Genome Biology - oalib

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Genome Biology

ISSN Print: 1465-6906

ISSN Online:

主页: http://genomebiology.com

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Helicos single molecule sequencing: unique capabilities and importance for molecular diagnostics

Patrice M Milos

PRDM9 points the zinc finger at meiotic recombination hotspots

Matthew J Neale

Quantifying the mechanisms of domain gain in animal proteins

Marija Buljan, Adam Frankish, Alex Bateman

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

Isheng J Tsai, Thomas D Otto, Matthew Berriman

Complex-trait analysis in plants

Thomas Mitchell-Olds

The devil's in the details

Gregory A Petsko

Modeling non-uniformity in short-read rates in RNA-Seq data

Jun Li, Hui Jiang, Wing Wong

Genome-wide prediction of transcription factor binding sites using an integrated model

Kyoung-Jae Won, Bing Ren, Wei Wang

Genome-wide functional analysis of human 5' untranslated region introns

Can Cenik, Adnan Derti, Joseph C Mellor, Gabriel F Berriz, Frederick P Roth

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Guoliang Li, Melissa J Fullwood, Han Xu, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius Vega, Pramila Nuwantha Ariyaratne, Yusoff Bin Mohamed, Hong-Sain Ooi, Chandana Tennakoon, Chia-Lin Wei, Yijun Ruan, Wing-Kin Sung

Cancer genomics identifies determinants of tumor biology

Elaine R Mardis

Direct sequencing of the human microbiome readily reveals community differences

Justin Kuczynski, Elizabeth K Costello, Diana R Nemergut, Jesse Zaneveld, Christian L Lauber, Dan Knights, Omry Koren, Noah Fierer, Scott T Kelley, Ruth E Ley, Jeffrey I Gordon, Rob Knight

A human functional protein interaction network and its application to cancer data analysis

Guanming Wu, Xin Feng, Lincoln Stein

Towards a comprehensive structural variation map of an individual human genome

Andy W Pang, Jeffrey R MacDonald, Dalila Pinto, John Wei, Muhammad A Rafiq, Donald F Conrad, Hansoo Park, Matthew E Hurles, Charles Lee, J Craig Venter, Ewen F Kirkness, Samuel Levy, Lars Feuk, Stephen W Scherer

RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast

Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J Rando

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino, Ryan H Moy, Ronald R Breaker

The amazing world of bacterial structured RNAs

Eric Westhof

Is canalization more than just a beautiful idea?

Kaoru Sato, Haruhiko Siomi

The yin and yang of chromatin spatial organization

Nathan F Cope, Peter Fraser, Christopher H Eskiw

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

Zhengdong D Zhang, Adam Frankish, Toby Hunt, Jennifer Harrow, Mark Gerstein

Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling

Marie JJ Huysman, Cindy Martens, Klaas Vandepoele, Jeroen Gillard, Edda Rayko, Marc Heijde, Chris Bowler, Dirk Inzé, Yves Peer, Lieven De Veylder, Wim Vyverman

DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex

Sarah Schaack, Eunjin Choi, Michael Lynch, Ellen J Pritham

Optimized design and data analysis of tag-based cytosine methylation assays

Masako Suzuki, Qiang Jing, Daniel Lia, Marién Pascual, Andrew McLellan, John M Greally

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

Christophe Dessimoz, Manuel Gil

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

David Hendrix, Michael Levine, Weiyang Shi

No stone unturned

Gregory A Petsko

Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats

Tiebing Liang, Mark W Kimpel, Jeanette N McClintick, Ashley R Skillman, Kevin McCall, Howard J Edenberg, Lucinda G Carr

Gene ontology analysis for RNA-seq: accounting for selection bias

Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack

Lost in translation

Gregory A Petsko

Histone tales: echoes from the past, prospects for the future

Chris Murgatroyd, Dietmar Spengler

Conserved developmental transcriptomes in evolutionarily divergent species

Anup Parikh, Edward Roshan Miranda, Mariko Katoh-Kurasawa, Danny Fuller, Gregor Rot, Lan Zagar, Tomaz Curk, Richard Sucgang, Rui Chen, Blaz Zupan, William F Loomis, Adam Kuspa, Gad Shaulsky

Genomic features defining exonic variants that modulate splicing

Adam Woolfe, James C Mullikin, Laura Elnitski

Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts

Ishita S Mehta, Manelle Amira, Amanda J Harvey, Joanna M Bridger

Evidence for natural antisense transcript-mediated inhibition of microRNA function

Mohammad Ali Faghihi, Ming Zhang, Jia Huang, Farzaneh Modarresi, Marcel P Van der Brug, Michael A Nalls, Mark R Cookson, Georges St-Laurent, Claes Wahlestedt

Skin microbiome in health and disease

Julie A Segre, Elizabeth A Grice, Heidi H Kong, Sean Conlan, Evan Snitkin, Lilia Mijares, Patrick Murray, Eric D Green, Maria L Turner

The rare biosphere: sorting out fact from fiction

Mitchell L Sogin, Hilary Morrison, Sandra McLellan, David Welch, Sue Huse

Looking for signatures of sex-specific demography and local adaptation on the X chromosome

Evelyne Heyer, Laure Segurel

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

Mark D Robinson, Alicia Oshlack

Genome-wide analysis of mRNA decay patterns during early Drosophila development

Stefan Thomsen, Simon Anders, Sarath Chandra Janga, Wolfgang Huber, Claudio R Alonso

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z Chen, Joel S Rozowsky, Ashutosh K Tewari, Naoki Kitabayashi, Benjamin J Moss, Mark S Chee, Francesca Demichelis, Mark A Rubin, Mark B Gerstein

Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development

Nathalie Billon, Raivo Kolde, Jüri Reimand, Miguel C Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani

Cloud-scale RNA-sequencing differential expression analysis with Myrna

Ben Langmead, Kasper D Hansen, Jeffrey T Leek

Multiple distinct small RNAs originate from the same microRNA precursors

Weixiong Zhang, Shang Gao, Xuefeng Zhou, Jing Xia, Padmanabhan Chellappan, Xiang Zhou, Xiaoming Zhang, Hailing Jin

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team

Dosage compensation and the global re-balancing of aneuploid genomes

Matthias Prestel, Christian Feller, Peter B Becker

Somatic structural rearrangements in genetically engineered mouse mammary tumors

Ignacio Varela, Christiaan Klijn, Phillip J Stephens, Laura J Mudie, Lucy Stebbings, Danushka Galappaththige, Hanneke van der Gulden, Eva Schut, Sjoerd Klarenbeek, Peter J Campbell, Lodewyk FA Wessels, Michael R Stratton, Jos Jonkers, P Andrew Futreal, David J Adams

Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level

Olivier Harismendy, Vikas Bansal, Gaurav Bhatia, Masakazu Nakano, Michael Scott, Xiaoyun Wang, Colette Dib, Edouard Turlotte, Jack C Sipe, Sarah S Murray, Jean Deleuze, Vineet Bafna, Eric J Topol, Kelly A Frazer

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