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		Research Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins Francisco Merchan, Adnane Boualem, Martin Crespi, Florian Frugier Genome Biology 2009, 10:R136 (1 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Functional homologous and non-homologous clusters of MIR genes that co-regulate target mRNA transcripts have been identified in plants
		Minireview Transcriptional regulation of metastatic [Id]entity by KLF17 Marcin P Iwanicki, Joan S Brugge Genome Biology 2009, 10:244 (30 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new player identified in the regulation of epithelial-to-mesenchyme transition, cell invasiveness and metastasis.
		Opinion Evolution, ecology and the engineered organism: lessons for synthetic biology Jeffrey M Skerker, Julius B Lucks, Adam P Arkin Genome Biology 2009, 10:114 (30 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An understanding of evolution and ecology will be critical to the success of synthetic biology.
		Minireview Panmixia postponed: ancestry-related assortative mating in contemporary human populations Andrew S Burrell, Todd R Disotell Genome Biology 2009, 10:245 (27 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A population study using human ancestry-informative markers reveals that the choice of a mate tends to be non-random in regard to specific ancestries within the group.
		Minireview Ubiquitous RNA-dependent RNA polymerase and gene silencing James A Birchler Genome Biology 2009, 10:243 (26 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery of a ubiquitous RNA-dependent RNA polymerase raises new questions about small RNA silencing mechanisms.
		Research Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication Radek Szklarczyk, Martijn A Huynen Genome Biology 2009, 10:R135 (24 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human mitochondrial proteome is shown to have expanded due to duplication of protein encoding genes and re-localization of these duplicated proteins.
		Comment Advice and dissent Gregory A Petsko Genome Biology 2009, 10:113 (24 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko reflects on what can happen when governments and their scientific advisors disagree.
		Software Searching for SNPs with cloud computing Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.
		Method COMIT: identification of noncoding motifs under selection in coding sequences Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, Jeffrey H Chuang Genome Biology 2009, 10:R133 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary COMIT is presented; an algorithm for detecting functional non-coding motifs in coding regions, separating nucleotide and amino acid effects.
		Research Ancestry-related assortative mating in Latino populations Neil Risch, Shweta Choudhry, Marc Via, Analabha Basu, Ronnie Sebro, Celeste Eng, Kenneth Beckman, Shannon Thyne, Rocio Chapela, Jose R Rodriguez-Santana, William Rodriguez-Cintron, Pedro C Avila, Elad Ziv, Esteban Gonzalez Burchard Genome Biology 2009, 10:R132 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Examination of ancestry-informative genetic markers shows that Puerto Rican and Mexican populations have shown strong assortative mating that continues to this day.
		Meeting report Biology inspires engineering Reine Byun, Attila Becskei Genome Biology 2009, 10:317 (19 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cold Spring Harbor Laboratory/Wellcome Trust Meeting on Engineering Principles in Biology, Cambridge, UK, 14-16 October 2009.
		Research CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features Kobby Essien, Sebastien Vigneau, Sofia Apreleva, Larry N Singh, Marisa S Bartolomei, Sridhar Hannenhalli Genome Biology 2009, 10:R131 (18 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CTCF DNA binding sites are classified into distinct functional classes, with distinct biological properties, shedding light on the differing functional roles of CTCF binding.
		Software BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, Serge Batalov, Christopher L Hodge, James Haase, Jeff Janes, Jon W Huss, Andrew I Su Genome Biology 2009, 10:R130 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BioGPS is a community based customisable gene annotation portal bringing together gene annotation resources on to a single platform.
		Research Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq Mehdi Motallebipour, Adam Ameur, Madhu Sudhan Reddy Bysani, Kalicharan Patra, Ola Wallerman, Jonathan Mangion, Melissa A Barker, Kevin J McKernan, Jan Komorowski, Claes Wadelius Genome Biology 2009, 10:R129 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary FOXA1 and FOXA3 binding patterns in HepG2 cells, together with their possible molecular interactions with FOXA2 and each other, are revealed by ChIP-seq.
		Method Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays Tatiana Popova, Elodie Manié, Dominique Stoppa-Lyonnet, Guillem Rigaill, Emmanuel Barillot, Marc Stern Genome Biology 2009, 10:R128 (11 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GAP, a method for analyzing complex cancer genome profiles from SNP arrays, performs well even with poor quality data and rearranged genomes
		Research Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis Rungnapa Pankla, Surachat Buddhisa, Matthew Berry, Derek M Blankenship, Gregory J Bancroft, Jacques Banchereau, Ganjana Lertmemongkolchai, Damien Chaussabel Genome Biology 2009, 10:R127 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A diagnostic signature for sepsis caused by Burkholderia pseudomallei infection was identified from transcriptional profiling of the blood of septicemia patients.
		Research Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora Shi Wang, Lingling Zhang, Eli Meyer, Mikhail V Matz Genome Biology 2009, 10:R126 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A high-resolution genetic linkage map for the coral Acropora millepora is constructed and compared with other metazoan genomes, revealing syntenic blocks.
		Research High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians Hajime Matsuzaki, Pei-Hua Wang, Jing Hu, Rich Rava, Glenn K Fu Genome Biology 2009, 10:R125 (9 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers.
		Research Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness Ana C Marques, Chris P Ponting Genome Biology 2009, 10:R124 (6 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative evolutionary analysis of two mouse long noncoding RNA libraries reveals a much larger pool of noncoding RNAs remains yet to be discovered.
		Research Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle Esther Castellano, Carmen Guerrero, Alejandro Núñez, Javier De Las Rivas, Eugenio Santos Genome Biology 2009, 10:R123 (6 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptional and functional analysis reveals that the H-Ras and N-Ras isoforms have different roles in the initial phases of the mouse cell cycle
		Research Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.) Mingxiong Pang, Andrew W Woodward, Vikram Agarwal, Xueying Guan, Misook Ha, Vanitharani Ramachandran, Xuemei Chen, Barbara A Triplett, David M Stelly, Z Jeffrey Chen Genome Biology 2009, 10:R122 (4 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton.
		Comment The dog days of autumn Gregory A Petsko Genome Biology 2009, 10:112 (4 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg's two dogs are impressed that only a few genes control the different lengths, growth patterns and curl of their coats.
		Research Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki, Masanori Suzuki Genome Biology 2009, 10:R121 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The knockdown of 78 transcription factors in differentiating human THP-1 cells using matrix RNAi reveals their interdependence
		Research Divergence of exonic splicing elements after gene duplication and the impact on gene structures Zhenguo Zhang, Li Zhou, Ping Wang, Yang Liu, Xianfeng Chen, Landian Hu, Xiangyin Kong Genome Biology 2009, 10:R120 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of human exonic splicing elements in duplicated genes reveals their important role in the generation of new gene structures.
		Minireview Comparing cellular proteomes by mass spectrometry Florian Fröhlich, Tobias C Walther Genome Biology 2009, 10:240 (28 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mass spectrometry and cryo-electron tomography together can enable absolute protein abundance to be determined.
		Meeting report Watching proteins in motion Mary Munson, Daniel N Bolon Genome Biology 2009, 10:316 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 23rd Protein Symposium 'Proteins in Motion', Boston, USA, 23-27 July 2009.
		Protein family review The SR protein family Peter J Shepard, Klemens J Hertel Genome Biology 2009, 10:242 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The SR proteins are not only involved in pre-mRNA splicing but in mRNA export and the initiation of translation.
		Minireview Runaway repeats force expansion of the Phytophthora infestans genome Mark Gijzen Genome Biology 2009, 10:241 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of the potato late blight pathogen Phytophthora infestans provides insight into the structure and evolution of its genome.
		Method An optimization framework for unsupervised identification of rare copy number variation from SNP array data Gökhan Yavaş, Mehmet Koyutürk, Meral Özsoyoğlu, Meetha P Gould, Thomas LaFramboise Genome Biology 2009, 10:R119 (23 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A highly sensitive and configurable method for calling copy number variants from SNP array data is presented that can identify even rare CNVs
		Research Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations Tom M Conrad, Andrew R Joyce, M Kenyon Applebee, Christian L Barrett, Bin Xie, Yuan Gao, Bernhard Ø Palsson Genome Biology 2009, 10:R118 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Escherichia coli strains that have evolved in the laboratory in response to lactate minimal media show a wide range of different genetic adaptations.
		Research Simultaneous transcription of duplicated var2csa gene copies in individual Plasmodium falciparum parasites Kim JM Brolin, Ulf Ribacke, Sandra Nilsson, Johan Ankarklev, Kirsten Moll, Mats Wahlgren, Qijun Chen Genome Biology 2009, 10:R117 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Duplicated var2csa genes in one strain of Plasmodium falciparum are simultaneously transcribed, challenging the dogma of mutual exclusive var gene transcription
		Method Enrichment of sequencing targets from the human genome by solution hybridization Ryan Tewhey, Masakazu Nakano, Xiaoyun Wang, Carlos Pabón-Peña, Barbara Novak, Angelica Giuffre, Eric Lin, Scott Happe, Doug N Roberts, Emily M LeProust, Eric J Topol, Olivier Harismendy, Kelly A Frazer Genome Biology 2009, 10:R116 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for target sequence enrichment from the human genome is described. This hybridization-based approach using oligonucleotide probes in solution has excellent sensitivity and accuracy for calling SNPs
		Method Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts Joshua Z Levin, Michael F Berger, Xian Adiconis, Peter Rogov, Alexandre Melnikov, Timothy Fennell, Chad Nusbaum, Levi A Garraway, Andreas Gnirke Genome Biology 2009, 10:R115 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Combining next-generation sequencing with capture of sequences from a relevant subset of a transcriptome produces an enhanced view of this subset
		Research Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell Peter von Dassow, Hiroyuki Ogata, Ian Probert, Patrick Wincker, Corinne Da Silva, Stéphane Audic, Jean-Michel Claverie, Colomban de Vargas Genome Biology 2009, 10:R114 (15 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An EST analysis of the phytoplankton Emiliania huxleyi reveals genes involved in haploid- and diploid-specific processes and provides insights into environmental adaptation.
		Research Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia Xiaobo Xia, Andrew L Kung Genome Biology 2009, 10:R113 (14 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip and microarray expression studies show that, in response to hypoxia, HIF-1 preferentially binds to and up-regulates already active genes.
		Method Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels Ian Sudbery, Jim Stalker, Jared T Simpson, Thomas Keane, Alistair G Rust, Matthew E Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve D Brown, Heng Li, Zemin Ning, Joseph H Nadeau, Colleen M Croniger, Richard Durbin, David J Adams Genome Biology 2009, 10:R112 (13 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Methods for accurate identification of nucleotide and structural variation using de novo short read sequencing of mouse chromosomes are described.
		Research Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Young-Joo Seol, Mina Jin, Jin-A Kim, Myung-Ho Lim, Jung Sun Kim, Seunghoon Baek, Beom-Soon Choi, Hee-Ju Yu, Dae-Soo Kim, Namshin Kim, Ki-Byung Lim, Soo-In Lee, Jang-Ho Hahn, Yong Pyo Lim, Ian Bancroft, Beom-Seok Park Genome Biology 2009, 10:R111 (12 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Euchromatic regions of the Brassica rapa genome were sequenced and mapped onto the corresponding regions in the Arabidopsis thaliana genome.
		Research NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis Christophe Rusniok, David Vallenet, Stéphanie Floquet, Helen Ewles, Coralie Mouzé-Soulama, Daniel Brown, Aurélie Lajus, Carmen Buchrieser, Claudine Médigue, Philippe Glaser, Vladimir Pelicic Genome Biology 2009, 10:R110 (9 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of a clinical isolate of Neisseria meningitidis is described. This and other reannotated Neisseria genomes are compiled in a database.
		Software A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome Cizhong Jiang, B Franklin Pugh Genome Biology 2009, 10:R109 (8 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Different genome-wide reference maps of Saccharomyces cerevisiae nucleosome positions are compiled and can be visualized on a browser.
		Research Genomic DNA k-mer spectra: models and modalities Benny Chor, David Horn, Nick Goldman, Yaron Levy, Tim Massingham Genome Biology 2009, 10:R108 (8 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genomes
		Research Defining the chromatin signature of inducible genes in T cells Pek S Lim, Kristine Hardy, Karen L Bunting, Lina Ma, Kaiman Peng, Xinxin Chen, Mary F Shannon Genome Biology 2009, 10:R107 (6 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Inducible genes in T cells show the chromatin characteristics of active genes, suggesting they are primed for transcription.
		Research Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions Nicolas Corradi, Karen L Haag, Jean-François Pombert, Dieter Ebert, Patrick J Keeling Genome Biology 2009, 10:R106 (6 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The draft genome sequence of Octosporea bayeri, a microsporidian pathogen of Daphnia, provides insights into the content and evolution of a large microsporidian genome
		Software MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock Genome Biology 2009, 10:R105 (5 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A software workflow to translate known differentially methylated regions into clinical biomarkers
		Research Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Kakoli Banerjee, Pike-See Cheah, Ping Z Cannon, Christopher N Hahn, Paul Q Thomas, Gordon K Smyth, Seong-Seng Tan, Tim Thomas, Hamish S Scott Genome Biology 2009, 10:R104 (2 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SAGE analysis reveals spatiotemporally regulated transcripts and overlapping sense and antisense transcripts that are important for mouse cerebral cortex development
		Method ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, David B Jaffe Genome Biology 2009, 10:R103 (1 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Allpaths2, a method for accurately assembling small genomes with high continuity using short paired reads.
		Correspondence Joining forces in the quest for orthologs Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis Genome Biology 2009, 10:403 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Building momentum to coordinate and leverage community orthology prediction resources.
		Protein family review The netrin protein family Sathyanath Rajasekharan, Timothy E Kennedy Genome Biology 2009, 10:239 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The netrins are a family of extracellular proteins that direct cell and axon migration during embryogenesis.
		Minireview Common variants in polygenic schizophrenia Joseph T Glessner, Hakon Hakonarson Genome Biology 2009, 10:236 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Schizophrenia is associated with both common single-nucleotide polymorphisms at the MHC locus and rare copy-number variants affecting many genes.
		Comment An issue to remember Gregory A Petsko Genome Biology 2009, 10:111 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Thumbing through a recent copy of a journal reveals unexpected riches.
		Research Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium Richard A Stabler, Miao He, Lisa Dawson, Melissa Martin, Esmeralda Valiente, Craig Corton, Trevor D Lawley, Mohammed Sebaihia, Michael A Quail, Graham Rose, Dale N Gerding, Maryse Gibert, Michel R Popoff, Julian Parkhill, Gordon Dougan, Brendan W Wren Genome Biology 2009, 10:R102 (25 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome comparison of non-epidemic and epidemic strains of Clostridium difficile reveals gene gains that could explain how a hypervirulent strain has emerged

	All
		Research Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins Francisco Merchan, Adnane Boualem, Martin Crespi, Florian Frugier Genome Biology 2009, 10:R136 (1 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Functional homologous and non-homologous clusters of MIR genes that co-regulate target mRNA transcripts have been identified in plants
		Minireview Transcriptional regulation of metastatic [Id]entity by KLF17 Marcin P Iwanicki, Joan S Brugge Genome Biology 2009, 10:244 (30 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new player identified in the regulation of epithelial-to-mesenchyme transition, cell invasiveness and metastasis.
		Opinion Evolution, ecology and the engineered organism: lessons for synthetic biology Jeffrey M Skerker, Julius B Lucks, Adam P Arkin Genome Biology 2009, 10:114 (30 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An understanding of evolution and ecology will be critical to the success of synthetic biology.
		Minireview Panmixia postponed: ancestry-related assortative mating in contemporary human populations Andrew S Burrell, Todd R Disotell Genome Biology 2009, 10:245 (27 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A population study using human ancestry-informative markers reveals that the choice of a mate tends to be non-random in regard to specific ancestries within the group.
		Minireview Ubiquitous RNA-dependent RNA polymerase and gene silencing James A Birchler Genome Biology 2009, 10:243 (26 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery of a ubiquitous RNA-dependent RNA polymerase raises new questions about small RNA silencing mechanisms.
		Research Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication Radek Szklarczyk, Martijn A Huynen Genome Biology 2009, 10:R135 (24 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human mitochondrial proteome is shown to have expanded due to duplication of protein encoding genes and re-localization of these duplicated proteins.
		Comment Advice and dissent Gregory A Petsko Genome Biology 2009, 10:113 (24 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko reflects on what can happen when governments and their scientific advisors disagree.
		Software Searching for SNPs with cloud computing Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.
		Method COMIT: identification of noncoding motifs under selection in coding sequences Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, Jeffrey H Chuang Genome Biology 2009, 10:R133 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary COMIT is presented; an algorithm for detecting functional non-coding motifs in coding regions, separating nucleotide and amino acid effects.
		Research Ancestry-related assortative mating in Latino populations Neil Risch, Shweta Choudhry, Marc Via, Analabha Basu, Ronnie Sebro, Celeste Eng, Kenneth Beckman, Shannon Thyne, Rocio Chapela, Jose R Rodriguez-Santana, William Rodriguez-Cintron, Pedro C Avila, Elad Ziv, Esteban Gonzalez Burchard Genome Biology 2009, 10:R132 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Examination of ancestry-informative genetic markers shows that Puerto Rican and Mexican populations have shown strong assortative mating that continues to this day.
		Meeting report Biology inspires engineering Reine Byun, Attila Becskei Genome Biology 2009, 10:317 (19 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cold Spring Harbor Laboratory/Wellcome Trust Meeting on Engineering Principles in Biology, Cambridge, UK, 14-16 October 2009.
		Research CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features Kobby Essien, Sebastien Vigneau, Sofia Apreleva, Larry N Singh, Marisa S Bartolomei, Sridhar Hannenhalli Genome Biology 2009, 10:R131 (18 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CTCF DNA binding sites are classified into distinct functional classes, with distinct biological properties, shedding light on the differing functional roles of CTCF binding.
		Software BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, Serge Batalov, Christopher L Hodge, James Haase, Jeff Janes, Jon W Huss, Andrew I Su Genome Biology 2009, 10:R130 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BioGPS is a community based customisable gene annotation portal bringing together gene annotation resources on to a single platform.
		Research Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq Mehdi Motallebipour, Adam Ameur, Madhu Sudhan Reddy Bysani, Kalicharan Patra, Ola Wallerman, Jonathan Mangion, Melissa A Barker, Kevin J McKernan, Jan Komorowski, Claes Wadelius Genome Biology 2009, 10:R129 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary FOXA1 and FOXA3 binding patterns in HepG2 cells, together with their possible molecular interactions with FOXA2 and each other, are revealed by ChIP-seq.
		Method Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays Tatiana Popova, Elodie Manié, Dominique Stoppa-Lyonnet, Guillem Rigaill, Emmanuel Barillot, Marc Stern Genome Biology 2009, 10:R128 (11 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GAP, a method for analyzing complex cancer genome profiles from SNP arrays, performs well even with poor quality data and rearranged genomes
		Research Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis Rungnapa Pankla, Surachat Buddhisa, Matthew Berry, Derek M Blankenship, Gregory J Bancroft, Jacques Banchereau, Ganjana Lertmemongkolchai, Damien Chaussabel Genome Biology 2009, 10:R127 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A diagnostic signature for sepsis caused by Burkholderia pseudomallei infection was identified from transcriptional profiling of the blood of septicemia patients.
		Research Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora Shi Wang, Lingling Zhang, Eli Meyer, Mikhail V Matz Genome Biology 2009, 10:R126 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A high-resolution genetic linkage map for the coral Acropora millepora is constructed and compared with other metazoan genomes, revealing syntenic blocks.
		Research High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians Hajime Matsuzaki, Pei-Hua Wang, Jing Hu, Rich Rava, Glenn K Fu Genome Biology 2009, 10:R125 (9 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers.
		Research Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness Ana C Marques, Chris P Ponting Genome Biology 2009, 10:R124 (6 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative evolutionary analysis of two mouse long noncoding RNA libraries reveals a much larger pool of noncoding RNAs remains yet to be discovered.
		Research Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle Esther Castellano, Carmen Guerrero, Alejandro Núñez, Javier De Las Rivas, Eugenio Santos Genome Biology 2009, 10:R123 (6 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptional and functional analysis reveals that the H-Ras and N-Ras isoforms have different roles in the initial phases of the mouse cell cycle
		Research Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.) Mingxiong Pang, Andrew W Woodward, Vikram Agarwal, Xueying Guan, Misook Ha, Vanitharani Ramachandran, Xuemei Chen, Barbara A Triplett, David M Stelly, Z Jeffrey Chen Genome Biology 2009, 10:R122 (4 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton.
		Comment The dog days of autumn Gregory A Petsko Genome Biology 2009, 10:112 (4 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg's two dogs are impressed that only a few genes control the different lengths, growth patterns and curl of their coats.
		Research Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki, Masanori Suzuki Genome Biology 2009, 10:R121 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The knockdown of 78 transcription factors in differentiating human THP-1 cells using matrix RNAi reveals their interdependence
		Research Divergence of exonic splicing elements after gene duplication and the impact on gene structures Zhenguo Zhang, Li Zhou, Ping Wang, Yang Liu, Xianfeng Chen, Landian Hu, Xiangyin Kong Genome Biology 2009, 10:R120 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of human exonic splicing elements in duplicated genes reveals their important role in the generation of new gene structures.
		Minireview Comparing cellular proteomes by mass spectrometry Florian Fröhlich, Tobias C Walther Genome Biology 2009, 10:240 (28 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mass spectrometry and cryo-electron tomography together can enable absolute protein abundance to be determined.
		Meeting report Watching proteins in motion Mary Munson, Daniel N Bolon Genome Biology 2009, 10:316 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 23rd Protein Symposium 'Proteins in Motion', Boston, USA, 23-27 July 2009.
		Protein family review The SR protein family Peter J Shepard, Klemens J Hertel Genome Biology 2009, 10:242 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The SR proteins are not only involved in pre-mRNA splicing but in mRNA export and the initiation of translation.
		Minireview Runaway repeats force expansion of the Phytophthora infestans genome Mark Gijzen Genome Biology 2009, 10:241 (27 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of the potato late blight pathogen Phytophthora infestans provides insight into the structure and evolution of its genome.
		Method An optimization framework for unsupervised identification of rare copy number variation from SNP array data Gökhan Yavaş, Mehmet Koyutürk, Meral Özsoyoğlu, Meetha P Gould, Thomas LaFramboise Genome Biology 2009, 10:R119 (23 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A highly sensitive and configurable method for calling copy number variants from SNP array data is presented that can identify even rare CNVs
		Research Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations Tom M Conrad, Andrew R Joyce, M Kenyon Applebee, Christian L Barrett, Bin Xie, Yuan Gao, Bernhard Ø Palsson Genome Biology 2009, 10:R118 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Escherichia coli strains that have evolved in the laboratory in response to lactate minimal media show a wide range of different genetic adaptations.
		Research Simultaneous transcription of duplicated var2csa gene copies in individual Plasmodium falciparum parasites Kim JM Brolin, Ulf Ribacke, Sandra Nilsson, Johan Ankarklev, Kirsten Moll, Mats Wahlgren, Qijun Chen Genome Biology 2009, 10:R117 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Duplicated var2csa genes in one strain of Plasmodium falciparum are simultaneously transcribed, challenging the dogma of mutual exclusive var gene transcription
		Method Enrichment of sequencing targets from the human genome by solution hybridization Ryan Tewhey, Masakazu Nakano, Xiaoyun Wang, Carlos Pabón-Peña, Barbara Novak, Angelica Giuffre, Eric Lin, Scott Happe, Doug N Roberts, Emily M LeProust, Eric J Topol, Olivier Harismendy, Kelly A Frazer Genome Biology 2009, 10:R116 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for target sequence enrichment from the human genome is described. This hybridization-based approach using oligonucleotide probes in solution has excellent sensitivity and accuracy for calling SNPs
		Method Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts Joshua Z Levin, Michael F Berger, Xian Adiconis, Peter Rogov, Alexandre Melnikov, Timothy Fennell, Chad Nusbaum, Levi A Garraway, Andreas Gnirke Genome Biology 2009, 10:R115 (16 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Combining next-generation sequencing with capture of sequences from a relevant subset of a transcriptome produces an enhanced view of this subset
		Research Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell Peter von Dassow, Hiroyuki Ogata, Ian Probert, Patrick Wincker, Corinne Da Silva, Stéphane Audic, Jean-Michel Claverie, Colomban de Vargas Genome Biology 2009, 10:R114 (15 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An EST analysis of the phytoplankton Emiliania huxleyi reveals genes involved in haploid- and diploid-specific processes and provides insights into environmental adaptation.
		Research Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia Xiaobo Xia, Andrew L Kung Genome Biology 2009, 10:R113 (14 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip and microarray expression studies show that, in response to hypoxia, HIF-1 preferentially binds to and up-regulates already active genes.
		Method Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels Ian Sudbery, Jim Stalker, Jared T Simpson, Thomas Keane, Alistair G Rust, Matthew E Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve D Brown, Heng Li, Zemin Ning, Joseph H Nadeau, Colleen M Croniger, Richard Durbin, David J Adams Genome Biology 2009, 10:R112 (13 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Methods for accurate identification of nucleotide and structural variation using de novo short read sequencing of mouse chromosomes are described.
		Research Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Young-Joo Seol, Mina Jin, Jin-A Kim, Myung-Ho Lim, Jung Sun Kim, Seunghoon Baek, Beom-Soon Choi, Hee-Ju Yu, Dae-Soo Kim, Namshin Kim, Ki-Byung Lim, Soo-In Lee, Jang-Ho Hahn, Yong Pyo Lim, Ian Bancroft, Beom-Seok Park Genome Biology 2009, 10:R111 (12 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Euchromatic regions of the Brassica rapa genome were sequenced and mapped onto the corresponding regions in the Arabidopsis thaliana genome.
		Research NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis Christophe Rusniok, David Vallenet, Stéphanie Floquet, Helen Ewles, Coralie Mouzé-Soulama, Daniel Brown, Aurélie Lajus, Carmen Buchrieser, Claudine Médigue, Philippe Glaser, Vladimir Pelicic Genome Biology 2009, 10:R110 (9 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of a clinical isolate of Neisseria meningitidis is described. This and other reannotated Neisseria genomes are compiled in a database.
		Software A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome Cizhong Jiang, B Franklin Pugh Genome Biology 2009, 10:R109 (8 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Different genome-wide reference maps of Saccharomyces cerevisiae nucleosome positions are compiled and can be visualized on a browser.
		Research Genomic DNA k-mer spectra: models and modalities Benny Chor, David Horn, Nick Goldman, Yaron Levy, Tim Massingham Genome Biology 2009, 10:R108 (8 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genomes
		Research Defining the chromatin signature of inducible genes in T cells Pek S Lim, Kristine Hardy, Karen L Bunting, Lina Ma, Kaiman Peng, Xinxin Chen, Mary F Shannon Genome Biology 2009, 10:R107 (6 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Inducible genes in T cells show the chromatin characteristics of active genes, suggesting they are primed for transcription.
		Research Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions Nicolas Corradi, Karen L Haag, Jean-François Pombert, Dieter Ebert, Patrick J Keeling Genome Biology 2009, 10:R106 (6 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The draft genome sequence of Octosporea bayeri, a microsporidian pathogen of Daphnia, provides insights into the content and evolution of a large microsporidian genome
		Software MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock Genome Biology 2009, 10:R105 (5 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A software workflow to translate known differentially methylated regions into clinical biomarkers
		Research Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Kakoli Banerjee, Pike-See Cheah, Ping Z Cannon, Christopher N Hahn, Paul Q Thomas, Gordon K Smyth, Seong-Seng Tan, Tim Thomas, Hamish S Scott Genome Biology 2009, 10:R104 (2 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SAGE analysis reveals spatiotemporally regulated transcripts and overlapping sense and antisense transcripts that are important for mouse cerebral cortex development
		Method ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, David B Jaffe Genome Biology 2009, 10:R103 (1 October 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Allpaths2, a method for accurately assembling small genomes with high continuity using short paired reads.
		Correspondence Joining forces in the quest for orthologs Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis Genome Biology 2009, 10:403 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Building momentum to coordinate and leverage community orthology prediction resources.
		Protein family review The netrin protein family Sathyanath Rajasekharan, Timothy E Kennedy Genome Biology 2009, 10:239 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The netrins are a family of extracellular proteins that direct cell and axon migration during embryogenesis.
		Minireview Common variants in polygenic schizophrenia Joseph T Glessner, Hakon Hakonarson Genome Biology 2009, 10:236 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Schizophrenia is associated with both common single-nucleotide polymorphisms at the MHC locus and rare copy-number variants affecting many genes.
		Comment An issue to remember Gregory A Petsko Genome Biology 2009, 10:111 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Thumbing through a recent copy of a journal reveals unexpected riches.
		Research Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium Richard A Stabler, Miao He, Lisa Dawson, Melissa Martin, Esmeralda Valiente, Craig Corton, Trevor D Lawley, Mohammed Sebaihia, Michael A Quail, Graham Rose, Dale N Gerding, Maryse Gibert, Michel R Popoff, Julian Parkhill, Gordon Dougan, Brendan W Wren Genome Biology 2009, 10:R102 (25 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome comparison of non-epidemic and epidemic strains of Clostridium difficile reveals gene gains that could explain how a hypervirulent strain has emerged