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  1. Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultiv...

    Authors: Amanda M Hulse-Kemp, Hamid Ashrafi, Xiuting Zheng, Fei Wang, Kevin A Hoegenauer, Andrea BV Maeda, S Samuel Yang, Kevin Stoffel, Marta Matvienko, Kimberly Clemons, Joshua A Udall, Allen Van Deynze, Don C Jones and David M Stelly
    Citation: BMC Genomics 2014 15:945
    Content type: Research article Published on:

  2. Polar overdominance at the ovine callipyge (CLPG) locus involves the post-transcriptional trans-inhibition of DLK1 in skeletal muscle of CLPG/CLPG sheep. The abundant maternally expressed microRNAs (miRNAs) mappi...

    Authors: Huijun Cheng, Xuewen Xu, Tracy Hadfield, Noelle Cockett, Carole Charlier, Michel Georges and Haruko Takeda
    Citation: BMC Genomics 2014 15:944
    Content type: Research article Published on:

  3. The fungal genus Sporothrix includes at least four human pathogenic species. One of these species, S. brasiliensis, is the causal agent of a major ongoing zoonotic outbreak of sporotrichosis in Brazil. Elsewhere,...

    Authors: Marcus M Teixeira, Luiz GP de Almeida, Paula Kubitschek-Barreira, Fernanda L Alves, Érika S Kioshima, Ana KR Abadio, Larissa Fernandes, Lorena S Derengowski, Karen S Ferreira, Rangel C Souza, Jeronimo C Ruiz, Nathalia C de Andrade, Hugo C Paes, André M Nicola, Patrícia Albuquerque, Alexandra L Gerber…
    Citation: BMC Genomics 2014 15:943
    Content type: Research article Published on:

  4. The oriental fruit fly, Bactrocera dorsalis, is an important pest of fruit and vegetable crops throughout Asia, and is considered a high risk pest for establishment in the mainland United States. It is a member o...

    Authors: Scott M Geib, Bernarda Calla, Brian Hall, Shaobin Hou and Nicholas C Manoukis
    Citation: BMC Genomics 2014 15:942
    Content type: Research article Published on:

  5. Previously we have examined the effect of maternal dietary n-3 long-chain polyunsaturated fatty acid (LCPUFA) supplementation during pregnancy on offspring fat mass. Considering the involvement of the placenta...

    Authors: Eva-Maria Sedlmeier, Stefanie Brunner, Daniela Much, Philipp Pagel, Susanne E Ulbrich, Heinrich HD Meyer, Ulrike Amann-Gassner, Hans Hauner and Bernhard L Bader
    Citation: BMC Genomics 2014 15:941
    Content type: Research article Published on:

  6. Werner Syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The gene responsible for WS encodes a DNA helicase/exonuclease protein believed to affect diffe...

    Authors: Alexandra Dallaire, Sophie Proulx, Martin J Simard and Michel Lebel
    Citation: BMC Genomics 2014 15:940
    Content type: Research article Published on:

  8. DNA damage (single or double-strand breaks) triggers adapted cellular responses. These responses are elicited through signalling pathways, which activate cell cycle checkpoints and basically lead to three cell...

    Authors: José CM Mombach, Cristhian A Bugs and Claudine Chaouiya
    Citation: BMC Genomics 2014 15(Suppl 7):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  9. The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and fo...

    Authors: Fabiana Barichello Mokry, Marcos Eli Buzanskas, Maurício de Alvarenga Mudadu, Daniela do Amaral Grossi, Roberto Hiroshi Higa, Ricardo Vieira Ventura, Andressa Oliveira de Lima, Mehdi Sargolzaei, Sarah Laguna Conceição Meirelles, Flávio Schramm Schenkel, Marcos Vinicius Gualberto Barbosa da Silva, Simone Cristina Méo Niciura, Maurício Mello de Alencar, Danísio Prado Munari and Luciana Correia de Almeida Regitano
    Citation: BMC Genomics 2014 15(Suppl 7):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  10. Over the last decades, a vast structural knowledge has been gathered on the HIV-1 protease (PR). Noticeably, most of the studies focused the B-subtype, which has the highest prevalence in developed countries. ...

    Authors: Mauricio GS Costa, Técio G Benetti-Barbosa, Nathan Desdouits, Arnaud Blondel, Paulo M Bisch, Pedro G Pascutti and Paulo R Batista
    Citation: BMC Genomics 2014 15(Suppl 7):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  11. This paper proposes a new methodology to simultaneously select the most relevant SNPs markers for the characterization of any measurable phenotype described by a continuous variable using Support Vector Regres...

    Authors: Fabrízzio Condé de Oliveira, Carlos Cristiano Hasenclever Borges, Fernanda Nascimento Almeida, Fabyano Fonseca e Silva, Rui da Silva Verneque, Marcos Vinicius GB da Silva and Wagner Arbex
    Citation: BMC Genomics 2014 15(Suppl 7):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  12. Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, there...

    Authors: Syed Shah Hassan, Sandeep Tiwari, Luís Carlos Guimarães, Syed Babar Jamal, Edson Folador, Neha Barve Sharma, Siomar de Castro Soares, Síntia Almeida, Amjad Ali, Arshad Islam, Fabiana Dias Póvoa, Vinicius Augusto Carvalho de Abreu, Neha Jain, Antaripa Bhattacharya, Lucky Juneja, Anderson Miyoshi…
    Citation: BMC Genomics 2014 15(Suppl 7):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  13. A challenge in precision medicine is the transformation of genomic data into knowledge that can be used to stratify patients into treatment groups based on predicted clinical response. Although clinical trials...

    Authors: Lindsay C Stetson, Taylor Pearl, Yanwen Chen and Jill S Barnholtz-Sloan
    Citation: BMC Genomics 2014 15(Suppl 7):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

    The Erratum to this article has been published in BMC Genomics 2015 16:481

  14. The dermatophyte Trichophyton rubrum is an anthropophilic filamentous fungus that infects keratinized tissues and is the most common etiologic agent isolated in human dermatophytoses. The clinical treatment of th...

    Authors: Gabriela Felix Persinoti, Nalu Teixeira de Aguiar Peres, Tiago Rinaldi Jacob, Antonio Rossi, Ricardo Zorzetto Vêncio and Nilce Maria Martinez-Rossi
    Citation: BMC Genomics 2014 15(Suppl 7):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  15. Alteromonas macleodii is a ubiquitous gammaproteobacterium shown to play a biogeochemical role in marine environments. Two A. macleodii strains (AltDE and AltDE1) isolated from the same sample (i.e., the same pla...

    Authors: Nikole E Kimes, Mario López-Pérez, Eva Ausó, Rohit Ghai and Francisco Rodriguez-Valera
    Citation: BMC Genomics 2014 15:938
    Content type: Research article Published on:

  16. The salmon louse, Lepeophtheirus salmonis, is an ectoparasite of salmonids that causes huge economic losses in salmon farming, and has also been causatively linked with declines of wild salmonid populations. L...

    Authors: Francois Besnier, Matthew Kent, Rasmus Skern-Mauritzen, Sigbjørn Lien, Ketil Malde, Rolf B Edvardsen, Simon Taylor, Lina ER Ljungfeldt, Frank Nilsen and Kevin A Glover
    Citation: BMC Genomics 2014 15:937
    Content type: Research article Published on:

  17. Prokaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria rema...

    Authors: Matthias Wietz, Natalie Millán-Aguiñaga and Paul R Jensen
    Citation: BMC Genomics 2014 15:936
    Content type: Research article Published on:

  18. Spring viraemia of carp virus (SVCV) has been identified as the causative agent of spring viraemia of carp (SVC) and it has caused significant losses in the cultured common carp (Cyprinus carpio) industry. The mo...

    Authors: Junfa Yuan, Yi Yang, Huihui Nie, Lijuan Li, Wangang Gu, Li Lin, Min Zou, Xueqin Liu, Min Wang and Zemao Gu
    Citation: BMC Genomics 2014 15:935
    Content type: Research article Published on:

  19. The detection and functional characterization of genomic structural variations are important for understanding the landscape of genetic variation in the chicken. A recently recognized aspect of genomic structu...

    Authors: Ruili Han, Pengkun Yang, Yadong Tian, Dandan Wang, Zengxuan Zhang, Lele Wang, Zhuanjian Li, Ruirui Jiang and Xiangtao Kang
    Citation: BMC Genomics 2014 15:934
    Content type: Research article Published on:

  20. The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbi...

    Authors: Meabh Beatty, Jasenka Guduric-Fuchs, Eoin Brown, Stephen Bridgett, Usha Chakravarthy, Ruth Esther Hogg and David Arthur Simpson
    Citation: BMC Genomics 2014 15:933
    Content type: Research article Published on:

  21. Phenotypes are variable within species, with high phenotypic variation in the fitness and cell morphology of natural yeast strains due to genetic variation. A gene deletion collection of yeast laboratory strai...

    Authors: Ming Yang, Shinsuke Ohnuki and Yoshikazu Ohya
    Citation: BMC Genomics 2014 15:932
    Content type: Research article Published on:

  22. Acholeplasma oculi belongs to the Acholeplasmataceae family, comprising the genera Acholeplasma and ‘Candidatus Phytoplasma’. Acholeplasmas are ubiquitous saprophytic bacteria. Several isolates are derived from p...

    Authors: Christin Siewert, Wolfgang R Hess, Bojan Duduk, Bruno Huettel, Richard Reinhardt, Carmen Büttner and Michael Kube
    Citation: BMC Genomics 2014 15:931
    Content type: Research article Published on:

  23. Vertebrate mitochondrial genomes (mitogenomes) are 16–18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved t...

    Authors: Yoshinori Kumazawa, Saaya Miura, Chiemi Yamada and Yasuyuki Hashiguchi
    Citation: BMC Genomics 2014 15:930
    Content type: Research article Published on:

  25. Wolbachia intracellular bacteria can manipulate the reproduction of their arthropod hosts, including inducing sterility between populations known as cytoplasmic incompatibility (CI). Certain strains have been ide...

    Authors: Elizabeth R Sutton, Simon R Harris, Julian Parkhill and Steven P Sinkins
    Citation: BMC Genomics 2014 15:928
    Content type: Research article Published on:

  27. Despite the intensive use of Bacillus thuringiensis israelensis (Bti) toxins for mosquito control, little is known about the long term effect of exposure to this cocktail of toxins on target mosquito populations....

    Authors: Laurence Després, Renaud Stalinski, Guillaume Tetreau, Margot Paris, Aurélie Bonin, Vincent Navratil, Stéphane Reynaud and Jean-Philippe David
    Citation: BMC Genomics 2014 15:926
    Content type: Research article Published on:

  29. Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved mul...

    Authors: Oleg Dmytrenko, Shelbi L Russell, Wesley T Loo, Kristina M Fontanez, Li Liao, Guus Roeselers, Raghav Sharma, Frank J Stewart, Irene LG Newton, Tanja Woyke, Dongying Wu, Jenna Morgan Lang, Jonathan A Eisen and Colleen M Cavanaugh
    Citation: BMC Genomics 2014 15:924
    Content type: Research article Published on:

  30. The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure – the syncytium – which it keeps alive for the duration of the life cycle and on whic...

    Authors: Peter Thorpe, Sophie Mantelin, Peter JA Cock, Vivian C Blok, Mirela C Coke, Sebastian Eves-van den Akker, Elena Guzeeva, Catherine J Lilley, Geert Smant, Adam J Reid, Kathryn M Wright, Peter E Urwin and John T Jones
    Citation: BMC Genomics 2014 15:923
    Content type: Research article Published on:

  31. Plant and animal methyltransferases are key enzymes involved in DNA methylation at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of ...

    Authors: Mélanie Thomas, Lise Pingault, Axel Poulet, Jorge Duarte, Mickaël Throude, Sébastien Faure, Jean-Philippe Pichon, Etienne Paux, Aline Valeska Probst and Christophe Tatout
    Citation: BMC Genomics 2014 15:922
    Content type: Research article Published on:

  32. The Mozambique tilapia Oreochromis mossambicus has the ability to adapt to a broad range of environmental salinities and has long been used for investigating iono-osmoregulation. However, to date most studies hav...

    Authors: Siew Hong Lam, Eei Yin Lui, Zhengjun Li, Shaojiang Cai, Wing-Kin Sung, Sinnakaruppan Mathavan, Toong Jin Lam and Yuen Kwong Ip
    Citation: BMC Genomics 2014 15:921
    Content type: Research article Published on:

  34. Ramie (Boehmeria nivea L.), popularly known as “China grass”, is one of the oldest crops in China and the second most important fiber crop in terms of area sown. Ramie fiber, extracted from the plant bast, is imp...

    Authors: Jie Chen, Zhihua Pei, Lunjin Dai, Bo Wang, Lijun Liu, Xia An and Dingxiang Peng
    Citation: BMC Genomics 2014 15:919
    Content type: Research article Published on:

  35. Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity an...

    Authors: Amirhossein Shamsaddini, Yang Pan, W Evan Johnson, Konstantinos Krampis, Mariya Shcheglovitova, Vahan Simonyan, Amy Zanne and Raja Mazumder
    Citation: BMC Genomics 2014 15:918
    Content type: Software Published on:

  36. Stick and leaf insects (Phasmatodea) are an exclusively leaf-feeding order of insects with no record of omnivory, unlike other “herbivorous” Polyneoptera. They represent an ideal system for investigating the a...

    Authors: Matan Shelomi, W Cameron Jasper, Joel Atallah, Lynn S Kimsey and Brian R Johnson
    Citation: BMC Genomics 2014 15:917
    Content type: Research article Published on:

  37. Acute kidney injury (AKI) is a common and serious complication of cardiac surgery using cardiopulmonary bypass (CPB). The pathogenesis is poorly understood and the study of AKI in rodent models has not led to ...

    Authors: Mohamed T Ghorbel, Nishith N Patel, Maimuna Sheikh, Gianni D Angelini, Massimo Caputo and Gavin J Murphy
    Citation: BMC Genomics 2014 15:916
    Content type: Research article Published on:

  38. Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent ...

    Authors: Pawel Tulinski, Birgitta Duim, Floyd R Wittink, Martijs J Jonker, Timo M Breit, Jos P van Putten, Jaap A Wagenaar and Ad C Fluit
    Citation: BMC Genomics 2014 15:915
    Content type: Research article Published on:

  39. Aerobic methanotrophs can grow in hostile volcanic environments and use methane as their sole source of energy. The discovery of three verrucomicrobial Methylacidiphilum strains has revealed diverse metabolic pat...

    Authors: Seyed Yahya Anvar, Jeroen Frank, Arjan Pol, Arnoud Schmitz, Ken Kraaijeveld, Johan T den Dunnen and Huub JM Op den Camp
    Citation: BMC Genomics 2014 15:914
    Content type: Research article Published on:

  41. Metatranscriptomics is rapidly expanding our knowledge of gene expression patterns and pathway dynamics in natural microbial communities. However, to cope with the challenges of environmental sampling, various...

    Authors: Adriana Alberti, Caroline Belser, Stéfan Engelen, Laurie Bertrand, Céline Orvain, Laura Brinas, Corinne Cruaud, Laurène Giraut, Corinne Da Silva, Cyril Firmo, Jean-Marc Aury and Patrick Wincker
    Citation: BMC Genomics 2014 15:912
    Content type: Methodology article Published on:

  42. Trypanosoma brucei subspecies infect humans and animals in sub-Saharan Africa. This early diverging eukaryote shows many novel features in basic biological processes, including the use of polycistronic transcript...

    Authors: Bryan C Jensen, Gowthaman Ramasamy, Elton J R Vasconcelos, Nicholas T Ingolia, Peter J Myler and Marilyn Parsons
    Citation: BMC Genomics 2014 15:911
    Content type: Research article Published on:

  43. Human Mesenchymal Stromal/Stem Cells (MSCs) are adult multipotent cells that behave in a highly plastic manner, inhabiting the stroma of several tissues. The potential utility of MSCs is nowadays strongly inve...

    Authors: Beatriz Roson-Burgo, Fermin Sanchez-Guijo, Consuelo Del Cañizo and Javier De Las Rivas
    Citation: BMC Genomics 2014 15:910
    Content type: Research article Published on:

  44. Sorghum [Sorghum bicolor (L.) Moench] is an important dry-land cereal of the world providing food, fodder, feed and fuel. Stay-green (delayed-leaf senescence) is a key attribute in sorghum determining its adaptat...

    Authors: Nagaraja Reddy Rama Reddy, Madhusudhana Ragimasalawada, Murali Mohan Sabbavarapu, Seetharama Nadoor and Jagannatha Vishnu Patil
    Citation: BMC Genomics 2014 15:909
    Content type: Research article Published on:

  45. Previous work on whole genome doubling in plants established the importance of gene functional category in provoking or suppressing duplicate gene loss, or fractionation. Other studies, particularly in Paramecium

    Authors: Eric CH Chen and David Sankoff
    Citation: BMC Genomics 2014 15(Suppl 6):S19
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  46. Clonal expansion is a process in which a single organism reproduces asexually, giving rise to a diversifying population. It is pervasive in nature, from within-host pathogen evolution to emergent infectious di...

    Authors: Hossein Khiabanian, Zachary Carpenter, Jeffrey Kugelman, Joseph Chan, Vladimir Trifonov, Elyse Nagle, Travis Warren, Patrick Iversen, Sina Bavari, Gustavo Palacios and Raul Rabadan
    Citation: BMC Genomics 2014 15(Suppl 6):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  47. The breakpoint graph and the de Bruijn graph are two key data structures in the studies of genome rearrangements and genome assembly. However, the classical breakpoint graphs are defined on two genomes (repres...

    Authors: Yu Lin, Sergey Nurk and Pavel A Pevzner
    Citation: BMC Genomics 2014 15(Suppl 6):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  48. The breakpoint median in the set S n of permutations on n terms is known to have some unusual behavior, especially if the input genomes are maximally different to each other...

    Authors: Arash Jamshidpey, Aryo Jamshidpey and David Sankoff
    Citation: BMC Genomics 2014 15(Suppl 6):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  49. The breakpoint median for a set of k ≥ 3 random genomes tends to approach (any) one of these genomes ("corners") as genome length increases, although there are diminishing proportion of medians equidistant from a...

    Authors: Caroline Anne Larlee, Chunfang Zheng and David Sankoff
    Citation: BMC Genomics 2014 15(Suppl 6):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

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