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  1. The nuclear receptor peroxisome proliferator-activated receptor alpha (PPARα) regulates responses to chemical or physical stress in part by altering expression of genes involved in proteome maintenance. Many o...

    Authors: Beena Vallanat, Steven P Anderson, Holly M Brown-Borg, Hongzu Ren, Sander Kersten, Sudhakar Jonnalagadda, Rajagopalan Srinivasan and J Christopher Corton
    Citation: BMC Genomics 2010 11:16
    Content type: Research article Published on:

  2. Microarray technologies produced large amount of data. In a previous study, we have shown the interest of k-Nearest Neighbour approach for restoring the missing gene expression values, and its positive impact of ...

    Authors: Magalie Celton, Alain Malpertuy, Gaëlle Lelandais and Alexandre G de Brevern
    Citation: BMC Genomics 2010 11:15
    Content type: Research article Published on:

  3. Snake mitochondrial genomes are of great interest in understanding mitogenomic evolution because of gene duplications and rearrangements and the fast evolutionary rate of their genes compared to other vertebra...

    Authors: Desirée A Douglas and David J Gower
    Citation: BMC Genomics 2010 11:14
    Content type: Research article Published on:

  4. Considerable progress has been made in our understanding of sex determination and dosage compensation mechanisms in model organisms such as C. elegans, Drosophila and M. musculus. Strikingly, the mechanism involv...

    Authors: Shaobing O Zhang, Sachin Mathur, Gaye Hattem, Olivier Tassy and Olivier Pourquié
    Citation: BMC Genomics 2010 11:13
    Content type: Research article Published on:

  5. Zinc is considered as an essential element for all living organisms, but it can be toxic at large concentrations. Bacteria therefore tightly regulate zinc metabolism. The Cg2502 protein of Corynebacterium glutami...

    Authors: Jasmin Schröder, Nina Jochmann, Dmitry A Rodionov and Andreas Tauch
    Citation: BMC Genomics 2010 11:12
    Content type: Research article Published on:

  6. Biological nitrogen fixation is highly controlled at the transcriptional level by regulatory networks that respond to the availability of fixed nitrogen. In many diazotrophs, addition of excess ammonium in the...

    Authors: Yongliang Yan, Shuzhen Ping, Junping Peng, Yunlei Han, Liang Li, Jian Yang, Yuetan Dou, Yan Li, Huili Fan, Ying Fan, Danhua Li, Yuhua Zhan, Ming Chen, Wei Lu, Wei Zhang, Qi Cheng…
    Citation: BMC Genomics 2010 11:11
    Content type: Research article Published on:

  7. During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during th...

    Authors: Kay Nieselt, Florian Battke, Alexander Herbig, Per Bruheim, Alexander Wentzel, Øyvind M Jakobsen, HÃ¥vard Sletta, Mohammad T Alam, Maria E Merlo, Jonathan Moore, Walid AM Omara, Edward R Morrissey, Miguel A Juarez-Hermosillo, Antonio Rodríguez-García, Merle Nentwich, Louise Thomas…
    Citation: BMC Genomics 2010 11:10
    Content type: Research article Published on:

  8. Non-genotoxic carcinogens are notoriously difficult to identify as they do not damage DNA directly and have diverse modes of action, necessitating long term in vivo studies. The early effects of the classic ro...

    Authors: Claire L Waterman, Richard A Currie, Lisa A Cottrell, Jacky Dow, Jayne Wright, Catherine J Waterfield and Julian L Griffin
    Citation: BMC Genomics 2010 11:9
    Content type: Research article Published on:

  10. RNAi screens via pooled short hairpin RNAs (shRNAs) have recently become a powerful tool for the identification of essential genes in mammalian cells. In the past years, several pooled large-scale shRNA screen...

    Authors: Michael Boettcher, Johannes Fredebohm, Amin Moghaddas Gholami, Yafit Hachmo, Iris Dotan, Dan Canaani and Jörg D Hoheisel
    Citation: BMC Genomics 2010 11:7
    Content type: Methodology article Published on:

  13. The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur dur...

    Authors: Thilo Borchardt, Mario Looso, Marc Bruckskotten, Patrick Weis, Julia Kruse and Thomas Braun
    Citation: BMC Genomics 2010 11:4
    Content type: Research article Published on:

  14. In most species of mammals, the TRB locus has the common feature of a library of TRBV genes positioned at the 5'- end of two in tandem aligned D-J-C gene clusters, each composed of a single TRBD gene, 6-7 TRBJ ge...

    Authors: Silvia Di Tommaso, Rachele Antonacci, Salvatrice Ciccarese and Serafina Massari
    Citation: BMC Genomics 2010 11:3
    Content type: Research article Published on:

  15. Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compar...

    Authors: Theo HM Smits, Sebastian Jaenicke, Fabio Rezzonico, Tim Kamber, Alexander Goesmann, Jürg E Frey and Brion Duffy
    Citation: BMC Genomics 2010 11:2
    Content type: Research article Published on:

  16. Methylotrophic yeast species (e.g. Hansenula polymorpha, Pichia pastoris) can grow on methanol as sole source of carbon and energy. These organisms are important cell factories for the production of recombinant p...

    Authors: Tim van Zutphen, Richard JS Baerends, Kim A Susanna, Anne de Jong, Oscar P Kuipers, Marten Veenhuis and Ida J van der Klei
    Citation: BMC Genomics 2010 11:1
    Content type: Research article Published on:

  17. The emergence of next-generation sequencing technology presents tremendous opportunities to accelerate the discovery of rare variants or mutations that underlie human genetic disorders. Although the complete s...

    Authors: Hane Lee, Brian D O'Connor, Barry Merriman, Vincent A Funari, Nils Homer, Zugen Chen, Daniel H Cohn and Stanley F Nelson
    Citation: BMC Genomics 2009 10:646
    Content type: Methodology article Published on:

  19. Plasmodium parasites are causative agents of malaria which affects >500 million people and claims ~2 million lives annually. The completion of Plasmodium genome sequencing and availability of PlasmoDB database ha...

    Authors: Tarun Kumar Bhatt, Charu Kapil, Sameena Khan, Mohamad Aman Jairajpuri, Vinay Sharma, Daniele Santoni, Francesco Silvestrini, Elisabetta Pizzi and Amit Sharma
    Citation: BMC Genomics 2009 10:644
    Content type: Research article Published on:

  20. New generation sequencing technology has allowed investigation of the small RNA populations of flowering plants at great depth. However, little is known about small RNAs in their reproductive cells, especially...

    Authors: Robert Grant-Downton, Gael Le Trionnaire, Ralf Schmid, Josefina Rodriguez-Enriquez, Said Hafidh, Saher Mehdi, David Twell and Hugh Dickinson
    Citation: BMC Genomics 2009 10:643
    Content type: Research article Published on:

  21. Emergence of multi-drug resistant (MDR) serotype 19A Streptococcus pneumoniae (SPN) is well-documented but causal factors remain unclear. Canadian SPN isolates (1993-2008, n = 11,083) were serotyped and in vitro ...

    Authors: Dylan R Pillai, Dea Shahinas, Alla Buzina, Remy A Pollock, Rachel Lau, Krishna Khairnar, Andrew Wong, David J Farrell, Karen Green, Allison McGeer and Donald E Low
    Citation: BMC Genomics 2009 10:642
    Content type: Research article Published on:

  22. Identification of specific genes and gene expression patterns important for bacterial survival, transmission and pathogenesis is critically needed to enable development of more effective pathogen control strat...

    Authors: Haley F Oliver, Renato H Orsi, Lalit Ponnala, Uri Keich, Wei Wang, Qi Sun, Samuel W Cartinhour, Melanie J Filiatrault, Martin Wiedmann and Kathryn J Boor
    Citation: BMC Genomics 2009 10:641
    Content type: Research article Published on:

  23. Due to their bi-directional replication machinery starting from a single finite origin, bacterial genomes show characteristic nucleotide compositional bias between the two replichores, which can be visualised ...

    Authors: Kazuharu Arakawa, Haruo Suzuki and Masaru Tomita
    Citation: BMC Genomics 2009 10:640
    Content type: Research article Published on:

  24. Prokaryotic microorganisms are able to survive and proliferate in severe environmental conditions. The increasing number of complete sequences of prokaryotic genomes has provided the basis for studying the mol...

    Authors: Konstantin V Gunbin, Dmitry A Afonnikov and Nikolay A Kolchanov
    Citation: BMC Genomics 2009 10:639
    Content type: Research article Published on:

  25. Selection for exercise-adapted phenotypes in the Thoroughbred racehorse has provided a valuable model system to understand molecular responses to exercise in skeletal muscle. Exercise stimulates immediate earl...

    Authors: Beatrice A McGivney, Suzanne S Eivers, David E MacHugh, James N MacLeod, Grace M O'Gorman, Stephen DE Park, Lisa M Katz and Emmeline W Hill
    Citation: BMC Genomics 2009 10:638
    Content type: Research article Published on:

  26. Deconjugation of ubiquitin and/or ubiquitin-like modified protein substrates is essential to modulate protein-protein interactions and, thus, signaling processes in cells. Although deubiquitylating (deubiquiti...

    Authors: William KF Tse, Birgit Eisenhaber, Steven HK Ho, Qimei Ng, Frank Eisenhaber and Yun-Jin Jiang
    Citation: BMC Genomics 2009 10:637
    Content type: Research article Published on:

  27. Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improv...

    Authors: José L Noguera, Carmen Rodríguez, Luis Varona, Anna Tomàs, Gloria Muñoz, Oscar Ramírez, Carmen Barragán, Meritxell Arqué, Jean P Bidanel, Marcel Amills, Cristina Ovilo and Armand Sánchez
    Citation: BMC Genomics 2009 10:636
    Content type: Research article Published on:

  29. Chlamydiae are obligate intracellular bacteria comprising some of the most important bacterial pathogens of animals and humans. Although chlamydial outer membrane proteins play a key role for attachment to and...

    Authors: Eva Heinz, Patrick Tischler, Thomas Rattei, Garry Myers, Michael Wagner and Matthias Horn
    Citation: BMC Genomics 2009 10:634
    Content type: Research article Published on:

  30. The full power of modern genetics has been applied to the study of speciation in only a small handful of genetic model species - all of which speciated allopatrically. Here we report the first large expressed ...

    Authors: Dietmar Schwarz, Hugh M Robertson, Jeffrey L Feder, Kranthi Varala, Matthew E Hudson, Gregory J Ragland, Daniel A Hahn and Stewart H Berlocher
    Citation: BMC Genomics 2009 10:633
    Content type: Research article Published on:

  31. Insect odorant binding proteins (OBPs) and chemosensory proteins (CSPs) play an important role in chemical communication of insects. Gene discovery of these proteins is a time-consuming task. In recent years, ...

    Authors: Ya-Long Xu, Peng He, Lan Zhang, Shao-Qing Fang, Shuang-Lin Dong, Yong-Jun Zhang and Fei Li
    Citation: BMC Genomics 2009 10:632
    Content type: Research article Published on:

  32. Defensins represent an important class of antimicrobial peptides. These effector molecules of the innate immune system act as endogenous antibiotics to protect the organism against infections with pathogenic m...

    Authors: Oliver Bruhn, Sven Paul, Jens Tetens and Georg Thaller
    Citation: BMC Genomics 2009 10:631
    Content type: Research article Published on:

  33. Accurate determination of orthology is central to comparative genomics. For vertebrates in particular, very large gene families, high rates of gene duplication and loss, multiple mechanisms of gene duplication...

    Authors: Jin Jun, Ion I Mandoiu and Craig E Nelson
    Citation: BMC Genomics 2009 10:630
    Content type: Research article Published on:

  34. Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been r...

    Authors: Carlos H Galeano, Andrea C Fernández, Marcela Gómez and Matthew W Blair
    Citation: BMC Genomics 2009 10:629
    Content type: Research article Published on:

  35. Transcription factors activate their target genes by binding to specific response elements. Many transcription factor families evolved from a common ancestor by gene duplication and subsequent divergent evolut...

    Authors: Tobias Brandt, Miriana Petrovich, Andreas C Joerger and Dmitry B Veprintsev
    Citation: BMC Genomics 2009 10:628
    Content type: Research article Published on:

  36. Coral reefs are expected to be severely impacted by rising seawater temperatures associated with climate change. This study used cDNA microarrays to investigate transcriptional effects of thermal stress in emb...

    Authors: Christian R Voolstra, Julia Schnetzer, Leonid Peshkin, Carly J Randall, Alina M Szmant and Mónica Medina
    Citation: BMC Genomics 2009 10:627
    Content type: Research article Published on:

  37. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) worldwide. In spite of its agricultural importance, the genomics and genet...

    Authors: Chuntao Yin, Xianming Chen, Xiaojie Wang, Qingmei Han, Zhensheng Kang and Scot H Hulbert
    Citation: BMC Genomics 2009 10:626
    Content type: Research article Published on:

  38. Pulmonary metastasis continues to be the most common cause of death in osteosarcoma. Indeed, the 5-year survival for newly diagnosed osteosarcoma patients has not significantly changed in over 20 years. Furthe...

    Authors: Melissa Paoloni, Sean Davis, Susan Lana, Stephen Withrow, Luca Sangiorgi, Piero Picci, Stephen Hewitt, Timothy Triche, Paul Meltzer and Chand Khanna
    Citation: BMC Genomics 2009 10:625
    Content type: Research article Published on:

  39. Transposable elements (TEs) are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have been shown to have important functions ...

    Authors: Florian Maumus, Andrew E Allen, Corinne Mhiri, Hanhua Hu, Kamel Jabbari, Assaf Vardi, Marie-Angèle Grandbastien and Chris Bowler
    Citation: BMC Genomics 2009 10:624
    Content type: Research article Published on:

  40. Understanding sequence conservation is important for the study of sequence evolution and for the identification of functional regions of the genome. Current studies often measure sequence conservation based on...

    Authors: Xiaohui Cai, Haiyan Hu and Xiaoman Li
    Citation: BMC Genomics 2009 10:623
    Content type: Research article Published on:

  41. Protein kinases are involved in diverse spectrum of cellular processes. Availability of draft version of the human genomic data in the year 2001 enabled recognition of repertoire of protein kinases. However, o...

    Authors: Krishanpal Anamika, Nicolas Garnier and Narayanaswamy Srinivasan
    Citation: BMC Genomics 2009 10:622
    Content type: Research article Published on:

  42. The maintenance of internal pH in bacterial cells is challenged by natural stress conditions, during host infection or in biotechnological production processes. Comprehensive transcriptomic and proteomic analy...

    Authors: Martin Follmann, Ines Ochrombel, Reinhard Krämer, Christian Trötschel, Ansgar Poetsch, Christian Rückert, Andrea Hüser, Marcus Persicke, Dominic Seiferling, Jörn Kalinowski and Kay Marin
    Citation: BMC Genomics 2009 10:621
    Content type: Research article Published on:

  43. Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 ...

    Authors: Daniel Klevebring, Nathaniel R Street, Noah Fahlgren, Kristin D Kasschau, James C Carrington, Joakim Lundeberg and Stefan Jansson
    Citation: BMC Genomics 2009 10:620
    Content type: Research article Published on:

  45. Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is increasingly being applied to study transcriptional regulation on a genome-wide scale. While numerous algorithms have rece...

    Authors: Teemu D Laajala, Sunil Raghav, Soile Tuomela, Riitta Lahesmaa, Tero Aittokallio and Laura L Elo
    Citation: BMC Genomics 2009 10:618
    Content type: Research article Published on:

  46. Whole genome gene expression profiling has revolutionized research in the past decade especially with the advent of microarrays. Recently, there have been significant improvements in whole blood RNA isolation ...

    Authors: Elizabeth H Robison, Tony S Mondala, Adam R Williams, Steven R Head, Daniel R Salomon and Sunil M Kurian
    Citation: BMC Genomics 2009 10:617
    Content type: Methodology article Published on:

  47. The Xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, Xanthomonas albilineans and Xylella fastidiosa. X. fastidiosa was the first completely sequenced plant pathogen. It is in...

    Authors: Isabelle Pieretti, Monique Royer, Valérie Barbe, Sébastien Carrere, Ralf Koebnik, Stéphane Cociancich, Arnaud Couloux, Armelle Darrasse, Jérôme Gouzy, Marie-Agnès Jacques, Emmanuelle Lauber, Charles Manceau, Sophie Mangenot, Stéphane Poussier, Béatrice Segurens, Boris Szurek…
    Citation: BMC Genomics 2009 10:616
    Content type: Research article Published on:

  48. Gastric cancers are generally classified into better differentiated intestinal-type tumor and poorly differentiated diffuse-type one according to Lauren's histological categorization. Although induction of pro...

    Authors: Hiraku Itadani, Hiroko Oshima, Masanobu Oshima and Hidehito Kotani
    Citation: BMC Genomics 2009 10:615
    Content type: Research article Published on:

  49. Human genetic variation produces the wide range of phenotypic differences that make us individual. However, little is known about the distribution of variation in the most conserved functional regions of the h...

    Authors: Scott Davidson, Andrew Starkey and Alasdair MacKenzie
    Citation: BMC Genomics 2009 10:614
    Content type: Research article Published on:

  50. Aspartic proteases are known to play an important role in the biology of nematode parasitism. This role is best characterised in blood-feeding nematodes, where they digest haemoglobin, but they are also likely...

    Authors: Luciane V Mello, Helen O'Meara, Daniel J Rigden and Steve Paterson
    Citation: BMC Genomics 2009 10:611
    Content type: Research article Published on:

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BMC Genomics

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