Kihoon Yoon's Top Recommendations

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	fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 24, No. 5. (1 March 2008), pp. 629-636. by Leping Li, Robert L. Bass, Yu Liang posted by 7 people bsamal wowalz GustavoLacerda maximilianh idonaldson csdhwang isimpson
	TFBS identification based on genetic algorithm with combined representations and adaptive post-processing [My Copy] Bioinformatics In Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 341-349. by Tak-Ming Chan, Kwong-Sak Leung, Kin-Hong Lee posted by 8 people bsamal wowalz nklee maximilianh idonaldson xili03 csdhwang isimpson
	Regulatory motif discovery using a population clustering evolutionary algorithm. [My Copy] IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (p 2007), pp. 403-414. by M. A. Lones, A. M. Tyrrell posted by 7 people Dulce wowalz nklee idonaldson xili03 csdhwang isimpson
	CoMoDis: composite motif discovery in mammalian genomes. [My Copy] Nucleic Acids Res, Vol. 35, No. 1. (2007) by I. J. Donaldson, B. Göttgens posted by 3 people Bioinformatics idonaldson csdhwang
	Additivity in protein-DNA interactions: how good an approximation is it? [My Copy] Nucleic Acids Res, Vol. 30, No. 20. (15 October 2002), pp. 4442-4451. by P. V. Benos, M. L. Bulyk, G. D. Stormo posted by 5 people aalibes erdos medic0747 emptyhb yevishere
	ABySS: a parallel assembler for short read sequence data. [My Copy] Genome research, Vol. 19, No. 6. (1 June 2009), pp. 1117-1123. by Jared T. Simpson, Kim Wong, Shaun D. Jackman, Jacqueline E. Schein, Steven J. Jones, Inanç Birol posted by 31 people jts darian jfr cthachuk hzoltan ramonvidal orzenil pachorip GustavoLacerda jonilaserson operon BergmanLab polivares reyez jasontsai n00c humburg dakelley jessopher idonaldson robsyme neils natstreet AaronDarling druvus rpatward dswan Mycology stajich jbhiatt erikarner
	Gene set-based module discovery in the breast cancer transcriptome [My Copy] BMC Bioinformatics, Vol. 10 (26 February 2009), 71. by Atsushi, Tetsu Akiyama posted by 4 people jfr Neuroblastoma fpattyn idonaldson
	Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes [My Copy] Genome Research, Vol. 19, No. 6. (1 June 2009), pp. 967-977. by Michael Y. Tolstorukov, Peter V. Kharchenko, Joseph A. Goldman, Robert E. Kingston, Peter J. Park posted by 4 people ashkelon13 hagechouchin443 humburg idonaldson
	ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks [My Copy] Bioinformatics, Vol. 25, No. 8. (15 April 2009), pp. 1091-1093. by Gabriela Bindea, Bernhard Mlecnik, Hubert Hackl, et al.Pornpimol Charoentong, Marie Tosolini, Amos Kirilovsky, Wolf-Herman Fridman, Franck Pages, Zlatko Trajanoski, Jerome Galon posted by 12 people icecrown jfr robert85 guhjy natstreet sjcockell Bioinformatics - CRUK Stew dswan idonaldson tosolini thomaskelder
	A Bayesian Hidden Markov Model for Motif Discovery Through Joint Modeling of Genomic Sequence and ChIP-Chip Data [My Copy] Biometrics, Vol. 9999, No. 9999. (2009) by Jonathan A. L. Gelfond, Mayetri Gupta, Joseph G. Ibrahim posted by 3 people wowalz maximilianh idonaldson
	Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites. [My Copy] Nucleic acids research (10 February 2009) by Keunsoo Kang, Jae Hoon H. Chung, Joomyeong Kim posted by 3 people clearbluespring idonaldson sebastien_vigneau
	Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 218-223. by Nicholas T. Ingolia, Sina Ghaemmaghami, John R. S. Newman, Jonathan S. Weissman posted by 22 people hzoltan jwfoley yyfwuhan gbloeb guhjy RockmanLab NYU Journal Review dpollard fenghezi gangcai idonaldson coela fpattyn jbhiatt kshundyak absterga myzhang bertelsen VGreiff provero microbiology_nijmegen kinestetika
	The evolution of Fox genes and their role in development and disease. [My Copy] Nature reviews. Genetics (10 March 2009) by Sridhar Hannenhalli, Klaus H H. Kaestner posted by 3 people fenghezi idonaldson provero
	TFCat: the curated catalog of mouse and human transcription factors. [My Copy] Genome biology, Vol. 10, No. 3. (2009) by Debra L. Fulton, Saravanan Sundararajan, Gwenael Badis, et al.Timothy R. Hughes, Wyeth W. Wasserman, Jared C. Roach, Rob Sladek posted by 10 people bsamal maximilianh megraw natstreet idonaldson bmajoros dolchan BergmanLab cisevol druvus
	Genome-wide analysis of histone H3 lysine 27 trimethylation by ChIP-chip in gastric cancer patients [My Copy] Journal of Gastroenterology by Li Zhang, Keli Zhong, Yong Dai, Hanxin Zhou posted by 1 person idonaldson
	Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 82. by Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn posted by 13 people bsamal daveGerrard ilyashl svenrahmann idonaldson maximilianh bmajoros nuin idoerg cis-regulatory-evolution BergmanLab cisevol dquest
	COTRASIF: conservation-aided transcription-factor-binding site finder [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 37, No. 7. (1 April 2009), e49. by Bogdan Tokovenko, Rostyslav Golda, Oleksiy Protas, Maria Obolenskaya, Anna El'skaya posted by 6 people bsamal Ensembl Compara citations avilella druvus nuin idonaldson
	Cloning-free regulated monitoring of reporter and gene expression [My Copy] BMC Molecular Biology, Vol. 10, No. 1. (08 March 2009), 20. by Latifa A. Haj, Wijdan A. Ahmadi, Maher A. Saif, Omer Demirkaya, Khalid Khabar posted by 3 people idonaldson BergmanLab daveGerrard
	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. [My Copy] Genome biology, Vol. 10, No. 3. (2009), R25. by Ben Langmead, Cole Trapnell, Mihai Pop, Steven L. Salzberg posted by 45 people jts oannes mijam nuin jfr hzoltan cthachuk darshan fstrozzi adijr debasis bozdagd BergmanLab polivares torfinnnome n00c talponer jmcq rschulz SIMR bioinformatics ghattem operon humburg idonaldson mmartin iSEEM skembel dquest heliopais djkt GeeSharpMinor bertelsen darian Notre Dame Bioinformatics semrich dakelley idoerg vmsr hpaces admash pdexheimer mhamada fpattyn natstreet druvus
	The correlations of the function and positional distribution of the cis-elements CArG around the TSS in the genes of Mus musculus. [My Copy] Genome / National Research Council Canada = Génome / Conseil national de recherches Canada, Vol. 52, No. 3. (March 2009), pp. 217-221. by X. Shen, B. Walsh, J. J. Li, H. X. Pang, W. J. Wang, S. H. Tao posted by 1 person idonaldson
	ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. [My Copy] BMC bioinformatics, Vol. 10 Suppl 1 (2009) by H. Sun, T. De Bie, V. Storms, et al.Q. Fu, T. Dhollander, K. Lemmens, A. Verstuyf, B. De Moor, K. Marchal posted by 2 people maximilianh idonaldson
	Local DNA topography correlates with functional noncoding regions of the human genome. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5925. (17 April 2009), pp. 389-392. by Stephen C. Parker, Loren Hansen, Hatice Ozel O. Abaan, Thomas D. Tullius, Elliott H. Margulies posted by 48 people arthegall provero rsaito BergmanLab daveGerrard operon sujaikumar antonkratz pradiptaray roys gjuggler benjaminsb gdb hagechouchin443 tomtullius scjparker psique orzenil emptyhb ilyashl coela VGreiff APRegier myzhang pkonings akundaje athma absterga rpatward timflutre Mycology stajich bpcusack jbhiatt djkt structural_bioinformatics dhlbh friendpine RockmanLab EisenLab cis-regulatory-evolution dpollard inesdesantiago JustinCrocker aprasad maximilianh idonaldson kshundyak
	Martini: using literature keywords to compare gene sets [My Copy] Nucl. Acids Res., Vol. 38, No. 1. (1 January 2010), pp. 26-38. by Theodoros G. Soldatos, Sean I. O'Donoghue, Venkata P. Satagopam, et al.Lars J. Jensen, Nigel P. Brown, Adriano Barbosa-Silva, Reinhard Schneider posted by 2 people idonaldson bsamal
	Epitope tagging of endogenous proteins for genome-wide chromatin immunoprecipitation analysis. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 567 (2009), pp. 87-98. by Zhenghe Wang posted by 1 person idonaldson
	Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping. [My Copy] BMC research notes, Vol. 2, No. 1. (16 December 2009) by Nicolas Buisine, Laurent Sachs posted by 1 person idonaldson
	A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments [My Copy] BMC Genomics, Vol. 10, No. 1. (18 December 2009), 618. by Teemu Laajala, Sunil Raghav, Soile Tuomela, Riitta Lahesmaa, Tero Aittokallio, Laura Elo posted by 3 people kshameer maximilianh idonaldson
	How does multiple testing correction work? [My Copy] Nature Biotechnology In Nat Biotech, Vol. 27, No. 12. (01 December 2009), pp. 1135-1137. by William S. Noble posted by 26 people arthegall GustavoLacerda icecrown psique MurphysLab roys gpyle Bioinformatics songpku Zephyrus tmmurali druvus vingron shikin dquest icq242500260 idonaldson frohike renatomilani megraw Orengo Group Journal Picks robertrentzsch daforerog greg brianb neils
	Characteristics of the CArG-SRF binding context in mammalian genomes [My Copy] Mammalian Genome In Mammalian Genome (3 December 2009) by Wenwu Wu, Xia Shen, Shiheng Tao posted by 1 person idonaldson
	Modeling tissue-specific structural patterns in human and mouse promoters [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 38, No. 1. (1 January 2010), pp. 17-25. by Alexis Vandenbon, Kenta Nakai posted by 2 people idonaldson bsamal
	Mining for coexpression across hundreds of datasets using novel rank aggregation and visualisation methods. [My Copy] Genome biology, Vol. 10, No. 12. (4 December 2009), R139. by Priit Adler, Raivo Kolde, Meelis Kull, et al.Aleksandr Tkachenko, Hedi Peterson, Juri Reimand, Jaak Vilo posted by 15 people GustavoLacerda idonaldson gotgenes rvidal neils provero julied515 kshameer Orengo Group Journal Picks lees ptrobajo daforerog druvus dandaman shikin
	A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data [My Copy] PLoS ONE In PLoS ONE, Vol. 4, No. 12. (1 December 2009), e8155. by Xin He, Chieh-Chun Chen, Feng Hong, et al.Fang Fang, Saurabh Sinha, Huck-Hui Ng, Sheng Zhong posted by 2 people emptyhb idonaldson
	Over-optimism in bioinformatics research [My Copy] Bioinformatics In Bioinformatics (26 November 2009), btp648. by Anne-Laure Boulesteix posted by 22 people GustavoLacerda tmmurali mikel_egana beapen idonaldson daforerog kshameer danielkcook thomaskelder meanerelk frohike pkonings daed VGreiff sjcockell burak phoenixzxl Zephyrus Journal picks dullhunk neils druvus
	DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (26 November 2009), 388. by Isabelle da Piedade, Man H. Tang, Olivier Elemento posted by 6 people xili03 idonaldson maximilianh oelemento barriot bedo
	MOODS: fast search for position weight matrix matches in DNA sequences [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3181-3182. by Janne Korhonen, Petri Martinmaki, Cinzia Pizzi, Pasi Rastas, Esko Ukkonen posted by 7 people Bioinformatics - CRUK Stew idonaldson Journal picks ppgardne farhat djkt
	Structural and dynamic changes of the serum response element and the core domain of serum response factor induced by their association [My Copy] Biochemical and Biophysical Research Communications (10 November 2009) by Josef Štěpánek, Kopecký Jr, Alberto Mezzetti, et al.Pierre-Yves Turpin, Denise Paulin, Bernard Alpert, Christian Zentz posted by 1 person idonaldson
	Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. [My Copy] Nucleic acids research (11 November 2009), gkp1012. by Kimberly R. Blahnik, Lei Dou, Henriette O'Geen, et al.Timothy McPhillips, Xiaoqin Xu, Alina R. Cao, Sushma Iyengar, Charles M. Nicolet, Bertram Ludäscher, Ian Korf, Peggy J. Farnham posted by 2 people fenghezi idonaldson
	JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles [My Copy] Nucl. Acids Res. (11 November 2009), gkp950. by Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, et al.David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin posted by 4 people kmdaily roys idonaldson daforerog
	Human-specific transcriptional regulation of CNS development genes by FOXP2. [My Copy] Nature, Vol. 462, No. 7270. (12 November 2009), pp. 213-217. by Genevieve Konopka, Jamee M. Bomar, Kellen Winden, et al.Giovanni Coppola, Zophonias O. Jonsson, Fuying Gao, Sophia Peng, Todd M. Preuss, James A. Wohlschlegel, Daniel H. Geschwind posted by 8 people provero idonaldson jeremymiller Geknitics qayub Journal picks yyfwuhan djkt
	BFAST: An Alignment Tool for Large Scale Genome Resequencing [My Copy] PloS one In PLoS ONE, Vol. 4, No. 11. (11 November 2009), e7767. by Nils Homer, Barry Merriman, Stanley F. Nelson posted by 10 people darian MarkFiers gdb oannes n00c friendpine zwang druvus torfinnnome idonaldson
	Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression [My Copy] Genome Research, Vol. 19, No. 12. (3 December 2009), pp. 2172-2184. by Yong Cheng, Weisheng Wu, Swathi Ashok Kumar, et al.Duonan Yu, Wulan Deng, Tamara Tripic, David C. King, Kuan-Bei Chen, Ying Zhang, Daniela Drautz, Belinda Giardine, Stephan C. Schuster, Webb Miller, Francesca Chiaromonte, Yu Zhang, Gerd A. Blobel, Mitchell J. Weiss, Ross C. Hardison posted by 4 people provero polivares djkt idonaldson
	Combinatorial binding predicts spatio-temporal cis-regulatory activity. [My Copy] Nature In Nature, Vol. 462, No. 7269. (5 November 2009), pp. 65-70. by Robert P. Zinzen, Charles Girardot, Julien Gagneur, Martina Braun, Eileen E. Furlong posted by 16 people marti gderwin idonaldson maximilianh cajunsushi emptyhb toszko roys inesdesantiago fenghezi balabu iskathy djkt megraw TRHvidsten pedrobeltrao
	Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling [My Copy] Cell, Vol. 139, No. 3. (30 October 2009), pp. 610-622. by Shaohui Hu, Zhi Xie, Akishi Onishi, et al.Xueping Yu, Lizhi Jiang, Jimmy Lin, Hee-sool Rho, Crystal Woodard, Hong Wang, Jun-Seop Jeong posted by 5 people psique tmmurali renatomilani idonaldson maximilianh
	A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays [My Copy] BMC Genomics, Vol. 10, No. 1. (27 October 2009), 497. by Danette Hartzell, Nathan Trinklein, Jacqui Mendez, et al.Nancy Murphy, Shelley Aldred, Keith Wood, Marjeta Urh posted by 1 person idonaldson
	G-compass: a web-based comparative genome browser between human and other vertebrate genomes [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 24. (15 December 2009), pp. 3321-3322. by Yoshihiro Kawahara, Ryuichi Sakate, Akihiro Matsuya, et al.Katsuhiko Murakami, Yoshiharu Sato, Hao Zhang, Takashi Gojobori, Takeshi Itoh, Tadashi Imanishi posted by 6 people nuin idonaldson kshameer operon neils druvus
	High-resolution nucleosome mapping reveals transcription-dependent promoter packaging [My Copy] Genome Research, Vol. 20, No. 1. (21 January 2010), pp. 90-100. by Assaf Weiner, Amanda Hughes, Moran Yassour, Oliver J. Rando, Nir Friedman posted by 9 people megraw lp2 TRHvidsten arthegall venancio natstreet Epigenetics sebastien_vigneau idonaldson
	Windshield splatter analysis with the Galaxy metagenomic pipeline [My Copy] Genome Research, Vol. 19, No. 11. (9 November 2009), pp. 2144-2153. by Sergei Kosakovsky Pond, Samir Wadhawan, Francesca Chiaromonte, et al.Guruprasad Ananda, Wen-Yu Chung, James Taylor, Anton Nekrutenko posted by 15 people dansullivanblk dutilh kiekyon Thaverkamp jmeppley seb1 microbiology_nijmegen Katje iSEEM djkt operon neils idonaldson jgill kshameer
	A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome [My Copy] Genome Biology, Vol. 10, No. 10. (2009), R109. by Cizhong Jiang, B. Franklin Pugh posted by 4 people idonaldson venancio aalibes lp2
	Discovering multiple realistic TFBS motifs based on a generalized model [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (7 October 2009), 321. by Tak M. Chan, Gang Li, Kwong S. Leung, Kin H. Lee posted by 5 people nuin heliopais idonaldson maximilianh ashishanand
	W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3191-3193. by Victor X. Jin, Jeff Apostolos, Naga S. Nagisetty, Peggy J. Farnham posted by 5 people bsamal idonaldson farhat nklee maximilianh
	Phosphorylation of the Human MicroRNA-Generating Complex Mediates MAPK/Erk Signaling [My Copy] Cell, Vol. 139, No. 1. (02 October 2009), pp. 112-122. by Zain Paroo, Xuecheng Ye, She Chen, Qinghua Liu posted by 5 people idonaldson microRNA heliopais gbloeb valeriehilgers
	A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG) [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2863-2864. by Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. De La Vega posted by 4 people seb1 idonaldson n00c druvus
	BayesPeak: Bayesian analysis of ChIP-seq data [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 299. by Christiana Spyrou, Rory Stark, Andy Lynch, Simon Tavare posted by 16 people Vincent_Rouilly Bioinformatics tonamswish dswan fenghezi inesdesantiago idonaldson JLab BergmanLab polivares mkiyer druvus Mycology stajich humburg rschulz
	CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses [My Copy] Nucl. Acids Res., Vol. 37, No. 19. (1 October 2009), pp. 6305-6315. by Helge G. Roider, Boris Lenhard, Aditi Kanhere, Stefan A. Haas, Martin Vingron posted by 5 people bmajoros BergmanLab daveGerrard idonaldson maximilianh
	Close encounters of the 3C kind: long-range chromatin interactions and transcriptional regulation [My Copy] Brief Funct Genomic Proteomic, Vol. 8, No. 4. (1 July 2009), pp. 297-309. by Robert-Jan Theo Sijtse Palstra posted by 1 person idonaldson
	The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. [My Copy] Blood, Vol. 113, No. 22. (28 May 2009), pp. 5456-5465. by Nicola K. Wilson, Diego Miranda-Saavedra, Sarah Kinston, et al.Nicolas Bonadies, Samuel D. Foster, Fernando Calero-Nieto, Mark A. Dawson, Ian J. Donaldson, Stephanie Dumon, Jonathan Frampton, Rekin's Janky, Xiao-Hong H. Sun, Sarah A. Teichmann, Andrew J. Bannister, Berthold Göttgens posted by 1 person idonaldson
	ID1 promotes expansion and survival of primary erythroid cells and is a target of JAK2V617F-STAT5 signaling. [My Copy] Blood, Vol. 114, No. 9. (27 August 2009), pp. 1820-1830. by Andrew D. Wood, Edwin Chen, Ian J. Donaldson, et al.Shilpa Hattangadi, Karly A. Burke, Mark A. Dawson, Diego Miranda-Saavedra, Harvey F. Lodish, Anthony R. Green, Berthold Göttgens posted by 1 person idonaldson
	ChIP\|[ndash]\|seq: advantages and challenges of a maturing technology [My Copy] Nature Reviews Genetics, Vol. 10, No. 10. (08 September 2009), pp. 669-680. by Peter J. Park posted by 32 people guhjy akakak hzoltan dchughes RyuOgawa heliopais giovenko inesdesantiago pradiptaray dakelley clearbluespring akundaje rdiaz kimorley leliavski humburg reyez Journal picks qayub fenghezi tonamswish Orengo Group Journal Picks robertrentzsch JLab BergmanLab polivares idonaldson rschulz CTCF Chromatin cvaldes danmaclean
	TagDust--a program to eliminate artifacts from next generation sequencing data [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2839-2840. by Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub posted by 25 people GustavoLacerda humburg darian orzenil hzoltan chvlyl operon kshameer djkt rtogawa seb1 idonaldson nuin debasis jgill GeeSharpMinor Journal picks sotacam torfinnnome walshtp heliopais jandot n00c rschulz druvus
	Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2739-2740. by Olivier Sand, Morgane Thomas-Chollier, Jacques van Helden posted by 5 people druvus inesdesantiago idonaldson natstreet sebastien_vigneau
	Updates to the RMAP short-read mapping software [My Copy] Bioinformatics In Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2841-2842. by Andrew D. Smith, Wen-Yu Chung, Emily Hodges, et al.Jude Kendall, Greg Hannon, James Hicks, Zhenyu Xuan, Michael Q. Zhang posted by 10 people seb1 darian natstreet djkt rtogawa idonaldson heliopais Journal picks n00c druvus
	From gene expression to gene regulatory networks in Arabidopsis thaliana [My Copy] BMC Systems Biology, Vol. 3, No. 1. (3 September 2009), 85. by Chris Needham, Iain Manfield, Andrew Bulpitt, Philip Gilmartin, David Westhead posted by 12 people icecrown drmacgregor idonaldson pengchy Borelli ptrobajo danmaclean TRHvidsten rmk barriot natstreet druvus
	Dissecting Nucleosome Free Regions by a Segmental Semi-Markov Model [My Copy] PLoS ONE, Vol. 4, No. 3. (6 March 2009), e4721. by Wei Sun, Wei Xie, Feng Xu, Michael Grunstein, Ker-Chau Li posted by 3 people BergmanLab cisevol idonaldson
	Chromatin poises miRNA- and protein-coding genes for expression. [My Copy] Genome research, Vol. 19, No. 10. (27 October 2009), pp. 1742-1751. by Artem Barski, Raja Jothi, Suresh Cuddapah, et al.Kairong Cui, Tae-Young Y. Roh, Dustin E. Schones, Keji Zhao posted by 12 people tonamswish microRNA heliopais samgj polivares megraw inesdesantiago Neuroblastoma fpattyn djkt fenghezi idonaldson
	A Quick Guide to Teaching R Programming to Computational Biology Students [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000482. by Stephen J. Eglen posted by 72 people mgaldino provero PabloMarin idonaldson bsamal nuin kaliczp maren sobolevnrm ltitodem zchen75 artaban421 natstreet jasonn tomhebbron psique Bioinformatics - CRUK Stew eshirdel guhjy polivares ajw fishtank diamantis fastjoe23 kshameer daveGerrard hrogers JoeBanks BergmanLab cisevol srijit hwright Ayest VGreiff welliegirl asadrahman rdiaz ptrobajo heliopais coffeerv Vincent_Rouilly marekrud tnhh barry ansobol Zephyrus walshtp bertelsen fgibson pkonings Borelli klauso dlizcano dswan skembel djkt jclau lwaldron phoenixzxl timhubbard eLearning in Leicester AJCann thegoose dullhunk brianb neils silberbauer daforerog Journal picks ppgardne druvus
	CEAS: cis-regulatory element annotation system [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2605-2606. by Hyunjin Shin, Tao Liu, Arjun K. Manrai, X. Shirley Liu posted by 7 people bsamal maximilianh druvus ewilban1 guhjy idonaldson nuin
	LookSeq: A browser-based viewer for deep sequencing data [My Copy] Genome Research, Vol. 19, No. 11. (29 November 2009), pp. 2125-2132. by Heinrich M. Manske, Dominic P. Kwiatkowski posted by 31 people humburg hzoltan darian dakelley tonamswish inesdesantiago Thaverkamp BergmanLab idonaldson heliopais owhitney GustavoLacerda ngehlenborg sandfire fpattyn xianjun katholt stubrown orzenil operon guhjy kongl Mycology stajich n00c torfinnnome nuin kshameer neils druvus natstreet
	Insights from genomic profiling of transcription factors [My Copy] Nature Reviews Genetics, Vol. 10, No. 9. (11 August 2009), pp. 605-616. by Peggy J. Farnham posted by 26 people GustavoLacerda vingron roys guhjy provero bsamal heliopais inesdesantiago fenghezi nklee samanthacooper fpattyn druvus frohike stubrown Journal picks qayub megraw TRHvidsten Chinnaiyan Lab mkiyer ericrpaquet ilyashl jbhiatt idonaldson danmaclean
	Statistical detection of cooperative transcription factors with similarity adjustment [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2103-2109. by Utz J. Pape, Holger Klein, Martin Vingron posted by 4 people bsamal idonaldson TRHvidsten djkt
	The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2730-2731. by John W. Nicol, Gregg A. Helt, Steven G. Blanchard, Archana Raja, Ann E. Loraine posted by 14 people n00c Bioinformatics Core Service jforment ronbun_2009au dokky inesdesantiago daforerog torfinnnome idonaldson pkonings sebastien_vigneau guhjy natstreet druvus
	Distinguishing direct versus indirect transcription factor-DNA interactions. [My Copy] Genome research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk posted by 15 people icecrown roys sebastien_vigneau oannes nklee djkt vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD[trade] system [My Copy] Nat Meth, Vol. 6, No. 4. (April 2009) by Anjali Shah posted by 1 person idonaldson
	RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2615-2616. by Nicole Cloonan, Qinying Xu, Geoffrey J. Faulkner, et al.Darrin F. Taylor, Dave T. P. Tang, Gabriel Kolle, Sean M. Grimmond posted by 16 people hzoltan idonaldson cthachuk ethanmj cassj GeeSharpMinor Journal picks sbmontgomery shyamsg natstreet dswan druvus samgj n00c guhjy GustavoLacerda
	Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions [My Copy] Genome Biology, Vol. 10, No. 7. (23 July 2009), R80. by Stewart MacArthur, Xiao Y. Li, Jingyi Li, et al.James Brown, Hou C. Chu, Lucy Zeng, Brandi Grondona, Aaron Hechmer, Lisa Simirenko, Soile Keranen, David Knowles, Mark Stapleton, Peter Bickel, Mark Biggin, Michael Eisen posted by 15 people bsamal venancio aalibes fenghezi idonaldson BergmanLab daveGerrard megraw scjparker maximilianh djkt isimpson Bioinformatics - CRUK Stew druvus
	Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP. [My Copy] Nucleic acids research, Vol. 37, No. 12. (1 July 2009), e85. by A. Ameur, A. Rada-Iglesias, J. Komorowski, C. Wadelius posted by 3 people guhjy idonaldson Journal picks
	ViTraM: visualization of transcriptional modules. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 18. (15 September 2009), pp. 2450-2451. by Hong Sun, Karen Lemmens, Tim Van den Bulcke, Kristof Engelen, Bart De Moor, Kathleen Marchal posted by 5 people idonaldson natstreet TRHvidsten guhjy frohike
	JBrowse: a next-generation genome browser. [My Copy] Genome research, Vol. 19, No. 9. (1 September 2009), pp. 1630-1638. by Mitchell E. Skinner, Andrew V. Uzilov, Lincoln D. Stein, Christopher J. Mungall, Ian H. Holmes posted by 33 people ongenetics dullhunk hzoltan darian mkiyer daforerog n00c torfinnnome fenghezi djkt WXuan Zephyrus idonaldson pkonings inesdesantiago jcbarret jamselem aprasad urgi polivares cassj guhjy giovanni druvus natstreet fpattyn BergmanLab cisevol danmaclean Journal picks timhubbard operon neils
	Managing and analyzing next-generation sequence data. [My Copy] PLoS computational biology In PLoS Comput Biol, Vol. 5, No. 6. (26 June 2009), e1000369. by Brent G. Richter, David P. Sexton posted by 54 people frohike michaelbarton Jporci kevinemamy heliopais Bioinformatics Core Service jforment jfr burak idoerg Geknitics cthachuk hzoltan chvlyl sameersoi hpaces gdv GeeSharpMinor idonaldson darian daveGerrard tharris Yanno inesdesantiago jcaddy agbiotec humburg Zephyrus daforerog stubrown GustavoLacerda torfinnnome natstreet BergmanLab polivares orzenil kongl guhjy druvus n00c leemond31 nuin operon jasontsai jmeppley rdiaz Bioinformatics dswan reyez kshameer TRHvidsten djkt Journal picks ppgardne
	Comparison of comparative genomic hybridization technologies across microarray platforms. [My Copy] Journal of biomolecular techniques : JBT, Vol. 20, No. 2. (April 2009), pp. 135-151. by Susan D. Hester, Laura Reid, Norma Nowak, et al.Wendell D. Jones, Joel S. Parker, Kevin Knudtson, William Ward, Jay Tiesman, Nancy D. Denslow posted by 3 people shikin rdiaz idonaldson
	Extracting transcription factor targets from ChIP-Seq data [My Copy] Nucl. Acids Res., Vol. 37, No. 17. (1 September 2009), e113. by Geetu Tuteja, Peter White, Jonathan Schug, Klaus H. Kaestner posted by 19 people hzoltan Vincent_Rouilly mfgreen ewilban1 idonaldson guhjy Chinnaiyan Lab mkiyer rschulz fenghezi clearbluespring thegoose robeirne inesdesantiago SIMR bioinformatics malcook BergmanLab polivares Journal picks
	Text-based over-representation analysis of microarray gene lists with annotation bias. [My Copy] Nucleic acids research, Vol. 37, No. 11. (1 June 2009), e79. by Hui Sun S. Leong, David Kipling posted by 4 people Orengo Group Journal Picks davidalee rdiaz idonaldson
	Circos: An information aesthetic for comparative genomics [My Copy] Genome Research, Vol. 19, No. 9. (18 September 2009), pp. 1639-1645. by Martin Krzywinski, Jacqueline Schein, Ä°nanã§ Birol, et al.Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones, Marco A. Marra posted by 14 people GustavoLacerda jmeppley jmanning2k djkt rdiaz pkonings natstreet chrisamiller aprasad BergmanLab cisevol nuin idonaldson kshameer
	The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes [My Copy] Genome research In Genome Research, Vol. 19, No. 7. (4 July 2009), pp. 1316-1323. by Kim D. Pruitt, Jennifer Harrow, Rachel A. Harte, et al.Craig Wallin, Mark Diekhans, Donna R. Maglott, Steve Searle, Catherine M. Farrell, Jane E. Loveland, Barbara J. Ruef, Elizabeth Hart, Marie-Marthe Suner, Melissa J. Landrum, Bronwen Aken, Sarah Ayling, Robert Baertsch, Julio Fernandez-Banet, Joshua L. Cherry, Val Curwen, Michael DiCuccio, Manolis Kellis, Jennifer Lee, Michael F. Lin, Michael Schuster, Andrew Shkeda, Clara Amid, Garth Brown, Oksana Dukhanina, Adam Frankish, Jennifer Hart, Bonnie L. Maidak, Jonathan Mudge, Michael R. Murphy, Terence Murphy, Jeena Rajan, Bhanu Rajput, Lillian D. Riddick, Catherine Snow, Charles Steward, David Webb, Janet A. Weber, Laurens Wilming, Wenyu Wu, Ewan Birney, David Haussler, Tim Hubbard, James Ostell, Richard Durbin, David Lipman posted by 8 people bpcusack jfr ptrobajo megraw timhubbard idonaldson Journal picks ppgardne
	Identifying regulatory elements in eukaryotic genomes [My Copy] Brief Funct Genomic Proteomic In Brief Funct Genomic Proteomic, Vol. 8, No. 4. (1 July 2009), pp. 215-230. by Leelavati Narlikar, Ivan Ovcharenko posted by 6 people bsamal daveGerrard Journal picks ppgardne natstreet idonaldson
	The Sequence Alignment/Map format and SAMtools. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 16. (15 August 2009), pp. 2078-2079. by Heng Li, Bob Handsaker, Alec Wysoker, et al.Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup posted by 32 people MarkFiers n00c darian cthachuk hzoltan seb1 heliopais urgi idonaldson GustavoLacerda stubrown cassj kshameer ciax BergmanLab polivares carlosjavierna jandot katholt jmcq guhjy orzenil jasontsai operon farhat Journal picks AlexBateman chrisamiller nuin natstreet sandfire druvus
	Computational methods for the detection of cis-regulatory modules [My Copy] Brief Bioinform In Brief Bioinform, Vol. 10, No. 5. (4 June 2009), pp. bbp025-524. by Peter V. Loo, Peter Marynen posted by 9 people mpizbioinfo bsamal reyez idonaldson kshameer nklee BergmanLab cisevol druvus
	SOAP2: an improved ultrafast tool for short read alignment. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1966-1967. by Ruiqiang Li, Chang Yu, Yingrui Li, et al.Tak-Wah W. Lam, Siu-Ming M. Yiu, Karsten Kristiansen, Jun Wang posted by 38 people jts Mycology stajich darian nuin hzoltan agbiotec torfinnnome natstreet cthachuk Bioinformatics Core Service jforment GustavoLacerda adijr bozdagd stubrown BergmanLab polivares guhjy Orengo Group Journal Picks ollieredfernwork operon cassj adamjamesreid Bioinformatics - CRUK Stew jamselem Bioinformatics dswan Journal picks idonaldson TRHvidsten humburg djkt farhat n00c jmeppley druvus
	Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes [My Copy] Nucl. Acids Res. In Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W247-252. by Federico Zambelli, Graziano Pesole, Giulio Pavesi posted by 8 people GustavoLacerda bsamal druvus natstreet idonaldson nklee nuin isimpson
	Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships [My Copy] Nucleic acids research In Nucl. Acids Res., Vol. 37, No. 13. (1 July 2009), e92. by Ken D. Yokoyama, Uwe Ohler, Gregory A. Wray posted by 3 people bsamal idonaldson maximilianh
	Fewer permutations, more accurate P-values [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i161-168. by Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich posted by 12 people heliopais jfr rdiaz Ayest farhat Journal picks AlexBateman bmajoros idonaldson TRHvidsten djkt sameersoi
	DISCOVER: a feature-based discriminative method for motif search in complex genomes [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i321-329. by Wenjie Fu, Pradipta Ray, Eric P. Xing posted by 8 people bsamal guhjy dquest Bioinformatics - CRUK Stew idonaldson thegoose maximilianh
	Efficient exact motif discovery [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i356-364. by Tobias Marschall, Sven Rahmann posted by 6 people bsamal wowalz dquest nuin idonaldson maximilianh
	NTAP: for NimbleGen tiling array ChIP-chip data analysis [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1838-1840. by Kun He, Xueyong Li, Junli Zhou, Xing-Wang Deng, Hongyu Zhao, Jingchu Luo posted by 5 people ashishanand Bioinformatics dswan idonaldson rschulz
	MEME SUITE: tools for motif discovery and searching. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), pp. W202-208. by Timothy L. Bailey, Mikael Boden, Fabian A. Buske, et al.Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble posted by 8 people bsamal suizifish jlike maximilianh natstreet idonaldson nuin cassj
	RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), gkp388. by Deepak Sharma, Debasisa Mohanty, Avadhesha Surolia posted by 5 people maximilianh idonaldson guhjy renatomilani cassj
	Fast and accurate short read alignment with Burrows-Wheeler transform. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1754-1760. by Heng Li, Richard Durbin posted by 41 people jts urgi agbiotec lianping hzoltan cthachuk maren bozdagd adijr heliopais jmanning2k GustavoLacerda stubrown jessopher guhjy katholt mkiyer jmcq idonaldson michaelbarton BergmanLab polivares darian orzenil cassj inesdesantiago TRHvidsten djkt operon SIMR bioinformatics ghattem n00c Bioinformatics danmaclean Journal picks ppgardne nuin rschulz natstreet druvus humburg
	Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1715-1721. by Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin posted by 15 people bsamal jfr tonamswish rdiaz fpattyn Journal picks jcbarret guhjy hendrik85 inesdesantiago nklee polivares ewilban1 idonaldson humburg
	SHRiMP: Accurate Mapping of Short Color-space Reads [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (22 May 2009), e1000386. by Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno posted by 28 people idonaldson heliopais jfr cthachuk hzoltan bozdagd ilanc burak guhjy djkt trfield n00c natstreet adijr druvus Bioinformatics - CRUK Stew farhat humburg kshameer operon Mycology stajich GeeSharpMinor Journal picks AlexBateman Bioinformatics barry
	An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome [My Copy] PLoS ONE, Vol. 4, No. 5. (12 May 2009), e5501. by Kyoung-Jae Won, Saurabh Agarwal, Li Shen, Robert Shoemaker, Bing Ren, Wei Wang posted by 5 people tonamswish guhjy idonaldson BergmanLab cisevol
	How to map billions of short reads onto genomes. [My Copy] Nature biotechnology, Vol. 27, No. 5. (01 May 2009), pp. 455-457. by Cole Trapnell, Steven L. Salzberg posted by 38 people michaelbarton frohike agbiotec burak cthachuk hzoltan tonamswish heliopais giovenko Bioinformatics jfr torfinnnome daforerog jonilaserson Chinnaiyan Lab mkiyer Annab darian BergmanLab polivares SIMR bioinformatics ghattem kiekyon n00c GeeSharpMinor guhjy nuin reyez orzenil Thaverkamp natstreet druvus fenghezi Bioinformatics - CRUK Stew inesdesantiago idonaldson neils
	FDR made easy in differential feature discovery and correlation analyses [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1461-1462. by Xuefeng B. Ling, Harvey Cohen, Joseph Jin, Irwin Lau, James Schilling posted by 8 people heliopais jfr rdiaz fishtank brianb nuin idonaldson guhjy