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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

Software   Open Access Highly Accessed

ggbio: an R package for extending the grammar of graphics for genomic data

Tengfei Yin, Dianne Cook, Michael Lawrence Genome Biology 2012, 13:R77 (31 August 2012)

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

A consistent, robust and versatile software tool for visualizing genomic data

Method   Open Access

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska, Bonnie Berger Genome Biology 2012, 13:R76 (31 August 2012)

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

Coev2Net is a method for assigning confidence to high-throughput protein-protein interaction predictions

Meeting report   Subscription Highly Accessed

The rise of translational bioinformatics

Yves A Lussier, Haiquan Li Genome Biology 2012, 13:319 (31 August 2012)

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

A report on the 20th International Conference On Intelligent Systems For Molecular Biology (ISMB), held at Long Beach, California, USA, July 15-17, 2012.

Comment   Free Highly Accessed

A modest proposal for an outreach section in scientific publications

Chris Gunter, Anne Osterrieder Genome Biology 2012, 13:168 (31 August 2012)

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

By Chris Gunter and Anne Osterrieder

Meeting report   Subscription

Turning pipe dreams into reality

Peter Li, Jeremy Goecks, Tin-Lap Lee Genome Biology 2012, 13:318 (30 August 2012)

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

The 2012 Galaxy meeting shows how the bioinformatic tools within Galaxy are developing and automating data analysis in the life sciences

Opinion   Subscription Highly Accessed

The tomato genome: implications for plant breeding, genomics and evolution

Aashish Ranjan, Yasunori Ichihashi, Neelima R Sinha Genome Biology 2012, 13:167 (30 August 2012)

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

The importance of the tomato genome for plant breeding and the future of crop research

Research   Open Access Highly Accessed

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

Alayne L Brunner, Andrew H Beck, Badreddin Edris, Robert T Sweeney, Shirley X Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W Foley, Daniela M Witten, Craig P Giacomini, Ryan A Flynn, Jonathan R Pollack, Robert Tibshirani, Howard Y Chang, Matt van de Rijn, Robert B West Genome Biology 2012, 13:R75 (28 August 2012)

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

Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs

Research   Open Access

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

Hervé Moreau, Bram Verhelst, Arnaud Couloux, Evelyne Derelle, Stephane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F Hohmann-Marriott, Gwenael Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele Genome Biology 2012, 13:R74 (24 August 2012)

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

The genome sequence of the marine green alga Bathycoccus prasinos, and a phylogenomic comparison with other Mammiellales species

Research   Open Access Highly Accessed

Novel origins of copy number variation in the dog genome

Jonas Berglund, Elisa M Nevalainen, Anna-Maja Molin, Michele Perloski, The LUPA Consortium, Catherine André, Michael C Zody, Ted Sharpe, Christophe Hitte, Kerstin Lindblad-Toh, Hannes Lohi, Matthew T Webster Genome Biology 2012, 13:R73 (23 August 2012)

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

CNVs were analyzed in dogs from 17 breeds, and were found to be associated with different features compared to other mammals

Research   Open Access

Sequencing and characterization of the FVB/NJ mouse genome

Kim Wong, Suzannah Bumpstead, Louise Van Der Weyden, Laura G Reinholdt, Laurens G Wilming, David J Adams, Thomas M Keane Genome Biology 2012, 13:R72 (23 August 2012)

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

The genome of the FVB/NJ mouse is sequenced, revealing variants specific to this strain

Research   Open Access Highly Accessed

A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers

Nathan P Palmer, Patrick R Schmid, Bonnie Berger, Isaac S Kohane Genome Biology 2012, 13:R71 (21 August 2012)

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

A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues

Research   Open Access

The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite

Andrea H Horakova, J Mauro Calabrese, Christine R McLaughlin, Deanna C Tremblay, Terry Magnuson, Brian P Chadwick Genome Biology 2012, 13:R70 (20 August 2012)

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

A characterization of the X-linked homogenous tandem repeat DXZ4 in mouse, and a subsequent analysis of conservation across mammals

Research   Open Access Highly Accessed

Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian Genome Biology 2012, 13:R69 (17 August 2012)

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

Genome-wide mapping of 5-formylcytosine in ES cells reveals an enrichment in promoter and exon CpG islands, and an association with transcription

Research   Open Access

Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins

Gary LeRoy, Iouri Chepelev, Peter A DiMaggio, Mario A Blanco, Barry M Zee, Keji Zhao, Benjamin A Garcia Genome Biology 2012, 13:R68 (16 August 2012)

Abstract | Full text | PDF | PubMed | F1000 Biology |  Editor’s summary

A novel proteogenomic strategy links the histone reader proteins Brd3 and Brd4 to HOX gene regulation

Research highlight   Subscription Highly Accessed

Genomes of extremophile crucifers: new platforms for comparative genomics and beyond

Simon M Dittami, Thierry Tonon Genome Biology 2012, 13:166 (16 August 2012)

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

Research Highlight: the genome sequences of extremophile crucifers provide valuable insights into the underlying mechanisms of stress tolerance in plants

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

Method   Open Access Highly Accessed

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule Genome Biology 2012, 13:R67 (3 August 2012)

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

The CLIP and iCLIP methods are compared for their utility in determining RNA binding protein binding sites

Review   Subscription Highly Accessed

Autism genetics: searching for specificity and convergence

Jamee M Berg, Daniel H Geschwind Genome Biology 2012, 13:247 (31 July 2012)

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

Daniel Geschwind and Jamee Berg review the genes associated with autism spectrum disorders: how might their functions relate to one another?

Research highlight   Subscription Highly Accessed

The aging epigenome: DNA methylation from the cradle to the grave

Marc Winnefeld, Frank Lyko Genome Biology 2012, 13:165 (30 July 2012)

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

Frank Lyko and Marc Winnefeld highlight a new survey of age-related epigenetic changes in newborn and centenarian methylomes

Research   Open Access

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation

Markus Lommer, Michael Specht, Alexandra-Sophie Roy, Lars Kraemer, Reidar Andreson, Magdalena A Gutowska, Juliane Wolf, Sonja V Bergner, Markus B Schilhabel, Ulrich C Klostermeier, Robert G Beiko, Philip Rosenstiel, Michael Hippler, Julie LaRoche Genome Biology 2012, 13:R66 (26 July 2012)

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

Transcriptomic and proteomic insights into the low-iron tolerance of Thalassoiosira oceanic, an oceanic diatom

Research   Open Access Highly Accessed

Developmental features of DNA methylation during activation of the embryonic zebrafish genome

Ingrid S Andersen, Andrew H Reiner, Håvard Aanes, Peter Aleström, Philippe Collas Genome Biology 2012, 13:R65 (25 July 2012)

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

DNA methylation patterning at developmental genes is assayed before, during and after zygotic genome activation

Research   Open Access Highly Accessed

Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates

Sean Conlan, Lilia A Mijares, NISC Comparative Sequencing Program, Jesse Becker, Robert W Blakesley, Gerard G Bouffard, Shelise Brooks, Holly Coleman, Jyoti Gupta, Natalie Gurson, Morgan Park, Brian Schmidt, Pamela J Thomas, Michael Otto, Heidi H Kong, Patrick R Murray, Julia A Segre Genome Biology 2012, 13:R64 (25 July 2012)

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

Comparative genomics of skin commensal and hospital infection-associated isolates uncovers a putative clinical biomarker

Research highlight   Subscription Highly Accessed

piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense

Allison C Billi, Mallory A Freeberg, John K Kim Genome Biology 2012, 13:164 (20 July 2012)

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

John Kim and colleagues discuss transgenerational genome surveillance and the recognition of non-self by the worm piRNA system

Research   Open Access

RNA processing in the minimal organism Nanoarchaeum equitans

Lennart Randau Genome Biology 2012, 13:R63 (18 July 2012)

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

RNA-seq in the minimal archaeon Nanoarchaeum equitans reveals details of unusual RNA processing such as trans splicing of tRNA molecules

Software   Open Access Highly Accessed

CIDeR: multifactorial interaction networks in human diseases

Martin Lechner, Veit Höhn, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Gabi Kastenmüller, Brigitte Waegele, Andreas Ruepp Genome Biology 2012, 13:R62 (18 July 2012)

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

A database of interactions in neurological and metabolic disorders, with a wide range of search options and graphical outputs

Meeting report   Subscription

Eastern genomics promises

Scott C Edmunds Genome Biology 2012, 13:317 (17 July 2012)

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

A report on the Bio-IT World Asia meeting, Marina Bay Sands, Singapore, 6-8 June 2012.

Research highlight   Subscription Highly Accessed

The greatest catch: big game fishing for mRNA-bound proteins

Christopher R Sibley, Jan Attig, Jernej Ule Genome Biology 2012, 13:163 (17 July 2012)

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

Jernej Ule and colleagues highlight two recent studies that have identified many novel RNA-binding proteins

Method   Open Access Highly Accessed

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman Genome Biology 2012, 13:R61 (11 July 2012)

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

A model-based SNP caller for bisulfite sequencing data improves methylation estimates and imprinting analysis

Method   Open Access

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples

Serena Dollive, Gregory L Peterfreund, Scott Sherrill-Mix, Kyle Bittinger, Rohini Sinha, Christian Hoffmann, Christopher S Nabel, David A Hill, David Artis, Michael A Bachman, Rebecca Custers-Allen, Stephanie Grunberg, Gary D Wu, James D Lewis, Frederic D Bushman Genome Biology 2012, 13:R60 (3 July 2012)

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

BROCC, a pipeline for the analysis of eukaryotes of microbiomes using conserved ribosomal rDNA sequences as markers

Research   Open Access

E2F mediates enhanced alternative polyadenylation in proliferation

Ran Elkon, Jarno Drost, Gijs van Haaften, Mathias Jenal, Mariette Schrier, Joachim AF Oude Vrielink, Reuven Agami Genome Biology 2012, 13:R59 (2 July 2012)

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

Transcriptome sequencing of two cell lines reveals shortened 3' UTRs and use of alternative polyadenylation sites associated with cell proliferation

Research   Open Access Highly Accessed

Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome

Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Tohru Masui, Yasuhiro Yasutomi, Naoki Osada Genome Biology 2012, 13:R58 (2 July 2012)

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

The Malaysian cynomolgus macaque genome sheds light on structural variation between primate species

Research   Open Access

Conserved rules govern genetic interaction degree across species

Elizabeth N Koch, Michael Costanzo, Jeremy Bellay, Raamesh Deshpande, Kate Chatfield-Reed, Gordon Chua, Gennaro D'Urso, Brenda J Andrews, Charles Boone, Chad L Myers Genome Biology 2012, 13:R57 (2 July 2012)

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

Genetic interaction degree is conserved between fission and budding yeast, but functional rewiring is also apparent

Review   Subscription

The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities

Jane WY Ng, Laura M Barrett, Andrew Wong, Diana Kuh, George Smith, Caroline L Relton Genome Biology 2012, 13:246 (29 June 2012)

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

Longitudinal cohort studies provide an opportunity to study how changes in epigenetic patterns occur in response to diverse factors

Comment   Subscription Highly Accessed

Out of Africa

Gregory A Petsko Genome Biology 2012, 13:162 (29 June 2012)

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

Greg Petsko suggests five disreputable ways of making a fortune in science.

Opinion   Subscription

Gene patents in the US - focusing on what really matters

Allison W Dobson, James P Evans Genome Biology 2012, 13:161 (29 June 2012)

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

With new technologies, concerns about gene patent claims regarding isolated DNA are becoming less relevant

Meeting report   Subscription

Dispatches from the functional phase of genome biology

Luke Jostins Genome Biology 2012, 13:316 (27 June 2012)

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

A report on the 25th annual meeting on The Biology of Genomes, Cold Spring Harbor, USA, 8-12 May 2012

Research highlight   Subscription

Deciphering membrane protein structures from protein sequences

Tilman Flock, AJ Venkatakrishnan, KR Vinothkumar, M Madan Babu Genome Biology 2012, 13:160 (27 June 2012)

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

Madan Babu and colleagues discuss how co-evolving residue pairs can be exploited to predict membrane protein topology

Software   Open Access Highly Accessed

Toward almost closed genomes with GapFiller

Marten Boetzer, Walter Pirovano Genome Biology 2012, 13:R56 (25 June 2012)

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

GapFiller is a method for automatically filling gaps in short read genome assemblies using the existing sequencing data

Method   Open Access

m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence

Jüri Reimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman, Nicholas M Luscombe Genome Biology 2012, 13:R55 (21 June 2012)

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

A computational method that identifies process-specific regulators from high-throughput data. Its utility is shown in an analysis that identifies cell cycle regulators

Research   Open Access

Regulation of alternative splicing by the circadian clock and food related cues

Nicholas J McGlincy, Amandine Valomon, Johanna E Chesham, Elizabeth S Maywood, Michael H Hastings, Jernej Ule Genome Biology 2012, 13:R54 (21 June 2012)

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

An extensive analysis of how the circadian clock and the physiological cue of feeding regulates alternative splicing in mice

Research highlight   Subscription

Transposable elements: not as quiet as a mouse

Rita Rebollo, Ying Zhang, Dixie L Mager Genome Biology 2012, 13:159 (20 June 2012)

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

Identification of over 100,000 transposon element variants in 18 mouse genomes reveals the role of negative selection in their evolution

Research   Open Access

Apple miRNAs and tasiRNAs with novel regulatory networks

Rui Xia, Hong Zhu, Yong-qiang An, Eric P Beers, Zongrang Liu Genome Biology 2012, 13:R47 (15 June 2012)

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

A comprehensive analysis of short regulatory RNAs including, miRNAs, siRNAs and tasiRNAs in the apple tree Malus domestica Golden Delicious

Research   Open Access Highly Accessed

Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms

Fredrik Barrenäs, Sreenivas Chavali, Alexessander Alves, Lachlan Coin, Marjo-Riitta Jarvelin, Rebecka Jörnsten, Michael A Langston, Adaikalavan Ramasamy, Gary Rogers, Hui Wang, Mikael Benson Genome Biology 2012, 13:R46 (15 June 2012)

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

Gene network analysis can predict novel disease-associated genes and finds significant overlap between phenotypically disparate complex diseases

Research   Open Access

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

Christoffer Nellåker, Thomas M Keane, Binnaz Yalcin, Kim Wong, Avigail Agam, T Grant Belgard, Jonathan Flint, David J Adams, Wayne N Frankel, Chris P Ponting Genome Biology 2012, 13:R45 (15 June 2012)

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

A comprehensive catalog of transposable elements across 18 mouse strains, and a subsequent analysis of selection acting on these transposable elements

Method   Open Access

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack Genome Biology 2012, 13:R44 (15 June 2012)

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

A method for normalizing the Illumina 450k methylation array data, allowing analysis of the genome-wide methylation status of the human genome

Research   Open Access Highly Accessed

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

Matthew N Davies, Manuela Volta, Ruth Pidsley, Katie Lunnon, Abhishek Dixit, Simon Lovestone, Cristian Coarfa, R Alan Harris, Aleksandar Milosavljevic, Claire Troakes, Safa Al-Sarraj, Richard Dobson, Leonard C Schalkwyk, Jonathan Mill Genome Biology 2012, 13:R43 (15 June 2012)

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

Differentially methylated regions are annotated using matched blood and brain samples from multiple individuals

Research   Open Access Highly Accessed

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

Nicola Segata, Susan Haake, Peter Mannon, Katherine P Lemon, Levi Waldron, Dirk Gevers, Curtis Huttenhower, Jacques Izard Genome Biology 2012, 13:R42 (14 June 2012)

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

The Human Microbiome Project's analysis of ten sites in the digestive tract of healthy human adults

Research   Open Access Highly Accessed

The multiplicity of divergence mechanisms in a single evolving population

Ram P Maharjan, Thomas Ferenci, Peter R Reeves, Yang Li, Bin Liu, Lei Wang Genome Biology 2012, 13:R41 (8 June 2012)

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

Whole genome sequencing of 8 laboratory populations of E. coli casts light on the mechanisms by which populations evolve

Opinion   Subscription

Power to the people: a wiki-governance model for biobanks

Edward S Dove, Yann Joly, Bartha M Knoppers Genome Biology 2012, 13:158 (29 May 2012)

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

Edward Dove and colleagues propose a wiki-governance model for biobanks that gives citizens the ability to collaborate in biobank governance and policymaking.

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