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  1. Nuclear receptors (NRs) are a large superfamily of proteins defined by a DNA-binding domain (DBD) and a ligand-binding domain (LBD). They function as transcriptional regulators to control expression of genes i...

    Authors: Dae-Sik Hwang, Bo-Young Lee, Hui-Su Kim, Min Chul Lee, Do-Hyun Kyung, Ae-Son Om, Jae-Sung Rhee and Jae-Seong Lee
    Citation: BMC Genomics 2014 15:993
    Content type: Research article Published on:

  3. Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been foun...

    Authors: João Perdigão, Hugo Silva, Diana Machado, Rita Macedo, Fernando Maltez, Carla Silva, Luisa Jordao, Isabel Couto, Kim Mallard, Francesc Coll, Grant A Hill-Cawthorne, Ruth McNerney, Arnab Pain, Taane G Clark, Miguel Viveiros and Isabel Portugal
    Citation: BMC Genomics 2014 15:991
    Content type: Research article Published on:

  6. Chromatin compactness has been considered a major determinant of gene activity and has been associated with specific chromatin modifications in studies on a few individual genetic loci. At the same time, genom...

    Authors: Beatrice Milon, Yezhou Sun, Weizhong Chang, Todd Creasy, Anup Mahurkar, Amol Shetty, Dmitry Nurminsky and Maria Nurminskaya
    Citation: BMC Genomics 2014 15:988
    Content type: Research article Published on:

  7. Arthropod venoms are invaluable sources of bioactive substances with biotechnological application. The limited availability of some venoms, such as those from ants, has restricted the knowledge about the compo...

    Authors: Wafa Bouzid, Marion Verdenaud, Christophe Klopp, Frédéric Ducancel, Céline Noirot and Angélique Vétillard
    Citation: BMC Genomics 2014 15:987
    Content type: Research article Published on:

  8. Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. Although this bacteria has been poorly studied, its genome has already been sequenced. Therefore, ...

    Authors: Hivana PMB Dall’Agnol, Rafael A Baraúna, Pablo HCG de Sá, Rommel TJ Ramos, Felipe Nóbrega, Catarina IP Nunes, Diego A das Graças, Adriana R Carneiro, Daniel M Santos, Adriano MC Pimenta, Marta SP Carepo, Vasco Azevedo, Vivian H Pellizari, Maria PC Schneider and Artur Silva
    Citation: BMC Genomics 2014 15:986
    Content type: Research article Published on:

  10. Panduratin A extracted from Boesenbergia rotunda is a flavonoid reported to possess a range of medicinal indications which include anti-dengue, anti-HIV, anti-cancer, antioxidant and anti-inflammatory properties....

    Authors: Noor Diyana Md-Mustafa, Norzulaani Khalid, Huan Gao, Zhiyu Peng, Mohd Firdaus Alimin, Noraini Bujang, Wong Sher Ming, Yusmin Mohd-Yusuf, Jennifer A Harikrishna and Rofina Yasmin Othman
    Citation: BMC Genomics 2014 15:984
    Content type: Research article Published on:

  11. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a diverse group of biologically active bacterial molecules. Due to the conserved genomic arrangement of many of the genes involved...

    Authors: Anne-Catrin Letzel, Sacha J Pidot and Christian Hertweck
    Citation: BMC Genomics 2014 15:983
    Content type: Research article Published on:

  12. Glaucoma is characterized by progressive loss of the visual field and death of retinal ganglion cells (RGCs), a process that is mediated, in part, by axonal injury. However, the molecular pathomechanisms linki...

    Authors: Masayuki Yasuda, Yuji Tanaka, Koji M Nishiguchi, Morin Ryu, Satoru Tsuda, Kazuichi Maruyama and Toru Nakazawa
    Citation: BMC Genomics 2014 15:982
    Content type: Research article Published on:

  13. Several individual studies have suggested that autosomal CpG methylation differs by sex both in terms of individual CpG sites and global autosomal CpG methylation. However, these findings have been inconsisten...

    Authors: Nina S McCarthy, Phillip E Melton, Gemma Cadby, Seyhan Yazar, Maria Franchina, Eric K Moses, David A Mackey and Alex W Hewitt
    Citation: BMC Genomics 2014 15:981
    Content type: Research article Published on:

  14. Phytophthora cactorum, a hemibiotrophic oomycete pathogen, can cause destructive diseases on numerous crops worldwide, leading to essential economic losses every year. However, little has been known about its mol...

    Authors: Xiao-Ren Chen, Bo-Yue Zhang, Yu-Ping Xing, Qi-Yuan Li, Yan-Peng Li, Yun-Hui Tong and Jing-You Xu
    Citation: BMC Genomics 2014 15:980
    Content type: Research article Published on:

  15. Many areas critical to agricultural production and research, such as the breeding and trait mapping in plants and livestock, require robust and scalable genotyping platforms. Genotyping-by-sequencing (GBS) is ...

    Authors: Christopher Heffelfinger, Christopher A Fragoso, Maria A Moreno, John D Overton, John P Mottinger, Hongyu Zhao, Joe Tohme and Stephen L Dellaporta
    Citation: BMC Genomics 2014 15:979
    Content type: Methodology article Published on:

  16. Human induced pluripotent stem cells (iPSCs) have a wide range of applications throughout the fields of basic research, disease modeling and drug screening. Epigenetic instable iPSCs with aberrant DNA methylat...

    Authors: Xiaojian Shao, Cuiyun Zhang, Ming-An Sun, Xuemei Lu and Hehuang Xie
    Citation: BMC Genomics 2014 15:978
    Content type: Research article Published on:

  17. Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the ...

    Authors: Alexandra Calteau, David P Fewer, Amel Latifi, Thérèse Coursin, Thierry Laurent, Jouni Jokela, Cheryl A Kerfeld, Kaarina Sivonen, Jörn Piel and Muriel Gugger
    Citation: BMC Genomics 2014 15:977
    Content type: Research article Published on:

  18. Micro-RNAs (miRNA) are attributed to the systems biological role of a regulatory mechanism of the expression of protein coding genes. Research has identified miRNAs dysregulations in several but distinct patho...

    Authors: Alfred Ultsch and Jörn Lötsch
    Citation: BMC Genomics 2014 15:976
    Content type: Research article Published on:

  19. Sex-determination genes drive the evolution of adjacent chromosomal regions. Sexually antagonistic selection favors the accumulation of inversions that reduce recombination in regions adjacent to the sex-deter...

    Authors: William J Gammerdinger, Matthew A Conte, Enoch A Acquah, Reade B Roberts and Thomas D Kocher
    Citation: BMC Genomics 2014 15:975
    Content type: Research article Published on:

  20. Jatropha curcas, whose seed content is approximately 30–40% oil, is an ideal feedstock for producing biodiesel and bio-jet fuels. However, Jatropha plants have a low number of female flowers, which results in low...

    Authors: Bang-Zhen Pan, Mao-Sheng Chen, Jun Ni and Zeng-Fu Xu
    Citation: BMC Genomics 2014 15:974
    Content type: Research article Published on:

  21. Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in...

    Authors: Thibaud Dugat, Valentin Loux, Sylvain Marthey, Marco Moroldo, Anne-Claire Lagrée, Henri-Jean Boulouis, Nadia Haddad and Renaud Maillard
    Citation: BMC Genomics 2014 15:973
    Content type: Research article Published on:

  22. While much recent research has expanded our understanding of the molecular interactions between aphids and their host plants, it is lacking for the soybean aphid, Aphis glycines. Since its North American invasion...

    Authors: Raman Bansal, MAR Mian, Omprakash Mittapalli and Andy P Michel
    Citation: BMC Genomics 2014 15:972
    Content type: Research article Published on:

  24. Streptomyces are widespread bacteria that contribute to the terrestrial carbon cycle and produce the majority of clinically useful antibiotics. While interspecific genomic diversity has been investigated among St...

    Authors: James R Doroghazi and Daniel H Buckley
    Citation: BMC Genomics 2014 15:970
    Content type: Research article Published on:

  26. 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

  27. 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

  28. 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

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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BMC Genomics

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