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Correspondence Re-examination of chimp protein kinases suggests "novel architectures" are gene prediction artifacts Keith Robison PMCID: PMC2823696 Finishing genomes with limited resources: lessons from an ensemble of microbial genomes Niranjan Nagarajan, Christopher Cook, MariaPia Di Bonaventura, Hong Ge, Allen Richards, Kimberly A Bishop-Lilly, Robert DeSalle, Timothy D Read, and Mihai Pop PMCID: PMC2864248 Touring Ensembl: A practical guide to genome browsing Giulietta M Spudich and Xosé M Fernández-Suárez PMCID: PMC2894802 Database DIGAP - a Database of Improved Gene Annotation for Phytopathogens Na Gao, Ling-Ling Chen, Hong-Fang Ji, Wei Wang, Ji-Wei Chang, Bei Gao, Lin Zhang, Shi-Cui Zhang, and Hong-Yu Zhang PMCID: PMC2825234 FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology Sandrine Grossetête, Bernard Labedan, and Olivier Lespinet PMCID: PMC2829015 Fungal Secretome Database: Integrated platform for annotation of fungal secretomes Jaeyoung Choi, Jongsun Park, Donghan Kim, Kyongyong Jung, Seogchan Kang, and Yong-Hwan Lee PMCID: PMC2836287 SoyTEdb: a comprehensive database of transposable elements in the soybean genome Jianchang Du, David Grant, Zhixi Tian, Rex T Nelson, Liucun Zhu, Randy C Shoemaker, and Jianxin Ma PMCID: PMC2830986 wDBTF: an integrated database resource for studying wheat transcription factor families Isabelle Romeuf, Dominique Tessier, Mireille Dardevet, Gérard Branlard, Gilles Charmet, and Catherine Ravel PMCID: PMC2858749 LEAPdb: a database for the late embryogenesis abundant proteins Gilles Hunault and Emmanuel Jaspard PMCID: PMC2858754 Ensembl variation resources Yuan Chen, Fiona Cunningham, Daniel Rios, William M McLaren, James Smith, Bethan Pritchard, Giulietta M Spudich, Simon Brent, Eugene Kulesha, Pablo Marin-Garcia, Damian Smedley, Ewan Birney, and Paul Flicek PMCID: PMC2894800 Database of exact tandem repeats in the Zebrafish genome Eric C Rouchka PMCID: PMC2901318 Research articles Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis Tim van Zutphen, Richard JS Baerends, Kim A Susanna, Anne de Jong, Oscar P Kuipers, Marten Veenhuis, and Ida J van der Klei PMCID: PMC2827406 Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity Theo HM Smits, Sebastian Jaenicke, Fabio Rezzonico, Tim Kamber, Alexander Goesmann, Jürg E Frey, and Brion Duffy PMCID: PMC2827408 Extensive analysis of D-J-C arrangements allows the identification of different mechanisms enhancing the diversity in sheep T cell receptor β-chain repertoire Silvia Di Tommaso, Rachele Antonacci, Salvatrice Ciccarese, and Serafina Massari PMCID: PMC2806336 Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish Thilo Borchardt, Mario Looso, Marc Bruckskotten, Patrick Weis, Julia Kruse, and Thomas Braun PMCID: PMC2823690 Normal colon epithelium: a dataset for the analysis of gene expression and alternative splicing events in colon disease Wilfrido Mojica and Lesleyann Hawthorn PMCID: PMC2823691 An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure? Yu Zhang and Brian Oliver PMCID: PMC2820458 Detecting positive selection from genome scans of linkage disequilibrium Chad D Huff, Henry C Harpending, and Alan R Rogers PMCID: PMC2820459 An integrated functional genomic study of acute phenobarbital exposure in the rat Claire L Waterman, Richard A Currie, Lisa A Cottrell, Jacky Dow, Jayne Wright, Catherine J Waterfield, and Julian L Griffin PMCID: PMC2826316 The dynamic architecture of the metabolic switch in Streptomyces coelicolor Kay Nieselt, Florian Battke, Alexander Herbig, Per Bruheim, Alexander Wentzel, Øyvind M Jakobsen, Håvard Sletta, Mohammad T Alam, Maria E Merlo, Jonathan Moore, Walid AM Omara, Edward R Morrissey, Miguel A Juarez-Hermosillo, Antonio Rodríguez-García, Merle Nentwich, Louise Thomas, Mudassar Iqbal, Roxane Legaie, William H Gaze, Gregory L Challis, Ritsert C Jansen, Lubbert Dijkhuizen, David A Rand, David L Wild, Michael Bonin, Jens Reuther, Wolfgang Wohlleben, Margaret CM Smith, Nigel J Burroughs, Juan F Martín, David A Hodgson, Eriko Takano, Rainer Breitling, Trond E Ellingsen, and Elizabeth MH Wellington PMCID: PMC2824715 Global transcriptional analysis of nitrogen fixation and ammonium repression in root-associated Pseudomonas stutzeri A1501 Yongliang Yan, Shuzhen Ping, Junping Peng, Yunlei Han, Liang Li, Jian Yang, Yuetan Dou, Yan Li, Huili Fan, Ying Fan, Danhua Li, Yuhua Zhan, Ming Chen, Wei Lu, Wei Zhang, Qi Cheng, Qi Jin, and Min Lin PMCID: PMC2820453 The Zur regulon of Corynebacterium glutamicum ATCC 13032 Jasmin Schröder, Nina Jochmann, Dmitry A Rodionov, and Andreas Tauch PMCID: PMC2823685 Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos Shaobing O Zhang, Sachin Mathur, Gaye Hattem, Olivier Tassy, and Olivier Pourquié PMCID: PMC2821371 Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution Desirée A Douglas and David J Gower PMCID: PMC2820454 Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments Magalie Celton, Alain Malpertuy, Gaëlle Lelandais, and Alexandre G de Brevern PMCID: PMC2827407 Analysis of the heat shock response in mouse liver reveals transcriptional dependence on the nuclear receptor peroxisome proliferator-activated receptor α (PPARα) Beena Vallanat, Steven P Anderson, Holly M Brown-Borg, Hongzu Ren, Sander Kersten, Sudhakar Jonnalagadda, Rajagopalan Srinivasan, and J Christopher Corton PMCID: PMC2823686 Glutamate, aspartate and nucleotide transporters in the SLC17 family form four main phylogenetic clusters: evolution and tissue expression Smitha Sreedharan, Jafar HA Shaik, Pawel K Olszewski, Allen S Levine, Helgi B Schiöth, and Robert Fredriksson PMCID: PMC2824716 Comparative transcriptomic analysis of follicle-enclosed oocyte maturational and developmental competence acquisition in two non-mammalian vertebrates Maella Gohin, Julien Bobe, and Franck Chesnel PMCID: PMC2821372 Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana Xiaoping Gou, Kai He, Hui Yang, Tong Yuan, Honghui Lin, Steven D Clouse, and Jia Li PMCID: PMC2817689 Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background Simone de Jong S, Tova F Fuller, Esther Janson, Eric Strengman, Steve Horvath, Martien JH Kas, and Roel A Ophoff PMCID: PMC2823687 Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates Robert W Blakesley, Nancy F Hansen, Jyoti Gupta, Jennifer C McDowell, Baishali Maskeri, Beatrice B Barnabas, Shelise Y Brooks, Holly Coleman, Payam Haghighi, Shi-Ling Ho, Karen Schandler, Sirintorn Stantripop, Jennifer L Vogt, Pamela J Thomas, NISC Comparative Sequencing Program, Gerard G Bouffard, and Eric D Green PMCID: PMC2827409 Acetylation of p65 at lysine 314 is important for late NF-κB-dependent gene expression Karin M Rothgiesser, Monika Fey, and Michael O Hottiger PMCID: PMC2823688 Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development Wen Huang, Brian S Yandell, and Hasan Khatib PMCID: PMC2824717 Comparison of clastogen-induced gene expression profiles in wild-type and DNA repair-deficient Rad54/Rad54B cells Anuska G Mahabir, Mirjam M Schaap, Jeroen LA Pennings, Jan van Benthem, Coenraad FM Hendriksen, and Harry van Steeg PMCID: PMC2824718 High-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylation David O Azorsa, RiLee H Robeson, Danielle Frost, Bessie Meec hoovet, Gillian R Brautigam, Chad Dickey, Christian Beaudry, Gargi D Basu, David R Holz, Joseph A Hernandez, Kristen M Bisanz, Leslie Gwinn, Andrew Grover, Joseph Rogers, Eric M Reiman, Michael Hutton, Dietrich A Stephan, Spyro Mousses, and Travis Dunckley PMCID: PMC2820455 1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1 Pavlo L Kovalenko, Zhentao Zhang, Min Cui, Steve K Clinton, and James C Fleet PMCID: PMC2820456 Regional regulation of transcription in the chicken genome Haisheng Nie, Richard PMA Crooijmans, John WM Bastiaansen, Hendrik-Jan Megens, and Martien AM Groenen PMCID: PMC2817690 Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens Heiko Vogel, Andrew J Heidel, David G Heckel, and Astrid T Groot PMCID: PMC2820457 Variable structure motifs for transcription factor binding sites John E Reid, Kenneth J Evans, Nigel Dyer, Lorenz Wernisch, and Sascha Ott PMCID: PMC2824720 Temperature increase prevails over acidification in gene expression modulation of amastigote differentiation in Leishmania infantum Pedro J Alcolea, Ana Alonso, Manuel J Gómez, Alicia Sánchez-Gorostiaga, Mercedes Moreno-Paz, Eduardo González-Pastor, Alfredo Toraño, Víctor Parro, and Vicente Larraga PMCID: PMC2845110 Integrative analysis of the heat shock response in Aspergillus fumigatus Daniela Albrecht, Reinhard Guthke, Axel A Brakhage, and Olaf Kniemeyer PMCID: PMC2820008 New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome Jihua Feng, Xianhua Dai, Qian Xiang, Zhiming Dai, Jiang Wang, Yangyang Deng, and Caisheng He PMCID: PMC2824721 In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum Emmanuel Bischoff and Catherine Vaquero PMCID: PMC2821373 Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum Laurent Bréhélin, Isabelle Florent, Olivier Gascuel, and Éric Maréchal PMCID: PMC2826313 The proteolytic system of lactic acid bacteria revisited: a genomic comparison Mengjin Liu, Jumamurat R Bayjanov, Bernadet Renckens, Arjen Nauta, and Roland J Siezen PMCID: PMC2827410 A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes - an open access resource for neuroscience and evolutionary biology Molly Craxton PMCID: PMC2823689 High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence David L Hyten, Steven B Cannon, Qijian Song, Nathan Weeks, Edward W Fickus, Randy C Shoemaker, James E Specht, Andrew D Farmer, Gregory D May, and Perry B Cregan PMCID: PMC2817691 Gene expression profiles in Atlantic salmon adipose-derived stromo-vascular fraction during differentiation into adipocytes Marijana Todorčević, Stanko Škugor, Aleksei Krasnov, and Bente Ruyter PMCID: PMC2824722 Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes Jessica E Butler, Nelson D Young, and Derek R Lovley PMCID: PMC2825233 Deletions of Immunoglobulin heavy chain and T cell receptor gene regions are uniquely associated with lymphoid blast transformation of chronic myeloid leukemia Elisabeth P Nacheva, Diana Brazma, Anna Virgili, Julie Howard-Reeves, Anastasios Chanalaris, Katya Gancheva, Margarita Apostolova, Mikel Valgañon, Helen Mazzullo, and Colin Grace PMCID: PMC2822760 Evolution and diversity of secretome genes in the apicomplexan parasite Theileria annulata William Weir, Tülin Karagenç, Margaret Baird, Andy Tait, and Brian R Shiels PMCID: PMC2826314 Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE) Ricardo Nilo, Carlos Saffie, Kathryn Lilley, Ricardo Baeza-Yates, Verónica Cambiazo, Reinaldo Campos-Vargas, Mauricio González , Lee A Meisel, Julio Retamales, Herman Silva, and Ariel Orellana PMCID: PMC2822761 Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes Jaroslav Nunvar, Tereza Huckova, and Irena Licha PMCID: PMC2817692 Novel OBP genes similar to hamster Aphrodisin in the bank vole, Myodes glareolus Romana Stopková, Zbyněk Zdráhal, Štěpán Ryba, Ondřej Šedo, Martin Šandera, and Pavel Stopka PMCID: PMC2824723 Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome Brian V Jones, Funing Sun, and Julian R Marchesi PMCID: PMC2822762 Expression profiling of prospero in the Drosophila larval chemosensory organ: Between growth and outgrowth Laure Guenin, Mahatsangy Raharijaona, Rémi Houlgatte, and Fawzia Baba-Aissa PMCID: PMC2826315 Intergenic, gene terminal, and intragenic CpG islands in the human genome Yulia A Medvedeva, Marina V Fridman, Nina J Oparina, Dmitry B Malko, Ekaterina O Ermakova, Ivan V Kulakovskiy, Andreas Heinzel, and Vsevolod J Makeev PMCID: PMC2817693 Identification of interacting transcription factors regulating tissue gene expression in human Zihua Hu and Steven M Gallo PMCID: PMC2822763 Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data Jun Yin, Sarah McLoughlin, Ian B Jeffery, Antonino Glaviano, Breandan Kennedy, and Desmond G Higgins PMCID: PMC2827411 An insight into the sialotranscriptome of the West Nile mosquito vector, Culex tarsalis Eric Calvo, Irma Sanchez-Vargas, Amanda J Favreau, Kent D Barbian, Van M Pham, Kenneth E Olson, and José MC Ribeiro PMCID: PMC2823692 Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development Guru Jagadeeswaran, Yun Zheng, Niranji Sumathipala, Haobo Jiang, Estela L Arrese, Jose L Soulages, Weixiong Zhang, and Ramanjulu Sunkar PMCID: PMC2824724 Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array Maarten Vercruysse, Maarten Fauvart, Lore Cloots, Kristof Engelen, Inge M Thijs, Kathleen Marchal, and Jan Michiels PMCID: PMC2881028 Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum Lili Hao, Pengfei Cai, Ning Jiang, Heng Wang, and Qijun Chen PMCID: PMC2820009 Gene expression profiling to identify eggshell proteins involved in physical defense of the chicken egg Vincent Jonchère, Sophie Réhault-Godbert, Christelle Hennequet-Antier, Cédric Cabau, Vonick Sibut, Larry A Cogburn, Yves Nys, and Joel Gautron PMCID: PMC2827412 Does replication groups scoring reduce false positive rate in SNP interaction discovery? Marko Toplak, Tomaz Curk, Janez Demsar, and Blaz Zupan PMCID: PMC2823693 Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation Rebecca L Nugent, Anna Johnsson, Brian Fleharty, Madelaine Gogol, Yongtao Xue-Franzén, Chris Seidel, Anthony PH Wright, and Susan L Forsburg PMCID: PMC2823694 Identical repeated backbone of the human genome Cinthya J Zepeda-Mendoza, Tzitziki Lemus, Omar Yáñez, Delfino García, David Valle-García, Karla F Meza-Sosa, María Gutiérrez-Arcelus, Yamile Márquez-Ortiz, Rocío Domínguez-Vidaña, Claudia Gonzaga-Jauregui, Margarita Flores, and Rafael Palacios PMCID: PMC2845111 Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs Yong Zhang, Jun Liu, Chunshi Jia, Tingting Li, Rimao Wu, Jie Wang, Ying Chen, Xiaoting Zou, Runsheng Chen, Xiu-Jie Wang, and Dahai Zhu PMCID: PMC2832892 Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans Jason S Maydan, Adam Lorch, Mark L Edgley, Stephane Flibotte, and Donald G Moerman PMCID: PMC2822765 Differences in the transcriptome signatures of two genetically related Entamoeba histolytica cell lines derived from the same isolate with different pathogenic properties Laura Biller, Paul H Davis, Manuela Tillack, Jenny Matthiesen, Hannelore Lotter, Samuel L Stanley, Jr, Egbert Tannich, and Iris Bruchhaus PMCID: PMC2823695 Changes in the genomic content of circulating Bordetella pertussis strains isolated from the Netherlands, Sweden, Japan and Australia: adaptive evolution or drift? Audrey J King, Tamara van Gorkom, Han GJ van der Heide, Abdolreza Advani, and Saskia van der Lee PMCID: PMC2834637 Tungsten carbide cobalt nanoparticles exert hypoxia-like effects on the gene expression level in human keratinocytes Wibke Busch, Dana Kühnel, Kristin Schirmer, and Stefan Scholz PMCID: PMC2824725 Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching Lori AS Snyder, Nicholas J Loman, James D Linton, Rebecca R Langdon, George M Weinstock, Brendan W Wren, and Mark J Pallen PMCID: PMC2823697 The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing Heiner Kuhl, Alfred Beck, Grzegorz Wozniak, Adelino VM Canario, Filip AM Volckaert, and Richard Reinhardt PMCID: PMC2837037 Transcriptome analysis reveals absence of unintended effects in drought-tolerant transgenic plants overexpressing the transcription factor ABF3 Ashraf Abdeen, Jaimie Schnell, and Brian Miki PMCID: PMC2837038 Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map Lisa A McGraw, Jamie K Davis, Josh J Lowman, Boudewijn FH ten Hallers, Maxim Koriabine, Larry J Young, Pieter J de Jong, M Katharine Rudd, and James W Thomas PMCID: PMC2824727 Relationship between operon preference and functional properties of persistent genes in bacterial genomes Marit S Bratlie, Jostein Johansen, and Finn Drabløs PMCID: PMC2837039 Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques Tiago S Hori, A Kurt Gamperl, Luis OB Afonso, Stewart C Johnson, Sophie Hubert, Jennifer Kimball, Sharen Bowman, and Matthew L Rise PMCID: PMC2830189 Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses Mukesh Jain, Challa Ghanashyam, and Annapurna Bhattacharjee PMCID: PMC2825235 Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells Lihan Zhou, Qing-En Lim, Guoqiang Wan, and Heng-Phon Too PMCID: PMC2831847 Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis Yogeswaran Lokanathan, Adura Mohd-Adnan, Kiew-Lian Wan, and Sheila Nathan PMCID: PMC2828411 Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data Chol-Hee Jung, Martin A Hansen, Igor V Makunin, Darren J Korbie, and John S Mattick PMCID: PMC2825236 Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola Yong-Li Zhou, Mei-Rong Xu, Ming-Fu Zhao, Xue-Wen Xie, Ling-Hua Zhu, Bin-Ying Fu, and Zhi-Kang Li PMCID: PMC2824728 Comparative evolutionary analysis of protein complexes in E. coli and yeast Adam J Reid, Juan AG Ranea, and Christine A Orengo PMCID: PMC2837643 Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome Alexandra M Lopes, Paul S Burgoyne, Andrew Ojarikre, Julien Bauer, Carole A Sargent, António Amorim, and Nabeel A Affara PMCID: PMC2837040 Comparative genomics reveals selective distribution and domain organization of FYVE and PX domain proteins across eukaryotic lineages Sumana Banerjee, Soumalee Basu, and Srimonti Sarkar PMCID: PMC2837644 Gene prioritization in Type 2 Diabetes using domain interactions and network analysis Amitabh Sharma, Sreenivas Chavali, Rubina Tabassum, Nikhil Tandon, and Dwaipayan Bharadwaj PMCID: PMC2824729 MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori Shiping Liu, Song Gao, Danyu Zhang, Jiyun Yin, Zhonghuai Xiang, and Qingyou Xia PMCID: PMC2835664 Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity Laurent X Nouvel, Pascal Sirand-Pugnet, Marc S Marenda, Eveline Sagné, Valérie Barbe, Sophie Mangenot, Chantal Schenowitz, Daniel Jacob, Aurélien Barré, Stéphane Claverol, Alain Blanchard, and Christine Citti PMCID: PMC2824730 Systematic overrepresentation of DNA termini and underrepresentation of subterminal regions among sequencing templates prepared from hydrodynamically sheared linear DNA molecules Sherri L Schwartz and Mark L Farman PMCID: PMC2824731 Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? Alexandros Bousios, Nikos Darzentas, Athanasios Tsaftaris, and Stephen R Pearce PMCID: PMC2829016 Transcriptional response of Burkholderia cenocepacia J2315 sessile cells to treatments with high doses of hydrogen peroxide and sodium hypochlorite Elke Peeters, Andrea Sass, Eshwar Mahenthiralingam, Hans Nelis, and Tom Coenye PMCID: PMC2830190 Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion Eva Trost, Susanne Götker, Jessica Schneider, Susanne Schneiker-Bekel, Rafael Szczepanowski, Alexandra Tilker, Prisca Viehoever, Walter Arnold, Thomas Bekel, Jochen Blom, Karl-Heinz Gartemann, Burkhard Linke, Alexander Goesmann, Alfred Pühler, Sanjay K Shukla, and Andreas Tauch PMCID: PMC2830990 Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications Chi Nam Ignatius Pang, Elisabeth Gasteiger, and Marc R Wilkins PMCID: PMC2830191 Comparative transcriptome analysis coupled to X-ray CT reveals sucrose supply and growth velocity as major determinants of potato tuber starch biosynthesis Stephanus J Ferreira, Melanie Senning, Sophia Sonnewald, Petra-Maria Keßling, Ralf Goldstein, and Uwe Sonnewald PMCID: PMC2827413 Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim Shaohua Zeng, Gong Xiao, Juan Guo, Zhangjun Fei, Yanqin Xu, Bruce A Roe, and Ying Wang PMCID: PMC2829513 Genome-wide analysis of rice ClpB/HSP100, ClpC and ClpD genes Amanjot Singh, Upasana Singh, Dheeraj Mittal, and Anil Grover PMCID: PMC2829514 Variability of gene expression profiles in human blood and lymphoblastoid cell lines Josine L Min, Amy Barrett, Tim Watts, Fredrik H Pettersson, Helen E Lockstone, Cecilia M Lindgren, Jennifer M Taylor, Maxine Allen, Krina T Zondervan, and Mark I McCarthy PMCID: PMC2841682 Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae) Jin Koh, Pamela S Soltis, and Douglas E Soltis PMCID: PMC2829515 Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs Vincent Deslandes, Martine Denicourt, Christiane Girard, Josée Harel, John HE Nash, and Mario Jacques PMCID: PMC2829017 Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics Christophe J Noël, Nicia Diaz, Thomas Sicheritz-Ponten, Lucie Safarikova, Jan Tachezy, Petrus Tang, Pier-Luigi Fiori, and Robert P Hirt PMCID: PMC2843621 Annotation and classification of the bovine T cell receptor delta genes Carolyn TA Herzig, Marie-Paule Lefranc, and Cynthia L Baldwin PMCID: PMC2846910 Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals Kahori Takane, Kosuke Fujishima, Yuka Watanabe, Asako Sato, Nobuto Saito, Masaru Tomita, and Akio Kanai PMCID: PMC2833159 Homopolymeric tracts represent a general regulatory mechanism in prokaryotes Renato H Orsi, Barbara M Bowen, and Martin Wiedmann PMCID: PMC2831843 Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus Sandip Paul, Anirban Dutta, Sumit K Bag, Sabyasachi Das, and Chitra Dutta PMCID: PMC2836286 Identification and analysis of in planta expressed genes of Magnaporthe oryzae Soonok Kim, Jongsun Park, Sook-Young Park, Thomas K Mitchell, and Yong-Hwan Lee PMCID: PMC2832786 U12 type introns were lost at multiple occasions during evolution Sebastian Bartschat and Tore Samuelsson PMCID: PMC2846911 Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate Georgina A Ankra-Badu, Daniel Shriner, Elisabeth Le Bihan-Duval, Sandrine Mignon-Grasteau, Frédérique Pitel, Catherine Beaumont, Michel J Duclos, Jean Simon, Tom E Porter, Alain Vignal, Larry A Cogburn, David B Allison, Nengjun Yi, and Samuel E Aggrey PMCID: PMC2830984 Genomics based analysis of interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication Jenny Zetterblad, Hong Qian, Sasan Zandi, Robert Månsson, Anna Lagergren, Frida Hansson, David Bryder, Nils Paulsson, and Mikael Sigvardsson PMCID: PMC2830985 Analysis of a normalised expressed sequence tag (EST) library from a key pollinator, the bumblebee Bombus terrestris Ben M Sadd, Michael Kube, Sven Klages, Richard Reinhardt, and Paul Schmid-Hempel PMCID: PMC2838840 Identification of candidates for cyclotide biosynthesis and cyclisation by expressed sequence tag analysis of Oldenlandia affinis Qiaoping Qin, Emily J McCallum, Quentin Kaas, Jan Suda, Ivana Saska, David J Craik, and Joshua S Mylne PMCID: PMC2838841 Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii Adam Labadorf, Alicia Link, Mark F Rogers, Julie Thomas, Anireddy SN Reddy, and Asa Ben-Hur PMCID: PMC2830987 Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum Israel Barrantes, Gernot Glockner, Sonja Meyer, and Wolfgang Marwan PMCID: PMC2837032 Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus Yu-Shin Nai, Chih-Yu Wu, Tai-Chuan Wang, Yun-Ru Chen, Wei-Hong Lau, Chu-Fang Lo, Meng-Feng Tsai, and Chung-Hsiung Wang PMCID: PMC2830988 General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species Marianna Polesani, Luisa Bortesi, Alberto Ferrarini, Anita Zamboni, Marianna Fasoli, Claudia Zadra, Arianna Lovato, Mario Pezzotti, Massimo Delledonne, and Annalisa Polverari PMCID: PMC2831845 Increased incidence of rare codon clusters at 5' and 3' gene termini:implications for function Thomas F Clarke, IV and Patricia L Clark PMCID: PMC2833160 Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus Rebecca L Skalsky, Dana L Vanlandingham, Frank Scholle, Stephen Higgs, and Bryan R Cullen PMCID: PMC2834634 High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak Matthew W Gilmour, Morag Graham, Gary Van Domselaar, Shaun Tyler, Heather Kent, Keri M Trout-Yakel, Oscar Larios, Vanessa Allen, Barbara Lee, and Celine Nadon PMCID: PMC2834635 Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis Hiroaki Sakai and Takeshi Itoh PMCID: PMC2831846 Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species Ming-Cheng Luo, Yaqin Ma, Frank M You, Olin D Anderson, David Kopecký, Hana Šimková, Jan Šafář, Jaroslav Doležel, Bikram Gill, Patrick E McGuire, and Jan Dvorak PMCID: PMC2836288 Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A Michael Widmann, P Benjamin Juhl, and Jürgen Pleiss PMCID: PMC2841678 Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes Nicola J Veitch, Paul CD Johnson, Urmi Trivedi, Sandra Terry, David Wildridge, and Annette MacLeod PMCID: PMC2837033 Comparative gene expression profiling between human cultured myotubes and skeletal muscle tissue Frederic Raymond, Sylviane Métairon, Martin Kussmann, Jaume Colomer, Andres Nascimento, Emma Mormeneo, Cèlia García-Martínez, and Anna M Gómez-Foix PMCID: PMC2838843 Expression profiling of mouse embryonic fibroblasts with a deletion in the helicase domain of the Werner Syndrome gene homologue treated with hydrogen peroxide Adam Labbé, Ramachander VN Turaga, Éric R Paquet, Chantal Garand, and Michel Lebel PMCID: PMC2838845 Defining species specific genome differences in malaria parasites Kingsley JL Liew, Guangan Hu, Zbynek Bozdech, and Preiser R Peter PMCID: PMC2837034 High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus Sofia Berlin, Ulf Lagercrantz, Sara von Arnold, Torbjörn Öst, and Ann Christin Rönnberg-Wästljung PMCID: PMC2834636 Identification and characterization of Tc1/mariner-like DNA transposons in genomes of the pathogenic fungi of the Paracoccidioides species complex Marjorie M Marini, Tamiris Zanforlin, Patrícia C Santos, Roberto RM Barros, Anne CP Guerra, Rosana Puccia, Maria SS Felipe, Marcelo Brigido, Célia MA Soares, Jerônimo C Ruiz, José F Silveira, and Patrícia S Cisalpino PMCID: PMC2836289 Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern Ann M Rose, Nigel J O'Neil, Mikhail Bilenky, Yaron S Butterfield, Nawar Malhis, Stephane Flibotte, Martin R Jones, Marco Marra, David L Baillie, and Steven JM Jones PMCID: PMC2837035 Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations Hsei-Wei Wang, Yu-Hsuan Wu, Jui-Yu Hsieh, Muh-Lii Liang, Meng-En Chao, Da-Jung Liu, Ming-Ta Hsu, and Tai-Tong Wong PMCID: PMC2837036 Comparative analysis of fungal protein kinases and associated domains Idit Kosti, Yael Mandel-Gutfreund, Fabian Glaser, and Benjamin A Horwitz PMCID: PMC2838846 Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles Robert R Kitchen, Vicky S Sabine, Andrew H Sims, E Jane Macaskill, Lorna Renshaw, Jeremy S Thomas, Jano I van Hemert, J Michael Dixon, and John MS Bartlett PMCID: PMC2843619 A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs Jun Hong Xia, Feng Liu, Ze Yuan Zhu, Jianjun Fu, Jianbin Feng, Jiale Li, and Gen Hua Yue PMCID: PMC2838847 Flux of transcript patterns during soybean seed development Sarah I Jones, Delkin O Gonzalez, and Lila O Vodkin PMCID: PMC2846912 Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing Yoshinao Ruike, Yukako Imanaka, Fumiaki Sato, Kazuharu Shimizu, and Gozoh Tsujimoto PMCID: PMC2838848 Escherichia coli infection induces distinct local and systemic transcriptome responses in the mammary gland Simone Mitterhuemer, Wolfram Petzl, Stefan Krebs, Daniel Mehne, Andrea Klanner, Eckhard Wolf, Holm Zerbe, and Helmut Blum PMCID: PMC2846913 Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data Ozren Polašek, Caroline Hayward, Celine Bellenguez, Veronique Vitart, Ivana Kolčić, Ruth McQuillan, Vanja Saftić, Ulf Gyllensten, James F Wilson, Igor Rudan, Alan F Wright, Harry Campbell, and Anne-Louise Leutenegger PMCID: PMC2848240 Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus Takashi Koyama, Shuichi Asakawa, Takayuki Katagiri, Atsushi Shimizu, Fernand F Fagutao, Rapeepat Mavichak, Mudjekeewis D Santos, Kanako Fuji, Takashi Sakamoto, Toshihide Kitakado, Hidehiro Kondo, Nobuyoshi Shimizu, Takashi Aoki, and Ikuo Hirono PMCID: PMC2838849 TobEA: an atlas of tobacco gene expression from seed to senescence Kieron D Edwards, Aureliano Bombarely, Geraint W Story, Fraser Allen, Lukas A Mueller, Steve A Coates, and Louise Jones PMCID: PMC2841117 Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes Melvin J Oliver, Andrew G Murdock, Brent D Mishler, Jennifer V Kuehl, Jeffrey L Boore, Dina F Mandoli, Karin DE Everett, Paul G Wolf, Aaron M Duffy, and Kenneth G Karol PMCID: PMC2841679 Whole genome analysis of p38 SAPK-mediated gene expression upon stress Isabel Ferreiro, Manel Joaquin, Abul Islam, Gonzalo Gomez-Lopez, Montserrat Barragan, Luís Lombardía, Orlando Domínguez, David G Pisano, Nuria Lopez-Bigas, Angel R Nebreda, and Francesc Posas PMCID: PMC2842250 Distribution of candidate genes for experimentally induced arthritis in rats Lars Andersson and Fredrik Ståhl PMCID: PMC2838850 Conservation and divergence of known apicomplexan transcriptional regulons Kobby Essien and Christian J Stoeckert, Jr PMCID: PMC2841118 MicroRNAs of Bombyx mori identified by Solexa sequencing Shiping Liu, Dong Li, Qibin Li, Ping Zhao, Zhonghuai Xiang, and Qingyou Xia PMCID: PMC2838851 Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa Palitha Dharmawardhana, Amy M Brunner, and Steven H Strauss PMCID: PMC2846914 Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements Danilo Licastro, Vincenzo A Gennarino, Francesca Petrera, Remo Sanges, Sandro Banfi, and Elia Stupka PMCID: PMC2847969 Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents Eva C Berglund, Christian Ehrenborg, Olga Vinnere Pettersson, Fredrik Granberg, Kristina Näslund, Martin Holmberg, and Siv GE Andersson PMCID: PMC2847970 Chemogenomic and transcriptome analysis identifies mode of action of the chemosensitizing agent CTBT (7-chlorotetrazolo[5,1-c]benzo[1,2,4]triazine) Monika Batova, Vlasta Klobucnikova, Zuzana Oblasova, Juraj Gregan, Pavol Zahradnik, Ivan Hapala, Julius Subik, and Christoph Schüller PMCID: PMC2841119 Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon Morten F Lukacs, Håvard Harstad, Hege G Bakke, Marianne Beetz-Sargent, Linda McKinnel, Krzysztof P Lubieniecki, Ben F Koop, and Unni Grimholt PMCID: PMC2846915 Unified translation repression mechanism for microRNAs and upstream AUGs Subramanian S Ajay, Brian D Athey, and Inhan Lee PMCID: PMC2842251 Transcriptome profiling of a Sinorhizobium meliloti fadD mutant reveals the role of rhizobactin 1021 biosynthesis and regulation genes in the control of swarming Joaquina Nogales, Ana Domínguez-Ferreras, Carol V Amaya-Gómez, Pieter van Dillewijn, Virginia Cuéllar, Juan Sanjuán, José Olivares, and María J Soto PMCID: PMC2848241 From QTL to candidate gene: Genetical genomics of simple and complex traits in potato using a pooling strategy Bjorn Kloosterman, Marian Oortwijn, Jan uitdeWilligen, Twan America, Ric de Vos, Richard GF Visser, and Christian WB Bachem PMCID: PMC2843620 Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs Junwu Ma, Nathalie Iannuccelli, Yanyu Duan, Weibing Huang, Beili Guo, Juliette Riquet, Lusheng Huang, and Denis Milan PMCID: PMC2850356 Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans) Geoffrey M Attardo, José MC Ribeiro, Yineng Wu, Matthew Berriman, and Serap Aksoy PMCID: PMC2846916 Functional annotation of novel lineage-specific genes using co-expression and promoter analysis Charu G Kumar, Robin E Everts, Juan J Loor, and Harris A Lewin PMCID: PMC2848242 Transcriptional and pathway analysis in the hypothalamus of newly hatched chicks during fasting and delayed feeding Stacy E Higgins, Laura E Ellestad, Nares Trakooljul, Fiona McCarthy, Jason Saliba, Larry A Cogburn, and Tom E Porter PMCID: PMC2848243 Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen Paul W O'Toole, William J Snelling, Carlos Canchaya, Brian M Forde, Kim R Hardie, Christine Josenhans, Robert LJ Graham, Geoff McMullan, Julian Parkhill, Eugenio Belda, and Stephen D Bentley PMCID: PMC2846917 Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery Thomas Neusser, Tino Polen, René Geissen, and Rolf Wagner PMCID: PMC2848244 TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation Virginie Bernard, Véronique Brunaud, and Alain Lecharny PMCID: PMC2842252 Large-scale transcriptome data reveals transcriptional activity of fission yeast LTR retrotransposons Tobias Mourier and Eske Willerslev PMCID: PMC2848245 Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer Brahim Mali, Markus A Grohme, Frank Förster, Thomas Dandekar, Martina Schnölzer, Dirk Reuter, Weronika Wełnicz, Ralph O Schill, and Marcus Frohme PMCID: PMC2848246 A sequence motif enriched in regions bound by the Drosophila dosage compensation complex Miguel Gallach, Vicente Arnau, Rodrigo Aldecoa, and Ignacio Marín PMCID: PMC2848247 The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants Pinja Jaspers, Kirk Overmyer, Michael Wrzaczek, Julia P Vainonen, Tiina Blomster, Jarkko Salojärvi, Ramesha A Reddy, and Jaakko Kangasjärvi PMCID: PMC2848248 Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus Ludovic V Mallet, Jennifer Becq, and Patrick Deschavanne PMCID: PMC2848249 Myosin individualized: single nucleotide polymorphisms in energy transduction Thomas P Burghardt, Kevin L Neff, Eric D Wieben, and Katalin Ajtai PMCID: PMC2848645 Expression profile of cuticular genes of silkworm, Bombyx mori Jiubo Liang, Liang Zhang, Zhonghuai Xiang, and Ningjia He PMCID: PMC2848646 QTL mapping for Mediterranean corn borer resistance in European flint germplasm using recombinant inbred lines Bernardo Ordas, Rosa A Malvar, Rogelio Santiago, and Ana Butron PMCID: PMC2841681 The embryonic genes Dkk3, Hoxd8, Hoxd9 and Tbx1 identify muscle types in a diet-independent and fiber-type unrelated way Janneke de Wilde, Martijn FM Hulshof, Mark V Boekschoten, Philip de Groot, Egbert Smit, and Edwin CM Mariman PMCID: PMC2847971 Phylogenetic analysis of fungal ABC transporters Andriy Kovalchuk and Arnold JM Driessen PMCID: PMC2848647 Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions Wei-Hua Chen, Juliette de Meaux, and Martin J Lercher PMCID: PMC2851598 Characterization of the ovine ribosomal protein SA gene and its pseudogenes Alice Van den Broeke, Mario Van Poucke, Ane Marcos-Carcavilla, Karine Hugot, Hélène Hayes, Maud Bertaud, Alex Van Zeveren, and Luc J Peelman PMCID: PMC2850357 Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery Thomas L Parchman, Katherine S Geist, Johan A Grahnen, Craig W Benkman, and C Alex Buerkle PMCID: PMC2851599 Legionella pneumophila pangenome reveals strain-specific virulence factors Giuseppe D'Auria, Nuria Jiménez-Hernández, Francesc Peris-Bondia, Andrés Moya, and Amparo Latorre PMCID: PMC2859405 Chromosomal evolution in the plant family Solanaceae Feinan Wu and Steven D Tanksley PMCID: PMC2847972 Complementary transcriptomic, lipidomic, and targeted functional genetic analyses in cultured Drosophila cells highlight the role of glycerophospholipid metabolism in Flock House virus RNA replication Kathryn M Castorena, Kenneth A Stapleford, and David J Miller PMCID: PMC2847973 Synteny mapping between common bean and soybean reveals extensive blocks of shared loci Phillip E McClean, Sujan Mamidi, Melody McConnell, Shireen Chikara, and Rian Lee PMCID: PMC2851600 Differential expression of genes in salivary glands of male Rhipicephalus (Boophilus)microplus in response to infection with Anaplasma marginale Zorica Zivkovic, Eliane Esteves, Consuelo Almazán, Sirlei Daffre, Ard M Nijhof, Katherine M Kocan, Frans Jongejan, and José de la Fuente PMCID: PMC2848250 Antimicrobial peptide-like genes in Nasonia vitripennis: a genomic perspective Caihuan Tian, Bin Gao, Qi Fang, Gongyin Ye, and Shunyi Zhu PMCID: PMC2853521 Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana Liam H Childs, Hanna Witucka-Wall, Torsten Günther, Ronan Sulpice, Maria V Korff, Mark Stitt, Dirk Walther, Karl J Schmid, and Thomas Altmann PMCID: PMC2850358 Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome Ralph Kissen, Per Winge, Diem Hong Thi Tran, Tommy S Jørstad, Trond R Størseth, Tone Christensen, and Atle M Bones PMCID: PMC2858750 Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua) Sophie Hubert, Brent Higgins, Tudor Borza, and Sharen Bowman PMCID: PMC2846918 Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles Annabelle Monnier, Silvia Liverani, Régis Bouvet, Béline Jesson, Jim Q Smith, Jean Mosser, Florence Corellou, and François-Yves Bouget PMCID: PMC2850359 Use of microarray technology to assess the time course of liver stress response after confinement exposure in gilthead sea bream (Sparus aurata L.) Josep A Calduch-Giner, Grace Davey, Alfonso Saera-Vila, Benoit Houeix, Anita Talbot, Patrick Prunet, Michael T Cairns, and Jaume Pérez-Sánchez PMCID: PMC2860363 Evidence of perturbations of cell cycle and DNA repair pathways as a consequence of human and murine NF1-haploinsufficiency Alexander Pemov, Caroline Park, Karlyne M Reilly, and Douglas R Stewart PMCID: PMC2858150 Molecular and evolutionary characteristics of the fraction of human alpha satellite DNA associated with CENP-A at the centromeres of chromosomes 1, 5, 19, and 21 Nathalie Pironon, Jacques Puechberty, and Gérard Roizès PMCID: PMC2853522 Reciprocal regulation of metabolic and signaling pathways Andreas S Barth, Ami Kumordzie, Carlo Colantuoni, Kenneth B Margulies, Thomas P Cappola, and Gordon F Tomaselli PMCID: PMC2861677 Genome-wide comparative analysis of metacaspases in unicellular and filamentous cyanobacteria Qiao Jiang, Song Qin, and Qing-yu Wu PMCID: PMC2853523 Transcriptome analysis reveals a major impact of JAK protein tyrosine kinase 2 (Tyk2) on the expression of interferon-responsive and metabolic genes Claus Vogl, Thomas Flatt, Bernd Fuhrmann, Elisabeth Hofmann, Barbara Wallner, Rita Stiefvater, Pavel Kovarik, Birgit Strobl, and Mathias Müller PMCID: PMC2864243 Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles Yongtao Xue-Franzén, Anna Johnsson, David Brodin, Johan Henriksson, Thomas R Bürglin, and Anthony PH Wright PMCID: PMC2861062 Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor Mohammad T Alam, Maria E Merlo, The STREAM Consortium, David A Hodgson, Elizabeth MH Wellington, Eriko Takano, and Rainer Breitling PMCID: PMC2853524 Downregulation of genes with a function in axon outgrowth and synapse formation in motor neurones of the VEGFδ/δ mouse model of amyotrophic lateral sclerosis Alice Brockington, Paul R Heath, Hazel Holden, Paul Kasher, Florian LP Bender, Filip Claes, Diether Lambrechts, Michael Sendtner, Peter Carmeliet, and Pamela J Shaw PMCID: PMC2861063 Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar Simone Scalabrin, Michela Troggio, Marco Moroldo, Massimo Pindo, Nicoletta Felice, Giuseppina Coppola, Giacomo Prete, Giulia Malacarne, Raffaella Marconi, Giorgia Faes, Irena Jurman, Stella Grando, Taco Jesse, Cinzia Segala, Giorgio Valle, Alberto Policriti, Paolo Fontana, Michele Morgante, and Riccardo Velasco PMCID: PMC2865496 The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues Peter Lorenz, Sabine Dietmann, Thomas Wilhelm, Dirk Koczan, Sandra Autran, Sophie Gad, Gaiping Wen, Guohui Ding, Yixue Li, Marie-Françoise Rousseau-Merck, and Hans-Juergen Thiesen PMCID: PMC2865497 The response to unfolded protein is involved in osmotolerance of Pichia pastoris Martin Dragosits, Johannes Stadlmann, Alexandra Graf, Brigitte Gasser, Michael Maurer, Michael Sauer, David P Kreil, Friedrich Altmann, and Diethard Mattanovich PMCID: PMC2867824 Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes Lokesh Kumar, Andrew Breakspear, Corby Kistler, Li-Jun Ma, and Xiaohui Xie PMCID: PMC2853525 Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes Sota Fujii, Tomohiko Kazama, Mari Yamada, and Kinya Toriyama PMCID: PMC2851602 Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics Koh Aoki, Kentaro Yano, Ayako Suzuki, Shingo Kawamura, Nozomu Sakurai, Kunihiro Suda, Atsushi Kurabayashi, Tatsuya Suzuki, Taneaki Tsugane, Manabu Watanabe, Kazuhide Ooga, Maiko Torii, Takanori Narita, Tadasu Shin-i, Yuji Kohara, Naoki Yamamoto, Hideki Takahashi, Yuichiro Watanabe, Mayumi Egusa, Motoichiro Kodama, Yuki Ichinose, Mari Kikuchi, Sumire Fukushima, Akiko Okabe, Tsutomu Arie, Yuko Sato, Katsumi Yazawa, Shinobu Satoh, Toshikazu Omura, Hiroshi Ezura, and Daisuke Shibata PMCID: PMC2859864 Mercury-induced hepatotoxicity in zebrafish: in vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation Choong Yong Ung, Siew Hong Lam, Mya Myintzu Hlaing, Cecilia Lanny Winata, Svetlana Korzh, Sinnakaruppan Mathavan, and Zhiyuan Gong PMCID: PMC2862047 An insight into the sialome of Glossina morsitans morsitans Juliana Alves-Silva, José MC Ribeiro, Jan Van Den Abbeele, Geoffrey Attardo, Zhengrong Hao, Lee R Haines, Marcelo B Soares, Matthew Berriman, Serap Aksoy, and Michael J Lehane PMCID: PMC2853526 Evidence for a lineage of virulent bacteriophages that target Campylobacter Andrew R Timms, Joanna Cambray-Young, Andrew E Scott, Nicola K Petty, Phillippa L Connerton, Louise Clarke, Kathy Seeger, Mike Quail, Nicola Cummings, Duncan J Maskell, Nicholas R Thomson, and Ian F Connerton PMCID: PMC2853527 Functional genomics of mountain pine beetle (Dendroctonus ponderosae) midguts and fat bodies Tidiane Aw, Karen Schlauch, Christopher I Keeling, Sharon Young, Jeremy C Bearfield, Gary J Blomquist, and Claus Tittiger PMCID: PMC2858752 Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology Jean-Philippe David, Eric Coissac, Christelle Melodelima, Rodolphe Poupardin, Muhammad Asam Riaz, Alexia Chandor-Proust, and Stéphane Reynaud PMCID: PMC2867825 Comparative genomics of metabolic networks of free-living and parasitic eukaryotes Barbara Nerima, Daniel Nilsson, and Pascal Mäser PMCID: PMC2858753 A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata) Alexander D Ball, Jessica Stapley, Deborah A Dawson, Tim R Birkhead, Terry Burke, and Jon Slate PMCID: PMC2864244 Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals Víctor Quesada, Gloria Velasco, Xose S Puente, Wesley C Warren, and Carlos López-Otín PMCID: PMC2865498 Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes Maria A Doyle, Robin B Gasser, Ben J Woodcroft, Ross S Hall, and Stuart A Ralph PMCID: PMC2867826 Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects Dominik Lutter, Carsten Marr, Jan Krumsiek, Elmar W Lang, and Fabian J Theis PMCID: PMC2865499 Differential transcript expression between the microfilariae of the filarial nematodes, Brugia malayi and B. pahangi Michael M Kariuki, Leonard B Hearne, and Brenda T Beerntsen PMCID: PMC2874553 Genome-wide comparison between IL-17 and combined TNF-alpha/IL-17 induced genes in primary murine hepatocytes Titus Sparna, Julia Rétey, Kathrin Schmich, Ute Albrecht, Katrin Naumann, Norbert Gretz, Hans-Peter Fischer, Johannes G Bode, and Irmgard Merfort PMCID: PMC2858152 Survey of transcripts expressed by the invasive juvenile stage of the liver fluke Fasciola hepatica Martín Cancela, Natalia Ruétalo, Nicolás Dell'Oca, Edileuza da Silva, Pablo Smircich, Gabriel Rinaldi, Leda Roche, Carlos Carmona, Fernando Alvarez-Valín, Arnaldo Zaha, and José F Tort PMCID: PMC2867827 The Alveolate Perkinsus marinus: Biological Insights from EST Gene Discovery Sandeep J Joseph, José A Fernández-Robledo, Malcolm J Gardner, Najib M El-Sayed, Chih-Horng Kuo, Eric J Schott, Haiming Wang, Jessica C Kissinger, and Gerardo R Vasta PMCID: PMC2868825 Age-related molecular genetic changes of murine bone marrow mesenchymal stem cells Amber Wilson, Lina A Shehadeh, Hong Yu, and Keith A Webster PMCID: PMC2873471 Whole transcriptome analysis of the hippocampus: toward a molecular portrait of epileptogenesis Oswaldo K Okamoto, Luciana Janjoppi, Felipe M Bonone, Aline P Pansani, Alexandre V da Silva, Fúlvio A Scorza, and Esper A Cavalheiro PMCID: PMC2859406 Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants Olga Novikova, Georgiy Smyshlyaev, and Alexander Blinov PMCID: PMC2864245 Identification of copy number variations and common deletion polymorphisms in cattle Joon Seol Bae, Hyun Sub Cheong, Lyoung Hyo Kim, Suk NamGung, Tae Joon Park, Ji-Yong Chun, Jason Yongha Kim, Charisse Flerida A Pasaje, Jin Sol Lee, and Hyoung Doo Shin PMCID: PMC2859865 A scenario of mitochondrial genome evolution in maize based on rearrangement events Aude Darracq, Jean-Stéphane Varré, and Pascal Touzet PMCID: PMC2859866 Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa Andreas Dötsch, Frank Klawonn, Michael Jarek, Maren Scharfe, Helmut Blöcker, and Susanne Häussler PMCID: PMC2864246 Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels John VW Becker, Linda Mtwisha, Bridget G Crampton, Stoyan Stoychev, Anna C van Brummelen, Shaun Reeksting, Abraham I Louw, Lyn-Marie Birkholtz, and Dalu T Mancama PMCID: PMC2867828 A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae Daniel C Koboldt, Julia Staisch, Bavithra Thillainathan, Karen Haines, Scott E Baird, Helen M Chamberlin, Eric S Haag, Raymond D Miller, and Bhagwati P Gupta PMCID: PMC2864247 Thioredoxin and glutathione systems differ in parasitic and free-living platyhelminths Lucía Otero, Mariana Bonilla, Anna V Protasio, Cecilia Fernández, Vadim N Gladyshev, and Gustavo Salinas PMCID: PMC2873472 Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii Leandro M Moreira, Nalvo F Almeida, Jr, Neha Potnis, Luciano A Digiampietri, Said S Adi, Julio C Bortolossi, Ana C da Silva, Aline M da Silva, Fabrício E de Moraes, Julio C de Oliveira, Robson F de Souza, Agda P Facincani, André L Ferraz, Maria I Ferro, Luiz R Furlan, Daniele F Gimenez, Jeffrey B Jones, Elliot W Kitajima, Marcelo L Laia, Rui P Leite, Jr, Milton Y Nishiyama, Julio Rodrigues Neto, Letícia A Nociti, David J Norman, Eric H Ostroski, Haroldo A Pereira, Jr, Brian J Staskawicz, Renata I Tezza, Jesus A Ferro, Boris A Vinatzer, and João C Setubal PMCID: PMC2883993 Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island Willem van Schaik, Janetta Top, David R Riley, Jos Boekhorst, Joyce EP Vrijenhoek, Claudia ME Schapendonk, Antoni PA Hendrickx, Isaäc J Nijman, Marc JM Bonten, Hervé Tettelin, and Rob JL Willems PMCID: PMC2858755 Genes related to the very early stage of ConA-induced fulminant hepatitis: a gene-chip-based study in a mouse model Feng Chen, Hai-Hong Zhu, Lin-Fu Zhou, Jie Li, Li-Ying Zhao, Shan-Shan Wu, Jing Wang, Wei Liu, and Zhi Chen PMCID: PMC2867829 Signal pathways JNK and NF-κB, identified by global gene expression profiling, are involved in regulation of TNFα-induced mPGES-1 and COX-2 expression in gingival fibroblasts Tove Båge, Johan Lindberg, Joakim Lundeberg, Thomas Modéer, and Tülay Yucel-Lindberg PMCID: PMC2873473 Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data Yukari Nishito, Yasunori Osana, Tsuyoshi Hachiya, Kris Popendorf, Atsushi Toyoda, Asao Fujiyama, Mitsuhiro Itaya, and Yasubumi Sakakibara PMCID: PMC2867830 A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti Jan-Philip Schlüter, Jan Reinkensmeier, Svenja Daschkey, Elena Evguenieva-Hackenberg, Stefan Janssen, Sebastian Jänicke, Jörg D Becker, Robert Giegerich, and Anke Becker PMCID: PMC2873474 Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type Qiang Xu, Yuanlong Liu, Andan Zhu, Xiaomeng Wu, Junli Ye, Keqin Yu, Wenwu Guo, and Xiuxin Deng PMCID: PMC2864249 The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation Qi-Long Qin, Xi-Ying Zhang, Xu-Min Wang, Gui-Ming Liu, Xiu-Lan Chen, Bin-Bin Xie, Hong-Yue Dang, Bai-Cheng Zhou, Jun Yu, and Yu-Zhong Zhang PMCID: PMC2864250 Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum Ines Yang, Uwe John, Sára Beszteri, Gernot Glöckner, Bernd Krock, Alexander Goesmann, and Allan D Cembella PMCID: PMC2874808 Small RNA expression and strain specificity in the rat Sam EV Linsen, Elzo de Wit, Ewart de Bruijn, and Edwin Cuppen PMCID: PMC2864251 The DUB/USP17 deubiquitinating enzymes: A gene family within a tandemly repeated sequence, is also embedded within the copy number variable Beta-defensin cluster James F Burrows, Christopher J Scott, and James A Johnston PMCID: PMC2874809 Transcriptome sequencing and development of an expression microarray platform for the domestic ferret Carl E Bruder, Suxia Yao, Francis Larson, Jeremy V Camp, Ronald Tapp, Alexis McBrayer, Nicholas Powers, Willy Valdivia Granda, and Colleen B Jonsson PMCID: PMC2873475 Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing Stefan Taudien, Marco Groth, Klaus Huse, Andreas Petzold, Karol Szafranski, Jochen Hampe, Philip Rosenstiel, Stefan Schreiber, and Matthias Platzer PMCID: PMC2873476 Gene expression changes in mononuclear cells in patients with metabolic syndrome after acute intake of phenol-rich virgin olive oil Antonio Camargo, Juan Ruano, Juan M Fernandez, Laurence D Parnell, Anabel Jimenez, Monica Santos-Gonzalez, Carmen Marin, Pablo Perez-Martinez, Marino Uceda, Jose Lopez-Miranda, and Francisco Perez-Jimenez PMCID: PMC2874810 Genome response to tissue plasminogen activator in experimental ischemic stroke Glen C Jickling, Xinhua Zhan, Bradley P Ander, Renée J Turner, Boryana Stamova, Huichun Xu, Yingfang Tian, Dazhi Liu, Ryan R Davis, Paul A Lapchak, and Frank R Sharp PMCID: PMC2875237 Reconstruction of xylose utilization pathway and regulons in Firmicutes Yang Gu, Yi Ding, Cong Ren, Zhe Sun, Dmitry A Rodionov, Weiwen Zhang, Sheng Yang, Chen Yang, and Weihong Jiang PMCID: PMC2873477 Validation of a mouse xenograft model system for gene expression analysis of human acute lymphoblastic leukaemia Amy L Samuels, Violet K Peeva, Rachael A Papa, Marin J Firth, Richard W Francis, Alex H Beesley, Richard B Lock, and Ursula R Kees PMCID: PMC2876122 Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns Anton Kratz, Erik Arner, Rintaro Saito, Atsutaka Kubosaki, Jun Kawai, Harukazu Suzuki, Piero Carninci, Takahiro Arakawa, Masaru Tomita, Yoshihide Hayashizaki, and Carsten O Daub PMCID: PMC2867832 Large genomic differences between the morphologically indistinguishable diplomonads Spironucleus barkhanus and Spironucleus salmonicida Katarina Roxström-Lindquist, Jon Jerlström-Hultqvist, Anders Jørgensen, Karin Troell, Staffan G Svärd, and Jan O Andersson PMCID: PMC2874811 Major role for mRNA stability in shaping the kinetics of gene induction Ran Elkon, Eitan Zlotorynski, Karen I Zeller, and Reuven Agami PMCID: PMC2864252 Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis Ingrid Lafontaine and Bernard Dujon PMCID: PMC2876123 Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes Jianping Wang, Bruce Roe, Simone Macmil, Qingyi Yu, Jan E Murray, Haibao Tang, Cuixia Chen, Fares Najar, Graham Wiley, John Bowers, Marie-Anne Van Sluys, Daniel S Rokhsar, Matthew E Hudson, Stephen P Moose, Andrew H Paterson, and Ray Ming PMCID: PMC2882929 De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis Chao Sun, Ying Li, Qiong Wu, Hongmei Luo, Yongzhen Sun, Jingyuan Song, Edmund MK Lui, and Shilin Chen PMCID: PMC2873478 Aryl hydrocarbon receptor (AHR)-regulated transcriptomic changes in rats sensitive or resistant to major dioxin toxicities Ivy D Moffat, Paul C Boutros, Hanbo Chen, Allan B Okey, and Raimo Pohjanvirta PMCID: PMC2881023 Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation Frank-Dietrich Müller, Anke Treuner-Lange, Johann Heider, Stuart M Huntley, and Penelope I Higgs PMCID: PMC2875238 Chronic activation of the epithelial immune system of the fruit fly's salivary glands has a negative effect on organismal growth and induces a peculiar set of target genes Ahmed Abdelsadik and Thomas Roeder PMCID: PMC2874812 Differences in transcription between free-living and CO2-activated third-stage larvae of Haemonchus contortus Cinzia Cantacessi, Bronwyn E Campbell, Neil D Young, Aaron R Jex, Ross S Hall, Paul JA Presidente, Jodi L Zawadzki, Weiwei Zhong, Boanerges Aleman-Meza, Alex Loukas, Paul W Sternberg, and Robin B Gasser PMCID: PMC2880303 Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms Toshio Yamamoto, Hideki Nagasaki, Jun-ichi Yonemaru, Kaworu Ebana, Maiko Nakajima, Taeko Shibaya, and Masahiro Yano PMCID: PMC2874813 EST analysis reveals putative genes involved in glycyrrhizin biosynthesis Ying Li, Hong-Mei Luo, Chao Sun, Jing-Yuan Song, Yong-Zhen Sun, Qiong Wu, Ning Wang, Hui Yao, André Steinmetz, and Shi-Lin Chen PMCID: PMC2886062 High-throughput marker discovery in melon using a self-designed oligo microarray Ron Ophir, Ravit Eshed, Rotem Harel-Beja, Galil Tzuri, Vitaly Portnoy, Yoseph Burger, Shai Uliel, Nurit Katzir, and Amir Sherman PMCID: PMC2874814 Genomic organization of eukaryotic tRNAs Clara Bermudez-Santana, Camille Stephan-Otto Attolini, Toralf Kirsten, Jan Engelhardt, Sonja J Prohaska, Stephan Steigele, and Peter F Stadler PMCID: PMC2888827 Deciphering the porcine intestinal microRNA transcriptome Soroush Sharbati, Marc R Friedländer, Jutta Sharbati, Lena Hoeke, Wei Chen, Andreas Keller, Peer F Stähler, Nikolaus Rajewsky, and Ralf Einspanier PMCID: PMC2873480 A survey of well conserved families of C2H2 zinc-finger genes in Daphnia Arun Seetharam, Yang Bai, and Gary W Stuart PMCID: PMC2889900 An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags Bo-Young Lee, Aimee E Howe, Matthew A Conte, Helena D'Cotta, Elodie Pepey, Jean-Francois Baroiller, Federica di Palma, Karen L Carleton, and Thomas D Kocher PMCID: PMC2874815 Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome Jong S Leong, Stuart G Jantzen, Kristian R von Schalburg, Glenn A Cooper, Amber M Messmer, Nancy Y Liao, Sarah Munro, Richard Moore, Robert A Holt, Steven JM Jones, William S Davidson, and Ben F Koop PMCID: PMC2886063 Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus) Marco Antonio Machado, Ana Luisa S Azevedo, Roberto L Teodoro, Maria A Pires, Maria Gabriela CD Peixoto, Célio de Freitas, Márcia Cristina A Prata, John Furlong, Marcos Vinicius GB da Silva, Simone EF Guimarães, Luciana CA Regitano, Luiz L Coutinho, Gustavo Gasparin, and Rui S Verneque PMCID: PMC2880304 Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum Fabrice Legeai, Guillaume Rizk, Thomas Walsh, Owain Edwards, Karl Gordon, Dominique Lavenier, Nathalie Leterme, Agnès Méreau, Jacques Nicolas, Denis Tagu, and Stéphanie Jaubert-Possamai PMCID: PMC2880305 A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling James R Bradford, Yvonne Hey, Tim Yates, Yaoyong Li, Stuart D Pepper, and Crispin J Miller PMCID: PMC2877694 Genome-wide in silico screen for CCCH-type zinc finger proteins of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major Susanne Kramer, Nicola C Kimblin, and Mark Carrington PMCID: PMC2873481 Copy number variation in the bovine genome João Fadista, Bo Thomsen, Lars-Erik Holm, and Christian Bendixen PMCID: PMC2902221 Frequent and recent retrotransposition of orthologous genes plays a role in the evolution of sperm glycolytic enzymes Soumya A Vemuganti, Fernando Pardo-Manuel de Villena, and Deborah A O'Brien PMCID: PMC2881024 Most transcription factor binding sites are in a few mosaic classes of the human genome Kenneth J Evans PMCID: PMC2881025 Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood Candida Vaz, Hafiz M Ahmad, Pratibha Sharma, Rashi Gupta, Lalit Kumar, Ritu Kulshreshtha, and Alok Bhattacharya PMCID: PMC2885365 In silico identification of the sea squirt selenoproteome Liang Jiang, Qiong Liu, and Jiazuan Ni PMCID: PMC2874816 Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser David A Fitzpatrick, Peadar O'Gaora, Kevin P Byrne, and Geraldine Butler PMCID: PMC2880306 Computational prediction of the osmoregulation network in Synechococcus sp. WH8102 Xizeng Mao, Victor Olman, Rhona Stuart, Ian T Paulsen, Brian Palenik, and Ying Xu PMCID: PMC2874817 Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response Yu Gao, Laurence Flori, Jérome Lecardonnel, Diane Esquerré, Zhi-Liang Hu, Angélique Teillaud, Gaëtan Lemonnier, Francois Lefèvre, Isabelle P Oswald, and Claire Rogel-Gaillard PMCID: PMC2881026 Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster Patricia Jumbo-Lucioni, Julien F Ayroles, Michelle Moses Chambers, Katherine W Jordan, Jeff Leips, Trudy FC Mackay, and Maria De Luca PMCID: PMC2880307 Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma Candy Kumps, Nadine Van Roy, Lien Heyrman, Dirk Goossens, Jurgen Del-Favero, Rosa Noguera, Jo Vandesompele, Frank Speleman, and Katleen De Preter PMCID: PMC2879279 A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis Marnix H Medema, Miaomiao Zhou, Sacha AFT van Hijum, Jolein Gloerich, Hans JCT Wessels, Roland J Siezen, and Marc Strous PMCID: PMC2881027 Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome Julie Lamontagne, Maxime Béland, Anik Forest, Alexandra Côté-Martin, Najib Nassif, Fadi Tomaki, Ignacio Moriyón, Edgardo Moreno, and Eustache Paramithiotis PMCID: PMC2877026 Massively parallel pyrosequencing-based transcriptome analyses of small brown planthopper (Laodelphax striatellus), a vector insect transmitting rice stripe virus (RSV) Fujie Zhang, Hongyan Guo, Huajun Zheng, Tong Zhou, Yijun Zhou, Shengyue Wang, Rongxiang Fang, Wei Qian, and Xiaoying Chen PMCID: PMC2885366 A critical assessment of cross-species detection of gene duplicates using comparative genomic hybridization Heather E Machado and Suzy CP Renn PMCID: PMC2876127 Comparison and consolidation of microarray data sets of human tissue expression Jenny Russ and Matthias E Futschik PMCID: PMC2885367 Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation Zhengyuan Wang, Sahar Abubucker, John Martin, Richard K Wilson, John Hawdon, and Makedonka Mitreva PMCID: PMC2882930 GC3 biology in corn, rice, sorghum and other grasses Tatiana V Tatarinova, Nickolai N Alexandrov, John B Bouck, and Kenneth A Feldmann PMCID: PMC2895627 Effects of Alu elements on global nucleosome positioning in the human genome Yoshiaki Tanaka, Riu Yamashita, Yutaka Suzuki, and Kenta Nakai PMCID: PMC2878307 Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon Shawn T O'Neil, Jason DK Dzurisin, Rory D Carmichael, Neil F Lobo, Scott J Emrich, and Jessica J Hellmann PMCID: PMC2887415 Plasmodium infection alters Anopheles gambiae detoxification gene expression Rute C Félix, Pie Müller, Vera Ribeiro, Hilary Ranson, and Henrique Silveira PMCID: PMC2885368 The collapse of gene complement following whole genome duplication David Sankoff, Chunfang Zheng, and Qian Zhu PMCID: PMC2896955 Gene expression changes during caste-specific neuronal development in the damp-wood termite Hodotermopsis sjostedti Yuki Ishikawa, Yasukazu Okada, Asano Ishikawa, Hitoshi Miyakawa, Shigeyuki Koshikawa, and Toru Miura PMCID: PMC2887416 A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masanori Kawakita, Takayuki Sakaguchi, and Nori Kurata PMCID: PMC2885369 Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif Dale Godfrey, Henrik Böhlenius, Carsten Pedersen, Ziguo Zhang, Jeppe Emmersen, and Hans Thordal-Christensen PMCID: PMC2886064 Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome Vladimir N Babenko, Igor V Makunin, Irina V Brusentsova, Elena S Belyaeva, Daniil A Maksimov, Stepan N Belyakin, Peter Maroy, Lyubov A Vasil'eva, and Igor F Zhimulev PMCID: PMC2887417 A deep investigation into the adipogenesis mechanism: Profile of microRNAs regulating adipogenesis by modulating the canonical Wnt/β-catenin signaling pathway Limei Qin, Yaosheng Chen, Yuna Niu, Weiquan Chen, Qiwei Wang, Shuqi Xiao, Anning Li, Ying Xie, Jing Li, Xiao Zhao, Zuyong He, and Delin Mo PMCID: PMC2895628 Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture Shuwei Li, Ching-Hua Shih, and Michael H Kohn PMCID: PMC2891614 Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes S Samuel Yang, Wayne Wenzhong Xu, Mesfin Tesfaye, JoAnn FS Lamb, Hans-Joachim G Jung, Kathryn A VandenBosch, Carroll P Vance, and John W Gronwald PMCID: PMC2893600 Genomic profiling of tumor initiating prostatospheres Maria Ana Duhagon, Elaine M Hurt, Jose R Sotelo-Silveira, Xiaohu Zhang, and William L Farrar PMCID: PMC2900264 Metabolic flexibility revealed in the genome of the cyst-forming α-1 proteobacterium Rhodospirillum centenum Yih-Kuang Lu, Jeremiah Marden, Mira Han, Wesley D Swingley, Stephen D Mastrian, Sugata Roy Chowdhury, Jicheng Hao, Tamer Helmy, Sun Kim, Ahmet A Kurdoglu, Heather J Matthies, David Rollo, Paul Stothard, Robert E Blankenship, Carl E Bauer, and Jeffrey W Touchman PMCID: PMC2890560 Genetic Structure of the Spanish Population Javier Gayán, José J Galan, Antonio González-Pérez, María Eugenia Sáez, María Teresa Martínez-Larrad, Carina Zabena, M Carmen Rivero, Ana Salinas, Reposo Ramírez-Lorca, Francisco J Morón, Jose Luis Royo, Concha Moreno-Rey, Juan Velasco, José M Carrasco, Eva Molero, Carolina Ochoa, María Dolores Ochoa, Marta Gutiérrez, Mercedes Reina, Rocío Pascual, Alejandro Romo-Astorga, Juan Luis Susillo-González, Enrique Vázquez, Luis M Real, Agustín Ruiz, and Manuel Serrano-Ríos PMCID: PMC2887418 Prediction of CpG-island function: CpG clustering vs. sliding-window methods Michael Hackenberg, Guillermo Barturen, Pedro Carpena, Pedro L Luque-Escamilla, Christopher Previti, and José L Oliver PMCID: PMC2887419 Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii Jochen Schmid, Dirk Müller-Hagen, Thomas Bekel, Laura Funk, Ulf Stahl, Volker Sieber, and Vera Meyer PMCID: PMC2887420 Cross-platform analysis of global microRNA expression technologies Carole L Yauk, Andrea Rowan-Carroll, John DH Stead, and Andrew Williams PMCID: PMC2890562 Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development Paola Piantoni, Massimo Bionaz, Daniel E Graugnard, Kristy M Daniels, Robin E Everts, Sandra L Rodriguez-Zas, Harris A Lewin, Hurley L Hurley, Michael Akers, and Juan J Loor PMCID: PMC2890563 Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics Luis David Alcaraz, Gabriel Moreno-Hagelsieb, Luis E Eguiarte, Valeria Souza, Luis Herrera-Estrella, and Gabriela Olmedo PMCID: PMC2890564 Benzo(a)pyrene induces similar gene expression changes in testis of DNA repair proficient and deficient mice Nicole Verhofstad, Jeroen LA Pennings, Conny ThM van Oostrom, Jan van Benthem, Frederik J van Schooten, Harry van Steeg, and Roger WL Godschalk PMCID: PMC2887421 Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius) Takahito Shikano, Jetty Ramadevi, Yukinori Shimada, and Juha Merilä PMCID: PMC2891615 A deletion mutation in bovine SLC4A2 is associated with osteopetrosis in Red Angus cattle Stacey N Meyers, Tara G McDaneld, Shannon L Swist, Brandy M Marron, David J Steffen, Donal O'Toole, Jeffrey R O'Connell, Jonathan E Beever, Tad S Sonstegard, and Timothy PL Smith PMCID: PMC2891616 Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa Li Q Wei, Wen Y Xu, Zhu Y Deng, Zhen Su, Yongbiao Xue, and Tai Wang PMCID: PMC2895629 Generation of a BAC-based physical map of the melon genome Víctor M González, Jordi Garcia-Mas, Pere Arús, and Pere Puigdomènech PMCID: PMC2894041 Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning Heather A Amthauer and Costas Tsatsoulis PMCID: PMC2890565 Factorial microarray analysis of zebra mussel (Dreissena polymorpha: Dreissenidae, Bivalvia) adhesion Wei Xu and Mohamed Faisal PMCID: PMC2894042 Bioinformatic identification and characterization of human endothelial cell-restricted genes Manoj Bhasin, Lei Yuan, Derin B Keskin, Hasan H Otu, Towia A Libermann, and Peter Oettgen PMCID: PMC2887814 Regulation of the cardiomyocyte transcriptome vs translatome by endothelin-1 and insulin: translational regulation of 5' terminal oligopyrimidine tract (TOP) mRNAs by insulin Thomais Markou, Andrew K Marshall, Timothy E Cullingford, El L Tham, Peter H Sugden, and Angela Clerk PMCID: PMC2900265 Transcriptomic analysis of dystrophin RNAi knockdown reveals a central role for dystrophin in muscle differentiation and contractile apparatus organization Mohammad M Ghahramani Seno, Capucine Trollet, Takis Athanasopoulos, Ian R Graham, Pingzhao Hu, and George Dickson PMCID: PMC2890566 Germline-dependent gene expression in distant non-gonadal somatic tissues of Drosophila Michael J Parisi, Vaijayanti Gupta, David Sturgill, James T Warren, Jean-Marc Jallon, John H Malone, Yu Zhang, Lawrence I Gilbert, and Brian Oliver PMCID: PMC2887422 Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays Ranjit Kumar, Pratik Shah, Edwin Swiatlo, Shane C Burgess, Mark L Lawrence, and Bindu Nanduri PMCID: PMC2887815 Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity Serena Ferraresso, Massimo Milan, Caterina Pellizzari, Nicola Vitulo, Richard Reinhardt, Adelino VM Canario, Tomaso Patarnello, and Luca Bargelloni PMCID: PMC2889902 Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes Francesca Orso, Davide Corà, Benedetta Ubezio, Paolo Provero, Michele Caselle, and Daniela Taverna PMCID: PMC2890567 Identification and analysis of immune-related transcriptome in Asian seabass Lates calcarifer Jun Hong Xia and Gen Hua Yue PMCID: PMC2893601 Copy number variation and cytidine analogue cytotoxicity: A genome-wide association approach Krishna R Kalari, Scott J Hebbring, High Seng Chai, Liang Li, Jean-Pierre A Kocher, Liewei Wang, and Richard M Weinshilboum PMCID: PMC2894803 Functional genomics of human bronchial epithelial cells directly interacting with conidia of Aspergillus fumigatus Pol Gomez, Tillie L Hackett, Margo M Moore, Darryl A Knight, and Scott J Tebbutt PMCID: PMC2897809 Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor Raoul Frijters, Wilco Fleuren, Erik JM Toonen, Jan P Tuckermann, Holger M Reichardt, Hans van der Maaden, Andrea van Elsas, Marie-Jose van Lierop, Wim Dokter, Jacob de Vlieg, and Wynand Alkema PMCID: PMC2895630 Transcriptomic responses in mouse brain exposed to chronic excess of the neurotransmitter glutamate Xinkun Wang, Xiaodong Bao, Ranu Pal, Abdulbaki Agbas, and Elias K Michaelis PMCID: PMC2896956 Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background Harry A Noyes, Morris Agaba, Susan Anderson, Alan L Archibald, Andy Brass, John Gibson, Laurence Hall, Helen Hulme, Sung Jong Oh, and Stephen Kemp PMCID: PMC2896378 Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing Melody S Clark, Michael AS Thorne, Florbela A Vieira, João CR Cardoso, Deborah M Power, and Lloyd S Peck PMCID: PMC2896379 The expression of genes coding for distinct types of glycine-rich proteins varies according to the biology of three metastriate ticks, Rhipicephalus (Boophilus) microplus, Rhipicephalus sanguineus and Amblyomma cajennense Sandra R Maruyama, Elen Anatriello, Jennifer M Anderson, José M Ribeiro, Lucinda G Brandão, Jesus G Valenzuela, Beatriz R Ferreira, Gustavo R Garcia, Matias PJ Szabó, Sonal Patel, Richard Bishop, and Isabel KF de Miranda-Santos PMCID: PMC2901319 Systematic investigation of global coordination among mRNA and protein in cellular society Haiyun Wang, Qi Wang, Utz J Pape, Bairong Shen, Jianhua Huang, Bin Wu, and Xia Li PMCID: PMC2900266 Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury Jesper Ryge, Ole Winther, Jacob Wienecke, Albin Sandelin, Ann-Charlotte Westerdahl, Hans Hultborn, and Ole Kiehn PMCID: PMC2900267 Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins Timothy G Lilburn, Jianying Gu, Hong Cai, and Yufeng Wang PMCID: PMC2890568 Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects Shu-jun Wei, Min Shi, Michael J Sharkey, Cornelis van Achterberg, and Xue-xin Chen PMCID: PMC2890569 Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits Angela Cánovas, Raquel Quintanilla, Marcel Amills, and Ramona N Pena PMCID: PMC2894043 Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus Felix D Guerrero, Paula Moolhuijzen, Daniel G Peterson, Shelby Bidwell, Elisabet Caler, Matthew Bellgard, Vishvanath M Nene, and Appolinaire Djikeng PMCID: PMC2893602 Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies Michael D Harwich, Jr, Joao M Alves, Gregory A Buck, Jerome F Strauss, III, Jennifer L Patterson, Aminat T Oki, Philippe H Girerd, and Kimberly K Jefferson PMCID: PMC2890570 Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis Maarten J Schijffelen, CH Edwin Boel, Jos AG van Strijp, and Ad C Fluit PMCID: PMC2900268 A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development Keren Byrne, Tony Vuocolo, Cedric Gondro, Jason D White, Noelle E Cockett, Tracy Hadfield, Christopher A Bidwell, Jolena N Waddell, and Ross L Tellam PMCID: PMC2894804 Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence Benoît Remenant, Bénédicte Coupat-Goutaland, Alice Guidot, Gilles Cellier, Emmanuel Wicker, Caitilyn Allen, Mark Fegan, Olivier Pruvost, Mounira Elbaz, Alexandra Calteau, Gregory Salvignol, Damien Mornico, Sophie Mangenot, Valérie Barbe, Claudine Médigue, and Philippe Prior PMCID: PMC2900269 Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS Delphine Fleury, Ming-Cheng Luo, Jan Dvorak, Luke Ramsay, Bikram S Gill, Olin D Anderson, Frank M You, Zahra Shoaei, Karin R Deal, and Peter Langridge PMCID: PMC2900270 Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types Shaogui Guo, Yi Zheng, Je-Gun Joung, Shiqiang Liu, Zhonghua Zhang, Oswald R Crasta, Bruno W Sobral, Yong Xu, Sanwen Huang, and Zhangjun Fei PMCID: PMC2897810 Expression of a retinoic acid signature in circulating CD34 cells from coronary artery disease patients Tineke CTM van der Pouw Kraan, Stephan H Schirmer, Joost O Fledderus, Perry D Moerland, Josefien M Baggen, Thomas A Leyen, Anja M van der Laan, Jan J Piek, Niels van Royen, and Anton JG Horrevoets PMCID: PMC2901320 Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae Michael Kube, Alexander M Migdoll, Isabel Gehring, Katja Heitmann, Yvonne Mayer, Heiner Kuhl, Florian Knaust, Klaus Geider, and Richard Reinhardt PMCID: PMC2897811 High resolution mapping of trypanosomosis resistance loci Tir2 and Tir3 using F12 advanced intercross lines with major locus Tir1 fixed for the susceptible allele Joseph K Nganga, Morris Soller, and Fuad A Iraqi PMCID: PMC2898758 Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training Beatrice A McGivney, Paul A McGettigan, John A Browne, Alexander CO Evans, Rita G Fonseca, Brendan J Loftus, Amanda Lohan, David E MacHugh, Barbara A Murphy, Lisa M Katz, and Emmeline W Hill PMCID: PMC2900271 Alternative splicing is frequent during early embryonic development in mouse Timothée Revil, Daniel Gaffney, Christel Dias, Jacek Majewski, and Loydie A Jerome-Majewska PMCID: PMC2898759 De novo characterization of a whitefly transcriptome and analysis of its gene expression during development Xiao-Wei Wang, Jun-Bo Luan, Jun-Min Li, Yan-Yuan Bao, Chuan-Xi Zhang, and Shu-Sheng Liu PMCID: PMC2898760 Software Genomics Portals: integrative web-platform for mining genomics data Kaustubh Shinde, Mukta Phatak, Freudenberg M Johannes, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jaroslaw Meller, and Mario Medvedovic PMCID: PMC2824719 Automated design of genomic Southern blot probes Mike DR Croning, David G Fricker, Noboru H Komiyama, and Seth GN Grant PMCID: PMC2830989 Library of molecular associations: curating the complex molecular basis of liver diseases Stefan Buchkremer, Jasmin Hendel, Markus Krupp, Arndt Weinmann, Kai Schlamp, Thorsten Maass, Frank Staib, Peter R Galle, and Andreas Teufel PMCID: PMC2851601 Methodology Articles Decoding pooled RNAi screens by means of barcode tiling arrays Michael Boettcher, Johannes Fredebohm, Amin Moghaddas Gholami, Yafit Hachmo, Iris Dotan, Dan Canaani, and Jörg D Hoheisel PMCID: PMC2824726 Genome-wide computational prediction of tandem gene arrays: application in yeasts Laurence Despons, Philippe V Baret, Lionel Frangeul, Véronique Leh Louis, Pascal Durrens, and Jean-Luc Souciet PMCID: PMC2822764 Tracking chromosomal positions of oligomers - a case study with Illumina's BovineSNP50 beadchip Armin O Schmitt, Ralf H Bortfeldt, and Gudrun A Brockmann PMCID: PMC2834638 Whole-genome sequencing of a laboratory-evolved yeast strain Carlos L Araya, Celia Payen, Maitreya J Dunham, and Stanley Fields PMCID: PMC2829512 Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility Koen Bossers, Bauke Ylstra, Ruud H Brakenhoff, Serge J Smeets, Joost Verhaagen, and Mark A van de Wiel PMCID: PMC2838842 Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH) Juan I Montoya-Burgos, Aurélia Foulon, and Ilham Bahechar PMCID: PMC2838844 Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing Julia Sandberg, Marten Neiman, Afshin Ahmadian, and Joakim Lundeberg PMCID: PMC2842249 Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs Srinivas Veerla, Markus Ringnér, and Mattias Höglund PMCID: PMC2841680 Transcribed-ultra conserved region expression profiling from low-input total RNA Paola Scaruffi, Sara Stigliani, Simona Coco, Franscesca Valdora, Carla De Vecchi, Stefano Bonassi, and Gian Paolo Tonini PMCID: PMC2838852 Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon Anti Vasemägi, Riho Gross, Daniel Palm, Tiit Paaver, and Craig R Primmer PMCID: PMC2838853 Improvement of tissue preparation for laser capture microdissection: application for cell type-specific miRNA expression profiling in colorectal tumors Shuyang Wang, Lei Wang, Tengfang Zhu, Xue Gao, Jian Li, Ying Wu, and Hongguang Zhu PMCID: PMC2853520 Detection of novel 3' untranslated region extensions with 3' expression microarrays Lieven Thorrez, Leon-Charles Tranchevent, Hui Ju Chang, Yves Moreau, and Frans Schuit PMCID: PMC2858751 DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing John C Castle, Matthew Biery, Heather Bouzek, Tao Xie, Ronghua Chen, Kira Misura, Stuart Jackson, Christopher D Armour, Jason M Johnson, Carol A Rohl, and Christopher K Raymond PMCID: PMC2867831 Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila Suzy CP Renn, Heather E Machado, Albyn Jones, Kosha Soneji, Rob J Kulathinal, and Hans A Hofmann PMCID: PMC2873954 A jackknife-like method for classification and uncertainty assessment of multi-category tumor samples using gene expression information Wensheng Zhang, Kelly Robbins, Yupeng Wang, Keith Bertrand, and Romdhane Rekaya PMCID: PMC2876124 Novel methods to identify biologically relevant genes for leukemia and prostate cancer from gene expression profiles Austin H Chen, Yin-Wu Tsau, and Ching-Heng Lin PMCID: PMC2873479 Amplified fragment length homoplasy: in silico analysis for model and non-model species Margot Paris, Benjamin Bonnes, Gentile Francesco Ficetola, Bénédicte N Poncet, and Laurence Després PMCID: PMC2875239 Consistent annotation of gene expression arrays Benoît Ballester, Nathan Johnson, Glenn Proctor, and Paul Flicek PMCID: PMC2894801 A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies Maxime Galan, Emmanuel Guivier, Gilles Caraux, Nathalie Charbonnel, and Jean-François Cosson PMCID: PMC2876125 A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC) libraries using High Resolution Melt analysis Giang TH Vu, Peter DS Caligari, and Mike J Wilkinson PMCID: PMC2881884 Towards a membrane proteome in Drosophila: a method for the isolation of plasma membrane Mansi R Khanna, Bruce A Stanley, and Graham H Thomas PMCID: PMC2876126 Genome-wide expression links the electron transfer pathway of Shewanella oneidensis to chemotaxis Shang-Kai Tai, GuanI Wu, Shinsheng Yuan, and Ker-Chau Li PMCID: PMC2886065 Inferring linkage disequilibrium from non-random samples† Minghui Wang, Tianye Jia, Ning Jiang, Lin Wang, Xiaohua Hu, and Zewei Luo PMCID: PMC2890561 Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays Cyril Degletagne, Céline Keime, Benjamin Rey, Marc de Dinechin, Fabien Forcheron, Paul Chuchana, Pierre Jouventin, Christian Gautier, and Claude Duchamp PMCID: PMC2901317 Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer Ruben Pio, David Blanco, Maria Jose Pajares, Elena Aibar, Olga Durany, Teresa Ezponda, Jackeline Agorreta, Javier Gomez-Roman, Miguel Angel Anton, Angel Rubio, Maria D Lozano, Jose M López-Picazo, Francesc Subirada, Tamara Maes, and Luis M Montuenga PMCID: PMC2889901 Corrections Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera Erica Mica, Viviana Piccolo, Massimo Delledonne, Alberto Ferrarini, Mario Pezzotti, Cesare Casati, Cristian Del Fabbro, Giorgio Valle, Alberto Policriti, Michele Morgante, Graziano Pesole, M Enrico Pè, and David S Horner PMCID: PMC2831844 Corrects: Erica Mica, et al. High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics. 2009; 10: 558. Correction: Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains Audrey J King, Tamara van Gorkom, Jeroen LA Pennings, Han GJ van der Heide, Qiushui He, Dimitri Diavatopoulos, Kees Heuvelman, Marjolein van Gent, Karin van Leeuwen, and Frits R Mooi PMCID: PMC2858151 Corrects: Audrey J King, et al. Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: Identification of genes absent from epidemic strains. BMC Genomics. 2008; 9: 311. Correction: Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach Ying Wang, Vinayak Brahmakshatriya, Huifeng Zhu, Blanca Lupiani, Sanjay M Reddy, Byung-Jun Yoon, Preethi H Gunaratne, Jong Hwan Kim, Rui Chen, Ashley L Benham, Junjun Wang, and Huaijun Zhou PMCID: PMC2896380 Corrects: Ying Wang, et al. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics. 2009; 10: 512. Other Issues: Journal List
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