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1.

7221
Accesses

Research   Open Access Highly Accessed

Characterizing and measuring bias in sequence data

Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum, David B Jaffe Genome Biology 2013, 14:R51 (29 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A comparison of the bias in sequencing data from four different platforms reveals that some human promoters are completelymissed

2.

4823
Accesses

Research   Open Access Highly Accessed

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida, David N Kuhn et al. Genome Biology 2013, 14:R53 (3 June 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

The genome sequence of Theobroma cacao Matina 1-6 allows the identification of a gene associated with pod color

3.

4541
Accesses

Review   Subscription Highly Accessed

Machine learning and genome annotation: a match meant to be?

Kevin Y Yip, Chao Cheng, Mark Gerstein Genome Biology 2013, 14:205 (29 May 2013)

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

Mark Gerstein, Kevin Yip and Chao Cheng present a beginner's guide to machine learning for genome annotation

4.

4150
Accesses

Software   Open Access Highly Accessed

REAPR: a universal tool for genome assembly evaluation

Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman, Thomas D Otto Genome Biology 2013, 14:R47 (27 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A new user-friendly software tool for genome assembly evaluation

5.

3978
Accesses

Research   Open Access Highly Accessed

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 | PubMed |  Editor’s summary

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

6.

3894
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

7.

3501
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 | F1000 Biology |  Editor’s summary

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

8.

2977
Accesses

Research   Open Access

The plasticity of the grapevine berry transcriptome

Silvia Dal Santo, Giovanni Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne, Mario Pezzotti Genome Biology 2013, 14:r54 (7 June 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A transcriptomic and metabolomic analysis of the plasticity of grapevine berry gene expression in response to development and the environment

9.

2970
Accesses

Research highlight   Subscription

New gene expression pipelines gush lncRNAs

Jiashi Wang, Bronwyn A Lucas, Lynne E Maquat Genome Biology 2013, 14:117 (24 May 2013)

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

The characterization of lncRNA expression during neuronal development is a useful resource for elucidating the functions of non-coding transcripts

10.

2869
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

11.

2764
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.

12.

2657
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.

13.

2559
Accesses

Method   Open Access Highly Accessed

Integrated analysis of recurrent properties of cancer genes to identify novel drivers

Matteo D'Antonio, Francesca D Ciccarelli Genome Biology 2013, 14:R52 (29 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A method to detect rare driver genes through integrated analysis of expression profiles, mutation effects and properties of known cancer genes

14.

2533
Accesses

Research   Open Access Highly Accessed

Mutations within lncRNAs are effectively selected against in fruitfly but not in human

Wilfried Haerty, Chris P Ponting Genome Biology 2013, 14:R49 (27 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Analysis of lncRNA conservation in fruitfly and humans shows that these elements are well conserved in insects, but not in mammals

15.

2522
Accesses

Research   Open Access Highly Accessed

DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus

Lucas JT Kaaij, Marc van de Wetering, Fang Fang, Benjamin Decato, Antoine Molaro, Harmen JG van de Werken, Johan H van Es, Jurian Schuijers, Elzo de Wit, Wouter de Laat, Gregory J Hannon, Hans C Clevers, Andrew D Smith, Rene F Ketting Genome Biology 2013, 14:R50 (28 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Intriguingly, DNA methylation in mouse intestinal cells does not change much during differentiation

16.

2443
Accesses

Meeting report   Subscription

Epigenetics and transgenerational inheritance

Emilie Brasset, Séverine Chambeyron Genome Biology 2013, 14:306 (24 May 2013)

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

A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, held at Churchill College, Cambridge, UK, April 11-12, 2013.

17.

2396
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 |  Editor’s summary

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

18.

2341
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.

19.

2292
Accesses

Research   Open Access

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

Shivendra Kishore, Andreas R Gruber, Dominik J Jedlinski, Afzal P Syed, Hadi Jorjani, Mihaela Zavolan Genome Biology 2013, 14:R45 (26 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

PAR-CLIP of snoRNA-associated proteins reveals the existence of extensive human loci that are processed into snoRNAs

20.

2242
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

21.

2208
Accesses

Research   Open Access

Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles

Nicole YP Souren, Pavlo Lutsik, Gilles Gasparoni, Sascha Tierling, Jasmin Gries, Matthias Riemenschneider, Jean-Pierre Fryns, Catherine Derom, Maurice P Zeegers, Jörn Walter Genome Biology 2013, 14:R44 (26 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Monozygotic twins discordant for birth weight have very similar DNA methylation profiles

22.

2160
Accesses

Research highlight   Subscription

Deep C diving: mapping the low-abundance modifications of the DNA demethylation pathway

John P Thomson, Jennifer M Hunter, Richard R Meehan Genome Biology 2013, 14:118 (29 May 2013)

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

Richard Meehan and colleagues highlight recent insights into the 5th, 6th, 7th and 8th DNA bases: 5mC, 5hmC, 5fC and 5caC

23.

2126
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

24.

2018
Accesses

Research   Open Access

5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes

Maja Klug, Sandra Schmidhofer, Claudia Gebhard, Reinhard Andreesen, Michael Rehli Genome Biology 2013, 14:R46 (26 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

TET2-mediated conversion of 5mC to 5hmC initiates active demethylation of the genome during monocyte differentiation

25.

1823
Accesses

Research   Open Access

Genome-wide analysis of functional sirtuin chromatin targets in yeast

Mingguang Li, Veena Valsakumar, Kunal Poorey, Stefan Bekiranov, Jeffrey S Smith Genome Biology 2013, 14:R48 (27 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Sirtuins regulate both glycolytic gene expression and condensin/cohesin deposition, suggesting a mechanistic link between metabolism and chromatin architecture

26.

1677
Accesses

Meeting report   Subscription

Genomic triumph meets clinical reality

Qasim Ayub, Yali Xue, Chris Tyler-Smith Genome Biology 2013, 14:307 (28 May 2013)

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

A report on the 'Genomic Disorders 2013 - from 60 years of DNA to human genomes in the clinic' meeting, held at Homerton College, Hills Road, Cambridge, UK, April 10-12, 2013.

27.

1628
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 | Full text | PDF | PubMed |  Editor’s summary

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

28.

1576
Accesses

Research highlight   Subscription

Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine

Sean M Cullen, Margaret A Goodell Genome Biology 2013, 14:116 (28 May 2013)

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

A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions

29.

1493
Accesses

Research highlight   Subscription

Plastic, fantastic! Phenotypic variance in the transcriptional landscape of the grape berry

Alisdair R Fernie, Takayuki Tohge Genome Biology 2013, 14:119 (7 June 2013)

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

A Research Highlight covering Mario Pezzotti's research article analyzing the plasticity of grape berrys in response to environmental changes

30.

1472
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

31.

1424
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.

32.

1402
Accesses

Research   Open Access

Inactive or moderately active human promoters are enriched for inter-individual epialleles

Carolina Gemma, Sreeram V Ramagopalan, Thomas A Down, Huriya Beyan, Mohammed I Hawa, Michelle L Holland, Paul J Hurd, Gavin Giovannoni, R David Leslie, George C Ebers, Vardhman K Rakyan Genome Biology 2013, 14:R43 (25 May 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions

33.

1386
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

34.

1298
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

35.

1265
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.

36.

1244
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

37.

1239
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.

38.

1190
Accesses

Research   Open Access

Comprehensive genotyping of the USA national maize inbred seed bank

Maria C Romay, Mark J Millard, Jeffrey C Glaubitz, Jason A Peiffer, Kelly L Swarts, Terry M Casstevens, Robert J Elshire, Charlotte B Acharya, Sharon E Mitchell, Sherry A Flint-Garcia, Michael D McMullen, James B Holland, Edward S Buckler, Candice A Gardner Genome Biology 2013, 14:R55 (11 June 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time

39.

1183
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

40.

1165
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

41.

1155
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.

42.

1116
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

43.

1123
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

44.

1118
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

45.

1101
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 | Cited on BioMed Central |  Editor’s summary

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

46.

1105
Accesses

Research   Open Access

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

María Muñoz-Amatriaín, Steven R Eichten, Thomas Wicker, Todd A Richmond, Martin Mascher, Burkhard Steuernagel, Uwe Scholz, Ruvini Ariyadasa, Manuel Spannagl, Thomas Nussbaumer, Klaus FX Mayer, Stefan Taudien, Matthias Platzer, Jeffrey A Jeddeloh, Nathan M Springer, Gary J Muehlbauer, Nils Stein Genome Biology 2013, 14:R58 (12 June 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations

47.

1100
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

48.

1089
Accesses

Research   Open Access

Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids

Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang, Xing Wang Deng Genome Biology 2013, 14:R57 (12 June 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids

49.

1064
Accesses

Research   Open Access Highly Accessed

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

André E Minoche, Juliane C Dohm, Heinz Himmelbauer Genome Biology 2011, 12:R112 (8 November 2011)

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

Error rates are compared in data from Illumina's HiSeq and GAIIx systems

50.

1055
Accesses

Research   Open Access Highly Accessed

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

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

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