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  2. High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is sup...

    Authors: Shicai Wang, Ioannis Pandis, Chao Wu, Sijin He, David Johnson, Ibrahim Emam, Florian Guitton and Yike Guo
    Citation: BMC Genomics 2014 15(Suppl 8):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 8

  3. A major application of RNA-Seq is to perform differential gene expression analysis. Many tools exist to analyze differentially expressed genes in the presence of biological replicates. Frequently, however, RNA...

    Authors: Sahar Al Seesi, Yvette Temate Tiagueu, Alexander Zelikovsky and Ion I Măndoiu
    Citation: BMC Genomics 2014 15(Suppl 8):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 8

  4. Many computational methods are available for assembly and annotation of newly sequenced microbial genomes. However, when new genomes are reported in the literature, there is frequently very little critical ana...

    Authors: Shatavia S Morrison, Roman Pyzh, Myung S Jeon, Carmen Amaro, Francisco J Roig, Craig Baker-Austin, James D Oliver and Cynthia J Gibas
    Citation: BMC Genomics 2014 15(Suppl 8):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 8

  5. Nematode-trapping fungi are soil-living fungi that capture and kill nematodes using special hyphal structures called traps. They display a large diversity of trapping mechanisms and differ in their host prefer...

    Authors: Karl-Magnus Andersson, Dharmendra Kumar, Johan Bentzer, Eva Friman, Dag Ahrén and Anders Tunlid
    Citation: BMC Genomics 2014 15:968
    Content type: Research article Published on:

  6. Brain and immune system are linked in a bi-directional manner. To date, it remained largely unknown why immune components become suppressed, enhanced, or remain unaffected in relation to psychosocial stress. T...

    Authors: Michael Oster, Eduard Muráni, Siriluck Ponsuksili, Richard B D’Eath, Simon P Turner, Gary Evans, Ludger Thölking, Esra Kurt, Ronald Klont, Aline Foury, Pierre Mormède and Klaus Wimmers
    Citation: BMC Genomics 2014 15:967
    Content type: Research article Published on:

  7. Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene f...

    Authors: Johannes A Hofberger, Beifei Zhou, Haibao Tang, Jonathan DG Jones and M Eric Schranz
    Citation: BMC Genomics 2014 15:966
    Content type: Research article Published on:

  8. Ectopic vascular calcifications represent a major clinical problem associated with cardiovascular disease and mortality. However, the mechanisms underlying pathological vascular calcifications are largely unkn...

    Authors: Rodrigo DAM Alves, Marco Eijken, Jeroen van de Peppel and Johannes PTM van Leeuwen
    Citation: BMC Genomics 2014 15:965
    Content type: Research article Published on:

  9. Pods of the vanilla orchid (Vanilla planifolia) accumulate large amounts of the flavor compound vanillin (3-methoxy, 4-hydroxy-benzaldehyde) as a glucoside during the later stages of their development. At earlier...

    Authors: Xiaolan Rao, Nick Krom, Yuhong Tang, Thomas Widiez, Daphna Havkin-Frenkel, Faith C Belanger, Richard A Dixon and Fang Chen
    Citation: BMC Genomics 2014 15:964
    Content type: Research article Published on:

  10. Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a lim...

    Authors: Can Alkan, Pinar Kavak, Mehmet Somel, Omer Gokcumen, Serkan Ugurlu, Ceren Saygi, Elif Dal, Kuyas Bugra, Tunga Güngör, S Cenk Sahinalp, Nesrin Özören and Cemalettin Bekpen
    Citation: BMC Genomics 2014 15:963
    Content type: Research article Published on:

  11. Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genome...

    Authors: Guoqiang Yi, Lujiang Qu, Jianfeng Liu, Yiyuan Yan, Guiyun Xu and Ning Yang
    Citation: BMC Genomics 2014 15:962
    Content type: Research article Published on:

  12. Heat shock transcriptional factors (Hsfs) play important roles in the processes of biotic and abiotic stresses as well as in plant development. Cotton (Gossypium hirsutum, 2n = 4x = (AD)2 = 52) is an important cr...

    Authors: Jun Wang, Na Sun, Ting Deng, Lida Zhang and Kaijing Zuo
    Citation: BMC Genomics 2014 15:961
    Content type: Research article Published on:

  13. Lassa virus and Marburg virus are two causative agents of viral hemorrhagic fever. Their diagnosis is difficult because patients infected with either pathogen present similar nonspecific symptoms early after i...

    Authors: Ignacio S Caballero, Judy Y Yen, Lisa E Hensley, Anna N Honko, Arthur J Goff and John H Connor
    Citation: BMC Genomics 2014 15:960
    Content type: Research article Published on:

  14. Over the course of its intraerythrocytic developmental cycle (IDC), the malaria parasite Plasmodium falciparum tightly orchestrates the rise and fall of transcript levels for hundreds of genes. Considerable debat...

    Authors: Ragini Rai, Lei Zhu, Haifen Chen, Archana Patkar Gupta, Siu Kwan Sze, Jie Zheng, Christiane Ruedl, Zbynek Bozdech and Mark Featherstone
    Citation: BMC Genomics 2014 15:959
    Content type: Research article Published on:

  15. Bacterial respiratory tract infections, mainly caused by Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are among the leading causes of global mortality and morbidity. Increased resist...

    Authors: Fredrick M Mobegi, Sacha AFT van Hijum, Peter Burghout, Hester J Bootsma, Stefan PW de Vries, Christa E van der Gaast-de Jongh, Elles Simonetti, Jeroen D Langereis, Peter WM Hermans, Marien I de Jonge and Aldert Zomer
    Citation: BMC Genomics 2014 15:958
    Content type: Research article Published on:

  16. The mango belongs to the genus Mangifera, consisting of numerous tropical fruiting trees in the flowering plant family, Anacardiaceae. Postharvest treatment by hot water brushing (HWB) for 15–20 s was introduced ...

    Authors: Neta Luria, Noa Sela, Mor Yaari, Oleg Feygenberg, Ilana Kobiler, Amnon Lers and Dov Prusky
    Citation: BMC Genomics 2014 15:957
    Content type: Research article Published on:

  17. 2b-RAD (type IIB endonucleases restriction-site associated DNA) approach was invented by Wang in 2012 and proven as a simple and flexible method for genome-wide genotyping. However, there is still plenty of ro...

    Authors: Yu Guo, Hui Yuan, Dongming Fang, Lianbo Song, Yan Liu, Yong Liu, Lu Wu, Jianping Yu, Zichao Li, Xun Xu and Hongliang Zhang
    Citation: BMC Genomics 2014 15:956
    Content type: Methodology article Published on:

  18. Few, if any, protozoan parasites are reported to exhibit extreme organ tropism like the flagellate Tritrichomonas foetus. In cattle, T. foetus infects the reproductive system causing abortion, whereas the infecti...

    Authors: Victoria Morin-Adeline, Rodrigo Lomas, Denis O’Meally, Colin Stack, Ana Conesa and Jan Šlapeta
    Citation: BMC Genomics 2014 15:955
    Content type: Research article Published on:

  19. Transcriptome analysis of porcine whole blood has several applications, which include deciphering genetic mechanisms for host responses to viral infection and vaccination. The abundance of alpha- and beta-glob...

    Authors: Igseo Choi, Hua Bao, Arun Kommadath, Afshin Hosseini, Xu Sun, Yan Meng, Paul Stothard, Graham S Plastow, Christopher K Tuggle, James M Reecy, Eric Fritz-Waters, Samuel M Abrams, Joan K Lunney and Le Luo Guan
    Citation: BMC Genomics 2014 15:954
    Content type: Methodology article Published on:

  20. MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA ...

    Authors: Jun Wu, Defu Wang, Yufeng Liu, Long Wang, Xin Qiao and Shaoling Zhang
    Citation: BMC Genomics 2014 15:953
    Content type: Research article Published on:

  21. Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were r...

    Authors: Hicham Benzekri, Paula Armesto, Xavier Cousin, Mireia Rovira, Diego Crespo, Manuel Alejandro Merlo, David Mazurais, Rocío Bautista, Darío Guerrero-Fernández, Noe Fernandez-Pozo, Marian Ponce, Carlos Infante, Jose Luis Zambonino, Sabine Nidelet, Marta Gut, Laureana Rebordinos…
    Citation: BMC Genomics 2014 15:952
    Content type: Research article Published on:

  22. Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH...

    Authors: Emma Timmins-Schiffman, William D Coffey, Wilber Hua, Brook L Nunn, Gary H Dickinson and Steven B Roberts
    Citation: BMC Genomics 2014 15:951
    Content type: Research article Published on:

  23. The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental...

    Authors: Vikas Belamkar, Nathan T Weeks, Arvind K Bharti, Andrew D Farmer, Michelle A Graham and Steven B Cannon
    Citation: BMC Genomics 2014 15:950
    Content type: Research article Published on:

  24. Vascular wilt caused by Fusarium oxysporum f. sp. ciceri Race 1 (Foc1) is a serious disease of chickpea (Cicer arietinum L.) accounting for approximately 10-15% annual crop loss. The fungus invades the plant via ...

    Authors: Moniya Chatterjee, Sumanti Gupta, Anirban Bhar, Dipankar Chakraborti, Debabrata Basu and Sampa Das
    Citation: BMC Genomics 2014 15:949
    Content type: Research article Published on:

  25. Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. Th...

    Authors: Christine F Baes, Marlies A Dolezal, James E Koltes, Beat Bapst, Eric Fritz-Waters, Sandra Jansen, Christine Flury, Heidi Signer-Hasler, Christian Stricker, Rohan Fernando, Ruedi Fries, Juerg Moll, Dorian J Garrick, James M Reecy and Birgit Gredler
    Citation: BMC Genomics 2014 15:948
    Content type: Methodology article Published on:

  26. Osteochondrosis (OC(D)) is a juvenile osteo-articular disorder affecting several mammalian species. In horses, OC(D) is considered as a multifactorial disease and has been described as a focal disruption of en...

    Authors: Clémence Desjardin, Julie Riviere, Anne Vaiman, Caroline Morgenthaler, Mathieu Diribarne, Michel Zivy, Céline Robert, Laurence Le Moyec, Laurence Wimel, Olivier Lepage, Claire Jacques, Edmond Cribiu and Laurent Schibler
    Citation: BMC Genomics 2014 15:947
    Content type: Research article Published on:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

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