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1.

Research article   Open Access

Male-specific fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains

Justin E Dalton, Justin M Fear, Simon Knott, Bruce S Baker, Lauren M McIntyre, Michelle N Arbeitman BMC Genomics 2013, 14:659 (27 September 2013)

Abstract | Provisional PDF | PubMed

2.

Research article   Open Access

Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls

Meeta Mistry, Jesse Gillis, Paul Pavlidis BMC Neuroscience 2013, 14:105 (26 September 2013)

Abstract | Full text | PDF | PubMed

3.

Research   Open Access

Organization of Plasmodium falciparum spliceosomal core complex and role of arginine methylation in its assembly

Manzar Hossain, Shweta Sharma, Reshma Korde, Shivani Kanodia, Monika Chugh, Khushboo Rawat, Pawan Malhotra Malaria Journal 2013, 12:333 (18 September 2013)

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

This paper compiles a substantial amount of experimental data that shed light on the organization of the spliceosome in Plasmodium.

4.

Database   Open Access Highly Accessed

Gentrepid V2.0: a web server for candidate disease gene prediction

Sara Ballouz, Jason Y Liu, Richard A George, Naresh Bains, Arthur Liu, Martin Oti, Bruno Gaeta, Diane Fatkin, Merridee A Wouters BMC Bioinformatics 2013, 14:249 (16 August 2013)

Abstract | Full text | PDF | PubMed

5.

Research   Open Access Highly Accessed

Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement

Kai Wang, Cecilia Kim, Jonathan Bradfield, Yunfei Guo, Elina Toskala, Frederick G Otieno, Cuiping Hou, Kelly Thomas, Christopher Cardinale, Gholson J Lyon, Ryan Golhar, Hakon Hakonarson Genome Medicine 2013, 5:67 (26 July 2013)

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

DNA and RNA sequencing identifies mutations within RBCK1 in children with a previously undiagnosed disease characterised by progressive muscular weakness and cardiomyopathy.

6.

Research   Open Access Highly Accessed

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanç Birol, Sébastien Boisvert, Jarrod A Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A Fonseca, Ganeshkumar Ganapathy, Richard A Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph B Hiatt, Isaac Y Ho et al. GigaScience 2013, 2:10 (22 July 2013)

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

Assemblathon 2 is the largest systematic assessment of how the process of genome assembly is carried out, with 21 participating teams submitting 43 entries based on data from 3 different genomes

7.

Poster presentation   Open Access

The structure of human olfactory space

Alexei Koulakov, Dmitry Rinberg BMC Neuroscience 2013, 14(Suppl 1):P323 (8 July 2013)

Full text | PDF

8.

Poster presentation   Open Access

Long-term memory stabilized by noise-induced rehearsal

Yi Wei, Alexei Koulakov BMC Neuroscience 2013, 14(Suppl 1):P220 (8 July 2013)

Full text | PDF

9.

Correspondence   Free Highly Accessed

The advantages of SMRT sequencing

Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013)

Abstract | Full text | PDF | PubMed | 2 comments |  Editor’s summary

Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform

10.

Comment   Free

The DNA60IFX contest

Michael C Schatz, James Taylor, Sven-Eric Schelhorn Genome Biology 2013, 14:124 (28 June 2013)

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

The curators and winner of Genome Biology's DNA60IFX challenge offer their thoughts on code cracking and crowd bioinformatics - includes full solutions

11.

Methodology Article   Open Access

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

Xiao Xu, Yuanhao Zhang, Jennie Williams, Eric Antoniou, W McCombie, Song Wu, Wei Zhu, Nicholas O Davidson, Paula Denoya, Ellen Li BMC Bioinformatics 2013, 14(Suppl 9):S1 (28 June 2013)

Abstract | Full text | PDF | PubMed

12.

Methodology   Open Access

A fluorometric assay for trehalose in the picomole range

Petronia Carillo, Regina Feil, Yves Gibon, Namiko Satoh-Nagasawa, David Jackson, Oliver E Bläsing, Mark Stitt, John Lunn Plant Methods 2013, 9:21 (20 June 2013)

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

Trehalose is a disaccharide that is found in a wide variety of species but whose functions are not always clear. The authors describe a novel assay, based on the use of recombinant bacterial trehalase, which is both sensitive and highly specific for trehalose. The method has been validated by studying diurnal patterns of trehalose content of Arabidopsis leaves and the effect of the maize ramosa3 mutant on trehalose levels in inflorescence primordia.

13.

Research   Open Access

CK2-dependent phosphorylation of occludin regulates the interaction with ZO-proteins and tight junction integrity

Max J Dörfel, Julie K Westphal, Christian Bellmann, Susanne M Krug, Jimmi Cording, Sonnhild Mittag, Rudolf Tauber, Michael Fromm, Ingolf E Blasig, Otmar Huber Cell Communication and Signaling 2013, 11:40 (10 June 2013)

Abstract | Full text | PDF | PubMed

14.

Research   Open Access

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Palitha Dharmawardhana, Liya Ren, Vindhya Amarasinghe, Marcela Monaco, Jim Thomason, Dean Ravenscroft, Susan McCouch, Doreen Ware, Pankaj Jaiswal Rice 2013, 6:15 (29 May 2013)

Abstract | Full text | PDF

15.

Research   Open Access Highly Accessed

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

Lucas TJ 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, René F Ketting Genome Biology 2013, 14:R50 (28 May 2013)

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

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

16.

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 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 | Full text | PDF | PubMed | Cited on BioMed Central | f1000 |  Editor’s summary

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

17.

Opinion   Subscription Highly Accessed

Sixty years of genome biology

W Ford 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

18.

Proceedings   Open Access

Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA)

Jesse Gillis, Paul Pavlidis BMC Bioinformatics 2013, 14(Suppl 3):S15 (22 April 2013)

Abstract | Full text | PDF | PubMed

19.

Research   Open Access Highly Accessed

Whole-genome sequencing in an autism multiplex family

Lingling Shi, Xu Zhang, Ryan Golhar, Frederick G Otieno, Mingze He, Cuiping Hou, Cecilia Kim, Brendan Keating, Gholson J Lyon, Kai Wang, Hakon Hakonarson Molecular Autism 2013, 4:8 (18 April 2013)

Abstract | Full text | PDF | PubMed

20.

Research   Open Access Highly Accessed

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

Jason O'Rawe, Tao Jiang, Guangqing Sun, Yiyang Wu, Wei Wang, Jingchu Hu, Paul Bodily, Lifeng Tian, Hakon Hakonarson, W Evan Johnson, Zhi Wei, Kai Wang, Gholson J Lyon Genome Medicine 2013, 5:28 (27 March 2013)

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

Head-to-head comparison of widely used variant calling pipelines including SOAP, GATK and Complete Genomics using default parameters reveals discrepancies between the pipelines.

21.

Research article   Open Access Highly Accessed

Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process

Liya Wang, Lincoln D Stein BMC Evolutionary Biology 2013, 13:57 (28 February 2013)

Abstract | Full text | PDF | PubMed

22.

Research   Open Access

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Yoshihiro Kawahara, Melissa de la Bastide, John P Hamilton, Hiroyuki Kanamori, W Richard McCombie, Shu Ouyang, David C Schwartz, Tsuyoshi Tanaka, Jianzhong Wu, Shiguo Zhou, Kevin L Childs, Rebecca M Davidson, Haining Lin, Lina Quesada-Ocampo, Brieanne Vaillancourt, Hiroaki Sakai, Sung Shin Lee, Jungsok Kim, Hisataka Numa, Takeshi Itoh, C Robin Buell, Takashi Matsumoto Rice 2013, 6:4 (6 February 2013)

Abstract | Full text | PDF

23.

Software   Open Access Highly Accessed

Kerfuffle: a web tool for multi-species gene colocalization analysis

Robert Aboukhalil, Bernard Fendler, Gurinder S Atwal BMC Bioinformatics 2013, 14:22 (17 January 2013)

Abstract | Full text | PDF | PubMed

24.

Software   Open Access Highly Accessed

The taxonomic name resolution service: an online tool for automated standardization of plant names

Brad Boyle, Nicole Hopkins, Zhenyuan Lu, Juan Antonio Raygoza Garay, Dmitry Mozzherin, Tony Rees, Naim Matasci, Martha L Narro, William H Piel, Sheldon J Mckay, Sonya Lowry, Chris Freeland, Robert K Peet, Brian J Enquist BMC Bioinformatics 2013, 14:16 (16 January 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

25.

Comment   Subscription Highly Accessed

Computational thinking in the era of big data biology

Michael C Schatz Genome Biology 2012, 13:177 (29 November 2012)

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

by Mike Schatz

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