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Genome Biology

ISSN Print: 1465-6906

ISSN Online:

Website: http://genomebiology.com

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Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

Falk Hildebrand, Anh THI LOAN Nguyen, Brigitta Brinkman, Roberto GARCIA Yunta, Benedicte Cauwe, Peter Vandenabeele, Adrian Liston, Jeroen Raes

CGAL: computing genome assembly likelihoods

Atif Rahman, Lior Pachter

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Daniel P Melters, Keith R Bradnam, Hugh A Young, Natalie Telis, Michael R May, J GRAHAM Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank, Jose Fernando Garcia, Joseph L DeRisi, Timothy Smith, Christian Tobias, Jeffrey Ross-Ibarra, Ian Korf, Simon WL Chan

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

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan, Xiangke Liao, Xiaoqian Zhu, Shaoliang Peng, Yingrui Li, Jun Wang, Guangwu Guo

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

Mallory A Freeberg, Ting Han, James J Moresco, Andy Kong, Yu-Cheng Yang, Zhi JOHN Lu, John R Yates, John K Kim

Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery

Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer

Accelerated exon evolution within primate segmental duplications

Belen Lorente-Galdos, Jonathan Bleyhl, Gabriel Santpere, Laura Vives, Oscar Ramirez, Jessica Hernandez, Roger Anglada, Gregory M Cooper, Arcadi Navarro, Evan E Eichler, Tomas Marques-Bonet

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Burglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Soon Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang

The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion

Henar Hernando, Claire Shannon-Lowe, Abul B M M K Islam, Fatima Al-Shahrour, Javier Rodriguez-Ubreva, Virginia C Rodriguez-Cortez, Biola M Javierre, Cristina Mangas, Agustin F Fernandez, Maribel Parra, Henri-Jacques Delecluse, Manel Esteller, Eduardo Lopez-Granados, Mario F Fraga, Nuria Lopez-Bigas, Esteban Ballestar

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King

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

Jong Kyoung Kim, John C Marioni

Genome-wide mapping of FOXM1 binding reveals co binding with estrogen receptor alpha in breast cancer cells

Deborah A Sanders, Caryn S Ross-Innes, Dario Beraldi, Jason S Carroll, Shankar Balasubramanian

Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs

Michelle Kudron, Wei Niu, Zhi Lu, Guilin Wang, Mark Gerstein, Michael Snyder, Valerie Reinke

Biogeography of the ecosystems of the healthy human body

Yanjiao Zhou, Hongyu Gao, Kathie A Mihindukulasuriya, Patricio S LA Rosa, Kristine M Wylie, Tatiana Vishnivetskaya, Mircea Podar, Barb Warner, Phillip I Tarr, David E Nelson, J Dennis Fortenberry, Martin J Holland, Sarah E Burr, William D Shannon, Erica Sodergren, George M Weinstock

Genome sequencing of the important oilseed crop Sesamum indicum L

Haiyang Zhang, Hongmei Miao, Lei Wang, Lingbo Qu, Hongyan Liu, Qiang Wang, Meiwang Yue

Science: it's a role model thing

Chris Gunter

Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies

Masayuki Sugawara, Brendan Epstein, Brian Badgley, Tatsuya Unno, Lei Xu, Jennifer Reese, Prasad Gyaneshwar, Roxanne Denny, Joann Mudge, Arvind K Bharti, Andrew D Farmer, Gregory D May, Jimmy E Woodward, Claudine Medigue, David Vallenet, Aurelie Lajus, Zoe Rouy, Betsy Martinez-Vaz, Peter Tiffin, Nevin D Young, Michael J Sadowsky

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya, Brian Ondov, Aaron E Darling, Adam M Phillippy, Mihai Pop

The passionate life of Simon Chan

Luca Comai

Old soldiers never die ....

Jacobus J Boomsma, Sanne Nygaard

Maternal-to-zygotic transition: soma versus germline

Martine Simonelig

Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pHc in Saccharomyces cerevisiae

Rick Orij, Malene L Urbanus, Franco J Vizeacoumar, Guri Giaever, Charles Boone, Corey Nislow, Stanley Brul, Gertien J Smits

Correlation of proteome-wide changes with social immunity behaviors provides insight into resistance to the parasitic mite, Varroa destructor, in the honey bee (Apis mellifera)

Robert Parker, M Marta Guarna, Andony P Melathopoulos, Kyung-Mee Moon, Rick White, Elizabeth Huxter, Stephen F Pernal, Leonard J Foster

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

Modeling gene expression using chromatin features in various cellular contexts

Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng

EpiExplorer: live exploration and global analysis of large epigenomic datasets

Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer, Christoph Bock

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason

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

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation

Jing-Quan Lim, Chandana Tennakoon, Guoliang Li, Eleanor Wong, Yijun Ruan, Chia-Lin Wei, Wing-Kin Sung

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome

John P Thomson, Harri Lempi？inen, Jamie A Hackett, Colm E Nestor, Arne Müller, Federico Bolognani, Edward J Oakeley, Dirk Schübeler, Rémi Terranova, Diana Reinhardt, Jonathan G Moggs, Richard R Meehan

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

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

E2F mediates enhanced alternative polyadenylation in proliferation

Ran Elkon, Jarno Drost, Gijs van Haaften, Mathias Jenal, Mariette Schrier, Joachim AF Oude Vrielink, Reuven Agami

A modest proposal for an outreach section in scientific publications

Chris Gunter, Anne Osterrieder

A quantitative literature-curated gold standard for kinase-substrate pairs

Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Youn, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews

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

A new approach for detecting low-level mutations in next-generation sequence data

Mingkun Li, Mark Stoneking

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Thomas Pr？schold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Alexandre Lomsadze, Mark Borodovsky, Jean-Michel Claverie, Igor V Grigoriev, James L Van Etten

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

Comparative multi-omics systems analysis of Escherichia coli strains B and K-12

Sung Yoon, Mee-Jung Han, Haeyoung Jeong, Choong Lee, Xiao-Xia Xia, Dae-Hee Lee, Ji Shim, Sang Lee, Tae Oh, Jihyun F Kim

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, Katleen De Preter, Gert Van Peer, Wim Van Criekinge, Ruth Ladenstein, Johannes H Schulte, Rosa Noguera, Raymond L Stallings, An Van Damme, Geneviève Laureys, Jo？lle Vermeulen, Tom Van Maerken, Frank Speleman, Jo Vandesompele

What can epigenomics do for you?

Alexander Meissner

The allure of the epigenome

Naomi Attar

Birds do it, bees do it, worms and ciliates do it too: DNA methylation from unexpected corners of the tree of life

Soojin V Yi

Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium

Simen M Kristoffersen, Chad Haase, M Ryan Weil, Karla D Passalacqua, Faheem Niazi, Stephen K Hutchison, Brian Desany, Anne-Brit Kolst？, Nicolas J Tourasse, Timothy D Read, Ole ？kstad

Population-specificity of human DNA methylation

Hunter B Fraser, Lucia L Lam, Sarah M Neumann, Michael S Kobor

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

Patrick Boyle, Kendell Clement, Hongcang Gu, Zachary D Smith, Michael Ziller, Jennifer L Fostel, Laurie Holmes, Jim Meldrim, Fontina Kelley, Andreas Gnirke, Alexander Meissner

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

Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

Zhen Shao, Yijing Zhang, Guo-Cheng Yuan, Stuart H Orkin, David J Waxman

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