Genome Biology | All articles

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

Supplements

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	All
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A study of the global binding of RNA binding proteins in yeast in response to stress
		Method 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
		Open letter 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sesame Genome Working Group describe the project for sequencing the sesame genome
		Review Host genomic influences on HIV/AIDS Stephen J O'Brien, Sher L Hendrickson Genome Biology 2013, 14:201 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How has the era of genomics advanced our understanding of HIV/AIDS epidemiology and pathogenesis?
		Research 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) Abstract \| Provisional PDF \| PubMed \| F1000 Biology \| Editor’s summary An analysis of centromere tandem repeats in 282 species reveals similar modes of evolution despite the lack of sequence conservation
		Comment The passionate life of Simon Chan Luca Comai Genome Biology 2013, 14:103 (30 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Luca Comai remembers the late Simon Chan, whose work on centromere evolution features in the current issue of Genome Biology
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study looks at segmental duplication genes in humans and macaques to elucidate exon evolution in primates
		Method CGAL: computing genome assembly likelihoods Atif Rahman, Lior Pachter Genome Biology 2013, 14:R8 (29 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A likelihood based approach for better estimation of genome assembly quality
		Comment A 10-step guide to party conversation for bioinformaticians Alicia Oshlack Genome Biology 2013, 14:104 (29 January 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Alicia Oshlack's 10-step guide to party conversation for bioinformaticians
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new framework for modeling stochastic gene expression in single cells yields insights into the regulatory role of histone modifications
		Meeting report From hybrids to hermaphrodites in population genetics Robert Verity, Jeannine Marquardt, Andrea Hatlen, Jasmin Zohren Genome Biology 2013, 14:301 (28 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 46th annual PopGroup conference, Glasgow, UK, December 18-21, 2012.
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Binding sites for FOXM1 are mapped in breast cancer cell lines with and without estrogen receptor
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study finds that enterotypes are not only present in mice, but also similar to those in humans
		Research highlight Acting on impulse: dissecting the dynamics of the NFAT transcriptional response Alon Kalo, Yaron Shav-Tal Genome Biology 2013, 14:102 (24 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Yaron Shav-Tal discusses isoform specifity in transcription factor dynamics, including the role of NFAT translocations out of the nucleus
		Research highlight Thick and thin fingers point out Turing waves Andrew D Economou, Jeremy BA Green Genome Biology 2013, 14:101 (24 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight on the mystery of finger formation: how Alan Turing's proposed reaction-diffusion mechanism underlies digit development
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The tissue specificity of Rb/E2F binding profiles enables the promotion of both somatic and germline transcriptional programs
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA hypomethylation is a key feature of Epstein-Barr virus-associated B cell proliferative transformation, and occurs via a passive demethylation process
		Software 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A modular, metagenomic analysis and assembly pipeline that inputs next-generation sequencing reads to generate genomic scaffolds and open reading frames
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary As part of the Human Microbiome Project, taxonomic analyses were performed on the bacteria from 22 body sites on 279 subjects
		Protein family review The ADAR protein family Yiannis A Savva, Leila E Rieder, Robert A Reenan Genome Biology 2012, 13:252 (28 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ADARs and RNA editing: a Protein Family Review by Robert Reenan and colleagues
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Different evolution rates of methicillin-resistant Staphylococcus aureus clone ST239 collected in different geographical locations are caused by fast global dissemination
		Research highlight 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of methicillin-resistant Staphylococcus aureus reveals its recombination trends, and highlights the challenges of phylogeographic analysis of these pathogens
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method using guilt-by-association principles to identify associations of unannotated gene sets
		Method Differential analysis of high-throughput quantitative genetic interaction data Gordon J Bean, Trey Ideker Genome Biology 2012, 13:R123 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method for the differential analysis of genetic interactions
		Research highlight A new era of human population genetics Alexander Platt, John Novembre Genome Biology 2012, 13:182 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Alexander Platt and John Novembre discuss what the 1000 Genomes Project teaches us about human population genetics
		Comment How to be wrong but useful Adam Kucharski Genome Biology 2012, 13:180 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Adam Kucharski, 2012's winner of the Wellcome Trust science writing prize, applauds Alan Turing, Nate Silver and the power of models
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DriverNet is a method for identifying driver mutations in cancer samples based on their effects on the transcriptional network
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study identifying microRNAs both facilitating and delaying fibroblast cell cycle re-entry from quiescence
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrative, probabilistic method for CNV discovery and genotyping
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of breakpoints in Drosophila melanogaster genomes reveals similarities and differences with breakpoint formation in humans
		Research 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) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Transmission events of Clostridium difficile are inferred from whole-genome sequencing of isolates and estimating divergence time of bacterial strains
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
		Meeting report Personal genomes and precision medicine Gareth Highnam, David Mittelman Genome Biology 2012, 13:324 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| 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
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer.
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription and degradation of mRNA in yeast is commonly coordinated through promoters
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of telomere length changes in a large collection of pediatric tumors
		Method A network module-based method for identifying cancer prognostic signatures Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MIRAGE is a gap-filling method for metabolic networks based on functional genomics data which is demonstrated, then applied to cyanobacterial networks
		Research highlight Dicer partners expand the repertoire of miRNA targets Lukasz Jaskiewicz, Mihaela Zavolan Genome Biology 2012, 13:179 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Lukasz Jaskiewicz and Mihaela Zavolan discusses how cofactors modify Dicer processing and, consequently, transcriptional networks
		Comment 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 \| Editor’s summary by Mike Schatz
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method that identifies regulatory elements by estimating motif densities around each gene, using overlapping neighborhoods in expression space
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins
		Research Transposable elements reveal a stem cell-specific class of long noncoding RNAs David Kelley, John Rinn Genome Biology 2012, 13:R107 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A characterization of the transposable element content of human lincRNAs to resolve the evolutionary origins of lincRNAs in the human genome
		Research highlight Why rodent pseudogenes refuse to retire Manyuan Long, Li Zhang Genome Biology 2012, 13:178 (20 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Functional entities or curmudgeonly junk? The ceRNA hypothesis may explain why many rodent pseudogenes resist evolutionary erosion
		Meeting report 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th International Congress of Plant Molecular Biology, Jeju, South Korea, October 21-26, 2012.
		Meeting report Strategies towards sequencing complex crop genomes James C Abbott, Sarah A Butcher Genome Biology 2012, 13:322 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 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.

	All
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A study of the global binding of RNA binding proteins in yeast in response to stress
		Method 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
		Open letter 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sesame Genome Working Group describe the project for sequencing the sesame genome
		Review Host genomic influences on HIV/AIDS Stephen J O'Brien, Sher L Hendrickson Genome Biology 2013, 14:201 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How has the era of genomics advanced our understanding of HIV/AIDS epidemiology and pathogenesis?
		Research 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) Abstract \| Provisional PDF \| PubMed \| F1000 Biology \| Editor’s summary An analysis of centromere tandem repeats in 282 species reveals similar modes of evolution despite the lack of sequence conservation
		Comment The passionate life of Simon Chan Luca Comai Genome Biology 2013, 14:103 (30 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Luca Comai remembers the late Simon Chan, whose work on centromere evolution features in the current issue of Genome Biology
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study looks at segmental duplication genes in humans and macaques to elucidate exon evolution in primates
		Method CGAL: computing genome assembly likelihoods Atif Rahman, Lior Pachter Genome Biology 2013, 14:R8 (29 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A likelihood based approach for better estimation of genome assembly quality
		Comment A 10-step guide to party conversation for bioinformaticians Alicia Oshlack Genome Biology 2013, 14:104 (29 January 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Alicia Oshlack's 10-step guide to party conversation for bioinformaticians
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new framework for modeling stochastic gene expression in single cells yields insights into the regulatory role of histone modifications
		Meeting report From hybrids to hermaphrodites in population genetics Robert Verity, Jeannine Marquardt, Andrea Hatlen, Jasmin Zohren Genome Biology 2013, 14:301 (28 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 46th annual PopGroup conference, Glasgow, UK, December 18-21, 2012.
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Binding sites for FOXM1 are mapped in breast cancer cell lines with and without estrogen receptor
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study finds that enterotypes are not only present in mice, but also similar to those in humans
		Research highlight Acting on impulse: dissecting the dynamics of the NFAT transcriptional response Alon Kalo, Yaron Shav-Tal Genome Biology 2013, 14:102 (24 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Yaron Shav-Tal discusses isoform specifity in transcription factor dynamics, including the role of NFAT translocations out of the nucleus
		Research highlight Thick and thin fingers point out Turing waves Andrew D Economou, Jeremy BA Green Genome Biology 2013, 14:101 (24 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight on the mystery of finger formation: how Alan Turing's proposed reaction-diffusion mechanism underlies digit development
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The tissue specificity of Rb/E2F binding profiles enables the promotion of both somatic and germline transcriptional programs
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA hypomethylation is a key feature of Epstein-Barr virus-associated B cell proliferative transformation, and occurs via a passive demethylation process
		Software 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A modular, metagenomic analysis and assembly pipeline that inputs next-generation sequencing reads to generate genomic scaffolds and open reading frames
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary As part of the Human Microbiome Project, taxonomic analyses were performed on the bacteria from 22 body sites on 279 subjects
		Protein family review The ADAR protein family Yiannis A Savva, Leila E Rieder, Robert A Reenan Genome Biology 2012, 13:252 (28 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ADARs and RNA editing: a Protein Family Review by Robert Reenan and colleagues
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Different evolution rates of methicillin-resistant Staphylococcus aureus clone ST239 collected in different geographical locations are caused by fast global dissemination
		Research highlight 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of methicillin-resistant Staphylococcus aureus reveals its recombination trends, and highlights the challenges of phylogeographic analysis of these pathogens
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method using guilt-by-association principles to identify associations of unannotated gene sets
		Method Differential analysis of high-throughput quantitative genetic interaction data Gordon J Bean, Trey Ideker Genome Biology 2012, 13:R123 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method for the differential analysis of genetic interactions
		Research highlight A new era of human population genetics Alexander Platt, John Novembre Genome Biology 2012, 13:182 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Alexander Platt and John Novembre discuss what the 1000 Genomes Project teaches us about human population genetics
		Comment How to be wrong but useful Adam Kucharski Genome Biology 2012, 13:180 (26 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Adam Kucharski, 2012's winner of the Wellcome Trust science writing prize, applauds Alan Turing, Nate Silver and the power of models
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DriverNet is a method for identifying driver mutations in cancer samples based on their effects on the transcriptional network
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study identifying microRNAs both facilitating and delaying fibroblast cell cycle re-entry from quiescence
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An integrative, probabilistic method for CNV discovery and genotyping
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of breakpoints in Drosophila melanogaster genomes reveals similarities and differences with breakpoint formation in humans
		Research 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) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Transmission events of Clostridium difficile are inferred from whole-genome sequencing of isolates and estimating divergence time of bacterial strains
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
		Meeting report Personal genomes and precision medicine Gareth Highnam, David Mittelman Genome Biology 2012, 13:324 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| 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
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that identifies media and knock-out conditions where a given reaction is essential for a measurable phenotype
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study the whole genome sequencing is used to reveal mutational signatures in gastric cancer.
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription and degradation of mRNA in yeast is commonly coordinated through promoters
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comprehensive analysis of telomere length changes in a large collection of pediatric tumors
		Method A network module-based method for identifying cancer prognostic signatures Guanming Wu, Lincoln Stein Genome Biology 2012, 13:R112 (10 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for identifying prognostic biomarkers from cancer gene expression datasets using gene functional network analysis
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MIRAGE is a gap-filling method for metabolic networks based on functional genomics data which is demonstrated, then applied to cyanobacterial networks
		Research highlight Dicer partners expand the repertoire of miRNA targets Lukasz Jaskiewicz, Mihaela Zavolan Genome Biology 2012, 13:179 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Lukasz Jaskiewicz and Mihaela Zavolan discusses how cofactors modify Dicer processing and, consequently, transcriptional networks
		Comment 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 \| Editor’s summary by Mike Schatz
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
		Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel method that identifies regulatory elements by estimating motif densities around each gene, using overlapping neighborhoods in expression space
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A proteomic study of the nuclear proteome of Plasmodium falciparum reveals novel nuclear proteins
		Research Transposable elements reveal a stem cell-specific class of long noncoding RNAs David Kelley, John Rinn Genome Biology 2012, 13:R107 (26 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A characterization of the transposable element content of human lincRNAs to resolve the evolutionary origins of lincRNAs in the human genome
		Research highlight Why rodent pseudogenes refuse to retire Manyuan Long, Li Zhang Genome Biology 2012, 13:178 (20 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Functional entities or curmudgeonly junk? The ceRNA hypothesis may explain why many rodent pseudogenes resist evolutionary erosion
		Meeting report 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 10th International Congress of Plant Molecular Biology, Jeju, South Korea, October 21-26, 2012.
		Meeting report Strategies towards sequencing complex crop genomes James C Abbott, Sarah A Butcher Genome Biology 2012, 13:322 (19 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 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.