Genome Biology - oalib

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Genome Biology

ISSN Print: 1465-6906

ISSN Online:

主页: http://genomebiology.com

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High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians

Hajime Matsuzaki, Pei-Hua Wang, Jing Hu, Rich Rava, Glenn K Fu

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

Mehdi Motallebipour, Adam Ameur, Madhu Sudhan Reddy Bysani, Kalicharan Patra, Ola Wallerman, Jonathan Mangion, Melissa A Barker, Kevin J McKernan, Jan Komorowski, Claes Wadelius

The dog days of autumn

Gregory A Petsko

Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling

King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Kakoli Banerjee, Pike-See Cheah, Ping Z Cannon, Christopher N Hahn, Paul Q Thomas, Gordon K Smyth, Seong-Seng Tan, Tim Thomas, Hamish S Scott

Structural and functional map of a bacterial nucleoid

Agustino Martínez-Antonio, Alejandra Medina-Rivera, Julio Collado-Vides

Transcriptional regulation of metastatic [Id]entity by KLF17

Marcin P Iwanicki, Joan S Brugge

Evolution, ecology and the engineered organism: lessons for synthetic biology

Jeffrey M Skerker, Julius B Lucks, Adam P Arkin

Panmixia postponed: ancestry-related assortative mating in contemporary human populations

Andrew S Burrell, Todd R Disotell

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, David B Jaffe

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

Desmond S Lun, Ashley Sherrid, Brian Weiner, David R Sherman, James E Galagan

NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis

Christophe Rusniok, David Vallenet, Stéphanie Floquet, Helen Ewles, Coralie Mouzé-Soulama, Daniel Brown, Aurélie Lajus, Carmen Buchrieser, Claudine Médigue, Philippe Glaser, Vladimir Pelicic

The netrin protein family

Sathyanath Rajasekharan, Timothy E Kennedy

Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae

Sandra Merz, Benedikt Westermann

Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Santiago F Elena

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans

Arun K Ramani, Andrew C Nelson, Philipp Kapranov, Ian Bell, Thomas R Gingeras, Andrew G Fraser

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

Tatiana Popova, Elodie Manié, Dominique Stoppa-Lyonnet, Guillem Rigaill, Emmanuel Barillot, Marc Stern

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

Joshua Z Levin, Michael F Berger, Xian Adiconis, Peter Rogov, Alexandre Melnikov, Timothy Fennell, Chad Nusbaum, Levi A Garraway, Andreas Gnirke

Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell

Peter von Dassow, Hiroyuki Ogata, Ian Probert, Patrick Wincker, Corinne Da Silva, Stéphane Audic, Jean-Michel Claverie, Colomban de Vargas

An issue to remember

Gregory A Petsko

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data

Christoph Bock, Konstantin Halachev, Joachim Büch, Thomas Lengauer

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg

TFCat: the curated catalog of mouse and human transcription factors

Debra L Fulton, Saravanan Sundararajan, Gwenael Badis, Timothy R Hughes, Wyeth W Wasserman, Jared C Roach, Rob Sladek

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

Bolan Linghu, Evan S Snitkin, Zhenjun Hu, Yu Xia, Charles DeLisi

The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus

Rachel Brower-Sinning, Donald M Carter, Corey J Crevar, Elodie Ghedin, Ted M Ross, Panayiotis V Benos

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

Jessica Severin, Andrew M Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J Balwierz, Michiel JL de Hoon, David A Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O Daub, Alistair RR Forrest

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

Ana C Marques, Chris P Ponting

Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle

Esther Castellano, Carmen Guerrero, Alejandro Nú？ez, Javier De Las Rivas, Eugenio Santos

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features

Kobby Essien, Sebastien Vigneau, Sofia Apreleva, Larry N Singh, Marisa S Bartolomei, Sridhar Hannenhalli

Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication

Radek Szklarczyk, Martijn A Huynen

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

Cizhong Jiang, B Franklin Pugh

MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays

Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock

Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis

Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki, Masanori Suzuki

Divergence of exonic splicing elements after gene duplication and the impact on gene structures

Zhenguo Zhang, Li Zhou, Ping Wang, Yang Liu, Xianfeng Chen, Landian Hu, Xiangyin Kong

Correlating measurements across samples improves accuracy of large-scale expression profile experiments

Mariano Alvarez, Pavel Sumazin, Presha Rajbhandari, Andrea Califano

Many LINE1 elements contribute to the transcriptome of human somatic cells

Sanjida H Rangwala, Lili Zhang, Haig H Kazazian

Nucleosome deposition and DNA methylation at coding region boundaries

Jung Choi, Jae-Bum Bae, Jaemyun Lyu, Tae-Yoon Kim, Young-Joon Kim

Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection

Nicoletta Bivi, Milena Romanello, Richard Harrison, Ian Clarke, David C Hoyle, Luigi Moro, Fulvia Ortolani, Antonella Bonetti, Franco Quadrifoglio, Gianluca Tell, Daniela Delneri

Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins

Francisco Merchan, Adnane Boualem, Martin Crespi, Florian Frugier

Non-imprinted allele-specific DNA methylation on human autosomes

Yingying Zhang, Christian Rohde, Richard Reinhardt, Claudia Voelcker-Rehage, Albert Jeltsch

Comparing cellular proteomes by mass spectrometry

Florian Fr？hlich, Tobias C Walther

Watching proteins in motion

Mary Munson, Daniel N Bolon

Simultaneous transcription of duplicated var2csa gene copies in individual Plasmodium falciparum parasites

Kim JM Brolin, Ulf Ribacke, Sandra Nilsson, Johan Ankarklev, Kirsten Moll, Mats Wahlgren, Qijun Chen

Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells

Britta Hartmann, Robert Castelo, Marco Blanchette, Stephanie Boue, Donald C Rio, Juan Valcárcel

Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis

Rungnapa Pankla, Surachat Buddhisa, Matthew Berry, Derek M Blankenship, Gregory J Bancroft, Jacques Banchereau, Ganjana Lertmemongkolchai, Damien Chaussabel

Insights into female sperm storage from the spermathecal fluid proteome of the honeybee Apis mellifera

Boris Baer, Holger Eubel, Nicolas L Taylor, Nicholas O'Toole, A Harvey Millar

A novel and universal method for microRNA RT-qPCR data normalization

Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele

Cytokinin and auxin intersection in root meristems

Elisabeth J Chapman, Mark Estelle

Defining the chromatin signature of inducible genes in T cells

Pek S Lim, Kristine Hardy, Karen L Bunting, Lina Ma, Kaiman Peng, Xinxin Chen, Mary F Shannon

COMIT: identification of noncoding motifs under selection in coding sequences

Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, Jeffrey H Chuang

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