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1.

9441
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 | Provisional PDF | PubMed |  Editor’s summary

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

2.

7164
Accesses

Editorial   Free Highly Accessed

Raymond Gosling: the man who crystallized genes

Naomi Attar Genome Biology 2013, 14:402 (25 April 2013)

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

"The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix

3.

6961
Accesses

Comment   Subscription Highly Accessed

After the gold rush

Neil Hall Genome Biology 2013, 14:115 (7 May 2013)

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

Neil Hall wonders whether genomics is ready for a plateau in sequencing costs

4.

5578
Accesses

Opinion   Subscription Highly Accessed

Sixty years of genome biology

W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013)

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

Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix

5.

5596
Accesses

Comment   Subscription Highly Accessed

How to evaluate a graduate studentship, or choosing the right doctoral advisor

Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013)

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

Duncan Odom has some sage advice for those considering PhD options

6.

5592
Accesses

Research   Open Access Highly Accessed

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability

7.

4468
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

John Abramyan, 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, LaDeana H Hillier, Alisha K Holloway, Daniel Janes, Fredric J Janzen, Cyriac Kandoth, Lesheng Kong, Jason de Koning, Yang Li et al. Genome Biology 2013, 14:R28 (28 March 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

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

8.

4189
Accesses

Method   Open Access Highly Accessed

Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq 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 | Provisional PDF | PubMed |  Editor’s summary

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

9.

3397
Accesses

Research   Open Access Highly Accessed

CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes

Quan Zhang, Mina Rho, Haixu Tang, Thomas G Doak, Yuzhen Ye Genome Biology 2013, 14:R40 (29 April 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements

10.

3106
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.

11.

3025
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

12.

2974
Accesses

Method   Open Access Highly Accessed

jMOSAiCS: joint analysis of multiple ChIP-seq datasets

Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sunduz Keles Genome Biology 2013, 14:R38 (29 April 2013)

Abstract | Provisional PDF |  Editor’s summary

A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM

13.

2829
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.

14.

2634
Accesses

Research   Open Access

Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors

Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors

15.

2455
Accesses

Research   Open Access Highly Accessed

Systematic biases in DNA copy number originate from isolation procedures

Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation

16.

2285
Accesses

Method   Open Access

EMu: probabilistic inference of mutational processes and their localization in the cancer genome

Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013)

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

A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active

17.

2117
Accesses

Research   Open Access

Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis

Srikanth Nagalla, Jeff W Chou, Mark C Willingham, Jimmy Ruiz, James P Vaughn, Purnima Dubey, Timothy L Lash, Stephen J Hamilton-Dutoit, Jonas Bergh, Christos Sotiriou, Michael A Black, Lance D Miller Genome Biology 2013, 14:R34 (29 April 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes

18.

2091
Accesses

Software   Open Access Highly Accessed

CRAC: an integrated approach to the analysis of RNA-seq reads

Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data

19.

1926
Accesses

Research   Open Access

DNA binding specificities of the long zinc-finger recombination protein PRDM9

Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals

20.

1824
Accesses

Research   Open Access

Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance

David Martino, Yuk Jin Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013)

Abstract | Provisional PDF |  Editor’s summary

A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status

21.

1761
Accesses

Research   Open Access Highly Accessed

Characterizing the admixed African ancestry of African Americans

Fouad Zakharia, Analabha Basu, Devin Absher, Themistocles L Assimes, Alan S Go, Mark A Hlatky, Carlos Iribarren, Joshua W Knowles, Jun Li, Balasubramanian Narasimhan, Steven Sidney, Audrey Southwick, Richard M Myers, Thomas Quertermous, Neil Risch, Hua Tang Genome Biology 2009, 10:R141 (22 December 2009)

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

Genome-wide SNP analyses reveal the admixed African genetic ancestry of African Americans.

22.

1736
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

23.

1695
Accesses

Research highlight   Subscription Highly Accessed

The fractured genome of HeLa cells

David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013)

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

David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome

24.

1572
Accesses

Research   Open Access Highly Accessed

Integrated miRNA and mRNA expression profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage

Min Zhu, Ming Yi, Chang Hee Kim, Chuxia Deng, Yi Li, Daniel Medina, Robert M Stephens, Jeffrey E Green Genome Biology 2011, 12:R77 (16 August 2011)

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

Expression profiling in mouse models of mammary tumors identifies miRNA signatures particular to lineages or driver oncogenes

25.

1526
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

26.

1512
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.

27.

1515
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

28.

1476
Accesses

Research   Open Access

p53 induces transcriptional and translational programs to suppress cell proliferation and growth

Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress

29.

1445
Accesses

Research highlight   Subscription

The complex binding of PRDM9

Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013)

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

A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9

30.

1457
Accesses

Research   Open Access Highly Accessed

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

Christopher I Keeling, Macaire MS Yuen, Nancy Y Liao, T Roderick Docking, Simon K Chan, Greg A Taylor, Diana L Palmquist, Shaun D Jackman, Anh Nguyen, Maria Li, Hannah Henderson, Jasmine K Janes, Yongjun Zhao, Pawan Pandoh, Richard Moore, Felix AH Sperling, Dezene PW Huber, Inanc Birol, Stephen JM Jones, Joerg Bohlmann Genome Biology 2013, 14:R27 (27 March 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

The genome sequence of the mountain pine beetle, only the second beetle genome to be sequenced

31.

1397
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 |  Editor’s summary

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

32.

1345
Accesses

Research   Open Access Highly Accessed

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

Xiaoming Zhang, Jing Xia, Yifan E Lii, Blanca E Barrera-Figueroa, Xuefeng Zhou, Shang Gao, Lu Lu, Dongdong Niu, Zheng Chen, Christy Leung, Timothy Wong, Huiming Zhang, Jianhua Guo, Yi Li, Renyi Liu, Wanqi Liang, Jian-Kang Zhu, Weixiong Zhang, Hailing Jin Genome Biology 2012, 13:R20 (22 March 2012)

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

In Arabidopsis and rice, natural antisense transcripts are processed into siRNAs by DCL1 and DCL3

33.

1330
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.

34.

1293
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

35.

1278
Accesses

Research   Open Access Highly Accessed

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration

Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Hoeffner, Marcus Krueger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013)

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

A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration

36.

1203
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.

37.

1203
Accesses

Research   Open Access Highly Accessed

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

Jong Kim, John C Marioni Genome Biology 2013, 14:R7 (28 January 2013)

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

A new framework for modeling stochastic gene expression in single cells yields insights into the regulatory role of histone modifications

38.

1187
Accesses

Meeting report   Free Highly Accessed

The future of genomic medicine is here

Konrad J Karczewski Genome Biology 2013, 14:304 (27 March 2013)

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

A report on the 6th annual Future of Genomic Medicine conference, held at the Scripps
Seaside Forum, La Jolla, CA, USA, March 7-8, 2013

39.

1186
Accesses

Research   Open Access Highly Accessed

Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes

Pedro G Ferreira, Solenn Patalano, Ritika Chauhan, Richard Ffrench-Constant, Toni Gabaldón, Roderic Guigó, Seirian Sumner Genome Biology 2013, 14:R20 (26 February 2013)

Abstract | Provisional PDF | PubMed | 2 comments |  Editor’s summary

An RNA-seq analysis of the genetic mechanisms controlling alternative phenotypes in the primitive eusocial wasp Polistes canadensis

40.

1173
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.

41.

1124
Accesses

Method   Open Access Highly Accessed

Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue

Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson Genome Biology 2013, 14:R24 (25 March 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples

42.

1117
Accesses

Review   Subscription Highly Accessed

Neurogenomics of speech and language disorders: the road ahead

Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013)

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

From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders

43.

1115
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

44.

1080
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

45.

1059
Accesses

Meeting report   Subscription

Single-cell biology meeting marks rebirth of an old science

Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013)

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

A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013

46.

1051
Accesses

Research   Open Access Highly Accessed

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper, Athos Bousvaros, Joshua Korzenik, Bruce E Sands, Ramnik J Xavier, Curtis Huttenhower Genome Biology 2012, 13:R79 (26 September 2012)

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

An analysis of the microbes and microbial metabolism present in intestinal biopsies and stool samples from 231 IBD and healthy subjects

47.

1049
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

48.

1044
Accesses

Research   Open Access Highly Accessed

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb-target genes

James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendegast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells

49.

1036
Accesses

Research   Open Access Highly Accessed

The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude.

Qingle Cai, Xiaoju Qian, Yongshan Lang, Yadan Luo, Shengkai Pan, Yuanyuan Hui, Caiyun Gou, Yue Cai, Meirong Hao, Jinyang Zhao, Songbo Wang, Zhaobao Wang, Xinming Zhang, Jinchao Liu, Longhai Luo, Yingrui Li, Jun Wang, Rongjun He, Fumin Lei, Jiaohui Xu Genome Biology 2013, 14:R29 (28 March 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

The ground tit genome, one of the highest quality avian genome assemblies to date, reveals potential mechanisms of high altitude adaptation

50.

1020
Accesses

Review   Subscription

Studying the microbiology of the indoor environment

Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013)

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

Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study

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