Genome Biology | Volume 14 Issue 1

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 14 Issue 1
	Comment
	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
	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 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 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
	Review
	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?
	Report
	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
	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 \| Full text \| 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
	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
	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 \| Full text \| PDF \| PubMed \| Editor’s summary The tissue specificity of Rb/E2F binding profiles enables the promotion of both somatic and germline transcriptional programs
	Research Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice Falk Hildebrand, Thi Loan Anh Nguyen, Brigitta Brinkman, Roberto Yunta, Benedicte Cauwe, Peter Vandenabeele, Adrian Liston, Jeroen Raes Genome Biology 2013, 14:R4 (24 January 2013) Abstract \| Full text \| 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 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 \| Full text \| PDF \| PubMed \| Editor’s summary Binding sites for FOXM1 are mapped in breast cancer cell lines with and without estrogen receptor
	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
	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 \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A new study looks at segmental duplication genes in humans and macaques to elucidate exon evolution in primates
	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 \| Full text \| 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
	Method CGAL: computing genome assembly likelihoods Atif Rahman, Lior Pachter Genome Biology 2013, 14:R8 (29 January 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A likelihood based approach for better estimation of genome assembly quality
	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 \| Full text \| 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
	Correspondence
	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

	Volume 14 Issue 1
	Comment
	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
	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 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 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
	Review
	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?
	Report
	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
	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 \| Full text \| 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
	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
	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 \| Full text \| PDF \| PubMed \| Editor’s summary The tissue specificity of Rb/E2F binding profiles enables the promotion of both somatic and germline transcriptional programs
	Research Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice Falk Hildebrand, Thi Loan Anh Nguyen, Brigitta Brinkman, Roberto Yunta, Benedicte Cauwe, Peter Vandenabeele, Adrian Liston, Jeroen Raes Genome Biology 2013, 14:R4 (24 January 2013) Abstract \| Full text \| 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 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 \| Full text \| PDF \| PubMed \| Editor’s summary Binding sites for FOXM1 are mapped in breast cancer cell lines with and without estrogen receptor
	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
	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 \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A new study looks at segmental duplication genes in humans and macaques to elucidate exon evolution in primates
	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 \| Full text \| 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
	Method CGAL: computing genome assembly likelihoods Atif Rahman, Lior Pachter Genome Biology 2013, 14:R8 (29 January 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A likelihood based approach for better estimation of genome assembly quality
	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 \| Full text \| 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
	Correspondence
	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

Explore Genome Biology

Articles

Volume 14 Issue 1

Comment

Review

Report

Research

Correspondence