|
|
Other Issues: Journal List
|
previous
|
next
|
latest
|
archive
Commentary Unlocking the bovine genome Ross L Tellam, Danielle G Lemay, Curtis P Van Tassell, Harris A Lewin, Kim C Worley, and Christine G Elsik PMCID: PMC2680899 Correspondence Correspondence regarding "Effect of active smoking on the human bronchial epithelium transcriptome" Scott D Zuyderduyn PMCID: PMC2656532 "Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes Jianfeng Ren, Xiao Liu, Guofan Zhang, Bin Liu, and Ximing Guo PMCID: PMC2652495 Database Fourmidable: a database for ant genomics Yannick Wurm, Paolo Uva, Frédéric Ricci, John Wang, Stephanie Jemielity, Christian Iseli, Laurent Falquet, and Laurent Keller PMCID: PMC2639375 RepPop: a database for repetitive elements in Populus trichocarpa Fengfeng Zhou and Ying Xu PMCID: PMC2645430 EPIC-DB: a proteomics database for studying Apicomplexan organisms Carlos J Madrid-Aliste, Joseph M Dybas, Ruth Hogue Angeletti, Louis M Weiss, Kami Kim, Istvan Simon, and Andras Fiser PMCID: PMC2652494 MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences Paola Venier, Cristiano De Pittà, Filippo Bernante, Laura Varotto, Barbara De Nardi, Giuseppe Bovo, Philippe Roch, Beatriz Novoa, Antonio Figueras, Alberto Pallavicini, and Gerolamo Lanfranchi PMCID: PMC2657158 SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data Adriane Menßen, Götz Edinger, Joachim R Grün, Ulrike Haase, Ria Baumgrass, Andreas Grützkau, Andreas Radbruch, Gerd-R Burmester, and Thomas Häupl PMCID: PMC2657156 IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes Wonhoon Lee, Jongsun Park, Jaeyoung Choi, Kyongyong Jung, Bongsoo Park, Donghan Kim, Jaeyoung Lee, Kyohun Ahn, Wonho Song, Seogchan Kang, Yong-Hwan Lee, and Seunghwan Lee PMCID: PMC2681477 plantsUPS: a database of plants' Ubiquitin Proteasome System Zhou Du, Xin Zhou, Li Li, and Zhen Su PMCID: PMC2690602 7TMRmine: a Web server for hierarchical mining of 7TMR proteins Guoqing Lu, Zhifang Wang, Alan M Jones, and Etsuko N Moriyama PMCID: PMC2718930 CellMiner: a relational database and query tool for the NCI-60 cancer cell lines Uma T Shankavaram, Sudhir Varma, David Kane, Margot Sunshine, Krishna K Chary, William C Reinhold, Yves Pommier, and John N Weinstein PMCID: PMC2709662 PairWise Neighbours database: overlaps and spacers among prokaryote genomes Albert Pallejà, Tomàs Reverter, Santiago Garcia-Vallvé, and Antoni Romeu PMCID: PMC2716372 Hmrbase: a database of hormones and their receptors Mamoon Rashid, Deepak Singla, Arun Sharma, Manish Kumar, and Gajendra PS Raghava PMCID: PMC2720991 P2CS: a two-component system resource for prokaryotic signal transduction research Mohamed Barakat, Philippe Ortet, Cécile Jourlin-Castelli, Mireille Ansaldi, Vincent Méjean, and David E Whitworth PMCID: PMC2716373 Genomic Resources of Magnaporthe oryzae (GROMO): A comprehensive and integrated database on rice blast fungus Shalabh Thakur, Sanjay Jha, Subhankar Roy-Barman, and Bharat Chattoo PMCID: PMC2721851 The Lactamase Engineering Database: a critical survey of TEM sequences in public databases Quan Ke Thai, Fabian Bös, and Jürgen Pleiss PMCID: PMC2742552 UFO: a web server for ultra-fast functional profiling of whole genome protein sequences Peter Meinicke PMCID: PMC2744726 ZifBASE: a database of zinc finger proteins and associated resources Mannu Jayakanthan, Jayaraman Muthukumaran, Sanniyasi Chandrasekar, Konika Chawla, Ankita Punetha, and Durai Sundar PMCID: PMC2746237 KAIKObase: An integrated silkworm genome database and data mining tool Michihiko Shimomura, Hiroshi Minami, Yoshitaka Suetsugu, Hajime Ohyanagi, Chikatada Satoh, Baltazar Antonio, Yoshiaki Nagamura, Keiko Kadono-Okuda, Hideyuki Kajiwara, Hideki Sezutsu, Javaregowda Nagaraju, Marian R Goldsmith, Qingyou Xia, Kimiko Yamamoto, and Kazuei Mita PMCID: PMC2770533 An expression database for roots of the model legume Medicago truncatula under salt stress Daofeng Li, Zhen Su, Jiangli Dong, and Tao Wang PMCID: PMC2779821 GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes Harald Hutter, Man-Ping Ng, and Nansheng Chen PMCID: PMC2779824 Research article The theory of discovering rare variants via DNA sequencing Michael C Wendl and Richard K Wilson PMCID: PMC2778663 Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-down José L Costa, Paul P Eijk, Mark A van de Wiel, Derk ten Berge, Fernando Schmitt, Carmen J Narvaez, JoEllen Welsh, and Bauke Ylstra PMCID: PMC2778664 Regulation of intestinal epithelial cells transcriptome by enteric glial cells: impact on intestinal epithelial barrier functions Laurianne Van Landeghem, Maxime M Mahé, Raluca Teusan, Jean Léger, Isabelle Guisle, Rémi Houlgatte, and Michel Neunlist PMCID: PMC2778665 Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family Marco Vedovato, Valeria Rossi, Joel B Dacks, and Francesco Filippini PMCID: PMC2779197 Evolution of genomic sequence inhomogeneity at mid-range scales Ashwin Prakash, Samuel S Shepard, Jie He, Benjamin Hart, Miao Chen, Surya P Amarachintha, Olga Mileyeva-Biebesheimer, Jason Bechtel, and Alexei Fedorov PMCID: PMC2779198 The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus Rob M de Graaf, Theo A van Alen, Bas E Dutilh, Jan WP Kuiper, Hanneke JAA van Zoggel, Minh Bao Huynh, Hans-Dieter Görtz, Martijn A Huynen, and Johannes HP Hackstein PMCID: PMC2779199 SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights Na Liu, Zhen-Dong Xiao, Chun-Hong Yu, Peng Shao, Yin-Tong Liang, Dao-Gang Guan, Jian-Hua Yang, Chun-Long Chen, Liang-Hu Qu, and Hui Zhou PMCID: PMC2780460 Endogenous control genes in complex vascular tissue samples Lasse Folkersen, Sanela Kurtovic, Anton Razuvaev, Hanna E Agardh, Anders Gabrielsen, and Gabrielle Paulsson-Berne PMCID: PMC2779820 Correlation of microsynteny conservation and disease gene distribution in mammalian genomes Simon C Lovell, Xiting Li, Nimmi R Weerasinghe, and Kathryn E Hentges PMCID: PMC2779822 Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization JM Friedman, Shelin Adam, Laura Arbour, Linlea Armstrong, Agnes Baross, Patricia Birch, Cornelius Boerkoel, Susanna Chan, David Chai, Allen D Delaney, Stephane Flibotte, William T Gibson, Sylvie Langlois, Emmanuelle Lemyre, H Irene Li, Patrick MacLeod, Joan Mathers, Jacques L Michaud, Barbara C McGillivray, Millan S Patel, Hong Qian, Guy A Rouleau, Margot I Van Allen, Siu-Li Yong, Farah R Zahir, Patrice Eydoux, and Marco A Marra PMCID: PMC2781027 Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues Christoffer Nellåker, Fang Li, Fredrik Uhrzander, Joanna Tyrcha, and Håkan Karlsson PMCID: PMC2779825 Software BioMart – biological queries made easy Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, and Arek Kasprzyk PMCID: PMC2649164 FragIdent – Automatic identification and characterisation of cDNA-fragments Dominik Seelow, Heike Goehler, and Katrin Hoffmann PMCID: PMC2672089 ESTPiper – a web-based analysis pipeline for expressed sequence tags Zuojian Tang, Jeong-Hyeon Choi, Chris Hemmerich, Ankita Sarangi, John K Colbourne, and Qunfeng Dong PMCID: PMC2676306 ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii Patrick May, Jan-Ole Christian, Stefan Kempa, and Dirk Walther PMCID: PMC2688524 BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks Carito Guziolowski, Annabel Bourdé, Francois Moreews, and Anne Siegel PMCID: PMC2693143 PAVE: Program for assembling and viewing ESTs Carol Soderlund, Eric Johnson, Matthew Bomhoff, and Anne Descour PMCID: PMC2748094 GEM-TREND: a web tool for gene expression data mining toward relevant network discovery Chunlai Feng, Michihiro Araki, Ryo Kunimoto, Akiko Tamon, Hiroki Makiguchi, Satoshi Niijima, Gozoh Tsujimoto, and Yasushi Okuno PMCID: PMC2748096 Research Articles A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution Sonja Jaari, Meng-Hua Li, and Juha Merilä PMCID: PMC2671524 Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer Mark S McClain, Carrie L Shaffer, Dawn A Israel, Richard M Peek, Jr, and Timothy L Cover PMCID: PMC2627912 Mining for single nucleotide polymorphisms in pig genome sequence data Hindrik HD Kerstens, Sonja Kollers, Arun Kommadath, Marisol del Rosario, Bert Dibbits, Sylvia M Kinders, Richard P Crooijmans, and Martien AM Groenen PMCID: PMC2637895 The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon Paul W Whitby, Thomas W Seale, Timothy M VanWagoner, Daniel J Morton, and Terrence L Stull PMCID: PMC2627913 Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast Craig Lawless, Richard D Pearson, Julian N Selley, Julia B Smirnova, Christopher M Grant, Mark P Ashe, Graham D Pavitt, and Simon J Hubbard PMCID: PMC2649001 Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend David M McGaughey, Zachary E Stine, Jimmy L Huynh, Ryan M Vinton, and Andrew S McCallion PMCID: PMC2630312 Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster Qianqian Zhu and Marc S Halfon PMCID: PMC2631479 A gene expression signature shared by human mature oocytes and embryonic stem cells Said Assou, Doris Cerecedo, Sylvie Tondeur, Véronique Pantesco, Outi Hovatta, Bernard Klein, Samir Hamamah, and John De Vos PMCID: PMC2628676 Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins Raghu Prasad Rao Metpally and Boojala Vijay B Reddy PMCID: PMC2653534 High-resolution mapping of plasmid transcriptomes in different host bacteria Masatoshi Miyakoshi, Hiromi Nishida, Masaki Shintani, Hisakazu Yamane, and Hideaki Nojiri PMCID: PMC2642839 Reconstruction and functional analysis of altered molecular pathways in human atherosclerotic arteries Stefano Cagnin, Michele Biscuola, Cristina Patuzzo, Elisabetta Trabetti, Alessandra Pasquali, Paolo Laveder, Giuseppe Faggian, Mauro Iafrancesco, Alessandro Mazzucco, Pier Franco Pignatti, and Gerolamo Lanfranchi PMCID: PMC2654039 Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Jiang Wang, Yangyang Deng, and Caisheng He PMCID: PMC2631480 Conservation in the face of diversity: multistrain analysis of an intracellular bacterium Michael J Dark, David R Herndon, Lowell S Kappmeyer, Mikel P Gonzales, Elizabeth Nordeen, Guy H Palmer, Donald P Knowles, Jr, and Kelly A Brayton PMCID: PMC2649000 Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates Toshiaki Matsui, Toshiyuki Yamamoto, Stefan Wyder, Evgeny M Zdobnov, and Tatsuhiko Kadowaki PMCID: PMC2656531 Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum Prathima Iengar and NV Joshi PMCID: PMC2662883 Genic regions of a large salamander genome contain long introns and novel genes Jeramiah J Smith, Srikrishna Putta, Wei Zhu, Gerald M Pao, Inder M Verma, Tony Hunter, Susan V Bryant, David M Gardiner, Timothy T Harkins, and S Randal Voss PMCID: PMC2633012 Mapping QTL affecting resistance to Marek's disease in an F6 advanced intercross population of commercial layer chickens Eliyahu M Heifetz, Janet E Fulton, Neil P O'Sullivan, James A Arthur, Hans Cheng, Jing Wang, Morris Soller, and Jack CM Dekkers PMCID: PMC2651900 Genetic diversity of canine olfactory receptors Stéphanie Robin, Sandrine Tacher, Maud Rimbault, Amaury Vaysse, Stéphane Dréano, Catherine André, Christophe Hitte, and Francis Galibert PMCID: PMC2635374 Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes Minli Xu and Zhengchang Su PMCID: PMC2633013 The G protein-coupled receptor subset of the dog genome is more similar to that in humans than rodents Tatjana Haitina, Robert Fredriksson, Steven M Foord, Helgi B Schiöth, and David E Gloriam PMCID: PMC2651185 Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome Chia-wei Wu, Timothy M Schramm, Shiguo Zhou, David C Schwartz, and Adel M Talaat PMCID: PMC2633350 Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida Adina Mwinyi, Achim Meyer, Christoph Bleidorn, Bernhard Lieb, Thomas Bartolomaeus, and Lars Podsiadlowski PMCID: PMC2639372 Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies Henrik Hornshøj, Emøke Bendixen, Lene N Conley, Pernille K Andersen, Jakob Hedegaard, Frank Panitz, and Christian Bendixen PMCID: PMC2633351 Microsatellite mapping of QTLs affecting resistance to coccidiosis (Eimeria tenella) in a Fayoumi × White Leghorn cross Marie-Hélène Pinard-van der Laan, Bertrand Bed'hom, Jean-Luc Coville, Frédérique Pitel, Katia Feve, Sophie Leroux, Hélène Legros, Aurélie Thomas, David Gourichon, Jean-Michel Repérant, and Paul Rault PMCID: PMC2633352 Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti Lisa Klasson, Zakaria Kambris, Peter E Cook, Thomas Walker, and Steven P Sinkins PMCID: PMC2647948 Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations Shihui Yang, Timothy J Tschaplinski, Nancy L Engle, Sue L Carroll, Stanton L Martin, Brian H Davison, Anthony V Palumbo, Miguel Rodriguez, Jr, and Steven D Brown PMCID: PMC2651186 Characterization of gene expression profiles for different types of mast cells pooled from mouse stomach subregions by an RNA amplification method Soken Tsuchiya, Yuki Tachida, Eri Segi-Nishida, Yasushi Okuno, Shigero Tamba, Gozoh Tsujimoto, Satoshi Tanaka, and Yukihiko Sugimoto PMCID: PMC2639374 Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi Kathryn E Holt, Nicholas R Thomson, John Wain, Gemma C Langridge, Rumina Hasan, Zulfiqar A Bhutta, Michael A Quail, Halina Norbertczak, Danielle Walker, Mark Simmonds, Brian White, Nathalie Bason, Karen Mungall, Gordon Dougan, and Julian Parkhill PMCID: PMC2658671 New DArT markers for oat provide enhanced map coverage and global germplasm characterization Nicholas A Tinker, Andrzej Kilian, Charlene P Wight, Katarzyna Heller-Uszynska, Peter Wenzl, Howard W Rines, Åsmund Bjørnstad, Catherine J Howarth, Jean-Luc Jannink, Joseph M Anderson, Brian G Rossnagel, Deon D Stuthman, Mark E Sorrells, Eric W Jackson, Stine Tuvesson, Frederic L Kolb, Olof Olsson, Luiz Carlos Federizzi, Marty L Carson, Herbert W Ohm, Stephen J Molnar, Graham J Scoles, Peter E Eckstein, J Michael Bonman, Alf Ceplitis, and Tim Langdon PMCID: PMC2661094 An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies Francesca D Frentiu, Marcin Adamski, Elizabeth A McGraw, Mark W Blows, and Stephen F Chenoweth PMCID: PMC2653539 Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don Xinguo Li, Harry X Wu, Shannon K Dillon, and Simon G Southerton PMCID: PMC2636829 Positive correlation between gene coexpression and positional clustering in the zebrafish genome Yen Kaow Ng, Wei Wu, and Louxin Zhang PMCID: PMC2654907 Large-scale inference of the point mutational spectrum in human segmental duplications Sigve Nakken, Einar A Rødland, Torbjørn Rognes, and Eivind Hovig PMCID: PMC2640414 Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway Thomas R Jørgensen, Theo Goosen, Cees AMJJ van den Hondel, Arthur FJ Ram, and Jens JL Iversen PMCID: PMC2639373 An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes David J Bertioli, Marcio C Moretzsohn, Lene H Madsen, Niels Sandal, Soraya CM Leal-Bertioli, Patricia M Guimarães, Birgit K Hougaard, Jakob Fredslund, Leif Schauser, Anna M Nielsen, Shusei Sato, Satoshi Tabata, Steven B Cannon, and Jens Stougaard PMCID: PMC2656529 A multiway analysis for identifying high integrity bovine BACs Abhirami Ratnakumar, Wesley Barris, Sean McWilliam, Rudiger Brauning, John C McEwan, Warren M Snelling, and Brian P Dalrymple PMCID: PMC2660975 Patterns of exon-intron architecture variation of genes in eukaryotic genomes Liucun Zhu, Ying Zhang, Wen Zhang, Sihai Yang, Jian-Qun Chen, and Dacheng Tian PMCID: PMC2636830 Tetraploid and hexaploid wheat varieties reveal large differences in expression of alpha-gliadins from homoeologous Gli-2 loci Elma MJ Salentijn, Svetlana V Goryunova, Noor Bas, Ingrid M van der Meer, Hetty C van den Broeck, Thomas Bastien, Luud JWJ Gilissen, and Marinus JM Smulders PMCID: PMC2636828 Infection and genotype remodel the entire soybean transcriptome Lecong Zhou, Santiago X Mideros, Lei Bao, Regina Hanlon, Felipe D Arredondo, Sucheta Tripathy, Konstantinos Krampis, Adam Jerauld, Clive Evans, Steven K St Martin, MA Saghai Maroof, Ina Hoeschele, Anne E Dorrance, and Brett M Tyler PMCID: PMC2662884 Generation of a predicted protein database from EST data and application to iTRAQ analyses in grape (Vitis vinifera cv. Cabernet Sauvignon) berries at ripening initiation Joost Lücker, Mario Laszczak, Derek Smith, and Steven T Lund PMCID: PMC2637896 Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22 Natalia Volfovsky, Taras K Oleksyk, Kristine C Cruz, Ann L Truelove, Robert M Stephens, and Michael W Smith PMCID: PMC2654908 A gene catalogue for post-diapause development of an anhydrobiotic arthropod Artemia franciscana Wie-Hua Chen, Xiaomeng Ge, Weiwei Wang, Jun Yu, and Songnian Hu PMCID: PMC2649162 Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data Theo A Knijnenburg, Jean-Marc G Daran, Marcel A van den Broek, Pascale AS Daran-Lapujade, Johannes H de Winde, Jack T Pronk, Marcel JT Reinders, and Lodewyk FA Wessels PMCID: PMC2640415 Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis Philip N Ward, Matthew TG Holden, James A Leigh, Nicola Lennard, Alexandra Bignell, Andy Barron, Louise Clark, Michael A Quail, John Woodward, Bart G Barrell, Sharon A Egan, Terence R Field, Duncan Maskell, Michael Kehoe, Christopher G Dowson, Neil Chanter, Adrian M Whatmore, Stephen D Bentley, and Julian Parkhill PMCID: PMC2657157 An Ac/Ds-mediated gene trap system for functional genomics in barley Katina Lazarow and Stephanie Lütticke PMCID: PMC2647555 Genome-wide analysis of chimpanzee genes with premature termination codons Anna Wetterbom, Ulf Gyllensten, Lucia Cavelier, and Tomas F Bergström PMCID: PMC2640416 The salivary gland transcriptome of the neotropical malaria vector Anopheles darlingi reveals accelerated evolution of genes relevant to hematophagy Eric Calvo, Van M Pham, Osvaldo Marinotti, John F Andersen, and José MC Ribeiro PMCID: PMC2644710 Sequence mining and transcript profiling to explore cyst nematode parasitism Axel A Elling, Makedonka Mitreva, Xiaowu Gai, John Martin, Justin Recknor, Eric L Davis, Richard S Hussey, Dan Nettleton, James P McCarter, and Thomas J Baum PMCID: PMC2640417 Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites Allison A Burrow, Laura E Williams, Levi CT Pierce, and Yuh-Hwa Wang PMCID: PMC2642838 Comparative genomic analysis of light-regulated transcripts in the Solanaceae Mariana Rutitzky, Hernan O Ghiglione, José A Curá, Jorge J Casal, and Marcelo J Yanovsky PMCID: PMC2644711 Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger James C Wright, Deana Sugden, Sue Francis-McIntyre, Isabel Riba-Garcia, Simon J Gaskell, Igor V Grigoriev, Scott E Baker, Robert J Beynon, and Simon J Hubbard PMCID: PMC2644712 Revisiting the missing protein-coding gene catalog of the domestic dog Thomas Derrien, Julien Thézé, Amaury Vaysse, Catherine André, Elaine A Ostrander, Francis Galibert, and Christophe Hitte PMCID: PMC2644713 Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach Hongbo Chen, Changchun Li, Mingdi Fang, Mengjin Zhu, Xinyun Li, Rui Zhou, Kui Li, and Shuhong Zhao PMCID: PMC2660370 Cloning, characterization and expression analysis of porcine microRNAs Alavala Matta Reddy, Yun Zheng, Guru Jagadeeswaran, Simone L Macmil, Wiley B Graham, Bruce A Roe, Udaya Desilva, Weixiong Zhang, and Ramanjulu Sunkar PMCID: PMC2644714 Differential gene expression in ADAM10 and mutant ADAM10 transgenic mice Claudia Prinzen, Dietrich Trümbach, Wolfgang Wurst, Kristina Endres, Rolf Postina, and Falk Fahrenholz PMCID: PMC2647556 Identification of genes differentially expressed as result of adenovirus type 5- and adenovirus type 12-transformation Janet Strath, Lindsay J Georgopoulos, Paul Kellam, and G Eric Blair PMCID: PMC2651901 Analysis of small nucleolar RNAs reveals unique genetic features in malaria parasites Prakash Chandra Mishra, Anuj Kumar, and Amit Sharma PMCID: PMC2656528 Desiccation survival in an Antarctic nematode: molecular analysis using expressed sequenced tags Bishwo N Adhikari, Diana H Wall, and Byron J Adams PMCID: PMC2667540 Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulation Lori AS Snyder, Jeff A Cole, and Mark J Pallen PMCID: PMC2649163 Escherichia coli genes affecting recipient ability in plasmid conjugation: Are there any? Daniel Pérez-Mendoza and Fernando de la Cruz PMCID: PMC2645431 Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives Marina Trouillas, Claire Saucourt, Bertrand Guillotin, Xavier Gauthereau, Li Ding, Frank Buchholz, Michael Xavier Doss, Agapios Sachinidis, Jurgen Hescheler, Oliver Hummel, Norbert Huebner, Raivo Kolde, Jaak Vilo, Herbert Schulz, and Hélène Bœuf PMCID: PMC2674464 Dynamic evolution of V1R putative pheromone receptors between Mus musculus and Mus spretus Vanessa C Kurzweil, Mike Getman, NISC Comparative Sequencing Program, Eric D Green, and Robert P Lane PMCID: PMC2644715 Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production Diana M Harris, Zita A van der Krogt, Paul Klaassen, Leonie M Raamsdonk, Susanne Hage, Marco A van den Berg, Roel AL Bovenberg, Jack T Pronk, and Jean-Marc Daran PMCID: PMC2657799 Synteny of Prunus and other model plant species Sook Jung, Derick Jiwan, Ilhyung Cho, Taein Lee, Albert Abbott, Bryon Sosinski, and Dorrie Main PMCID: PMC2647949 MicroRNA transcriptome profiles during swine skeletal muscle development Tara G McDaneld, Timothy PL Smith, Matthew E Doumit, Jeremy R Miles, Luiz L Coutinho, Tad S Sonstegard, Lakshmi K Matukumalli, Dan J Nonneman, and Ralph T Wiedmann PMCID: PMC2646747 Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization Yan Zhang, Dmitry A Rodionov, Mikhail S Gelfand, and Vadim N Gladyshev PMCID: PMC2667541 The mitochondrial genomes of Ancylostoma caninum and Bunostomum phlebotomum – two hookworms of animal health and zoonotic importance Aaron R Jex, Andrea Waeschenbach, Min Hu, Jan A van Wyk, Ian Beveridge, D Timothy J Littlewood, and Robin B Gasser PMCID: PMC2656527 Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis Matthew S Lebo, Laura E Sanders, Fengzhu Sun, and Michelle N Arbeitman PMCID: PMC2656526 Genome-wide identification of Xenopus matrix metalloproteinases: conservation and unique duplications in amphibians Liezhen Fu, Biswajit Das, Smita Mathew, and Yun-Bo Shi PMCID: PMC2656525 Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation Chaobo Tong, Baocheng Guo, and Shunping He PMCID: PMC2653535 Ultraspecific probes for high throughput HLA typing Chen Feng, Catherine Putonti, Meizhuo Zhang, Rick Eggers, Rahul Mitra, Mike Hogan, Krishna Jayaraman, and Yuriy Fofanov PMCID: PMC2661095 Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs Peng Shao, Jian-Hua Yang, Hui Zhou, Dao-Gang Guan, and Liang-Hu Qu PMCID: PMC2653536 Systematic identification of genes involved in divergent skeletal muscle growth rates of broiler and layer chickens Qi Zheng, Yong Zhang, Ying Chen, Ning Yang, Xiu-Jie Wang, and Dahai Zhu PMCID: PMC2656524 Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae Julien Gouré, Wendy A Findlay, Vincent Deslandes, Anne Bouevitch, Simon J Foote, Janet I MacInnes, James W Coulton, John HE Nash, and Mario Jacques PMCID: PMC2653537 Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis Miguel Pérez-Enciso, André LJ Ferraz, Ana Ojeda, and Manel López-Béjar PMCID: PMC2656523 Expression profiling and Ingenuity biological function analyses of interleukin-6- versus nerve growth factor-stimulated PC12 cells Dieter Kunz, Gaby Walker, Marc Bedoucha, Ulrich Certa, Pia März-Weiss, Beatrice Dimitriades-Schmutz, and Uwe Otten PMCID: PMC2657914 Genomic sequence, organization and characteristics of a new nucleopolyhedrovirus isolated from Clanis bilineata larva Shan-Ying Zhu, Jian-Ping Yi, Wei-De Shen, Li-Qun Wang, Hua-Gang He, Yong Wang, Bing Li, and Wen-Bing Wang PMCID: PMC2650706 Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites Baochen Shi, Xiangqian Guo, Tao Wu, Sitong Sheng, Jie Wang, Geir Skogerbø, Xiaopeng Zhu, and Runsheng Chen PMCID: PMC2651899 Global gene expression analysis reveals reduced abundance of putative microRNA targets in human prostate tumours Ruping Sun, Xuping Fu, Yao Li, Yi Xie, and Yumin Mao PMCID: PMC2653538 Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis Benjamin Stich and Albrecht E Melchinger PMCID: PMC2676307 Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle Wouter Coppieters, Ted HM Mes, Tom Druet, Frédéric Farnir, Nico Tamma, Chris Schrooten, Albert WCA Cornelissen, Michel Georges, and Harm W Ploeger PMCID: PMC2657155 Rapid evolution of mammalian X-linked testis microRNAs Xuejiang Guo, Bing Su, Zuomin Zhou, and Jiahao Sha PMCID: PMC2660371 Influence of genetic background on the occurrence of chromosomal rearrangements in Saccharomyces cerevisiae Emilie S Fritsch, Joseph Schacherer, Claudine Bleykasten-Grosshans, Jean-Luc Souciet, Serge Potier, and Jacky de Montigny PMCID: PMC2674068 An integrated approach for the systematic identification and characterization of heart-enriched genes with unknown functions Shizuka Uchida, André Schneider, Marion Wiesnet, Benno Jungblut, Polina Zarjitskaya, Katharina Jenniches, Karsten grosse Kreymborg, Werner Seeger, and Thomas Braun PMCID: PMC2657154 Intergenic regions of Borrelia plasmids contain phylogenetically conserved RNA secondary structure motifs Nicholas Delihas PMCID: PMC2674063 A gene-rich linkage map in the dioecious species Actinidia chinensis (kiwifruit) reveals putative X/Y sex-determining chromosomes Lena G Fraser, Gianna K Tsang, Paul M Datson, H Nihal De Silva, Catherine F Harvey, Geoffrey P Gill, Ross N Crowhurst, and Mark A McNeilage PMCID: PMC2661093 Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species Jessica E Butler, Nelson D Young, and Derek R Lovley PMCID: PMC2669807 Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources? Frédéric Boyer, Gwennaële Fichant, Jérémie Berthod, Yves Vandenbrouck, and Ina Attree PMCID: PMC2660368 Genetic basis of arsenite and cadmium tolerance in Saccharomyces cerevisiae Michael Thorsen, Gabriel G Perrone, Erik Kristiansson, Mathew Traini, Tian Ye, Ian W Dawes, Olle Nerman, and Markus J Tamás PMCID: PMC2660369 Missing call bias in high-throughput genotyping Wenqing Fu, Yi Wang, Ying Wang, Rui Li, Rong Lin, and Li Jin PMCID: PMC2670840 The complete mitochondrial genome of the house dust mite Dermatophagoides pteronyssinus (Trouessart): a novel gene arrangement among arthropods Wannes Dermauw, Thomas Van Leeuwen, Bartel Vanholme, and Luc Tirry PMCID: PMC2680895 Discovering genes associated with dormancy in the monogonont rotifer Brachionus plicatilis Nadav Y Denekamp, Michael AS Thorne, Melody S Clark, Michael Kube, Richard Reinhardt, and Esther Lubzens PMCID: PMC2667189 Identification of candidate genes for human pituitary development by EST analysis Yueyun Ma, Xiaofei Qi, Jianjun Du, Shaojun Song, Dongyun Feng, Jia Qi, Zhidong Zhu, Xin Zhang, Huasheng Xiao, Zeguang Han, and Xiaoke Hao PMCID: PMC2664823 Induction of lipid oxidation by polyunsaturated fatty acids of marine origin in small intestine of mice fed a high-fat diet Evert M van Schothorst, Pavel Flachs, Nicole LW Franssen-van Hal, Ondrej Kuda, Annelies Bunschoten, Jos Molthoff, Carolien Vink, Guido JEJ Hooiveld, Jan Kopecky, and Jaap Keijer PMCID: PMC2662879 Population-specific gene expression in the plant pathogenic nematode Heterodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of the Glycine max genotype Peking Vincent P Klink, Parsa Hosseini, Margaret H MacDonald, Nadim W Alkharouf, and Benjamin F Matthews PMCID: PMC2662880 Transcriptomic basis for an antiserum against Micrurus corallinus (coral snake) venom Luciana I Leão, Paulo L Ho, and Inacio de LM Junqueira-de-Azevedo PMCID: PMC2662881 Identification of pro-angiogenic markers in blood vessels from stroked-affected brain tissue using laser-capture microdissection Mark Slevin, Jerzy Krupinski, Norma Rovira, Marta Turu, Ana Luque, Maribel Baldellou, Coral Sanfeliu, Nuria de Vera, and Lina Badimon PMCID: PMC2664824 Molecular determinants archetypical to the phylum Nematoda Yong Yin, John Martin, Sahar Abubucker, Zhengyuan Wang, Lucjan Wyrwicz, Leszek Rychlewski, James P McCarter, Richard K Wilson, and Makedonka Mitreva PMCID: PMC2666764 Independent evolution of neurotoxin and flagellar genetic loci in proteolytic Clostridium botulinum Andrew T Carter, Catherine J Paul, David R Mason, Susan M Twine, Mark J Alston, Susan M Logan, John W Austin, and Michael W Peck PMCID: PMC2674064 Analysis of tarantula skeletal muscle protein sequences and identification of transcriptional isoforms Jingui Zhu, Yongqiao Sun, Fa-Qing Zhao, Jun Yu, Roger Craig, and Songnian Hu PMCID: PMC2674065 Uncovering new signaling proteins and potential drug targets through the interactome analysis of Mycobacterium tuberculosis Tao Cui, Lei Zhang, Xizhou Wang, and Zheng-Guo He PMCID: PMC2671525 Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes José Osorio y Fortéa, Emilie de La Llave, Béatrice Regnault, Jean-Yves Coppée, Geneviève Milon, Thierry Lang, and Eric Prina PMCID: PMC2666765 Sugarcane genes associated with sucrose content Flávia S Papini-Terzi, Flávia R Rocha, Ricardo ZN Vêncio, Juliana M Felix, Diana S Branco, Alessandro J Waclawovsky, Luiz EV Del Bem, Carolina G Lembke, Maximiller DL Costa, Milton Y Nishiyama, Jr, Renato Vicentini, Michel GA Vincentz, Eugênio C Ulian, Marcelo Menossi, and Glaucia M Souza PMCID: PMC2666766 Prediction of disease-related mutations affecting protein localization Kirsti Laurila and Mauno Vihinen PMCID: PMC2680896 Biocomputational prediction of non-coding RNAs in model cyanobacteria Björn Voß, Jens Georg, Verena Schön, Susanne Ude, and Wolfgang R Hess PMCID: PMC2662882 Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster Sergey V Nuzhdin, Jennifer A Brisson, Andrew Pickering, Marta L Wayne, Lawrence G Harshman, and Lauren M McIntyre PMCID: PMC2674066 Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array Xingyi Hang, Peiyao Li, Zhifeng Li, Wubin Qu, Ying Yu, Hualing Li, Zhiyong Shen, Hao Zheng, Yan Gao, Yonghong Wu, Minghua Deng, Zhixian Sun, and Chenggang Zhang PMCID: PMC2678155 Identifying components of the hair-cell interactome involved in cochlear amplification Jing Zheng, Charles T Anderson, Katharine K Miller, MaryAnn Cheatham, and Peter Dallos PMCID: PMC2669096 Developmental gene expression profiles of the human pathogen Schistosoma japonicum Geoffrey N Gobert, Luke Moertel, Paul J Brindley, and Donald P McManus PMCID: PMC2670322 Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae William J Jo, Jeung Hyoun Kim, Eric Oh, Daniel Jaramillo, Patricia Holman, Alex V Loguinov, Adam P Arkin, Corey Nislow, Guri Giaever, and Chris D Vulpe PMCID: PMC2669097 Snapshot of iron response in Shewanella oneidensis by gene network reconstruction Yunfeng Yang, Daniel P Harris, Feng Luo, Wenlu Xiong, Marcin Joachimiak, Liyou Wu, Paramvir Dehal, Janet Jacobsen, Zamin Yang, Anthony V Palumbo, Adam P Arkin, and Jizhong Zhou PMCID: PMC2667191 The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA David Roy Smith and Robert W Lee PMCID: PMC2670323 Genomic regions with distinct genomic distance conservation in vertebrate genomes Hong Sun, Geir Skogerbø, Xiaohui Zheng, Wei Liu, and Yixue Li PMCID: PMC2667192 A robust linkage map of the porcine autosomes based on gene-associated SNPs Rikke KK Vingborg, Vivi R Gregersen, Bujie Zhan, Frank Panitz, Anette Høj, Kirsten K Sørensen, Lone B Madsen, Knud Larsen, Henrik Hornshøj, Xuefei Wang, and Christian Bendixen PMCID: PMC2674067 Comparative expression pathway analysis of human and canine mammary tumors Paolo Uva, Luigi Aurisicchio, James Watters, Andrey Loboda, Amit Kulkarni, John Castle, Fabio Palombo, Valentina Viti, Giuseppe Mesiti, Valentina Zappulli, Laura Marconato, Francesca Abramo, Gennaro Ciliberto, Armin Lahm, Nicola La Monica, and Emanuele de Rinaldis PMCID: PMC2670324 A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta Xin Shen, Xiaoyin Ma, Jianfeng Ren, and Fangqing Zhao PMCID: PMC2667193 Gene expression signature of cerebellar hypoplasia in a mouse model of Down syndrome during postnatal development Julien Laffaire, Isabelle Rivals, Luce Dauphinot, Fabien Pasteau, Rosine Wehrle, Benoit Larrat, Tania Vitalis, Randal X Moldrich, Jean Rossier, Ralph Sinkus, Yann Herault, Isabelle Dusart, and Marie-Claude Potier PMCID: PMC2678156 Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups Swarup Kumar Parida, Vivek Dalal, Ashok Kumar Singh, Nagendra Kumar Singh, and Trilochan Mohapatra PMCID: PMC2680414 Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio) by transcriptome profiling Liraz Levi, Irena Pekarski, Ellen Gutman, Paolo Fortina, Terry Hyslop, Jakob Biran, Berta Levavi-Sivan, and Esther Lubzens PMCID: PMC2678157 Adipogenic and energy metabolism gene networks in longissimus lumborum during rapid post-weaning growth in Angus and Angus × Simmental cattle fed high-starch or low-starch diets Daniel E Graugnard, Paola Piantoni, Massimo Bionaz, Larry L Berger, Dan B Faulkner, and Juan J Loor PMCID: PMC2676302 Determination of enriched histone modifications in non-genic portions of the human genome Jeffrey A Rosenfeld, Zhibin Wang, Dustin E Schones, Keji Zhao, Rob DeSalle, and Michael Q Zhang PMCID: PMC2667539 Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse Christine Steinhoff, Martina Paulsen, Szymon Kielbasa, Jörn Walter, and Martin Vingron PMCID: PMC2671526 The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota Iain J Anderson, Lakshmi Dharmarajan, Jason Rodriguez, Sean Hooper, Iris Porat, Luke E Ulrich, James G Elkins, Kostas Mavromatis, Hui Sun, Miriam Land, Alla Lapidus, Susan Lucas, Kerrie Barry, Harald Huber, Igor B Zhulin, William B Whitman, Biswarup Mukhopadhyay, Carl Woese, James Bristow, and Nikos Kyrpides PMCID: PMC2678158 The evolution of isochore patterns in vertebrate genomes Maria Costantini, Rosalia Cammarano, and Giorgio Bernardi PMCID: PMC2678159 Early iron-deficiency-induced transcriptional changes in Arabidopsis roots as revealed by microarray analyses Thomas J Buckhout, Thomas JW Yang, and Wolfgang Schmidt PMCID: PMC2676303 Identification and characterization of new miRNAs cloned from normal mouse mammary gland Nezha Sdassi, Licia Silveri, Johann Laubier, Gaëlle Tilly, José Costa, Sarah Layani, Jean-Luc Vilotte, and Fabienne Le Provost PMCID: PMC2683868 Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone Bastien Llamas, Ricardo A Verdugo, Gary A Churchill, and Christian F Deschepper PMCID: PMC2679052 Norepinephrine transport-mediated gene expression in noradrenergic neurogenesis Yao Fei Hu, Marc G Caron, and Maya Sieber-Blum PMCID: PMC2679758 Histone acetylations mark origins of polycistronic transcription in Leishmania major Sean Thomas, Amanda Green, Nancy R Sturm, David A Campbell, and Peter J Myler PMCID: PMC2679053 Learning from microarray interlaboratory studies: measures of precision for gene expression David L Duewer, Wendell D Jones, Laura H Reid, and Marc Salit PMCID: PMC2679054 Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome Edouard I Severing, Aalt DJ van Dijk, Willem J Stiekema, and Roeland CHJ van Ham PMCID: PMC2674458 Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana Kei Iida, Hailing Jin, and Jian-Kang Zhu PMCID: PMC2674459 The complete mitochondrial genomes of two band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus Chuan Ma, Chunxiang Liu, Pengcheng Yang, and Le Kang PMCID: PMC2674460 Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax Elena Sarropoulou, Pilar Sepulcre, Laura Poisa-Beiro, Victoriano Mulero, José Meseguer, Antonio Figueras, Beatriz Novoa, Vasso Terzoglou, Richard Reinhardt, Antonios Magoulas, and Georgios Kotoulas PMCID: PMC2674461 Genome evolution driven by host adaptations results in a more virulent and antimicrobial-resistant Streptococcus pneumoniae serotype 14 Feng Ding, Petrus Tang, Mei-Hua Hsu, Peng Cui, Songnian Hu, Jun Yu, and Cheng-Hsun Chiu PMCID: PMC2678160 Whole genome amplification and real-time PCR in forensic casework Emiliano Giardina, Ilenia Pietrangeli, Claudia Martone, Stefania Zampatti, Patrizio Marsala, Luciano Gabriele, Omero Ricci, Gianluca Solla, Paola Asili, Giovanni Arcudi, Aldo Spinella, and Giuseppe Novelli PMCID: PMC2675535 Evolution of alternative and constitutive regions of mammalian 5'UTRs Alissa M Resch, Aleksey Y Ogurtsov, Igor B Rogozin, Svetlana A Shabalina, and Eugene V Koonin PMCID: PMC2674463 A transcriptional sketch of a primary human breast cancer by 454 deep sequencing Alessandro Guffanti, Michele Iacono, Paride Pelucchi, Namshin Kim, Giulia Soldà, Larry J Croft, Ryan J Taft, Ermanno Rizzi, Marjan Askarian-Amiri, Raoul J Bonnal, Maurizio Callari, Flavio Mignone, Graziano Pesole, Giovanni Bertalot, Luigi Rossi Bernardi, Alberto Albertini, Christopher Lee, John S Mattick, Ileana Zucchi, and Gianluca De Bellis PMCID: PMC2678161 Functional annotation of the human retinal pigment epithelium transcriptome Judith C Booij, Simone van Soest, Sigrid MA Swagemakers, Anke HW Essing, Annemieke JMH Verkerk, Peter J van der Spek, Theo GMF Gorgels, and Arthur AB Bergen PMCID: PMC2679759 Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli Ye Jin, Rory M Watt, Antoine Danchin, and Jian-dong Huang PMCID: PMC2676305 Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction Pierre-Edouard Fournier, Khalid El Karkouri, Quentin Leroy, Catherine Robert, Bernadette Giumelli, Patricia Renesto, Cristina Socolovschi, Philippe Parola, Stéphane Audic, and Didier Raoult PMCID: PMC2694212 Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa Kuem Hee Jang and Ui Wook Hwang PMCID: PMC2678162 The γ-gliadin multigene family in common wheat (Triticum aestivum) and its closely related species Peng-Fei Qi, Yu-Ming Wei, Thérèse Ouellet, Qing Chen, Xin Tan, and You-Liang Zheng PMCID: PMC2685405 The cytochrome P450 (CYP) gene superfamily in Daphnia pulex William S Baldwin, Peter B Marko, and David R Nelson PMCID: PMC2678163 The ABC transporter gene family of Daphnia pulex Armin Sturm, Phil Cunningham, and Michael Dean PMCID: PMC2680897 LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia Thomas Fröhlich, Georg J Arnold, Rainer Fritsch, Tobias Mayr, and Christian Laforsch PMCID: PMC2674882 Comparative metagenomics of Daphnia symbionts Weihong Qi, Guang Nong, James F Preston, Frida Ben-Ami, and Dieter Ebert PMCID: PMC2678164 Reconstructing the phylogeny of 21 completely sequenced arthropod species based on their motor proteins Florian Odronitz, Sebastian Becker, and Martin Kollmar PMCID: PMC2674883 The components of the Daphnia pulex immune system as revealed by complete genome sequencing Seanna J McTaggart, Claire Conlon, John K Colbourne, Mark L Blaxter, and Tom J Little PMCID: PMC2685406 Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility Jean M Feugang, Abdullah Kaya, Grier P Page, Lang Chen, Tapan Mehta, Kashif Hirani, Lynne Nazareth, Einko Topper, Richard Gibbs, and Erdogan Memili PMCID: PMC2684547 Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae) Sean MacEachern, John McEwan, and Mike Goddard PMCID: PMC2694835 Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits William Barendse, Blair E Harrison, Rowan J Bunch, Merle B Thomas, and Lex B Turner PMCID: PMC2681478 Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle? Sean MacEachern, John McEwan, Alan McCulloch, Andrew Mather, Keith Savin, and Mike Goddard PMCID: PMC2681479 Bos taurus genome assembly Yue Liu, Xiang Qin, Xing-Zhi Henry Song, Huaiyang Jiang, Yufeng Shen, K James Durbin, Sigbjørn Lien, Matthew Peter Kent, Marte Sodeland, Yanru Ren, Lan Zhang, Erica Sodergren, Paul Havlak, Kim C Worley, George M Weinstock, and Richard A Gibbs PMCID: PMC2686734 An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle Sean MacEachern, Ben Hayes, John McEwan, and Mike Goddard PMCID: PMC2681480 A high resolution RH map of the bovine major histocompatibility complex Candice L Brinkmeyer-Langford, Christopher P Childers, Krista L Fritz, Ashley L Gustafson-Seabury, Marian Cothran, Terje Raudsepp, James E Womack, and Loren C Skow PMCID: PMC2682492 Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis Alper Uzun, Nelida Rodriguez-Osorio, Abdullah Kaya, Hongfeng Wang, John J Parrish, Valentin A Ilyin, and Erdogan Memili PMCID: PMC2684548 QTL global meta-analysis: are trait determining genes clustered? Hanni Salih and David L Adelson PMCID: PMC2683869 Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes Bhanu Prakash VL Telugu, Angela M Walker, and Jonathan A Green PMCID: PMC2682831 Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6 Rosemarie Weikard, Tom Goldammer, Annett Eberlein, and Christa Kuehn PMCID: PMC2681481 Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies Angela M Walker and R Michael Roberts PMCID: PMC2680415 Analysis of the complement and molecular evolution of tRNA genes in cow Dave TP Tang, Evgeny A Glazov, Sean M McWilliam, Wesley C Barris, and Brian P Dalrymple PMCID: PMC2680898 Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts Helen Piontkivska, Mary Q Yang, Denis M Larkin, Harris A Lewin, James Reecy, and Laura Elnitski PMCID: PMC2688522 Transcriptional reprogramming of gene expression in bovine somatic cell chromatin transfer embryos Nelida Rodriguez-Osorio, Zhongde Wang, Poothappillai Kasinathan, Grier P Page, James M Robl, and Erdogan Memili PMCID: PMC2695822 Genomic organization and classification of the bovine WC1 genes and expression by peripheral blood gamma delta T cells Carolyn TA Herzig and Cynthia L Baldwin PMCID: PMC2681482 Genomic analysis reveals extensive gene duplication within the bovine TRB locus Timothy Connelley, Jan Aerts, Andy Law, and W Ivan Morrison PMCID: PMC2685407 Comparative genomics of Enterococcus faecalis from healthy Norwegian infants Margrete Solheim, Ågot Aakra, Lars G Snipen, Dag A Brede, and Ingolf F Nes PMCID: PMC2680900 Parallel DNA pyrosequencing unveils new zebrafish microRNAs Ana R Soares, Patrícia M Pereira, Bruno Santos, Conceição Egas, Ana C Gomes, Joel Arrais, José L Oliveira, Gabriela R Moura, and Manuel AS Santos PMCID: PMC2684549 Molecular profiles of Quadriceps muscle in myostatin-null mice reveal PI3K and apoptotic pathways as myostatin targets Ilham Chelh, Bruno Meunier, Brigitte Picard, Mark James Reecy, Catherine Chevalier, Jean-François Hocquette, and Isabelle Cassar-Malek PMCID: PMC2684550 Gene set internal coherence in the context of functional profiling David Montaner, Pablo Minguez, Fátima Al-Shahrour, and Joaquín Dopazo PMCID: PMC2680416 M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island Alexandre Panchaud, Lionel Guy, François Collyn, Marisa Haenni, Masanobu Nakata, Andreas Podbielski, Philippe Moreillon, and Claude-Alain H Roten PMCID: PMC2683870 Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis Marianne Gamper, Volker Viereck, Verena Geissbühler, Jakob Eberhard, Jochen Binder, Carlo Moll, Hubert Rehrauer, and René Moser PMCID: PMC2686735 Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa L. reveals their developmental and stress regulation Hemant R Kushwaha, Anil K Singh, Sudhir K Sopory, Sneh L Singla-Pareek, and Ashwani Pareek PMCID: PMC2694836 Activation of p53-regulated pro-apoptotic signaling pathways in PrP-mediated myopathy Jingjing Liang, Debra Parchaliuk, Sarah Medina, Garrett Sorensen, Laura Landry, Shenghai Huang, Meiling Wang, Qingzhong Kong, and Stephanie A Booth PMCID: PMC2683871 Distinct patterns of gene and protein expression elicited by organophosphorus pesticides in Caenorhabditis elegans John A Lewis, Maria Szilagyi, Elizabeth Gehman, William E Dennis, and David A Jackson PMCID: PMC2689271 Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery Matthew C Hale, Cory R McCormick, James R Jackson, and J Andrew DeWoody PMCID: PMC2688523 In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity Ate van der Burgt, Mark WJE Fiers, Jan-Peter Nap, and Roeland CHJ van Ham PMCID: PMC2688010 Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1 Xiaodong Bai, Byron J Adams, Todd A Ciche, Sandra Clifton, Randy Gaugler, Saskia A Hogenhout, John Spieth, Paul W Sternberg, Richard K Wilson, and Parwinder S Grewal PMCID: PMC2686736 Identifying genes related to choriogenesis in insect panoistic ovaries by Suppression Subtractive Hybridization Paula Irles, Xavier Bellés, and M Dolors Piulachs PMCID: PMC2683872 Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility Grace M O'Gorman, Stephen DE Park, Emmeline W Hill, Kieran G Meade, Paul M Coussens, Morris Agaba, Jan Naessens, Stephen J Kemp, and David E MacHugh PMCID: PMC2685408 Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila Chengjie Fu, Jie Xiong, and Wei Miao PMCID: PMC2691746 Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2 Alan L Kwan, Linya Li, David C Kulp, Susan K Dutcher, and Gary D Stormo PMCID: PMC2694837 An integrated RH map of porcine chromosome 10 Jian-Gang Ma, Hiroshi Yasue, Katie E Eyer, Hideki Hiraiwa, Takeshi Shimogiri, Stacey N Meyers, Jonathan E Beever, Lawrence B Schook, Craig W Beattie, and Wan-Sheng Liu PMCID: PMC2689272 Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay Laurent G Deluc, David R Quilici, Alain Decendit, Jérôme Grimplet, Matthew D Wheatley, Karen A Schlauch, Jean-Michel Mérillon, John C Cushman, and Grant R Cramer PMCID: PMC2701440 Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE Xin Wang, Yongjun Zhao, Kim Wong, Peter Ehlers, Yuji Kohara, Steven J Jones, Marco A Marra, Robert A Holt, Donald G Moerman, and Dave Hansen PMCID: PMC2686737 Identification and target prediction of miRNAs specifically expressed in rat neural tissue You-Jia Hua, Zhong-Yi Tang, Kang Tu, Li Zhu, Yi-Xue Li, Lu Xie, and Hua-Sheng Xiao PMCID: PMC2688525 Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays Minjie Wang, Xiaoli Qi, Shutang Zhao, Shougong Zhang, and Meng-Zhu Lu PMCID: PMC2685409 Comparative genomics of Toll-like receptor signalling in five species Oliver C Jann, Annemarie King, Nestor Lopez Corrales, Susan I Anderson, Kirsty Jensen, Tahar Ait-ali, Haizhou Tang, Chunhua Wu, Noelle E Cockett, Alan L Archibald, and Elizabeth J Glass PMCID: PMC2689273 Ixodes scapularis tick serine proteinase inhibitor (serpin) gene family; annotation and transcriptional analysis Albert Mulenga, Rabuesak Khumthong, and Katelyn C Chalaire PMCID: PMC2689274 Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data Yu-Ping Wang and Kuo-Bin Li PMCID: PMC2686738 Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx Eli Meyer, Galina V Aglyamova, Shi Wang, Jade Buchanan-Carter, David Abrego, John K Colbourne, Bette L Willis, and Mikhail V Matz PMCID: PMC2689275 A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila Li Wang, Zhidong Tu, and Fengzhu Sun PMCID: PMC2697172 Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays Joshua S Bloom, Zia Khan, Leonid Kruglyak, Mona Singh, and Amy A Caudy PMCID: PMC2686739 Molecular identification of differentially regulated genes in the hydrothermal-vent species Bathymodiolus thermophilus and Paralvinella pandorae in response to temperature Isabelle Boutet, Didier Jollivet, Bruce Shillito, Dario Moraga, and Arnaud Tanguy PMCID: PMC2689276 An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines Jian Li, Fei Gao, Ning Li, Shengting Li, Guangliang Yin, Geng Tian, Shangang Jia, Kai Wang, Xiuqing Zhang, Huanming Yang, Anders Lade Nielsen, and Lars Bolund PMCID: PMC2696471 Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of Iridoviridae Youhua Huang, Xiaohong Huang, Hong Liu, Jie Gong, Zhengliang Ouyang, Huachun Cui, Jianhao Cao, Yingtao Zhao, Xiujie Wang, Yulin Jiang, and Qiwei Qin PMCID: PMC2689277 Effect of continuous light on diurnal rhythms in Cyanothece sp. ATCC 51142 Thanura Elvitigala, Jana Stöckel, Bijoy K Ghosh, and Himadri B Pakrasi PMCID: PMC2695482 Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches Bruce R Southey, Sandra L Rodriguez-Zas, and Jonathan V Sweedler PMCID: PMC2698874 A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment Shani Tzahor, Dikla Man-Aharonovich, Benjamin C Kirkup, Tali Yogev, Ilana Berman-Frank, Martin F Polz, Oded Béjà, and Yael Mandel-Gutfreund PMCID: PMC2696472 Distinct gene-expression profiles characterize mammary tumors developed in transgenic mice expressing constitutively active and C-terminally truncated variants of STAT5 Tali Eilon and Itamar Barash PMCID: PMC2689279 Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites Norma E Padilla-Mejía, Luis E Florencio-Martínez, Elisa E Figueroa-Angulo, Rebeca G Manning-Cela, Rosaura Hernández-Rivas, Peter J Myler, and Santiago Martínez-Calvillo PMCID: PMC2695483 Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells K Emelie M Blomberg, Nicole Boucheron, Jessica M Lindvall, Liang Yu, Julia Raberger, Anna Berglöf, Wilfried Ellmeier, and CI Edvard Smith PMCID: PMC2689280 Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis Daniel A Hahn, Gregory J Ragland, D DeWayne Shoemaker, and David L Denlinger PMCID: PMC2700817 A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism Isabelle Florent, Betina M Porcel, Elodie Guillaume, Corinne Da Silva, François Artiguenave, Eric Maréchal, Laurent Bréhélin, Olivier Gascuel, Sébastien Charneau, Patrick Wincker, and Philippe Grellier PMCID: PMC2695484 Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene Benjamin Nota, Mirte Bosse, Bauke Ylstra, Nico M van Straalen, and Dick Roelofs PMCID: PMC2688526 A comparative approach to elucidate chloroplast genome replication Neeraja M Krishnan and Basuthkar J Rao PMCID: PMC2695485 Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes Yuan Wu, Jian Yang, Fan Yang, Tao Liu, Wenchuan Leng, Yonglie Chu, and Qi Jin PMCID: PMC2693141 Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain Helena MB Seth-Smith, Simon R Harris, Kenneth Persson, Pete Marsh, Andrew Barron, Alexandra Bignell, Carina Bjartling, Louise Clark, Lesley T Cutcliffe, Paul R Lambden, Nicola Lennard, Sarah J Lockey, Michael A Quail, Omar Salim, Rachel J Skilton, Yibing Wang, Martin J Holland, Julian Parkhill, Nicholas R Thomson, and Ian N Clarke PMCID: PMC2693142 Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome Martin Smith, Frédéric Bringaud, and Barbara Papadopoulou PMCID: PMC2689281 A transcript profiling approach reveals the zinc finger transcription factor ZNF191 is a pleiotropic factor Jianzhong Li, Xia Chen, Xuelian Gong, Ying Liu, Hao Feng, Lei Qiu, Zhenlin Hu, and Junping Zhang PMCID: PMC2694838 Gene expression during Drosophila melanogaster egg development before and after reproductive diapause Dean A Baker and Steven Russell PMCID: PMC2700134 A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping Maria Domenica Moccia, Christine Oger-Desfeux, Gabriel AB Marais, and Alex Widmer PMCID: PMC2689282 Systems level analysis of two-component signal transduction systems in Erwinia amylovora: Role in virulence, regulation of amylovoran biosynthesis and swarming motility Youfu Zhao, Dongping Wang, Sridevi Nakka, George W Sundin, and Schuyler S Korban PMCID: PMC2698875 Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight Per Wahlberg, Örjan Carlborg, Mario Foglio, Xavier Tordoir, Ann-Christine Syvänen, Mark Lathrop, Ivo G Gut, Paul B Siegel, and Leif Andersson PMCID: PMC2695486 DDX11L: a novel transcript family emerging from human subtelomeric regions Valerio Costa, Amelia Casamassimi, Roberta Roberto, Fernando Gianfrancesco, Maria R Matarazzo, Michele D'Urso, Maurizio D'Esposito, Mariano Rocchi, and Alfredo Ciccodicola PMCID: PMC2705379 Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays Amy N Bernardo, Peter J Bradbury, Hongxiang Ma, Shengwa Hu, Robert L Bowden, Edward S Buckler, and Guihua Bai PMCID: PMC2698007 Cytokine-dependent and–independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling Jaime A Costales, Johanna P Daily, and Barbara A Burleigh PMCID: PMC2709661 Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array Tristan E Coram, Matthew L Settles, and Xianming Chen PMCID: PMC2694213 Transcriptional analysis of the mammalian heart with special reference to its endocrine function Monica Forero McGrath and Adolfo J de Bold PMCID: PMC2694839 Chromosome level assembly of the hybrid Trypanosoma cruzi genome D Brent Weatherly, Courtney Boehlke, and Rick L Tarleton PMCID: PMC2698008 Probing the endosperm gene expression landscape in Brassica napus Yi Huang, Liang Chen, Liping Wang, Kannan Vijayan, Sieu Phan, Ziying Liu, Lianglu Wan, Andrew Ross, Daoquan Xiang, Raju Datla, Youlian Pan, and Jitao Zou PMCID: PMC2702316 Genome-wide transcriptomic profiling of Anopheles gambiae hemocytes reveals pathogen-specific signatures upon bacterial challenge and Plasmodium berghei infection Luke A Baton, Anne Robertson, Emma Warr, Michael R Strand, and George Dimopoulos PMCID: PMC2703655 Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont Shinichi Sunagawa, Emily C Wilson, Michael Thaler, Marc L Smith, Carlo Caruso, John R Pringle, Virginia M Weis, Mónica Medina, and Jodi A Schwarz PMCID: PMC2702317 Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing Timothy B Sackton and Andrew G Clark PMCID: PMC2701966 Gene expression profiling within the spleen of Clostridium perfringens-challenged Broilers fed antibiotic-medicated and non-medicated diets Aimie J Sarson, Ying Wang, Zhumei Kang, Scot E Dowd, Yang Lu, Hai Yu, Yanming Han, Huaijun Zhou, and Joshua Gong PMCID: PMC2703656 Molecular signature of cell cycle exit induced in human T lymphoblasts by IL-2 withdrawal Magdalena Chechlinska, Jan Konrad Siwicki, Monika Gos, Malgorzata Oczko-Wojciechowska, Michal Jarzab, Aleksandra Pfeifer, Barbara Jarzab, and Jan Steffen PMCID: PMC2706892 Gene expression profiling of intestinal regeneration in the sea cucumber Pablo A Ortiz-Pineda, Francisco Ramírez-Gómez, Judit Pérez-Ortiz, Sebastián González-Díaz, Francisco Santiago-De Jesús, Josue Hernández-Pasos, Cristina Del Valle-Avila, Carmencita Rojas-Cartagena, Edna C Suárez-Castillo, Karen Tossas, Ana T Méndez-Merced, José L Roig-López, Humberto Ortiz-Zuazaga, and José E García-Arrarás PMCID: PMC2711116 The repertoire of G-protein-coupled receptors in Xenopus tropicalis Yanping Ji, Zhen Zhang, and Yinghe Hu PMCID: PMC2709155 Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing Shrinivasrao P Mane, Clive Evans, Kristal L Cooper, Oswald R Crasta, Otto Folkerts, Stephen K Hutchison, Timothy T Harkins, Danielle Thierry-Mieg, Jean Thierry-Mieg, and Roderick V Jensen PMCID: PMC2707382 Gene expression profiling in peanut using high density oligonucleotide microarrays Paxton Payton, Kameswara Rao Kottapalli, Diane Rowland, Wilson Faircloth, Baozhu Guo, Mark Burow, Naveen Puppala, and Maria Gallo PMCID: PMC2703657 Epistatic interactions modulate the evolution of mammalian mitochondrial respiratory complex components Luísa Azevedo, João Carneiro, Barbara van Asch, Ana Moleirinho, Filipe Pereira, and António Amorim PMCID: PMC2711975 Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3 Ben-Wen Li, Amy C Rush, Makedonka Mitreva, Yong Yin, David Spiro, Elodie Ghedin, and Gary J Weil PMCID: PMC2708187 Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique' Michelle M Meyer, Tyler D Ames, Daniel P Smith, Zasha Weinberg, Michael S Schwalbach, Stephen J Giovannoni, and Ronald R Breaker PMCID: PMC2704228 Definition, conservation and epigenetics of housekeeping and tissue-enriched genes Xinwei She, Carol A Rohl, John C Castle, Amit V Kulkarni, Jason M Johnson, and Ronghua Chen PMCID: PMC2706266 Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events Sónia S Albuquerque, Céline Carret, Ana Rita Grosso, Alice S Tarun, Xinxia Peng, Stefan HI Kappe, Miguel Prudêncio, and Maria M Mota PMCID: PMC2706893 Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns Kanako Kawaura, Keiichi Mochida, Akiko Enju, Yasushi Totoki, Atsushi Toyoda, Yoshiyuki Sakaki, Chikatoshi Kai, Jun Kawai, Yoshihide Hayashizaki, Motoaki Seki, Kazuo Shinozaki, and Yasunari Ogihara PMCID: PMC2703658 Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes Jeff W Chou and Pierre R Bushel PMCID: PMC2706894 Mapping of heterologous expressed sequence tags as an alternative to microarrays for study of defense responses in plants Alexander M Boutanaev, Olga A Postnikova, and Lev G Nemchinov PMCID: PMC2706895 Maternal diabetes alters transcriptional programs in the developing embryo Gabriela Pavlinkova, J Michael Salbaum, and Claudia Kappen PMCID: PMC2715936 Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis Farkhanda S Khowaja, Gareth J Norton, Brigitte Courtois, and Adam H Price PMCID: PMC2708188 Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout Hooman K Moghadam, Moira M Ferguson, and Roy G Danzmann PMCID: PMC2711117 Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome Alessio Aprile, Anna M Mastrangelo, Anna M De Leonardis, Gabor Galiba, Enrica Roncaglia, Francesco Ferrari, Luigi De Bellis, Luana Turchi, Giovanni Giuliano, and Luigi Cattivelli PMCID: PMC2713995 Impact of animal strain on gene expression in a rat model of acute cardiac rejection Katherine J Deans, Peter C Minneci, Hao Chen, Steven J Kern, Carolea Logun, Sara Alsaaty, Kelly J Norsworthy, Stephanie M Theel, Joel D Sennesh, Jennifer J Barb, Peter J Munson, Robert L Danner, and Michael A Solomon PMCID: PMC2711118 Analysis of salivary transcripts and antigens of the sand fly Phlebotomus arabicus Jitka Hostomská, Věra Volfová, Jianbing Mu, Mark Garfield, Iva Rohoušová, Petr Volf, Jesus G Valenzuela, and Ryan C Jochim PMCID: PMC2714351 Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species Chengcang Wu, Dina Proestou, Dorothy Carter, Erica Nicholson, Filippe Santos, Shaying Zhao, Hong-Bin Zhang, and Marian R Goldsmith PMCID: PMC2718931 Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation Xi Wang, Georg Haberer, and Klaus FX Mayer PMCID: PMC2714861 Comparative transcriptomics in the Triticeae Andreas W Schreiber, Tim Sutton, Rico A Caldo, Elena Kalashyan, Ben Lovell, Gwenda Mayo, Gary J Muehlbauer, Arnis Druka, Robbie Waugh, Roger P Wise, Peter Langridge, and Ute Baumann PMCID: PMC2717122 Expressed sequence tags from larval gut of the European corn borer (Ostrinia nubilalis): Exploring candidate genes potentially involved in Bacillus thuringiensis toxicity and resistance Chitvan Khajuria, Yu Cheng Zhu, Ming-Shun Chen, Lawrent L Buschman, Randall A Higgins, Jianxiu Yao, Andre LB Crespo, Blair D Siegfried, Subbaratnam Muthukrishnan, and Kun Yan Zhu PMCID: PMC2717985 In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence Chad R Laing, Cody Buchanan, Eduardo N Taboada, Yongxiang Zhang, Mohamed A Karmali, James E Thomas, and Victor PJ Gannon PMCID: PMC2719669 Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression Stefanie De Bodt, Sebastian Proost, Klaas Vandepoele, Pierre Rouzé, and Yves Van de Peer PMCID: PMC2719670 cDNA-AFLP analysis reveals differential gene expression in compatible interaction of wheat challenged with Puccinia striiformis f. sp. tritici Xiaojie Wang, Chunlei Tang, Gang Zhang, Yingchun Li, Chenfang Wang, Bo Liu, Zhipeng Qu, Jie Zhao, Qingmei Han, Lili Huang, Xianming Chen, and Zhensheng Kang PMCID: PMC2717123 Transcriptome analysis of the venom gland of the scorpion Scorpiops jendeki: implication for the evolution of the scorpion venom arsenal Yibao Ma, Ruiming Zhao, Yawen He, Songryong Li, Jun Liu, Yingliang Wu, Zhijian Cao, and Wenxin Li PMCID: PMC2713264 Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH) Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell, and Ian G Charles PMCID: PMC2721850 Disorders of sex development expose transcriptional autonomy of genetic sex and androgen-programmed hormonal sex in human blood leukocytes Paul-Martin Holterhus, Jan-Hendrik Bebermeier, Ralf Werner, Janos Demeter, Annette Richter-Unruh, Gunnar Cario, Mahesh Appari, Reiner Siebert, Felix Riepe, James D Brooks, and Olaf Hiort PMCID: PMC2713997 A BAC-based physical map of the Hessian fly genome anchored to polytene chromosomes Rajat Aggarwal, Thiago R Benatti, Navdeep Gill, Chaoyang Zhao, Ming-Shun Chen, John P Fellers, Brandon J Schemerhorn, and Jeff J Stuart PMCID: PMC2709663 Differential expression proteomics to investigate responses and resistance to Orobanche crenata in Medicago truncatula Ma Ángeles Castillejo, Ana M Maldonado, Eliane Dumas-Gaudot, Mónica Fernández-Aparicio, Rafael Susín, Rubiales Diego, and Jesús V Jorrín PMCID: PMC2714000 Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus Christian Obermeier, Bashir Hosseini, Wolfgang Friedt, and Rod Snowdon PMCID: PMC2719671 Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex Galeb S Abu-Ali, David W Lacher, Lukas M Wick, Weihong Qi, and Thomas S Whittam PMCID: PMC2713265 Whole genome expression analysis within the angiotensin II-apolipoprotein E deficient mouse model of abdominal aortic aneurysm Catherine Rush, Moses Nyara, Joseph V Moxon, Alexandra Trollope, Bradford Cullen, and Jonathan Golledge PMCID: PMC2728106 Analysis of expression in the Anopheles gambiae developing testes reveals rapidly evolving lineage-specific genes in mosquitoes Elzbieta Krzywinska and Jaroslaw Krzywinski PMCID: PMC2713267 Systemic treatment of xenografts with vaccinia virus GLV-1h68 reveals the immunologic facet of oncolytic therapy Andrea Worschech, Nanhai Chen, Yong A Yu, Qian Zhang, Zoltan Pos, Stephanie Weibel, Viktoria Raab, Marianna Sabatino, Alessandro Monaco, Hui Liu, Vladia Monsurró, R Mark Buller, David F Stroncek, Ena Wang, Aladar A Szalay, and Francesco M Marincola PMCID: PMC2713268 Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens Paul Wilkinson, Nicholas R Waterfield, Lisa Crossman, Craig Corton, Maria Sanchez-Contreras, Isabella Vlisidou, Andrew Barron, Alexandra Bignell, Louise Clark, Douglas Ormond, Matthew Mayho, Nathalie Bason, Frances Smith, Mark Simmonds, Carol Churcher, David Harris, Nicholas R Thompson, Michael Quail, Julian Parkhill, and Richard H ffrench-Constant PMCID: PMC2717986 Expressional dynamics of minisatellite 33.15 tagged spermatozoal transcriptome in Bubalus bubalis Jyoti Srivastava, Sanjay Premi, Sudhir Kumar, and Sher Ali PMCID: PMC2713999 Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Jiang Wang, Yangyang Deng, and Caisheng He PMCID: PMC2713269 Coordinated patterns of gene expressions for adult muscle build-up in transgenic mice expressing myostatin propeptide Baoping Zhao, Eileena J Li, Robert J Wall, and Jinzeng Yang PMCID: PMC2713998 Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model Jin Hwan Do, Rui Yamaguchi, and Satoru Miyano PMCID: PMC2714559 Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen Natàlia Garcia-Reyero, Kevin J Kroll, Li Liu, Edward F Orlando, Karen H Watanabe, María S Sepúlveda, Daniel L Villeneuve, Edward J Perkins, Gerald T Ankley, and Nancy D Denslow PMCID: PMC2713996 Genomic evidence for non-random endemic populations of decaying exons from mammalian genes David DeLima Morais and Paul M Harrison PMCID: PMC2718932 MHC-linked and un-linked class I genes in the wallaby Hannah V Siddle, Janine E Deakin, Penny Coggill, Elizabeth Hart, Yuanyuan Cheng, Emily SW Wong, Jennifer Harrow, Stephan Beck, and Katherine Belov PMCID: PMC2719672 Genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30 John M Taylor, Sofiane Ghorbel, and Christophe Nicot PMCID: PMC2723137 Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs Hiroyuki Wakaguri, Yutaka Suzuki, Masahide Sasaki, Sumio Sugano, and Junichi Watanabe PMCID: PMC2722674 Divergence in function and expression of the NOD26-like intrinsic proteins in plants Qingpo Liu, Huasen Wang, Zhonghua Zhang, Jiasheng Wu, Ying Feng, and Zhujun Zhu PMCID: PMC2726226 In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach Lukas Chavez, Abha S Bais, Martin Vingron, Hans Lehrach, James Adjaye, and Ralf Herwig PMCID: PMC2714862 Identification and characterization of pseudogenes in the rice gene complement Françoise Thibaud-Nissen, Shu Ouyang, and C Robin Buell PMCID: PMC2724416 A method for identifying alternative or cryptic donor splice sites within gene and mRNA sequences. Comparisons among sequences from vertebrates, echinoderms and other groups Katherine M Buckley, Liliana D Florea, and L Courtney Smith PMCID: PMC2721852 Gene expression patterns in heterozygous Plk4 murine embryonic fibroblasts Alan Morettin, Alejandra Ward, Jordan Nantais, and John W Hudson PMCID: PMC2727538 High, clustered, nucleotide diversity in the genome of Anopheles gambiae revealed through pooled-template sequencing: implications for high-throughput genotyping protocols Craig S Wilding, David Weetman, Keith Steen, and Martin J Donnelly PMCID: PMC2723138 Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates Adrian F Gombart, Tsuyako Saito, and H Phillip Koeffler PMCID: PMC2716374 GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation Murat A Abdurashitov, Valery A Chernukhin, Danila A Gonchar, and Sergey Kh Degtyarev PMCID: PMC2722675 A Myc-regulated transcriptional network controls B-cell fate in response to BCR triggering Jernej Murn, Irena Mlinaric-Rascan, Pierre Vaigot, Olivier Alibert, Vincent Frouin, and Xavier Gidrol PMCID: PMC2722676 Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues Anita Grigoriadis, Gavin R Oliver, Austin Tanney, Howard Kendrick, Matt J Smalley, Parmjit Jat, and A Munro Neville PMCID: PMC2721853 A comparison of RNA amplification techniques at sub-nanogram input concentration Julie E Lang, Mark Jesus M Magbanua, Janet H Scott, G Mike Makrigiorgos, Gang Wang, Scot Federman, Laura J Esserman, John W Park, and Christopher M Haqq PMCID: PMC2724417 Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells Mike J Mason, Guoping Fan, Kathrin Plath, Qing Zhou, and Steve Horvath PMCID: PMC2727539 Surviving the cold: molecular analyses of insect cryoprotective dehydration in the Arctic springtail Megaphorura arctica (Tullberg) Melody S Clark, Michael AS Thorne, Jelena Purać, Gavin Burns, Guy Hillyard, Željko D Popović, Gordana Grubor-Lajšić, and M Roger Worland PMCID: PMC2726227 Polymorphic segmental duplication in the nematode Caenorhabditis elegans Ismael A Vergara, Allan K Mah, Jim C Huang, Maja Tarailo-Graovac, Robert C Johnsen, David L Baillie, and Nansheng Chen PMCID: PMC2728738 The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements Fabrício R Lopes, Joana C Silva, Marlene Benchimol, Gustavo GL Costa, Gonçalo AG Pereira, and Claudia MA Carareto PMCID: PMC2725143 Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens Ching Leang, Julia Krushkal, Toshiyuki Ueki, Marko Puljic, Jun Sun, Katy Juárez, Cinthia Núñez, Gemma Reguera, Raymond DiDonato, Bradley Postier, Ronald M Adkins, and Derek R Lovley PMCID: PMC2725144 The Odorant Binding Protein Gene Family from the Genome of Silkworm, Bombyx mori Da-Ping Gong, Hui-Jie Zhang, Ping Zhao, Qing-You Xia, and Zhong-Huai Xiang PMCID: PMC2722677 Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis Cécile Sabourault, Philippe Ganot, Emeline Deleury, Denis Allemand, and Paola Furla PMCID: PMC2727540 Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty Mark S Longo, Dawn M Carone, NISC Comparative Sequencing Program, Eric D Green, Michael J O'Neill, and Rachel J O'Neill PMCID: PMC2736999 Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation Claire Lemaitre, Lamia Zaghloul, Marie-France Sagot, Christian Gautier, Alain Arneodo, Eric Tannier, and Benjamin Audit PMCID: PMC2722678 A comparative genomics approach to understanding the biosynthesis of the sunscreen scytonemin in cyanobacteria Tanya Soule, Kendra Palmer, Qunjie Gao, Ruth M Potrafka, Valerie Stout, and Ferran Garcia-Pichel PMCID: PMC2726228 Detection of differentially expressed genes between Erhualian and Large White placentas on day 75 and 90 of gestation Quan-Yong Zhou, Ming-Di Fang, Ting-Hua Huang, Chang-Chun Li, Mei Yu, and Shu-Hong Zhao PMCID: PMC2724418 Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD Elena Bosch, Hafid Laayouni, Carlos Morcillo-Suarez, Ferran Casals, Andrés Moreno-Estrada, Anna Ferrer-Admetlla, Michelle Gardner, Araceli Rosa, Arcadi Navarro, David Comas, Jan Graffelman, Francesc Calafell, and Jaume Bertranpetit PMCID: PMC2723139 A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression Wen Juan Mo, Xu Ping Fu, Xiao Tian Han, Guang Yuan Yang, Ji Gang Zhang, Feng Hua Guo, Yan Huang, Yu Min Mao, Yao Li, and Yi Xie PMCID: PMC2737000 Gene expression profiles in mouse embryo fibroblasts lacking stathmin, a microtubule regulatory protein, reveal changes in the expression of genes contributing to cell motility Danielle N Ringhoff and Lynne Cassimeris PMCID: PMC2725145 Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing Erik Kristiansson, Noomi Asker, Lars Förlin, and DG Joakim Larsson PMCID: PMC2725146 Stretches of alternating pyrimidine/purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes Jon Bohlin, Simon P Hardy, and David W Ussery PMCID: PMC2728739 Proteomic-based identification of maternal proteins in mature mouse oocytes Ping Zhang, Xiaojian Ni, Ying Guo, Xuejiang Guo, Yufeng Wang, Zuomin Zhou, Ran Huo, and Jiahao Sha PMCID: PMC2730056 Type I interferon receptor-independent and -dependent host transcriptional responses to mouse hepatitis coronavirus infection in vivo Matthijs Raaben, Marian JA Groot Koerkamp, Peter JM Rottier, and Cornelis AM de Haan PMCID: PMC2728740 Brucella microti: the genome sequence of an emerging pathogen Stéphane Audic, Magali Lescot, Jean-Michel Claverie, and Holger C Scholz PMCID: PMC2743711 Gene copy number variation throughout the Plasmodium falciparum genome Ian H Cheeseman, Natalia Gomez-Escobar, Celine K Carret, Alasdair Ivens, Lindsay B Stewart, Kevin KA Tetteh, and David J Conway PMCID: PMC2732925 Statistical aspects of discerning indel-type structural variation via DNA sequence alignment Michael C Wendl and Richard K Wilson PMCID: PMC2748092 A proposed syntax for Minimotif Semantics, version 1 Jay Vyas, Ronald J Nowling, Mark W Maciejewski, Sanguthevar Rajasekaran, Michael R Gryk, and Martin R Schiller PMCID: PMC2733157 Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae) Richard H Baker, Jenna Morgan, Xianhui Wang, Jeffrey L Boore, and Gerald S Wilkinson PMCID: PMC2737001 Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes Nicolas Smargiasso, Valérie Gabelica, Christian Damblon, Frédéric Rosu, Edwin De Pauw, Marie-Paule Teulade-Fichou, J Alexandra Rowe, and Antoine Claessens PMCID: PMC2736202 Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor Anita Zamboni, Pamela Gatto, Alessandro Cestaro, Stefania Pilati, Roberto Viola, Fulvio Mattivi, Claudio Moser, and Riccardo Velasco PMCID: PMC2743712 Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea Lars Podsiadlowski, Anke Braband, Torsten H Struck, Jörn von Döhren, and Thomas Bartolomaeus PMCID: PMC2728741 Correlations between RNA and protein expression profiles in 23 human cell lines Marcus Gry, Rebecca Rimini, Sara Strömberg, Anna Asplund, Fredrik Pontén, Mathias Uhlén, and Peter Nilsson PMCID: PMC2728742 Complexity of the MSG gene family of Pneumocystis carinii Scott P Keely and James R Stringer PMCID: PMC2743713 Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait Thomas Moen, Matthew Baranski, Anna K Sonesson, and Sissel Kjøglum PMCID: PMC2728743 The adult boar testicular and epididymal transcriptomes Benoît Guyonnet, Guillemette Marot, Jean-Louis Dacheux, Marie-José Mercat, Sandrine Schwob, Florence Jaffrézic, and Jean-Luc Gatti PMCID: PMC2738690 Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling Paul Lacaze, Sobia Raza, Garwin Sing, David Page, Thorsten Forster, Petter Storm, Marie Craigon, Tarif Awad, Peter Ghazal, and Tom C Freeman PMCID: PMC2741489 Identification and expression of differentially expressed genes in the hard clam, Mercenaria mercenaria, in response to quahog parasite unknown (QPX) Mickael Perrigault, Arnaud Tanguy, and Bassem Allam PMCID: PMC2752465 High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs Nicole AR Walter, Daniel Bottomly, Ted Laderas, Michael A Mooney, Priscila Darakjian, Robert P Searles, Christina A Harrington, Shannon K McWeeney, Robert Hitzemann, and Kari J Buck PMCID: PMC2743714 The degree of microbiome complexity influences the epithelial response to infection Jeffrey J Mans, Kate von Lackum, Cassandra Dorsey, Shaun Willis, Shannon M Wallet, Henry V Baker, Richard J Lamont, and Martin Handfield PMCID: PMC2736203 What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae) David A Rasmussen and Mohamed AF Noor PMCID: PMC2735751 Involvement of potential pathways in malignant transformation from Oral Leukoplakia to Oral Squamous Cell Carcinoma revealed by proteomic analysis Zhi Wang, Xiaodong Feng, Xinyu Liu, Lu Jiang, Xin Zeng, Ning Ji, Jing Li, Longjiang Li, and Qianming Chen PMCID: PMC2746235 Effect of CAR activation on selected metabolic pathways in normal and hyperlipidemic mouse livers Tadeja Režen, Viola Tamasi, Anita Lövgren-Sandblom, Ingemar Björkhem, Urs A Meyer, and Damjana Rozman PMCID: PMC2739862 Generation, annotation, and analysis of ESTs from midgut tissue of adult female Anopheles stephensi mosquitoes Deepak P Patil, Santosh Atanur, Dhiraj P Dhotre, D Anantharam, Vineet S Mahajan, Sandeep A Walujkar, Rakesh K Chandode, Girish J Kulkarni, Pankaj S Ghate, Abhishek Srivastav, Kannayakanahalli M Dayananda, Neha Gupta, Bhakti Bhagwat, Rajendra R Joshi, Devendra T Mourya, Milind S Patole, and Yogesh S Shouche PMCID: PMC2743715 Mitochondrial dysregulation and oxidative stress in patients with chronic kidney disease Simona Granata, Gianluigi Zaza, Simona Simone, Gaetano Villani, Dominga Latorre, Paola Pontrelli, Massimo Carella, Francesco Paolo Schena, Giuseppe Grandaliano, and Giovanni Pertosa PMCID: PMC2737002 An integrated genetic linkage map for silkworms with three parental combinations and its application to the mapping of single genes and QTL Shuai Zhan, Jianhua Huang, Qiuhong Guo, Yunpo Zhao, Weihua Li, Xuexia Miao, Marian R Goldsmith, Muwang Li, and Yongping Huang PMCID: PMC2741490 Properties of untranslated regions of the S. cerevisiae genome Tamir Tuller, Eytan Ruppin, and Martin Kupiec PMCID: PMC2737003 Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes Koji Numata, Yuko Osada, Yuki Okada, Rintaro Saito, Noriko Hiraiwa, Hajime Nakaoka, Naoyuki Yamamoto, Kazufumi Watanabe, Kazue Okubo, Chihiro Kohama, Akio Kanai, Kuniya Abe, and Hidenori Kiyosawa PMCID: PMC2741491 Rice sHsp genes: genomic organization and expression profiling under stress and development Neelam K Sarkar, Yeon-Ki Kim, and Anil Grover PMCID: PMC2746236 Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans Raquel Quatrini, Corinne Appia-Ayme, Yann Denis, Eugenia Jedlicki, David S Holmes, and Violaine Bonnefoy PMCID: PMC2754497 A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528 David J Studholme, Selena Gimenez Ibanez, Daniel MacLean, Jeffery L Dangl, Jeff H Chang, and John P Rathjen PMCID: PMC2745422 A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain Trine B Rounge, Thomas Rohrlack, Alexander J Nederbragt, Tom Kristensen, and Kjetill S Jakobsen PMCID: PMC2739229 Implications of high level pseudogene transcription in Mycobacterium leprae Diana L Williams, Richard A Slayden, Amol Amin, Alejandra N Martinez, Tana L Pittman, Alex Mira, Anirban Mitra, Valakunja Nagaraja, Norman E Morrison, Milton Moraes, and Thomas P Gillis PMCID: PMC2753549 Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress Harkamal Walia, Clyde Wilson, Abdelbagi M Ismail, Timothy J Close, and Xinping Cui PMCID: PMC2739230 Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development Fiammetta Alagna, Nunzio D'Agostino, Laura Torchia, Maurizio Servili, Rosa Rao, Marco Pietrella, Giovanni Giuliano, Maria Luisa Chiusano, Luciana Baldoni, and Gaetano Perrotta PMCID: PMC2748093 CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations Bart PP van Houte, Thomas W Binsl, Hannes Hettling, Walter Pirovano, and Jaap Heringa PMCID: PMC2748095 Two distinct groups of porcine enteropathogenic Escherichia coli strains of serogroup O45 are revealed by comparative genomic hybridization and virulence gene microarray Guillaume Bruant, Yongxiang Zhang, Philippe Garneau, Justin Wong, Chad Laing, John M Fairbrother, Victor PJ Gannon, and Josée Harel PMCID: PMC2749873 Transcriptional profiling reveals developmental relationship and distinct biological functions of CD16+ and CD16- monocyte subsets Petronela Ancuta, Kuang-Yu Liu, Vikas Misra, Vanessa Sue Wacleche, Annie Gosselin, Xiaobo Zhou, and Dana Gabuzda PMCID: PMC2741492 Streptococcus pneumoniae nasopharyngeal colonization induces type I interferons and interferon-induced gene expression Elizabeth A Joyce, Stephen J Popper, and Stanley Falkow PMCID: PMC2743716 Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients Christiaan GJ Saris, Steve Horvath, Paul WJ van Vught, Michael A van Es, Hylke M Blauw, Tova F Fuller, Peter Langfelder, Joseph DeYoung, John HJ Wokke, Jan H Veldink, Leonard H van den Berg, and Roel A Ophoff PMCID: PMC2743717 Molecular mechanisms of tungstate-induced pancreatic plasticity: a transcriptomics approach Jordi Altirriba, Albert Barbera, Héctor Del Zotto, Belen Nadal, Sandra Piquer, Alex Sánchez-Pla, Juan J Gagliardino, and Ramon Gomis PMCID: PMC2741493 Hypoxic transcription gene profiles under the modulation of nitric oxide in nuclear run on-microarray and proteomics Emeka I Igwe, Silke Essler, Natalie Al-Furoukh, Nathalie Dehne, and Bernhard Brüne PMCID: PMC2743718 Transcriptional response of the model planctomycete Rhodopirellula baltica SH1T to changing environmental conditions Patricia Wecker, Christine Klockow, Andreas Ellrott, Christian Quast, Philipp Langhammer, Jens Harder, and Frank Oliver Glöckner PMCID: PMC2754498 Sequence features associated with microRNA strand selection in humans and flies Hai Yang Hu, Zheng Yan, Ying Xu, Hao Hu, Corinna Menzel, Yan Hong Zhou, Wei Chen, and Philipp Khaitovich PMCID: PMC2751786 Isolation and sequence analysis of the wheat B genome subtelomeric DNA Elena A Salina, Ekaterina M Sergeeva, Irina G Adonina, Andrey B Shcherban, Dmitry A Afonnikov, Harry Belcram, Cecile Huneau, and Boulos Chalhoub PMCID: PMC2756281 Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity Nasheeman Ashraf, Deepali Ghai, Pranjan Barman, Swaraj Basu, Nagaraju Gangisetty, Mihir K Mandal, Niranjan Chakraborty, Asis Datta, and Subhra Chakraborty PMCID: PMC2755012 Comparative analysis of the mammalian WNT4 promoter Hongshi Yu, Andrew J Pask, Geoffrey Shaw, and Marilyn B Renfree PMCID: PMC2758904 GATA3 is a master regulator of the transcriptional response to low-dose ionizing radiation in human keratinocytes Florian Bonin, Manuella Molina, Claude Malet, Chantal Ginestet, Odile Berthier-Vergnes, Michèle T Martin, and Jérôme Lamartine PMCID: PMC2753551 Genome-wide analysis of Tol2 transposon reintegration in zebrafish Igor Kondrychyn, Marta Garcia-Lecea, Alexander Emelyanov, Sergey Parinov, and Vladimir Korzh PMCID: PMC2753552 Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation Sergei A Manakov, Seth GN Grant, and Anton J Enright PMCID: PMC2759968 Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation Tamara Aid-Pavlidis, Pavlos Pavlidis, and Tõnis Timmusk PMCID: PMC2748098 Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality Paula Vizoso, Lee A Meisel, Andrés Tittarelli, Mariano Latorre, Juan Saba, Rodrigo Caroca, Jonathan Maldonado, Veronica Cambiazo, Reinaldo Campos-Vargas, Mauricio Gonzalez, Ariel Orellana, and Herman Silva PMCID: PMC2748099 Genome-wide analysis of signal peptide functionality in Lactobacillus plantarum WCFS1 Geir Mathiesen, Anita Sveen, May Bente Brurberg, Lasse Fredriksen, Lars Axelsson, and Vincent GH Eijsink PMCID: PMC2748100 Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei Sarah Kabani, Katelyn Fenn, Alan Ross, Al Ivens, Terry K Smith, Peter Ghazal, and Keith Matthews PMCID: PMC2753553 A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus M Carmen Marques, Hugo Alonso-Cantabrana, Javier Forment, Raquel Arribas, Santiago Alamar, Vicente Conejero, and Miguel A Perez-Amador PMCID: PMC2754500 Transcriptome analysis of the responses of Staphylococcus aureus to antimicrobial peptides and characterization of the roles of vraDE and vraSR in antimicrobial resistance Milla Pietiäinen, Patrice François, Hanne-Leena Hyyryläinen, Manuela Tangomo, Vera Sass, Hans-Georg Sahl, Jacques Schrenzel, and Vesa P Kontinen PMCID: PMC2748101 Gene array analysis of adrenal glands in broiler chickens following ACTH treatment Clara Bureau, Christelle Hennequet-Antier, Michel Couty, and Daniel Guémené PMCID: PMC2751787 The relationship between the evolution of microRNA targets and the length of their UTRs Chao Cheng, Nitin Bhardwaj, and Mark Gerstein PMCID: PMC2758905 Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa HyeRan Kim, Su Ryun Choi, Jina Bae, Chang Pyo Hong, Seo Yeon Lee, Md Jamil Hossain, Dan Van Nguyen, Mina Jin, Beom-Seok Park, Jea-Wook Bang, Ian Bancroft, and Yong Pyo Lim PMCID: PMC2761421 Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis Ruisheng An, Srinand Sreevatsan, and Parwinder S Grewal PMCID: PMC2760582 New insights into molecular pathways associated with flatfish ovarian development and atresia revealed by transcriptional analysis Angèle Tingaud-Sequeira, François Chauvigné, Juanjo Lozano, María J Agulleiro, Esther Asensio, and Joan Cerdà PMCID: PMC2751788 Assessing the genomic evidence for conserved transcribed pseudogenes under selection Amit N Khachane and Paul M Harrison PMCID: PMC2753554 Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa Mark W Davey, Neil S Graham, Bartel Vanholme, Rony Swennen, Sean T May, and Johan Keulemans PMCID: PMC2761422 Pepsin homologues in bacteria Neil D Rawlings and Alex Bateman PMCID: PMC2761423 Zooplankton diversity analysis through single-gene sequencing of a community sample Ryuji J Machida, Yasuyuki Hashiguchi, Mutsumi Nishida, and Shuhei Nishida PMCID: PMC2751789 Phase Coupled Meta-analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast Saumyadipta Pyne, Roee Gutman, Chang Sik Kim, and Bruce Futcher PMCID: PMC2753555 Reciprocal regulation by the CepIR and CciIR quorum sensing systems in Burkholderia cenocepacia Eoin P O'Grady, Duber F Viteri, Rebecca J Malott, and Pamela A Sokol PMCID: PMC2753556 Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer Federica Avondo, Paola Roncaglia, Nicoletta Crescenzio, Helena Krmac, Emanuela Garelli, Marta Armiraglio, Carlotta Castagnoli, Maria Francesca Campagnoli, Ugo Ramenghi, Stefano Gustincich, Claudio Santoro, and Irma Dianzani PMCID: PMC2760583 Identification and characterization of miRNAs expressed in the bovine ovary Md Munir Hossain, Nasser Ghanem, Michael Hoelker, Franca Rings, Chirawath Phatsara, Ernst Tholen, Karl Schellander, and Dawit Tesfaye PMCID: PMC2762473 Osteopontin: an early innate immune marker of Escherichia coli mastitis harbors genetic polymorphisms with possible links with resistance to mastitis Karin Alain, Niel A Karrow, Catherine Thibault, Jessika St-Pierre, Martin Lessard, and Nathalie Bissonnette PMCID: PMC2761946 Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction Emanuele Bultrini, Kevin Brick, Srayanta Mukherjee, Yang Zhang, Francesco Silvestrini, Pietro Alano, and Elisabetta Pizzi PMCID: PMC2756283 A comparison of reptilian and avian olfactory receptor gene repertoires: Species-specific expansion of group γ genes in birds Silke S Steiger, Vladimir Y Kuryshev, Marcus C Stensmyr, Bart Kempenaers, and Jakob C Mueller PMCID: PMC2758906 Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens Carla Risso, Jun Sun, Kai Zhuang, Radhakrishnan Mahadevan, Robert DeBoy, Wael Ismail, Susmita Shrivastava, Heather Huot, Sagar Kothari, Sean Daugherty, Olivia Bui, Christophe H Schilling, Derek R Lovley, and Barbara A Methé PMCID: PMC2755013 Expression profiling of skeletal muscle following acute and chronic β2-adrenergic stimulation: implications for hypertrophy, metabolism and circadian rhythm Michael A Pearen, James G Ryall, Gordon S Lynch, and George EO Muscat PMCID: PMC2758907 Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response Jingyu Zhang, Yunyuan Xu, Qing Huan, and Kang Chong PMCID: PMC2759970 Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5 Marcelo Bertalan, Rodolpho Albano, Vânia de Pádua, Luc Rouws, Cristian Rojas, Adriana Hemerly, Kátia Teixeira, Stefan Schwab, Jean Araujo, André Oliveira, Leonardo França, Viviane Magalhães, Sylvia Alquéres, Alexander Cardoso, Wellington Almeida, Marcio Martins Loureiro, Eduardo Nogueira, Daniela Cidade, Denise Oliveira, Tatiana Simão, Jacyara Macedo, Ana Valadão, Marcela Dreschsel, Flávia Freitas, Marcia Vidal, Helma Guedes, Elisete Rodrigues, Carlos Meneses, Paulo Brioso, Luciana Pozzer, Daniel Figueiredo, Helena Montano, Jadier Junior, Gonçalo de Souza Filho, Victor Martin Quintana Flores, Beatriz Ferreira, Alan Branco, Paula Gonzalez, Heloisa Guillobel, Melissa Lemos, Luiz Seibel, José Macedo, Marcio Alves-Ferreira, Gilberto Sachetto-Martins, Ana Coelho, Eidy Santos, Gilda Amaral, Anna Neves, Ana Beatriz Pacheco, Daniela Carvalho, Letícia Lery, Paulo Bisch, Shaila C Rössle, Turán Ürményi, Alessandra Rael Pereira, Rosane Silva, Edson Rondinelli, Wanda von Krüger, Orlando Martins, José Ivo Baldani, and Paulo CG Ferreira PMCID: PMC2765452 Transcriptome analysis of the central nervous system of the mollusc Lymnaea stagnalis Z-P Feng, Z Zhang, RE van Kesteren, VA Straub, P van Nierop, K Jin, N Nejatbakhsh, JI Goldberg, GE Spencer, MS Yeoman, W Wildering, JR Coorssen, RP Croll, LT Buck, NI Syed, and AB Smit PMCID: PMC2760584 Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways Carsten Külheim, Suat Hui Yeoh, Jens Maintz, William J Foley, and Gavin F Moran PMCID: PMC2760585 Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database Davide Scaglione, Alberto Acquadro, Ezio Portis, Christopher A Taylor, Sergio Lanteri, and Steven J Knapp PMCID: PMC2760586 MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori) Shiping Liu, Liang Zhang, Qibin Li, Ping Zhao, Jun Duan, Daojun Cheng, Zhonghuai Xiang, and Qingyou Xia PMCID: PMC2761947 Transcriptomic and proteomic analyses of seasonal photoperiodism in the pea aphid G Le Trionnaire, F Francis, S Jaubert-Possamai, J Bonhomme, E De Pauw, J-P Gauthier, E Haubruge, F Legeai, N Prunier-Leterme, J-C Simon, S Tanguy, and D Tagu PMCID: PMC2763885 Enrichment of a set of microRNAs during the cotton fiber development Pieter Bas Kwak, Qin Qin Wang, Xu Sheng Chen, Cheng Xiang Qiu, and Zhi Min Yang PMCID: PMC2760587 DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum Hai-Chun Jing, Carlos Bayon, Kostya Kanyuka, Simon Berry, Peter Wenzl, Eric Huttner, Andrzej Kilian, and Kim E Hammond-Kosack PMCID: PMC2764732 Combined phylogeny and neighborhood analysis of the evolution of the ABC transporters conferring multiple drug resistance in hemiascomycete yeasts Marie-Line Seret, Julie F Diffels, André Goffeau, and Philippe V Baret PMCID: PMC2763886 'Bois noir' phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine Matjaž Hren, Petra Nikolić, Ana Rotter, Andrej Blejec, Nancy Terrier, Maja Ravnikar, Marina Dermastia, and Kristina Gruden PMCID: PMC2761425 Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae Eija Rintala, Mervi Toivari, Juha-Pekka Pitkänen, Marilyn G Wiebe, Laura Ruohonen, and Merja Penttilä PMCID: PMC2767370 A first generation BAC-based physical map of the rainbow trout genome Yniv Palti, Ming-Cheng Luo, Yuqin Hu, Carine Genet, Frank M You, Roger L Vallejo, Gary H Thorgaard, Paul A Wheeler, and Caird E Rexroad, III PMCID: PMC2763887 The word landscape of the non-coding segments of the Arabidopsis thaliana genome Jens Lichtenberg, Alper Yilmaz, Joshua D Welch, Kyle Kurz, Xiaoyu Liang, Frank Drews, Klaus Ecker, Stephen S Lee, Matt Geisler, Erich Grotewold, and Lonnie R Welch PMCID: PMC2770528 Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum Claudia C Copeland, Manja Marz, Dominic Rose, Jana Hertel, Paul J Brindley, Clara Bermudez Santana, Stephanie Kehr, Camille Stephan-Otto Attolini, and Peter F Stadler PMCID: PMC2770079 Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing Wei Wang, Yejun Wang, Qing Zhang, Yan Qi, and Dianjing Guo PMCID: PMC2763888 Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding Sung-Chur Sim, Matthew D Robbins, Charles Chilcott, Tong Zhu, and David M Francis PMCID: PMC2763011 An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.) Albert Mascarell-Creus, Joaquin Cañizares, Josep Vilarrasa-Blasi, Santiago Mora-García, José Blanca, Daniel Gonzalez-Ibeas, Montserrat Saladié, Cristina Roig, Wim Deleu, Belén Picó-Silvent, Nuria López-Bigas, Miguel A Aranda, Jordi Garcia-Mas, Fernando Nuez, Pere Puigdomènech, and Ana I Caño-Delgado PMCID: PMC2767371 Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia Derek M Bickhart, Johann P Gogarten, Pascal Lapierre, Louis S Tisa, Philippe Normand, and David R Benson PMCID: PMC2770080 Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades Frank Förster, Chuanguang Liang, Alexander Shkumatov, Daniela Beisser, Julia C Engelmann, Martina Schnölzer, Marcus Frohme, Tobias Müller, Ralph O Schill, and Thomas Dandekar PMCID: PMC2768748 A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life Crysten E Haas, Dmitry A Rodionov, Janette Kropat, Davin Malasarn, Sabeeha S Merchant, and Valérie de Crécy-Lagard PMCID: PMC2770081 Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes Sylvain Foret, Robert Kucharski, Yvonne Pittelkow, Gabrielle A Lockett, and Ryszard Maleszka PMCID: PMC2768749 Development and mapping of DArT markers within the Festuca - Lolium complex David Kopecký, Jan Bartoš, Adam J Lukaszewski, James H Baird, Vladimír Černoch, Roland Kölliker, Odd Arne Rognli, Helene Blois, Vanessa Caig, Thomas Lübberstedt, Bruno Studer, Paul Shaw, Jaroslav Doležel, and Andrzej Kilian PMCID: PMC2770082 The l1-l2 regularization framework unmasks the hypoxia signature hidden in the transcriptome of a set of heterogeneous neuroblastoma cell lines Paolo Fardin, Annalisa Barla, Sofia Mosci, Lorenzo Rosasco, Alessandro Verri, and Luigi Varesio PMCID: PMC2768750 Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae Ji Qi, Asela J Wijeratne, Lynn P Tomsho, Yi Hu, Stephan C Schuster, and Hong Ma PMCID: PMC2770529 Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries Tammy L Romanuik, Gang Wang, Robert A Holt, Steven JM Jones, Marco A Marra, and Marianne D Sadar PMCID: PMC2766392 Maternal high fat diet during pregnancy and lactation alters hepatic expression of insulin like growth factor-2 and key microRNAs in the adult offspring Junlong Zhang, Fang Zhang, Xavier Didelot, Kimberley D Bruce, Felino R Cagampang, Manu Vatish, Mark Hanson, Hendrik Lehnert, Antonio Ceriello, and Christopher D Byrne PMCID: PMC2770530 Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity Yuen-Jong Liu, Deyou Zheng, Suganthi Balasubramanian, Nicholas Carriero, Ekta Khurana, Rebecca Robilotto, and Mark B Gerstein PMCID: PMC2770531 Characterization of the oxidative stress stimulon and PerR regulon of Campylobacter jejuni Kiran Palyada, Yi-Qian Sun, Annika Flint, James Butcher, Hemant Naikare, and Alain Stintzi PMCID: PMC2772861 Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei Bryan C Jensen, Dhileep Sivam, Charles T Kifer, Peter J Myler, and Marilyn Parsons PMCID: PMC2771046 Glycogenome expression dynamics during mouse C2C12 myoblast differentiation suggests a sequential reorganization of membrane glycoconjugates Mathilde Janot, Aymeric Audfray, Céline Loriol, Agnès Germot, Abderrahman Maftah, and Fabrice Dupuy PMCID: PMC2772862 Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses? John W Stiller, Jinling Huang, Qin Ding, Jing Tian, and Carol Goodwillie PMCID: PMC2770532 Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering Jon Bohlin, Eystein Skjerve, and David W Ussery PMCID: PMC2770534 Analysis of regulatory protease sequences identified through bioinformatic data mining of the Schistosoma mansoni genome David H Bos, Chris Mayfield, and Dennis J Minchella PMCID: PMC2772863 Identification and analysis of serpin-family genes by homology and synteny across the 12 sequenced Drosophilid genomes Matthew Garrett, Ane Fullaondo, Laurent Troxler, Gos Micklem, and David Gubb PMCID: PMC2770083 Whole-genome analysis of pseudorabies virus gene expression by real-time quantitative RT-PCR assay Dóra Tombácz, Judit S Tóth, Pál Petrovszki, and Zsolt Boldogkői PMCID: PMC2775753 Expulsion of Trichuris muris is associated with increased expression of angiogenin 4 in the gut and increased acidity of mucins within the goblet cell Riccardo D'Elia, Matthew L deSchoolmeester, Leo AH Zeef, Steven H Wright, Alan D Pemberton, and Kathryn J Else PMCID: PMC2774869 Quality control in microarray assessment of gene expression in human airway epithelium Tina Raman, Timothy P O'Connor, Neil R Hackett, Wei Wang, Ben-Gary Harvey, Marc A Attiyeh, David T Dang, Matthew Teater, and Ronald G Crystal PMCID: PMC2774870 Exploring the molecular basis of insecticide resistance in the dengue vector Aedes aegypti: a case study in Martinique Island (French West Indies) Sébastien Marcombe, Rodolphe Poupardin, Frederic Darriet, Stéphane Reynaud, Julien Bonnet, Clare Strode, Cecile Brengues, André Yébakima, Hilary Ranson, Vincent Corbel, and Jean-Philippe David PMCID: PMC2770535 Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons Rafael Queiroz, Corinna Benz, Kurt Fellenberg, Jörg D Hoheisel, and Christine Clayton PMCID: PMC2772864 A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat Yong Q Gu, Yaqin Ma, Naxin Huo, John P Vogel, Frank M You, Gerard R Lazo, William M Nelson, Carol Soderlund, Jan Dvorak, Olin D Anderson, and Ming-Cheng Luo PMCID: PMC2774330 A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays Danette D Hartzell, Nathan D Trinklein, Jacqui Mendez, Nancy Murphy, Shelley F Aldred, Keith Wood, and Marjeta Urh PMCID: PMC2774331 Inherent promoter bidirectionality facilitates maintenance of sequence integrity and transcription of parasitic DNA in mammalian genomes Paul Kalitsis and Richard Saffery PMCID: PMC2777200 Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex Susanne A Thomson, William S Baldwin, Ying H Wang, Gwijun Kwon, and Gerald A LeBlanc PMCID: PMC2774871 Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens Chris J Stubben, Melanie L Duffield, Ian A Cooper, Donna C Ford, Jason D Gans, Andrey V Karlyshev, Bryan Lingard, Petra CF Oyston, Anna de Rochefort, Jian Song, Brendan W Wren, Rick W Titball, and Murray Wolinsky PMCID: PMC2774872 Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar) Rune Andreassen, Sigbjørn Lunner, and Bjørn Høyheim PMCID: PMC2774873 Hepatic gene expression profiling reveals protective responses in Atlantic salmon vaccinated against furunculosis Stanko Škugor, Sven Martin Jørgensen, Bjarne Gjerde, and Aleksei Krasnov PMCID: PMC2775754 EST and microarray analysis of horn development in Onthophagus beetles Teiya Kijimoto, James Costello, Zuojian Tang, Armin P Moczek, and Justen Andrews PMCID: PMC2777201 Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics Elisabeth Jamet, David Roujol, Hélène San-Clemente, Muhammad Irshad, Ludivine Soubigou-Taconnat, Jean-Pierre Renou, and Rafael Pont-Lezica PMCID: PMC2774874 Phylogenetic relatedness and host plant growth form influence gene expression of the polyphagous comma butterfly (Polygonia c-album) Hanna M Heidel-Fischer, Dalial Freitak, Niklas Janz, Lina Söderlind, Heiko Vogel, and Sören Nylin PMCID: PMC2775755 Computational prediction of splicing regulatory elements shared by Tetrapoda organisms Alexander Churbanov, Igor Vořechovský, and Chindo Hicks PMCID: PMC2777938 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, Junjun Wang, and Huaijun Zhou PMCID: PMC2777939 Methodology Articles Gene expression profiling of whole blood: Comparison of target preparation methods for accurate and reproducible microarray analysis Kristina Vartanian, Rachel Slottke, Timothy Johnstone, Amanda Casale, Stephen R Planck, Dongseok Choi, Justine R Smith, James T Rosenbaum, and Christina A Harrington PMCID: PMC2649161 A novel regulatory event-based gene set analysis method for exploring global functional changes in heterogeneous genomic data sets Chien-Yi Tung, Chih-Hung Jen, Ming-Ta Hsu, Hsei-Wei Wang, and Chi-Hung Lin PMCID: PMC2637897 A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms Ming-Cheng Luo, Kenong Xu, Yaqin Ma, Karin R Deal, Charles M Nicolet, and Jan Dvorak PMCID: PMC2647554 Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome Andreas Dötsch, Claudia Pommerenke, Florian Bredenbruch, Robert Geffers, and Susanne Häussler PMCID: PMC2658670 Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach Marie de Tayrac, Sébastien Lê, Marc Aubry, Jean Mosser, and François Husson PMCID: PMC2636827 Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing Philippe Lefrançois, Ghia M Euskirchen, Raymond K Auerbach, Joel Rozowsky, Theodore Gibson, Christopher M Yellman, Mark Gerstein, and Michael Snyder PMCID: PMC2656530 Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes Steven P Wilder, Pamela J Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, and Dominique Gauguier PMCID: PMC2652496 Digital PCR provides sensitive and absolute calibration for high throughput sequencing Richard A White, III, Paul C Blainey, H Christina Fan, and Stephen R Quake PMCID: PMC2667538 A simple and efficient method for isolating polymorphic microsatellites from cDNA Gen Hua Yue, Ze Yuan Zhu, Chun Ming Wang, and Jun Hong Xia PMCID: PMC2667190 Detection of genomic deletions in rice using oligonucleotide microarrays Myron Bruce, Ann Hess, Jianfa Bai, Ramil Mauleon, M Genaleen Diaz, Nobuko Sugiyama, Alicia Bordeos, Guo-Liang Wang, Hei Leung, and Jan E Leach PMCID: PMC2666768 A signature-based method for indexing cell cycle phase distribution from microarray profiles Hideaki Mizuno, Yoshito Nakanishi, Nobuya Ishii, Akinori Sarai, and Kunio Kitada PMCID: PMC2676301 Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences Liane Fendt, Bettina Zimmermann, Martin Daniaux, and Walther Parson PMCID: PMC2669098 Gene expression profiling to characterize sediment toxicity – a pilot study using Caenorhabditis elegans whole genome microarrays Ralph Menzel, Suresh C Swain, Sebastian Hoess, Evelyn Claus, Stefanie Menzel, Christian EW Steinberg, Georg Reifferscheid, and Stephen R Stürzenbaum PMCID: PMC2674462 Estimating accuracy of RNA-Seq and microarrays with proteomics Xing Fu, Ning Fu, Song Guo, Zheng Yan, Ying Xu, Hao Hu, Corinna Menzel, Wei Chen, Yixue Li, Rong Zeng, and Philipp Khaitovich PMCID: PMC2676304 Systematic identification of transcription factors associated with patient survival in cancers Chao Cheng, Lei M Li, Pedro Alves, and Mark Gerstein PMCID: PMC2686740 Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling Mathieu Clément-Ziza, David Gentien, Stanislas Lyonnet, Jean-Paul Thiery, Claude Besmond, and Charles Decraene PMCID: PMC2700135 Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation Zuogang Peng, Navin Elango, Derek E Wildman, and Soojin V Yi PMCID: PMC2693144 Biases in Drosophila melanogaster protein trap screens Jelena Aleksic, Ranko Lazic, Ilka Müller, Steven R Russell, and Boris Adryan PMCID: PMC2695487 Genome-wide scans using archived neonatal dried blood spot samples Mads V Hollegaard, Jonas Grauholm, Anders Børglum, Mette Nyegaard, Bent Nørgaard-Pedersen, Torben Ørntoft, Preben B Mortensen, Carsten Wiuf, Ole Mors, Michael Didriksen, Poul Thorsen, and David M Hougaard PMCID: PMC2713266 Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing Julio C Vega-Arreguín, Enrique Ibarra-Laclette, Beatriz Jiménez-Moraila, Octavio Martínez, Jean Philippe Vielle-Calzada, Luis Herrera-Estrella, and Alfredo Herrera-Estrella PMCID: PMC2714558 Primer fabrication using polymerase mediated oligonucleotide synthesis Murray J Cairns, Torsten Thomas, Carolina E Beltran, and Daniel Tillett PMCID: PMC2733156 Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome Andreia J Amaral, Hendrik-Jan Megens, Hindrik HD Kerstens, Henri CM Heuven, Bert Dibbits, Richard PMA Crooijmans, Johan T den Dunnen, and Martien AM Groenen PMCID: PMC2739861 Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis Yongxin Chen, Jonathan AL Gelfond, Linda M McManus, and Paula K Shireman PMCID: PMC2753550 Rapid high-throughput analysis of DNaseI hypersensitive sites using a modified Multiplex Ligation-dependent Probe Amplification approach Thomas Ohnesorg, Stefanie Eggers, Wouter N Leonhard, Andrew H Sinclair, and Stefan J White PMCID: PMC2748097 Allele-specific expression assays using Solexa Bradley J Main, Ryan D Bickel, Lauren M McIntyre, Rita M Graze, Peter P Calabrese, and Sergey V Nuzhdin PMCID: PMC2749874 Improvement of the clinical applicability of the Genomic Grade Index through a qRT-PCR test performed on frozen and formalin-fixed paraffin-embedded tissues Jérôme Toussaint, Anieta M Sieuwerts, Benjamin Haibe-Kains, Christine Desmedt, Ghizlane Rouas, Adrian L Harris, Denis Larsimont, Martine Piccart, John A Foekens, Virginie Durbecq, and Christos Sotiriou PMCID: PMC2756282 A flexible whole-genome microarray for transcriptomics in three-spine stickleback (Gasterosteus aculeatus) Erica H Leder, Juha Merilä, and Craig R Primmer PMCID: PMC2754499 Relative power and sample size analysis on gene expression profiling data M van Iterson, PAC 't Hoen, P Pedotti, GJEJ Hooiveld, JT den Dunnen, GJB van Ommen, JM Boer, and RX Menezes PMCID: PMC2759969 Quadruplex MAPH: improvement of throughput in high-resolution copy number screening Jess Tyson, Tamsin MO Majerus, Susan Walker, and John AL Armour PMCID: PMC2761424 A comparative analysis of DNA barcode microarray feature size Ron Ammar, Andrew M Smith, Lawrence E Heisler, Guri Giaever, and Corey Nislow PMCID: PMC2765990 Transposon-mediated BAC transgenesis in zebrafish and mice Maximiliano L Suster, Kenta Sumiyama, and Koichi Kawakami PMCID: PMC2768751 Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey Hindrik HD Kerstens, Richard PMA Crooijmans, Albertine Veenendaal, Bert W Dibbits, Thomas FC Chin-A-Woeng, Johan T den Dunnen, and Martien AM Groenen PMCID: PMC2772860 A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp John MJ Herbert, Francesca M Buffa, Henrik Vorschmitt, Stuart Egginton, and Roy Bicknell PMCID: PMC2771047 Information-theoretic gene-gene and gene-environment interaction analysis of quantitative traits Pritam Chanda, Lara Sucheston, Song Liu, Aidong Zhang, and Murali Ramanathan PMCID: PMC2779196 Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation Kevin CH Ha, Jasmin Coulombe-Huntington, and Jacek Majewski PMCID: PMC2780461 New methods to analyse microarray data that partially lack a reference signal Neeltje Carpaij, Ad C Fluit, Jodi A Lindsay, Marc JM Bonten, and Rob JL Willems PMCID: PMC2779823 Corrections Gene expression and isoform variation analysis using Affymetrix exon arrays Amandine Bemmo, David Benovoy, Tony Kwan, Daniel J Gaffney, Roderick V Jensen, and Jacek Majewski PMCID: PMC2666767 Corrects: Amandine Bemmo, et al. Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays. BMC Genomics. 2008; 9: 529. The extracellular Leucine-Rich Repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns Jackie Dolan, Karen Walshe, Samantha Alsbury, Karsten Hokamp, Sean O'Keeffe, Tatsuya Okafuji, Suzanne FC Miller, Guy Tear, and Kevin J Mitchell PMCID: PMC2689278 Corrects: Jackie Dolan, et al. The extracellular Leucine-Rich Repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns. BMC Genomics. 2007; 8: 320. Other Issues: Journal List
|
previous
|
next
|
latest
|
archive
|
