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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)
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A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status |
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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)
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The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability |
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After the gold rush
Neil Hall Genome Biology 2013, 14:115 (7 May 2013)
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Neil Hall wonders whether genomics is ready for a plateau in sequencing costs |
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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)
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Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements |
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EMu: probabilistic inference of mutational processes and their localization in the cancer genome
Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013)
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A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active |
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jMOSAiCS: joint analysis of multiple ChIP-seq datasets
Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sunduz Keles Genome Biology 2013, 14:R38 (29 April 2013)
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A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM |
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Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors
Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013)
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A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors |
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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)
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An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
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How to evaluate a graduate studentship, or choosing the right doctoral advisor
Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013)
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Duncan Odom has some sage advice for those considering PhD options |
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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)
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A major update to TopHat, the popular Bowtie-based spliced aligner |
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Raymond Gosling: the man who crystallized genes
Naomi Attar Genome Biology 2013, 14:402 (25 April 2013)
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"The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix |
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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)
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Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix |
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DNA binding specificities of the long zinc-finger recombination protein PRDM9
Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013)
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A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
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Systematic biases in DNA copy number originate from isolation procedures
Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013)
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A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation |
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The complex binding of PRDM9
Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013)
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A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9 |
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Single-cell biology meeting marks rebirth of an old science
Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013)
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A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013 |
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Neurogenomics of speech and language disorders: the road ahead
Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013)
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From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders |
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p53 induces transcriptional and translational programs to suppress cell proliferation and growth
Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013)
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p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress |
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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)
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Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility |
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The fractured genome of HeLa cells
David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013)
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David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome |
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CRAC: an integrated approach to the analysis of RNA-seq reads
Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013)
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Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data |
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The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude.
Qingle Cai, Xiaoju Qian, Yongshan Lang, Yadan Luo, Shengkai Pan, Yuanyuan Hui, Caiyun Gou, Yue Cai, Meirong Hao, Jinyang Zhao, Songbo Wang, Zhaobao Wang, Xinming Zhang, Jinchao Liu, Longhai Luo, Yingrui Li, Jun Wang, Rongjun He, Fumin Lei, Jiaohui Xu Genome Biology 2013, 14:R29 (28 March 2013)
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The ground tit genome, one of the highest quality avian genome assemblies to date, reveals potential mechanisms of high altitude adaptation |
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The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
John Abramyan, 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, LaDeana H Hillier, Alisha K Holloway, Daniel Janes, Fredric J Janzen, Cyriac Kandoth, Lesheng Kong, Jason de Koning, Yang Li et al.
Genome Biology 2013, 14:R28 (28 March 2013)
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The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing |
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Clinical applications of sequencing take center stage
Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013)
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A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013 |
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Recent progress in the use of genetics to understand links between type 2 diabetes and related metabolic traits
Hanieh Yaghootkar, Timothy M Frayling Genome Biology 2013, 14:203 (28 March 2013)
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Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes |
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Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest
Christopher I Keeling, Macaire MS Yuen, Nancy Y Liao, T Roderick Docking, Simon K Chan, Greg A Taylor, Diana L Palmquist, Shaun D Jackman, Anh Nguyen, Maria Li, Hannah Henderson, Jasmine K Janes, Yongjun Zhao, Pawan Pandoh, Richard Moore, Felix AH Sperling, Dezene PW Huber, Inanc Birol, Stephen JM Jones, Joerg Bohlmann Genome Biology 2013, 14:R27 (27 March 2013)
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The genome sequence of the mountain pine beetle, only the second beetle genome to be sequenced |
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The future of genomic medicine is here
Konrad J Karczewski Genome Biology 2013, 14:304 (27 March 2013)
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A report on the 6th annual Future of Genomic Medicine conference, held at the Scripps
Seaside Forum, La Jolla, CA, USA, March 7-8, 2013 |
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Pushing the (nuclear) envelope into meiosis
Abby F Dernburg Genome Biology 2013, 14:110 (27 March 2013)
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Abby Dernburg discusses recent research linking nuclear lamins to chromosome pairing in meiosis |
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Sequestration: inadvertently killing biomedical research to score political points
Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013)
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Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction |
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RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes
Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grutzner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013)
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A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation |
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Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb-target genes
James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendegast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013)
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An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells |
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Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue
Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson Genome Biology 2013, 14:R24 (25 March 2013)
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Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples |
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Go retro and get a GRIP
Kim Wong, David J Adams, Thomas M Keane Genome Biology 2013, 14:108 (19 March 2013)
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David Adams and colleagues grapple with the GRIPs (gene retrocopy insertion polymorphisms) identified by Ewing et al in this month's issue |
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DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels
Huiying Zhao, Yuedong Yang, Hai Lin, Xinjun Zhang, Matthew Mort, David N Copper, Yunlong Liu, Yaoqi Zhou Genome Biology 2013, 14:R23 (13 March 2013)
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DDIG-in is a method for predicting the deleterious effects of short indels |
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Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
Adam D Ewing, Tracy J Ballinger, Dent Earl, Broad Institute Genome Sequencing and Analysis Program and Platform, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013)
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An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues |
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DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes
Dvir Aran, Sivan Sabato, Asaf Hellman Genome Biology 2013, 14:R21 (12 March 2013)
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A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers |
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Studying the microbiology of the indoor environment
Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013)
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Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study |
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Food for thought from plant and animal genomes
Emily Abrash Genome Biology 2013, 14:302 (27 February 2013)
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A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013. |
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Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes
Pedro G Ferreira, Solenn Patalano, Ritika Chauhan, Richard Ffrench-Constant, Toni Gabaldón, Roderic Guigó, Seirian Sumner Genome Biology 2013, 14:R20 (26 February 2013)
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An RNA-seq analysis of the genetic mechanisms controlling alternative phenotypes in the primitive eusocial wasp Polistes canadensis |
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A CRISPR way to engineer the human genome
Sivaprakash Ramalingam, Narayana Annaluru, Srinivasan Chandrasegaran Genome Biology 2013, 14:107 (26 February 2013)
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Srinivasan Chandrasegaran and colleagues explain how recent advances in mammalian genome engineering exploit the natural properties of the bacterial CRISPR system |
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Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes
Cecilia Alsmark, Peter G Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T Martin Embley, Robert P Hirt Genome Biology 2013, 14:R19 (25 February 2013)
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A survey of the genomes of eukaryotic microbial parasites reveals extensive lateral gene transfer from prokaryotes |
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The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila
Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, Renato Paro Genome Biology 2013, 14:R18 (25 February 2013)
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Editor’s summary
The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression |
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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 Genome Biology 2013, 14:R17 (20 February 2013)
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Sequencing the genomes of 48 strains of Sinorhizobium reveals a large heterogeneity in strategies for colonization in this family |
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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)
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A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration |
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What is it about 'eye of newt'?
Yuliana Mihaylova, A Aziz Aboobaker Genome Biology 2013, 14:106 (20 February 2013)
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Aziz Aboobaker and Yuliana Mihaylova muse on the peculiar powers that led 'eye of newt' to find favor with Macbeth's witches |
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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 Genome Biology 2013, 14:R15 (18 February 2013)
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Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity |
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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 Genome Biology 2013, 14:R14 (15 February 2013)
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A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner |
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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 Lu, John R Yates, John K Kim Genome Biology 2013, 14:R13 (14 February 2013)
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A study of the global binding of RNA binding proteins in yeast in response to stress |
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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 Genome Biology 2013, 14:R12 (14 February 2013)
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SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements |
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Science: it's a role model thing
Chris Gunter Genome Biology 2013, 14:105 (14 February 2013)
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To coincide with International Women's Day on March 8, Chris Gunter ask how important role models are to improving female representation in science |
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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 Bürglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris 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, Peter Hegemann, Hillel Fromm, Didier Raoult, Gilbert Greub, Diego Miranda-Saavedra, Nansheng Chen, Piers Nash et al.
Genome Biology 2013, 14:R11 (1 February 2013)
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Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling |
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Genome sequencing of the important oilseed crop Sesamum indicum L
Haiyang Zhang, Hongmei Miao, Lei Wang, Lingbo Qu, Hongyan Liu, Qiang Wang, Meiwang Yue Genome Biology 2013, 14:401 (31 January 2013)
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The Sesame Genome Working Group describe the project for sequencing the sesame genome |
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Host genomic influences on HIV/AIDS
Stephen J O'Brien, Sher L Hendrickson Genome Biology 2013, 14:201 (31 January 2013)
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How has the era of genomics advanced our understanding of HIV/AIDS epidemiology and pathogenesis? |
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Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
Daniël P Melters, Keith R Bradnam, Hugh A Young, Natalie Telis, Michael R May, J Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank, José Garcia, Joseph L DeRisi, Timothy Smith, Christian Tobias, Jeffrey Ross-Ibarra, Ian Korf, Simon WL Chan Genome Biology 2013, 14:R10 (30 January 2013)
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| F1000 Biology
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An analysis of centromere tandem repeats in 282 species reveals similar modes of evolution despite the lack of sequence conservation |
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The passionate life of Simon Chan
Luca Comai Genome Biology 2013, 14:103 (30 January 2013)
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Luca Comai remembers the late Simon Chan, whose work on centromere evolution features in the current issue of Genome Biology |
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Accelerated exon evolution within primate segmental duplications
Belen Lorente-Galdos, Jonathan Bleyhl, Gabriel Santpere, Laura Vives, Oscar Ramírez, Jessica Hernandez, Roger Anglada, Gregory M Cooper, Arcadi Navarro, Evan E Eichler, Tomas Marques-Bonet Genome Biology 2013, 14:R9 (29 January 2013)
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A new study looks at segmental duplication genes in humans and macaques to elucidate exon evolution in primates |
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CGAL: computing genome assembly likelihoods
Atif Rahman, Lior Pachter Genome Biology 2013, 14:R8 (29 January 2013)
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A likelihood based approach for better estimation of genome assembly quality |
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A 10-step guide to party conversation for bioinformaticians
Alicia Oshlack Genome Biology 2013, 14:104 (29 January 2013)
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Alicia Oshlack's 10-step guide to party conversation for bioinformaticians |
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Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data
Jong Kim, John C Marioni Genome Biology 2013, 14:R7 (28 January 2013)
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A new framework for modeling stochastic gene expression in single cells yields insights into the regulatory role of histone modifications |
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From hybrids to hermaphrodites in population genetics
Robert Verity, Jeannine Marquardt, Andrea Hatlen, Jasmin Zohren Genome Biology 2013, 14:301 (28 January 2013)
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A report on the 46th annual PopGroup conference, Glasgow, UK, December 18-21, 2012. |
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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 Genome Biology 2013, 14:R6 (24 January 2013)
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Binding sites for FOXM1 are mapped in breast cancer cell lines with and without estrogen receptor |
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Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
Falk Hildebrand, Thi Nguyen, Brigitta Brinkman, Roberto Yunta, Benedicte Cauwe, Peter Vandenabeele, Adrian Liston, Jeroen Raes Genome Biology 2013, 14:R4 (24 January 2013)
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A new study finds that enterotypes are not only present in mice, but also similar to those in humans |
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Acting on impulse: dissecting the dynamics of the NFAT transcriptional response
Alon Kalo, Yaron Shav-Tal Genome Biology 2013, 14:102 (24 January 2013)
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Yaron Shav-Tal discusses isoform specifity in transcription factor dynamics, including the role of NFAT translocations out of the nucleus |
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Thick and thin fingers point out Turing waves
Andrew D Economou, Jeremy BA Green Genome Biology 2013, 14:101 (24 January 2013)
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Editor’s summary
A Research Highlight on the mystery of finger formation: how Alan Turing's proposed reaction-diffusion mechanism underlies digit development |
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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 Genome Biology 2013, 14:R5 (23 January 2013)
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The tissue specificity of Rb/E2F binding profiles enables the promotion of both somatic and germline transcriptional programs |
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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 Islam, Fatima Al-Shahrour, Javier Rodríguez-Ubreva, Virginia C Rodríguez-Cortez, Biola M Javierre, Cristina Mangas, Agustín F Fernández, Maribel Parra, Henri-Jacques Delecluse, Manel Esteller, Eduardo López-Granados, Mario F Fraga, Nuria López-Bigas, Esteban Ballestar Genome Biology 2013, 14:R3 (15 January 2013)
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DNA hypomethylation is a key feature of Epstein-Barr virus-associated B cell proliferative transformation, and occurs via a passive demethylation process |
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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 Genome Biology 2013, 14:R2 (15 January 2013)
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Editor’s summary
A modular, metagenomic analysis and assembly pipeline that inputs next-generation sequencing reads to generate genomic scaffolds and open reading frames |
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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 Fortenberry, Martin J Holland, Sarah E Burr, William D Shannon, Erica Sodergren, George M Weinstock Genome Biology 2013, 14:R1 (14 January 2013)
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Editor’s summary
As part of the Human Microbiome Project, taxonomic analyses were performed on the bacteria from 22 body sites on 279 subjects |
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The ADAR protein family
Yiannis A Savva, Leila E Rieder, Robert A Reenan Genome Biology 2012, 13:252 (28 December 2012)
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ADARs and RNA editing: a Protein Family Review by Robert Reenan and colleagues |
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Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus
Santiago Castillo-Ramírez, Jukka Corander, Pekka Marttinen, Mona Aldeljawi, William P Hanage, Henrik Westh, Kit Boye, Zeynep Gulay, Stephen D Bentley, Julian Parkhill, Matthew T Holden, Edward J Feil Genome Biology 2012, 13:R126 (27 December 2012)
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Different evolution rates of methicillin-resistant Staphylococcus aureus clone ST239 collected in different geographical locations are caused by fast global dissemination |
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Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone
Todd J Treangen, Adam M Phillippy Genome Biology 2012, 13:181 (27 December 2012)
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A study of methicillin-resistant Staphylococcus aureus reveals its recombination trends, and highlights the challenges of phylogeographic analysis of these pathogens |
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RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network
Peggy I Wang, Sohyun Hwang, Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, Edward M Marcotte Genome Biology 2012, 13:R125 (26 December 2012)
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A method using guilt-by-association principles to identify associations of unannotated gene sets |
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Differential analysis of high-throughput quantitative genetic interaction data
Gordon J Bean, Trey Ideker Genome Biology 2012, 13:R123 (26 December 2012)
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A new method for the differential analysis of genetic interactions
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A new era of human population genetics
Alexander Platt, John Novembre Genome Biology 2012, 13:182 (26 December 2012)
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Alexander Platt and John Novembre discuss what the 1000 Genomes Project teaches us about human population genetics |
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How to be wrong but useful
Adam Kucharski Genome Biology 2012, 13:180 (26 December 2012)
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Adam Kucharski, 2012's winner of the Wellcome Trust science writing prize, applauds Alan Turing, Nate Silver and the power of models |
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DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer
Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G Huntsman, Carlos Caldas, Samuel A Aparicio, Sohrab P Shah Genome Biology 2012, 13:R124 (22 December 2012)
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DriverNet is a method for identifying driver mutations in cancer samples based on their effects on the transcriptional network |
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Ray Meta: scalable de novo metagenome assembly and profiling
Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012)
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A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
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A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts
Eric J Suh, Matthew Y Remillard, Aster Legesse-Miller, Elizabeth L Johnson, Johanna MS Lemons, Talia R Chapman, Joshua J Forman, Mina Kojima, Eric S Silberman, Hilary A Coller Genome Biology 2012, 13:R121 (22 December 2012)
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A study identifying microRNAs both facilitating and delaying fibroblast cell cycle re-entry from quiescence |
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cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data
Evangelos Bellos, Michael R Johnson, Lachlan J M Coin Genome Biology 2012, 13:R120 (22 December 2012)
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An integrative, probabilistic method for CNV discovery and genotyping |
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Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing
Margarida Cardoso-Moreira, J Arguello, Andrew G Clark Genome Biology 2012, 13:R119 (22 December 2012)
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Sequencing of breakpoints in Drosophila melanogaster genomes reveals similarities and differences with breakpoint formation in humans
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Microevolutionary analysis of Clostridium difficile genomes to investigate transmission
Xavier Didelot, David W Eyre, Madeleine Cule, Camilla LC Ip, M Ansari, David Griffiths, Alison Vaughan, Lily O'Connor, Tanya Golubchik, Elizabeth M Batty, Paolo Piazza, Daniel J Wilson, Rory Bowden, Peter J Donnelly, Kate E Dingle, Mark Wilcox, A Walker, Derrick W Crook, Tim E A Peto, Rosalind M Harding Genome Biology 2012, 13:R118 (21 December 2012)
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Editor’s summary
Transmission events of Clostridium difficile are inferred from whole-genome sequencing of isolates and estimating divergence time of bacterial strains
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Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements
Xue Dong, Julia Reimer, Ulrike Göbel, Julia Engelhorn, Fei He, Heiko Schoof, Franziska Turck Genome Biology 2012, 13:R117 (19 December 2012)
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An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
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Personal genomes and precision medicine
Gareth Highnam, David Mittelman Genome Biology 2012, 13:324 (19 December 2012)
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Editor’s summary
A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012 |
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FOCAL: an experimental design tool for systematizing metabolic discoveries and model
development
Christopher J Tervo, Jennifer L Reed Genome Biology 2012, 13:R116 (13 December 2012)
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Editor’s summary
A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype |
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Whole-genome reconstruction and mutational signatures in gastric cancer
Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Zang, Fei Yao, Pierre-Étienne Jacques, Audrey SM Teo, Ioana Cutcutache, Zhenshui Zhang, Wah Lee, Yee Sia, Song Gao, Pramila N Ariyaratne, Andrea Ho, Xing Woo, Lavanya Veeravali, Choon Ong, Niantao Deng, Kartiki V Desai, Chiea Khor, Martin L Hibberd, Atif Shahab, Jaideepraj Rao, Mengchu Wu, Ming Teh, Feng Zhu, Sze Chin, Brendan Pang, Jimmy BY So, Guillaume Bourque et al.
Genome Biology 2012, 13:R115 (13 December 2012)
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Editor’s summary
In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer. |
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Widespread promoter-mediated coordination of transcription and mRNA degradation
Mally Dori-Bachash, Ophir Shalem, Yair S Manor, Yitzhak Pilpel, Itay Tirosh Genome Biology 2012, 13:R114 (13 December 2012)
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Transcription and degradation of mRNA in yeast is commonly coordinated through promoters
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Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data
Matthew Parker, Xiang Chen, Armita Bahrami, James Dalton, Michael Rusch, Gang Wu, John Easton, Nai-Kong Cheung, Michael Dyer, Elaine R Mardis, Richard K Wilson, Charles Mullighan, Richard Gilbertson, Suzanne J Baker, Gerard Zambetti, David W Ellison, James R Downing, Jinghui Zhang, the Pediatric Cancer Genome Project Genome Biology 2012, 13:R113 (11 December 2012)
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Editor’s summary
A comprehensive analysis of telomere length changes in a large collection of pediatric tumors
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A network module-based method for identifying cancer prognostic signatures
Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012)
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A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis |
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MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
Edward Vitkin, Tomer Shlomi Genome Biology 2012, 13:R111 (29 November 2012)
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MIRAGE is a gap-filling method for metabolic networks based on functional genomics data which is demonstrated, then applied to cyanobacterial networks
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Dicer partners expand the repertoire of miRNA targets
Lukasz Jaskiewicz, Mihaela Zavolan Genome Biology 2012, 13:179 (29 November 2012)
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A Research Highlight by Lukasz Jaskiewicz and Mihaela Zavolan discusses how cofactors modify Dicer processing and, consequently, transcriptional networks
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Computational thinking in the era of big data biology
Michael C Schatz Genome Biology 2012, 13:177 (29 November 2012)
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by Mike Schatz
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Human genes with CpG island promoters have a distinct transcription-associated chromatin organization
Tanya Vavouri, Ben Lehner Genome Biology 2012, 13:R110 (27 November 2012)
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A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
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Computational discovery of regulatory elements in a continuous expression space
Mathieu Lajoie, Olivier Gascuel, Vincent Lefort, Laurent Bréhélin Genome Biology 2012, 13:R109 (27 November 2012)
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A novel method that identifies regulatory elements by estimating motif densities around each gene, using overlapping neighborhoods in expression space
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Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum
Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph, Till S Voss Genome Biology 2012, 13:R108 (26 November 2012)
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A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins
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Transposable elements reveal a stem cell-specific class of long noncoding RNAs
David Kelley, John Rinn Genome Biology 2012, 13:R107 (26 November 2012)
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Editor’s summary
A characterization of the transposable element content of human lincRNAs to resolve the evolutionary origins of lincRNAs in the human genome
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Why rodent pseudogenes refuse to retire
Manyuan Long, Li Zhang Genome Biology 2012, 13:178 (20 November 2012)
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Functional entities or curmudgeonly junk? The ceRNA hypothesis may explain why many rodent pseudogenes resist evolutionary erosion
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International plant molecular biology: a bright future for green science
Sibum Sung, Enamul Huq, Z Jeffrey Chen Genome Biology 2012, 13:323 (19 November 2012)
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Editor’s summary
A report on the 10th International Congress of Plant Molecular Biology, Jeju, South Korea, October 21-26, 2012.
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Strategies towards sequencing complex crop genomes
James C Abbott, Sarah A Butcher Genome Biology 2012, 13:322 (19 November 2012)
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A report on the Strategies for de novo assemblies of complex crop genomes workshop held at The Genome Analysis Centre, Norwich, UK, 8-10 October 2012.
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Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling
Mariona Nadal-Ribelles, Núria Conde, Oscar Flores, Juan González-Vallinas, Eduardo Eyras, Modesto Orozco, Eulàlia de Nadal, Francesc Posas Genome Biology 2012, 13:R106 (18 November 2012)
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Hog1 bypasses gene expression regulation by targeting RNA polymerase II machinery and inducing chromatin remodeling at stress-responsive loci
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A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis
Simon E Alfred, Anuradha Surendra, Chris Le, Ken Lin, Alexander Mok, Iain M Wallace, Michael Proctor, Malene L Urbanus, Guri Giaever, Corey Nislow Genome Biology 2012, 13:R105 (18 November 2012)
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Editor’s summary
An automated small molecule screening method for Chlamydomonas reinhardtii, and its application to identify bioactive compounds for agriculture, biofuels and therapeutics
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