubrown smgomez SUN_RUPING tonamswish bertelsen dayjm Ciccarelli Lab cicca fenghezi koyanagicl path skjq blueprint-epigenomics jwernegreen ecological genomics seminar sergiodealencar agongdai GustavoLacerda maehler orzenil abhishek_tiwari Hanzhij scleighbrown liuqi515 daforerog giovanni NGS_Array_References seb1 druvus TRHvidsten simonalpha muratsincan giovenko kshameer lauraclarke michaelzeller GeeSharpMinor Diego_Prada shikin aswinsainarain avilella caspertm epigenetics ccristi cmgoodman operon sebastien_vigneau saravana antonkratz eutopia daphnehuang golharam lindenb phoenixzxl scole Abstract Copy My Attachments My Copy Abstract In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing ...
	✔ Computational methods for transcriptome annotation and quantification using RNA-seq [Quick Edit] [CiTO] Nature Methods, Vol. 8, No. 6. (27 May 2011), pp. 469-477, doi:10.1038/nmeth.1613 by Manuel Garber, Manfred G. Grabherr, Mitchell Guttman, Cole Trapnell posted by 70 people lennyheath dullhunk mfrichar SUN_RUPING gdauria fiannell gwallau golharam BioNica tonamswish Journal picks srirampc 2007lab giovanni kclbioinf ongenetics arjun_citeulike fenghezi nosbod nailest duartemolha orzenil farhat shikin gdb sergiodealencar salbougouffa kozillo megraw torfinnnome druvus jessy_ wardweistra jfr path fuadgwadry Gig77 aheilbut maximilianh superhardfuture sotacam sbarbit konrad_foerstner lgatto guhjy shiyongliu djkt udivi kshameer Vincent_Rouilly jainsley avilella gwajnberg luzdary smgomez pickw epigenetics rpiro blueprint-epigenomics squalet GustavoLacerda antonkratz lauraclarke cantalapiedra katussa astoddard Laur705 dakelley Bioinformatics roys Abstract Copy My Attachments My Copy Abstract High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes ...
	✔ A quick guide to large-scale genomic data mining. [Quick Edit] [CiTO] PLoS computational biology, Vol. 6, No. 5. (27 May 2010), e1000779, doi:10.1371/journal.pcbi.1000779 by Curtis Huttenhower, Oliver Hofmann posted by 57 people misonneh MGEL Short Reading guhjy dullhunk ptrobajo farhat rdiaz rtogawa KamilSlowikowski fstrozzi dswan giovenko sotacam rbritto abhishek_tiwari 2007lab corgan Bioinformatics mrvaidya kshameer Galaxy galaxyproject sunhao100 kou_jinsei golharam euclid druvus heliopais rvosa FAB-lab phoenixzxl robertorun giovanni antonkratz lennyheath doaa_altarawy nailest xiaoheilong daforerog neils operon agomez chenmengjie87 Yanno jdreyf Hanzhij jtcribbs karthikraman garson626 Journal picks chvlyl jeremymiller NextGenSeQ dondon kclbioinf nosbod lokesht Copy My Attachments My Copy
	✔ A scaling normalization method for differential expression analysis of RNA-seq data [Quick Edit] [CiTO] Genome Biology, Vol. 11, No. 3. (2 March 2010), R25, doi:10.1186/gb-2010-11-3-r25 by Mark Robinson, Alicia Oshlack posted by 65 people jwfoley orzenil Translational interest scryrps bgranger djkt jforment mhz richrr dakelley shikin fstrozzi cxmmw685 daveGerrard corybarr dswan rpiro kclbioinf lp2 nailest jeanmonlong sotacam astoddard superliwei tonamswish Bioinformatics antonkratz Bioinformatics Core Service golharam guhjy heathervincent avantikalal ikarus97 sebastien_vigneau giovanni zufar chica roys GustavoLacerda jimineep gdr konrad_foerstner davidliwei gdb tmarstrand druvus idonaldson nosbod heliopais Journal picks YukiShindo konradpaszkiewicz chvlyl chenmengjie87 michaelzeller cswarth michafla ptrobajo lwaldron dgu natstreet ivan_kel SUN_RUPING PollardWall tobiasg82 Abstract Copy My Attachments My Copy Abstract The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA. In order to discover biologically important changes in expression, we show that normalization continues to be an essential step in the analysis. We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets. ...
	✔ Full-length transcriptome assembly from RNA-Seq data without a reference genome. [Quick Edit] [CiTO] Nature biotechnology, Vol. 29, No. 7. (15 July 2011), pp. 644-652, doi:10.1038/nbt.1883 by Manfred G. Grabherr, Brian J. Haas, Moran Yassour, et al.Joshua Z. Levin, Dawn A. Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng, Zehua Chen, Evan Mauceli, Nir Hacohen, Andreas Gnirke, Nicholas Rhind, Federica di Palma, Bruce W. Birren, Chad Nusbaum, Kerstin Lindblad-Toh, Nir Friedman, Aviv Regev posted by 71 people ongenetics jforment mikelove osvaldoreisss salaba mfrichar yylin semrich Laur705 dswan operon natstreet srirampc 2007lab agongdai bcondon zhidkov aswinsainarain SUN_RUPING diamantis gjkaur madav Notre Dame Bioinformatics emptyhb 01_pachinko_pagan avilella sujaikumar kentsis salbougouffa lennyheath Journal picks debasis djkt PollardWall torfinnnome fenghezi daveGerrard pickw davidliwei dakelley mbalint pauljaparrigor cantalapiedra cerca sergiodealencar accopeland GustavoLacerda gdauria smgomez dwood NextGenSeQ mgoldman guhjy robinson_jt phoenixzxl rs Bioinformatics Core Service seb1 Schmidtc druvus oannes mtaylo roedelsberg simonalpha dullhunk michaelzeller orzenil nailest kshameer arjun_citeulike fuadgwadry Abstract Copy My Attachments My Copy Abstract Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse ...
	✔ Computational solutions to large-scale data management and analysis. [Quick Edit] [CiTO] Nature reviews. Genetics, Vol. 11, No. 9. (01 September 2010), pp. 647-657, doi:10.1038/nrg2857 by Eric E. Schadt, Michael D. Linderman, Jon Sorenson, Lawrence Lee, Garry P. Nolan posted by 54 people ct586 martingleditzsch adamwebb dullhunk Scis0000002 colinmolter operon karthikraman Yanno seb1 giovanni ptrobajo qfwills Hanzhij golharam phoenixzxl druvus adampah lokesht dgront TRHvidsten lp2 abhishek_tiwari sergiodealencar CoffeeCat poirel klauso galaxyproject alaincoletta daforerog Journal picks martainn Galaxy megraw dswan Bioinformatics peterli shikin steenhoff theboyfree BergmanLab qayub farhat rossmounce davidweisss mafree guhjy antonkratz scryrps nicklynch cisevol htp_drug_discovery dakelley bioinformatics classics Abstract Copy My Attachments My Copy Abstract Today we can generate hundreds of gigabases of DNA and RNA sequencing data in a week for less than US$5,000. The astonishing rate of data generation by these low-cost, high-throughput technologies in genomics is being matched by that of other technologies, such as real-time imaging and mass spectrometry-based flow cytometry. Success in the life sciences will depend on our ability to properly interpret the large-scale, ...
	✔ Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation [Quick Edit] [CiTO] Nature Biotechnology, Vol. 28, No. 5. (2 May 2010), pp. 511-515, doi:10.1038/nbt.1621 by Cole Trapnell, Brian A. Williams, Geo Pertea, et al.Ali Mortazavi, Gordon Kwan, Marijke J. van Baren, Steven L. Salzberg, Barbara J. Wold, Lior Pachter posted by 80 people easih YukiShindo alnnfiai sotacam pickw davidliwei NGS_Array_References agingumbrella srirampc jgarbe shikin sannenygaard giovanni SUN_RUPING nailest nedwards osvaldoreisss ishmael cerca seb1 darshan kozillo timflutre natstreet GustavoLacerda manto aprasad justinhjohnson antonkratz buske torfinnnome fiannell lennyheath jeanmonlong stajich gingi dakelley BlaxterLab AaronArvey semrich avantikalal mfrichar kevinemamy jasontsai chriswallace astoddard scchou tnkysr path EisenLab fenghezi dswan Bolozna kshameer neils orzenil roedelsberg guhjy wardweistra provero Journal picks heliopais sujaikumar Neuroblastoma pauljaparrigor fpattyn brianb daveGerrard drjoey stubrown Schmidtc agongdai accopeland MarkFiers alebalbin lywinter golharam ongenetics cxmmw685 Mycology Abstract Copy My Attachments My Copy Abstract High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed >430 million paired 75-bp RNA-Seq reads from a mouse myoblast cell line over a ...
	✔ Computational methods for discovering structural variation with next-generation sequencing. [Quick Edit] [CiTO] Nature methods, Vol. 6, No. 11 Suppl. (15 November 2009), pp. S13-S20, doi:10.1038/nmeth.1374 by Paul Medvedev, Monica Stanciu, Michael Brudno posted by 59 people druvus scole desany SUN_RUPING pickw kshameer fatgarfield Journal picks guhjy kclbioinf accopeland robertrentzsch muratsincan heliopais sameersoi pst jfr mikelove toszko giovenko owenlancaster Jporci diamantis golharam ddahlem sjcockell gdv qayub justinhjohnson siiner chrisamiller tonamswish Ethence dondon debasis farhat seb1 Orengo Group Journal Picks GustavoLacerda nosbod yotamd giovanni Bioinformatics operon michaelbarton n00c GeeSharpMinor Peiyong mmparks shikin cantalapiedra oannes74 kiekyon azazello jasontsai abhishek_tiwari Gig77 isaacturner orzenil Abstract Copy My Attachments My Copy Abstract In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation ...
	✔ From RNA-seq reads to differential expression results [Quick Edit] [CiTO] Genome Biology, Vol. 11, No. 12. (22 December 2010), 220, doi:10.1186/gb-2010-11-12-220 by Alicia Oshlack, Mark Robinson, Matthew Young posted by 59 people sotacam malvikasharan chica vingron szilva mikelove dayjm Ciccarelli Lab dandaman daveGerrard mhz shikin GustavoLacerda Jporci Evangelia epigenetics TRHvidsten konrad_foerstner druvus nailest orzenil shandar tonamswish ongenetics osvaldoreisss giovenko cicca gbloeb daphnehuang cxmmw685 PollardWall ingridfetter nlapalu SUN_RUPING phoenixzxl giovanni richrr djkt cantalapiedra natstreet antonkratz gdb kshameer NGS_Array_References fstrozzi fuadgwadry roedelsberg kclbioinf mlog jimineep nosbod BergmanLab wardweistra GeeSharpMinor farhat Vincent_Rouilly megraw Journal picks dullhunk Abstract Copy My Attachments My Copy Abstract Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression. ...
	✔ Genotype and SNP calling from next-generation sequencing data [Quick Edit] [CiTO] Nat Rev Genet, Vol. 12, No. 6. (18 June 2011), pp. 443-451, doi:10.1038/nrg2986 by Rasmus Nielsen, Joshua S. Paul, Anders Albrechtsen, Yun S. Song posted by 44 people slack---line idonaldson daed Ciccarelli Lab edotter jeanmonlong shikin golharam kshameer smiddha daforerog cicca epigenetics loopback007 songpku LucioAlencar jameswasmuth smgomez natstreet MBekritsky shaas szilva diamantis lokesht misonneh torfinnnome nickolay path simonalpha Gig77 dakelley druvus arjun_citeulike lennyheath dswan muratsincan Florenceg huangkiekyon orzenil Journal picks nailest alexanderzelikovsky pickw giovanni Abstract Copy My Attachments My Copy Abstract Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies. ...
	✔ Initial impact of the sequencing of the human genome. [Quick Edit] [CiTO] Nature, Vol. 470, No. 7333. (10 February 2011), pp. 187-197, doi:10.1038/nature09792 by Eric S. Lander posted by 46 people druvus ongenetics BlaxterLab lp2 cdsouthan sukuM johnomics minseven tiberio daforerog karthikraman yockeyc1 ricardoaugusto Yanno kshameer chuuc0 ammurira Ciccarelli Lab brucecochrane heathervincent ajaymalik misonneh guhjy cabbagesofdoom thompsonneildoman tonamswish cisevol cdj39 LeilaTA koyanagicl seb1 Journal picks provero colinmolter operon daed dakelley cicca tlehto BergmanLab giovanni Bioinformatics theboyfree brianb dullhunk TRHvidsten Abstract Copy My Attachments My Copy Abstract The sequence of the human genome has dramatically accelerated biomedical research. Here I explore its impact, in the decade since its publication, on our understanding of the biological functions encoded in the genome, on the biological basis of inherited diseases and cancer, and on the evolution and history of the human species. I also discuss the road ahead in fulfilling the promise of genomics for ...
	✔ Computation for ChIP-seq and RNA-seq studies [Quick Edit] [CiTO] Nat Meth In Nat Meth, Vol. 6, No. 11s. (15 November 2009), pp. S22-S32, doi:10.1038/nmeth.1371 by Shirley Pepke, Barbara Wold, Ali Mortazavi posted by 76 people heathervincent ongenetics xueliangwei inesdesantiago molnet-macs urgi abhishek_tiwari stubrown maximilianh antluiz jameswasmuth molnet-mna alebalbin kshameer golharam TorstenWaldminghaus GustavoLacerda aprasad Orengo Group Journal Picks agbiotec chvlyl jfr rschulz robertrentzsch hzoltan mpizbioinfo giovenko sebastien_vigneau ACGT2010_NGSinstrumentsAndAlgorithms polivares Sherman_Lab Hanzhij cajunsushi rneches phansen druvus manduca darian ikarus97 02_ceuratrans pauljaparrigor GeeSharpMinor sotacam avilella xingxu martainn heliopais Sheidan Baschl lennyheath muratsincan epigenetics idonaldson mfrichar guhjy debasis n00c TMichael gdb giovanni shikin tobiasg82 nailest jwfoley Vincent_Rouilly tnkysr tonamswish oannes74 farhat justinhjohnson humburg fenghezi pst robertorun lucacozzuto lwaldron Abstract Copy My Attachments My Copy Abstract Genome-wide measurements of protein-DNA interactions and transcriptomes are increasingly done by deep DNA sequencing methods (ChIP-seq and RNA-seq). The power and richness of these counting-based measurements comes at the cost of routinely handling tens to hundreds of millions of reads. Whereas early adopters necessarily developed their own custom computer code to analyze the first ChIP-seq and RNA-seq datasets, a new generation of more sophisticated algorithms and software tools are emerging to assist in the analysis phase of these projects. Here we ...
	✔ Widespread RNA and DNA Sequence Differences in the Human Transcriptome [Quick Edit] [CiTO] Science, Vol. 333, No. 6038. (01 July 2011), pp. 53-58, doi:10.1126/science.1207018 by Mingyao Li, Isabel X. Wang, Yun Li, et al.Alan Bruzel, Allison L. Richards, Jonathan M. Toung, Vivian G. Cheung posted by 53 people sebastien_vigneau heliopais lp2 tcezard khobta cdj39 AaronArvey TRHvidsten mizuki Ciccarelli Lab NextGenSeQ scole jfr operon ongenetics achinerarias Journal picks phoenixzxl druvus mariannemonicadebrito BlaxterLab cicca 2007lab gdb jbhiatt bioexamples shikin koyanagicl arjun_citeulike hyunjin4jc imremager konrad_foerstner rschulz nailest zufar lalpert diamantis provero egonw skjq fenghezi amueller wieceka1 dakelley qayub neils giovanni dullhunk megraw sergiodealencar djkt zhaodj pickw Abstract Copy My Attachments My Copy Abstract The transmission of information from DNA to RNA is a critical process. We compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that of the DNA. All 12 possible categories of discordances were observed. These differences were nonrandom as many sites ...
	✔ The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data [Quick Edit] [CiTO] Genome Research, Vol. 20, No. 9. (01 September 2010), pp. 1297-1303, doi:10.1101/gr.107524.110 by Aaron McKenna, Matthew Hanna, Eric Banks, et al.Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly, Mark A. DePristo posted by 52 people gwallau alnnfiai druvus NextGenSeQ Scis0000002 sujaikumar operon neils n00c darian torfinnnome dakelley antonkratz Ciccarelli Lab agbiotec stubrown heliopais sergiodealencar TRHvidsten Bioinformatics natstreet Hanzhij golharam ramonvidal2 PollardWall BlaxterLab dswan gdb petkraw guhjy fuadgwadry roys APRegier diamantis gdauria abhishek_tiwari kamilkonowalik dzunkova maren fawn giovanni djkt GeeSharpMinor kshameer 2007lab muratsincan RFMcC orzenil Gig77 roedelsberg shikin fiannell Abstract Copy My Attachments My Copy Abstract An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms ...
	✔ Assembly algorithms for next-generation sequencing data. [Quick Edit] [CiTO] Genomics, Vol. 95, No. 6. (06 June 2010), pp. 315-327, doi:10.1016/j.ygeno.2010.03.001 by Jason R. Miller, Sergey Koren, Granger Sutton posted by 72 people farhat ayansamanta michaelbarton robsyme mbalint dswan azazello davidmam fstrozzi epigenetics aprasad shikin accopeland isaacturner pablocarb darian lennyheath seb1 natstreet isimpson Karljv jablackshaw alexbowe cantalapiedra SciLifeLab Stockholm swear000 wolbachia gorifabio APRegier thiago_r Ethence Bioinformatics agongdai muratsincan alnnfiai snow88935 PollardWall kamilkonowalik epermal avilella druvus dzunkova fawn skembel operon zhuojie scryrps dutilh bluto Journal picks djkt Hanzhij ongenetics elzed phoenixzxl bobherbst scchou abhishek_tiwari sujaikumar giovenko mwinz n00c mpizbioinfo kfrousios brking69 torfinnnome bobcottingham kou_jinsei dullhunk kshameer torbennielsen hroest Abstract Copy My Attachments My Copy Abstract The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing ...
	✔ Network medicine: a network-based approach to human disease. [Quick Edit] [CiTO] Nature reviews. Genetics, Vol. 12, No. 1. (01 January 2011), pp. 56-68, doi:10.1038/nrg2918 by Albert-László L. Barabási, Natali Gulbahce, Joseph Loscalzo posted by 53 people tunepers guhjy hyeyoungcho kshameer abhishek_tiwari provero theboyfree rpiro tonamswish vvoorr karthikraman hwangwoochang yaredo Journal picks egonw kaarsinogen Scis0000002 cdsouthan BISL swmason ddahlem epmp MartinMcDonald tomhebbron seb1 daed phoenixzxl tmmurali Bolozna qayub dakelley heathervincent tozammel apocapoc fenghezi sebastien_vigneau pablocarb shikin BT5240: Computational Systems Biology peterli jcrump daforerog megraw smgomez skjq lokesht misonneh jimineep schwartzjmc pmcmullen krzstefaniak eesruiz Bioinformatics Abstract Copy My Attachments My Copy Abstract Given the functional interdependencies between the molecular components in a human cell, a disease is rarely a consequence of an abnormality in a single gene, but reflects the perturbations of the complex intracellular and intercellular network that links tissue and organ systems. The emerging tools of network medicine offer a platform to explore systematically not only the molecular complexity of a particular disease, leading to ...
	✔ The case for cloud computing in genome informatics [Quick Edit] [CiTO] Genome Biology, Vol. 11, No. 5. (5 May 2010), 207, doi:10.1186/gb-2010-11-5-207 by Lincoln Stein posted by 58 people Galaxy galaxyproject Journal picks manikath MarkFiers LucioAlencar gthorisson BlaxterLab abhishek_tiwari agbiotec torfinnnome farhat rossmounce Bioinformatics maximilianh shikin rdiaz hark tonamswish hagechouchin443 dullhunk Hanzhij mschatz seb1 jamesmorris agomez oinizan CoffeeCat n00c druvus cerami chvlyl tnhh ShantanuPal walshtp avilella daforerog phoenixzxl johnomics seong-hyeuknam dutilh operon SciLifeLab Stockholm nicklynch andrea_bio MReyad kshameer diamantis rvosa jfr pekrau justinhjohnson mikel_egana FAB-lab mgssal antonio-pgarcia irishoconnor AndrewPoirrette Abstract Copy My Attachments My Copy Abstract With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud. ...
	✔ Tackling the widespread and critical impact of batch effects in high-throughput data. [Quick Edit] [CiTO] Nature reviews. Genetics, Vol. 11, No. 10. (14 October 2010), pp. 733-739, doi:10.1038/nrg2825 by Jeffrey T. Leek, Robert B. Scharpf, Héctor Corrada C. Bravo, et al.David Simcha, Benjamin Langmead, W. Evan Johnson, Donald Geman, Keith Baggerly, Rafael A. Irizarry posted by 40 people torfinnnome mikelove Journal picks maximilianh BergmanLab GWAS misonneh ptrobajo sebastien_vigneau dakelley bertelsen cnv cisevol farhat easih blueprint-epigenomics SciLifeLab Stockholm muratsincan zufar djkt neils timflutre fenghezi TRHvidsten pekrau qayub vz33 guhjy johncearls mhz minseven idonaldson ppgardne lauraclarke debasis 2007lab Bioinformatics rmk shikin giovanni Abstract Copy My Attachments My Copy Abstract High-throughput technologies are widely used, for example to assay genetic variants, gene and protein expression, and epigenetic modifications. One often overlooked complication with such studies is batch effects, which occur because measurements are affected by laboratory conditions, reagent lots and personnel differences. This becomes a major problem when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. Using both published ...
	✔ Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. [Quick Edit] [CiTO] Nature protocols, Vol. 7, No. 3. (1 March 2012), pp. 562-578, doi:10.1038/nprot.2012.016 by Cole Trapnell, Adam Roberts, Loyal Goff, et al.Geo Pertea, Daehwan Kim, David R. Kelley, Harold Pimentel, Steven L. Salzberg, John L. Rinn, Lior Pachter posted by 53 people wardweistra cantalapiedra jameswasmuth NGS_Array_References farhat aelefsinioti dakelley BioNica tonamswish SUN_RUPING mlog miguelastico mleung djkt daveGerrard nailest nickolay dswan salaba darian phoenixzxl wuchunyan sujaikumar darrenjw gonzalez ongenetics druvus nickholway galaxyproject torfinnnome kshameer golharam GeeSharpMinor guhjy babakap siarheimanakov path drmacgregor operon drjoey IGV idonaldson pickw natstreet hpaces sjcockell lauraclarke slk505 Galaxy roedelsberg rpiro heathervincent blueprint-epigenomics Abstract Copy My Attachments My Copy Abstract Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to ...
	✔ Assemblathon 1: a competitive assessment of de novo short read assembly methods. [Quick Edit] [CiTO] Genome research, Vol. 21, No. 12. (16 December 2011), pp. 2224-2241, doi:10.1101/gr.126599.111 by Dent Earl, Keith Bradnam, John St John, et al.Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken O. Yu, Vince Buffalo, Daniel R. Zerbino, Mark Diekhans, Ngan Nguyen, Pramila Nuwantha N. Ariyaratne, Wing-Kin K. Sung, Zemin Ning, Matthias Haimel, Jared T. Simpson, Nuno A. Fonseca, İnanç Birol, T. Roderick Docking, Isaac Y. Ho, Daniel S. Rokhsar, Rayan Chikhi, Dominique Lavenier, Guillaume Chapuis, Delphine Naquin, Nicolas Maillet, Michael C. Schatz, David R. Kelley, Adam M. Phillippy, Sergey Koren, Shiaw-Pyng P. Yang, Wei Wu, Wen-Chi C. Chou, Anuj Srivastava, Timothy I. Shaw, J. Graham Ruby, Peter Skewes-Cox, Miguel Betegon, Michelle T. Dimon, Victor Solovyev, Igor Seledtsov, Petr Kosarev, Denis Vorobyev, Ricardo Ramirez-Gonzalez, Richard Leggett, Dan MacLean, Fangfang Xia, Ruibang Luo, Zhenyu Li, Yinlong Xie, Binghang Liu, Sante Gnerre, Iain MacCallum, Dariusz Przybylski, Filipe J. Ribeiro, Shuangye Yin, Ted Sharpe, Giles Hall, Paul J. Kersey, Richard Durbin, Shaun D. Jackman, Jarrod A. Chapman, Xiaoqiu Huang, Joseph L. DeRisi, Mario Caccamo, Yingrui Li, David B. Jaffe, Richard E. Green, David Haussler, Ian Korf, Benedict Paten posted by 42 people diguzim emptyhb simonalpha scole Bioinformatics dakelley djkt BergmanLab nickholway michaelbarton accopeland megraw jts aswinsainarain cisevol jforment PollardWall fsm Journal picks pauljaparrigor dposada TRHvidsten shikin Bioinformatics Core Service avilella kshameer orzenil dbk BlaxterLab sujaikumar druvus torfinnnome neils natstreet seb1 pickw leomrtns heathervincent lennyheath phoenixzxl daveGerrard oinizan Abstract Copy My Attachments My Copy Abstract Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina ...
	✔ The Roots of Bioinformatics [Quick Edit] [CiTO] PLoS Comput Biol, Vol. 6, No. 6. (24 June 2010), e1000809, doi:10.1371/journal.pcbi.1000809 by David B. Searls posted by 74 people ct586 bioinformatics classics nailest aheilbut antonio-pgarcia steeleam dullhunk Bioinformatics operon MReyad karthikraman dswan pablocarb yash1 FAB-lab TMichael Gig77 banso golharam phoenixzxl irishoconnor RFMcC orzenil MBekritsky perkeo swmason Hanzhij qfwills sujaikumar kshameer minostro stajich Mycology silberbauer cisevol BergmanLab McNallyR scole JoeVinegar lmichan yuifu tnhh sebwielgoss nanomuthu azureohn tmmurali arsyed egonw chemhackerutm htp_drug_discovery JoseBrox jain applebyb rvosa mrvaidya poirel arpaton alexandreconde mittinatten elvinado chenmengjie87 druvus Sal dynamite_owner daforerog JERollins Yanno LucioAlencar pinney rdiaz farhat TRHvidsten Journal picks pedrobeltrao Copy My Attachments My Copy
	✔ Next-generation transcriptome assembly [Quick Edit] [CiTO] Nature Reviews Genetics, Vol. 12, No. 10. (7 September 2011), pp. 671-682, doi:10.1038/nrg3068 by Jeffrey A. Martin, Zhong Wang posted by 59 people skjq roys UGDG dakelley babakap lennyheath rpiro NGS_Array_References darian toszko Bioinformatics Core Service antonkratz dwood sujaikumar davidliwei pickw druvus MPorsch golharam mingzhi path heathervincent mblaxter GustavoLacerda provero konrad_foerstner dchughes pauljaparrigor nickolay malvikasharan ammurira IanDay torfinnnome avilella SUN_RUPING guhjy michaelzeller agbiotec astoddard cosmixx PabloMarin karthikraman gdr Journal picks operon Laur705 kshameer accopeland jforment cantalapiedra jbhiatt orzenil agongdai BlaxterLab TRHvidsten epigenetics 01_pachinko_pagan simonalpha Gig77 Abstract Copy My Attachments My Copy Abstract Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This ...
	✔ Basic local alignment search tool. [Quick Edit] [CiTO] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410, doi:10.1006/jmbi.1990.9999 by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted by 141 people indigoviolet monkey_boy moborg AustinC APRegier coela florisbuijzen krapnik sjcockell davidng yylin benwei accopeland Callum MolBI drekol969 agongdai parnell mtaschuk TLVincent richter80 bertelsen Blackbeard evaf cjeans wenhan Thaverkamp granujilla dbk-lab dzunkova BioNica EisenLab myui GustavoLacerda pwais mcbla n00c Keksle incovoma Microbial-Ecology T_lab alessandroparini daforerog robert85 esyoun VGreiff danbolser dfdong aschriner Sadgad AnnaHerDu jofiel dragonrez kaarsinogen siebertm beatrizfernandez caporaso arcticrasta balajis jmeppley camster laurabailey thegoose2 idoerg pachorip azazello sujaikumar chburrus mgomes hiec thuanvh RebeccaHamer kazemi rabio RMGraze biomedical-nlp shung john76 gurupoornam epermal daveGerrard nailest mbaddar2 wltrimble nexus23 gracia18 gorifabio henrylin pickw ichbins81 jtomasch wenboj gktaylor maria_hauser treangen Neeperando dutilh timflutre dgront dullhunk rshe PolymeraseI jablackshaw xili03 ea smallBumblebee dfspspirit dwood mschatz eduberrocal johanviklund sobolevnrm renatomilani laurobeltrao jrhill thekungfumonkey Chindok kfrousios isaacturner agbiotec Richmonp niallhaslam fergus humburg timhubbard rpetrenko mmartin C. elegans / WormBase tharris dmp Ayest yas michC CitoJam lusk sgoetz marti ashaytan TOchi jwm alexg Abstract Copy My Attachments My Copy Abstract A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; ...
	✔ Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia [Quick Edit] [CiTO] PLoS Comput Biol, Vol. 7, No. 1. (6 January 2011), e1002001, doi:10.1371/journal.pcbi.1002001 by Philip E. Bourne posted by 67 people arjun_citeulike Cavor MathBio TRHvidsten ongenetics steff_came McCammon stubrown ishmael theboyfree nelas koyanagicl bgo Hanzhij littlelamb dullhunk cabbagesofdoom rsantana flieder PollardWall Journal picks bdessailly jrom sriesenfeld Gig77 rossmounce dbk thiago_r fatgarfield alextrial operon renatomilani torfinnnome Bioinformatics druvus mojin fgb emptyhb irishoconnor dswan neylufer GustavoLacerda tozammel pigironjoe djkt aduong farhat gotgenes bionano yuifu ahmetbakan srthomas vkbelle gorifabio jhyin bitar Edwards Lab - molecular evolution & bioinformatics phoenixzxl golharam Yanno dvasya dlobo guiraldelli barry daforerog ppgardne kshameer Copy My Attachments My Copy
	✔ Genome evolution and adaptation in a long-term experiment with Escherichia coli [Quick Edit] [CiTO] Nature, Vol. 461, No. 7268. (29 October 2009), pp. 1243-1247, doi:10.1038/nature08480 by Jeffrey E. Barrick, Dong S. Yu, Sung H. Yoon, et al.Haeyoung Jeong, Tae K. Oh, Dominique Schneider, Richard E. Lenski, Jihyun F. Kim posted by 66 people mikeeck andreasweller DrRichardBadge druvus BergmanLab diamantis Journal picks treangen iSEEM dbikard Asclepius Garamonfok qayub tjandra josepe nurban sawasthi kintoki dokky gjuggler TorstenWaldminghaus dutilh imchelo TMichael spongelab Hanzhij nzm maren Pedro Martinez EvoDevo lab Barcelona jasontsai aprasad isaacturner timflutre ilyashl Katieleonard venancio ronbun_2009au johanviklund yuki-nagato JoseBrox hawksjohnd jtcribbs rebeccamancy codonusage jhc dennisk gwallau jasonvo robfsouza martainn Meve_Val mamoru kevin_purcell psique pmalkus samubernard biomcgary zwang aaltenburger yyfwuhan jjray djkt lp2 operon michaelbarton richardfranzese Abstract Copy My Attachments My Copy Abstract The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that ...
	✔ Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing [Quick Edit] [CiTO] Science, Vol. 328, No. 5978. (30 April 2010), pp. 636-639, doi:10.1126/science.1186802 by Jared C. Roach, Gustavo Glusman, Arian F. A. Smit, et al.Chad D. Huff, Robert Hubley, Paul T. Shannon, Lee Rowen, Krishna P. Pant, Nathan Goodman, Michael Bamshad, Jay Shendure, Radoje Drmanac, Lynn B. Jorde, Leroy Hood, David J. Galas posted by 43 people nailest druvus ppgardne kou_jinsei daforerog dswan aylwyn dennisk muratsincan paulrejto djkt giovanni yyfwuhan qayub rvosa FAB-lab barry kshameer darian Yanno karthikraman kslibrarian chadhuff Journal picks 2007lab PollardWall NextGenSeQ roedelsberg jessopher Gig77 thomasbleazard daed jzm10nyc pickw Bioinformatics aethelwine chburrus hawksjohnd golharam mrvaidya dakelley torfinnnome merpublic Abstract Copy My Attachments My Copy Abstract We analyzed the whole-genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors (resulting in > 99.999% accuracy), and identify very rare single-nucleotide polymorphisms. We also directly estimated a human intergeneration mutation rate of approximately 1.1 x 10(-8) per position per haploid genome. Both offspring in ...
	✔ Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. [Quick Edit] [CiTO] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 23. (9 June 2009), pp. 9362-9367, doi:10.1073/pnas.0903103106 by Lucia A. Hindorff, Praveen Sethupathy, Heather A. Junkins, et al.Erin M. Ramos, Jayashri P. Mehta, Francis S. Collins, Teri A. Manolio posted by 27 people engelhardt emmameaburn Borelli dakelley kshameer rdiaz daforerog tunepers BergmanLab liqbbi heathervincent kaarsinogen daed provero arjun_citeulike nicholso chriswallace shikin mikelove nailest xingxu misonneh guhjy zufar pkonings jsatkosk cisevol Abstract Copy My Attachments My Copy Abstract We have developed an online catalog of SNP-trait associations from published genome-wide association studies for use in investigating genomic characteristics of trait/disease-associated SNPs (TASs). Reported TASs were common [median risk allele frequency 36%, interquartile range (IQR) 21%-53%] and were associated with modest effect sizes [median odds ratio (OR) 1.33, IQR 1.20-1.61]. Among 20 genomic annotation sets, reported TASs were significantly overrepresented only in nonsynonymous sites ...
	✔ The power of protein interaction networks for associating genes with diseases. [Quick Edit] [CiTO] Bioinformatics (Oxford, England), Vol. 26, No. 8. (15 April 2010), pp. 1057-1063, doi:10.1093/bioinformatics/btq076 by Saket Navlakha, Carl Kingsford posted by 39 people astoddard neils Scis0000002 phoenixzxl kiekyon renatomilani provero abhishek_tiwari nosbod RobertSOakes chenmengjie87 grahamc PollardWall daforerog ess30 Orengo Group Journal Picks eesruiz aschriner zufar hawksjohnd jtcribbs bioinformatics classics daed druvus jimineep kaarsinogen tclough kclbioinf yl191991 annaritz guhjy liblab cisevol tony_c flbarroso djkt Mycology iSEEM sharpton Abstract Copy My Attachments My Copy Abstract Understanding the association between genetic diseases and their causal genes is an important problem concerning human health. With the recent influx of high-throughput data describing interactions between gene products, scientists have been provided a new avenue through which these associations can be inferred. Despite the recent interest in this problem, however, there is little understanding of the relative benefits and drawbacks underlying the proposed techniques. ...
	✔ A global map of human gene expression [Quick Edit] [CiTO] Nat Biotech, Vol. 28, No. 4. (01 April 2010), pp. 322-324, doi:10.1038/nbt0410-322 by Margus Lukk, Misha Kapushesky, Janne Nikkila, et al.Helen Parkinson, Angela Goncalves, Wolfgang Huber, Esko Ukkonen, Alvis Brazma posted by 39 people mikeeck nailest kmdaily dullhunk druvus jfr brianb guhjy heathervincent njciteulike provero arjun_citeulike tonamswish aceol CFriedel phoenixzxl daed kristen carelcad zivganor chrisamiller shikin alaincoletta pedrobeltrao tunepers operon ptrobajo aaltenburger manto natstreet Orengo Group Journal Picks robertrentzsch mikeolero karthikraman idonaldson gjuggler neils GeeSharpMinor Journal picks Abstract Copy My Attachments My Copy Abstract Although there is only one human genome sequence, different genes are expressed in many different cell types and tissues, as well as in different developmental stages or diseases. The structure of this 'expression space' is still largely unknown, as most transcriptomics experiments focus on sampling small regions. ...
	✔ De novo assembly and genotyping of variants using colored de Bruijn graphs [Quick Edit] [CiTO] Nat Genet, Vol. 44, No. 2. (08 February 2012), pp. 226-232, doi:10.1038/ng.1028 by Zamin Iqbal, Mario Caccamo, Isaac Turner, Paul Flicek, Gil McVean posted by 40 people Bioinformatics nailest barry GustavoLacerda inodebruijn lennyheath orzenil jts UGDG timflutre qayub PollardWall druvus natstreet accopeland sujaikumar kaminskipodinski Gig77 dswan kshameer dbk ajaymalik cisevol jforment Bioinformatics Core Service seb1 golharam PabloMarin megraw fsm djkt pbellec SUN_RUPING pickw dullhunk Laur705 dakelley TRHvidsten Journal picks isaacturner Abstract Copy My Attachments My Copy Abstract Detecting genetic variants that are highly divergent from a reference sequence remains a major challenge in genome sequencing. We introduce de novo assembly algorithms using colored de Bruijn graphs for detecting and genotyping simple and complex genetic variants in an individual or population. We provide an efficient software implementation, Cortex, the first de novo assembler capable of assembling multiple eukaryotic genomes simultaneously. Four applications of ...
	✔ Genome structural variation discovery and genotyping. [Quick Edit] [CiTO] Nature reviews. Genetics, Vol. 12, No. 5. (01 May 2011), pp. 363-376, doi:10.1038/nrg2958 by Can Alkan, Bradley P. Coe, Evan E. Eichler posted by 33 people shikin daveGerrard shaas SUN_RUPING isaacturner guhjy scole aswinsainarain ehoogend giovanni golharam epermal muratsincan Journal picks kshameer dakelley tonamswish n00c jeanmonlong mmparks dullhunk kyoohyoungrho seb1 songpku natstreet maximilianh rpiro daforerog simonalpha pickw Gig77 druvus megraw Abstract Copy My Attachments My Copy Abstract Comparisons of human genomes show that more base pairs are altered as a result of structural variation - including copy number variation - than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the ...
	✔ Transcriptome genetics using second generation sequencing in a Caucasian population. [Quick Edit] [CiTO] Nature, Vol. 464, No. 7289. (1 April 2010), pp. 773-777, doi:10.1038/nature08903 by Stephen B. Montgomery, Micha Sammeth, Maria Gutierrez-Arcelus, et al.Radoslaw P. Lach, Catherine Ingle, James Nisbett, Roderic Guigo, Emmanouil T. Dermitzakis posted by 33 people giovanni provero guhjy daveGerrard SeaBird BergmanLab dakelley daed AaronArvey TRHvidsten kshameer avilella druvus pedrobeltrao lp2 daforerog natstreet yyfwuhan jeanmonlong babakap timflutre ongenetics sleighbrown robfsouza PollardWall shikin fenghezi kclbioinf nicholso qilin djkt nosbod matthiasheinig Abstract Copy My Attachments My Copy Abstract Gene expression is an important phenotype that informs about genetic and environmental effects on cellular state. Many studies have previously identified genetic variants for gene expression phenotypes using custom and commercially available microarrays. Second generation sequencing technologies are now providing unprecedented access to the fine structure of the transcriptome. We have sequenced the mRNA fraction of the transcriptome in 60 extended HapMap individuals of European ...
	✔ Genome-wide allele-specific analysis: insights into regulatory variation. [Quick Edit] [CiTO] Nature reviews. Genetics, Vol. 11, No. 8. (22 August 2010), pp. 533-538, doi:10.1038/nrg2815 by Tomi Pastinen posted by 25 people kshameer aswinsainarain qayub guhjy daed sleighbrown provero daforerog druvus xingxu sachanwi812 darian lp2 misonneh djkt natstreet engelhardt chriswillmott Journal picks fenghezi giovanni dakelley jameswasmuth dchughes TRHvidsten Abstract Copy My Attachments My Copy Abstract Functional genomics is rapidly progressing towards the elucidation of elements that are crucial for the cis-regulatory control of gene expression, and population-based studies of disease and gene expression traits are yielding widespread evidence of the influence of non-coding variants on trait variance. Recently, genome-wide allele-specific approaches that harness high-throughput sequencing technology have started to allow direct evaluation of how these cis-regulatory polymorphisms control gene expression ...
	✔ Fast and accurate long-read alignment with Burrows-Wheeler transform. [Quick Edit] [CiTO] Bioinformatics (Oxford, England), Vol. 26, No. 5. (1 March 2010), pp. 589-595, doi:10.1093/bioinformatics/btp698 by Heng Li, Richard Durbin posted by 53 people mmparks cantalapiedra seb1 bertelsen kshameer epermal diamantis unyanee azazello PollardWall polivares daed accopeland natstreet muratsincan FAB-lab rvosa darian Gig77 mschatz jrgardner mikaels goldmanskitchen n00c ccristi RFMcC roys sharpton sdepark scole srirampc dakelley djkt LucioAlencar drcyber balajis farhat torfinnnome druvus APRegier aethelwine tonamswish chrisamiller guteng BergmanLab darshan GustavoLacerda mpetri lp2 jts iSEEM taroleo justinhjohnson Abstract Copy My Attachments My Copy Abstract Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected ...
	✔ Genome sequencing in microfabricated high-density picolitre reactors. [Quick Edit] [CiTO] Nature In Nature, Vol. 437, No. 7057. (15 September 2005), pp. 376-380, doi:10.1038/nature03959 by Marcel Margulies, Michael Egholm, William E. Altman, et al.Said Attiya, Joel S. Bader, Lisa A. Bemben, Jan Berka, Michael S. Braverman, Yi-Ju J. Chen, Zhoutao Chen, Scott B. Dewell, Lei Du, Joseph M. Fierro, Xavier V. Gomes, Brian C. Godwin, Wen He, Scott Helgesen, Chun Heen H. Ho, Chun He H. Ho, Gerard P. Irzyk, Szilveszter C. Jando, Maria L. Alenquer, Thomas P. Jarvie, Kshama B. Jirage, Jong-Bum B. Kim, James R. Knight, Janna R. Lanza, John H. Leamon, Steven M. Lefkowitz, Ming Lei, Jing Li, Kenton L. Lohman, Hong Lu, Vinod B. Makhijani, Keith E. McDade, Michael P. McKenna, Eugene W. Myers, Elizabeth Nickerson, John R. Nobile, Ramona Plant, Bernard P. Puc, Michael T. Ronan, George T. Roth, Gary J. Sarkis, Jan Fredrik F. Simons, John W. Simpson, Maithreyan Srinivasan, Karrie R. Tartaro, Alexander Tomasz, Kari A. Vogt, Greg A. Volkmer, Shally H. Wang, Yong Wang, Michael P. Weiner, Pengguang Yu, Richard F. Begley, Jonathan M. Rothberg posted by 62 people Florenceg shikin farhat wenhan JAShapiro jbhiatt idoerg daforerog michaelbarton jonilaserson pachorip seb1 heliopais dutilh chriswillmott jlgreen iSEEM agongdai testertom Microbial-Ecology emmameaburn cantalapiedra toszko druvus gatech-compgenomics natldawson bpb Dbarker06 sujaikumar wltrimble sandfire katiehumphry GustavoLacerda Green Lab erbon RMGraze jmeppley bjorns natstreet n00c APRegier pmcmullen carpi GIG xingxu leechuck beatrizfernandez mmartin stubrown LucioAlencar isaacturner orzenil rshe azazello alessandrobrozzi dayjm arve balajis AaronDarling treangen usagi-kirin tpreeprem Abstract Copy My Attachments My Copy Abstract The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, ...
	✔ Software for systems biology: from tools to integrated platforms [Quick Edit] [CiTO] Nat Rev Genet, Vol. 12, No. 12. (03 December 2011), pp. 821-832, doi:10.1038/nrg3096 by Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin, Hiroaki Kitano posted by 34 people cppxm kshameer cdsouthan kozo2 mikel_egana galaxyproject ttshinar darrenjw karthikraman tonamswish karlward druvus scook005 TRHvidsten alhufton Journal picks megraw GeeSharpMinor dullhunk lmichan fairybasslet renatomilani egonw misonneh nailest jdreyf guhjy Biiiogeek daveGerrard shikin Galaxy schwartzjmc JeremyZucker skjq Abstract Copy My Attachments My Copy Abstract Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers ...
	✔ edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. [Quick Edit] [CiTO] Bioinformatics (Oxford, England), Vol. 26, No. 1. (1 January 2010), pp. 139-140, doi:10.1093/bioinformatics/btp616 by Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth posted by 38 people tonamswish natstreet pickw jwfoley guhjy darshan Bioinformatics giovanni michaelzeller operon orzenil jimineep daveGerrard nailest jfr fuadgwadry jdutheil ikarus97 Scott2283 mikelove SUN_RUPING mhz shikin antonkratz farhat zhouyu heliopais lwaldron GustavoLacerda jforment sotacam druvus dandaman justinhjohnson Yanno djkt Bioinformatics Core Service hzoltan Abstract Copy My Attachments My Copy Abstract SUMMARY: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression ...
	✔ Human DNA methylomes at base resolution show widespread epigenomic differences. [Quick Edit] [CiTO] Nature In Nature, Vol. 462, No. 7271. (19 November 2009), pp. 315-322, doi:10.1038/nature08514 by Ryan Lister, Mattia Pelizzola, Robert H. Dowen, et al.R. David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R. Nery, Leonard Lee, Zhen Ye, Que-Minh M. Ngo, Lee Edsall, Jessica Antosiewicz-Bourget, Ron Stewart, Victor Ruotti, A. Harvey Millar, James A. Thomson, Bing Ren, Joseph R. Ecker posted by 59 people kshameer easydin pickw devinmhellesen toates provero yuifu Epigenetics YukiShindo ongenetics mamitamura CTCF colinveal frohike daforerog ethanmj liqbbi rschulz clearbluespring tonamswish neils malay hyojinkang viren4388 gderwin timflutre rdillon TMichael Zapparoli daveGerrard MiriamBauer Journal picks qayub dswan gjuggler JLab dennisk tag gdb hagechouchin443 RyuOgawa jonathanmg gbloeb fenghezi polivares BergmanLab megraw djkt roedelsberg jrifon rsaito guhjy greg psebastian Scis0000002 justinhjohnson suizifish akakak jessopher Abstract Copy My Attachments My Copy Abstract DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of ...
	✔ An integrated encyclopedia of DNA elements in the human genome [Quick Edit] [CiTO] Nature, Vol. 489, No. 7414. (05 September 2012), pp. 57-74, doi:10.1038/nature11247 posted by 54 people surajitmicro liuqi515 mikel_egana chica nailest bioinfo_bz dakelley kshameer Bolozna babs-keil valenciabraham lp2 paulbattlestarbible dogentili antonkratz loopback007 omeran isaacturner facarlisle pickw tnkysr fuadgwadry roys khobta qayub Journal picks wangj26 daed babakap nedwards TRHvidsten polivares Yanno hiec dbk sujaikumar shikin gthorisson richrr pablocarb tonamswish fsm djkt dullhunk eng_manee druvus jimineep jjray Información digital 2013-1 heathervincent maria77 timflutre robatlas jwfoley Abstract Copy My Attachments My Copy Abstract The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. ...
	✔ Accurate and comprehensive sequencing of personal genomes [Quick Edit] [CiTO] Genome Research, Vol. 21, No. 9. (01 September 2011), pp. 1498-1505, doi:10.1101/gr.123638.111 by Subramanian S. Ajay, Stephen C. J. Parker, Hatice O. Abaan, Karin V. Fuentes Fajardo, Elliott H. Margulies posted by 38 people nailest muratsincan jason_kennedy kmdaily UGDG PabloMarin simonalpha orzenil bjruef dbensasson daforerog qayub lp2 marti Gig77 kshameer pickw gaosong0329 PollardWall djkt astoddard operon dswan anoopmandaher Ciccarelli Lab torfinnnome aswinsainarain abc623 Journal picks dullhunk gdb jbhiatt golharam giovanni druvus natstreet avilella xwbcn Abstract Copy My Attachments My Copy Abstract An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms ...
	✔ Annotating non-coding regions of the genome [Quick Edit] [CiTO] Nature Reviews Genetics, Vol. 11, No. 8. (13 July 2010), pp. 559-571, doi:10.1038/nrg2814 by Roger P. Alexander, Gang Fang, Joel Rozowsky, Michael Snyder, Mark B. Gerstein posted by 37 people eng_manee daed APRegier kshameer lp2 smiddha vezzi vvoorr dullhunk fstrozzi djkt toates gdr avilella dakelley Journal picks nklee elipapa mhz Orengo Group Journal Picks operon Bioinformatics misonneh musze istevens druvus daforerog 02_ceuratrans Struan_Murray robertrentzsch scole PollardWall tony_c tmmurali tellis antonkratz TRHvidsten Abstract Copy My Attachments My Copy Abstract Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and ...
	✔ De novo assembly of human genomes with massively parallel short read sequencing [Quick Edit] [CiTO] Genome Research, Vol. 20, No. 2. (1 February 2010), pp. 265-272, doi:10.1101/gr.097261.109 by Ruiqiang Li, Hongmei Zhu, Jue Ruan, et al.Wubin Qian, Xiaodong Fang, Zhongbin Shi, Yingrui Li, Shengting Li, Gao Shan, Karsten Kristiansen, Songgang Li, Huanming Yang, Jian Wang, Jun Wang posted by 48 people torfinnnome Bioinformatics mbalint thiago_r n00c stubrown gaosong0329 semrich guhjy alnnfiai vplagnol isaacturner epermal natstreet golharam Journal picks agongdai druvus accopeland seb1 qayub roedelsberg xueliangwei avantikalal justinhjohnson steeleam peterli operon aethelwine djkt darian dakelley kfrousios sannenygaard meanerelk farhat scchou jts Hanzhij kshameer bluto idonaldson amartins orzenil GustavoLacerda owenlancaster jessopher Laur705 Abstract Copy My Attachments My Copy Abstract Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of ...
	✔ A high-resolution map of human evolutionary constraint using 29 mammals [Quick Edit] [CiTO] Nature, Vol. 478, No. 7370. (12 October 2011), pp. 476-482, doi:10.1038/nature10530 by Kerstin Lindblad-Toh, Manuel Garber, Or Zuk, et al.Michael F. Lin, Brian J. Parker, Stefan Washietl, Pouya Kheradpour, Jason Ernst, Gregory Jordan, Evan Mauceli, Lucas D. Ward, Craig B. Lowe, Alisha K. Holloway, Michele Clamp, Sante Gnerre, Jessica Alfoldi, Kathryn Beal, Jean Chang, Hiram Clawson, James Cuff, Federica Di Palma, Stephen Fitzgerald, Paul Flicek, Mitchell Guttman, Melissa J. Hubisz, David B. Jaffe, Irwin Jungreis, W. James Kent, Dennis Kostka, Marcia Lara, Andre L. Martins, Tim Massingham, Ida Moltke, Brian J. Raney, Matthew D. Rasmussen, Jim Robinson, Alexander Stark, Albert J. Vilella, Jiayu Wen, Xiaohui Xie, Michael C. Zody, Kim C. Worley, Christie L. Kovar, Donna M. Muzny, Richard A. Gibbs, Wesley C. Warren, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Ewan Birney, Elliott H. Margulies, Javier Herrero, Eric D. Green, David Haussler, Adam Siepel, Nick Goldman, Katherine S. Pollard, Jakob S. Pedersen, Eric S. Lander, Manolis Kellis posted by 42 people vingron nklee jrobinso roys lokesht Journal picks amueller cicca provero michaelzeller Avilella papers eng_manee colmryan PollardWall djkt sujaikumar astoddard IGV avilella druvus isaacturner koyanagicl jessopher dariabedulina dakelley RajeevVikram aprasad kshameer TRHvidsten drjoey ptrobajo shikin qayub Ciccarelli Lab fsm skjq cappuccinolin1 dullhunk OJKirtley daveGerrard lp2 Gig77 Abstract Copy My Attachments My Copy Abstract The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon ...
	✔ Comparative analysis of algorithms for next-generation sequencing read alignment [Quick Edit] [CiTO] Bioinformatics, Vol. 27, No. 20. (15 October 2011), pp. 2790-2796, doi:10.1093/bioinformatics/btr477 by Matthew Ruffalo, Thomas LaFramboise, Mehmet Koyutürk posted by 38 people giovenko simonalpha rs cantalapiedra Ciccarelli Lab heathervincent muratsincan sjcockell irishoconnor ParkinsonLab_at_MaRS BioNica egatti arjun_citeulike diamantis djkt Gig77 oinizan druvus gaosong0329 petkraw shikin Bioinformatics Core Service SUN_RUPING scole Journal picks TRHvidsten lp2 alnnfiai natstreet drjoey phoenixzxl nailest golharam BergmanLab cisevol dswan operon jforment Abstract Copy My Attachments My Copy Abstract Motivation: The advent of next-generation sequencing (NGS) techniques presents many novel opportunities for many applications in life sciences. The vast number of short reads produced by these techniques, however, pose significant computational challenges. The first step in many types of genomic analysis is the mapping of short reads to a reference genome, and several groups have developed dedicated algorithms and software packages to perform this function. As the developers of these packages optimize their algorithms with respect to various considerations, the ...
	✔ Initial sequencing and analysis of the human genome [Quick Edit] [CiTO] Nature, Vol. 409, No. 6822. (15 February 2001), pp. 860-921, doi:10.1038/35057062 posted by 98 people epigenetics Proteinkinases mqbphcw3 fisherp Gig77 Cortel dgront LabCompMed azazello taroleo 5escarletmdg bicko eng_manee daforerog vplagnol mikeybadr nailest BioNica n00c jts jnemecek kaulms cthachuk nagendraproj astoddard dakelley christoph_standfuss tchaumie mschatz dullhunk LauraEMont pmcmullen jo_davies brant kiekyon mscscpp monik23 aethelwine kcf5 michaeldavid2002 absterga davidsanchezm mlog dragonrez rshe T_lab japrin druvus smichan jmanning2k bozdagd wimufi dutilh walmsley1991 polivares yoanjacquemin timflutre pablocarb ThomasDOtto cmor kentz EduardoSantiago muditha timhubbard sgoetz xdeupi motahari VGreiff psique CIBERLITERATURA UNAM lmichan isaacturner fayroz_farouk haarcuba olympos toxic rsaito reyez petkraw davidweisss aprasad incovoma gg EmmanuelTG accopeland sujaikumar humburg GermanErlenkamp antonkratz Dax42 jecastillo saminda gjuggler TMichael yas djkt micromassive balajis Abstract Copy My Attachments My Copy Abstract The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence. ...
	✔ Insights from genomic profiling of transcription factors [Quick Edit] [CiTO] Nat Rev Genet, Vol. 10, No. 9. (11 September 2009), pp. 605-616, doi:10.1038/nrg2636 by Peggy J. Farnham posted by 50 people druvus fenghezi bsamal GustavoLacerda ayansamanta atulchin aswinsainarain provero danmaclean roedelsberg qayub sleighbrown dakelley Chinnaiyan Lab balajis Richmonp samanthacooper robatlas ggy ericrpaquet nklee pcarbo jameswasmuth PabloMarin giovanni fpattyn heliopais guhjy timflutre mkiyer Jporci 02_ceuratrans avilella idonaldson stubrown natstreet jbhiatt ilyashl Journal picks roys duemcke mwinz AaronArvey maximilianh sebastien_vigneau aaltenburger vingron frohike megraw TRHvidsten Abstract Copy My Attachments My Copy Abstract A crucial question in the field of gene regulation is whether the location at which a transcription factor binds influences its effectiveness or the mechanism by which it regulates transcription. Comprehensive transcription factor binding maps are needed to address these issues, and genome-wide mapping is now possible thanks to the technological advances of ChIP–chip and ChIP–seq. This Review discusses how recent genomic profiling of transcription factors gives insight into how binding specificity is achieved and what features of chromatin influence ...
	✔ Efficient de novo assembly of large genomes using compressed data structures [Quick Edit] [CiTO] Genome Research, Vol. 22, No. 3. (01 March 2012), pp. 549-556, doi:10.1101/gr.126953.111 by Jared T. Simpson, Richard Durbin posted by 41 people polivares djkt jforment roedelsberg sujaikumar BergmanLab orzenil natstreet fsm lennyheath Ciccarelli Lab jts wltrimble darian astoddard druvus mblaxter jbhiatt scole oinizan farhat Gig77 isaacturner Bioinformatics Core Service nickholway thiago_r pickw salaba BlaxterLab inodebruijn cisevol dakelley cantalapiedra GustavoLacerda accopeland dposada NGS_Array_References daveGerrard TRHvidsten Journal picks dullhunk Abstract Copy My Attachments My Copy Abstract An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms ...
	✔ PubMed and beyond: a survey of web tools for searching biomedical literature [Quick Edit] [CiTO] Database, Vol. 2011 (01 January 2011), doi:10.1093/database/baq036 by Zhiyong Lu posted by 41 people Journal picks Biiiogeek cambia benfqt daforerog lynnefox guhjy peony sobolevnrm ajaymalik cisevol jtcribbs henk-cul NIlz zimbo1 Evidence-based-medicine misonneh bgood lesikv dswan cdsouthan A_Carrasco mfenner dullhunk StephanMatthiesen druvus guillermina mikel_egana abhishek_tiwari Gobbledygook BergmanLab neils aheilbut Publicase banso lmichan Gaetan Demeter lxm fairybasslet irenas Abstract Copy My Attachments My Copy Abstract The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology ...
	✔ Improving RNA-Seq expression estimates by correcting for fragment bias [Quick Edit] [CiTO] Genome Biology, Vol. 12, No. 3. (1 September 2011), pp. R22-14, doi:10.1186/gb-2011-12-3-r22 by Adam Roberts, Cole Trapnell, Julie Donaghey, John Rinn, Lior Pachter posted by 41 people joelrosa BlaxterLab ongenetics dandaman Gig77 operon neils daveGerrard siarheimanakov gdb shikin torfinnnome sotacam Journal picks nailest kshameer heathervincent sujaikumar TRHvidsten ptrobajo srirampc lbarquist GustavoLacerda davidliwei cosmixx arjun_citeulike SUN_RUPING astoddard natstreet megraw ikarus97 orzenil PollardWall djkt jforment mikelove dakelley konrad_foerstner timflutre druvus Bioinformatics Core Service Abstract Copy My Attachments My Copy Abstract The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies. ...
	✔ The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants [Quick Edit] [CiTO] Nucleic Acids Research, Vol. 38, No. 6. (1 April 2010), pp. 1767-1771, doi:10.1093/nar/gkp1137 by Peter J. A. Cock, Christopher J. Fields, Naohisa Goto, Michael L. Heuer, Peter M. Rice posted by 44 people andrea_bio hpaces aheilbut druvus gjuggler muratsincan natstreet chburrus sujaikumar seb1 BergmanLab elzed GustavoLacerda meanerelk jmanning2k antonkratz golharam YukiShindo TiagoCites Gig77 orzenil nuin wltrimble n00c LucioAlencar mbalint jfr Journal picks YukaH kmegy oannes dakelley heliopais accopeland kshameer machar farhat Bioinformatics epermal ppgardne daveGerrard justinhjohnson cisevol chriscole Abstract Copy My Attachments My Copy Abstract FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava ...
	✔ A census of human transcription factors: function, expression and evolution [Quick Edit] [CiTO] Nat Rev Genet, Vol. 10, No. 4. (01 April 2009), pp. 252-263, doi:10.1038/nrg2538 by Juan M. Vaquerizas, Sarah K. Kummerfeld, Sarah A. Teichmann, Nicholas M. Luscombe posted by 42 people vingron nklee dakelley avilella oannes sleighbrown PollardWall arjun_citeulike peterli babakap djkt pcarbo jwfoley kaarsinogen absterga ggy PabloMarin provero poirel balajis manto Hashem lwaldron robert85 mysickova isbkramer kshameer marti megraw druvus gjuggler engelhardt nuin Bioinformatics daforerog idonaldson dennisk daveGerrard tony_c AaronArvey kmdaily cassj Abstract Copy My Attachments My Copy Abstract Transcription factors are key cellular components that control gene expression: their activities determine how cells function and respond to the environment. Currently, there is great interest in research into human transcriptional regulation. However, surprisingly little is known about these regulators themselves. For example, how many transcription factors does the human genome contain? How are they expressed in different tissues? Are they evolutionarily conserved? Here, we present an analysis of 1,391 manually curated sequence-specific DNA-binding transcription factors, their functions, genomic organization and ...
	✔ Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. [Quick Edit] [CiTO] Science (New York, N.Y.), Vol. 328, No. 5981. (21 May 2010), pp. 1036-1040, doi:10.1126/science.1186176 by Dominic Schmidt, Michael D. Wilson, Benoit Ballester, et al.Petra C. Schwalie, Gordon D. Brown, Aileen Marshall, Claudia Kutter, Stephen Watt, Celia P. Martinez-Jimenez, Sarah Mackay, Iannis Talianidis, Paul Flicek, Duncan T. Odom posted by 51 people siarheimanakov Journal picks tony_c idonaldson cis-regulatory-evolution ShouyongPeng jjray dutilh TRHvidsten jonathanmg dakelley clearbluespring alhufton Richmonp roedelsberg mwinz adegrass Ensembl Compara citations emptyhb stubrown nklee JeremyZucker isaacturner matthiasheinig mysickova rschulz kmdaily gjuggler djkt sleighbrown szymon_kielbasa rolandkrause BergmanLab cisevol robertrentzsch dullhunk roys ggy paulschlesinger michaelzeller daveGerrard robatlas morgane Orengo Group Journal Picks tmmurali sriesenfeld xwbcn provero vingron avilella PollardWall Abstract Copy My Attachments My Copy Abstract Transcription factors (TFs) direct gene expression by binding to DNA regulatory regions. To explore the evolution of gene regulation, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine experimentally the genome-wide occupancy of two TFs, CCAAT/enhancer-binding protein alpha and hepatocyte nuclear factor 4 alpha, in the livers of five vertebrates. Although each TF displays highly conserved DNA binding preferences, most binding is species-specific, and ...
	✔ Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS [Quick Edit] [CiTO] PLoS Genet, Vol. 6, No. 4. (1 April 2010), e1000888, doi:10.1371/journal.pgen.1000888 by Dan L. Nicolae, Eric Gamazon, Wei Zhang, Shiwei Duan, M. Eileen Dolan, Nancy J. Cox posted by 21 people natstreet tonamswish lp2 djkt pcarbo misonneh colmryan timflutre engelhardt neckart1 nailest PollardWall tony_c songpku giovanni tunepers qilin nicholso chenli xingxu guhjy Abstract Copy My Attachments My Copy Abstract Although genome-wide association studies (GWAS) of complex traits have yielded more reproducible associations than had been discovered using any other approach, the loci characterized to date do not account for much of the heritability to such traits and, in general, have not led to improved understanding of the biology underlying complex phenotypes. Using a web site we developed to serve results of expression quantitative trait locus (eQTL) studies in lymphoblastoid cell lines from HapMap samples (http://www.scandb.org), we show that single nucleotide ...
	✔ An integrated semiconductor device enabling non-optical genome sequencing [Quick Edit] [CiTO] Nature, Vol. 475, No. 7356. (20 July 2011), pp. 348-352, doi:10.1038/nature10242 by Jonathan M. Rothberg, Wolfgang Hinz, Todd M. Rearick, et al.Jonathan Schultz, William Mileski, Mel Davey, John H. Leamon, Kim Johnson, Mark J. Milgrew, Matthew Edwards, Jeremy Hoon, Jan F. Simons, David Marran, Jason W. Myers, John F. Davidson, Annika Branting, John R. Nobile, Bernard P. Puc, David Light, Travis A. Clark, Martin Huber, Jeffrey T. Branciforte, Isaac B. Stoner, Simon E. Cawley, Michael Lyons, Yutao Fu, Nils Homer, Marina Sedova, Xin Miao, Brian Reed, Jeffrey Sabina, Erika Feierstein, Michelle Schorn, Mohammad Alanjary, Eileen Dimalanta, Devin Dressman, Rachel Kasinskas, Tanya Sokolsky, Jacqueline A. Fidanza, Eugeni Namsaraev, Kevin J. McKernan, Alan Williams, G. Thomas Roth, James Bustillo posted by 38 people Florenceg CarlosEH druvus cdsouthan lxm1117 dakelley cantalapiedra konrad_foerstner heathervincent dwhong qayub ankitam kristgy guhjy pickw dayjm simonalpha daveGerrard salbougouffa dutilh alabarga PollardWall djkt aswinsainarain drjoey cabbagesofdoom torfinnnome Journal picks dullhunk sebotic sergiodealencar orzenil sjcockell darian eyliu BergmanLab cisevol seb1 Abstract Copy My Attachments My Copy Abstract The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed ...
	✔ BEDTools: a flexible suite of utilities for comparing genomic features [Quick Edit] [CiTO] Bioinformatics, Vol. 26, No. 6. (15 March 2010), pp. 841-842, doi:10.1093/bioinformatics/btq033 by Aaron R. Quinlan, Ira M. Hall posted by 43 people seb1 jforment iris42 avilella orzenil robfsouza morgane guhjy kshameer mojones GustavoLacerda sujaikumar nailest druvus galaxyproject Galaxy BergmanLab torfinnnome 02_ceuratrans timflutre Bioinformatics dswan jgarbe daveGerrard polivares heliopais Bioinformatics Core Service vz33 n00c daed aprasad SUN_RUPING theboyfree elzed nuin Eduvernois jmanning2k accopeland natstreet siarheimanakov mikelove BlaxterLab path Abstract Copy My Attachments My Copy Abstract Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. ...
	✔ BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. [Quick Edit] [CiTO] Nature methods, Vol. 6, No. 9. (09 September 2009), pp. 677-681, doi:10.1038/nmeth.1363 by Ken Chen, John W. Wallis, Michael D. McLellan, et al.David E. Larson, Joelle M. Kalicki, Craig S. Pohl, Sean D. McGrath, Michael C. Wendl, Qunyuan Zhang, Devin P. Locke, Xiaoqi Shi, Robert S. Fulton, Timothy J. Ley, Richard K. Wilson, Li Ding, Elaine R. Mardis posted by 45 people sitalange natstreet daed Leaflet orzenil dutilh isaacturner maren pickw siiner Journal picks golharam kclbioinf mwinz rneches balajis diamantis darian yylin aheilbut tonamswish muratsincan kshameer chburrus danmaclean MCB-CNV operon dakelley fenghezi jasontsai mmparks jeanmonlong accopeland gdb nosbod druvus captaineguy qayub SUN_RUPING ayansamanta shikin roedelsberg heliopais n00c stubrown Abstract Copy My Attachments My Copy Abstract Detection and characterization of genomic structural variation are important for understanding the landscape of genetic variation in human populations and in complex diseases such as cancer. Recent studies demonstrate the feasibility of detecting structural variation using next-generation, short-insert, paired-end sequencing reads. However, the utility of these reads is not entirely clear, nor are the analysis methods with which accurate detection can be achieved. The algorithm ...
	✔ Exome sequencing identifies the cause of a mendelian disorder [Quick Edit] [CiTO] Nature Genetics In Nat Genet, Vol. 42, No. 1. (13 November 2009), pp. 30-35, doi:10.1038/ng.499 by Sarah B. Ng, Kati J. Buckingham, Choli Lee, et al.Abigail W. Bigham, Holly K. Tabor, Karin M. Dent, Chad D. Huff, Paul T. Shannon, Ethylin W. Jabs, Deborah A. Nickerson, Jay Shendure, Michael J. Bamshad posted by 36 people FranziMe guhjy stubrown daforerog n00c chrisamiller pekrau balajis kclbioinf kfrousios chburrus psique tonamswish avilella sergiodealencar operon kshameer nosbod dswan vplagnol cajunsushi absterga muratsincan frohike Peiyong druvus pickw darian golharam jame0taylor chadhuff shikin pst seb1 Yanno kuma0077 Abstract Copy My Attachments My Copy Abstract We demonstrate the first successful application of exome sequencing to discover the gene for a rare mendelian disorder of unknown cause, Miller syndrome (MIM%263750). For four affected individuals in three independent kindreds, we captured and sequenced coding regions to a mean coverage of 40x and sufficient depth to call variants at approximately 97% of each targeted exome. Filtering against public SNP databases and eight HapMap ...
	✔ Integration and visualization of systems biology data in context of the genome. [Quick Edit] [CiTO] BMC bioinformatics, Vol. 11, No. 1. (19 July 2010), 382, doi:10.1186/1471-2105-11-382 by J. Christopher Bare, Tie Koide, David J. Reiss, Dan Tenenbaum, Nitin S. Baliga posted by 27 people jforment farhat scryrps jildau IGV neils daforerog rneches guhjy dullhunk shikin sillitoe rcr1991 rbritto Scott2283 cisevol kshameer Bioinformatics Core Service druvus erexhepa misonneh phoenixzxl Journal picks Orengo Group Journal Picks karthikraman Bioinformatics nuin Abstract Copy My Attachments My Copy Abstract High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. The Gaggle ...
	✔ Genetic analysis of variation in transcription factor binding in yeast. [Quick Edit] [CiTO] Nature, Vol. 464, No. 7292. (22 April 2010), pp. 1187-1191, doi:10.1038/nature08934 by Wei Zheng, Hongyu Zhao, Eugenio Mancera, Lars M. Steinmetz, Michael Snyder posted by 30 people yyfwuhan raiyar cis-regulatory-evolution daed lp2 dakelley roys gdb provero emptyhb dullhunk pedrobeltrao TRHvidsten jtcribbs chvlyl rdowell karthikraman Journal picks jjray seaver mjoach megraw djkt PollardWall mox cambray chris cisevol AaronArvey songpku Abstract Copy My Attachments My Copy Abstract Variation in transcriptional regulation is thought to be a major cause of phenotypic diversity. Although widespread differences in gene expression among individuals of a species have been observed, studies to examine the variability of transcription factor binding on a global scale have not been performed, and thus the extent and underlying genetic basis of transcription factor binding diversity is unknown. By mapping differences in transcription ...
	✔ A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies [Quick Edit] [CiTO] PLoS ONE, Vol. 6, No. 3. (14 March 2011), e17915, doi:10.1371/journal.pone.0017915 by Wenyu Zhang, Jiajia Chen, Yang Yang, Yifei Tang, Jing Shang, Bairong Shen posted by 38 people n00c BergmanLab jmeppley farhat kamilkonowalik CorinYeats gwallau zhaodj orzenil GustavoLacerda mfrichar natstreet simonalpha indignacious rvosa natldawson BlaxterLab daisukekomura avilella abhishek_tiwari fuadgwadry hspitia oinizan dullhunk FAB-lab operon druvus cisevol aheilbut Journal picks sujaikumar aldens mblaxter NGS Orengo Group Journal Picks walshtp kshameer seb1 Abstract Copy My Attachments My Copy Abstract The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, ...
	✔ Efficient storage of high throughput DNA sequencing data using reference-based compression [Quick Edit] [CiTO] Genome Research, Vol. 21, No. 5. (1 May 2011), pp. 734-740, doi:10.1101/gr.114819.110 by Markus Hsi-Yang Fritz, Rasko Leinonen, Guy Cochrane, Ewan Birney posted by 39 people accopeland timhubbard abhishek_tiwari jforment Bioinformatics Core Service gdb pickw lennyheath Ciccarelli Lab jwfoley pauljaparrigor nickholway 2007lab aheilbut guhjy natstreet SUN_RUPING Scis0000002 hillan NextGenSeQ Bioinformatics kshameer Orengo Group Journal Picks philcarter fsm operon golharam neils PollardWall djkt koyanagicl oinizan druvus farhat cicca johanviklund dullhunk Journal picks giovenko Abstract Copy My Attachments My Copy Abstract Data storage costs have become an appreciable proportion of total cost in the creation and analysis of DNA sequence data. Of particular concern is that the rate of increase in DNA sequencing is significantly outstripping the rate of increase in disk storage capacity. In this paper we present a new reference-based compression method that efficiently compresses DNA sequences for storage. Our approach works for resequencing experiments that target well-studied genomes. We align new sequences to a reference genome and then encode ...
	✔ A comprehensive catalogue of somatic mutations from a human cancer genome. [Quick Edit] [CiTO] Nature, Vol. 463, No. 7278. (14 January 2010), pp. 191-196, doi:10.1038/nature08658 by Erin D. Pleasance, R. Keira Cheetham, Philip J. Stephens, et al.David J. McBride, Sean J. Humphray, Chris D. Greenman, Ignacio Varela, Meng-Lay L. Lin, Gonzalo R. Ordóñez, Graham R. Bignell, Kai Ye, Julie Alipaz, Markus J. Bauer, David Beare, Adam Butler, Richard J. Carter, Lina Chen, Anthony J. Cox, Sarah Edkins, Paula I. Kokko-Gonzales, Niall A. Gormley, Russell J. Grocock, Christian D. Haudenschild, Matthew M. Hims, Terena James, Mingming Jia, Zoya Kingsbury, Catherine Leroy, John Marshall, Andrew Menzies, Laura J. Mudie, Zemin Ning, Tom Royce, Ole B. Schulz-Trieglaff, Anastassia Spiridou, Lucy A. Stebbings, Lukasz Szajkowski, Jon Teague, David Williamson, Lynda Chin, Mark T. Ross, Peter J. Campbell, David R. Bentley, P. Andrew Futreal, Michael R. Stratton posted by 33 people nailest druvus pickw mysickova daed neils frohike owenlancaster songpku renatomilani alaincoletta jame0taylor isaacturner eisei BioNica n00c japrin guhjy srp33 cdsouthan mskathleen bertelsen golharam sebotic kuma0077 njciteulike chrisamiller dakelley Annab wkretzsch bpcusack ealloza pavanghatty Abstract Copy My Attachments My Copy Abstract All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights ...
	✔ An integrated map of genetic variation from 1,092 human genomes [Quick Edit] [CiTO] Nature, Vol. 491, No. 7422. (31 October 2012), pp. 56-65, doi:10.1038/nature11632 posted by 31 people cdsouthan kshameer lp2 brianb PabloMarin Journal picks qayub AaronArvey muratsincan vb1 isbkramer nailest djkt jfr gsaunders pickw dullhunk repeaterphone jtcribbs fergus guhjy jeanmonlong mmparks Terkko UGDG druvus dakelley wieceka1 rdillon daforerog dswan Abstract Copy My Attachments My Copy Abstract By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide ...
	✔ An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man [Quick Edit] [CiTO] Cell, Vol. 140, No. 5. (5 March 2010), pp. 744-752, doi:10.1016/j.cell.2010.01.044 by Timothy Ravasi, Harukazu Suzuki, Carlo V. Cannistraci, et al.Shintaro Katayama, Vladimir B. Bajic, Kai Tan, Altuna Akalin, Sebastian Schmeier, Mutsumi Kanamori-Katayama, Nicolas Bertin, Piero Carninci, Carsten O. Daub, Alistair R. R. Forrest, Julian Gough, Sean Grimmond, Jung-Hoon Han, Takehiro Hashimoto, Winston Hide, Oliver Hofmann, Atanas Kamburov, Mandeep Kaur, Hideya Kawaji, Atsutaka Kubosaki, Timo Lassmann, Erik van Nimwegen, Cameron R. MacPherson, Chihiro Ogawa, Aleksandar Radovanovic, Ariel Schwartz, Rohan D. Teasdale, Jesper Tegnér, Boris Lenhard, Sarah A. Teichmann, Takahiro Arakawa, Noriko Ninomiya, Kayoko Murakami, Michihira Tagami, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ryoko Ishihara, Yayoi Kitazume, Jun Kawai, David A. Hume, Trey Ideker, Yoshihide Hayashizaki posted by 44 people grahamc seaver mysickova ayansamanta meldon absterga szymon_kielbasa bertelsen cisevol qayub michaelzeller sriesenfeld kshameer zhanglimdacc alhufton dutilh ajank lp2 PollardWall DNA repair and transcription roys khobta balabu arjun_citeulike jonathanmg taherl djkt provero guhjy lokesht avilella maximilianh roedelsberg dakelley isbkramer YukiShindo biomcgary vingron BergmanLab daveGerrard klein_h gbloeb Journal picks leelarcombe Abstract Copy My Attachments My Copy Abstract Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of ...
	✔ Limitations of next-generation genome sequence assembly [Quick Edit] [CiTO] Nature Methods, Vol. 8, No. 1. (21 November 2010), pp. 61-65, doi:10.1038/nmeth.1527 by Can Alkan, Saba Sajjadian, Evan E. Eichler posted by 44 people pedrobeltrao Rodrigocorrea elzed johnomics konrad_foerstner SUN_RUPING Hanzhij machar konradpaszkiewicz sinhashruti avilella pickw Ciccarelli Lab yylin dakelley operon heliopais Journal picks kozo2 thiago_r fiannell 01_pachinko_pagan APRegier accopeland sujaikumar lennyheath orzenil zufar bertelsen disteld druvus kshameer scole porejide natstreet abhishek_tiwari BlaxterLab LucioAlencar n00c seb1 qayub Bioinformatics michaelbarton cdsouthan Abstract Copy My Attachments My Copy Abstract High-throughput sequencing technologies promise to transform the fields of genetics and comparative biology by delivering tens of thousands of genomes in the near future. Although it is feasible to construct de novo genome assemblies in a few months, there has been relatively little attention to what is lost by sole application of short sequence reads. We compared the recent de novo assemblies using the short ...
	✔ Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. [Quick Edit] [CiTO] Nature methods, Vol. 6, No. 9. (02 September 2009), pp. 673-676, doi:10.1038/nmeth.1358 by Arthur Brady, Steven L. Salzberg posted by 39 people mikeeck Orengo Group Journal Picks azazello dutilh rneches setubal esyoun Mycology salbougouffa matsen sharpton Journal picks gorifabio stajich wltrimble aschriner jbhiatt AaronDarling natldawson djkt robertrentzsch skennedy8 01_pachinko_pagan dakelley skembel virushunter CorinYeats avilella rebeccamaelamb sriesenfeld bluto iSEEM elipapa seb1 Thaverkamp jmeppley druvus chburrus idoerg Abstract Copy My Attachments My Copy Abstract Metagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a sample. New sequencing technologies have made metagenomics easier, by making sequencing faster, and more difficult, by ...
	✔ CNV-seq, a new method to detect copy number variation using high-throughput sequencing [Quick Edit] [CiTO] BMC Bioinformatics, Vol. 10, No. 1. (2009), 80, doi:10.1186/1471-2105-10-80 by Chao Xie, Martti Tammi posted by 42 people operon MCB-CNV cthachuk steeleam neils Bioinformatics svenrahmann sameersoi darian stubrown Ethence eutopia GustavoLacerda kshameer thomasbleazard xiechao pickw natstreet polivares path shikin rdiaz bmenten n00c hzoltan Sheidan mikelove slakov vplagnol dakelley owenlancaster guhjy justinhjohnson druvus orzenil humburg biovils semrich pkonings dswan sleepingcell magusina Abstract Copy My Attachments My Copy Abstract BACKGROUND:DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations.RESULTS:Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the ...
	✔ Cloud computing and the DNA data race [Quick Edit] [CiTO] Nature Biotechnology, Vol. 28, No. 7. (01 July 2010), pp. 691-693, doi:10.1038/nbt0710-691 by Michael C. Schatz, Ben Langmead, Steven L. Salzberg posted by 42 people brianb Journal picks chenmengjie87 cisevol rolandkrause guhjy APRegier LucioAlencar cerami mschatz seb1 CoffeeCat cantalapiedra vingron Hanzhij neoblue77 megraw yash1 andrea_bio mliroz Yanno rtogawa BergmanLab jfr BlaxterLab sujaikumar dullhunk sjcockell ppgardne galaxyproject Galaxy nedwards Bioinformatics scole abhishek_tiwari n00c ongenetics agbiotec cabbagesofdoom druvus perkeo gthorisson Abstract Copy My Attachments My Copy Abstract Given the accumulation of DNA sequence data sets at ever-faster rates, what are the key factors you should consider when using distributed and multicore computing systems for analysis? In the race between DNA sequencing throughput and computer speed, sequencing is winning by a mile. Sequencing throughput has recently been improving at a rate of about fivefold per year1, whereas computer performance generally follows 'Moore's Law', doubling only every 18 or 24 months2. ...
	✔ Gene ontology analysis for RNA-seq: accounting for selection bias [Quick Edit] [CiTO] Genome Biology, Vol. 11, No. 2. (4 February 2010), R14, doi:10.1186/gb-2010-11-2-r14 by Matthew Young, Matthew Wakefield, Gordon Smyth, Alicia Oshlack posted by 36 people nailest nanonan gdb pickw Bioinformatics Bioinformatics Core Service druvus 01_pachinko_pagan TRHvidsten ishmael guhjy cxmmw685 djkt jforment dgu sotacam konrad_foerstner idonaldson golharam GustavoLacerda mikelove ikarus97 venancio ShouyongPeng PollardWall acadaccts kimbie dswan antonkratz dandaman avilella natstreet kshameer MVEverett mpizbioinfo kclbioinf Abstract Copy My Attachments My Copy Abstract We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology. ...
	✔ The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease [Quick Edit] [CiTO] Science, Vol. 313, No. 5795. (29 September 2006), pp. 1929-1935, doi:10.1126/science.1132939 by Justin Lamb, Emily D. Crawford, David Peck, et al.Joshua W. Modell, Irene C. Blat, Matthew J. Wrobel, Jim Lerner, Jean-Philippe Brunet, Aravind Subramanian, Kenneth N. Ross, Michael Reich, Haley Hieronymus, Guo Wei, Scott A. Armstrong, Stephen J. Haggarty, Paul A. Clemons, Ru Wei, Steven A. Carr, Eric S. Lander, Todd R. Golub posted by 59 people kengg yas AbnerCYH gbloeb ilyashl sgoetz koikoi steenhoff giovenko peterli mox BragilMassoud jeremymiller cdsouthan shikin aheilbut ipark-kaist ezra daforerog zufar Plantandetc koller Dulcinea GeschwindLab mitko balajis askrajiv daed marcius mingzhi uknandal2010 bertelsen lhonigberg jfr jdiggans egonw ealloza daveGerrard Yanno massivemayhem mlovell pablomendes juusoparkkinen yaredo BioinfoCIPF T_lab Bioinformatics Computational-Genomics Biostatistics lp2 cmap Neuroscience venomousanimal dansullivanblk guhjy kuhn neveaire frohike SGU-CIPF Abstract Copy My Attachments My Copy Abstract To pursue a systematic approach to the discovery of functional connections among diseases, genetic perturbation, and drug action, we have created the first installment of a reference collection of gene-expression profiles from cultured human cells treated with bioactive small molecules, together with pattern-matching software to mine these data. We demonstrate that this “Connectivity Map” resource can be used to find connections among small molecules sharing a mechanism of action, chemicals and physiological processes, and diseases and drugs. These results indicate the ...
	✔ A formal test of the theory of universal common ancestry [Quick Edit] [CiTO] Nature, Vol. 465, No. 7295. (13 May 2010), pp. 219-222, doi:10.1038/nature09014 by Douglas L. Theobald posted by 41 people nailest gwallau damm aaltenburger andreassorge hiec mrvaidya darekmyszor djkt skembel qayub lokesht fergus jtcribbs Katje seaver biomcgary edevost druvus bobcottingham alhufton PollardWall galtay 4waldron wheedhee guillermina maletich dutilh joybrata sqooby Journal picks dullhunk provero operon dinnes TRHvidsten robfsouza TwistedBacteria shikin megraw iSEEM Abstract Copy My Attachments My Copy Abstract Universal common ancestry (UCA) is a central pillar of modern evolutionary theory. As first suggested by Darwin, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past. The classic evidence for UCA, although massive, is largely restricted to 'local' common ancestry-for example, of specific phyla rather than the entirety of life-and has yet to fully integrate the recent advances from modern phylogenetics and ...
	✔ VarScan: variant detection in massively parallel sequencing of individual and pooled samples [Quick Edit] [CiTO] Bioinformatics, Vol. 25, No. 17. (01 September 2009), pp. 2283-2285, doi:10.1093/bioinformatics/btp373 by Daniel C. Koboldt, Ken Chen, Todd Wylie, et al.David E. Larson, Michael D. McLellan, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Li Ding posted by 36 people aalap_mogre heliopais Peiyong malcook dswan stajich Mycology jeanmonlong gwajnberg golharam djkt guhjy gdauria caroline_odling elzed maren junehlee humburg darian seb1 dakelley Journal picks n00c druvus SIMR bioinformatics BioNica mkiyer hzoltan oinizan Bioinformatics epermal orzenil natstreet pickw APRegier PabloMarin Abstract Copy My Attachments My Copy Abstract Summary: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The unprecedented throughput and relatively short read lengths of Roche/454, Illumina/Solexa, and other platforms have spurred development of a new generation of sequence alignment algorithms. Yet detection of sequence variants based on short read alignments remains challenging, and most currently available tools are limited to a single platform or aligner type. We present VarScan, an open source tool ...
	✔ BLAST+: architecture and applications. [Quick Edit] [CiTO] BMC bioinformatics, Vol. 10, No. 1. (2009), 421, doi:10.1186/1471-2105-10-421 by Christiam Camacho, George Coulouris, Vahram Avagyan, et al.Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L. Madden posted by 45 people jwm druvus nuin kshameer walshtp operon maximilianh natstreet justinhjohnson Orengo Group Journal Picks pansapiens leelarcombe dutilh gawbul n00c guhjy Journal picks jeargle torfinnnome karthikraman alicezelman kvalyi richardbickerton sillitoe ndiaz rschaeff SUN_RUPING kinestetika nailest accopeland cisevol Schmidtc georgeg mbalint hiec nlapalu phoenixzxl BergmanLab kiekyon wenboj GustavoLacerda michaelbarton zhangce chriscole heliopais Abstract Copy My Attachments My Copy Abstract Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. ...
	✔ Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps [Quick Edit] [CiTO] Genome Biology, Vol. 11, No. 4. (2010), R41, doi:10.1186/gb-2010-11-4-r41 by Isheng Tsai, Thomas Otto, Matthew Berriman posted by 31 people justinhjohnson dakelley elzed GustavoLacerda djkt avilella roedelsberg iSEEM orzenil accopeland Bioinformatics n00c cisevol Journal picks dandaman utrivedi dswan sharpton dutilh BlaxterLab konrad_foerstner davidmam michaelbarton BergmanLab APRegier natstreet natalia_martins PollardWall Mycology jasontsai druvus Abstract Copy My Attachments My Copy Abstract Advances in sequencing technology allow genomes to be sequenced at vastly decreased costs. However, the assembled data frequently are highly fragmented with many gaps. We present a practical approach that uses Illumina sequences to improve draft genome assemblies by aligning sequences against contig ends and performing local assemblies to produce gap-spanning contigs. The continuity of a draft genome can thus be substantially improved, often without the need to generate new data. ...
	✔ BamTools: a C++ API and toolkit for analyzing and managing BAM files [Quick Edit] [CiTO] Bioinformatics, Vol. 27, No. 12. (15 June 2011), pp. 1691-1692, doi:10.1093/bioinformatics/btr174 by Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael P. Strömberg, Gabor T. Marth posted by 29 people seb1 druvus Journal picks djkt APRegier cisevol BergmanLab idonaldson SUN_RUPING simonalpha roedelsberg jforment dswan jts nailest muratsincan accopeland Bioinformatics Core Service adthrasher kshameer orzenil pickw 2007lab Ciccarelli Lab cicca mikelove n00c natstreet pareng Abstract Copy My Attachments My Copy Abstract Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. ...
	✔ Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. [Quick Edit] [CiTO] Nature reviews. Genetics, Vol. 12, No. 9. (18 September 2011), pp. 628-640, doi:10.1038/nrg3046 by Gregory M. Cooper, Jay Shendure posted by 33 people lauraclarke dakelley pedrobeltrao pickw jbhiatt lp2 natstreet PabloMarin UGDG astoddard gthorisson druvus darian martainn rpiro colmryan golharam brianb Gig77 maribeljuev phoenixzxl JanHendric kshameer Orengo Group Journal Picks daforerog shikin provero qayub Bioinformatics kmdaily Journal picks guhjy dwhong Abstract Copy My Attachments My Copy Abstract Genome and exome sequencing yield extensive catalogues of human genetic variation. However, pinpointing the few phenotypically causal variants among the many variants present in human genomes remains a major challenge, particularly for rare and complex traits wherein genetic information alone is often insufficient. Here, we review approaches to estimate the deleteriousness of single nucleotide variants (SNVs), which can be used to prioritize disease-causal variants. We ...
	✔ Uncovering the roles of rare variants in common disease through whole-genome sequencing [Quick Edit] [CiTO] Nature Reviews Genetics, Vol. 11, No. 6. (01 June 2010), pp. 415-425, doi:10.1038/nrg2779 by Elizabeth T. Cirulli, David B. Goldstein posted by 23 people astoddard songpku daforerog idonaldson guhjy provero lp2 n00c humburg druvus kshameer natstreet aheilbut dondon minseven nailest tunepers rrwedel zufar daed darian giovanni slack---line Abstract Copy My Attachments My Copy Abstract Although genome-wide association (GWA) studies for common variants have thus far succeeded in explaining only a modest fraction of the genetic components of human common diseases, recent advances in next-generation sequencing technologies could rapidly facilitate substantial progress. This outcome is expected if much of the missing genetic control is due to gene variants that are too rare to be picked up by GWA studies and have relatively large effects on risk. Here, we evaluate the evidence for an important role of ...
	✔ Testing for an Unusual Distribution of Rare Variants [Quick Edit] [CiTO] PLoS Genet, Vol. 7, No. 3. (3 March 2011), e1001322, doi:10.1371/journal.pgen.1001322 by Benjamin M. Neale, Manuel A. Rivas, Benjamin F. Voight, et al.David Altshuler, Bernie Devlin, Marju Orho-Melander, Sekar Kathiresan, Shaun M. Purcell, Kathryn Roeder, Mark J. Daly posted by 18 people sriesenfeld djkt emptyhb Journal picks dullhunk qayub Bioinformatics ongenetics guhjy daed songpku golharam FranziMe mikelove humburg PollardWall kshameer giovanni Abstract Copy My Attachments My Copy Abstract Technological advances make it possible to use high-throughput sequencing as a primary discovery tool of medical genetics, specifically for assaying rare variation. Still this approach faces the analytic challenge that the influence of very rare variants can only be evaluated effectively as a group. A further complication is that any given rare variant could have no effect, could increase risk, or could be protective. We propose here the C-alpha test statistic as a novel approach for testing for the presence of ...
	✔ How to visually interpret biological data using networks [Quick Edit] [CiTO] Nat Biotech In Nat Biotech, Vol. 27, No. 10. (01 October 2009), pp. 921-924, doi:10.1038/nbt.1567 by Daniele Merico, David Gfeller, Gary D. Bader posted by 42 people nailest Gig77 megraw rdiaz AJCann qayub Journal picks richardbickerton jtcribbs danielmehnert CFriedel konrad_foerstner rolandkrause jfr lokesht pigironjoe wwweagle agomez ashishvt nrnb fuenfgeld toates hawksjohnd sgsfak fbergmann allysonlister abhishek_tiwari daforerog guhjy beete ngehlenborg Yanno Geknitics perkeo mhamidi OliverHarriman grahamc tmmurali fgibson gotgenes druvus dullhunk Abstract Copy My Attachments My Copy Abstract Networks in biology can appear complex and difficult to decipher. Merico et al. illustrate how to interpret biological networks with the help of frequently used visualization and analysis patterns. Networks represent relationships. In a biological context, many different types of relationships can be measured, such as physical interactions between proteins or genetic interactions revealed by combinations of mutations. ...
	✔ Assembly of large genomes using second-generation sequencing [Quick Edit] [CiTO] Genome Research, Vol. 20, No. 9. (1 September 2010), pp. 1165-1173, doi:10.1101/gr.101360.109 by Michael C. Schatz, Arthur L. Delcher, Steven L. Salzberg posted by 38 people SciLifeLab Stockholm ongenetics seb1 nailest robsyme diguzim ptrobajo stajich dullhunk scole darian oinizan jamselem djkt fstrozzi dchughes fenghezi dakelley abhishek_tiwari maximilianh daveGerrard roys GustavoLacerda Gig77 golharam n00c Journal picks Mycology Dadou venura idonaldson agbiotec lennyheath accopeland mschatz druvus PollardWall tony_c Abstract Copy My Attachments My Copy Abstract Second-generation sequencing technology can now be used to sequence an entire human genome in a matter of days and at low cost. Sequence read lengths, initially very short, have rapidly increased since the technology first appeared, and we now are seeing a growing number of efforts to sequence large genomes de novo from these short reads. In this Perspective, we describe the issues associated with short-read assembly, the different types of data produced by second-gen sequencers, and the latest assembly algorithms ...
	✔ Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome [Quick Edit] [CiTO] Science, Vol. 329, No. 5987. (02 July 2010), pp. 52-56, doi:10.1126/science.1190719 by Daniel G. Gibson, John I. Glass, Carole Lartigue, et al.Vladimir N. Noskov, Ray-Yuan Chuang, Mikkel A. Algire, Gwynedd A. Benders, Michael G. Montague, Li Ma, Monzia M. Moodie, Chuck Merryman, Sanjay Vashee, Radha Krishnakumar, Nacyra Assad-Garcia, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Lei Young, Zhi-Qing Qi, Thomas H. Segall-Shapiro, Christopher H. Calvey, Prashanth P. Parmar, Clyde A. Hutchison, Hamilton O. Smith, J. Craig Venter posted by 75 people dzunkova cambray babelfish911 aiwagan pablocarb operon sjcockell dswan karthikraman JoramJvR gstan TwistedBacteria trm005 nschaeff hawksjohnd coela wieceka1 tellis galtay GeeSharpMinor aaltenburger clab JeremyZucker MikolkaMikolka cobi lizbiogen LucioAlencar tedrubin Journal picks guhjy prasad3130 gracia18 pvdg gjuggler dumont Photoinduced polylepis rhashemi antonio-pgarcia oteri sanjaydosaj nzm scottfranklin666 Scis0000002 kou_jinsei VGreiff abhishek_tiwari chriswillmott marcio yuki-nagato popwongpalee gogodidi pkapoorvijay frohike TRHvidsten provero bobcottingham antonkratz gotgenes dullhunk torfinnnome tbsaid81 dbikard PHYSICSofLIFE toates joybrata onurvarol danielmcgownjr mikeeck jdoconnell kevinemamy pmcmullen coppagejd gkroch JoseBrox Abstract Copy My Attachments My Copy Abstract We report the design, synthesis, and assembly of the 1.08–mega–base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including “watermark” sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and ...
	✔ Diversity of human copy number variation and multicopy genes. [Quick Edit] [CiTO] Science (New York, N.Y.), Vol. 330, No. 6004. (29 October 2010), pp. 641-646, doi:10.1126/science.1197005 by Peter H. Sudmant, Jacob O. Kitzman, Francesca Antonacci, et al.Can Alkan, Maika Malig, Anya Tsalenko, Nick Sampas, Laurakay Bruhn, Jay Shendure, 1000 Genomes Project, Evan E. Eichler posted by 30 people xianfan AaronArvey mmparks Journal picks hawksjohnd ppgardne lp2 sriesenfeld pickw provero absterga isaacturner guhjy hpaces maren ongenetics PollardWall daforerog BergmanLab chburrus Ayest MCB-CNV maximilianh giovanni dakelley Terkko djkt zufar daveGerrard dullhunk Abstract Copy My Attachments My Copy Abstract Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in ...
	✔ Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [Quick Edit] [CiTO] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402, doi:10.1093/nar/25.17.3389 by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted by 120 people johnlapage petrabarus captaineguy rschaeff happy_manatee bicko newton1234 iakes Sadgad LBMP-FFCLRP nlapalu manzanita kiekyon indigoviolet whitead fenz mijam daforerog yylin nuke2005 knaseanka operon michaelzeller CharlesM dullhunk tfuji GustavoLacerda jbhiatt shung BioNica parnell dakelley viktor21614 nanomuthu idoerg pjcite swp09 Sjitprasutwit LucioAlencar pwais tjimenez sebk niallhaslam abovell jrhill paulshealy granujilla timflutre mirzazadeh dgront Richmonp wenboj mcbla bjorns biomedical-nlp dutilh epermal mgomes Jiang Research Group HawkinsJohnC jmeppley sannenygaard indignacious natldawson beatrizfernandez chad_davis mariakmejia agbiotec kengg mrvaidya edvin caporaso maria_hauser rshe RebeccaHamer setar eweaver maehler alicezelman sobolevnrm ekrzepka kaarsinogen LeilaTA ucbcjbm cpwardell robert adijr balajis kgutwin mra928 accopeland sujaikumar TLVincent janasont jdelcampo marti grottenolm References for 3DSim paper mbaddar2 timhubbard johanviklund david_parsons azazello sillitoe saunders ksliu bandrewfox massivemayhem CitoJam jackpotDelight huichun Plantandetc Microbial-Ecology n00c rabio aengisch siebertm miguel treangen EisenLab Abstract Copy My Attachments My Copy Abstract The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating ...
	✔ A beginner's guide to eukaryotic genome annotation [Quick Edit] [CiTO] Nature Reviews Genetics, Vol. 13, No. 5. (18 April 2012), pp. 329-342, doi:10.1038/nrg3174 by Mark Yandell, Daniel Ence posted by 27 people MGEL Short Reading misonneh Journal picks guhjy nailest rdillon dakelley IGV lokesht cisevol epigenetics NGS_Array_References Gig77 druvus kshameer mjbell orzenil muratsincan songpku qayub lutfanlazuardi inodebruijn megraw dullhunk aprasad BergmanLab TRHvidsten Abstract Copy My Attachments My Copy Abstract The falling cost of genome sequencing is having a marked impact on the research community with respect to which genomes are sequenced and how and where they are annotated. Genome annotation projects have generally become small-scale affairs that are often carried out by an individual laboratory. Although annotating a eukaryotic genome assembly is now within the reach of non-experts, it remains a challenging task. Here we provide an overview of the genome annotation process and the available tools and describe some ...
	✔ DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. [Quick Edit] [CiTO] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 26, No. 1. (1 January 2010), pp. 136-138, doi:10.1093/bioinformatics/btp612 by Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang posted by 36 people tonamswish ramonvidal jwfoley Bioinformatics justinhjohnson scryrps Scott2283 GustavoLacerda cxmmw685 darshan druvus guhjy pickw heliopais shikin jforment Bioinformatics Core Service scchou natstreet rpiro juokcho jmeppley sotacam GeeSharpMinor hzoltan torfinnnome jfr ikarus97 davidliwei Laur705 ongenetics SUN_RUPING djkt lwaldron junehlee dandaman Abstract Copy My Attachments My Copy Abstract SUMMARY: High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. In this package, we integrated three existing methods, and introduced two novel methods based on MA-plot to detect and visualize gene expression difference. AVAILABILITY: The R package and a quick-start ...
	✔ A guide to web tools to prioritize candidate genes. [Quick Edit] [CiTO] Briefings in bioinformatics, Vol. 12, No. 1. (01 January 2011), pp. 22-32, doi:10.1093/bib/bbq007 by Léon-Charles C. Tranchevent, Francisco Bonachela B. Capdevila, Daniela Nitsch, Bart De Moor, Patrick De Causmaecker, Yves Moreau posted by 30 people rpiro nosbod lokesht Journal picks daforerog liblab muratsincan guhjy bborgeson kmdaily samhubble poirel druvus renatomilani BergmanLab kees steenhoff sobolevnrm Bioinformatics abhishek_tiwari dbk cisevol dswan rbritto giovanni karthikraman dullhunk provero kclbioinf kshameer Abstract Copy My Attachments My Copy Abstract Finding the most promising genes among large lists of candidate genes has been defined as the gene prioritization problem. It is a recurrent problem in genetics in which genetic conditions are reported to be associated with chromosomal regions. In the last decade, several different computational approaches have been developed to tackle this challenging task. In this study, we review 19 computational solutions for human gene ...
	✔ Lost in translation: an assessment and perspective for computational microRNA target identification [Quick Edit] [CiTO] Bioinformatics In Bioinformatics, Vol. 25, No. 23. (01 December 2009), pp. 3049-3055, doi:10.1093/bioinformatics/btp565 by Panagiotis Alexiou, Manolis Maragkakis, Giorgos L. Papadopoulos, Martin Reczko, Artemis G. Hatzigeorgiou posted by 34 people kintoki qfwills Orengo Group Journal Picks frohike daforerog Stew jperkins dswan guhjy daveGerrard toni_marco lwaldron kshameer dandaman Journal picks heliopais Jporci pattersonee Bioinformatics - CRUK apaydin Bioinformatics Core Service renatomilani justinhjohnson GustavoLacerda jfr microRNA tonamswish jakalssj3 shikin lp2 ikarus97 jforment fstrozzi hyojinkang Abstract Copy My Attachments My Copy Abstract MicroRNAs (miRNAs) are a class of short endogenously expressed RNA molecules that regulate gene expression by binding directly to the messenger RNA of protein coding genes. They have been found to confer a novel layer of genetic regulation in a wide range of biological processes. Computational miRNA target prediction remains one of the key means used to decipher the role of miRNAs in development and disease. Here we introduce the basic idea behind the experimental identification of miRNA targets and present ...
	✔ Measuring the evolutionary rewiring of biological networks. [Quick Edit] [CiTO] PLoS computational biology, Vol. 7, No. 1. (6 January 2011), e1001050, doi:10.1371/journal.pcbi.1001050 by Chong Shou, Nitin Bhardwaj, Hugo Y. Lam, et al.Koon-Kiu K. Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein posted by 41 people druvus pedrobeltrao friendpine danbumbarger lmichan biomcgary alextrial karthikraman vvoorr emptyhb rpiro heathervincent johanviklund gotgenes djkt skjq abhishek_tiwari Biiiogeek CFriedel 02_ceuratrans pkatz aswinsainarain arjun_citeulike hwangwoochang atulchin lxm1117 manto PollardWall tozammel Journal picks dullhunk cabbagesofdoom phoenixzxl BlaxterLab sujaikumar provero colmryan daed kaarsinogen TRHvidsten avilella Abstract Copy My Attachments My Copy Abstract We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in ...
	✔ The mystery of missing heritability: Genetic interactions create phantom heritability [Quick Edit] [CiTO] Proceedings of the National Academy of Sciences, Vol. 109, No. 4. (24 January 2012), pp. 1193-1198, doi:10.1073/pnas.1119675109 by Or Zuk, Eliana Hechter, Shamil R. Sunyaev, Eric S. Lander posted by 27 people ongenetics vingron lp2 Borelli mikelove cdsouthan dakelley nailest pcarbo jdreyf chuuc0 dullhunk daforerog avilella astoddard robert PollardWall djkt tsuvitai songpku furmanlab Journal picks ddahlem timflutre natstreet guhjy gthorisson Abstract Copy My Attachments My Copy Abstract Human genetics has been haunted by the mystery of “missing heritability” of common traits. Although studies have discovered >1,200 variants associated with common diseases and traits, these variants typically appear to explain only a minority of the heritability. The proportion of heritability explained by a set of variants is the ratio of (i) the heritability due to these variants (numerator), estimated directly from their observed effects, to (ii) the total heritability (denominator), inferred indirectly from population data. The prevailing view has ...
	✔ RNA-Seq gene expression estimation with read mapping uncertainty [Quick Edit] [CiTO] Bioinformatics, Vol. 26, No. 4. (15 February 2010), pp. 493-500, doi:10.1093/bioinformatics/btp692 by Bo Li, Victor Ruotti, Ron M. Stewart, James A. Thomson, Colin N. Dewey posted by 42 people natstreet engelhardt druvus srirampc timflutre orzenil APRegier sotacam n00c dswan ikarus97 Bioinformatics Core Service jforment alebalbin Bioinformatics lp2 jimineep dgu djkt TRHvidsten daed davidmam GustavoLacerda cxmmw685 jwfoley buske justinhjohnson konrad_foerstner ongenetics scchou duemcke davidliwei FBI golharam heliopais fstrozzi dakelley guhjy ShouyongPeng idonaldson rs arthegall Abstract Copy My Attachments My Copy Abstract Motivation: RNA-Seq is a promising new technology for accurately measuring gene expression levels. Expression estimation with RNA-Seq requires the mapping of relatively short sequencing reads to a reference genome or transcript set. Because reads are generally shorter than transcripts from which they are derived, a single read may map to multiple genes and isoforms, complicating expression analyses. Previous computational methods either discard reads that map to multiple locations or allocate them to genes heuristically.Results: We present a generative statistical model and ...
	✔ Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks [Quick Edit] [CiTO] PLoS Comput Biol, Vol. 6, No. 6. (24 June 2010), e1000807, doi:10.1371/journal.pcbi.1000807 by Javier De Las Rivas, Celia Fontanillo posted by 30 people Sal huichun richrr heathervincent jjray Journal picks guhjy schwartzjmc dullhunk georgeg fuenfgeld CorinYeats kshameer colmryan Scis0000002 giovenko sudarshaniisc daforerog lokesht cabbagesofdoom Orengo Group Journal Picks eesruiz tonamswish dynamite_owner Yanno karthikraman shikin poirel TRHvidsten Bioinformatics Copy My Attachments My Copy
	✔ Interactome networks and human disease. [Quick Edit] [CiTO] Cell, Vol. 144, No. 6. (18 March 2011), pp. 986-998, doi:10.1016/j.cell.2011.02.016 by Marc Vidal, Michael E. Cusick, Albert-László L. Barabási posted by 27 people Evangelia provero kshameer Bioinformatics astoddard phoenixzxl rpiro guhjy karthikraman Yanno Scis0000002 pankajpandey flbarroso junehlee peterli colmryan jongrae seb1 schwartzjmc jimineep poirel jtcribbs shiyongliu huichun skjq misonneh daed Abstract Copy My Attachments My Copy Abstract Complex biological systems and cellular networks may underlie most genotype to phenotype relationships. Here, we review basic concepts in network biology, discussing different types of interactome networks and the insights that can come from analyzing them. We elaborate on why interactome networks are important to consider in biology, how they can be mapped and integrated with each other, what global properties are starting to emerge ...
	✔ Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks [Quick Edit] [CiTO] Genome Research, Vol. 13, No. 11. (1 November 2003), pp. 2498-2504, doi:10.1101/gr.1239303 by Paul Shannon, Andrew Markiel, Owen Ozier, et al.Nitin S. Baliga, Jonathan T. Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker posted by 68 people ndiaz tonamswish FAB-lab Evangelia PabloR Stew Borelli ajank dIEMoSIRIS janani137 chibatching higueruelo jlh64 AndreasS01 tunepers nolodie daveGerrard yggdrasil nailest federicoapelt koikoi hagi Mehlhorn amueller robert85 vvoorr phoenixzxl nrnb pickw yagyav neerjakatiyar ceciklein badi Fedo dragonrez chrahn daforerog jjack shikin thomaskelder JeremyZucker fastjoe23 dagmar frohike tvdbulck balajis giovenko capitall panghouse APRegier schwartzjmc kentz ganden saunders guhjy schuylrp FranziMe carmaus carlk robingauba rvosa vjethava shung MoSi-Rostock compneur pmendes cswinburne natstreet Abstract Copy My Attachments My Copy Abstract Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, ...
	✔ Correction of sequencing errors in a mixed set of reads [Quick Edit] [CiTO] Bioinformatics, Vol. 26, No. 10. (15 May 2010), pp. 1284-1290, doi:10.1093/bioinformatics/btq151 by Leena Salmela posted by 27 people natstreet GeeSharpMinor MVEverett jforment djkt PollardWall chburrus BlaxterLab operon iSEEM n00c orzenil drcyber epermal machar druvus srirampc dakelley accopeland avilella sujaikumar Bioinformatics ikarus97 sharpton Bioinformatics Core Service dswan 01_pachinko_pagan Abstract Copy My Attachments My Copy Abstract Motivation: High-throughput sequencing technologies produce large sets of short reads that may contain errors. These sequencing errors make de novo assembly challenging. Error correction aims to reduce the error rate prior assembly. Many de novo sequencing projects use reads from several sequencing technologies to get the benefits of all used technologies and to alleviate their shortcomings. However, combining such a mixed set of reads is problematic as many tools are specific to one sequencing platform. The SOLiD sequencing platform is especially ...
	✔ Disease signatures are robust across tissues and experiments. [Quick Edit] [CiTO] Molecular systems biology, Vol. 5 (15 September 2009), doi:10.1038/msb.2009.66 by Joel T. Dudley, Robert Tibshirani, Tarangini Deshpande, Atul J. Butte posted by 27 people nailest oceanblue zufar phoenixzxl winterschlaefer dswan klo renatomilani HermanSontrop alaincoletta giovanni jclau peterli neils bertelsen SciLifeLab Stockholm guhjy jfr icecrown frohike tmmurali grahamc ptrobajo mingzhi ngehlenborg daforerog brianb Abstract Copy My Attachments My Copy Abstract Meta-analyses combining gene expression microarray experiments offer new insights into the molecular pathophysiology of disease not evident from individual experiments. Although the established technical reproducibility of microarrays serves as a basis for meta-analysis, pathophysiological reproducibility across experiments is not well established. In this study, we carried out a large-scale analysis of disease-associated experiments obtained from NCBI GEO, and evaluated their concordance across a broad range of diseases and tissue types. On evaluating 429 experiments, representing 238 diseases and 122 tissues from ...
	✔ Network motifs: simple building blocks of complex networks. [Quick Edit] [CiTO] Science (New York, N.Y.), Vol. 298, No. 5594. (25 October 2002), pp. 824-827, doi:10.1126/science.298.5594.824 by R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon posted by 133 people prabhatshankar iris_2001 griota poirel subhacom ChaTo FAB-lab kubyaddi dbk-lab ocs pbull RafG ypjones antonkratz nailest complex networks korakot imouthesmp dullhunk atulchin st3vil ethkim favremar hryk christianholz maralena BT5240: Computational Systems Biology karthikraman zibuyu Evangelia Philosophy_of_Information michaelmampaey ddahlem heliopais Md_2007 daforerog arsyed mjoach jaspervoskuilen megraw kimbie koikoi netzwerkerin shikin wwweagle krisl jtaylor mullonc sudarshaniisc josepe i-stevenson orahcio babakap balicea lenov tfogal winterstream jovillal tmaillart rebeccamancy carlk sgsfak GEB antonio-pgarcia phoenixzxl Bolozna Sergey_gerbek WaterLily2 cswinburne ADMiRes jasonjgs39 vtraag Borelli renatomilani tomhebbron alexg darian nurban karfunkel dlobo wei_tang arpaton skjq johanneskoester operon lfriedl Richmonp brewbooks aalibes neveaire Yitapi galyardt fierykylin isbkramer mtagaya chenmengjie87 mawds andreassorge nicholasflann rajs2010 ssb gurkanbebek applesnow davidbindel scoodnim maehler matijapolajnar roys sergiun Kovanen chasmand dquinby schwartzjmc Blog_and_Wiki_Research Telpecarne jlizier stefanoallesina cmor kaarsinogen wnpx donade GeneGo ColDyn kdl beefer lawraga adampah balabu makrehchi Akimasa camster tny cmm Abstract Copy My Attachments My Copy Abstract Complex networks are studied across many fields of science. To uncover their structural design principles, we defined "network motifs," patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic ...
	✔ Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing [Quick Edit] [CiTO] Briefings in Bioinformatics In Brief Bioinform, Vol. 11, No. 2. (01 March 2010), pp. 181-197, doi:10.1093/bib/bbp046 by David S. Horner, Giulio Pavesi, Tiziana Castrignanò, et al.Paolo D. De Meo, Sabino Liuni, Michael Sammeth, Ernesto Picardi, Graziano Pesole posted by 41 people sushant_mishra oinizan orzenil cisevol lmichan ikarus97 dullhunk Jporci siiner LauraEMont GustavoLacerda jsatkosk MVEverett scryrps kshameer guhjy Biiiogeek sergiodealencar farhat bioinformatics classics abhishek_tiwari golharam tfb785 ShouyongPeng lipido idonaldson giovenko nuin michaelbarton darian qm greg Journal picks heliopais elipapa burak torfinnnome operon wilbur renatomilani druvus Abstract Copy My Attachments My Copy Abstract Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called ‘next-generation’ sequencing platforms, with several others anticipated to become available shortly. The previously unimaginable scale and economy of these methods, coupled with their enthusiastic uptake by the scientific community and the potential for further improvements in accuracy and read length, suggest ...
	✔ Tabix: fast retrieval of sequence features from generic TAB-delimited files [Quick Edit] [CiTO] Bioinformatics, Vol. 27, No. 5. (01 March 2011), pp. 718-719, doi:10.1093/bioinformatics/btq671 by Heng Li posted by 31 people LuciaPu dullhunk heliopais jamesmorris BlaxterLab n00c BergmanLab antonkratz theboyfree Journal picks dswan mhz Bioinformatics Core Service lp2 mjbell abhishek_tiwari cisevol nigelhardy kshameer farhat astoddard Gig77 skjq sujaikumar timflutre jforment avilella sebastien_vigneau Bioinformatics druvus guhjy Abstract Copy My Attachments My Copy Abstract Summary: Tabix is the first generic tool that indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves features overlapping specified regions. Tabix features include few seek function calls per query, data compression with gzip compatibility and direct FTP/HTTP access. Tabix is implemented as a free command-line tool as well as a library in C, Java, Perl and Python. It is particularly useful for manually examining local genomic features on the command ...
	✔ RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. [Quick Edit] [CiTO] BMC bioinformatics, Vol. 12, No. 1. (2011), 323, doi:10.1186/1471-2105-12-323 by Bo Li, Colin N. Dewey posted by 36 people daed davidliwei ecircuit dennisk roys aheilbut graslevy pickw phoenixzxl shikin shandar jforment ongenetics tonamswish daveGerrard jameswasmuth mfrichar kshameer srirampc 01_pachinko_pagan SUN_RUPING idonaldson Vincent_Rouilly natstreet dakelley etkimura fuadgwadry pauljaparrigor avilella seb1 druvus sergiodealencar TRHvidsten orzenil Bioinformatics Core Service torfinnnome Abstract Copy My Attachments My Copy Abstract RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant ...

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