Research article  

Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages

Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynänen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R Steffensen, Carsten Carlberg BMC Genomics 2012, 13:50 (31 January 2012)

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Research article  

Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice

Rumdeep K Grewal, Sumanti Gupta, Sampa Das BMC Genomics 2012, 13:49 (31 January 2012)

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Methodology article  

Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle

Hermann Schwarzenbacher, Marlies Dolezal, Krzysztof Flisikowski, Franz Seefried, Christine Wurmser, Christian Schlötterer, Ruedi Fries BMC Genomics 2012, 13:48 (30 January 2012)

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Methodology article  

Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome

Romain Philippe, Frédéric Choulet, Etienne Paux, Jan van Oeveren, Jifeng Tang, Alexander HJ Wittenberg, Antoine Janssen, Michiel JT van Eijk, Keith Stormo, Adriana Alberti, Patrick Wincker, Eduard Akhunov, Edwin van der Vossen, Catherine Feuillet BMC Genomics 2012, 13:47 (30 January 2012)

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Research article  

Identification of differentially expressed genes in SHSY5Y cells exposed to okadaic acid by suppression subtractive hybridization

Vanessa Valdiglesias, Juan Fernández-Tajes, Eduardo Pásaro, Josefina Méndez, Blanca Laffon BMC Genomics 2012, 13:46 (27 January 2012)

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Research article  

Transcriptional profiling of bovine milk using RNA sequencing

Saumya Wickramasinghe, Gonzalo Rincon, Alma Islas-Trejo, Juan F Medrano BMC Genomics 2012, 13:45 (25 January 2012)

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Database  

miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes

Andrew E Bruno, Li Li, James L Kalabus, Yuzhuo Pan, Aiming Yu, Zihua Hu BMC Genomics 2012, 13:44 (25 January 2012)

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Methodology article  

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis

Jing Tu, Qinyu Ge, Shengqin Wang, Lei Wang, Beili Sun, Qi Yang, Yunfei Bai, Zuhong Lu BMC Genomics 2012, 13:43 (25 January 2012)

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Research article  

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

Michiel E Adriaens, Magali Jaillard, Lars MT Eijssen, Claus-Dieter Mayer, Chris TA Evelo BMC Genomics 2012, 13:42 (25 January 2012)

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Research article  

The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis

Domenico De Paola, Federica Cattonaro, Domenico Pignone, Gabriella Sonnante BMC Genomics 2012, 13:41 (24 January 2012)

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Research article  

Genetic diversity of human RNase 8

Calvin C Chan, Jennifer M Moser, Kimberly D Dyer, Caroline M Percopo, Helene F Rosenberg BMC Genomics 2012, 13:40 (24 January 2012)

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Research article  

The core and unique proteins of haloarchaea

Melinda D Capes, Priya DasSarma, Shiladitya DasSarma BMC Genomics 2012, 13:39 (24 January 2012)

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Research article  

Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae

Haruo Suzuki, Tristan Lefébure, Paulina Bitar, Michael J Stanhope BMC Genomics 2012, 13:38 (24 January 2012)

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Research article  

Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida

Geir Å Hansen, Rafi Ahmad, Erik Hjerde, Christopher G Fenton, Nils-Peder Willassen, Peik Haugen BMC Genomics 2012, 13:37 (24 January 2012)

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Research article  

A metabolomic strategy defines the regulation of lipid content and global metabolism by Δ9 desaturases in Caenorhabditis elegans

Cecilia Castro, Funda Sar, W Robert Shaw, Masanori Mishima, Eric A Miska, Julian L Griffin BMC Genomics 2012, 13:36 (20 January 2012)

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Database  

IntegromeDB: an integrated system and biological search engine

Michael Baitaluk, Sergey Kozhenkov, Yulia Dubinina, Julia Ponomarenko BMC Genomics 2012, 13:35 (19 January 2012)

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Methodology article  

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

John P Didion, Hyuna Yang, Keith Sheppard, Chen-Ping Fu, Leonard McMillan, Fernando de Villena, Gary A Churchill BMC Genomics 2012, 13:34 (19 January 2012)

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Research article  

Transcriptional ontogeny of the developing liver

Janice S Lee, William O Ward, Geremy Knapp, Hongzu Ren, Beena Vallanat, Barbara Abbott, Karen Ho, Seth J Karp, J Corton BMC Genomics 2012, 13:33 (19 January 2012)

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Research article  

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

Marc W Allard, Yan Luo, Errol Strain, Cong Li, Christine E. Keys, Insook Son, Robert Stones, Steven M. Musser, Eric W. Brown BMC Genomics 2012, 13:32 (19 January 2012)

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Research article  

Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes

Kristopher J Irizarry, Sukhaswami B Malladi, Xiangming Gao, Katherine Mitsouras, Lynda Melendez, Patricia A Burris, Jeffrey A Brockman, Samer W Al-Murrani BMC Genomics 2012, 13:31 (18 January 2012)

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Research article  

Microarray analysis on germfree mice elucidates the primary target of a traditional Japanese medicine juzentaihoto: acceleration of IFN-α response via affecting the ISGF3-IRF7 signaling cascade

Kaori Munakata, Kiyoe Takashima, Mitsue Nishiyama, Naoko Asano, Akihito Mase, Kyoji Hioki, Yasuyuki Ohnishi, Masahiro Yamamoto, Kenji Watanabe BMC Genomics 2012, 13:30 (18 January 2012)

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Research article  

Centromere-associated repeat arrays on Trypanosoma brucei chromosomes are much more extensive than predicted

Maria C Echeverry, Christopher Bot, Samson O Obado, Martin C Taylor, John M Kelly BMC Genomics 2012, 13:29 (18 January 2012)

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Research article  

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA

Anastasios Mastrokolias, Johan T den Dunnen, GertJan B van Ommen, Peter AC 't Hoen, Willeke MC van Roon-Mom BMC Genomics 2012, 13:28 (18 January 2012)

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Research article  

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

Kelly J Vining, Kyle R Pomraning, Larry J Wilhelm, Henry D Priest, Matteo Pellegrini, Todd C Mockler, Michael Freitag, Steven H Strauss BMC Genomics 2012, 13:27 (17 January 2012)

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Research article  

Postmortem cardiac tissue maintains gene expression profile even after late harvesting

Simone Gupta, Marc K Halushka, Gina M Hilton, Dan E Arking BMC Genomics 2012, 13:26 (17 January 2012)

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Research article  

The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression

Vinoy K Ramachandran, Neil Shearer, Jobin J Jacob, Cynthia M Sharma, Arthur Thompson BMC Genomics 2012, 13:25 (17 January 2012)

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Research article  

Estimation of linkage disequilibrium in four US pig breeds

Yvonne M Badke, Ronald O Bates, Catherine W Ernst, Clint Schwab, Juan P Steibel BMC Genomics 2012, 13:24 (17 January 2012)

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Research article  

Quantification and accurate normalisation of small RNAs through new custom RT-qPCR arrays demonstrates Salmonella-induced microRNAs in human monocytes

Soroush Sharbati, Jutta Sharbati, Lena Hoeke, Marc Bohmer, Ralf Einspanier BMC Genomics 2012, 13:23 (16 January 2012)

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Research article  

Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds

Vivi R Gregersen, Lene N Conley, Kirsten K Sørensen, Bernt Guldbrandtsen, Ingela H Velander, Christian Bendixen BMC Genomics 2012, 13:22 (13 January 2012)

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Research article  

Characterisation of full-length cDNA sequences provides insights into the Eimeria tenellatranscriptome

Nadzirah Amiruddin, Xin-Wei Lee, Damer P Blake, Yutaka Suzuki, Yea-Ling Tay, Lik-Sin Lim, Fiona M Tomley, Junichi Watanabe, Chihiro Sugimoto, Kiew-Lian Wan BMC Genomics 2012, 13:21 (13 January 2012)

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Methodology article  

Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

Binod B Sahu, Rishi Sumit, Subodh K Srivastava, Madan K Bhattacharyya BMC Genomics 2012, 13:20 (13 January 2012)

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Research article  

Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq

Chao Feng, Ming Chen, Chang-jie Xu, Lin Bai, Xue-ren Yin, Xian Li, Andrew C Allan, Ian B Ferguson, Kun-song Chen BMC Genomics 2012, 13:19 (13 January 2012)

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Methodology article  

Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing

Tyson Koepke, Scott Schaeffer, Vandhana Krishnan, Derick Jiwan, Artemus Harper, Matthew Whiting, Nnadozie Oraguzie, Amit Dhingra BMC Genomics 2012, 13:18 (12 January 2012)

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Research article  

Lipopolysaccharide priming enhances expression of effectors of immune defence while decreasing expression of pro-inflammatory cytokines in mammary epithelia cells from cows

Juliane Günther, Wolfram Petzl, Holm Zerbe, Hans-Joachim Schuberth, Dirk Koczan, Leopold Goetze, Hans-Martin Seyfert BMC Genomics 2012, 13:17 (12 January 2012)

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Research article  

Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

Michael P Mullen, Christopher J Creevey, Donagh P Berry, Matt S McCabe, David A Magee, Dawn J Howard, Aideen P Killeen, Stephen D Park, Paul A McGettigan, Matt C Lucy, David E MacHugh, Sinead M Waters BMC Genomics 2012, 13:16 (11 January 2012)

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Research article  

Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea

Bin Wu, Ying Li, Haixia Yan, Yimian Ma, Hongmei Luo, Lichai Yuan, Shilin Chen, Shanfa Lu BMC Genomics 2012, 13:15 (10 January 2012)

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Research article  

Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

Jonathan L Klassen, Cameron R Currie BMC Genomics 2012, 13:14 (10 January 2012)

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Research article  

SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

Patrick Ollitrault, Javier Terol, Andres Garcia-Lor, Aurélie Bérard, Aurélie Chauveau, Yann Froelicher, Caroline Belzile, Raphaël Morillon, Luis Navarro, Dominique Brunel, Manuel Talon BMC Genomics 2012, 13:13 (10 January 2012)

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Research article  

A searchable cross-platform gene expression database reveals connections between drug treatments and disease

Gareth Williams BMC Genomics 2012, 13:12 (10 January 2012)

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Research article  

Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development

Teshome T Bizuayehu, Carlos FC Lanes, Tomasz Furmanek, Bård O Karlsen, Jorge MO Fernandes, Steinar D Johansen, Igor Babiak BMC Genomics 2012, 13:11 (10 January 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Research article  

Transcriptome changes during fruit development and ripening of sweet orange (Citrus sinensis)

Keqin Yu, Qiang Xu, Xinlei Da, Fei Guo, Yuduan Ding, Xiuxin Deng BMC Genomics 2012, 13:10 (10 January 2012)

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Research article  

Rootstock-regulated gene expression patterns associated with fire blight resistance in apple

Philip J Jensen, Noemi Halbrendt, Gennaro Fazio, Izabela Makalowska, Naomi Altman, Craig Praul, Siela N Maximova, Henry K Ngugi, Robert M Crassweller, James W Travis, Timothy W McNellis BMC Genomics 2012, 13:9 (9 January 2012)

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Research article  

Quantitative Interactor Screening with next-generation Sequencing (QIS-Seq) identifies Arabidopsis thaliana MLO2 as a target of the Pseudomonas syringae type III effector HopZ2

Jennifer D Lewis, Janet Wan, Rachel Ford, Yunchen Gong, Pauline Fung, Hardeep Nahal, Pauline W Wang, Darrell Desveaux, David S Guttman BMC Genomics 2012, 13:8 (9 January 2012)

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Research article  

Sculpting the maturation, softening and ethylene pathway: The influences of microRNAs on tomato fruits

Jinhua Zuo, Benzhong Zhu, Daqi Fu, Yi Zhu, Yuanzheng Ma, Lihong Chi, Zheng Ju, Yunxiang Wang, Baiqiang Zhai, Yunbo Luo BMC Genomics 2012, 13:7 (9 January 2012)

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Research article  

RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug

Praveen Mamidala, Asela J Wijeratne, Saranga Wijeratne, Karl Kornacker, Babu Sudhamalla, Loren J Rivera-Vega, Andrew Hoelmer, Tea Meulia, Susan C Jones, Omprakash Mittapalli BMC Genomics 2012, 13:6 (6 January 2012)

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Research article  

Controversies in modern evolutionary biology: the imperative for error detection and quality control

Francisco Prosdocimi, Benjamin Linard, Pierre Pontarotti, Olivier Poch, Julie D Thompson BMC Genomics 2012, 13:5 (4 January 2012)

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Research article  

Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

Alan D Winter, William Weir, Martin Hunt, Matthew Berriman, John S Gilleard, Eileen Devaney, Collette Britton BMC Genomics 2012, 13:4 (4 January 2012)

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Research article  

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

Davide Scaglione, Alberto Acquadro, Ezio Portis, Matteo Tirone, Steven J Knapp, Sergio Lanteri BMC Genomics 2012, 13:3 (3 January 2012)

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Research article  

Yeast-based assay identifies novel Shh/Gli target genes in vertebrate development

Luis A Milla, Claudio R Cortés, Christian Hodar Q, Maritza G Oñate, Veronica Cambiazo, Shawn M Burgess, Verónica Palma BMC Genomics 2012, 13:2 (3 January 2012)

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Methodology article  

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

Samuel O Oyola, Thomas D Otto, Yong Gu, Gareth Maslen, Magnus Manske, Susana Campino, Daniel J Turner, Bronwyn MacInnis, Dominic P Kwiatkowski, Harold P Swerdlow, Michael A Quail BMC Genomics 2012, 13:1 (3 January 2012)

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