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1.

34576
Accesses

Method   Open Access Highly Accessed

Differential expression analysis for sequence count data

Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment | F1000 Biology |  Editor’s summary

DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments

2.

31177
Accesses

Software   Open Access Highly Accessed

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

Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R25 (4 March 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.

3.

27870
Accesses

Research   Open Access Highly Accessed

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman Genome Biology 2002, 3:research0034-research0034.11 (18 June 2002)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment |  Editor’s summary

Using real-time reverse transcription PCR ten housekeeping genes from different abundance and functional classes in various human tissues were evaluated. The conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested.

4.

27852
Accesses

Research   Open Access Highly Accessed

VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer

Georges St Laurent, Dmitry Shtokalo, Biao Dong, Michael R Tackett, Xiaoxuan Fan, Sandra Lazorthes, Estelle Nicolas, Nianli Sang, Timothy J Triche, Timothy A McCaffrey, Weidong Xiao, Philipp Kapranov Genome Biology 2013, 14:R73 (22 July 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

The expression of vlincRNAs from retroviral promoters is correlated with pluripotency and malignancy

5.

26880
Accesses

Research   Open Access Highly Accessed

Functional analysis of transcription factor binding sites in human promoters

Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Aldred, Nathan D Trinklein, Richard M Myers, Zhiping Weng Genome Biology 2012, 13:R50 (5 September 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

TFBSs are predicted from ENCODE data, and experiments in four cell lines find 70% to be functional

6.

23101
Accesses

Research   Open Access Highly Accessed

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder, Mark Gerstein Genome Biology 2012, 13:R48 (5 September 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions

7.

22137
Accesses

Research   Open Access Highly Accessed

Modeling gene expression using chromatin features in various cellular contexts

Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method

8.

20644
Accesses

Review   Free Highly Accessed

From RNA-seq reads to differential expression results

Alicia Oshlack, Mark D Robinson, Matthew D Young Genome Biology 2010, 11:220 (22 December 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.

9.

20110
Accesses

Comment   Subscription Highly Accessed

A 10-step guide to party conversation for bioinformaticians

Alicia Oshlack Genome Biology 2013, 14:104 (29 January 2013)

Abstract | Full text | PDF | PubMed | 1 comment |  Editor’s summary

Alicia Oshlack's 10-step guide to party conversation for bioinformaticians

10.

19939
Accesses

Research   Open Access Highly Accessed

The GENCODE pseudogene resource

Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng Mu, Rachel Harte, Suganthi Balasubramanian, Andrea Tanzer, Mark Diekhans, Alexandre Reymond, Tim J Hubbard, Jennifer Harrow, Mark B Gerstein Genome Biology 2012, 13:R51 (5 September 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The GENCODE pseudogene resource includes evidence for dead genes undergoing resurrection

11.

19299
Accesses

Research   Open Access Highly Accessed

Analysis of variation at transcription factor binding sites in Drosophila and humans

Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, Ewan Birney Genome Biology 2012, 13:R49 (5 September 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Transcription factor binding site variability in fly and human provides evidence for a buffering phenomenon

12.

18243
Accesses

Method   Open Access Highly Accessed

A scaling normalization method for differential expression analysis of RNA-seq data

Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A novel and empirical method for normalization of RNA-seq data is presented

13.

18183
Accesses

Method   Open Access Highly Accessed

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield Genome Biology 2011, 12:R44 (19 May 2011)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Reconstructing full length rRNA sequences from short reads to estimate microbial community structure

14.

16367
Accesses

Method   Open Access Highly Accessed

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg Genome Biology 2013, 14:R36 (25 April 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

A major update to TopHat, the popular Bowtie-based spliced aligner

15.

15567
Accesses

Research   Open Access Highly Accessed

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

H Bradley Shaffer, Patrick Minx, Daniel E Warren, Andrew M Shedlock, Robert C Thomson, Nicole Valenzuela, John Abramyan, Chris T Amemiya, Daleen Badenhorst, Kyle K Biggar, Glen M Borchert, Christopher W Botka, Rachel M Bowden, Edward L Braun, Anne M Bronikowski, Benoit G Bruneau, Leslie T Buck, Blanche Capel, Todd A Castoe, Mike Czerwinski, Kim D Delehaunty, Scott V Edwards, Catrina C Fronick, Matthew K Fujita, Lucinda Fulton, Tina A Graves, Richard E Green, Wilfried Haerty, Ramkumar Hariharan, Omar Hernandez et al. Genome Biology 2013, 14:R28 (28 March 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing

16.

15508
Accesses

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)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment | F1000 Biology |  Editor’s summary

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

17.

14068
Accesses

Method   Open Access Highly Accessed

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda Genome Biology 2013, 14:R31 (17 April 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility

18.

14038
Accesses

Method   Open Access Highly Accessed

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li, X Shirley Liu Genome Biology 2008, 9:R137 (17 September 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

MACS performs model-based analysis of ChIP-Seq data generated by short read sequencers.

19.

13808
Accesses

Software   Open Access Highly Accessed

The Transcription Factor Encyclopedia

Dimas Yusuf, Stefanie L Butland, Magdalena I Swanson, Eugene Bolotin, Amy Ticoll, Warren A Cheung, Xiao Cindy Zhang, Christopher TD Dickman, Debra L Fulton, Jonathan S Lim, Jake M Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N de Leeuw, Elizabeth M Simpson, Gerhart U Ryffel, Eric W-F Lam, Ralf Kist, Miranda SC Wilson, Raquel Marco-Ferreres, Jan J Brosens, Leonardo L Beccari, Paola Bovolenta, Bérénice A Benayoun, Lara J Monteiro, Helma DC Schwenen, Lars Grontved, Elizabeth Wederell, Susanne Mandrup, Reiner A Veitia et al. Genome Biology 2012, 13:R24 (29 March 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment |  Editor’s summary

A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system

20.

13510
Accesses

Method   Open Access Highly Accessed

Improving RNA-Seq expression estimates by correcting for fragment bias

Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

An extension to Cufflinks corrects bias in RNA-seq datasets

21.

13494
Accesses

Method   Open Access Highly Accessed

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke Genome Biology 2011, 12:R18 (21 February 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

The optimization of PCR amplification steps in Illumina libraries significantly reduces sequencing bias

22.

13291
Accesses

Method   Open Access Highly Accessed

Bioconductor: open software development for computational biology and bioinformatics

Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang Genome Biology 2004, 5:R80 (15 September 2004)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.

23.

13143
Accesses

Research   Open Access Highly Accessed

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

Seth Frietze, Rui Wang, Lijing Yao, Yu Tak, Zhenqing Ye, Malaina Gaddis, Heather Witt, Peggy J Farnham, Victor X Jin Genome Biology 2012, 13:R52 (5 September 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The transcription factor TCF7L2 can be tethered to the genome by GATA3, and therefore can target sites lacking its own motif

24.

13027
Accesses

Software   Open Access Highly Accessed

CellProfiler: image analysis software for identifying and quantifying cell phenotypes

Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Kang, Ola Friman, David A Guertin, Joo Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini Genome Biology 2006, 7:R100 (31 October 2006)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

CellProfiler, the first free, open-source system for flexible and high-throughput cell image analysis is described.

25.

12913
Accesses

Open letter   Free Highly Accessed

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Mouse ENCODE Consortium, John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al. Genome Biology 2012, 13:418 (13 August 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome

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