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  1. Oral squamous cell carcinoma (OSCC) is one of the most common forms of cancer associated with the presence of precancerous oral leukoplakia. Given the poor prognosis associated with oral leukoplakia, and the d...

    Authors: Zhi Wang, Xiaodong Feng, Xinyu Liu, Lu Jiang, Xin Zeng, Ning Ji, Jing Li, Longjiang Li and Qianming Chen
    Citation: BMC Genomics 2009 10:383
    Content type: Research article Published on:

  2. The declining cost of DNA sequencing is making genome sequencing a feasible option for more organisms, including many of interest to ecologists and evolutionary biologists. While obtaining high-depth, complete...

    Authors: David A Rasmussen and Mohamed AF Noor
    Citation: BMC Genomics 2009 10:382
    Content type: Research article Published on:

  3. To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression programs. To investigate the mechanis...

    Authors: Fabio Parisi, Bernhard Sonderegger, Pratyaksha Wirapati, Mauro Delorenzi and Felix Naef
    Citation: BMC Genomics 2009 10:381
    Content type: Research article Published on:

  4. The human microflora is known to be extremely complex, yet most pathogenesis research is conducted in mono-species models of infection. Consequently, it remains unclear whether the level of complexity of a hos...

    Authors: Jeffrey J Mans, Kate von Lackum, Cassandra Dorsey, Shaun Willis, Shannon M Wallet, Henry V Baker, Richard J Lamont and Martin Handfield
    Citation: BMC Genomics 2009 10:380
    Content type: Research article Published on:

  5. Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not...

    Authors: 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
    Citation: BMC Genomics 2009 10:379
    Content type: Research article Published on:

  6. Reactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in...

    Authors: Bhupendra Chaudhary, Ran Hovav, Lex Flagel, Ron Mittler and Jonathan F Wendel
    Citation: BMC Genomics 2009 10:378
    Content type: Research article Published on:

  7. The hard clam, Mercenaria mercenaria, has been affected by severe mortality episodes associated with the protistan parasite QPX (Quahog Parasite Unknown) for several years. Despite the commercial importance of ha...

    Authors: Mickael Perrigault, Arnaud Tanguy and Bassem Allam
    Citation: BMC Genomics 2009 10:377
    Content type: Research article Published on:

  8. Soybeans grown in the upper Midwestern United States often suffer from iron deficiency chlorosis, which results in yield loss at the end of the season. To better understand the effect of iron availability on s...

    Authors: Jamie A O'Rourke, Rex T Nelson, David Grant, Jeremy Schmutz, Jane Grimwood, Steven Cannon, Carroll P Vance, Michelle A Graham and Randy C Shoemaker
    Citation: BMC Genomics 2009 10:376
    Content type: Research article Published on:

  9. Venomous animals incapacitate their prey using complex venoms that can contain hundreds of unique protein toxins. The realisation that many of these toxins may have pharmaceutical and insecticidal potential du...

    Authors: David LA Wood, Tomas Miljenović, Shuzhi Cai, Robert J Raven, Quentin Kaas, Pierre Escoubas, Volker Herzig, David Wilson and Glenn F King
    Citation: BMC Genomics 2009 10:375
    Content type: Database Published on:

  10. Although the Illumina 1 G Genome Analyzer generates billions of base pairs of sequence data, challenges arise in sequence selection due to the varying sequence quality. Therefore, in the framework of the Inter...

    Authors: 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
    Citation: BMC Genomics 2009 10:374
    Content type: Methodology article Published on:

  11. Hepatitis C virus (HCV) is a major cause of chronic liver disease by infecting over 170 million people worldwide. Recent studies have shown that microRNAs (miRNAs), a class of small non-coding regulatory RNAs,...

    Authors: Xinxia Peng, Yu Li, Kathie-Anne Walters, Elizabeth R Rosenzweig, Sharon L Lederer, Lauri D Aicher, Sean Proll and Michael G Katze
    Citation: BMC Genomics 2009 10:373
    Content type: Research article Published on:

  12. Interferons (IFNs) are potent antiviral cytokines capable of reprogramming the macrophage phenotype through the induction of interferon-stimulated genes (ISGs). Here we have used targeted RNA interference to s...

    Authors: Paul Lacaze, Sobia Raza, Garwin Sing, David Page, Thorsten Forster, Petter Storm, Marie Craigon, Tarif Awad, Peter Ghazal and Tom C Freeman
    Citation: BMC Genomics 2009 10:372
    Content type: Research article Published on:

  13. Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced b...

    Authors: Qingyi Yu, Eric Tong, Rachel L Skelton, John E Bowers, Meghan R Jones, Jan E Murray, Shaobin Hou, Peizhu Guan, Ricelle A Acob, Ming-Cheng Luo, Paul H Moore, Maqsudul Alam, Andrew H Paterson and Ray Ming
    Citation: BMC Genomics 2009 10:371
    Content type: Research article Published on:

  14. Chronic chagasic cardiomyopathy is a debilitating and frequently fatal outcome of human infection with the protozoan parasite, Trypanosoma cruzi. Microarray analysis of gene expression during the T. cruzi life-cy...

    Authors: Todd A Minning, D Brent Weatherly, James Atwood III, Ron Orlando and Rick L Tarleton
    Citation: BMC Genomics 2009 10:370
    Content type: Research article Published on:

  15. Mammalians gamete production takes place in the testis but when they exit this organ, although spermatozoa have acquired a specialized and distinct morphology, they are immotile and infertile. It is only after...

    Authors: Benoît Guyonnet, Guillemette Marot, Jean-Louis Dacheux, Marie-José Mercat, Sandrine Schwob, Florence Jaffrézic and Jean-Luc Gatti
    Citation: BMC Genomics 2009 10:369
    Content type: Research article Published on:

  16. Infectious pancreatic necrosis (IPN) is one of the most prevalent and economically devastating diseases in Atlantic salmon (Salmo salar) farming worldwide. The disease causes large mortalities at both the fry- an...

    Authors: Thomas Moen, Matthew Baranski, Anna K Sonesson and Sissel Kjøglum
    Citation: BMC Genomics 2009 10:368
    Content type: Research article Published on:

  17. The relationship between the parasitic fungus Pneumocystis carinii and its host, the laboratory rat, presumably involves features that allow the fungus to circumvent attacks by the immune system. It is hypothesiz...

    Authors: Scott P Keely and James R Stringer
    Citation: BMC Genomics 2009 10:367
    Content type: Research article Published on:

  19. The Central Dogma of biology holds, in famously simplified terms, that DNA makes RNA makes proteins, but there is considerable uncertainty regarding the general, genome-wide correlation between levels of RNA a...

    Authors: Marcus Gry, Rebecca Rimini, Sara Strömberg, Anna Asplund, Fredrik Pontén, Mathias Uhlén and Peter Nilsson
    Citation: BMC Genomics 2009 10:365
    Content type: Research article Published on:

  20. The new animal phylogeny established several taxa which were not identified by morphological analyses, most prominently the Ecdysozoa (arthropods, roundworms, priapulids and others) and Lophotrochozoa (mollusc...

    Authors: Lars Podsiadlowski, Anke Braband, Torsten H Struck, Jörn von Döhren and Thomas Bartolomaeus
    Citation: BMC Genomics 2009 10:364
    Content type: Research article Published on:

  21. In response to pathogen attack, grapevine synthesizes phytoalexins belonging to the family of stilbenes. Grapevine cell cultures represent a good model system for studying the basic mechanisms of plant respons...

    Authors: Anita Zamboni, Pamela Gatto, Alessandro Cestaro, Stefania Pilati, Roberto Viola, Fulvio Mattivi, Claudio Moser and Riccardo Velasco
    Citation: BMC Genomics 2009 10:363
    Content type: Research article Published on:

  22. Guanine-rich nucleic acid sequences are capable of folding into an intramolecular four-stranded structure called a G-quadruplex. When found in gene promoter regions, G-quadruplexes can downregulate gene expres...

    Authors: Nicolas Smargiasso, Valérie Gabelica, Christian Damblon, Frédéric Rosu, Edwin De Pauw, Marie-Paule Teulade-Fichou, J Alexandra Rowe and Antoine Claessens
    Citation: BMC Genomics 2009 10:362
    Content type: Research article Published on:

  23. Many species of stalk-eyed flies (Diopsidae) possess highly-exaggerated, sexually dimorphic eye-stalks that play an important role in the mating system of these flies. Eye-stalks are increasingly being used as...

    Authors: Richard H Baker, Jenna Morgan, Xianhui Wang, Jeffrey L Boore and Gerald S Wilkinson
    Citation: BMC Genomics 2009 10:361
    Content type: Research article Published on:

  24. One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as p...

    Authors: Jay Vyas, Ronald J Nowling, Mark W Maciejewski, Sanguthevar Rajasekaran, Michael R Gryk and Martin R Schiller
    Citation: BMC Genomics 2009 10:360
    Content type: Research article Published on:

  26. Streptococcus mutans is the major pathogen of dental caries, and it occasionally causes infective endocarditis. While the pathogenicity of this species is distinct from other human pathogenic streptococci, the sp...

    Authors: Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takashi Ooshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada and Ichiro Nakagawa
    Citation: BMC Genomics 2009 10:358
    Content type: Research article Published on:

  27. The availability of the complete chicken (Gallus gallus) genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH) and microarray resources facilitate comparative ge...

    Authors: Benjamin M Skinner, Lindsay BW Robertson, Helen G Tempest, Elizabeth J Langley, Dimitris Ioannou, Katie E Fowler, Richard PMA Crooijmans, Anthony D Hall, Darren K Griffin and Martin Völker
    Citation: BMC Genomics 2009 10:357
    Content type: Research article Published on:

  28. 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:

  30. 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:

  31. Gene copy number variation (CNV) is responsible for several important phenotypes of the malaria parasite Plasmodium falciparum, including drug resistance, loss of infected erythrocyte cytoadherence and alteration...

    Authors: Ian H Cheeseman, Natalia Gomez-Escobar, Celine K Carret, Alasdair Ivens, Lindsay B Stewart, Kevin KA Tetteh and David J Conway
    Citation: BMC Genomics 2009 10:353
    Content type: Research article Published on:

  32. 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:

  33. 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:

  34. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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