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Open letter   Free Highly Accessed

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   Subscription

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   Open Access Highly Accessed

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 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   Free Highly Accessed

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   Open Access Highly Accessed

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 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   Open Access Highly Accessed

CGAL: computing genome assembly likelihoods

Atif Rahman, Lior Pachter Genome Biology 2013, 14:R8 (29 January 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

A likelihood based approach for better estimation of genome assembly quality

Comment   Subscription Highly Accessed

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   Open Access Highly Accessed

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 | Provisional 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   Subscription

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   Open Access

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   Open Access Highly Accessed

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   Subscription

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   Subscription

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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 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   Subscription

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   Open Access

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   Subscription

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   Open Access

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   Open Access

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   Subscription Highly Accessed

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   Subscription

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   Open Access

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

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