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Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection
Omer Gokcumen, Paul L Babb, Rebecca C Iskow, Qihui Zhu, Xinghua Shi, Ryan E Mills, Iuliana Ionita-Laza, Eric J Vallender, Andrew G Clark, Welkin E Johnson, Charles Lee Genome Biology 2011, 12:R52 (31 May 2011)
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Identification of overlapping copy number variation hotspots in chimpanzee, macaque and human
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Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths
Jacob Enk, Alison Devault, Regis Debruyne, Christine E King, Todd Treangen, Dennis O'Rourke, Steven L Salzberg, Daniel Fisher, Ross MacPhee, Hendrik Poinar Genome Biology 2011, 12:R51 (31 May 2011)
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A surprising mtDNA phylogeny suggests that North American woolly mammoths bred with the distinct Columbian mammoth species
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Moving pictures of the human microbiome
J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I Gordon, Rob Knight Genome Biology 2011, 12:R50 (30 May 2011)
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| F1000 Biology
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Editor’s summary
The dynamism of microbiome populations is seen in daily samples from a landmark multi-body site, multi-individual study
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Mapping of disease-associated variants in admixed populations
Daniel Shriner, Adebowale Adeyemo, Edward Ramos, Guanjie Chen, Charles N Rotimi Genome Biology 2011, 12:223 (30 May 2011)
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High-throughput genotyping and sequencing will enable refined estimation of ancestry, thus enhancing disease loci identification in admixed populations
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In praise of model organisms
Gregory A Petsko Genome Biology 2011, 12:115 (30 May 2011)
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Basic research in model organisms is crucial and needs defending against claims that it is irrelevant to human biology and disease.
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The volatile microbiome
George M Weinstock Genome Biology 2011, 12:114 (30 May 2011)
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George Weinstock highlights Genome Biology's latest research article on human microbiota
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A mystery unveiled
Yves Van de Peer Genome Biology 2011, 12:113 (30 May 2011)
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A recent phylogenomic study has provided new evidence for two ancient whole genome duplications in plants, with potential importance for the evolution of seed and flowering plants
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Path finding methods accounting for stoichiometry in metabolic networks
Jon Pey, Joaquín Prada, John E Beasley, Francisco J Planes Genome Biology 2011, 12:R49 (27 May 2011)
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The incorporation of stoichiometry into path finding improves metabolic network analysis
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A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure
Andrea Zuccolo, John E Bowers, James C Estill, Zhiyong Xiong, Meizhong Luo, Aswathy Sebastian, José Goicoechea, Kristi Collura, Yeisoo Yu, Yuannian Jiao, Jill Duarte, Haibao Tang, Saravanaraj Ayyampalayam, Steve Rounsley, Dave Kudrna, Andrew H Paterson, J Pires, Andre Chanderbali, Douglas E Soltis, Srikar Chamala, Brad Barbazuk, Pamela S Soltis, Victor A Albert, Hong Ma, Dina Mandoli, Jody Banks, John E Carlson, Jeffrey Tomkins, Claude W dePamphilis, Rod A Wing, Jim Leebens-Mack et al.
Genome Biology 2011, 12:R48 (27 May 2011)
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Mapping an outlier helps reconstruct the polyploidy timeline in angiosperms
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A high resolution map of a cyanobacterial transcriptome
Vikram Vijayan, Isha H Jain, Erin K O'Shea Genome Biology 2011, 12:R47 (25 May 2011)
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A detailed transcriptome analysis of the cyanobacterium Synechococcus elongatus reveals widespread non coding transcription and transcript architecture
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Copy number polymorphisms and anticancer pharmacogenomics
Eric R Gamazon, R Stephanie Huang, M Eileen Dolan, Nancy J Cox Genome Biology 2011, 12:R46 (25 May 2011)
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Copy number polymorphisms are shown to significantly contribute to the sensitivity to anticancer drugs
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A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi
James K Hane, Thierry Rouxel, Barbara J Howlett, Gert HJ Kema, Stephen B Goodwin, Richard P Oliver Genome Biology 2011, 12:R45 (24 May 2011)
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Mesosynteny, in which genes are maintained on the same chromosome but in different orders, is revealed in different ascomycete species
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EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield Genome Biology 2011, 12:R44 (19 May 2011)
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Reconstructing full length rRNA sequences from short reads to estimate microbial community structure
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Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
Sean Thomas, Xiao-Yong Li, Peter J Sabo, Richard Sandstrom, Robert E Thurman, Theresa K Canfield, Erika Giste, William Fisher, Ann Hammonds, Susan E Celniker, Mark D Biggin, John A Stamatoyannopoulos Genome Biology 2011, 12:R43 (11 May 2011)
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A map of the dynamically changing chromatin landscape throughout Drosophila development.
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Modulated contact frequencies at gene-rich loci support a statistical helix model for mammalian chromatin organization
Franck Court, Julie Miro, Caroline Braem, Marie-Noëlle Lelay-Taha, Audrey Brisebarre, Florian Atger, Thierry Gostan, Michaël Weber, Guy Cathala, Thierry Forné Genome Biology 2011, 12:R42 (10 May 2011)
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Gene-rich mammalian chromatin is shown by 3C-qPCR and polymer modeling to adopt a helical conformation
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GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz Genome Biology 2011, 12:R41 (28 April 2011)
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Identification of genes affected by somatic copy number variations that drive human cancer growth.
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Vive la différence: biogenesis and evolution of microRNAs in plants and animals
Michael J Axtell, Jakub O Westholm, Eric C Lai Genome Biology 2011, 12:221 (28 April 2011)
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The differences in biogenesis, function and evolution of plant and animal microRNAs contribute to, and are the result of, distinct evolutionary characteristics in the two kingdoms.
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The cullin protein family
Antonio Sarikas, Thomas Hartmann, Zhen-Qiang Pan Genome Biology 2011, 12:220 (28 April 2011)
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Cullin proteins are molecular scaffolds involved in the posttranslational modification of cellular proteins by ubiquitin.
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The blue marble
Gregory A Petsko Genome Biology 2011, 12:112 (28 April 2011)
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A picture speaks a thousand words.
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Mapping meiotic breaks: Spo11 oligonucleotides precisely mark the spots
Patty Hwang, Neil Hunter Genome Biology 2011, 12:111 (28 April 2011)
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Mapping double-strand breaks reveals the characteristics of meiotic hotspots.
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Observations on shifted cumulative regulation
Chao Ye, Ying Liu, Xuegong Zhang Genome Biology 2011, 12:404 (27 April 2011)
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A response to Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation by F He, J Buer, AP Zeng and R Balling. Genome Biol 2007, 8:R181.
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A top-down view on DNA replication and recombination from 9,000 feet above sea level
Erik Johansson, Christian Speck, Andrei Chabes Genome Biology 2011, 12:304 (27 April 2011)
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A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February - 4 March 2011.
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Correction: Closing gaps in the human genome using sequencing by synthesis
Manuel Garber, Michael C Zody, Harindra C Arachchi, Aaron Berlin, Sante Gnerre, Lisa M Green, Niall Lennon, Chad Nusbaum Genome Biology 2011, 12:403 (19 April 2011)
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Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
Christian P Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth, Diego A Martinez, Irina S Druzhinina, Michael Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A Horwitz, Prasun K Mukherjee, Mala Mukherjee, László Kredics, Luis D Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte G Cervantes-Badillo, Jean Challacombe, Olga Chertkov, Kevin McCluskey, Fanny Coulpier, Nandan Deshpande, Hans von Döhren, Daniel J Ebbole, Edgardo U Esquivel-Naranjo, Erzsébet Fekete, Michel Flipphi, Fabian Glaser, Elida Y Gómez-Rodríguez, Sabine Gruber et al.
Genome Biology 2011, 12:R40 (18 April 2011)
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Analysis of two novel genomes from the biocontrol agent genus Trichoderma
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A quantitative literature-curated gold standard for kinase-substrate pairs
Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Young, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews Genome Biology 2011, 12:R39 (14 April 2011)
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A yeast kinase interaction database is presented, for kinase-gene and kinase-protein interactions
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Discovery of permuted and recently split transfer RNAs in Archaea
Patricia P Chan, Aaron E Cozen, Todd M Lowe Genome Biology 2011, 12:R38 (13 April 2011)
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Discovery of novel split and permuted archaeal tRNAs argues against a single, early origin in Archaea
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Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome
Christine R McLaughlin, Brian P Chadwick Genome Biology 2011, 12:R37 (13 April 2011)
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Potential roles of the human DXZ4 macrosatellite in CTCF binding and X inactivation are revealed through functional conservation in primates.
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An enigmatic satellite
William Amos Genome Biology 2011, 12:110 (13 April 2011)
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A conserved, transcribed X-linked satellite DNA that defies X-inactivation.
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Genome-wide survey of post-meiotic segregation during yeast recombination
Eugenio Mancera, Richard Bourgon, Wolfgang Huber, Lars M Steinmetz Genome Biology 2011, 12:R36 (11 April 2011)
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The first genome-wide study of post-meiotic segregation, in which mismatches in heteroduplex DNA are left unrepaired, performed in yeast
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What does biologically meaningful mean? A perspective on gene regulatory network validation
Albertha JM Walhout Genome Biology 2011, 12:109 (11 April 2011)
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Deciding whether gene regulatory interactions are biologically meaningful is not as simple as it might seem.
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An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations
John C Tan, Becky A Miller, Asako Tan, Jigar J Patel, Ian H Cheeseman, Tim JC Anderson, Magnus Manske, Gareth Maslen, Dominic P Kwiatkowski, Michael T Ferdig Genome Biology 2011, 12:R35 (8 April 2011)
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A Plasmodium falciparum genotyping array for determining variation in field samples with human DNA contamination.
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The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
Xiao-Yong Li, Sean Thomas, Peter J Sabo, Michael B Eisen, John A Stamatoyannopoulos, Mark D Biggin Genome Biology 2011, 12:R34 (7 April 2011)
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Chromatin accessibility influences the binding of Drosophila transcription factors.
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High recombination rates and hotspots in a Plasmodium falciparum genetic cross
Hongying Jiang, Na Li, Vivek Gopalan, Martine M Zilversmit, Sudhir Varma, Vijayaraj Nagarajan, Jian Li, Jianbing Mu, Karen Hayton, Bruce Henschen, Ming Yi, Robert Stephens, Gilean McVean, Philip Awadalla, Thomas E Wellems, Xin-zhuan Su Genome Biology 2011, 12:R33 (4 April 2011)
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The identification of Plasmodium falciparum recombination rates, hotspots and a potential PRDM9 candidate.
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The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics
Tara A Gianoulis, Ashish Agarwal, Michael Snyder, Mark B Gerstein Genome Biology 2011, 12:R32 (31 March 2011)
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Making connections between unrelated tabulated genomics datasets
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A vertebrate case study of the quality of assemblies derived from next-generation sequences
Liang Ye, LaDeana W Hillier, Patrick Minx, Nay Thane, Devin P Locke, John C Martin, Lei Chen, Makedonka Mitreva, Jason R Miller, Kevin V Haub, David J Dooling, Elaine R Mardis, Richard K Wilson, George M Weinstock, Wesley C Warren Genome Biology 2011, 12:R31 (31 March 2011)
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Editor’s summary
In a comparative analysis, the chicken genome is assembled using Sanger, Illumina or 454 reads from the same biological sample
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The walking dead
Gregory A Petsko Genome Biology 2011, 12:108 (31 March 2011)
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Creationism, academic freedom and funding: keeping the zombie out of science.
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Control of endogenous gene expression timing by introns
Annelie Oswald, Andrew C Oates Genome Biology 2011, 12:107 (29 March 2011)
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Comparison of gene expression from transgenes and endogenous genes with or without introns reveals a time-regulating role of introns in natural biological systems
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ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes
Alessandro M Varani, Patricia Siguier, Edith Gourbeyre, Vincent Charneau, Mick Chandler Genome Biology 2011, 12:R30 (28 March 2011)
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ISsaga is a tool for identifying and annotating insertion sequences in prokaryotic genomes.
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High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype
Rosangela Sozzani, Philip N Benfey Genome Biology 2011, 12:219 (28 March 2011)
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A review of new methods for high-throughput phenotyping of multicellular organisms.
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Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite
France Denoeud, Michaël Roussel, Benjamin Noel, Ivan Wawrzyniak, Corinne Da Silva, Marie Diogon, Eric Viscogliosi, Céline Brochier-Armanet, Arnaud Couloux, Julie Poulain, Béatrice Segurens, Véronique Anthouard, Catherine Texier, Nicolas Blot, Philippe Poirier, Geok Choo Ng, Kevin SW Tan, François Artiguenave, Olivier Jaillon, Jean-Marc Aury, Frédéric Delbac, Patrick Wincker, Christian P Vivarès, Hicham El Alaoui Genome Biology 2011, 12:R29 (25 March 2011)
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| F1000 Biology
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Editor’s summary
The genome sequence of the anaerobic stramenopile, Blastocystis, reveals the pathogenic potential of this important human parasite.
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Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis
Kevin Ashelford, Maria E Eriksson, Christopher M Allen, Rosalinda D'Amore, Mikael Johansson, Peter Gould, Suzanne Kay, Andrew J Millar, Neil Hall, Anthony Hall Genome Biology 2011, 12:R28 (23 March 2011)
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Re-sequencing of the Ws-2 Arabidopsis accession and a comparison with the reference accession reveals a novel circadian clock mutation.
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A genome-wide view of mutation rate co-variation using multivariate analyses
Guruprasad Ananda, Francesca Chiaromonte, Kateryna D Makova Genome Biology 2011, 12:R27 (22 March 2011)
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Local genomic features influence the rate of different types of mutations in primate genomes
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Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities
Frank J Stewart, Adrian K Sharma, Jessica A Bryant, John M Eppley, Edward F DeLong Genome Biology 2011, 12:R26 (22 March 2011)
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Analysis of several metagenomic datasets reveals that highly expressed genes are more conserved than less highly expressed ones
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Closure of the NCBI SRA and implications for the long-term future of genomics data storage
GB Editorial Team Genome Biology 2011, 12:402 (22 March 2011)
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Closure of the NCBI SRA and implications for the long-term future of genomics data storage
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Genome-wide assessment of imprinted expression in human cells
Lisanne Morcos, Bing Ge, Vonda Koka, Kevin CL Lam, Dmitry K Pokholok, Kevin L Gunderson, Alexandre Montpetit, Dominique J Verlaan, Tomi Pastinen Genome Biology 2011, 12:R25 (21 March 2011)
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Editor’s summary
A genome-wide survey of allelic expression bias in human cells suggests only a very small number of human genes are imprinted
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Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells
Alexander Cecil, Carina Rikanović, Knut Ohlsen, Chunguang Liang, Jörg Bernhardt, Tobias A Oelschlaeger, Tanja Gulder, Gerhard Bringmann, Ulrike Holzgrabe, Matthias Unger, Thomas Dandekar Genome Biology 2011, 12:R24 (21 March 2011)
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Editor’s summary
Gene expression analysis and metabolic modeling offer insights into an antibiotic’s target
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The role of imprinted genes in humans
Gudrun E Moore, Rebecca Oakey Genome Biology 2011, 12:106 (21 March 2011)
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Editor’s summary
Imprinting in humans seems to be less prevalent than in mice.
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'Next-generation' sequencing becomes 'now-generation'
Daniel E Neafsey, Brian J Haas Genome Biology 2011, 12:303 (18 March 2011)
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A report on the Advances in Genome Biology & Technology conference, Marco Island, USA, 2-5 February 2011.
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Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation
Claudia C Weber, Laurence D Hurst Genome Biology 2011, 12:R23 (17 March 2011)
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Editor’s summary
The conservation of syntenic gene order previously described in yeast is not apparent in D. melanogaster
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The transient receptor potential family of ion channels
Bernd Nilius, Grzegorz Owsianik Genome Biology 2011, 12:218 (17 March 2011)
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Editor’s summary
The transient receptor potential (TRP) of ion channels activate voltage-dependent ion channels and are involved in physiological processes such as sensation of stimuli and ion homeostasis
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