dakelley's library 262 articles Export

	Cancer genome sequencing: a review [My Copy] Hum. Mol. Genet., Vol. 18, No. R2. (15 October 2009), pp. R163-168. by Elaine R. Mardis, Richard K. Wilson posted to short-reads review cancer by dakelley on 2009-11-02 17:13:02 as along with 2 people desany jmanning2k
	Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2878-2881. by Bas E. Dutilh, Martijn A. Huynen, Marc Strous posted to short-reads sequence-alignment metagenomics assembly by dakelley on 2009-11-02 04:32:58 as along with 7 people and 1 group druvus kinestetika ThomasDOtto jasontsai skembel sharpton jmeppley iSEEM
	De novo transcriptome assembly with ABySS [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2872-2877. by Inanc Birol, Shaun D. Jackman, Cydney B. Nielsen, et al.Jenny Q. Qian, Richard Varhol, Greg Stazyk, Ryan D. Morin, Yongjun Zhao, Martin Hirst, Jacqueline E. Schein, Doug E. Horsman, Joseph M. Connors, Randy D. Gascoyne, Marco A. Marra, Steven J. M. Jones posted to short-reads rna-seq de-bruijn assembly by dakelley on 2009-11-02 04:28:46 as along with 9 people dswan torfinnnome TRHvidsten rtogawa ramonvidal stubrown darshan GustavoLacerda druvus
	Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2865-2871. by Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning posted to structural_variation short-reads by dakelley on 2009-11-01 22:41:59 as along with 5 people torfinnnome n00c natstreet druvus vplagnol
	Maximum likelihood genome assembly. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 16, No. 8. (August 2009), pp. 1101-1116. by Paul Medvedev, Michael Brudno posted to theory assembly by dakelley on 2009-10-28 20:31:10 as along with 7 people nuin walshtp djkt n00c natstreet druvus operon
	Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms [My Copy] Nature Methods, Vol. 6, No. 10. (20 September 2009), pp. 767-772. by Tim van Opijnen, Kip L. Bodi, Andrew Camilli posted to genetic-interactions by dakelley on 2009-10-26 22:32:31 as along with 1 person lp2
	Hierarchical Scaffolding With Bambus [My Copy] Genome Research, Vol. 14, No. 1. (January 2004), pp. 149-159. by Mihai Pop, Daniel S. Kosack, Steven L. Salzberg posted to scaffolding assembly by dakelley on 2009-10-26 18:16:23 as along with 4 people and 1 group druvus azazello wenhan Neeperando MBLAB
	BreakDancer: an algorithm for high-resolution mapping of genomic structural variation [My Copy] Nat Meth, Vol. 6, No. 9. (09 August 2009), pp. 677-681. 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 to structural_variation by dakelley on 2009-10-26 05:18:19 as along with 9 people and 1 group fenghezi daed natstreet druvus sitalange qayub gdb jasontsai danmaclean Journal picks
	ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads [My Copy] Genome Biology, Vol. 10, No. 10. (1 October 2009), R103. by Iain MacCallum, Dariusz Przybylski, Sante Gnerre, et al.Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance Shea, Louise Williams, Sarah Young, Chad Nusbaum, David Jaffe posted to short-reads scaffolding de-bruijn assembly by dakelley on 2009-10-23 18:39:55 as along with 10 people and 1 group djkt n00c azazello jgill GustavoLacerda ramonvidal justinhjohnson stajich druvus neils Mycology
	A simple, fast, and accurate method of phylogenomic inference [My Copy] Genome Biology, Vol. 9, No. 10. (13 October 2008), R151. by Martin Wu, Jonathan Eisen posted to metagenomics classification by dakelley on 2009-10-22 20:51:16 as along with 12 people and 2 groups jeargle AaronDarling zwang cgaugain treangen Katje operon ellakat scryrps djkt aramata druvus microbiology_nijmegen iSEEM
	Unsupervised statistical clustering of environmental shotgun sequences [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 316. by Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff, Joshua Weitz posted to metagenomics clustering by dakelley on 2009-10-22 20:50:47 as along with 2 people druvus BioInfoCites
	Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing. [My Copy] Journal of biomedicine & biotechnology, Vol. 2008, No. 1. (2008) by Chon-Kit Kenneth K. Chan, Arthur L. Hsu, Sen-Lin L. Tang, Saman K. Halgamuge posted to metagenomics clustering by dakelley on 2009-10-19 21:26:31 as along with 4 people idoerg azazello druvus alexisfjdufresne
	CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads [My Copy] Research in Computational Molecular Biology (2008), pp. 17-28. by Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai, Jonathan Eisen posted to metagenomics clustering by dakelley on 2009-10-19 21:15:32 as
	Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification [My Copy] Bioinformatics, Vol. 24, No. 14. (15 July 2008), pp. 1568-1574. by Christian Martin, Naryttza N. Diaz, Jorg Ontrup, Tim W. Nattkemper posted to metagenomics clustering by dakelley on 2009-10-19 18:01:16 as along with 2 people inesdesantiago nklee
	Open source clustering software. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 9. (12 June 2004), pp. 1453-1454. by M. J. de Hoon, S. Imoto, J. Nolan, S. Miyano posted to clustering by dakelley on 2009-10-16 23:17:46 as along with 25 people and 7 groups rabio klexa oteri arlam ilyashl matterhorn cswinburne mtagaya macowell davidbroadhurst eme oilcan rahul Ayest balajis piscinero metamerist digisoki wnpx rafamayo atopcu ccr calu karlmicha chad_davis Structural Biology Group TorVergata Fluid-Mechanics-and-Thermal-Science-Research astro SRL Computational_Systems_Biology XMLDataManagement BUiGEM
	Phylogenetic Signals in DNA Composition: Limitations and Prospects [My Copy] Mol Biol Evol, Vol. 26, No. 5. (1 May 2009), pp. 1163-1169. by Jan Mrazek posted to genome_signatures by dakelley on 2009-10-16 23:17:11 as along with 5 people and 1 group jmeppley skembel djkt druvus nuin iSEEM
	Fuzzy Genome Sequence Assembly for Single and Environmental Genomes [My Copy] Fuzzy Systems in Bioinformatics and Computational Biology (2009), pp. 19-44. by Sara Nasser, Adrienne Breland, Frederick Harris, Monica Nicolescu, Gregory Vert posted to metagenomics clustering by dakelley on 2009-10-16 23:05:41 as
	Evidence-Based Clustering of Reads and Taxonomic Analysis of Metagenomic Data [My Copy] Pattern Recognition in Bioinformatics (2009), pp. 102-112. by Gianluigi Folino, Fabio Gori, Mike Jetten, Elena Marchiori posted to metagenomics clustering by dakelley on 2009-10-16 22:57:41 as
	Clustering Metagenome Short Reads Using Weighted Proteins [My Copy] Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (2009), pp. 152-163. by Gianluigi Folino, Fabio Gori, Mike Jetten, Elena Marchiori posted to metagenomics clustering by dakelley on 2009-10-16 22:55:23 as
	Community-wide analysis of microbial genome sequence signatures [My Copy] Genome Biology, Vol. 10, No. 8. (2009), R85. by Gregory Dick, Anders Andersson, Brett Baker, et al.Sheri Simmons, Brian Thomas, A. Pepper Yelton, Jillian Banfield posted to metagenomics genome_signatures clustering by dakelley on 2009-10-16 22:48:54 as along with 7 people and 2 groups druvus bdessailly skembel djkt jonilaserson neils barriot Orengo Group Journal Picks iSEEM
	Genomic Signatures in De Bruijn Chains [My Copy] Algorithms in Bioinformatics (2007), pp. 216-227. by Lenwood Heath, Amrita Pati posted to genome_signatures by dakelley on 2009-10-16 22:34:47 as
	Application of tetranucleotide frequencies for the assignment of genomic fragments [My Copy] Environmental Microbiology, Vol. 6, No. 9. (September 2004), pp. 938-947. by Hanno Teeling, Anke Meyerdierks, Margarete Bauer, Rudolf Amann, Frank O. Glöckner posted to metagenomics genome_signatures clustering by dakelley on 2009-10-16 22:27:24 as along with 7 people Thaverkamp azazello druvus michC bluto george_g mcox
	BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing [My Copy] Genome Research, Vol. 19, No. 10. (6 October 2009), pp. 1884-1895. by Wei-Chun Kao, Kristian Stevens, Yun S. Song posted to short-reads base_calling by dakelley on 2009-10-15 21:03:49 as along with 12 people and 2 groups lp2 megraw rdiaz torfinnnome djkt n00c farhat druvus polivares stajich fpattyn jbhiatt BergmanLab Mycology
	An MCMC algorithm for haplotype assembly from whole-genome sequence data [My Copy] Genome Research, Vol. 18, No. 8. (August 2008), pp. 1336-1346. by Vikas Bansal, Aaron L. Halpern, Nelson Axelrod, Vineet Bafna posted to haplotype by dakelley on 2009-10-14 03:46:18 as along with 1 person xingxu
	OSLay: optimal syntenic layout of unfinished assemblies [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. 1573-1579. by Daniel C. Richter, Stephan C. Schuster, Daniel H. Huson posted to scaffold comparative_assembly assembly by dakelley on 2009-10-13 16:48:11 as along with 4 people n00c AaronDarling azazello GustavoLacerda
	Parametric complexity of sequence assembly: theory and applications to next generation sequencing. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 16, No. 7. (July 2009), pp. 897-908. by Niranjan Nagarajan, Mihai Pop posted to theory assembly by dakelley on 2009-10-13 15:49:40 as along with 3 people n00c sitalange nuin
	Personalized copy number and segmental duplication maps using next-generation sequencing. [My Copy] Nature genetics, Vol. 41, No. 10. (30 October 2009), pp. 1061-1067. by Can Alkan, Jeffrey M. Kidd, Tomas Marques-Bonet, et al.Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O. Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs, Evan E. Eichler posted to structural_variation duplications by dakelley on 2009-10-13 06:00:15 as along with 28 people and 1 group leemachado daed gbenson n00c bozdagd sbmontgomery eshirdel merpublic shyamsg scmelton qayub natstreet fenghezi Annab djkt nuin xingxu jamesmorris rdiaz brant torfinnnome jandot pkonings danmaclean daforerog frohike rschulz gangcai Journal picks
	Correcting base-assignment errors in repeat regions of shotgun assembly. [My Copy] IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 4, No. 1. (r 2007), pp. 54-64. by Degui Zhi, Uri Keich, Pavel Pevzner, Steffen Heber, Haixu Tang posted to duplications assembly by dakelley on 2009-10-12 21:38:04 as along with 2 people n00c ojabado
	A scaffold analysis tool using mate-pair information in genome sequencing. [My Copy] Journal of biomedicine & biotechnology, Vol. 2008 (2008) by Pan-Gyu G. Kim, Hwan-Gue G. Cho, Kiejung Park posted to scaffold assembly by dakelley on 2009-10-12 21:37:07 as along with 2 people orzenil Neeperando
	A machine-learning approach to combined evidence validation of genome assemblies [My Copy] Bioinformatics, Vol. 24, No. 6. (15 March 2008), pp. 744-750. by Jeong-Hyeon Choi, Sun Kim, Haixu Tang, Justen Andrews, Don G. Gilbert, John K. Colbourne posted to post-assembly assembly by dakelley on 2009-10-09 23:36:32 as along with 7 people thegoose2 orzenil GustavoLacerda Neeperando tharris ttuechler bertelsen
	The greedy path-merging algorithm for contig scaffolding [My Copy] J. ACM, Vol. 49, No. 5. (September 2002), pp. 603-615. by Daniel H. Huson, Knut Reinert, Eugene W. Myers posted to theory assembly by dakelley on 2009-10-09 22:45:01 as along with 2 people and 1 group azazello tpreeprem gatech-compgenomics
	A new statistical method for haplotype reconstruction from population data. [My Copy] American journal of human genetics, Vol. 68, No. 4. (April 2001), pp. 978-989. by M. Stephens, N. J. Smith, P. Donnelly posted to haplotype by dakelley on 2009-10-08 19:57:57 as along with 3 people ekostem misonneh kieran101
	Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction [My Copy] Research in Computational Molecular Biology (2009), pp. 271-284. by Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel posted to haplotype by dakelley on 2009-10-05 19:04:34 as along with 1 person jonilaserson
	Principles for the buffering of genetic variation. [My Copy] Science, Vol. 291, No. 5506. (9 February 2001), pp. 1001-1004. by J. L. Hartman, B. Garvik, L. Hartwell posted to genetic-interactions by dakelley on 2009-10-02 22:10:35 as along with 4 people rdowell ajbattle nirfriedman patrycja_missiuro
	The impact of retrotransposons on human genome evolution [My Copy] Nature Reviews Genetics, Vol. 10, No. 10. (01 October 2009), pp. 691-703. by Richard Cordaux, Mark A. Batzer posted to review mobile_genetic_elements by dakelley on 2009-09-29 22:03:14 as along with 4 people and 1 group docv fenghezi Annab qayub Journal picks
	ChIP-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 to review chip-seq by dakelley on 2009-09-29 21:59:53 as along with 22 people and 6 groups dchughes RyuOgawa heliopais giovenko inesdesantiago pradiptaray clearbluespring akundaje rdiaz kimorley leliavski humburg reyez qayub fenghezi tonamswish robertrentzsch polivares idonaldson rschulz cvaldes danmaclean Journal picks Orengo Group Journal Picks JLab BergmanLab CTCF Chromatin
	Building on basic metagenomics with complementary technologies [My Copy] Genome Biology, Vol. 8, No. 12. (28 December 2007), 231. by Falk Warnecke, Philip Hugenholtz posted to metagenomics class by dakelley on 2009-09-28 23:26:29 as along with 3 people and 3 groups alexisfjdufresne mjetten jlgreen microbiology_nijmegen Green Lab iSEEM
	Clustering Variable Length Sequences by Eigenvector Decomposition Using HMM [My Copy] Structural, Syntactic, and Statistical Pattern Recognition (2004), pp. 352-360. by Fatih Porikli posted to hmm clustering by dakelley on 2009-09-28 01:08:43 as
	Assembling the Marine Metagenome, One Cell at a Time [My Copy] PLoS ONE, Vol. 4, No. 4. (23 April 2009), e5299. by Tanja Woyke, Gary Xie, Alex Copeland, et al.José M. González, Cliff Han, Hajnalka Kiss, Jimmy H. Saw, Pavel Senin, Chi Yang, Sourav Chatterji, Jan-Fang Cheng, Jonathan A. Eisen, Michael E. Sieracki, Ramunas Stepanauskas posted to metagenomics assembly by dakelley on 2009-09-24 21:23:08 as along with 10 people and 3 groups inquil hwright jonilaserson jlgreen chocolate2009 jmeppley vaulot Thaverkamp neils skoch3 iSEEM Papers recommended by the Roscoff Plankton Group Microbial-Ecology
	Similarity-Based Clustering of Sequences Using Hidden Markov Models [My Copy] In Machine Learning and Data Mining in Pattern Recognition, vol. LNAI 2734 (2003), pp. 86-95. by Manuele Bicego, Vittorio Murino, Mario A. T. Figueiredo posted to hmm clustering by dakelley on 2009-09-23 22:27:57 as
	G.: Clustering sequence data using hidden Markov model representation [My Copy] In In: Proc. of SPIE’99 Conf. on Data Mining and Knowledge Discovery: Theory (1999), pp. 14-21. by Cen Li, Gautam Biswas posted to hmm clustering by dakelley on 2009-09-23 22:27:43 as
	A Hidden Markov Model-based approach to sequential data clustering [My Copy] Vol. 2396 (2002), pp. 734-742. by Antonello Panuccio, Manuele Bicego, Vittorio Murino posted to hmm clustering by dakelley on 2009-09-23 22:27:12 as
	HMM clustering for connected word recognition [My Copy] Acoustics, Speech, and Signal Processing, 1989. ICASSP-89., 1989 International Conference on (06 August 1989), pp. 405-408 vol.1. by L. R. Rabiner, C. H. Lee, B. H. Juang, J. G. Wilpon posted to hmm clustering by dakelley on 2009-09-23 22:26:37 as
	Clustering Sequences with Hidden Markov Models [My Copy] In Advances in Neural Information Processing Systems, Vol. 9 (1997), pp. 648-654. by Padhraic Smyth posted to hmm clustering by dakelley on 2009-09-23 22:25:53 as along with 3 people jrodriguez donade ChaTo
	Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile [My Copy] Cell, Vol. 123, No. 3. (4 November 2005), pp. 507-519. by Maya Schuldiner, Sean R. Collins, Natalie J. Thompson, et al.Vladimir Denic, Arunashree Bhamidipati, Thanuja Punna, Jan Ihmels, Brenda Andrews, Charles Boone, Jack F. Greenblatt posted to genetic-interactions by dakelley on 2009-09-22 04:38:54 as along with 13 people and 2 groups thegoose2 colmryan nzm ajbattle chasmand tharris adiel okarsligil balajis nirfriedman jtaylor cjhall hplatero C. elegans / WormBase Bioinformatics
	TopHat: discovering splice junctions with RNA-Seq [My Copy] Bioinformatics, Vol. 25, No. 9. (1 May 2009), pp. 1105-1111. by Cole Trapnell, Lior Pachter, Steven L. Salzberg posted to rna-seq by dakelley on 2009-09-21 22:41:19 as along with 21 people and 2 groups heliopais druvus GustavoLacerda stubrown polivares torfinnnome jmcq mtagaya jonilaserson gdb guhjy ThomasDOtto n00c ghattem xingxu djkt vplagnol bertelsen natstreet idoerg vmsr BergmanLab SIMR bioinformatics
	CloudBurst: highly sensitive read mapping with MapReduce [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1363-1369. by Michael C. Schatz posted to sequence-alignment hpc by dakelley on 2009-09-21 22:39:58 as along with 30 people and 2 groups jfr walshtp idonaldson orzenil heliopais bozdagd agbiotec jandot guhjy n00c cymacs semrich nuin operon AlexBateman fgibson rschulz dswan mitko djkt humburg jmeppley coela vagoskar svenrahmann natstreet brianb Neeperando druvus neils KCL & UCL Bioinformatics Bioinformatics
	Get the most out of your metagenome: computational analysis of environmental sequence data. [My Copy] Current opinion in microbiology, Vol. 10, No. 5. (October 2007), pp. 490-498. by Jeroen Raes, Konrad Ulrich U. Foerstner, Peer Bork posted to review metagenomics by dakelley on 2009-09-21 22:21:03 as along with 3 people and 1 group idoerg Pascalichouchou druvus iSEEM
	MetaGene: prokaryotic gene finding from environmental genome shotgun sequences [My Copy] Nucl. Acids Res., Vol. 34, No. 19. (14 November 2006), pp. 5623-5630. by Hideki Noguchi, Jungho Park, Toshihisa Takagi posted to metagenomics gene-finding class by dakelley on 2009-09-21 15:44:20 as along with 5 people and 1 group Thaverkamp jlgreen jmeppley alexl mcox iSEEM
	Sensitive and accurate detection of copy number variants using read depth of coverage [My Copy] Genome Research, Vol. 19, No. 9. (5 September 2009), pp. 1586-1592. by Seungtai Yoon, Zhenyu Xuan, Vladimir Makarov, Kenny Ye, Jonathan Sebat posted to structural_variation by dakelley on 2009-09-09 23:19:43 as along with 7 people woodson8 scmelton torfinnnome n00c rdiaz jbhiatt pkonings

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assembly	62
genetic-interactions	32
short-reads	32
networks	27
metagenomics	26
duplications	22
review	22
structural_variation	18
clustering	17
haplotype	17
sequence-alignment	13
de-bruijn	9
gene-regulation	9
modularity	9
theory	9
gene-finding	8
hmm	8
epigenetics	7
genome	7
network-evolution	7
classification	6
genomics	6
post-assembly	6
biology	5
rna-seq	5
cancer	4
crf	4
genome_signatures	4
scaffolding	4
statistics	4
transcription	4
base_calling	3
comparative_assembly	3
hpc	3
molecular-evolution	3
svm	3
chip-seq	2
class	2
cow	2
intro	2
machine-learning	2
rna	2
scaffold	2
visualization	2
gene-annotation	1
genome-evolution	1
mirna	1
mobile_genetic_elements	1
parallel	1
trimming	1
virology	1

dakelley's library 262 articles Export

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