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		Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
		Comment After the gold rush Neil Hall Genome Biology 2013, 14:115 (7 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
		Method EMu: probabilistic inference of mutational processes and their localization in the cancer genome Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
		Method jMOSAiCS: joint analysis of multiple ChIP-seq datasets Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sunduz Keles Genome Biology 2013, 14:R38 (29 April 2013) Abstract \| Provisional PDF \| Editor’s summary A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
		Research Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
		Research Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis Srikanth Nagalla, Jeff W Chou, Mark C Willingham, Jimmy Ruiz, James P Vaughn, Purnima Dubey, Timothy L Lash, Stephen J Hamilton-Dutoit, Jonas Bergh, Christos Sotiriou, Michael A Black, Lance D Miller Genome Biology 2013, 14:R34 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
		Comment How to evaluate a graduate studentship, or choosing the right doctoral advisor Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Duncan Odom has some sage advice for those considering PhD options
		Method TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg Genome Biology 2013, 14:R36 (25 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A major update to TopHat, the popular Bowtie-based spliced aligner
		Editorial Raymond Gosling: the man who crystallized genes Naomi Attar Genome Biology 2013, 14:402 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary "The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
		Opinion Sixty years of genome biology W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
		Research DNA binding specificities of the long zinc-finger recombination protein PRDM9 Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
		Research Systematic biases in DNA copy number originate from isolation procedures Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation
		Research highlight The complex binding of PRDM9 Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
		Meeting report Single-cell biology meeting marks rebirth of an old science Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013
		Review Neurogenomics of speech and language disorders: the road ahead Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders
		Research p53 induces transcriptional and translational programs to suppress cell proliferation and growth Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress
		Method Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda Genome Biology 2013, 14:R31 (17 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
		Research highlight The fractured genome of HeLa cells David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome
		Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data
		Research The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude. Qingle Cai, Xiaoju Qian, Yongshan Lang, Yadan Luo, Shengkai Pan, Yuanyuan Hui, Caiyun Gou, Yue Cai, Meirong Hao, Jinyang Zhao, Songbo Wang, Zhaobao Wang, Xinming Zhang, Jinchao Liu, Longhai Luo, Yingrui Li, Jun Wang, Rongjun He, Fumin Lei, Jiaohui Xu Genome Biology 2013, 14:R29 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The ground tit genome, one of the highest quality avian genome assemblies to date, reveals potential mechanisms of high altitude adaptation
		Research The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage John Abramyan, Daleen Badenhorst, Kyle K Biggar, Glen M Borchert, Christopher W Botka, Rachel M Bowden, Edward L Braun, Anne M Bronikowski, Benoit G Bruneau, Leslie T Buck, Blanche Capel, Todd A Castoe, Mike Czerwinski, Kim D Delehaunty, Scott V Edwards, Catrina C Fronick, Matthew K Fujita, Lucinda Fulton, Tina A Graves, Richard E Green, Wilfried Haerty, Ramkumar Hariharan, LaDeana H Hillier, Alisha K Holloway, Daniel Janes, Fredric J Janzen, Cyriac Kandoth, Lesheng Kong, Jason de Koning, Yang Li et al. Genome Biology 2013, 14:R28 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing
		Meeting report Clinical applications of sequencing take center stage Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013
		Review Recent progress in the use of genetics to understand links between type 2 diabetes and related metabolic traits Hanieh Yaghootkar, Timothy M Frayling Genome Biology 2013, 14:203 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes
		Research Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest Christopher I Keeling, Macaire MS Yuen, Nancy Y Liao, T Roderick Docking, Simon K Chan, Greg A Taylor, Diana L Palmquist, Shaun D Jackman, Anh Nguyen, Maria Li, Hannah Henderson, Jasmine K Janes, Yongjun Zhao, Pawan Pandoh, Richard Moore, Felix AH Sperling, Dezene PW Huber, Inanc Birol, Stephen JM Jones, Joerg Bohlmann Genome Biology 2013, 14:R27 (27 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome sequence of the mountain pine beetle, only the second beetle genome to be sequenced
		Meeting report The future of genomic medicine is here Konrad J Karczewski Genome Biology 2013, 14:304 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 6th annual Future of Genomic Medicine conference, held at the Scripps Seaside Forum, La Jolla, CA, USA, March 7-8, 2013
		Research highlight Pushing the (nuclear) envelope into meiosis Abby F Dernburg Genome Biology 2013, 14:110 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Abby Dernburg discusses recent research linking nuclear lamins to chromosome pairing in meiosis
		Comment Sequestration: inadvertently killing biomedical research to score political points Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction
		Research RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grutzner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
		Research Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb-target genes James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendegast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells
		Method Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson Genome Biology 2013, 14:R24 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples
		Research highlight Go retro and get a GRIP Kim Wong, David J Adams, Thomas M Keane Genome Biology 2013, 14:108 (19 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Adams and colleagues grapple with the GRIPs (gene retrocopy insertion polymorphisms) identified by Ewing et al in this month's issue
		Method DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels Huiying Zhao, Yuedong Yang, Hai Lin, Xinjun Zhang, Matthew Mort, David N Copper, Yunlong Liu, Yaoqi Zhou Genome Biology 2013, 14:R23 (13 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary DDIG-in is a method for predicting the deleterious effects of short indels
		Research Retrotransposition of gene transcripts leads to structural variation in mammalian genomes Adam D Ewing, Tracy J Ballinger, Dent Earl, Broad Institute Genome Sequencing and Analysis Program and Platform, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
		Research DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes Dvir Aran, Sivan Sabato, Asaf Hellman Genome Biology 2013, 14:R21 (12 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers
		Review Studying the microbiology of the indoor environment Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study
		Meeting report Food for thought from plant and animal genomes Emily Abrash Genome Biology 2013, 14:302 (27 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.
		Research highlight A CRISPR way to engineer the human genome Sivaprakash Ramalingam, Narayana Annaluru, Srinivasan Chandrasegaran Genome Biology 2013, 14:107 (26 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Srinivasan Chandrasegaran and colleagues explain how recent advances in mammalian genome engineering exploit the natural properties of the bacterial CRISPR system
		Research Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes Cecilia Alsmark, Peter G Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T Martin Embley, Robert P Hirt Genome Biology 2013, 14:R19 (25 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A survey of the genomes of eukaryotic microbial parasites reveals extensive lateral gene transfer from prokaryotes
		Research The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, Renato Paro Genome Biology 2013, 14:R18 (25 February 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression
		Research Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies Masayuki Sugawara, Brendan Epstein, Brian Badgley, Tatsuya Unno, Lei Xu, Jennifer Reese, Prasad Gyaneshwar, Roxanne Denny, Joann Mudge, Arvind K Bharti, Andrew D Farmer, Gregory D May, Jimmy E Woodward, Claudine Medigue, David Vallenet, Aurelie Lajus, Zoe Rouy, Betsy Martinez-Vaz, Peter Tiffin, Nevin D Young, Michael J Sadowsky Genome Biology 2013, 14:R17 (20 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Sequencing the genomes of 48 strains of Sinorhizobium reveals a large heterogeneity in strategies for colonization in this family
		Research A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Hoeffner, Marcus Krueger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
		Research highlight What is it about 'eye of newt'? Yuliana Mihaylova, A Aziz Aboobaker Genome Biology 2013, 14:106 (20 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Aziz Aboobaker and Yuliana Mihaylova muse on the peculiar powers that led 'eye of newt' to find favor with Macbeth's witches
		Research Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King Genome Biology 2013, 14:R15 (18 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity
		Research Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer Genome Biology 2013, 14:R14 (15 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
		Research Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae Mallory A Freeberg, Ting Han, James J Moresco, Andy Kong, Yu-Cheng Yang, Zhi Lu, John R Yates, John K Kim Genome Biology 2013, 14:R13 (14 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A study of the global binding of RNA binding proteins in yeast in response to stress
		Method SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan, Xiangke Liao, Xiaoqian Zhu, Shaoliang Peng, Yingrui Li, Jun Wang, Guangwu Guo Genome Biology 2013, 14:R12 (14 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements
		Comment Science: it's a role model thing Chris Gunter Genome Biology 2013, 14:105 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary To coincide with International Women's Day on March 8, Chris Gunter ask how important role models are to improving female representation in science
		Research Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Bürglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang, Peter Hegemann, Hillel Fromm, Didier Raoult, Gilbert Greub, Diego Miranda-Saavedra, Nansheng Chen, Piers Nash et al. Genome Biology 2013, 14:R11 (1 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
		Open letter Genome sequencing of the important oilseed crop Sesamum indicum L Haiyang Zhang, Hongmei Miao, Lei Wang, Lingbo Qu, Hongyan Liu, Qiang Wang, Meiwang Yue Genome Biology 2013, 14:401 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sesame Genome Working Group describe the project for sequencing the sesame genome
		Review Host genomic influences on HIV/AIDS Stephen J O'Brien, Sher L Hendrickson Genome Biology 2013, 14:201 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How has the era of genomics advanced our understanding of HIV/AIDS epidemiology and pathogenesis?

	All
		Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
		Comment After the gold rush Neil Hall Genome Biology 2013, 14:115 (7 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
		Method EMu: probabilistic inference of mutational processes and their localization in the cancer genome Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
		Method jMOSAiCS: joint analysis of multiple ChIP-seq datasets Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sunduz Keles Genome Biology 2013, 14:R38 (29 April 2013) Abstract \| Provisional PDF \| Editor’s summary A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
		Research Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
		Research Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis Srikanth Nagalla, Jeff W Chou, Mark C Willingham, Jimmy Ruiz, James P Vaughn, Purnima Dubey, Timothy L Lash, Stephen J Hamilton-Dutoit, Jonas Bergh, Christos Sotiriou, Michael A Black, Lance D Miller Genome Biology 2013, 14:R34 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
		Comment How to evaluate a graduate studentship, or choosing the right doctoral advisor Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Duncan Odom has some sage advice for those considering PhD options
		Method TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg Genome Biology 2013, 14:R36 (25 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A major update to TopHat, the popular Bowtie-based spliced aligner
		Editorial Raymond Gosling: the man who crystallized genes Naomi Attar Genome Biology 2013, 14:402 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary "The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
		Opinion Sixty years of genome biology W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
		Research DNA binding specificities of the long zinc-finger recombination protein PRDM9 Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
		Research Systematic biases in DNA copy number originate from isolation procedures Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation
		Research highlight The complex binding of PRDM9 Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
		Meeting report Single-cell biology meeting marks rebirth of an old science Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013
		Review Neurogenomics of speech and language disorders: the road ahead Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders
		Research p53 induces transcriptional and translational programs to suppress cell proliferation and growth Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress
		Method Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda Genome Biology 2013, 14:R31 (17 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
		Research highlight The fractured genome of HeLa cells David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome
		Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data
		Research The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude. Qingle Cai, Xiaoju Qian, Yongshan Lang, Yadan Luo, Shengkai Pan, Yuanyuan Hui, Caiyun Gou, Yue Cai, Meirong Hao, Jinyang Zhao, Songbo Wang, Zhaobao Wang, Xinming Zhang, Jinchao Liu, Longhai Luo, Yingrui Li, Jun Wang, Rongjun He, Fumin Lei, Jiaohui Xu Genome Biology 2013, 14:R29 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The ground tit genome, one of the highest quality avian genome assemblies to date, reveals potential mechanisms of high altitude adaptation
		Research The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage John Abramyan, Daleen Badenhorst, Kyle K Biggar, Glen M Borchert, Christopher W Botka, Rachel M Bowden, Edward L Braun, Anne M Bronikowski, Benoit G Bruneau, Leslie T Buck, Blanche Capel, Todd A Castoe, Mike Czerwinski, Kim D Delehaunty, Scott V Edwards, Catrina C Fronick, Matthew K Fujita, Lucinda Fulton, Tina A Graves, Richard E Green, Wilfried Haerty, Ramkumar Hariharan, LaDeana H Hillier, Alisha K Holloway, Daniel Janes, Fredric J Janzen, Cyriac Kandoth, Lesheng Kong, Jason de Koning, Yang Li et al. Genome Biology 2013, 14:R28 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing
		Meeting report Clinical applications of sequencing take center stage Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013
		Review Recent progress in the use of genetics to understand links between type 2 diabetes and related metabolic traits Hanieh Yaghootkar, Timothy M Frayling Genome Biology 2013, 14:203 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes
		Research Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest Christopher I Keeling, Macaire MS Yuen, Nancy Y Liao, T Roderick Docking, Simon K Chan, Greg A Taylor, Diana L Palmquist, Shaun D Jackman, Anh Nguyen, Maria Li, Hannah Henderson, Jasmine K Janes, Yongjun Zhao, Pawan Pandoh, Richard Moore, Felix AH Sperling, Dezene PW Huber, Inanc Birol, Stephen JM Jones, Joerg Bohlmann Genome Biology 2013, 14:R27 (27 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome sequence of the mountain pine beetle, only the second beetle genome to be sequenced
		Meeting report The future of genomic medicine is here Konrad J Karczewski Genome Biology 2013, 14:304 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 6th annual Future of Genomic Medicine conference, held at the Scripps Seaside Forum, La Jolla, CA, USA, March 7-8, 2013
		Research highlight Pushing the (nuclear) envelope into meiosis Abby F Dernburg Genome Biology 2013, 14:110 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Abby Dernburg discusses recent research linking nuclear lamins to chromosome pairing in meiosis
		Comment Sequestration: inadvertently killing biomedical research to score political points Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction
		Research RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grutzner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
		Research Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb-target genes James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendegast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells
		Method Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson Genome Biology 2013, 14:R24 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples
		Research highlight Go retro and get a GRIP Kim Wong, David J Adams, Thomas M Keane Genome Biology 2013, 14:108 (19 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Adams and colleagues grapple with the GRIPs (gene retrocopy insertion polymorphisms) identified by Ewing et al in this month's issue
		Method DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels Huiying Zhao, Yuedong Yang, Hai Lin, Xinjun Zhang, Matthew Mort, David N Copper, Yunlong Liu, Yaoqi Zhou Genome Biology 2013, 14:R23 (13 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary DDIG-in is a method for predicting the deleterious effects of short indels
		Research Retrotransposition of gene transcripts leads to structural variation in mammalian genomes Adam D Ewing, Tracy J Ballinger, Dent Earl, Broad Institute Genome Sequencing and Analysis Program and Platform, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
		Research DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes Dvir Aran, Sivan Sabato, Asaf Hellman Genome Biology 2013, 14:R21 (12 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers
		Review Studying the microbiology of the indoor environment Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study
		Meeting report Food for thought from plant and animal genomes Emily Abrash Genome Biology 2013, 14:302 (27 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.
		Research highlight A CRISPR way to engineer the human genome Sivaprakash Ramalingam, Narayana Annaluru, Srinivasan Chandrasegaran Genome Biology 2013, 14:107 (26 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Srinivasan Chandrasegaran and colleagues explain how recent advances in mammalian genome engineering exploit the natural properties of the bacterial CRISPR system
		Research Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes Cecilia Alsmark, Peter G Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T Martin Embley, Robert P Hirt Genome Biology 2013, 14:R19 (25 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A survey of the genomes of eukaryotic microbial parasites reveals extensive lateral gene transfer from prokaryotes
		Research The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, Renato Paro Genome Biology 2013, 14:R18 (25 February 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression
		Research Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies Masayuki Sugawara, Brendan Epstein, Brian Badgley, Tatsuya Unno, Lei Xu, Jennifer Reese, Prasad Gyaneshwar, Roxanne Denny, Joann Mudge, Arvind K Bharti, Andrew D Farmer, Gregory D May, Jimmy E Woodward, Claudine Medigue, David Vallenet, Aurelie Lajus, Zoe Rouy, Betsy Martinez-Vaz, Peter Tiffin, Nevin D Young, Michael J Sadowsky Genome Biology 2013, 14:R17 (20 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Sequencing the genomes of 48 strains of Sinorhizobium reveals a large heterogeneity in strategies for colonization in this family
		Research A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Hoeffner, Marcus Krueger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
		Research highlight What is it about 'eye of newt'? Yuliana Mihaylova, A Aziz Aboobaker Genome Biology 2013, 14:106 (20 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Aziz Aboobaker and Yuliana Mihaylova muse on the peculiar powers that led 'eye of newt' to find favor with Macbeth's witches
		Research Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King Genome Biology 2013, 14:R15 (18 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity
		Research Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery Nikolaj Zuleger, Shelagh Boyle, David A Kelly, Jose I de las Heras, Vassiliki Lazou, Nadia Korfali, Dzmitry G Batrakou, K Natalie Randles, Glenn E Morris, David J Harrison, Wendy A Bickmore, Eric C Schirmer Genome Biology 2013, 14:R14 (15 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
		Research Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae Mallory A Freeberg, Ting Han, James J Moresco, Andy Kong, Yu-Cheng Yang, Zhi Lu, John R Yates, John K Kim Genome Biology 2013, 14:R13 (14 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A study of the global binding of RNA binding proteins in yeast in response to stress
		Method SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data Wenlong Jia, Kunlong Qiu, Minghui He, Pengfei Song, Quan Zhou, Feng Zhou, Yuan Yu, Dandan Zhu, Michael L Nickerson, Shengqing Wan, Xiangke Liao, Xiaoqian Zhu, Shaoliang Peng, Yingrui Li, Jun Wang, Guangwu Guo Genome Biology 2013, 14:R12 (14 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements
		Comment Science: it's a role model thing Chris Gunter Genome Biology 2013, 14:105 (14 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary To coincide with International Women's Day on March 8, Chris Gunter ask how important role models are to improving female representation in science
		Research Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Bürglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang, Peter Hegemann, Hillel Fromm, Didier Raoult, Gilbert Greub, Diego Miranda-Saavedra, Nansheng Chen, Piers Nash et al. Genome Biology 2013, 14:R11 (1 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
		Open letter Genome sequencing of the important oilseed crop Sesamum indicum L Haiyang Zhang, Hongmei Miao, Lei Wang, Lingbo Qu, Hongyan Liu, Qiang Wang, Meiwang Yue Genome Biology 2013, 14:401 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Sesame Genome Working Group describe the project for sequencing the sesame genome
		Review Host genomic influences on HIV/AIDS Stephen J O'Brien, Sher L Hendrickson Genome Biology 2013, 14:201 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How has the era of genomics advanced our understanding of HIV/AIDS epidemiology and pathogenesis?