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  1. Colletotrichum truncatum is a haploid, hemibiotrophic, ascomycete fungal pathogen that causes anthracnose disease on many economically important leguminous crops. This pathogen exploits sequential biotrophic- and...

    Authors: Vijai Bhadauria, Sabine Banniza, Albert Vandenberg, Gopalan Selvaraj and Yangdou Wei
    Citation: BMC Genomics 2011 12:327
  2. In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jaw...

    Authors: Huan Qiu, Falk Hildebrand, Shigehiro Kuraku and Axel Meyer
    Citation: BMC Genomics 2011 12:325
  3. Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. B...

    Authors: Daniela Kalhoefer, Sebastian Thole, Sonja Voget, Rüdiger Lehmann, Heiko Liesegang, Antje Wollher, Rolf Daniel, Meinhard Simon and Thorsten Brinkhoff
    Citation: BMC Genomics 2011 12:324
  4. Next-generation sequencing technologies can effectively detect the entire spectrum of genomic variation and provide a powerful tool for systematic exploration of the universe of common, low frequency and rare ...

    Authors: Hoicheong Siu, Yun Zhu, Li Jin and Momiao Xiong
    Citation: BMC Genomics 2011 12:322
  5. The regulatory information encoded in the DNA of promoter regions usually enforces a minimal, non-zero distance between the coding regions of neighboring genes. However, the size of this minimal regulatory spa...

    Authors: Wei-Hua Chen, Wu Wei and Martin J Lercher
    Citation: BMC Genomics 2011 12:320
  6. In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics...

    Authors: BP Mallikarjuna Swamy, Prashant Vikram, Shalabh Dixit, HU Ahmed and Arvind Kumar
    Citation: BMC Genomics 2011 12:319
  7. 'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and comple...

    Authors: Saber Qanbari, Daniel Gianola, Ben Hayes, Flavio Schenkel, Steve Miller, Stephen Moore, Georg Thaller and Henner Simianer
    Citation: BMC Genomics 2011 12:318
  8. Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to ...

    Authors: Barbara Feldmeyer, Christopher W Wheat, Nicolas Krezdorn, Björn Rotter and Markus Pfenninger
    Citation: BMC Genomics 2011 12:317
  9. 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
  10. 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
  11. 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

  12. 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

  13. Mass spectrometry-based metabolomics analyses have the potential to complement sequence-based methods of genome annotation, but only if raw mass spectral data can be linked to specific metabolic pathways. In u...

    Authors: Benjamin P Bowen, Curt R Fischer, Richard Baran, Jillian F Banfield and Trent Northen
    Citation: BMC Genomics 2011 12(Suppl 1):S6

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

  14. 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

  15. 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

  16. Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically...

    Authors: Dmitry A Rodionov, Pavel S Novichkov, Elena D Stavrovskaya, Irina A Rodionova, Xiaoqing Li, Marat D Kazanov, Dmitry A Ravcheev, Anna V Gerasimova, Alexey E Kazakov, Galina Yu Kovaleva, Elizabeth A Permina, Olga N Laikova, Ross Overbeek, Margaret F Romine, James K Fredrickson, Adam P Arkin…
    Citation: BMC Genomics 2011 12(Suppl 1):S3

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

  17. 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

  18. 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

  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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

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