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		Research Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor) Lei-Ying Zheng, Xiao-Sen Guo, Bing He, Lian-Jun Sun, Yao Peng, Shan-Shan Dong, Teng-Fei Liu, Shuye Jiang, Srinivasan Ramachandran, Chun-Ming Liu, Hai-Chun Jing Genome Biology 2011, 12:R114 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomes from three strains of Sorghum bicolor (one grain and two sweet) have been sequenced and compared with the reference genome
		Research highlight Wrangling for microRNAs provokes much crosstalk Ana C Marques, Jennifer Tan, Chris P Ponting Genome Biology 2011, 12:132 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chris Ponting highlights recent articles on competitive endogenous RNAs that illustrate how miRNA response elements enable crosstalk between transcripts
		Research Discovery of active enhancers through bidirectional expression of short transcripts Michael F Melgar, Francis S Collins, Praveen Sethupathy Genome Biology 2011, 12:R113 (14 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Regions showing bidirectional expression of short transcripts can be used to identify active enhancers
		Protein family review Tissue inhibitors of metalloproteinases Gillian Murphy Genome Biology 2011, 12:233 (11 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As metalloproteinase-independent functions are discovered for TIMPs, future work will focus on identifying receptors and downstream signaling mechanisms
		Research Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems André E Minoche, Juliane C Dohm, Heinz Himmelbauer Genome Biology 2011, 12:R112 (8 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Error rates are compared in data from Illumina's HiSeq and GAIIx systems
		Method Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors Chao Cheng, Chong Shou, Kevin Y Yip, Mark B Gerstein Genome Biology 2011, 12:R111 (7 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that uses both chromatin features and motif identification to predict transcription factor binding sites
		Research Composite effects of gene determinants on the translation speed and density of ribosomes Tamir Tuller, Isana Veksler-Lublinsky, Nir Gazit, Martin Kupiec, Eytan Ruppin, Michal Ziv-Ukelson Genome Biology 2011, 12:R110 (3 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Codon usage, amino acid charge and mRNA folding energy all correlate with translation speed and ribosome density
		Comment Bailing out Gregory A Petsko Genome Biology 2011, 12:131 (29 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Let us shout to the public and private sectors, this is not the time to be bailing out
		Review Genome-wide association studies in plants: the missing heritability is in the field Benjamin Brachi, Geoffrey P Morris, Justin O Borevitz Genome Biology 2011, 12:232 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Justin Borevitz on how high-power association mapping is going back 'into the field' through the combination of genomics and population biology
		Research highlight 1, 2, 3: Counting the fingers on a chicken wing Martin D Carkett, Malcolm PO Logan Genome Biology 2011, 12:130 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Malcolm Logan on an RNA-seq approach to clarifying a long-standing dispute between paleontologists and embryologists
		Research Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles Maya Botzman, Hanah Margalit Genome Biology 2011, 12:R109 (27 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Application of a new method to prokaryotic genomes reveals an association between lifestyle and codon bias
		Protein family review The rhomboid protease family: a decade of progress on function and mechanism Sinisa Urban, Seth W Dickey Genome Biology 2011, 12:231 (27 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The rhomboid family of membrane-immersed proteases are found in all domains of life and have been implicated in several human diseases.
		Method Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity Markus Rasmussen, Magnus Sundström, Hanna Kultima, Johan Botling, Patrick Micke, Helgi Birgisson, Bengt Glimelius, Anders Isaksson Genome Biology 2011, 12:R108 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TAPS is a method for identifying allele-specific copy number changes in tumor samples
		Research The draft genome of the carcinogenic human liver fluke Clonorchis sinensis Xiaoyun Wang, Wenjun Chen, Yan Huang, Jiufeng Sun, Jingtao Men, Hailiang Liu, Fang Luo, Lei Guo, Xiaoli Lv, Chuanhuan Deng, Chenhui Zhou, Yongxiu Fan, Xuerong Li, Lisi Huang, Yue Hu, Chi Liang, Xuchu Hu, Jin Xu, Xinbing Yu Genome Biology 2011, 12:R107 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A draft genome sequence of the liver fluke Clonorchis sinensis, which is a leading cause of liver cancer in Asia
		Meeting report Moving beyond genome sequencing into personalized genomic medicine: biological and computing challenges David M Kristensen Genome Biology 2011, 12:308 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Beyond the Genome meeting, the Universities at Shady Grove, Rockville, Maryland, USA, 19-22 September 2011
		Review Bacterial epidemiology and biology - lessons from genome sequencing Julian Parkhill, Brendan W Wren Genome Biology 2011, 12:230 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Brendan Wren and Julian Parkhill on how a new era in microbial genomics has solved ancient controversies and promises to revolutionize our understanding of bacterial pathogens
		Research Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics Vinoy K Ramachandran, Alison K East, Ramakrishnan Karunakaran, J Allan Downie, Philip S Poole Genome Biology 2011, 12:R106 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription is measured in Rhizobium leguminosarum grown on roots of a host plant, a non-host legume and a non-leguminous plant
		Method Integrating diverse genomic data using gene sets Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani Genome Biology 2011, 12:R105 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for integrating multiple genomic data types for the identification of enriched gene sets
		Method High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord Genome Biology 2011, 12:R104 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
		Research The draft genome and transcriptome of Cannabis sativa Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
		Editorial How hemp got high Naomi Attar Genome Biology 2011, 12:409 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Senior Assistant Editor Naomi Attar discusses the genome sequence of cannabis
		Correction Correction: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Mogens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2011, 12:140 (20 October 2011) Abstract \| Full text \| PDF
		Research Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer Wigard P Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S Vermaat, Markus J van Roosmalen, Stef van Lieshout, Isaac J Nijman, Wijnand Roessingh, Ruben van 't Slot, José van de Belt, Victor Guryev, Marco Koudijs, Emile Voest, Edwin Cuppen Genome Biology 2011, 12:R103 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromothripsis is found to be a common mechanism driving structural rearrangement in primary colorectal cancer and metastases
		Review Revealing the molecular signatures of host-pathogen interactions Chiea-Chuen Khor, Martin L Hibberd Genome Biology 2011, 12:229 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide association studies and pathogen sequencing are revealing unexpected insights into host-pathogen interactions
		Method SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Wolfgang Huber, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:R101 (18 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method to detect condition-specific gene expression from microarray data
		Research Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
		Research Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin, Aindrila Mukhopadhyay Genome Biology 2011, 12:R99 (12 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary All response regulators in the genome of Desulfovibrius vulgaris are identified, as are all their target genes
		Research The transcriptional landscape of Chlamydia pneumoniae Marco Albrecht, Cynthia M Sharma, Marcus T Dittrich, Tobias Müller, Richard Reinhardt, Jörg Vogel, Thomas Rudel Genome Biology 2011, 12:R98 (11 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The life cycle of the obligate intracellular human pathogen C. pneumoniae has a dynamic transcriptional landscape
		Research A comparative analysis of exome capture Jennifer S Parla, Ivan Iossifov, Ian Grabill, Mona S Spector, Melissa Kramer, W Richard McCombie Genome Biology 2011, 12:R97 (29 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The coverage of two solution exome capture kits is compared
		Comment The one new journal we might actually need Gregory A Petsko Genome Biology 2011, 12:129 (29 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The one thing that I actually do want for Christmas: another scientific journal
		Research First somatic mutation of E2F1 in a critical DNA binding residue discovered in well-differentiated papillary mesothelioma of the peritoneum Willie Yu, Waraporn Chan-On, Melissa Teo, Choon Ong, Ioana Cutcutache, George E Allen, Bernice Wong, Swe Myint, Kiat Lim, P Mathijs Voorhoeve, Steve Rozen, Khee Soo, Patrick Tan, Bin Teh Genome Biology 2011, 12:R96 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An E2F1 somatic mutation is discovered in a rare form of cancer by exome sequencing
		Research Comprehensive comparison of three commercial human whole-exome capture platforms Asan, Yu Xu, Hui Jiang, Chris Tyler-Smith, Yali Xue, Tao Jiang, Jiawei Wang, Mingzhi Wu, Xiao Liu, Geng Tian, Jun Wang, Jian Wang, Huangming Yang, Xiuqing Zhang Genome Biology 2011, 12:R95 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of three human exome-capture platforms shows that NimbleGen's SeqCap EZ gives the best efficacy of exome capture and SNP detection
		Research Comparison of solution-based exome capture methods for next generation sequencing Anna-Maija Sulonen, Pekka Ellonen, Henrikki Almusa, Maija Lepistö, Samuli Eldfors, Sari Hannula, Timo Miettinen, Henna Tyynismaa, Perttu Salo, Caroline Heckman, Heikki Joensuu, Taneli Raivio, Anu Suomalainen, Janna Saarela Genome Biology 2011, 12:R94 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Roche NimbleGen and Agilent solution-based exome capture kits are compared. NimbleGen kits give more accurate alignments to target regions
		Method Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis Tejasvi S Niranjan, Abby Adamczyk, Héctor Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry, Tao Wang Genome Biology 2011, 12:R93 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two methods are presented, SRFIM and SERVIC4E, for detecting rare variants in pooled exome samples
		Research Exome sequencing identifies a novel missense variant in RRM2B associated with autosomal recessive progressive external ophthalmoplegia Atsushi Takata, Maiko Kato, Masayuki Nakamura, Takeo Yoshikawa, Shigenobu Kanba, Akira Sano, Tadafumi Kato Genome Biology 2011, 12:R92 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Exome sequencing in a single recessive case of progressive external ophthalmoplegia identifies a novel missense variant in RRM2B as a potential causative mutation
		Research SHROOM3 is a novel candidate for heterotaxy identified by whole exome sequencing Muhammad Tariq, John W Belmont, Seema Lalani, Teresa Smolarek, Stephanie M Ware Genome Biology 2011, 12:R91 (21 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recessive missense mutation in SHROOM3, which is associated with heterotaxy is identified using exome sequencing
		Research Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice Jennifer M Hilton, Morag A Lewis, M'hamed Grati, Neil Ingham, Selina Pearson, Roman A Laskowski, David J Adams, Karen P Steel Genome Biology 2011, 12:R90 (21 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exome sequencing was used to identify a potentially causative mutation in the Dearish mouse, a model for otitis media
		Research Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families Zippora Brownstein, Lilach M Friedman, Hashem Shahin, Varda Oron-Karni, Nitzan Kol, Amal Rayyan, Thomas Parzefall, Dorit Lev, Stavit Shalev, Moshe Frydman, Bella Davidov, Mordechai Shohat, Michele Rahile, Sari Lieberman, Ephrat Levy-Lahad, Ming K Lee, Noam Shomron, Mary-Claire King, Tom Walsh, Moien Kanaan, Karen B Avraham Genome Biology 2011, 12:R89 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Targeted capture and sequencing of genomic DNA from subjects with inherited hearing loss offers an effective screen for mutations
		Research Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome Cyrille Saintenac, Dayou Jiang, Eduard D Akhunov Genome Biology 2011, 12:R88 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat
		Research Expanding whole exome resequencing into non-human primates Eric J Vallender Genome Biology 2011, 12:R87 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human DNA capture tools are used to capture and sequence non-human primate DNA
		Method Mutation discovery in mice by whole exome sequencing Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R Corrigan, Michelle Curtain, Yueming Ding, Mark D'Ascenzo, Daniel J Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy Rowe, Frank J Probst, David E Bergstrom, Stephen A Murray, Carol Bult, Joel Richardson, Benjamin T Kile, Ivo Gut, Jorg Hager, Snaevar Sigurdsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad-Toh, Michael L Cunningham, Timothy C Cox, Monica J Justice, Mona S Spector, Scott W Lowe, Thomas Albert, Leah Donahue, Jeffrey Jeddeloh, Jay Shendure, Laura G Reinholdt et al. Genome Biology 2011, 12:R86 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary In solution capture reagents are developed for the mouse exome and demonstrated in multiple inbred strains and novel mutant strains
		Method Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes Katherine R Smith, Catherine J Bromhead, Michael S Hildebrand, A Eliot Shearer, Paul J Lockhart, Hossein Najmabadi, Richard J Leventer, George McGillivray, David J Amor, Richard J Smith, Melanie Bahlo Genome Biology 2011, 12:R85 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for performing linkage analysis from exome sequencing variant data is presented
		Research The functional spectrum of low-frequency coding variation Gabor T Marth, Fuli Yu, Amit R Indap, Kiran Garimella, Simon Gravel, Wen Leong, Chris Tyler-Smith, Matthew Bainbridge, Tom Blackwell, Xiangqun Zheng-Bradley, Yuan Chen, Danny Challis, Laura Clarke, Edward V Ball, Kristian Cibulskis, David N Cooper, Bob Fulton, Chris Hartl, Dan Koboldt, Donna Muzny, Richard Smith, Carrie Sougnez, Chip Stewart, Alistair Ward, Jin Yu, Yali Xue, David Altshuler, Carlos D Bustamante, Andrew G Clark, Mark Daly, Mark DePristo, Paul Flicek, Stacey Gabriel, Elaine Mardis, Aarno Palotie, Richard Gibbs, the 1000 Genomes Project et al. Genome Biology 2011, 12:R84 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 1000 Genomes Project presents exome sequence data for 1000 genes from 700 individuals, better defining low frequency variants
		Editorial Next-generation human genetics Jay Shendure Genome Biology 2011, 12:408 (14 September 2011) Abstract \| Full text \| PDF \| Editor’s summary Exome and genome sequencing are reshaping the landscape of human genetics; Jay Shendure discusses the lessons learnt and opportunities opened
		Editorial The exome factor Hannah Stower Genome Biology 2011, 12:407 (14 September 2011) Abstract \| Full text \| PDF \| Editor’s summary Special Issues Editor, Hannah Stower, introduces Genome Biology's issue on exome sequencing
		Review Unlocking Mendelian disease using exome sequencing Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A Veltman Genome Biology 2011, 12:228 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In the past 2 years, exome sequencing has provided significant new insights into the causes of both Mendelian and sporadic genetic diseases
		Review Computational and statistical approaches to analyzing variants identified by exome sequencing Nathan O Stitziel, Adam Kiezun, Shamil Sunyaev Genome Biology 2011, 12:227 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many computational and statistical methods are now available to narrow down causal variants in exome sequencing data, for both Mendelian and complex diseases
		Opinion Exome sequencing: the expert view Leslie G Biesecker, Kevin V Shianna, Jim C Mullikin Genome Biology 2011, 12:128 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three leaders in the field of exome sequencing discuss why the approach is so popular and how it is contributing to genomics
		Opinion The promise and limitations of population exomics for human evolution studies Jacob A Tennessen, Timothy D O'Connor, Michael J Bamshad, Joshua M Akey Genome Biology 2011, 12:127 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality
		Comment Nothing to do and all day to do it in Gregory A Petsko Genome Biology 2011, 12:126 (31 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The perfect end to a perfect vacation day

	All
		Research Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor) Lei-Ying Zheng, Xiao-Sen Guo, Bing He, Lian-Jun Sun, Yao Peng, Shan-Shan Dong, Teng-Fei Liu, Shuye Jiang, Srinivasan Ramachandran, Chun-Ming Liu, Hai-Chun Jing Genome Biology 2011, 12:R114 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomes from three strains of Sorghum bicolor (one grain and two sweet) have been sequenced and compared with the reference genome
		Research highlight Wrangling for microRNAs provokes much crosstalk Ana C Marques, Jennifer Tan, Chris P Ponting Genome Biology 2011, 12:132 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chris Ponting highlights recent articles on competitive endogenous RNAs that illustrate how miRNA response elements enable crosstalk between transcripts
		Research Discovery of active enhancers through bidirectional expression of short transcripts Michael F Melgar, Francis S Collins, Praveen Sethupathy Genome Biology 2011, 12:R113 (14 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Regions showing bidirectional expression of short transcripts can be used to identify active enhancers
		Protein family review Tissue inhibitors of metalloproteinases Gillian Murphy Genome Biology 2011, 12:233 (11 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As metalloproteinase-independent functions are discovered for TIMPs, future work will focus on identifying receptors and downstream signaling mechanisms
		Research Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems André E Minoche, Juliane C Dohm, Heinz Himmelbauer Genome Biology 2011, 12:R112 (8 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Error rates are compared in data from Illumina's HiSeq and GAIIx systems
		Method Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors Chao Cheng, Chong Shou, Kevin Y Yip, Mark B Gerstein Genome Biology 2011, 12:R111 (7 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method that uses both chromatin features and motif identification to predict transcription factor binding sites
		Research Composite effects of gene determinants on the translation speed and density of ribosomes Tamir Tuller, Isana Veksler-Lublinsky, Nir Gazit, Martin Kupiec, Eytan Ruppin, Michal Ziv-Ukelson Genome Biology 2011, 12:R110 (3 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Codon usage, amino acid charge and mRNA folding energy all correlate with translation speed and ribosome density
		Comment Bailing out Gregory A Petsko Genome Biology 2011, 12:131 (29 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Let us shout to the public and private sectors, this is not the time to be bailing out
		Review Genome-wide association studies in plants: the missing heritability is in the field Benjamin Brachi, Geoffrey P Morris, Justin O Borevitz Genome Biology 2011, 12:232 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Justin Borevitz on how high-power association mapping is going back 'into the field' through the combination of genomics and population biology
		Research highlight 1, 2, 3: Counting the fingers on a chicken wing Martin D Carkett, Malcolm PO Logan Genome Biology 2011, 12:130 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Malcolm Logan on an RNA-seq approach to clarifying a long-standing dispute between paleontologists and embryologists
		Research Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles Maya Botzman, Hanah Margalit Genome Biology 2011, 12:R109 (27 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Application of a new method to prokaryotic genomes reveals an association between lifestyle and codon bias
		Protein family review The rhomboid protease family: a decade of progress on function and mechanism Sinisa Urban, Seth W Dickey Genome Biology 2011, 12:231 (27 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The rhomboid family of membrane-immersed proteases are found in all domains of life and have been implicated in several human diseases.
		Method Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity Markus Rasmussen, Magnus Sundström, Hanna Kultima, Johan Botling, Patrick Micke, Helgi Birgisson, Bengt Glimelius, Anders Isaksson Genome Biology 2011, 12:R108 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TAPS is a method for identifying allele-specific copy number changes in tumor samples
		Research The draft genome of the carcinogenic human liver fluke Clonorchis sinensis Xiaoyun Wang, Wenjun Chen, Yan Huang, Jiufeng Sun, Jingtao Men, Hailiang Liu, Fang Luo, Lei Guo, Xiaoli Lv, Chuanhuan Deng, Chenhui Zhou, Yongxiu Fan, Xuerong Li, Lisi Huang, Yue Hu, Chi Liang, Xuchu Hu, Jin Xu, Xinbing Yu Genome Biology 2011, 12:R107 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A draft genome sequence of the liver fluke Clonorchis sinensis, which is a leading cause of liver cancer in Asia
		Meeting report Moving beyond genome sequencing into personalized genomic medicine: biological and computing challenges David M Kristensen Genome Biology 2011, 12:308 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Beyond the Genome meeting, the Universities at Shady Grove, Rockville, Maryland, USA, 19-22 September 2011
		Review Bacterial epidemiology and biology - lessons from genome sequencing Julian Parkhill, Brendan W Wren Genome Biology 2011, 12:230 (24 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Brendan Wren and Julian Parkhill on how a new era in microbial genomics has solved ancient controversies and promises to revolutionize our understanding of bacterial pathogens
		Research Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics Vinoy K Ramachandran, Alison K East, Ramakrishnan Karunakaran, J Allan Downie, Philip S Poole Genome Biology 2011, 12:R106 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription is measured in Rhizobium leguminosarum grown on roots of a host plant, a non-host legume and a non-leguminous plant
		Method Integrating diverse genomic data using gene sets Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, Giovanni Parmigiani Genome Biology 2011, 12:R105 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for integrating multiple genomic data types for the identification of enriched gene sets
		Method High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord Genome Biology 2011, 12:R104 (21 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
		Research The draft genome and transcriptome of Cannabis sativa Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
		Editorial How hemp got high Naomi Attar Genome Biology 2011, 12:409 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Senior Assistant Editor Naomi Attar discusses the genome sequence of cannabis
		Correction Correction: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Mogens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2011, 12:140 (20 October 2011) Abstract \| Full text \| PDF
		Research Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer Wigard P Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S Vermaat, Markus J van Roosmalen, Stef van Lieshout, Isaac J Nijman, Wijnand Roessingh, Ruben van 't Slot, José van de Belt, Victor Guryev, Marco Koudijs, Emile Voest, Edwin Cuppen Genome Biology 2011, 12:R103 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromothripsis is found to be a common mechanism driving structural rearrangement in primary colorectal cancer and metastases
		Review Revealing the molecular signatures of host-pathogen interactions Chiea-Chuen Khor, Martin L Hibberd Genome Biology 2011, 12:229 (19 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide association studies and pathogen sequencing are revealing unexpected insights into host-pathogen interactions
		Method SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Wolfgang Huber, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:R101 (18 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method to detect condition-specific gene expression from microarray data
		Research Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
		Research Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin, Aindrila Mukhopadhyay Genome Biology 2011, 12:R99 (12 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary All response regulators in the genome of Desulfovibrius vulgaris are identified, as are all their target genes
		Research The transcriptional landscape of Chlamydia pneumoniae Marco Albrecht, Cynthia M Sharma, Marcus T Dittrich, Tobias Müller, Richard Reinhardt, Jörg Vogel, Thomas Rudel Genome Biology 2011, 12:R98 (11 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The life cycle of the obligate intracellular human pathogen C. pneumoniae has a dynamic transcriptional landscape
		Research A comparative analysis of exome capture Jennifer S Parla, Ivan Iossifov, Ian Grabill, Mona S Spector, Melissa Kramer, W Richard McCombie Genome Biology 2011, 12:R97 (29 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The coverage of two solution exome capture kits is compared
		Comment The one new journal we might actually need Gregory A Petsko Genome Biology 2011, 12:129 (29 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The one thing that I actually do want for Christmas: another scientific journal
		Research First somatic mutation of E2F1 in a critical DNA binding residue discovered in well-differentiated papillary mesothelioma of the peritoneum Willie Yu, Waraporn Chan-On, Melissa Teo, Choon Ong, Ioana Cutcutache, George E Allen, Bernice Wong, Swe Myint, Kiat Lim, P Mathijs Voorhoeve, Steve Rozen, Khee Soo, Patrick Tan, Bin Teh Genome Biology 2011, 12:R96 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An E2F1 somatic mutation is discovered in a rare form of cancer by exome sequencing
		Research Comprehensive comparison of three commercial human whole-exome capture platforms Asan, Yu Xu, Hui Jiang, Chris Tyler-Smith, Yali Xue, Tao Jiang, Jiawei Wang, Mingzhi Wu, Xiao Liu, Geng Tian, Jun Wang, Jian Wang, Huangming Yang, Xiuqing Zhang Genome Biology 2011, 12:R95 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of three human exome-capture platforms shows that NimbleGen's SeqCap EZ gives the best efficacy of exome capture and SNP detection
		Research Comparison of solution-based exome capture methods for next generation sequencing Anna-Maija Sulonen, Pekka Ellonen, Henrikki Almusa, Maija Lepistö, Samuli Eldfors, Sari Hannula, Timo Miettinen, Henna Tyynismaa, Perttu Salo, Caroline Heckman, Heikki Joensuu, Taneli Raivio, Anu Suomalainen, Janna Saarela Genome Biology 2011, 12:R94 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Roche NimbleGen and Agilent solution-based exome capture kits are compared. NimbleGen kits give more accurate alignments to target regions
		Method Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis Tejasvi S Niranjan, Abby Adamczyk, Héctor Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry, Tao Wang Genome Biology 2011, 12:R93 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two methods are presented, SRFIM and SERVIC4E, for detecting rare variants in pooled exome samples
		Research Exome sequencing identifies a novel missense variant in RRM2B associated with autosomal recessive progressive external ophthalmoplegia Atsushi Takata, Maiko Kato, Masayuki Nakamura, Takeo Yoshikawa, Shigenobu Kanba, Akira Sano, Tadafumi Kato Genome Biology 2011, 12:R92 (28 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Exome sequencing in a single recessive case of progressive external ophthalmoplegia identifies a novel missense variant in RRM2B as a potential causative mutation
		Research SHROOM3 is a novel candidate for heterotaxy identified by whole exome sequencing Muhammad Tariq, John W Belmont, Seema Lalani, Teresa Smolarek, Stephanie M Ware Genome Biology 2011, 12:R91 (21 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recessive missense mutation in SHROOM3, which is associated with heterotaxy is identified using exome sequencing
		Research Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice Jennifer M Hilton, Morag A Lewis, M'hamed Grati, Neil Ingham, Selina Pearson, Roman A Laskowski, David J Adams, Karen P Steel Genome Biology 2011, 12:R90 (21 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exome sequencing was used to identify a potentially causative mutation in the Dearish mouse, a model for otitis media
		Research Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families Zippora Brownstein, Lilach M Friedman, Hashem Shahin, Varda Oron-Karni, Nitzan Kol, Amal Rayyan, Thomas Parzefall, Dorit Lev, Stavit Shalev, Moshe Frydman, Bella Davidov, Mordechai Shohat, Michele Rahile, Sari Lieberman, Ephrat Levy-Lahad, Ming K Lee, Noam Shomron, Mary-Claire King, Tom Walsh, Moien Kanaan, Karen B Avraham Genome Biology 2011, 12:R89 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Targeted capture and sequencing of genomic DNA from subjects with inherited hearing loss offers an effective screen for mutations
		Research Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome Cyrille Saintenac, Dayou Jiang, Eduard D Akhunov Genome Biology 2011, 12:R88 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat
		Research Expanding whole exome resequencing into non-human primates Eric J Vallender Genome Biology 2011, 12:R87 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human DNA capture tools are used to capture and sequence non-human primate DNA
		Method Mutation discovery in mice by whole exome sequencing Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R Corrigan, Michelle Curtain, Yueming Ding, Mark D'Ascenzo, Daniel J Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy Rowe, Frank J Probst, David E Bergstrom, Stephen A Murray, Carol Bult, Joel Richardson, Benjamin T Kile, Ivo Gut, Jorg Hager, Snaevar Sigurdsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad-Toh, Michael L Cunningham, Timothy C Cox, Monica J Justice, Mona S Spector, Scott W Lowe, Thomas Albert, Leah Donahue, Jeffrey Jeddeloh, Jay Shendure, Laura G Reinholdt et al. Genome Biology 2011, 12:R86 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary In solution capture reagents are developed for the mouse exome and demonstrated in multiple inbred strains and novel mutant strains
		Method Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes Katherine R Smith, Catherine J Bromhead, Michael S Hildebrand, A Eliot Shearer, Paul J Lockhart, Hossein Najmabadi, Richard J Leventer, George McGillivray, David J Amor, Richard J Smith, Melanie Bahlo Genome Biology 2011, 12:R85 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for performing linkage analysis from exome sequencing variant data is presented
		Research The functional spectrum of low-frequency coding variation Gabor T Marth, Fuli Yu, Amit R Indap, Kiran Garimella, Simon Gravel, Wen Leong, Chris Tyler-Smith, Matthew Bainbridge, Tom Blackwell, Xiangqun Zheng-Bradley, Yuan Chen, Danny Challis, Laura Clarke, Edward V Ball, Kristian Cibulskis, David N Cooper, Bob Fulton, Chris Hartl, Dan Koboldt, Donna Muzny, Richard Smith, Carrie Sougnez, Chip Stewart, Alistair Ward, Jin Yu, Yali Xue, David Altshuler, Carlos D Bustamante, Andrew G Clark, Mark Daly, Mark DePristo, Paul Flicek, Stacey Gabriel, Elaine Mardis, Aarno Palotie, Richard Gibbs, the 1000 Genomes Project et al. Genome Biology 2011, 12:R84 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 1000 Genomes Project presents exome sequence data for 1000 genes from 700 individuals, better defining low frequency variants
		Editorial Next-generation human genetics Jay Shendure Genome Biology 2011, 12:408 (14 September 2011) Abstract \| Full text \| PDF \| Editor’s summary Exome and genome sequencing are reshaping the landscape of human genetics; Jay Shendure discusses the lessons learnt and opportunities opened
		Editorial The exome factor Hannah Stower Genome Biology 2011, 12:407 (14 September 2011) Abstract \| Full text \| PDF \| Editor’s summary Special Issues Editor, Hannah Stower, introduces Genome Biology's issue on exome sequencing
		Review Unlocking Mendelian disease using exome sequencing Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A Veltman Genome Biology 2011, 12:228 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In the past 2 years, exome sequencing has provided significant new insights into the causes of both Mendelian and sporadic genetic diseases
		Review Computational and statistical approaches to analyzing variants identified by exome sequencing Nathan O Stitziel, Adam Kiezun, Shamil Sunyaev Genome Biology 2011, 12:227 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many computational and statistical methods are now available to narrow down causal variants in exome sequencing data, for both Mendelian and complex diseases
		Opinion Exome sequencing: the expert view Leslie G Biesecker, Kevin V Shianna, Jim C Mullikin Genome Biology 2011, 12:128 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three leaders in the field of exome sequencing discuss why the approach is so popular and how it is contributing to genomics
		Opinion The promise and limitations of population exomics for human evolution studies Jacob A Tennessen, Timothy D O'Connor, Michael J Bamshad, Joshua M Akey Genome Biology 2011, 12:127 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality
		Comment Nothing to do and all day to do it in Gregory A Petsko Genome Biology 2011, 12:126 (31 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The perfect end to a perfect vacation day