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
		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 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 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 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 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 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 \| 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 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 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 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

	All
		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 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 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 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 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 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 \| 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 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 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 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