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  1. Compelling evidence exists that magnetic fields modulate living systems. To date, however, rigorous studies have focused on identifying the molecular-level biosensor (e.g., radical ion pairs or membranes) or o...

    Authors: Zhiyun Wang, Anshu Sarje, Pao-Lin Che and Kevin J Yarema
    Citation: BMC Genomics 2009 10:356
    Content type: Research article Published on:

  2. The recently described Type VI Secretion System (T6SS) represents a new paradigm of protein secretion in bacteria. A number of bioinformatic studies have been conducted to identify T6SS gene clusters in the av...

    Authors: Carlos J Blondel, Juan C Jiménez, Inés Contreras and Carlos A Santiviago
    Citation: BMC Genomics 2009 10:354
    Content type: Research article Published on:

  3. Using a combination of pyrosequencing and conventional Sanger sequencing, the complete genome sequence of the recently described novel Brucella species, Brucella microti, was determined. B. microti is a member of...

    Authors: Stéphane Audic, Magali Lescot, Jean-Michel Claverie and Holger C Scholz
    Citation: BMC Genomics 2009 10:352
    Content type: Research article Published on:

  4. Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating inte...

    Authors: Kennan Kellaris Salinero, Keith Keller, William S Feil, Helene Feil, Stephan Trong, Genevieve Di Bartolo and Alla Lapidus
    Citation: BMC Genomics 2009 10:351
    Content type: Research article Published on:

  5. The role of type I IFNs in protecting against coronavirus (CoV) infections is not fully understood. While CoVs are poor inducers of type I IFNs in tissue culture, several studies have demonstrated the importan...

    Authors: Matthijs Raaben, Marian JA Groot Koerkamp, Peter JM Rottier and Cornelis AM de Haan
    Citation: BMC Genomics 2009 10:350
    Content type: Research article Published on:

  7. The mature mouse oocyte contains the full complement of maternal proteins required for fertilization, reprogramming, zygotic gene activation (ZGA), and the early stages of embryogenesis. However, due to limita...

    Authors: Ping Zhang, Xiaojian Ni, Ying Guo, Xuejiang Guo, Yufeng Wang, Zuomin Zhou, Ran Huo and Jiahao Sha
    Citation: BMC Genomics 2009 10:348
    Content type: Research article Published on:

  8. We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional...

    Authors: P Kerr Wall, Jim Leebens-Mack, André S Chanderbali, Abdelali Barakat, Erik Wolcott, Haiying Liang, Lena Landherr, Lynn P Tomsho, Yi Hu, John E Carlson, Hong Ma, Stephan C Schuster, Douglas E Soltis, Pamela S Soltis, Naomi Altman and Claude W dePamphilis
    Citation: BMC Genomics 2009 10:347
    Content type: Methodology article Published on:

  9. The genomic fractions of purine (RR) and alternating pyrimidine/purine (YR) stretches of 10 base pairs or more, have been linked to genomic AT content, the formation of different DNA helices, strand-biased gen...

    Authors: Jon Bohlin, Simon P Hardy and David W Ussery
    Citation: BMC Genomics 2009 10:346
    Content type: Research article Published on:

  10. The teleost Zoarces viviparus (eelpout) lives along the coasts of Northern Europe and has long been an established model organism for marine ecology and environmental monitoring. The scarce information about this...

    Authors: Erik Kristiansson, Noomi Asker, Lars Förlin and DG Joakim Larsson
    Citation: BMC Genomics 2009 10:345
    Content type: Research article Published on:

  11. Custom solid phase oligonucleotide synthesis is an important foundation supporting nearly every aspect of current genomics. In spite of the demand for oligonucleotide primers, their synthesis remains relativel...

    Authors: Murray J Cairns, Torsten Thomas, Carolina E Beltran and Daniel Tillett
    Citation: BMC Genomics 2009 10:344
    Content type: Methodology article Published on:

  12. Stathmin (STMN1) protein functions to regulate assembly of the microtubule cytoskeleton by destabilizing microtubule polymers. Stathmin over-expression has been correlated with cancer stage progression, while ...

    Authors: Danielle N Ringhoff and Lynne Cassimeris
    Citation: BMC Genomics 2009 10:343
    Content type: Research article Published on:

  13. Epidemiological studies showed that physical exercise, specifically moderate lifelong training, is protective against cardiovascular morbidity and mortality. Most experimental work has focused into the effects...

    Authors: Betti Giusti, Marina Marini, Luciana Rossi, Ilaria Lapini, Alberto Magi, Andrea Capalbo, Rosa Lapalombella, Simona di Tullio, Michele Samaja, Fabio Esposito, Vittoria Margonato, Maria Boddi, Rosanna Abbate and Arsenio Veicsteinas
    Citation: BMC Genomics 2009 10:342
    Content type: Research article Published on:

  14. Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This repo...

    Authors: Elodie Fleury, Arnaud Huvet, Christophe Lelong, Julien de Lorgeril, Viviane Boulo, Yannick Gueguen, Evelyne Bachère, Arnaud Tanguy, Dario Moraga, Caroline Fabioux, Penelope Lindeque, Jenny Shaw, Richard Reinhardt, Patrick Prunet, Grace Davey, Sylvie Lapègue…
    Citation: BMC Genomics 2009 10:341
    Content type: Database Published on:

  15. The identification of gene differential co-expression patterns between cancer stages is a newly developing method to reveal the underlying molecular mechanisms of carcinogenesis. Most researches of this subjec...

    Authors: 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
    Citation: BMC Genomics 2009 10:340
    Content type: Research article Published on:

  16. Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-...

    Authors: Lee G Miles, Sally R Isberg, Travis C Glenn, Stacey L Lance, Pauline Dalzell, Peter C Thomson and Chris Moran
    Citation: BMC Genomics 2009 10:339
    Content type: Research article Published on:

  17. It is well known that the pattern of linkage disequilibrium varies between human populations, with remarkable geographical stratification. Indirect association studies routinely exploit linkage disequilibrium ...

    Authors: 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
    Citation: BMC Genomics 2009 10:338
    Content type: Research article Published on:

  18. Placental efficiency is strongly associated with litter size, fetal weight and prenatal mortality. Together with its rapid growth during late gestation, the Large White pig breed shows a significant increase i...

    Authors: Quan-Yong Zhou, Ming-Di Fang, Ting-Hua Huang, Chang-Chun Li, Mei Yu and Shu-Hong Zhao
    Citation: BMC Genomics 2009 10:337
    Content type: Research article Published on:

  19. The extracellular sunscreen scytonemin is the most common and widespread indole-alkaloid among cyanobacteria. Previous research using the cyanobacterium Nostoc punctiforme ATCC 29133 revealed a unique 18-gene clu...

    Authors: Tanya Soule, Kendra Palmer, Qunjie Gao, Ruth M Potrafka, Valerie Stout and Ferran Garcia-Pichel
    Citation: BMC Genomics 2009 10:336
    Content type: Research article Published on:

  20. The Intergenic Breakage Model, which is the current model of structural genome evolution, considers that evolutionary rearrangement breakages happen with a uniform propensity along the genome but are selected ...

    Authors: Claire Lemaitre, Lamia Zaghloul, Marie-France Sagot, Christian Gautier, Alain Arneodo, Eric Tannier and Benjamin Audit
    Citation: BMC Genomics 2009 10:335
    Content type: Research article Published on:

  21. Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species...

    Authors: Mark S Longo, Dawn M Carone, Eric D Green, Michael J O'Neill and Rachel J O'Neill
    Citation: BMC Genomics 2009 10:334
    Content type: Research article Published on:

  22. Coral reef ecosystems are renowned for their diversity and beauty. Their immense ecological success is due to a symbiotic association between cnidarian hosts and unicellular dinoflagellate algae, known as zoox...

    Authors: Cécile Sabourault, Philippe Ganot, Emeline Deleury, Denis Allemand and Paola Furla
    Citation: BMC Genomics 2009 10:333
    Content type: Research article Published on:

  24. The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to deve...

    Authors: 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
    Citation: BMC Genomics 2009 10:331
    Content type: Research article Published on:

  25. For three decades the Mutator system was thought to be exclusive of plants, until the first homolog representatives were characterized in fungi and in early-diverging amoebas earlier in this decade.

    Authors: Fabrício R Lopes, Joana C Silva, Marlene Benchimol, Gustavo GL Costa, Gonçalo AG Pereira and Claudia MA Carareto
    Citation: BMC Genomics 2009 10:330
    Content type: Research article Published on:

  26. The nematode Caenorhabditis elegans was the first multicellular organism to have its genome fully sequenced. Over the last 10 years since the original publication in 1998, the C. elegans genome has been scrutiniz...

    Authors: Ismael A Vergara, Allan K Mah, Jim C Huang, Maja Tarailo-Graovac, Robert C Johnsen, David L Baillie and Nansheng Chen
    Citation: BMC Genomics 2009 10:329
    Content type: Research article Published on:

  27. Insects provide tractable models for enhancing our understanding of the physiological and cellular processes that enable survival at extreme low temperatures. They possess three main strategies to survive the ...

    Authors: Melody S Clark, Michael AS Thorne, Jelena Purać, Gavin Burns, Guy Hillyard, Željko D Popović, Gordana Grubor-Lajšić and M Roger Worland
    Citation: BMC Genomics 2009 10:328
    Content type: Research article Published on:

  28. Recent work has revealed that a core group of transcription factors (TFs) regulates the key characteristics of embryonic stem (ES) cells: pluripotency and self-renewal. Current efforts focus on identifying gen...

    Authors: Mike J Mason, Guoping Fan, Kathrin Plath, Qing Zhou and Steve Horvath
    Citation: BMC Genomics 2009 10:327
    Content type: Research article Published on:

  29. Gene expression profiling of small numbers of cells requires high-fidelity amplification of sub-nanogram amounts of RNA. Several methods for RNA amplification are available; however, there has been little cons...

    Authors: 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
    Citation: BMC Genomics 2009 10:326
    Content type: Research article Published on:

  30. The free-living nematode Caenorhabditis elegans makes a developmental decision based on environmental conditions: larvae either arrest as dauer larva, or continue development into reproductive adults. There is na...

    Authors: Simon C Harvey, Gary LA Barker, Alison Shorto and Mark E Viney
    Citation: BMC Genomics 2009 10:325
    Content type: Research article Published on:

  31. More than 20% of human transcripts have naturally occurring antisense products (or natural antisense transcripts – NATs), some of which may play a key role in a range of human diseases. To date, several databa...

    Authors: Anita Grigoriadis, Gavin R Oliver, Austin Tanney, Howard Kendrick, Matt J Smalley, Parmjit Jat and A Munro Neville
    Citation: BMC Genomics 2009 10:324
    Content type: Research article Published on:

  32. The B cell antigen receptor (BCR) is a signaling complex that mediates the differentiation of stage-specific cell fate decisions in B lymphocytes. While several studies have shown differences in signal transdu...

    Authors: Jernej Murn, Irena Mlinaric-Rascan, Pierre Vaigot, Olivier Alibert, Vincent Frouin and Xavier Gidrol
    Citation: BMC Genomics 2009 10:323
    Content type: Research article Published on:

  33. Patterns of mouse DNA hydrolysis with restriction enzymes are coincided with calculated diagrams of genomic DNA digestion in silico, except presence of additional bright bands, which correspond to monomer and dim...

    Authors: Murat A Abdurashitov, Valery A Chernukhin, Danila A Gonchar and Sergey Kh Degtyarev
    Citation: BMC Genomics 2009 10:322
    Content type: Research article Published on:

  34. About 45% of the human genome is comprised of mobile transposable elements or "junk DNA". The exaptation or co-option of these elements to provide important cellular functions is hypothesized to have played a ...

    Authors: Adrian F Gombart, Tsuyako Saito and H Phillip Koeffler
    Citation: BMC Genomics 2009 10:321
    Content type: Research article Published on:

  35. Association mapping approaches are dependent upon discovery and validation of single nucleotide polymorphisms (SNPs). To further association studies in Anopheles gambiae we conducted a major resequencing programm...

    Authors: Craig S Wilding, David Weetman, Keith Steen and Martin J Donnelly
    Citation: BMC Genomics 2009 10:320
    Content type: Research article Published on:

  37. As the amount of genome sequencing data grows, so does the problem of computational gene identification, and in particular, the splicing signals that flank exon borders. Traditional methods for identifying spl...

    Authors: Katherine M Buckley, Liliana D Florea and L Courtney Smith
    Citation: BMC Genomics 2009 10:318
    Content type: Research article Published on:

  39. Magnaporthe oryzae, rice blast fungus, is the most devastating pathogen of rice. It has emerged as a model phytopathogen for the study of host-pathogen interactions. A large body of data has been generated on dif...

    Authors: Shalabh Thakur, Sanjay Jha, Subhankar Roy-Barman and Bharat Chattoo
    Citation: BMC Genomics 2009 10:316
    Content type: Database Published on:

  40. With the escalation of high throughput prokaryotic genome sequencing, there is an ever-increasing need for databases that characterise, catalogue and present data relating to particular gene sets and genomes/m...

    Authors: Mohamed Barakat, Philippe Ortet, Cécile Jourlin-Castelli, Mireille Ansaldi, Vincent Méjean and David E Whitworth
    Citation: BMC Genomics 2009 10:315
    Content type: Database Published on:

  41. The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self renewal are controlled by a tran...

    Authors: Lukas Chavez, Abha S Bais, Martin Vingron, Hans Lehrach, James Adjaye and Ralf Herwig
    Citation: BMC Genomics 2009 10:314
    Content type: Research article Published on:

  42. NOD26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional diver...

    Authors: Qingpo Liu, Huasen Wang, Zhonghua Zhang, Jiasheng Wu, Ying Feng and Zhujun Zhu
    Citation: BMC Genomics 2009 10:313
    Content type: Research article Published on:

  43. Apicomplexan parasites are causative agents of various diseases including malaria and have been targets of extensive genomic sequencing. We generated 5'-EST collections for six apicomplexa parasites using our ...

    Authors: Hiroyuki Wakaguri, Yutaka Suzuki, Masahide Sasaki, Sumio Sugano and Junichi Watanabe
    Citation: BMC Genomics 2009 10:312
    Content type: Research article Published on:

  44. Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group th...

    Authors: Xueyan Shan, David A Ray, John A Bunge and Daniel G Peterson
    Citation: BMC Genomics 2009 10(Suppl 2):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  45. Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species. Moreover, due to its u...

    Authors: David W Burt, Wilfrid Carrë, Mark Fell, Andy S Law, Parker B Antin, Donna R Maglott, Janet A Weber, Carl J Schmidt, Shane C Burgess and Fiona M McCarthy
    Citation: BMC Genomics 2009 10(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  46. Pasteurella multocida is a gram-negative bacterial pathogen that has a broad host range. One of the diseases it causes is fowl cholera in poultry. The availability of the genome sequence of avian P. multocida iso...

    Authors: Bindu Nanduri, Leslie A Shack, Shane C Burgess and Mark L Lawrence
    Citation: BMC Genomics 2009 10(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  47. With the threat of emerging infectious diseases such as avian influenza, whose natural hosts are thought to be a variety of wild water birds including duck, we are armed with very few genomic resources to inve...

    Authors: Tamsyn M Crowley, Volker R Haring, Simon Burggraaf and Robert J Moore
    Citation: BMC Genomics 2009 10(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  48. The genome sequence and a high-density SNP map are now available for the chicken and can be used to identify genetic markers for use in marker-assisted selection (MAS). Effective MAS requires high linkage dise...

    Authors: Behnam Abasht, Erin Sandford, Jesus Arango, Petek Settar, Janet E Fulton, Neil P O'Sullivan, Abebe Hassen, David Habier, Rohan L Fernando, Jack CM Dekkers and Susan J Lamont
    Citation: BMC Genomics 2009 10(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

  50. The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the bi...

    Authors: Susan M Bridges, Shane C Burgess and Fiona M McCarthy
    Citation: BMC Genomics 2009 10(Suppl 2):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

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