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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. It has been recognized cancer cells acquire characters reminiscent of those of normal stem cells, and the degree of stem cell gene expression correlates with patient prognosis. Lgr5(+) or CD133(+) epithelial s...

    Authors: Shing-Jyh Chang, Tao-Yeuan Wang, Chan-Yen Tsai, Tzu-Fang Hu, Margaret Dah-Tsyr Chang and Hsei-Wei Wang
    Citation: BMC Genomics 2009 10:613
  33. Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their...

    Authors: Trevor J Pemberton, Conner I Sandefur, Mattias Jakobsson and Noah A Rosenberg
    Citation: BMC Genomics 2009 10:612
  34. 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
  35. Epigenetic modifications of histones and regulation of chromatin structure have been implicated in regulation of virulence gene families in P. falciparum. To better understand chromatin-mediated gene regulation, ...

    Authors: Scott J Westenberger, Long Cui, Neekesh Dharia, Elizabeth Winzeler and Liwang Cui
    Citation: BMC Genomics 2009 10:610
  36. The success of a biological control agent depends on key traits, particularly reproductive potential, environmental tolerance, and ability to be cultured. These traits can deteriorate rapidly when the biologic...

    Authors: Bishwo N Adhikari, Chin-Yo Lin, Xiaodong Bai, Todd A Ciche, Parwinder S Grewal, Adler R Dillman, John M Chaston, David I Shapiro-Ilan, Anwar L Bilgrami, Randy Gaugler, Paul W Sternberg and Byron J Adams
    Citation: BMC Genomics 2009 10:609
  37. The delta smelt (Hypomesus transpacificus) is a pelagic fish species listed as endangered under both the USA Federal and Californian State Endangered Species Acts and considered an indicator of ecosystem health i...

    Authors: Richard E Connon, Juergen Geist, Janice Pfeiff, Alexander V Loguinov, Leandro S D'Abronzo, Henri Wintz, Christopher D Vulpe and Inge Werner
    Citation: BMC Genomics 2009 10:608
  38. Microsporidia are obligate intracellular eukaryotic parasites with genomes ranging in size from 2.3 Mbp to more than 20 Mbp. The extremely small (2.9 Mbp) and highly compact (~1 gene/kb) genome of the human pa...

    Authors: Eric Peyretaillade, Olivier Gonçalves, Sébastien Terrat, Eric Dugat-Bony, Patrick Wincker, Robert S Cornman, Jay D Evans, Frédéric Delbac and Pierre Peyret
    Citation: BMC Genomics 2009 10:607
  39. Host defense peptides are a critical component of the innate immune system. Human alpha- and beta-defensin genes are subject to copy number variation (CNV) and historically the organization of mouse alpha-defe...

    Authors: Clara Amid, Linda M Rehaume, Kelly L Brown, James GR Gilbert, Gordon Dougan, Robert EW Hancock and Jennifer L Harrow
    Citation: BMC Genomics 2009 10:606
  40. Current models propose that mitochondrial DNA macrohaplogroups M and N evolved from haplogroup L3 soon after modern humans left Africa. Increasingly, however, analysis of isolated populations is filling in the...

    Authors: François-X Ricaut, Harilanto Razafindrazaka, Murray P Cox, Jean-M Dugoujon, Evelyne Guitard, Clement Sambo, Maru Mormina, Marta Mirazon-Lahr, Bertrand Ludes and Eric Crubézy
    Citation: BMC Genomics 2009 10:605
  41. With the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species (orthologs) is of fundamental importance to facilitate functional annotation...

    Authors: Raffaele Mazza, Francesco Strozzi, Andrea Caprera, Paolo Ajmone-Marsan and John L Williams
    Citation: BMC Genomics 2009 10:604
  42. Strepsiptera are an unusual group of sexually dimorphic, entomophagous parasitoids whose evolutionary origins remain elusive. The lineage leading to Mengenilla australiensis (Family Mengenillidae) is the sister g...

    Authors: Dino P McMahon, Alexander Hayward and Jeyaraney Kathirithamby
    Citation: BMC Genomics 2009 10:603
  43. The nucleosome is the fundamental unit of eukaryotic genomes. Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo. However, h...

    Authors: Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Yangyang Deng and Jiang Wang
    Citation: BMC Genomics 2009 10:602
  44. Metamorphosis is an important process in the life cycle of holometabolous insects and is regulated by insect hormones. During metamorphosis, the epidermis goes through a significant transformation at the bioch...

    Authors: Qiang Fu, Peng-Cheng Liu, Jin-Xing Wang, Qi-Sheng Song and Xiao-Fan Zhao
    Citation: BMC Genomics 2009 10:600
  45. Atypical tRNAs are functional minimal tRNAs, lacking either the D- or T-arm. They are significantly shorter than typical cloverleaf tRNAs. Widespread occurrence of atypical tRNAs was first demonstrated for sec...

    Authors: Pavel B Klimov and Barry M OConnor
    Citation: BMC Genomics 2009 10:598
  46. The application of high-throughput genomic tools in nutrition research is a widespread practice. However, it is becoming increasingly clear that the outcome of individual expression studies is insufficient for...

    Authors: Duccio Cavalieri, Enrica Calura, Chiara Romualdi, Emmanuela Marchi, Marijana Radonjic, Ben Van Ommen and Michael Müller
    Citation: BMC Genomics 2009 10:596

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