Genome Biology

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead*, Cole Trapnell, Mihai Pop and Steven L Salzberg

Genome Biology 2009, 10:R25 doi:10.1186/gb-2009-10-3-r25

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BioMed Central: 79 citations

Proceedings   Open Access

Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy

Yanni Sun, Osama Aljawad, Jikai Lei, Alex Liu BMC Bioinformatics 2012, 13(Suppl 3):S12 (21 March 2012)

Research article   Open Access

Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages

Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynanen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R Steffensen, Carsten Carlberg BMC Genomics 2012, 13:50 (31 January 2012)

Technical Note   Open Access Highly Accessed

BarraCUDA - a fast short read sequence aligner using graphics processing units

Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S H Yeo, Brian Y H Lam BMC Research Notes 2012, 5:27 (13 January 2012)

Research article   Open Access

The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs

Peter Arensburger, Robert H Hice, Jennifer A Wright, Nancy L Craig, Peter W Atkinson BMC Genomics 2011, 12:606 (15 December 2011)

Proceedings   Open Access Highly Accessed

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Qiong-Yi Zhao, Yi Wang, Yi-Meng Kong, Da Luo, Xuan Li, Pei Hao BMC Bioinformatics 2011, 12(Suppl 14):S2 (14 December 2011)

Research article   Open Access Highly Accessed

Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

Geng Chen, Ruiyuan Li, Leming Shi, Junyi Qi, Pengzhan Hu, Jian Luo, Mingyao Liu, Tieliu Shi BMC Genomics 2011, 12:590 (2 December 2011)

Research   Open Access

Characterization of the abomasal transcriptome for mechanisms of resistance to gastrointestinal nematodes in cattle

Robert W Li, Manuela Rinaldi, Anthony V Capuco Veterinary Research 2011, 42:114 (30 November 2011)

Proceedings   Open Access

UASIS: Universal Automatic SNP Identification System

Danny C C Poo, Shaojiang Cai, James T L Mah BMC Genomics 2011, 12(Suppl 3):S9 (30 November 2011)

Proceedings   Open Access

Perfect Hamming code with a hash table for faster genome mapping

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda BMC Genomics 2011, 12(Suppl 3):S8 (30 November 2011)

Review   Open Access Highly Accessed

Next-generation sequencing technologies and applications for human genetic history and forensics

Eva C Berglund, Anna Kiialainen, Ann-Christine Syvänen Investigative Genetics 2011, 2:23 (24 November 2011)

Research article   Open Access Highly Accessed

Identification and correction of systematic error in high-throughput sequence data

Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David IK Martin, Meromit Singer, Lior Pachter BMC Bioinformatics 2011, 12:451 (21 November 2011)

Technical Note   Open Access Highly Accessed

Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen

Robert M Givens, Larry D Mesner, Joyce L Hamlin, Michael J Buck, Joel A Huberman BMC Research Notes 2011, 4:499 (16 November 2011)

Research article   Open Access

Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis

Xiaowei S Chen, David Penny, Lesley J Collins BMC Genomics 2011, 12:550 (6 November 2011)

Research article   Open Access Highly Accessed

RNA-Seq improves annotation of protein-coding genes in the cucumber genome

Zhen Li, Zhonghua Zhang, Pengcheng Yan, Sanwen Huang, Zhangjun Fei, Kui Lin BMC Genomics 2011, 12:540 (2 November 2011)

Research article   Open Access

Transcript profiling reveals expression differences in wild-type and glabrous soybean lines

Matt Hunt, Navneet Kaur, Martina Stromvik, Lila Vodkin BMC Plant Biology 2011, 11:145 (26 October 2011)

Method   Open Access Highly Accessed

High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord Genome Biology 2011, 12:R104 (21 October 2011)

The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method

Research article   Open Access

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazumitsu Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi, Yasuyuki Ohkawa BMC Genomics 2011, 12:516 (20 October 2011)

Research   Open Access Highly Accessed

The draft genome and transcriptome of Cannabis sativa

Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011)

The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity

Research article   Open Access

Transcriptome map of mouse isochores

Stilianos Arhondakis, Kimon Frousios, Costas S Iliopoulos, Solon P Pissis, German Tischler, Sophia Kossida BMC Genomics 2011, 12:511 (17 October 2011)

Research article   Open Access Highly Accessed

De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes

Matthew G Links, Eric Holub, Rays HY Jiang, Andrew G Sharpe, Dwayne Hegedus, Elena Beynon, Dean Sillito, Wayne E Clarke, Shihomi Uzuhashi, Mohammad H Borhan BMC Genomics 2011, 12:503 (13 October 2011)

Research article   Open Access

Establishing the baseline level of repetitive element expression in the human cortex

Svitlana Tyekucheva, Robert H Yolken, W McCombie, Jennifer Parla, Melissa Kramer, Sarah J Wheelan, Sarven Sabunciyan BMC Genomics 2011, 12:495 (10 October 2011)

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Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6

Chung-Il An, Yao Dong, Nobuko Hagiwara BMC Developmental Biology 2011, 11:59 (10 October 2011)

Research article   Open Access

Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence

Dario Cantu, Stephen P Pearce, Assaf Distelfeld, Michael W Christiansen, Cristobal Uauy, Eduard Akhunov, Tzion Fahima, Jorge Dubcovsky BMC Genomics 2011, 12:492 (7 October 2011)

Research article   Open Access

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

Özgen Deniz, Oscar Flores, Federica Battistini, Alberto Pérez, Montserrat Soler-López, Modesto Orozco BMC Genomics 2011, 12:489 (7 October 2011)

Research   Open Access Highly Accessed

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data

Iros Barozzi, Alberto Termanini, Saverio Minucci, Gioacchino Natoli Biology Direct 2011, 6:51 (6 October 2011)

Fish the ChIPs is a computational pipeline for complete ChIP-Seq data analysis of unlimited samples; it can be run on any Unix machine while providing a graphic interface for Mac.

Proceedings   Open Access

STELLAR: fast and exact local alignments

Birte Kehr, David Weese, Knut Reinert BMC Bioinformatics 2011, 12(Suppl 9):S15 (5 October 2011)

Method   Open Access

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

Tejasvi S Niranjan, Abby Adamczyk, Héctor Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry, Tao Wang Genome Biology 2011, 12:R93 (28 September 2011)

Two methods are presented, SRFIM and SERVIC4E, for detecting rare variants in pooled exome samples

Research article   Open Access

Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

Jaime I Davila, Maria P Arrieta-Montiel, Yashitola Wamboldt, Jun Cao, Joerg Hagmann, Vikas Shedge, Ying-Zhi Xu, Detlef Weigel, Sally A Mackenzie BMC Biology 2011, 9:64 (27 September 2011)

Research   Open Access Highly Accessed

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

Cyrille Saintenac, Dayou Jiang, Eduard D Akhunov Genome Biology 2011, 12:R88 (14 September 2011)

Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat

Research   Open Access

Expanding whole exome resequencing into non-human primates

Eric J Vallender Genome Biology 2011, 12:R87 (14 September 2011)

Human DNA capture tools are used to capture and sequence non-human primate DNA

Software   Open Access Highly Accessed

WebMGA: a customizable web server for fast metagenomic sequence analysis

Sitao Wu, Zhengwei Zhu, Liming Fu, Beifang Niu, Weizhong Li BMC Genomics 2011, 12:444 (7 September 2011)

Research article   Open Access

Retrotransposon-centered analysis of piRNA targeting shows a shift from active to passive retrotransposon transcription in developing mouse testes

Tobias Mourier BMC Genomics 2011, 12:440 (1 September 2011)

Research   Open Access Highly Accessed

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, Hongshi Yu, Kirsty R Short, Hannah V Siddle, Stephen R Frankenberg, Keng Chew, Brandon R Menzies, Jessica M Stringer, Shunsuke Suzuki, Timothy A Hore, Margaret L Delbridge et al. Genome Biology 2011, 12:R81 (19 August 2011)

This article is part of a collection on The tammar wallaby genome...

The tammar wallaby genome and transcriptome sequences yield insights into many aspects of mammalian biology

Software   Open Access Highly Accessed

SAMQA: error classification and validation of high-throughput sequenced read data

Thomas Robinson, Sarah Killcoyne, Ryan Bressler, John Boyle BMC Genomics 2011, 12:419 (18 August 2011)

Method   Open Access Highly Accessed

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

David L Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L Skalsky, Jack D Keene, Uwe Ohler Genome Biology 2011, 12:R79 (18 August 2011)

A method for identifying RNA binding sites and miRNA target motifs from PAR-CLIP data

Research   Open Access Highly Accessed

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer Genome Biology 2011, 12:R76 (16 August 2011)

Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea

Method   Open Access Highly Accessed

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

Daehwan Kim, Steven L Salzberg Genome Biology 2011, 12:R72 (11 August 2011)

A tool for discovery of fusion transcripts in RNA-seq data, based on the efficient TopHat algorithm

Software   Open Access Highly Accessed

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin N Dewey BMC Bioinformatics 2011, 12:323 (4 August 2011)

RSEM is a new user-friendly software tool for quantifying transcript abundance from RNA-seq data that does not rely on a reference genome and is particularly useful for quantification with de novo transcriptome assemblies

Correspondence   Open Access Highly Accessed

Addressing challenges in the production and analysis of illumina sequencing data

Martin Kircher, Patricia Heyn, Janet Kelso BMC Genomics 2011, 12:382 (29 July 2011)

Janet Kelso and colleagues review the potential problems and suggested solutions for users of Illumina sequencers, including general principles for library preparation, image analysis, run parameters and handling of sequences containing adapter chimeras.

Software   Open Access Highly Accessed

ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

Brad A Friedman, Tom Maniatis Genome Biology 2011, 12:R69 (28 July 2011)

A web-based RNA-seq and microarray analysis tool

Proceedings   Open Access

A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data

Yufeng Shen, Yiwei Gu, Itsik Pe’er BMC Bioinformatics 2011, 12(Suppl 6):S4 (28 July 2011)

Proceedings   Open Access

Assembly of non-unique insertion content using next-generation sequencing

Nathaniel Parrish, Farhad Hormozdiari, Eleazar Eskin BMC Bioinformatics 2011, 12(Suppl 6):S3 (28 July 2011)

Methodology article   Open Access

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data

Hyunsoo Kim, Yingtao Bi, Sharmistha Pal, Ravi Gupta, Ramana V Davuluri BMC Bioinformatics 2011, 12:305 (27 July 2011)

Software   Open Access Highly Accessed

Applications of the pipeline environment for visual informatics and genomics computations

Ivo D Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A Knowles, Andrew P Clark, John D Van Horn, Joseph Ames, Carl Kesselman, Arthur W Toga BMC Bioinformatics 2011, 12:304 (26 July 2011)

Methodology article   Open Access Highly Accessed

Identification of genomic indels and structural variations using split reads

Zhengdong D Zhang, Jiang Du, Hugo Lam, Alex Abyzov, Alexander E Urban, Michael Snyder, Mark Gerstein BMC Genomics 2011, 12:375 (25 July 2011)

A new method for the identification of structural variations and indels based on split reads in short read sequencing allows discovery of the precise location and sequence of structural variants covering the whole size spectrum.

Research article   Open Access Highly Accessed

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

Prabin Bajgain, Bryce A Richardson, Jared C Price, Richard C Cronn, Joshua A Udall BMC Genomics 2011, 12:370 (18 July 2011)

Research   Open Access Highly Accessed

A comparative analysis of DNA methylation across human embryonic stem cell lines

Pao-Yang Chen, Suhua Feng, Jong Joo, Steve E Jacobsen, Matteo Pellegrini Genome Biology 2011, 12:R62 (6 July 2011)

A comparison of DNA methylation in three human embryonic stem cell lines

Research article   Open Access Highly Accessed

Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

Melissa ML Wong, Charles H Cannon, Ratnam Wickneswari BMC Genomics 2011, 12:342 (5 July 2011)

Software   Open Access Highly Accessed

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

Xutao Deng BMC Bioinformatics 2011, 12:267 (29 June 2011)

Research article   Open Access Highly Accessed

Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus

Roberto A Barrero, Gabriel Keeble-Gagnère, Bing Zhang, Paula Moolhuijzen, Kazuho Ikeo, Yoshio Tateno, Takashi Gojobori, Felix D Guerrero, Ala Lew-Tabor, Matthew Bellgard BMC Genomics 2011, 12:328 (24 June 2011)

Anciently acquired microRNAs, discovered in the cattle tick Rhipicephalus microplus, tend to be highly conserved and ubiquitously expressed across tissues and life stages when compared to newly acquired tick-specific miRNAs.

Method   Open Access Highly Accessed

Sniper: improved SNP discovery by multiply mapping deep sequenced reads

Daniel F Simola, Junhyong Kim Genome Biology 2011, 12:R55 (20 June 2011)

A method for improved SNP discovery in next-generation sequencing data

Research article   Open Access Highly Accessed

The characterisation of piRNA-related 19mers in the mouse

Harald M Oey, Neil A Youngson, Emma Whitelaw BMC Genomics 2011, 12:315 (15 June 2011)

Technical Note   Open Access Highly Accessed

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping

Tung Nguyen, Weisong Shi, Douglas Ruden BMC Research Notes 2011, 4:171 (6 June 2011)

Review   Open Access Highly Accessed

Microarrays, deep sequencing and the true measure of the transcriptome

John H Malone, Brian Oliver BMC Biology 2011, 9:34 (31 May 2011)

Global measures of gene expression can now be extracted either from microarrays or from RNA-seq, which do not always seem to give the same answer. Malone and Oliver review the advantages and limitations of each and conclude that, with some important exceptions, they tell the same story.

Methodology article   Open Access Highly Accessed

A novel and well-defined benchmarking method for second generation read mapping

Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert BMC Bioinformatics 2011, 12:210 (26 May 2011)

Research   Open Access Highly Accessed

A high resolution map of a cyanobacterial transcriptome

Vikram Vijayan, Isha H Jain, Erin K O'Shea Genome Biology 2011, 12:R47 (25 May 2011)

A detailed transcriptome analysis of the cyanobacterium Synechococcus elongatus reveals widespread non coding transcription and transcript architecture

Proceedings   Open Access

Enhancing genome assemblies by integrating non-sequence based data

Thomas N Heider, James Lindsay, Chenwei Wang, Rachel J O’Neill, Andrew J Pask BMC Proceedings 2011, 5(Suppl 2):S7 (28 April 2011)

Research   Open Access

Repeat-aware modeling and correction of short read errors

Xiao Yang, Srinivas Aluru, Karin S Dorman BMC Bioinformatics 2011, 12(Suppl 1):S52 (15 February 2011)

Research   Open Access

A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns

Sung-Joon Park, Kenta Nakai BMC Bioinformatics 2011, 12(Suppl 1):S50 (15 February 2011)

Research   Open Access

UMARS: Un-MAppable Reads Solution

Sung-Chou Li, Wen-Ching Chan, Chun-Hung Lai, Kuo-Wang Tsai, Chun-Nan Hsu, Yuh-Shan Jou, Hua-Chien Chen, Chun-Hong Chen, Wen-chang Lin BMC Bioinformatics 2011, 12(Suppl 1):S9 (15 February 2011)

Research   Open Access

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

Shaun Mahony, Esteban O Mazzoni, Scott McCuine, Richard A Young, Hynek Wichterle, David K Gifford Genome Biology 2011, 12:R2 (13 January 2011)

ChIP-seq for retinoic acid receptor binding during early neuronal differentiation reveals a complex landscape of transcriptional control.

Proceedings   Open Access Highly Accessed

Galaxy CloudMan: delivering cloud compute clusters

Enis Afgan, Dannon Baker, Nate Coraor, Brad Chapman, Anton Nekrutenko, James Taylor BMC Bioinformatics 2010, 11(Suppl 12):S4 (21 December 2010)

Proceedings   Open Access Highly Accessed

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

Ronald C Taylor BMC Bioinformatics 2010, 11(Suppl 12):S1 (21 December 2010)

Proceedings   Open Access

NGSQC: cross-platform quality analysis pipeline for deep sequencing data

Manhong Dai, Robert C Thompson, Christopher Maher, Rafael Contreras-Galindo, Mark H Kaplan, David M Markovitz, Gil Omenn, Fan Meng BMC Genomics 2010, 11(Suppl 4):S7 (2 December 2010)

Proceedings   Open Access

Quail Genomics: a knowledgebase for Northern bobwhite

Arun Rawat, Kurt A Gust, Mohamed O Elasri, Edward J Perkins BMC Bioinformatics 2010, 11(Suppl 6):S13 (7 October 2010)

Research highlight   Free Highly Accessed

The missing graphical user interface for genomics

Michael C Schatz Genome Biology 2010, 11:128 (25 August 2010)

The Galaxy package for genomic analysis empowers regular users through a much-needed and user-friendly graphical web interface.

Software   Open Access Highly Accessed

Cloud-scale RNA-sequencing differential expression analysis with Myrna

Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010)

This article is part of a collection on Cloud computing tools and...

Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.

Poster presentation   Open Access

Next-gen sequencing of multi-drug resistant Acinetobacter baumannii to determine antibiotic resistance genotypes

Leon Dent, Dana Marshall, Robert Hulette, Siddharth Pratap BMC Bioinformatics 2010, 11(Suppl 4):P16 (23 July 2010)

Research   Open Access Highly Accessed

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010)

The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.

Software   Open Access

Design and evaluation of genome-wide libraries for RNA interference screens

Thomas Horn, Thomas Sandmann, Michael Boutros Genome Biology 2010, 11:R61 (15 June 2010)

NEXT-RNAi allows the design and evaluation of genome-wide RNAi screens in any organism.

Research article   Open Access

Effects of Alu elements on global nucleosome positioning in the human genome

Yoshiaki Tanaka, Riu Yamashita, Yutaka Suzuki, Kenta Nakai BMC Genomics 2010, 11:309 (17 May 2010)

Software   Open Access Highly Accessed

BS Seeker: precise mapping for bisulfite sequencing

Pao-Yang Chen, Shawn J Cokus, Matteo Pellegrini BMC Bioinformatics 2010, 11:203 (23 April 2010)

Research article   Open Access Highly Accessed

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

James H Bullard, Elizabeth Purdom, Kasper D Hansen, Sandrine Dudoit BMC Bioinformatics 2010, 11:94 (18 February 2010)

Research article   Open Access Highly Accessed

An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data

Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A Wilson, Dabing Zhang BMC Bioinformatics 2010, 11:81 (9 February 2010)

Method   Open Access Highly Accessed

Gene ontology analysis for RNA-seq: accounting for selection bias

Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack Genome Biology 2010, 11:R14 (4 February 2010)

GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq

Software   Open Access

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes

Chunguang Liang, Alexander Schmid, María López-Sánchez, Andres Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar BMC Bioinformatics 2009, 10:391 (29 November 2009)

Software   Open Access Highly Accessed

Searching for SNPs with cloud computing

Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009)

This article is part of a collection on Cloud computing tools and...

Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.

Software   Open Access Highly Accessed

Simultaneous alignment of short reads against multiple genomes

Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, Detlef Weigel Genome Biology 2009, 10:R98 (17 September 2009)

New software for the alignment of short-read sequence data to multiple genomes allows identification of polymorphisms that cannot be identified by alignment to a single reference genome.

Minireview   Free

The need for speed

Paul Flicek Genome Biology 2009, 10:212 (27 March 2009)

A new sequence-alignment algorithm that uses advanced data structures to help data analysis keep pace with data generation.