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 Contrasting chromatin organization of CpG islands and exons in the human genome Jung Kyoon Choi Genome Biology 2010, 11:R70 (5 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of CpG methylation and histone positioning finds that these both help to define exons.
		Comment Hand-made biology Gregory A Petsko Genome Biology 2010, 11:124 (30 June 2010) Full text \| PDF \| PubMed \| Editor’s summary The genomics era Shelley, Craig Venter, has refocused attention on synthetic biology by creating a bacterium.
		Method Estimating enrichment of repetitive elements from high-throughput sequence data Daniel S Day, Lovelace J Luquette, Peter J Park, Peter V Kharchenko Genome Biology 2010, 11:R69 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors present a method for estimating repetitive sequence content in high-throughput sequencing data, including from ChIP-seq experiments
		Protein family review A hitchhiker's guide to the MADS world of plants Lydia Gramzow, Guenter Theissen Genome Biology 2010, 11:214 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The MADS-domain transcription factors, a protein family of crucial importance in plant development.
		Meeting report Genomics through the lens of next-generation sequencing John A Capra, Lucia Carbone, Samantha J Riesenfeld, Jeffrey D Wall Genome Biology 2010, 11:306 (25 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 23rd annual meeting on 'The Biology of Genomes', 11-15 May 2010, Cold Spring Harbor, USA.
		Review Escape from X inactivation in mice and humans Joel B Berletch, Fan Yang, Christine M Disteche Genome Biology 2010, 11:213 (24 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Species-specific differences in X-linked genes that escape inactivation suggest a role in the evolution of sex differences.
		Research Molecular evolution of genes in avian genomes Kiwoong Nam, Carina Mugal, Benoit Nabholz, Holger Schielzeth, Jochen BW Wolf, Niclas Backström, Axel Künstner, Christopher N Balakrishnan, Andreas Heger, Chris P Ponting, David F Clayton, Hans Ellegren Genome Biology 2010, 11:R68 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Evolutionary analysis of the gene content of the chicken and zebrafinch genomes relative to other vertebrate lineages reveals avian specific patterns of evolution.
		Research The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle Francisco Ferrezuelo, Neus Colomina, Bruce Futcher, Martí Aldea Genome Biology 2010, 11:R67 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Over-expression of CLN3 and integration with other data sets allows the elucidation of the Cln3 transcriptional network in yeast.
		Research Deficiency in mouse Y chromosome long arm gene complement is associated with sperm DNA damage Yasuhiro Yamauchi, Jonathan M Riel, Zoia Stoytcheva, Paul S Burgoyne, Monika A Ward Genome Biology 2010, 11:R66 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Defects on the mouse Y chromosome lead to DNA damage in sperm resulting in reduced efficiency of in vitro fertilization
		Research Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts Meryem Mekouar, Isabelle Blanc-Lenfle, Christophe Ozanne, Corinne Da Silva, Corinne Cruaud, Patrick Wincker, Claude Gaillardin, Cécile Neuvéglise Genome Biology 2010, 11:R65 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Yarrowia lipolytica genes are intron rich and found to be subject to structural constraints resulting in an unusual gene structure.
		Research A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes Rossella De Cegli, Antonio Romito, Simona Iacobacci, Lei Mao, Mario Lauria, Anthony O Fedele, Joachim Klose, Christelle Borel, Patrick Descombes, Stylianos E Antonarakis, Diego di Bernardo, Sandro Banfi, Andrea Ballabio, Gilda Cobellis Genome Biology 2010, 11:R64 (22 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mouse embryonic stem cell bank of inducible human chromosome 21 gene expression is shown to be an important resource for investigating trisomy.
		Research highlight MicroRNA processing without Dicer Anne Dueck, Gunter Meister Genome Biology 2010, 11:123 (21 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microRNA essential for life is processed by Argonaute endonuclease activity.
		Research Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels Maja Klug, Sven Heinz, Claudia Gebhard, Lucia Schwarzfischer, Stefan W Krause, Reinhard Andreesen, Michael Rehli Genome Biology 2010, 11:R63 (18 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Active CpG methylation is demonstrated in the differentiation of human peripheral blood monocytes and shown to correlate with histone modifications but not transcription.
		Method Whole exome capture in solution with 3 Gbp of data Matthew N Bainbridge, Min Wang, Daniel L Burgess, Christie Kovar, Matthew J Rodesch, Mark D'Ascenzo, Jacob Kitzman, Yuan-Qing Wu, Irene Newsham, Todd A Richmond, Jeffrey A Jeddeloh, Donna Muzny, Thomas J Albert, Richard A Gibbs Genome Biology 2010, 11:R62 (17 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for whole exome capture, using just 3Gbp of raw sequence data. Rare coding alleles can be identified in large-scale studies.
		Software Design and evaluation of genome-wide libraries for RNA interference screens Thomas Horn, Thomas Sandmann, Michael Boutros Genome Biology 2010, 11:R61 (15 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary NEXT-RNAi allows the design and evaluation of genome-wide RNAi screens in any organism.
		Method Global fitness profiling of fission yeast deletion strains by barcode sequencing Tian Han, Xing-Ya Xu, Mei-Jun Zhang, Xu Peng, Li-Lin Du Genome Biology 2010, 11:R60 (10 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The barcode sequences used in creating the Schizosaccharomyces pombe deletion collection are reported.
		Meeting report Genome-wide insights into eukaryotic transcriptional control James A Goodrich, Jennifer F Kugel Genome Biology 2010, 11:305 (7 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium on Dynamics of Eukaryotic Transcription during Development, Big Sky, Montana, USA, 7-12 April 2010.
		Correction Correction: Diatom genomes come of age Assaf Vardi, Kimberlee Thamatrakoln, Kay D Bidle, Paul G Falkowski Genome Biology 2010, 11:401 (4 June 2010) Full text \| PDF \| PubMed
		Research The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates Noa Sela, Eddo Kim, Gil Ast Genome Biology 2010, 11:R59 (2 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the influence of transposable elements on non-mammalian vertebrate and invertebrate transcriptomes reveals a link between intron length and exonization.
		Research Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode Shai S Shen-Orr, Yitzhak Pilpel, Craig P Hunter Genome Biology 2010, 11:R58 (1 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of maternal and zygotic transcripts reveals regulatory differences between mammals and egg- laying animals.
		Research highlight Dramatic changes in transcription factor binding over evolutionary time Matthew T Weirauch, Timothy R Hughes Genome Biology 2010, 11:122 (1 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates.
		Research Screening the human exome: a comparison of whole genome and whole transcriptome sequencing Elizabeth T Cirulli, Abanish Singh, Kevin V Shianna, Dongliang Ge, Jason P Smith, Jessica M Maia, Erin L Heinzen, James J Goedert, David B Goldstein, the Center for HIV/AIDS Vaccine Immunology (CHAVI) Genome Biology 2010, 11:R57 (28 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq is an efficient and cheaper alternative, compared with whole genome sequencing, for identifying coding variants in humans.
		Research Evidence for natural antisense transcript-mediated inhibition of microRNA function Mohammad Ali Faghihi, Ming Zhang, Jia Huang, Farzaneh Modarresi, Marcel P Van der Brug, Michael A Nalls, Mark R Cookson, Georges St-Laurent, Claes Wahlestedt Genome Biology 2010, 11:R56 (27 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The BACE1-antisense transcript and miR-485-5p have antagonistic regulatory effects on BACE1 transcript expression and are dysregulated in Alzheimer’s disease patients.
		Meeting report mRNA: a complex(ed) life Michaela Müller, Karla M Neugebauer, Christian Eckmann Genome Biology 2010, 11:304 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the EMBL conference 'The Complex Life of mRNA: From Synthesis to Decay', Heidelberg, Germany, 18-21 March 2010.
		Meeting report Sequences to systems Manolis Kellis, John L Rinn Genome Biology 2010, 11:303 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the seventh annual meeting on Systems Biology: Global Regulation of Gene Expression, 23-27 March 2010, Cold Spring Harbor, USA.
		Research highlight Membrane traffic in the post-genomic era Peter Hein, Mark von Zastrow Genome Biology 2010, 11:119 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A multi-parametric genetic screening approach sheds light on integrated control of the endocytic pathway in mammalian cells.
		Research Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult Rachel A Heimeier, Biswajit Das, Daniel R Buchholz, Maria Fiorentino, Yun-Bo Shi Genome Biology 2010, 11:R55 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The developmental transcriptome of the Xenopus laevis intestine, from embryo to adult, reveals insights into the regulation of gut development in all vertebrates.
		Research Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus Claudia Steglich, Debbie Lindell, Matthias Futschik, Trent Rector, Robert Steen, Sallie W Chisholm Genome Biology 2010, 11:R54 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA half lives in the slow growing cyanobacteria Prochlorococcus are surprisingly short and may enable rapid responses to environmental change.
		Research A human functional protein interaction network and its application to cancer data analysis Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.
		Research Towards a comprehensive structural variation map of an individual human genome Andy W Pang, Jeffrey R MacDonald, Dalila Pinto, John Wei, Muhammad A Rafiq, Donald F Conrad, Hansoo Park, Matthew E Hurles, Charles Lee, J Craig Venter, Ewen F Kirkness, Samuel Levy, Lars Feuk, Stephen W Scherer Genome Biology 2010, 11:R52 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive map of structural variation in the human genome provides a reference dataset for analyses of future personal genomes.
		Meeting report Microbial signaling and systems biology Alistair JP Brown Genome Biology 2010, 11:302 (17 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the symposium on Signaling and Systems Biology held during the Society for General Microbiology Spring Meeting, 29-30 March 2010, Edinburgh, UK
		Research highlight Interesting things come in small packages Edward F DeLong Genome Biology 2010, 11:118 (14 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An unusual uncultivated nitrogen-fixing cyanobacterium lacks many of the signature features of typical cyanobacteria.
		Research Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes Charles Hebert, Hugues Roest Crollius Genome Biology 2010, 11:R51 (12 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Human genes contain a 10 bp repeat of RR dinucleotides focused around the first nucleosome position suggesting a role in transcriptional control.
		Method Modeling non-uniformity in short-read rates in RNA-Seq data Jun Li, Hui Jiang, Wing Wong Genome Biology 2010, 11:R50 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Methods for modeling read counts from short read RNA-seq data.
		Research Widespread remodeling of mid-coding sequence nucleosomes by Isw1 Itay Tirosh, Nadejda Sigal, Naama Barkai Genome Biology 2010, 11:R49 (10 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In yeast, the chromatin remodeler Isw1 shifts nucleosomes from mid-coding, to more 5’ regions of genes and may regulate transcriptional elongation.
		Method Computational challenges in the analysis of ancient DNA Kay Prüfer, Udo Stenzel, Michael Hofreiter, Svante Pääbo, Janet Kelso, Richard E Green Genome Biology 2010, 11:R47 (6 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method of next-generation sequencing analysis is presented which takes into account the biases characteristic of ancient, including Neandertal, DNA samples.
		Review GWASs and the age of human as the model organism for autoimmune genetic research Robert Plenge Genome Biology 2010, 11:212 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Humans should perhaps be the model organism for autoimmune disease studies, considering the success of GWAS studies uncovering risk alleles.
		Review Cancer genomics identifies determinants of tumor biology Elaine R Mardis Genome Biology 2010, 11:211 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Whole-genome analysis of human tumors has identified some unsuspected tumor-associated genes
		Review Direct sequencing of the human microbiome readily reveals community differences Justin Kuczynski, Elizabeth K Costello, Diana R Nemergut, Jesse Zaneveld, Christian L Lauber, Dan Knights, Omry Koren, Noah Fierer, Scott T Kelley, Ruth E Ley, Jeffrey I Gordon, Rob Knight Genome Biology 2010, 11:210 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Future sequencing of the human microbiota will require greater breadth rather than depth.
		Review The origin and early evolution of eukaryotes in the light of phylogenomics Eugene V Koonin Genome Biology 2010, 11:209 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and new phylogenies of eukaryote groups suggest a scenario in which the mitochondrial endosymbiosis triggered the origin of eukaryotes.
		Review The next frontier of systems biology: higher-order and interspecies interactions Michael A Fischbach, Nevan J Krogan Genome Biology 2010, 11:208 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systems biology is set to go beyond single species to the study of interspecies interactions.
		Review The case for cloud computing in genome informatics Lincoln D Stein Genome Biology 2010, 11:207 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 3 comments \| Editor’s summary With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics.
		Review Between a chicken and a grape: estimating the number of human genes Mihaela Pertea, Steven L Salzberg Genome Biology 2010, 11:206 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The number of genes in the human genome is still an estimate.
		Comment And they said it wouldn't last... Gregory A Petsko Genome Biology 2010, 11:121 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the 10 years that Genome Biology has been published the scientific changes have been amazing, as have the changes in the culture of science.
		Editorial A decade and genome of change Clare Garvey Genome Biology 2010, 11:120 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Innovations in genomic technologies have generated huge advances in biomedical research over the last decade.
		Research The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum Marcin Piechota, Michal Korostynski, Wojciech Solecki, Agnieszka Gieryk, Michal Slezak, Wiktor Bilecki, Barbara Ziolkowska, Elzbieta Kostrzewa, Iwona Cymerman, Lukasz Swiech, Jacek Jaworski, Ryszard Przewlocki Genome Biology 2010, 11:R48 (4 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcriptional response to six commonly-abused drugs was assessed in the mouse brain revealing common modules of drug-induced genes.
		Research DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex Sarah Schaack, Eunjin Choi, Michael Lynch, Ellen J Pritham Genome Biology 2010, 11:R46 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Transposable elements in Daphnia pulex are identified and the impact of sex on their evolution is experimentally assessed
		Review Are homologies in vertebrate sex determination due to shared ancestry or to limited options? Jennifer A Marshall Graves, Catherine L Peichel Genome Biology 2010, 11:205 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The bewildering array of different sex-determination systems in vertebrates is built on a common set of genes and chromosomes.
		Comment The devil's in the details Gregory A Petsko Genome Biology 2010, 11:117 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Cures Acceleration Network brought in by the US Health Care Reform Bill looks good but could take funding from other research.
		Research highlight Mapping the complexity of transcription control in higher eukaryotes Pavel Tomancak, Uwe Ohler Genome Biology 2010, 11:115 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent large analyses suggest the importance of combinatorial regulation by broadly expressed transcription factors rather than expression domains characterized by highly specific factors.

	All
		Research Contrasting chromatin organization of CpG islands and exons in the human genome Jung Kyoon Choi Genome Biology 2010, 11:R70 (5 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of CpG methylation and histone positioning finds that these both help to define exons.
		Comment Hand-made biology Gregory A Petsko Genome Biology 2010, 11:124 (30 June 2010) Full text \| PDF \| PubMed \| Editor’s summary The genomics era Shelley, Craig Venter, has refocused attention on synthetic biology by creating a bacterium.
		Method Estimating enrichment of repetitive elements from high-throughput sequence data Daniel S Day, Lovelace J Luquette, Peter J Park, Peter V Kharchenko Genome Biology 2010, 11:R69 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The authors present a method for estimating repetitive sequence content in high-throughput sequencing data, including from ChIP-seq experiments
		Protein family review A hitchhiker's guide to the MADS world of plants Lydia Gramzow, Guenter Theissen Genome Biology 2010, 11:214 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The MADS-domain transcription factors, a protein family of crucial importance in plant development.
		Meeting report Genomics through the lens of next-generation sequencing John A Capra, Lucia Carbone, Samantha J Riesenfeld, Jeffrey D Wall Genome Biology 2010, 11:306 (25 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 23rd annual meeting on 'The Biology of Genomes', 11-15 May 2010, Cold Spring Harbor, USA.
		Review Escape from X inactivation in mice and humans Joel B Berletch, Fan Yang, Christine M Disteche Genome Biology 2010, 11:213 (24 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Species-specific differences in X-linked genes that escape inactivation suggest a role in the evolution of sex differences.
		Research Molecular evolution of genes in avian genomes Kiwoong Nam, Carina Mugal, Benoit Nabholz, Holger Schielzeth, Jochen BW Wolf, Niclas Backström, Axel Künstner, Christopher N Balakrishnan, Andreas Heger, Chris P Ponting, David F Clayton, Hans Ellegren Genome Biology 2010, 11:R68 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Evolutionary analysis of the gene content of the chicken and zebrafinch genomes relative to other vertebrate lineages reveals avian specific patterns of evolution.
		Research The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle Francisco Ferrezuelo, Neus Colomina, Bruce Futcher, Martí Aldea Genome Biology 2010, 11:R67 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Over-expression of CLN3 and integration with other data sets allows the elucidation of the Cln3 transcriptional network in yeast.
		Research Deficiency in mouse Y chromosome long arm gene complement is associated with sperm DNA damage Yasuhiro Yamauchi, Jonathan M Riel, Zoia Stoytcheva, Paul S Burgoyne, Monika A Ward Genome Biology 2010, 11:R66 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Defects on the mouse Y chromosome lead to DNA damage in sperm resulting in reduced efficiency of in vitro fertilization
		Research Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts Meryem Mekouar, Isabelle Blanc-Lenfle, Christophe Ozanne, Corinne Da Silva, Corinne Cruaud, Patrick Wincker, Claude Gaillardin, Cécile Neuvéglise Genome Biology 2010, 11:R65 (23 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Yarrowia lipolytica genes are intron rich and found to be subject to structural constraints resulting in an unusual gene structure.
		Research A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes Rossella De Cegli, Antonio Romito, Simona Iacobacci, Lei Mao, Mario Lauria, Anthony O Fedele, Joachim Klose, Christelle Borel, Patrick Descombes, Stylianos E Antonarakis, Diego di Bernardo, Sandro Banfi, Andrea Ballabio, Gilda Cobellis Genome Biology 2010, 11:R64 (22 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mouse embryonic stem cell bank of inducible human chromosome 21 gene expression is shown to be an important resource for investigating trisomy.
		Research highlight MicroRNA processing without Dicer Anne Dueck, Gunter Meister Genome Biology 2010, 11:123 (21 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microRNA essential for life is processed by Argonaute endonuclease activity.
		Research Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels Maja Klug, Sven Heinz, Claudia Gebhard, Lucia Schwarzfischer, Stefan W Krause, Reinhard Andreesen, Michael Rehli Genome Biology 2010, 11:R63 (18 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Active CpG methylation is demonstrated in the differentiation of human peripheral blood monocytes and shown to correlate with histone modifications but not transcription.
		Method Whole exome capture in solution with 3 Gbp of data Matthew N Bainbridge, Min Wang, Daniel L Burgess, Christie Kovar, Matthew J Rodesch, Mark D'Ascenzo, Jacob Kitzman, Yuan-Qing Wu, Irene Newsham, Todd A Richmond, Jeffrey A Jeddeloh, Donna Muzny, Thomas J Albert, Richard A Gibbs Genome Biology 2010, 11:R62 (17 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for whole exome capture, using just 3Gbp of raw sequence data. Rare coding alleles can be identified in large-scale studies.
		Software Design and evaluation of genome-wide libraries for RNA interference screens Thomas Horn, Thomas Sandmann, Michael Boutros Genome Biology 2010, 11:R61 (15 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary NEXT-RNAi allows the design and evaluation of genome-wide RNAi screens in any organism.
		Method Global fitness profiling of fission yeast deletion strains by barcode sequencing Tian Han, Xing-Ya Xu, Mei-Jun Zhang, Xu Peng, Li-Lin Du Genome Biology 2010, 11:R60 (10 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The barcode sequences used in creating the Schizosaccharomyces pombe deletion collection are reported.
		Meeting report Genome-wide insights into eukaryotic transcriptional control James A Goodrich, Jennifer F Kugel Genome Biology 2010, 11:305 (7 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Keystone Symposium on Dynamics of Eukaryotic Transcription during Development, Big Sky, Montana, USA, 7-12 April 2010.
		Correction Correction: Diatom genomes come of age Assaf Vardi, Kimberlee Thamatrakoln, Kay D Bidle, Paul G Falkowski Genome Biology 2010, 11:401 (4 June 2010) Full text \| PDF \| PubMed
		Research The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates Noa Sela, Eddo Kim, Gil Ast Genome Biology 2010, 11:R59 (2 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the influence of transposable elements on non-mammalian vertebrate and invertebrate transcriptomes reveals a link between intron length and exonization.
		Research Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode Shai S Shen-Orr, Yitzhak Pilpel, Craig P Hunter Genome Biology 2010, 11:R58 (1 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of maternal and zygotic transcripts reveals regulatory differences between mammals and egg- laying animals.
		Research highlight Dramatic changes in transcription factor binding over evolutionary time Matthew T Weirauch, Timothy R Hughes Genome Biology 2010, 11:122 (1 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates.
		Research Screening the human exome: a comparison of whole genome and whole transcriptome sequencing Elizabeth T Cirulli, Abanish Singh, Kevin V Shianna, Dongliang Ge, Jason P Smith, Jessica M Maia, Erin L Heinzen, James J Goedert, David B Goldstein, the Center for HIV/AIDS Vaccine Immunology (CHAVI) Genome Biology 2010, 11:R57 (28 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-seq is an efficient and cheaper alternative, compared with whole genome sequencing, for identifying coding variants in humans.
		Research Evidence for natural antisense transcript-mediated inhibition of microRNA function Mohammad Ali Faghihi, Ming Zhang, Jia Huang, Farzaneh Modarresi, Marcel P Van der Brug, Michael A Nalls, Mark R Cookson, Georges St-Laurent, Claes Wahlestedt Genome Biology 2010, 11:R56 (27 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The BACE1-antisense transcript and miR-485-5p have antagonistic regulatory effects on BACE1 transcript expression and are dysregulated in Alzheimer’s disease patients.
		Meeting report mRNA: a complex(ed) life Michaela Müller, Karla M Neugebauer, Christian Eckmann Genome Biology 2010, 11:304 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the EMBL conference 'The Complex Life of mRNA: From Synthesis to Decay', Heidelberg, Germany, 18-21 March 2010.
		Meeting report Sequences to systems Manolis Kellis, John L Rinn Genome Biology 2010, 11:303 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the seventh annual meeting on Systems Biology: Global Regulation of Gene Expression, 23-27 March 2010, Cold Spring Harbor, USA.
		Research highlight Membrane traffic in the post-genomic era Peter Hein, Mark von Zastrow Genome Biology 2010, 11:119 (25 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A multi-parametric genetic screening approach sheds light on integrated control of the endocytic pathway in mammalian cells.
		Research Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult Rachel A Heimeier, Biswajit Das, Daniel R Buchholz, Maria Fiorentino, Yun-Bo Shi Genome Biology 2010, 11:R55 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The developmental transcriptome of the Xenopus laevis intestine, from embryo to adult, reveals insights into the regulation of gut development in all vertebrates.
		Research Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus Claudia Steglich, Debbie Lindell, Matthias Futschik, Trent Rector, Robert Steen, Sallie W Chisholm Genome Biology 2010, 11:R54 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA half lives in the slow growing cyanobacteria Prochlorococcus are surprisingly short and may enable rapid responses to environmental change.
		Research A human functional protein interaction network and its application to cancer data analysis Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.
		Research Towards a comprehensive structural variation map of an individual human genome Andy W Pang, Jeffrey R MacDonald, Dalila Pinto, John Wei, Muhammad A Rafiq, Donald F Conrad, Hansoo Park, Matthew E Hurles, Charles Lee, J Craig Venter, Ewen F Kirkness, Samuel Levy, Lars Feuk, Stephen W Scherer Genome Biology 2010, 11:R52 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive map of structural variation in the human genome provides a reference dataset for analyses of future personal genomes.
		Meeting report Microbial signaling and systems biology Alistair JP Brown Genome Biology 2010, 11:302 (17 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the symposium on Signaling and Systems Biology held during the Society for General Microbiology Spring Meeting, 29-30 March 2010, Edinburgh, UK
		Research highlight Interesting things come in small packages Edward F DeLong Genome Biology 2010, 11:118 (14 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An unusual uncultivated nitrogen-fixing cyanobacterium lacks many of the signature features of typical cyanobacteria.
		Research Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes Charles Hebert, Hugues Roest Crollius Genome Biology 2010, 11:R51 (12 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Human genes contain a 10 bp repeat of RR dinucleotides focused around the first nucleosome position suggesting a role in transcriptional control.
		Method Modeling non-uniformity in short-read rates in RNA-Seq data Jun Li, Hui Jiang, Wing Wong Genome Biology 2010, 11:R50 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Methods for modeling read counts from short read RNA-seq data.
		Research Widespread remodeling of mid-coding sequence nucleosomes by Isw1 Itay Tirosh, Nadejda Sigal, Naama Barkai Genome Biology 2010, 11:R49 (10 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In yeast, the chromatin remodeler Isw1 shifts nucleosomes from mid-coding, to more 5’ regions of genes and may regulate transcriptional elongation.
		Method Computational challenges in the analysis of ancient DNA Kay Prüfer, Udo Stenzel, Michael Hofreiter, Svante Pääbo, Janet Kelso, Richard E Green Genome Biology 2010, 11:R47 (6 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method of next-generation sequencing analysis is presented which takes into account the biases characteristic of ancient, including Neandertal, DNA samples.
		Review GWASs and the age of human as the model organism for autoimmune genetic research Robert Plenge Genome Biology 2010, 11:212 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Humans should perhaps be the model organism for autoimmune disease studies, considering the success of GWAS studies uncovering risk alleles.
		Review Cancer genomics identifies determinants of tumor biology Elaine R Mardis Genome Biology 2010, 11:211 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Whole-genome analysis of human tumors has identified some unsuspected tumor-associated genes
		Review Direct sequencing of the human microbiome readily reveals community differences Justin Kuczynski, Elizabeth K Costello, Diana R Nemergut, Jesse Zaneveld, Christian L Lauber, Dan Knights, Omry Koren, Noah Fierer, Scott T Kelley, Ruth E Ley, Jeffrey I Gordon, Rob Knight Genome Biology 2010, 11:210 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Future sequencing of the human microbiota will require greater breadth rather than depth.
		Review The origin and early evolution of eukaryotes in the light of phylogenomics Eugene V Koonin Genome Biology 2010, 11:209 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genomics and new phylogenies of eukaryote groups suggest a scenario in which the mitochondrial endosymbiosis triggered the origin of eukaryotes.
		Review The next frontier of systems biology: higher-order and interspecies interactions Michael A Fischbach, Nevan J Krogan Genome Biology 2010, 11:208 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systems biology is set to go beyond single species to the study of interspecies interactions.
		Review The case for cloud computing in genome informatics Lincoln D Stein Genome Biology 2010, 11:207 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 3 comments \| Editor’s summary With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics.
		Review Between a chicken and a grape: estimating the number of human genes Mihaela Pertea, Steven L Salzberg Genome Biology 2010, 11:206 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The number of genes in the human genome is still an estimate.
		Comment And they said it wouldn't last... Gregory A Petsko Genome Biology 2010, 11:121 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the 10 years that Genome Biology has been published the scientific changes have been amazing, as have the changes in the culture of science.
		Editorial A decade and genome of change Clare Garvey Genome Biology 2010, 11:120 (5 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Innovations in genomic technologies have generated huge advances in biomedical research over the last decade.
		Research The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum Marcin Piechota, Michal Korostynski, Wojciech Solecki, Agnieszka Gieryk, Michal Slezak, Wiktor Bilecki, Barbara Ziolkowska, Elzbieta Kostrzewa, Iwona Cymerman, Lukasz Swiech, Jacek Jaworski, Ryszard Przewlocki Genome Biology 2010, 11:R48 (4 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcriptional response to six commonly-abused drugs was assessed in the mouse brain revealing common modules of drug-induced genes.
		Research DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex Sarah Schaack, Eunjin Choi, Michael Lynch, Ellen J Pritham Genome Biology 2010, 11:R46 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Transposable elements in Daphnia pulex are identified and the impact of sex on their evolution is experimentally assessed
		Review Are homologies in vertebrate sex determination due to shared ancestry or to limited options? Jennifer A Marshall Graves, Catherine L Peichel Genome Biology 2010, 11:205 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The bewildering array of different sex-determination systems in vertebrates is built on a common set of genes and chromosomes.
		Comment The devil's in the details Gregory A Petsko Genome Biology 2010, 11:117 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Cures Acceleration Network brought in by the US Health Care Reform Bill looks good but could take funding from other research.
		Research highlight Mapping the complexity of transcription control in higher eukaryotes Pavel Tomancak, Uwe Ohler Genome Biology 2010, 11:115 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent large analyses suggest the importance of combinatorial regulation by broadly expressed transcription factors rather than expression domains characterized by highly specific factors.