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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)
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The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
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After the gold rush
Neil Hall Genome Biology 2013, 14:115 (7 May 2013)
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Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
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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)
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A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
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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)
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A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
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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)
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A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
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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)
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An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
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How to evaluate a graduate studentship, or choosing the right doctoral advisor
Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013)
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Duncan Odom has some sage advice for those considering PhD options
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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)
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A major update to TopHat, the popular Bowtie-based spliced aligner
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Raymond Gosling: the man who crystallized genes
Naomi Attar Genome Biology 2013, 14:402 (25 April 2013)
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"The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
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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)
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Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
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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)
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A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
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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)
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A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation
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The complex binding of PRDM9
Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013)
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A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
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Single-cell biology meeting marks rebirth of an old science
Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013)
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A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013
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Neurogenomics of speech and language disorders: the road ahead
Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013)
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From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders
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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)
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p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress
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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)
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Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
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The fractured genome of HeLa cells
David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013)
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David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome
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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)
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Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data
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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)
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The ground tit genome, one of the highest quality avian genome assemblies to date, reveals potential mechanisms of high altitude adaptation
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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)
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The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing
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Clinical applications of sequencing take center stage
Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013)
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A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013
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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)
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Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes
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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)
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The genome sequence of the mountain pine beetle, only the second beetle genome to be sequenced
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The future of genomic medicine is here
Konrad J Karczewski Genome Biology 2013, 14:304 (27 March 2013)
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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
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Pushing the (nuclear) envelope into meiosis
Abby F Dernburg Genome Biology 2013, 14:110 (27 March 2013)
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Abby Dernburg discusses recent research linking nuclear lamins to chromosome pairing in meiosis
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Sequestration: inadvertently killing biomedical research to score political points
Jeffrey T Leek, Steven L Salzberg Genome Biology 2013, 14:109 (27 March 2013)
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Steven Salzberg and Jeff Leek are concerned about the Sequester's impact on biomedical research, and argue for a change in policy direction
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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)
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A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
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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)
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An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells
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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)
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Patchwork is a method for determining allele-specific copy number variation in sequenced tumor samples
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Go retro and get a GRIP
Kim Wong, David J Adams, Thomas M Keane Genome Biology 2013, 14:108 (19 March 2013)
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David Adams and colleagues grapple with the GRIPs (gene retrocopy insertion polymorphisms) identified by Ewing et al in this month's issue
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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)
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DDIG-in is a method for predicting the deleterious effects of short indels
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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)
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An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
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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)
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A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers
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Studying the microbiology of the indoor environment
Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013)
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Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study
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Food for thought from plant and animal genomes
Emily Abrash Genome Biology 2013, 14:302 (27 February 2013)
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A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.
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A CRISPR way to engineer the human genome
Sivaprakash Ramalingam, Narayana Annaluru, Srinivasan Chandrasegaran Genome Biology 2013, 14:107 (26 February 2013)
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Srinivasan Chandrasegaran and colleagues explain how recent advances in mammalian genome engineering exploit the natural properties of the bacterial CRISPR system
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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)
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A survey of the genomes of eukaryotic microbial parasites reveals extensive lateral gene transfer from prokaryotes
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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)
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The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression
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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)
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Sequencing the genomes of 48 strains of Sinorhizobium reveals a large heterogeneity in strategies for colonization in this family
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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)
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A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
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What is it about 'eye of newt'?
Yuliana Mihaylova, A Aziz Aboobaker Genome Biology 2013, 14:106 (20 February 2013)
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Aziz Aboobaker and Yuliana Mihaylova muse on the peculiar powers that led 'eye of newt' to find favor with Macbeth's witches
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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)
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Genome sequencing of Salpingoeca rosetta reveals insights into the genome composition of the metazoan ancestor and the evolution of multicellularity
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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)
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A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
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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)
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A study of the global binding of RNA binding proteins in yeast in response to stress
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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)
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SOAPfuse is a method for detecting fusion transcripts in RNA-seq data that has a high detection rate and low computational requirements
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Science: it's a role model thing
Chris Gunter Genome Biology 2013, 14:105 (14 February 2013)
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To coincide with International Women's Day on March 8, Chris Gunter ask how important role models are to improving female representation in science
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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)
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Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
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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)
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The Sesame Genome Working Group describe the project for sequencing the sesame genome
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Host genomic influences on HIV/AIDS
Stephen J O'Brien, Sher L Hendrickson Genome Biology 2013, 14:201 (31 January 2013)
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How has the era of genomics advanced our understanding of HIV/AIDS epidemiology and pathogenesis?
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