Genome Biology | Most Forwarded

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	All
	1.	Method ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb Genome Biology 2011, 12:R67 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq
	2.	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
	3.	Research highlight Runaway transcription Jiannan Guo, Tiandao Li, David H Price Genome Biology 2013, 14:133 (30 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Price proposes that 7SK snRNA is a key barrier to runaway transcription - in contrast to the inept engineer Casey Jones
	4.	Research RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grützner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
	5.	Editorial Raymond Gosling: the man who crystallized genes Naomi Attar Genome Biology 2013, 14:402 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary "The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
	6.	Research Comprehensive genotyping of the USA national maize inbred seed bank Maria C Romay, Mark J Millard, Jeffrey C Glaubitz, Jason A Peiffer, Kelly L Swarts, Terry M Casstevens, Robert J Elshire, Charlotte B Acharya, Sharon E Mitchell, Sherry A Flint-Garcia, Michael D McMullen, James B Holland, Edward S Buckler, Candice A Gardner Genome Biology 2013, 14:R55 (11 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time
	7.	Research Aging effects on DNA methylation modules in human brain and blood tissue Steve Horvath, Yafeng Zhang, Peter Langfelder, René S Kahn, Marco PM Boks, Kristel van Eijk, Leonard H van den Berg, Roel A Ophoff Genome Biology 2012, 13:R97 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An age-related co-methylation module in human brain and blood tissue includes genes associated with Alzheimer's disease
	8.	Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
	9.	Method Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, 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 \| Full text \| PDF \| PubMed \| Editor’s summary Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
	10.	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 \| Full text \| PDF \| PubMed \| Editor’s summary A new study identifies nuclear envelope proteins which may reposition human chromosomes in a tissue-specific manner
	11.	Research Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance David Martino, Yuk Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
	12.	Review From RNA-seq reads to differential expression results Alicia Oshlack, Mark D Robinson, Matthew D Young Genome Biology 2010, 11:220 (22 December 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
	13.	Research A blood based 12-miRNA signature of Alzheimer disease patients Petra Leidinger, Christina Backes, Stephanie Deutscher, Katja Schmitt, Sabine C Mueller, Karen Frese, Jan Haas, Klemens Ruprecht, Friedemann Paul, Cord Stähler, Christoph JG Lang, Benjamin Meder, Tamas Bartfai, Eckart Meese, Andreas Keller Genome Biology 2013, 14:R78 (29 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A 12-miRNA signature in blood samples can be used to detect Alzheimer’s disease and other neurological disorders
	14.	Software MetAMOS: a modular and open source metagenomic assembly and analysis pipeline Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya, Brian Ondov, Aaron E Darling, Adam M Phillippy, Mihai Pop Genome Biology 2013, 14:R2 (15 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A modular, metagenomic analysis and assembly pipeline that inputs next-generation sequencing reads to generate genomic scaffolds and open reading frames
	15.	Method Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E Mason, Nicholas D Socci, Doron Betel Genome Biology 2013, 14:R95 (10 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An evaluation of differential gene expression analysis methods for RNA-seq data using the SEQC gold standard dataset
	16.	Correspondence The advantages of SMRT sequencing Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013) Abstract \| Full text \| PDF \| PubMed \| 2 comments \| Editor’s summary Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform
	17.	Method Ray Meta: scalable de novo metagenome assembly and profiling Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
	18.	Software REAPR: a universal tool for genome assembly evaluation Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman, Thomas D Otto Genome Biology 2013, 14:R47 (27 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new user-friendly software tool for genome assembly evaluation
	19.	Software methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason Genome Biology 2012, 13:R87 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An R package (incorporating multiple analysis tools) automates and simplifies the characterization of methylation datasets
	20.	Editorial Plant genomics: sowing the seeds of success Gemma D Bilsborough Genome Biology 2013, 14:404 (28 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome Biology's Special Issue Editor, Gemma Bilsborough, gives an overview of our plant genomics issue
	21.	Research Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford progeria syndrome cells Ishita S Mehta, Christopher H Eskiw, Halime D Arican, Ian R Kill, Joanna M Bridger Genome Biology 2011, 12:R74 (12 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Treating cultured cells from Hutchinson-Gilford progeria patients with farnesyltransferase inhibitors restores wildtype chromosome dynamics
	22.	Software Toward almost closed genomes with GapFiller Marten Boetzer, Walter Pirovano Genome Biology 2012, 13:R56 (25 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GapFiller is a method for automatically filling gaps in short read genome assemblies using the existing sequencing data
	23.	Poster presentation CIPRO 2.5: Ciona intestinalis Protein Database - a unique integrated repository of large-scale omics data, bioinformatic analyses, and curated annotation, with ability for user rating and comments Toshinori Endo, Keisuke Ueno, Kouki Yonezawa, Katsuhiko Mineta, Kohji Hotta, Yutaka Satou, Lixy Yamada, Michio Ogasawara, Hiroki Takahashi, Ayako Nakajima, Mia Nakachi, Mamoru Nomura, Junko Yaguchi, Alu Konno, Yasunori Sasakura, Akiyasu C Yoshizawa, Hisaaki Taniguchi, Chisato Yamasaki, Miho Sera, Tadashi Imanishi, Kazuo Inaba Genome Biology 2010, 11(Suppl 1):P11 (11 October 2010) Full text \| PDF
	24.	Research The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida, David N Kuhn et al. Genome Biology 2013, 14:R53 (3 June 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of Theobroma cacao Matina 1-6 allows the identification of a gene associated with pod color
	25.	Method Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes Georgia Giannoukos, Dawn M Ciulla, Katherine Huang, Brian J Haas, Jacques Izard, Joshua Z Levin, Jonathan Livny, Ashlee M Earl, Dirk Gevers, Doyle V Ward, Chad Nusbaum, Bruce W Birren, Andreas Gnirke Genome Biology 2012, 13:r23 (28 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented for transcriptome sequencing of complex bacterial mixtures or communities