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  1. 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
    Content type: Research article Published on:

  2. 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
    Content type: Research article Published on:

  3. 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
    Content type: Research article Published on:

  4. 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
    Content type: Research article Published on:

  5. 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
    Content type: Research article Published on:

  6. 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
    Content type: Research article Published on:

  7. 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
    Content type: Research article Published on:

  8. 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
    Content type: Research article Published on:

  9. 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
    Content type: Research article Published on:

  10. 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
    Content type: Research article Published on:

  11. 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
    Content type: Research article Published on:

  12. 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
    Content type: Research article Published on:

  13. 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
    Content type: Research article Published on:

  14. 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
    Content type: Proceedings Published on:

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

  15. 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
    Content type: Proceedings Published on:

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

  16. 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
    Content type: Proceedings Published on:

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

  17. 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
    Content type: Proceedings Published on:

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

  19. 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
    Content type: Proceedings Published on:

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

  20. 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
    Content type: Proceedings Published on:

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

  21. 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
    Content type: Proceedings Published on:

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

  22. 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
    Content type: Proceedings Published on:

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

  23. 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
    Content type: Proceedings Published on:

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

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Research article Published on:

  27. 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
    Content type: Research article Published on:

  28. 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
    Content type: Research article Published on:

  30. 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
    Content type: Research article Published on:

  31. 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
    Content type: Research article Published on:

  32. 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
    Content type: Research article Published on:

  33. 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
    Content type: Research article Published on:

  34. 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
    Content type: Research article Published on:

  35. Cellular glucose availability is crucial for the functioning of most biological processes. Our understanding of the glucose regulatory system has been greatly advanced by studying the model organism Saccharomyces...

    Authors: Eva Apweiler, Katrin Sameith, Thanasis Margaritis, Nathalie Brabers, Loes van de Pasch, Linda V Bakker, Dik van Leenen, Frank CP Holstege and Patrick Kemmeren
    Citation: BMC Genomics 2012 13:239
    Content type: Research article Published on:

  36. There is considerable interest in developing high-throughput genotyping with single nucleotide polymorphisms (SNPs) for the identification of genes affecting important ecological or economical traits. SNPs are...

    Authors: Mekki Boussaha, René Guyomard, Cédric Cabau, Diane Esquerré and Edwige Quillet
    Citation: BMC Genomics 2012 13:238
    Content type: Research article Published on:

  37. Many plant genes have been identified through whole genome and deep transcriptome sequencing and other methods; yet our knowledge on the function of many of these genes remains limited. The integration and ana...

    Authors: Tyler J Wilson, Liming Lai, Yuguang Ban and Steven X Ge
    Citation: BMC Genomics 2012 13:237
    Content type: Research article Published on:

  39. Recent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. A detailed characterisation of the population structure and linkage disequilibrium (LD) is essenti...

    Authors: Katharina V Alheit, Hans Peter Maurer, Jochen C Reif, Matthew R Tucker, Volker Hahn, Elmar A Weissmann and Tobias Würschum
    Citation: BMC Genomics 2012 13:235
    Content type: Research article Published on:

  40. Cowpea [Vigna unguiculata (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot he...

    Authors: Marti Pottorff, Jeffrey D Ehlers, Christian Fatokun, Philip A Roberts and Timothy J Close
    Citation: BMC Genomics 2012 13:234
    Content type: Research article Published on:

  41. Losses of slaughter-weight pigs due to transport stress are both welfare and economic concerns to pork producers. Historically, the HAL-1843 mutation in ryanodine receptor 1 was considered responsible for most...

    Authors: Dan J Nonneman, Tami Brown-Brandl, Shuna A Jones, Ralph T Wiedmann and Gary A Rohrer
    Citation: BMC Genomics 2012 13:233
    Content type: Research article Published on:

  42. The morphogenesis of the cerebral cortex depends on the precise control of gene expression during development. Small non-coding RNAs, including microRNAs and other groups of small RNAs, play profound roles in ...

    Authors: Mao-jin Yao, Gang Chen, Ping-ping Zhao, Ming-hua Lu, Jiang Jian, Mo-fang Liu and Xiao-bing Yuan
    Citation: BMC Genomics 2012 13:232
    Content type: Research article Published on:

  43. Buckwheat, consisting of two cultivated species Fagopyrum tataricum and F. esculentum, is the richest source of flavonoid rutin. Vegetative tissues of both the Fagopyrum species contain almost similar amount of r...

    Authors: Nidhi Gupta, Pradeep Kumar Naik and Rajinder Singh Chauhan
    Citation: BMC Genomics 2012 13:231
    Content type: Research article Published on:

  44. Term clustering, by measuring the string similarities between terms, is known within the natural language processing community to be an effective method for improving the quality of texts and dictionaries. How...

    Authors: Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi and Akinori Yonezawa
    Citation: BMC Genomics 2012 13(Suppl 3):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  45. RNA secondary structure plays a scaffolding role for RNA tertiary conformation. Accurate secondary structure prediction can not only identify double-stranded helices and single stranded-loops but also help pro...

    Authors: Pooya Shareghi, Yingfeng Wang, Russell Malmberg and Liming Cai
    Citation: BMC Genomics 2012 13(Suppl 3):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  46. Computational approaches to generate hypotheses from biomedical literature have been studied intensively in recent years. Nevertheless, it still remains a challenge to automatically discover novel, cross-silo ...

    Authors: Jayasimha Reddy Katukuri, Ying Xie, Vijay V Raghavan and Ashish Gupta
    Citation: BMC Genomics 2012 13(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  47. One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, ...

    Authors: Hasan M Jamil
    Citation: BMC Genomics 2012 13(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  48. MiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa. Confident identification of MiRNA-Target Interactions (MTI) is vital to unde...

    Authors: Jiandong Ding, Danqing Li, Uwe Ohler, Jihong Guan and Shuigeng Zhou
    Citation: BMC Genomics 2012 13(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  49. In the biomedical domain, there are immense data and tremendous increase of genomics and biomedical relevant publications. The wealth of information has led to an increasing amount of interest in and need for ...

    Authors: Yan Chen, Xiaoshi Yin, Zhoujun Li, Xiaohua Hu and Jimmy Xiangji Huang
    Citation: BMC Genomics 2012 13(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

  50. Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway that catalyzes the deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pa...

    Authors: Ujwal R Bagal, James H Leebens-Mack, W Walter Lorenz and Jeffrey FD Dean
    Citation: BMC Genomics 2012 13(Suppl 3):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 3

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