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  1. African Green Monkeys (AGM) are amongst the most frequently used nonhuman primate models in clinical and biomedical research, nevertheless only few genomic resources exist for this species. Such information wo...

    Authors: Nicolas Tchitchek, Béatrice Jacquelin, Patrick Wincker, Carole Dossat, Corinne Da Silva, Jean Weissenbach, Antoine Blancher, Michaela Müller-Trutwin and Arndt Benecke
    Citation: BMC Genomics 2012 13:279
  2. Avian influenza virus (AIV) outbreaks are worldwide threats to both poultry and humans. Our previous study suggested microRNAs (miRNAs) play significant roles in the regulation of host response to AIV infectio...

    Authors: Ying Wang, Vinayak Brahmakshatriya, Blanca Lupiani, Sanjay M Reddy, Benjamin Soibam, Ashley L Benham, Preethi Gunaratne, Hsiao-ching Liu, Nares Trakooljul, Nancy Ing, Ron Okimoto and Huaijun Zhou
    Citation: BMC Genomics 2012 13:278
  3. Celiac disease (CD) is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the p...

    Authors: Elma MJ Salentijn, D Cristina Mitea, Svetlana V Goryunova, Ingrid M van der Meer, Ismael Padioleau, Luud JWJ Gilissen, Frits Koning and Marinus JM Smulders
    Citation: BMC Genomics 2012 13:277
  4. Human T cell leukemia virus type 1 (HTLV-1) Tax is a potent activator of viral and cellular gene expression that interacts with a number of cellular proteins. Many reports show that Tax is capable of regulatin...

    Authors: Mariluz Arainga, Hironobu Murakami and Yoko Aida
    Citation: BMC Genomics 2012 13:275
  5. The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, t...

    Authors: Jon Christensen, Sara El-Gebali, Manuela Natoli, Thierry Sengstag, Mauro Delorenzi, Susanne Bentz, Hanifa Bouzourene, Martin Rumbo, Armando Felsani, Sanna Siissalo, Jouni Hirvonen, Maya R Vila, Piercarlo Saletti, Michel Aguet and Pascale Anderle
    Citation: BMC Genomics 2012 13:274
  6. Copy Number Variations (CNVs) have been shown important in both normal phenotypic variability and disease susceptibility, and are increasingly accepted as another important source of genetic variation compleme...

    Authors: Jiying Wang, Jicai Jiang, Weixuan Fu, Li Jiang, Xiangdong Ding, Jian-Feng Liu and Qin Zhang
    Citation: BMC Genomics 2012 13:273
  7. Transposable elements (TEs), both DNA transposons and retrotransposons, are genetic elements with the main characteristic of being able to mobilize and amplify their own representation within genomes, utilizin...

    Authors: Rita D Fernández-Medina, José M C Ribeiro, Claudia M A Carareto, Luciane Velasque and Cláudio J Struchiner
    Citation: BMC Genomics 2012 13:272
  8. Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due t...

    Authors: Erik M Lehnert, Matthew S Burriesci and John R Pringle
    Citation: BMC Genomics 2012 13:271
  9. A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcri...

    Authors: Prateek Tripathi, Roel C Rabara, Tanner J Langum, Ashley K Boken, Deena L Rushton, Darius D Boomsma, Charles I Rinerson, Jennifer Rabara, R Neil Reese, Xianfeng Chen, Jai S Rohila and Paul J Rushton
    Citation: BMC Genomics 2012 13:270
  10. Phakopsora pachyrhizi is an obligate fungal pathogen causing Asian soybean rust (ASR). A dual approach was taken to examine the molecular and biochemical processes occurring during the development of appressoria,...

    Authors: Christine L Stone, Michael B McMahon, Laurie L Fortis, Alberto Nuñez, Gary W Smythers, Douglas G Luster and Reid D Frederick
    Citation: BMC Genomics 2012 13:269
  11. Prior to this study, relatively few strains of Francisella had been genome-sequenced. Previously published Francisella genome sequences were largely restricted to the zoonotic agent F. tularensis. Only limited da...

    Authors: Andreas Sjödin, Kerstin Svensson, Caroline Öhrman, Jon Ahlinder, Petter Lindgren, Samuel Duodu, Anders Johansson, Duncan J Colquhoun, Pär Larsson and Mats Forsman
    Citation: BMC Genomics 2012 13:268
  12. Chitosan oligosaccharide (COS), a deacetylated derivative of chitin, is an abundant, and renewable natural polymer. COS has higher antimicrobial properties than chitosan and is presumed to act by disrupting/pe...

    Authors: Maria DLA Jaime, Luis Vicente Lopez-Llorca, Ana Conesa, Anna Y Lee, Michael Proctor, Lawrence E Heisler, Marinella Gebbia, Guri Giaever, J Timothy Westwood and Corey Nislow
    Citation: BMC Genomics 2012 13:267
  13. De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Ammopiptanthus mongolicus, a super-...

    Authors: Yijun Zhou, Fei Gao, Ran Liu, Jinchao Feng and Hongjie Li
    Citation: BMC Genomics 2012 13:266
  14. Epulopiscium sp. type B, a large intestinal bacterial symbiont of the surgeonfish Naso tonganus, does not reproduce by binary fission. Instead, it forms multiple intracellular offspring using a process with morph...

    Authors: David A Miller, Garret Suen, Kendall D Clements and Esther R Angert
    Citation: BMC Genomics 2012 13:265
  15. MicroRNAs (miRNAs) modulate gene expression in different tissues and at diverse developmental stages, including grain development in japonica rice. To identify novel miRNAs in indica rice and to study their ex...

    Authors: Ying Lan, Ning Su, Yi Shen, Rongzhi Zhang, Fuqing Wu, Zhijun Cheng, Jiulin Wang, Xin Zhang, Xiupin Guo, Cailin Lei, Jie Wang, Ling Jiang, Long Mao and Jianmin Wan
    Citation: BMC Genomics 2012 13:264
  16. Malaria caused by Plasmodium vivax is an experimentally neglected severe disease with a substantial burden on human health. Because of technical limitations, little is known about the biology of this important hu...

    Authors: A Taylor Bright, Ryan Tewhey, Shira Abeles, Raul Chuquiyauri, Alejandro Llanos-Cuentas, Marcelo U Ferreira, Nicholas J Schork, Joseph M Vinetz and Elizabeth A Winzeler
    Citation: BMC Genomics 2012 13:262
  17. Bats are the natural reservoir host for a range of emerging and re-emerging viruses, including SARS-like coronaviruses, Ebola viruses, henipaviruses and Rabies viruses. However, the mechanisms responsible for ...

    Authors: Anthony T Papenfuss, Michelle L Baker, Zhi-Ping Feng, Mary Tachedjian, Gary Crameri, Chris Cowled, Justin Ng, Vijaya Janardhana, Hume E Field and Lin-Fa Wang
    Citation: BMC Genomics 2012 13:261
  18. Evolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal s...

    Authors: Evaristus Chibunna Mbanefo, Yu Chuanxin, Mihoko Kikuchi, Mohammed Nasir Shuaibu, Daniel Boamah, Masashi Kirinoki, Naoko Hayashi, Yuichi Chigusa, Yoshio Osada, Shinjiro Hamano and Kenji Hirayama
    Citation: BMC Genomics 2012 13:260
  19. Next-generation sequencing methods have contributed to rapid progress in the fields of genomics and population genetics. Using this high-throughput and cost-effective technology, a number of studies have estim...

    Authors: Soo Hyung Eo and J Andrew DeWoody
    Citation: BMC Genomics 2012 13:259
  20. Mycobacterium ulcerans is an unusual bacterial pathogen with elusive origins. While closely related to the aquatic dwelling M. marinum, M. ulcerans has evolved the ability to produce the immunosuppressive polyket...

    Authors: Kenneth D Doig, Kathryn E Holt, Janet AM Fyfe, Caroline J Lavender, Miriam Eddyani, Françoise Portaels, Dorothy Yeboah-Manu, Gerd Pluschke, Torsten Seemann and Timothy P Stinear
    Citation: BMC Genomics 2012 13:258
  21. Scaleless (sc/sc) chickens carry a single recessive mutation that causes a lack of almost all body feathers, as well as foot scales and spurs, due to a failure of skin patterning during embryogenesis. This sponta...

    Authors: Kirsty L Wells, Yair Hadad, Danny Ben-Avraham, Jossi Hillel, Avigdor Cahaner and Denis J Headon
    Citation: BMC Genomics 2012 13:257
  22. Escherichia coli is an important species of bacteria that can live as a harmless inhabitant of the guts of many animals, as a pathogen causing life-threatening conditions or freely in the non-host environment. Th...

    Authors: Xavier Didelot, Guillaume Méric, Daniel Falush and Aaron E Darling
    Citation: BMC Genomics 2012 13:256
  23. Telomeres are nucleoprotein complexes at the end of linear eukaryotic chromosomes which maintain the genome integrity by regulating telomere length, preventing recombination and end to end fusion events. Multi...

    Authors: Easwaran Sreesankar, Ramamoorthy Senthilkumar, Vellaichamy Bharathi, Rakesh K Mishra and Krishnaveni Mishra
    Citation: BMC Genomics 2012 13:255
  24. An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer ...

    Authors: Amit Sinha, Ralf J Sommer and Christoph Dieterich
    Citation: BMC Genomics 2012 13:254
  25. CCCH zinc finger proteins contain a typical motif of three cysteines and one histidine residues and serve regulatory functions at all stages of mRNA metabolism. In plants, CCCH type zinc finger proteins compri...

    Authors: Guohua Chai, Ruibo Hu, Dongyuan Zhang, Guang Qi, Ran Zuo, Yingping Cao, Peng Chen, Yingzhen Kong and Gongke Zhou
    Citation: BMC Genomics 2012 13:253
  26. The complex balance between environmental and host factors is an important determinant of susceptibility to infection. Disturbances of this equilibrium may result in multifactorial diseases as illustrated by t...

    Authors: Rafael Diego Rosa, Julien de Lorgeril, Patrick Tailliez, Roman Bruno, David Piquemal and Evelyne Bachère
    Citation: BMC Genomics 2012 13:252
  27. The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo ...

    Authors: Hongshi Yu, James Lindsay, Zhi-Ping Feng, Stephen Frankenberg, Yanqiu Hu, Dawn Carone, Geoff Shaw, Andrew J Pask, Rachel O’Neill, Anthony T Papenfuss and Marilyn B Renfree
    Citation: BMC Genomics 2012 13:251
  28. Weaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessati...

    Authors: Aran O’Loughlin, David J Lynn, Mark McGee, Sean Doyle, Matthew McCabe and Bernadette Earley
    Citation: BMC Genomics 2012 13:250
  29. Non-synonymous single nucleotide polymorphisms (nsSNPs) alter the protein sequence and can cause disease. The impact has been described by reliable experiments for relatively few mutations. Here, we study pred...

    Authors: Christian Schaefer, Yana Bromberg, Dominik Achten and Burkhard Rost
    Citation: BMC Genomics 2012 13(Suppl 4):S11

    This article is part of a Supplement: Volume 13 Supplement 4

  30. Mutations as sources of evolution have long been the focus of attention in the biomedical literature. Accessing the mutational information and their impacts on protein properties facilitates research in variou...

    Authors: Nona Naderi and René Witte
    Citation: BMC Genomics 2012 13(Suppl 4):S10

    This article is part of a Supplement: Volume 13 Supplement 4

  31. Large-scale tumor sequencing projects are now underway to identify genetic mutations that drive tumor initiation and development. Most studies take a gene-based approach to identifying driver mutations, highli...

    Authors: Nathan L Nehrt, Thomas A Peterson, DoHwan Park and Maricel G Kann
    Citation: BMC Genomics 2012 13(Suppl 4):S9

    This article is part of a Supplement: Volume 13 Supplement 4

  32. Various computational methods are presently available to classify whether a protein variation is disease-associated or not. However data derived from recent technological advancements make it feasible to exten...

    Authors: Pier Luigi Martelli, Piero Fariselli, Eva Balzani and Rita Casadio
    Citation: BMC Genomics 2012 13(Suppl 4):S8

    This article is part of a Supplement: Volume 13 Supplement 4

  33. The structure of RiboNucleic Acid (RNA) has the potential to be altered by a Single Nucleotide Polymorphism (SNP). Disease-associated SNPs mapping to non-coding regions of the genome that are transcribed into ...

    Authors: Justin Ritz, Joshua S Martin and Alain Laederach
    Citation: BMC Genomics 2012 13(Suppl 4):S6

    This article is part of a Supplement: Volume 13 Supplement 4

  34. Non-synonymous coding SNPs (nsSNPs) that are associated to disease can also be related with alterations in protein stability. Computational methods are available to predict the effect of single amino acid subs...

    Authors: Ezequiel Juritz, Maria Silvina Fornasari, Pier Luigi Martelli, Piero Fariselli, Rita Casadio and Gustavo Parisi
    Citation: BMC Genomics 2012 13(Suppl 4):S5

    This article is part of a Supplement: Volume 13 Supplement 4

  35. Amino acid point mutations (nsSNPs) may change protein structure and function. However, no method directly predicts the impact of mutations on structure. Here, we compare pairs of pentamers (five consecutive r...

    Authors: Christian Schaefer and Burkhard Rost
    Citation: BMC Genomics 2012 13(Suppl 4):S4

    This article is part of a Supplement: Volume 13 Supplement 4

  36. Most of the many mutations described in human protein kinases are tolerated without significant disruption of the corresponding structures or molecular functions, while some of them have been associated to a v...

    Authors: Jose MG Izarzugaza, Angela del Pozo, Miguel Vazquez and Alfonso Valencia
    Citation: BMC Genomics 2012 13(Suppl 4):S3

    This article is part of a Supplement: Volume 13 Supplement 4

  37. Prediction methods are increasingly used in biosciences to forecast diverse features and characteristics. Binary two-state classifiers are the most common applications. They are usually based on machine learni...

    Authors: Mauno Vihinen
    Citation: BMC Genomics 2012 13(Suppl 4):S2

    This article is part of a Supplement: Volume 13 Supplement 4

  38. The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemio...

    Authors: Alejandro Reyes, Andrea Sandoval, Andrés Cubillos-Ruiz, Katherine E Varley, Ivan Hernández-Neuta, Sofía Samper, Carlos Martín, María Jesús García, Viviana Ritacco, Lucelly López, Jaime Robledo, María Mercedes Zambrano, Robi D Mitra and Patricia Del Portillo
    Citation: BMC Genomics 2012 13:249
  39. Bacillus thuringiensis var. israelensis (Bti) is a natural larval mosquito pathogen producing pore-forming toxins targeting the midgut of Diptera larvae. It is used worldwide for mosquito control. Resistance mech...

    Authors: Guillaume Tetreau, Krishnareddy Bayyareddy, Christopher M Jones, Renaud Stalinski, Muhammad A Riaz, Margot Paris, Jean-Philippe David, Michael J Adang and Laurence Després
    Citation: BMC Genomics 2012 13:248
  40. Polyploidy often results in considerable changes in gene expression, both immediately and over evolutionary time. New phenotypes often arise with polyploid formation and may contribute to the fitness of polypl...

    Authors: Janet Higgins, Andreas Magusin, Martin Trick, Fiona Fraser and Ian Bancroft
    Citation: BMC Genomics 2012 13:247
  41. Gene duplication has had a major impact on genome evolution. Localized (or tandem) duplication resulting from unequal crossing over and whole genome duplication are believed to be the two dominant mechanisms c...

    Authors: Jianguo Lu, Eric Peatman, Haibao Tang, Joshua Lewis and Zhanjiang Liu
    Citation: BMC Genomics 2012 13:246
  42. Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have i...

    Authors: Ross D Houston, John W Davey, Stephen C Bishop, Natalie R Lowe, Jose C Mota-Velasco, Alastair Hamilton, Derrick R Guy, Alan E Tinch, Marian L Thomson, Mark L Blaxter, Karim Gharbi, James E Bron and John B Taggart
    Citation: BMC Genomics 2012 13:244
  43. Carotenoids are a heterogeneous group of plant isoprenoids primarily involved in photosynthesis. In plants the cleavage of carotenoids leads to the formation of the phytohormones abscisic acid and strigolacton...

    Authors: Philip R Young, Justin G Lashbrooke, Erik Alexandersson, Dan Jacobson, Claudio Moser, Riccardo Velasco and Melané A Vivier
    Citation: BMC Genomics 2012 13:243
  44. Plants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor), egg laying by the elm leaf be...

    Authors: Kerstin Büchel, Eric McDowell, Will Nelson, Anne Descour, Jonathan Gershenzon, Monika Hilker, Carol Soderlund, David R Gang, Trevor Fenning and Torsten Meiners
    Citation: BMC Genomics 2012 13:242
  45. Genotypes obtained with commercial SNP arrays have been extensively used in many large case-control or population-based cohorts for SNP-based genome-wide association studies for a multitude of traits. Yet, the...

    Authors: Armand Valsesia, Brian J Stevenson, Dawn Waterworth, Vincent Mooser, Peter Vollenweider, Gérard Waeber, C Victor Jongeneel, Jacques S Beckmann, Zoltán Kutalik and Sven Bergmann
    Citation: BMC Genomics 2012 13:241
  46. Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (

    Authors: Corey J Hudson, Jules S Freeman, Anand RK Kullan, César D Petroli, Carolina P Sansaloni, Andrzej Kilian, Frank Detering, Dario Grattapaglia, Brad M Potts, Alexander A Myburg and René E Vaillancourt
    Citation: BMC Genomics 2012 13:240

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