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  1. Inflammatory bowel disease (IBD) is used to describe a state of idiopathic, chronic inflammation of the gastrointestinal tract. The two main phenotypes of IBD are Crohn's disease (CD) and ulcerative colitis (U...

    Authors: Rebecca Munk Vejborg, Viktoria Hancock, Andreas M Petersen, Karen A Krogfelt and Per Klemm
    Citation: BMC Genomics 2011 12:316
  2. Piwi interacting RNA, or piRNA, is a class of small RNA almost exclusively expressed in the germline where they serve essential roles in retrotransposon silencing. There are two types, primary and secondary pi...

    Authors: Harald M Oey, Neil A Youngson and Emma Whitelaw
    Citation: BMC Genomics 2011 12:315
  3. Transporter proteins are one of an organism’s primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and...

    Authors: Sarah E Giuliani, Ashley M Frank, Danielle M Corgliano, Catherine Seifert, Loren Hauser and Frank R Collart
    Citation: BMC Genomics 2011 12(Suppl 1):S8

    This article is part of a Supplement: Volume 12 Supplement 1

  4. Correct annotation of function is essential if one is to take full advantage of the vast amounts of genomic sequence data. The accuracy of sequence-based functional annotations is often variable, particularly ...

    Authors: Yihong Chen, Ethel Apolinario, Libuse Brachova, Zvi Kelman, Zhuo Li, Basil J Nikolau, Lucas Showman, Kevin Sowers and John Orban
    Citation: BMC Genomics 2011 12(Suppl 1):S7

    This article is part of a Supplement: Volume 12 Supplement 1

  5. In order to carry out experimental gene annotation, DNA encoding open reading frames (ORFs) derived from real genes (termed "genic") in the correct frame is required. When genes are correctly assigned, isolati...

    Authors: Sara D'Angelo, Nileena Velappan, Flavio Mignone, Claudio Santoro, Daniele Sblattero, Csaba Kiss and Andrew RM Bradbury
    Citation: BMC Genomics 2011 12(Suppl 1):S5

    This article is part of a Supplement: Volume 12 Supplement 1

  6. Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the C. reinhardtii genome has made ...

    Authors: Lila Ghamsari, Santhanam Balaji, Yun Shen, Xinping Yang, Dawit Balcha, Changyu Fan, Tong Hao, Haiyuan Yu, Jason A Papin and Kourosh Salehi-Ashtiani
    Citation: BMC Genomics 2011 12(Suppl 1):S4

    This article is part of a Supplement: Volume 12 Supplement 1

  7. Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown or vag...

    Authors: Svetlana Gerdes, Basma El Yacoubi, Marc Bailly, Ian K Blaby, Crysten E Blaby-Haas, Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Jeffrey C Waller, Andreas Wilke, Ross Overbeek, Andrew D Hanson and Valérie de Crécy-Lagard
    Citation: BMC Genomics 2011 12(Suppl 1):S2

    This article is part of a Supplement: Volume 12 Supplement 1

  8. Genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function. While a variety of computational tools have been developed for this purpose, err...

    Authors: Margaret F Romine
    Citation: BMC Genomics 2011 12(Suppl 1):S1

    This article is part of a Supplement: Volume 12 Supplement 1

  9. Rainbow trout (Oncorhynchus mykiss) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmoni...

    Authors: Carine Genet, Patrice Dehais, Yniv Palti, Guangtu Gao, Frederick Gavory, Patrick Wincker, Edwige Quillet and Mekki Boussaha
    Citation: BMC Genomics 2011 12:314
  10. DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have develope...

    Authors: Srinivasan Yegnasubramanian, Zhijin Wu, Michael C Haffner, David Esopi, Martin J Aryee, Raghav Badrinath, Tony L He, James D Morgan, Benilton Carvalho, Qizhi Zheng, Angelo M De Marzo, Rafael A Irizarry and William G Nelson
    Citation: BMC Genomics 2011 12:313
  11. Noncoding RNA (ncRNA) has been recognized as an important regulator of gene expression networks in Bacteria and Eucaryota. Little is known about ncRNA in thermococcal archaea except for the eukaryotic-like C/D...

    Authors: Kounthéa Phok, Annick Moisan, Dana Rinaldi, Nicolas Brucato, Agamemnon J Carpousis, Christine Gaspin and Béatrice Clouet-d'Orval
    Citation: BMC Genomics 2011 12:312
  12. Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits o...

    Authors: Gloria L Fawcett, Muthuswamy Raveendran, David Rio Deiros, David Chen, Fuli Yu, Ronald Alan Harris, Yanru Ren, Donna M Muzny, Jeffrey G Reid, David A Wheeler, Kimberly C Worley, Steven E Shelton, Ned H Kalin, Aleksandar Milosavljevic, Richard Gibbs and Jeffrey Rogers
    Citation: BMC Genomics 2011 12:311
  13. Fish has been deemed suitable to study the complex mechanisms of vertebrate skeletogenesis and gilthead seabream (Sparus aurata), a marine teleost with acellular bone, has been successfully used in recent years t...

    Authors: Daniel M Tiago, Vincent Laizé, Luca Bargelloni, Serena Ferraresso, Chiara Romualdi and M Leonor Cancela
    Citation: BMC Genomics 2011 12:310
  14. Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especial...

    Authors: Luisa Orsini, Mieke Jansen, Erika L Souche, Sarah Geldof and Luc De Meester
    Citation: BMC Genomics 2011 12:309
  15. The larvae of the greater wax moth Galleria mellonella are increasingly used (i) as mini-hosts to study pathogenesis and virulence factors of prominent bacterial and fungal human pathogens, (ii) as a whole-animal...

    Authors: Heiko Vogel, Boran Altincicek, Gernot Glöckner and Andreas Vilcinskas
    Citation: BMC Genomics 2011 12:308
  16. Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs...

    Authors: Franceli R Kulcheski, Luiz FV de Oliveira, Lorrayne G Molina, Maurício P Almerão, Fabiana A Rodrigues, Juliana Marcolino, Joice F Barbosa, Renata Stolf-Moreira, Alexandre L Nepomuceno, Francismar C Marcelino-Guimarães, Ricardo V Abdelnoor, Leandro C Nascimento, Marcelo F Carazzolle, Gonçalo AG Pereira and Rogério Margis
    Citation: BMC Genomics 2011 12:307
  17. Seminal fluid plays an important role in successful fertilization, but knowledge of the full suite of proteins transferred from males to females during copulation is incomplete. The list of ejaculated proteins...

    Authors: Matthew D Dean, Geoffrey D Findlay, Michael R Hoopmann, Christine C Wu, Michael J MacCoss, Willie J Swanson and Michael W Nachman
    Citation: BMC Genomics 2011 12:306
  18. The intestinal mucosa is characterized by complex metabolic and immunological processes driven highly dynamic gene expression programs. With the advent of next generation sequencing and its utilization for the...

    Authors: Ulrich C Klostermeier, Matthias Barann, Michael Wittig, Robert Häsler, Andre Franke, Olga Gavrilova, Benjamin Kreck, Christian Sina, Markus B Schilhabel, Stefan Schreiber and Philip Rosenstiel
    Citation: BMC Genomics 2011 12:305
  19. The eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on th...

    Authors: Lorenzo Barchi, Sergio Lanteri, Ezio Portis, Alberto Acquadro, Giampiero Valè, Laura Toppino and Giuseppe Leonardo Rotino
    Citation: BMC Genomics 2011 12:304
  20. Folding and intermingling of chromosomes has the potential of bringing close to each other loci that are very distant genomically or even on different chromosomes. On the other hand, genomic rearrangements als...

    Authors: Amélie S Véron, Claire Lemaitre, Christian Gautier, Vincent Lacroix and Marie-France Sagot
    Citation: BMC Genomics 2011 12:303
  21. Current breeding approaches in potato rely almost entirely on phenotypic evaluations; molecular markers, with the exception of a few linked to disease resistance traits, are not widely used. Large-scale sequen...

    Authors: John P Hamilton, Candice N Hansey, Brett R Whitty, Kevin Stoffel, Alicia N Massa, Allen Van Deynze, Walter S De Jong, David S Douches and C Robin Buell
    Citation: BMC Genomics 2011 12:302
  22. Eucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly ...

    Authors: Jean-Marc Gion, Audrey Carouché, Sylvie Deweer, Franck Bedon, Frédérique Pichavant, Jean-Paul Charpentier, Henri Baillères, Philippe Rozenberg, Victor Carocha, Nina Ognouabi, Daniel Verhaegen, Jacqueline Grima-Pettenati, Philippe Vigneron and Christophe Plomion
    Citation: BMC Genomics 2011 12:301
  23. To identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes r...

    Authors: Debbie Laudencia-Chingcuanco, Seedhabadee Ganeshan, Frank You, Brian Fowler, Ravindra Chibbar and Olin Anderson
    Citation: BMC Genomics 2011 12:299
  24. Gene expression is known to vary extensively among tissues and between sexes. However, detailed descriptions of tissue- and sex-specific gene expression are available for only a few model organisms. A new stud...

    Authors: Rayna Stamboliyska and John Parsch
    Citation: BMC Genomics 2011 12:297
  25. The mosquito, Anopheles gambiae, is the primary vector of human malaria, a disease responsible for millions of deaths each year. To improve strategies for controlling transmission of the causative parasite, Plasm...

    Authors: Dean A Baker, Tony Nolan, Bettina Fischer, Alex Pinder, Andrea Crisanti and Steven Russell
    Citation: BMC Genomics 2011 12:296
  26. Human killer immunoglobulin-like receptors (KIRs) play a critical role in governing the immune response to neoplastic and infectious disease. Rhesus macaques serve as important animal models for many human dis...

    Authors: Anna J Moreland, Lisbeth A Guethlein, R Keith Reeves, Karl W Broman, R Paul Johnson, Peter Parham, David H O'Connor and Benjamin N Bimber
    Citation: BMC Genomics 2011 12:295
  27. Vibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emerg...

    Authors: Yuansha Chen, O Colin Stine, Jonathan H Badger, Ana I Gil, G Balakrish Nair, Mitsuaki Nishibuchi and Derrick E Fouts
    Citation: BMC Genomics 2011 12:294
  28. RNA-seq is revolutionizing the way we study transcriptomes. mRNA can be surveyed without prior knowledge of gene transcripts. Alternative splicing of transcript isoforms and the identification of previously un...

    Authors: Lauren M McIntyre, Kenneth K Lopiano, Alison M Morse, Victor Amin, Ann L Oberg, Linda J Young and Sergey V Nuzhdin
    Citation: BMC Genomics 2011 12:293
  29. One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to...

    Authors: Patricia Faivre Rampant, Isabelle Lesur, Clément Boussardon, Frédérique Bitton, Marie-Laure Martin-Magniette, Catherine Bodénès, Grégoire Le Provost, Hélène Bergès, Sylvia Fluch, Antoine Kremer and Christophe Plomion
    Citation: BMC Genomics 2011 12:292
  30. Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study e...

    Authors: Jason W Sahl, J Kristie Johnson, Anthony D Harris, Adam M Phillippy, William W Hsiao, Kerri A Thom and David A Rasko
    Citation: BMC Genomics 2011 12:291
  31. Non-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific impo...

    Authors: Lu Wang, Xiang Yu, Han Wang, Yi-Zhen Lu, Marjo de Ruiter, Marcel Prins and Yu-Ke He
    Citation: BMC Genomics 2011 12:289
  32. Emerging knowledge of the impact of small RNAs as important cellular regulators has prompted an explosion of small transcriptome sequencing projects. Although significant progress has been made towards small R...

    Authors: Cristiano C Nunes, Malali Gowda, Joshua Sailsbery, Minfeng Xue, Feng Chen, Douglas E Brown, YeonYee Oh, Thomas K Mitchell and Ralph A Dean
    Citation: BMC Genomics 2011 12:288
  33. Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is ...

    Authors: Paul J McMurdie, Laura A Hug, Elizabeth A Edwards, Susan Holmes and Alfred M Spormann
    Citation: BMC Genomics 2011 12:287
  34. The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping ...

    Authors: Jose M Blanca, Laura Pascual, Peio Ziarsolo, Fernando Nuez and Joaquin Cañizares
    Citation: BMC Genomics 2011 12:285
  35. The recent development of next generation sequencing technologies has made it possible to generate very large amounts of sequence data in species with little or no genome information. Combined with the large p...

    Authors: Anna W Santure, Jake Gratten, Jim A Mossman, Ben C Sheldon and Jon Slate
    Citation: BMC Genomics 2011 12:283
  36. Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of...

    Authors: Brian B Oakley, Eldin Talundzic, Cesar A Morales, Kelli L Hiett, Gregory R Siragusa, Nikolay V Volozhantsev and Bruce S Seal
    Citation: BMC Genomics 2011 12:282
  37. Glucagon is an important hormone in the regulation of glucose homeostasis, particularly in the maintenance of euglycemia and prevention of hypoglycemia. In type 2 Diabetes Mellitus (T2DM), glucagon levels are ...

    Authors: Jianxin Yang, Margit L MacDougall, Michael T McDowell, Li Xi, Ru Wei, William J Zavadoski, Mark P Molloy, John D Baker, Max Kuhn, Over Cabrera and Judith L Treadway
    Citation: BMC Genomics 2011 12:281
  38. DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the...

    Authors: Lucian Ilie, Silvana Ilie, Shima Khoshraftar and Anahita Mansouri Bigvand
    Citation: BMC Genomics 2011 12:280
  39. Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. We used a genomic tiling array to dr...

    Authors: Sota Fujii, Takushi Toda, Shunsuke Kikuchi, Ryutaro Suzuki, Koji Yokoyama, Hiroko Tsuchida, Kentaro Yano and Kinya Toriyama
    Citation: BMC Genomics 2011 12:279
  40. In animals, signaling of Bone Morphogenetic Proteins (BMPs) is essential for dorsoventral (DV) patterning of the embryo, but how BMP signaling evolved with changes in embryonic DV differentiation is largely un...

    Authors: Steffen Lemke, Dionysios A Antonopoulos, Folker Meyer, Marc H Domanus and Urs Schmidt-Ott
    Citation: BMC Genomics 2011 12:278
  41. MicroRNAs (miRNAs) play important roles in embryonic stem cell (ESC) self-renewal and pluripotency. Numerous studies have revealed human and mouse ESC miRNA profiles. As a model for human-related study, the rh...

    Authors: Zhenghua Sun, Qiang Wei, Yanfeng Zhang, Xiechao He, Weizhi Ji and Bing Su
    Citation: BMC Genomics 2011 12:276
  42. Entamoeba histolytica, an enteric protozoan parasite, causes amebic colitis and extra intestinal abscesses in millions of inhabitants of endemic areas. E. histolytica completely lacks glutathione metabolism but p...

    Authors: Afzal Husain, Ghulam Jeelani, Dan Sato and Tomoyoshi Nozaki
    Citation: BMC Genomics 2011 12:275
  43. In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referre...

    Authors: Martien AM Groenen, Hendrik-Jan Megens, Yalda Zare, Wesley C Warren, LaDeana W Hillier, Richard PMA Crooijmans, Addie Vereijken, Ron Okimoto, William M Muir and Hans H Cheng
    Citation: BMC Genomics 2011 12:274
  44. Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. ...

    Authors: Dana Barth and Thomas U Berendonk
    Citation: BMC Genomics 2011 12:272

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