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  1. Genome-wide association studies (GWAS) identify regions of the genome that are associated with particular traits, but do not typically identify specific causative genetic elements. For example, while a large n...

    Authors: Jay Pendse, Prasanna V Ramachandran, Jianbo Na, Narisu Narisu, Jill L Fink, Ross L Cagan, Francis S Collins and Thomas J Baranski
    Citation: BMC Genomics 2013 14:136
    Content type: Research article Published on:

  2. Genomic resources within the phylum Arthropoda are largely limited to the true insects but are beginning to include unexplored subphyla, such as the Crustacea and Chelicerata. Investigations of these understud...

    Authors: Amanda K Gibson, Zach Smith, Clay Fuqua, Keith Clay and John K Colbourne
    Citation: BMC Genomics 2013 14:135
    Content type: Research article Published on:

  3. Transcriptome analysis in combination with pathway-focused bioassays is suggested to be a helpful approach for gaining deeper insights into the complex mechanisms of action of herbal multicomponent preparation...

    Authors: Angela Klein, Oliver A Wrulich, Marcel Jenny, Peter Gruber, Kathrin Becker, Dietmar Fuchs, Johanna M Gostner and Florian Ãœberall
    Citation: BMC Genomics 2013 14:133
    Content type: Research article Published on:

  4. One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign sc...

    Authors: Dominik Grimm, Jörg Hagmann, Daniel Koenig, Detlef Weigel and Karsten Borgwardt
    Citation: BMC Genomics 2013 14:132
    Content type: Methodology article Published on:

  5. Copy number variations (CNVs) are widespread in the human or animal genome and are a significant source of genetic variation, which has been demonstrated to play an important role in phenotypic diversity. Adva...

    Authors: Li Jiang, Jicai Jiang, Jie Yang, Xuan Liu, Jiying Wang, Haifei Wang, Xiangdong Ding, Jianfeng Liu and Qin Zhang
    Citation: BMC Genomics 2013 14:131
    Content type: Research article Published on:

  6. As well known, both natural and synthetic steroidal compounds are powerful endocrine disrupting compounds (EDCs) which can cause reproductive toxicity and affect cellular development in mammals and thus are ge...

    Authors: Zhi-Zhen Li, Xiao-Fei Li, Wei Yang, Xiang Dong, Jie Yu, Shu-Liang Zhu, Man Li, Li Xie and Wang-Yu Tong
    Citation: BMC Genomics 2013 14:130
    Content type: Research article Published on:

  7. Understanding the genetic basis of diseases is key to the development of better diagnoses and treatments. Unfortunately, only a small fraction of the existing data linking genes to phenotypes is available thro...

    Authors: Elodie Portales-Casamar, Carolyn Ch’ng, Frances Lui, Nicolas St-Georges, Anton Zoubarev, Artemis Y Lai, Mark Lee, Cathy Kwok, Willie Kwok, Luchia Tseng and Paul Pavlidis
    Citation: BMC Genomics 2013 14:129
    Content type: Database Published on:

  8. The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the...

    Authors: Nuno Sepúlveda, Susana G Campino, Samuel A Assefa, Colin J Sutherland, Arnab Pain and Taane G Clark
    Citation: BMC Genomics 2013 14:128
    Content type: Methodology article Published on:

  9. Genetic susceptibility to colonic inflammation is poorly defined at the gene level. Although Genome Wide Association studies (GWAS) have identified loci in the human genome which confer susceptibility to Infla...

    Authors: Scott E Levison, Paul Fisher, Jenny Hankinson, Leo Zeef, Steve Eyre, William E Ollier, John T McLaughlin, Andy Brass, Richard K Grencis and Joanne L Pennock
    Citation: BMC Genomics 2013 14:127
    Content type: Research article Published on:

  10. Staphylococcus aureus is a widely distributed human pathogen capable of infecting almost every ecological niche of the host. As a result, it is responsible for causing many different diseases. S. aureus has a vas...

    Authors: Jose Antonio Ibarra, Ernesto Pérez-Rueda, Ronan K Carroll and Lindsey N Shaw
    Citation: BMC Genomics 2013 14:126
    Content type: Research article Published on:

  11. Ramie fiber, extracted from vegetative organ stem bast, is one of the most important natural fibers. Understanding the molecular mechanisms of the vegetative growth of the ramie and the formation and developme...

    Authors: Touming Liu, Siyuan Zhu, Qingming Tang, Ping Chen, Yongting Yu and Shouwei Tang
    Citation: BMC Genomics 2013 14:125
    Content type: Research article Published on:

  12. Copy number variations (CNVs) represent a significant source of genomic structural variation. Their length ranges from approximately one hundred to millions of base pair. Genome-wide screenings have clarified ...

    Authors: Francesco Cicconardi, Giovanni Chillemi, Anna Tramontano, Cinzia Marchitelli, Alessio Valentini, Paolo Ajmone-Marsan and Alessandro Nardone
    Citation: BMC Genomics 2013 14:124
    Content type: Research article Published on:

  13. Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies...

    Authors: Eva Jiménez-Guri, Jaime Huerta-Cepas, Luca Cozzuto, Karl R Wotton, Hui Kang, Heinz Himmelbauer, Guglielmo Roma, Toni Gabaldón and Johannes Jaeger
    Citation: BMC Genomics 2013 14:123
    Content type: Research article Published on:

  14. Human genome is enriched with thousands of conserved non-coding elements (CNEs). Recently, a medium throughput strategy was employed to analyze the ability of human CNEs to drive tissue specific expression dur...

    Authors: Nazia Parveen, Ayesha Masood, Nouman Iftikhar, Bushra F Minhas, Rashid Minhas, Uzma Nawaz and Amir Ali Abbasi
    Citation: BMC Genomics 2013 14:122
    Content type: Research article Published on:

  15. Trichoderma is a genus of mycotrophic filamentous fungi (teleomorph Hypocrea) which possess a bright variety of biotrophic and saprotrophic lifestyles. The ability to parasitize and/or kill other fungi (mycoparas...

    Authors: Lea Atanasova, Stephane Le Crom, Sabine Gruber, Fanny Coulpier, Verena Seidl-Seiboth, Christian P Kubicek and Irina S Druzhinina
    Citation: BMC Genomics 2013 14:121
    Content type: Research article Published on:

  16. High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution...

    Authors: Régine Delourme, Cyril Falentin, Berline Fopa Fomeju, Marie Boillot, Gilles Lassalle, Isabelle André, Jorge Duarte, Valérie Gauthier, Nicole Lucante, Amandine Marty, Maryline Pauchon, Jean-Philippe Pichon, Nicolas Ribière, Gwenn Trotoux, Philippe Blanchard, Nathalie Rivière…
    Citation: BMC Genomics 2013 14:120
    Content type: Research article Published on:

  17. The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains. A single LS chromosome in the Fol4287 r...

    Authors: Sarah M Schmidt, Petra M Houterman, Ines Schreiver, Lisong Ma, Stefan Amyotte, Biju Chellappan, Sjef Boeren, Frank L W Takken and Martijn Rep
    Citation: BMC Genomics 2013 14:119
    Content type: Research article Published on:

  18. Cooperia oncophora and Ostertagia ostertagi are among the most important gastrointestinal nematodes of cattle worldwide. The economic losses caused by these parasites are on the order of hundreds of millions of d...

    Authors: Esley Heizer, Dante S Zarlenga, Bruce Rosa, Xin Gao, Robin B Gasser, Jessie De Graef, Peter Geldhof and Makedonka Mitreva
    Citation: BMC Genomics 2013 14:118
    Content type: Research article Published on:

  20. The guanine nucleotide binding protein (G protein)-coupled receptors (GPCRs) regulate cell growth, proliferation and differentiation. G proteins are also implicated in erythroid differentiation, and some of th...

    Authors: Vladan P Čokić, Reginald D Smith, Angélique Biancotto, Constance T Noguchi, Raj K Puri and Alan N Schechter
    Citation: BMC Genomics 2013 14:116
    Content type: Research article Published on:

  21. Two species of wild silkworms, the Chinese oak silkworm (Antheraea pernyi) and the castor silkworm Philosamia cynthia ricini, can acquire a serious disease caused by Nucleopolyhedrin Viruses (NPVs) (known as Anpe...

    Authors: Heying Qian, Yuehua Zhang, Yejun Wu, Pingiang Sun, Shanying Zhu, Xijie Guo, Kun Gao, Anying Xu and Wenbing Wang
    Citation: BMC Genomics 2013 14:115
    Content type: Research article Published on:

  22. Orthoptera, the largest polyneopteran insect order, contains 2 suborders and 235 subfamilies. Orthoptera mitochondrial genomes (mitogenomes) follow the ancestral insect gene order, with the exception of a trnD-tr...

    Authors: Chunxiang Liu, Jia Chang, Chuan Ma, Ling Li and Shanyi Zhou
    Citation: BMC Genomics 2013 14:114
    Content type: Research article Published on:

  23. In humans, cleft palate (CP) accounts for one of the largest number of birth defects with a complex genetic and environmental etiology. TGFβ3 has been established as an important regulator of palatal fusion in...

    Authors: Ferhat Ozturk, You Li, Xiujuan Zhu, Chittibabu Guda and Ali Nawshad
    Citation: BMC Genomics 2013 14:113
    Content type: Research article Published on:

  24. As one of the most dominant bacterial groups on Earth, cyanobacteria play a pivotal role in the global carbon cycling and the Earth atmosphere composition. Understanding their molecular responses to environmen...

    Authors: Jiangxin Wang, Gang Wu, Lei Chen and Weiwen Zhang
    Citation: BMC Genomics 2013 14:112
    Content type: Research article Published on:

  25. MicroRNAs are a population of short non-coding RNAs with widespread negative regulatory impact on mRNA translation. Unrestricted somatic stem cells (USSC) are a rare population in human cord blood that can be ...

    Authors: Hans-Ingo Trompeter, Janine Dreesen, Eugenie Hermann, Katharina M Iwaniuk, Markus Hafner, Neil Renwick, Thomas Tuschl and Peter Wernet
    Citation: BMC Genomics 2013 14:111
    Content type: Research article Published on:

  26. Identifying similarities and differences in the molecular constitutions of various types of cancer is one of the key challenges in cancer research. The appearances of a cancer depend on complex molecular inter...

    Authors: Sungwon Jung, Michael Verdicchio, Jeff Kiefer, Daniel Von Hoff, Michael Berens, Michael Bittner and Seungchan Kim
    Citation: BMC Genomics 2013 14:110
    Content type: Methodology article Published on:

  27. Plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) proteins encoded by resistance genes play an important role in the responses of plants to various pathogens, including viruses, bacteria, fungi, an...

    Authors: Hongjian Wan, Wei Yuan, Kailiang Bo, Jia Shen, Xin Pang and Jinfeng Chen
    Citation: BMC Genomics 2013 14:109
    Content type: Research article Published on:

  28. Genome-wide association studies have identified thousands of SNP variants associated with hundreds of phenotypes. For most associations the causal variants and the molecular mechanisms underlying pathogenesis ...

    Authors: Alida S D Kindt, Pau Navarro, Colin A M Semple and Chris S Haley
    Citation: BMC Genomics 2013 14:108
    Content type: Research article Published on:

  29. Pyropia haitanensis is an economically important mariculture crop in China and is also valuable in life science research. However, the lack of genetic information of this organism hinders the understanding of the...

    Authors: Chaotian Xie, Bing Li, Yan Xu, Dehua Ji and Changsheng Chen
    Citation: BMC Genomics 2013 14:107
    Content type: Research article Published on:

  30. The core promoter is the region flanking the transcription start site (TSS) that directs formation of the pre-initiation complex. Core promoters have been studied intensively in mammals and yeast, but not in m...

    Authors: Sourav Roy, Laetitia Poidevin, Tao Jiang and Howard S Judelson
    Citation: BMC Genomics 2013 14:106
    Content type: Research article Published on:

  31. For safe clinical application of engineered cartilage made from mesenchymal stem cells (MSCs), molecular mechanisms for chondrogenic differentiation must be known in detail. Changes in gene expression and extr...

    Authors: Sarah R Herlofsen, Jan Christian Bryne, Torill Høiby, Li Wang, Robbyn Issner, Xiaolan Zhang, Michael J Coyne, Patrick Boyle, Hongcang Gu, Leonardo A Meza-Zepeda, Philippe Collas, Tarjei S Mikkelsen and Jan E Brinchmann
    Citation: BMC Genomics 2013 14:105
    Content type: Research article Published on:

  32. MicroRNAs (miRNAs) are short non-coding regulatory RNAs that control gene expression usually producing translational repression and gene silencing. High-throughput sequencing technologies have revealed heterog...

    Authors: Franc Llorens, Mónica Bañez-Coronel, Lorena Pantano, Jose Antonio del Río, Isidre Ferrer, Xavier Estivill and Eulàlia Martí
    Citation: BMC Genomics 2013 14:104
    Content type: Research article Published on:

  33. Tandem repeats (TRs) in the mitochondrial (mt) genome control region have been documented in a wide variety of vertebrate species. The mechanism by which repeated tracts originate and undergo duplication and d...

    Authors: Wei Shi, Xiao-Yu Kong, Zhong-Ming Wang, Shan-Shan Yu, Hai-Xia Chen and Elizabeth A De Stasio
    Citation: BMC Genomics 2013 14:103
    Content type: Research article Published on:

  34. Detection of significant differentially expressed genes (DEGs) from DNA microarray datasets is a common routine task conducted in biomedical research. For the detection of DEGs, numerous methods are proposed. ...

    Authors: Koki Tsuyuzaki, Daisuke Tominaga, Yeondae Kwon and Satoru Miyazaki
    Citation: BMC Genomics 2013 14(Suppl 2):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  35. Biological data acquisition is raising new challenges, both in data analysis and handling. Not only is it proving hard to analyze the data at the rate it is generated today, but simply reading and transferring...

    Authors: Konstantin Tretyakov, Sven Laur, Geert Smant, Jaak Vilo and Pjotr Prins
    Citation: BMC Genomics 2013 14(Suppl 2):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  36. Long intergenic non-coding RNAs (lincRNAs) are emerging as a novel class of non-coding RNAs and potent gene regulators. High-throughput RNA-sequencing combined with de novo assembly promises quantity discovery of...

    Authors: Kun Sun, Xiaona Chen, Peiyong Jiang, Xiaofeng Song, Huating Wang and Hao Sun
    Citation: BMC Genomics 2013 14(Suppl 2):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  37. Classification is the problem of assigning each input object to one of a finite number of classes. This problem has been extensively studied in machine learning and statistics, and there are numerous applicati...

    Authors: Mark Menor, Kyungim Baek and Guylaine Poisson
    Citation: BMC Genomics 2013 14(Suppl 2):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  38. Haplotype information is useful for various genetic analyses, including genome-wide association studies. Determining haplotypes experimentally is difficult and there are several computational approaches that i...

    Authors: Hirotaka Matsumoto and Hisanori Kiryu
    Citation: BMC Genomics 2013 14(Suppl 2):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  39. Investigation of conformational changes in a protein is a prerequisite to understand its biological function. To explore these conformational changes in proteins we developed a strategy with the combination of...

    Authors: MNV Prasad Gajula, KP Vogel, Anil Rai, Franziska Dietrich and HJ Steinhoff
    Citation: BMC Genomics 2013 14(Suppl 2):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  40. microRNAs (miRNAs) are tiny endogenous RNAs that have been discovered in animals and plants, and direct the post-transcriptional regulation of target mRNAs for degradation or translational repression via bindi...

    Authors: Toyofumi Fujiwara and Tetsushi Yada
    Citation: BMC Genomics 2013 14(Suppl 2):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  41. Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation in human DNA. The sequence of SNPs in each of the two copies of a given chromosome in a diploid organism is referred to as a...

    Authors: Fei Deng, Wenjuan Cui and Lusheng Wang
    Citation: BMC Genomics 2013 14(Suppl 2):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  42. Protein structure comparison and classification is an effective method for exploring protein structure-function relations. This problem is computationally challenging. Many different computational approaches f...

    Authors: Cody Ashby, Daniel Johnson, Karl Walker, Iyad A Kanj, Ge Xia and Xiuzhen Huang
    Citation: BMC Genomics 2013 14(Suppl 2):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 2

  43. Many studies have revealed correlations between breast tumour phenotypes, variations in gene expression, and patient survival outcomes. The molecular heterogeneity between breast tumours revealed by these stud...

    Authors: Yi Kan Wang, Cristin G Print and Edmund J Crampin
    Citation: BMC Genomics 2013 14:102
    Content type: Research article Published on:

  44. Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase t...

    Authors: Anneleen Van Geystelen, Ronny Decorte and Maarten HD Larmuseau
    Citation: BMC Genomics 2013 14:101
    Content type: Methodology article Published on:

  45. White clover (Trifolium repens L.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white c...

    Authors: Istvan Nagy, Susanne Barth, Jeanne Mehenni-Ciz, Michael T Abberton and Dan Milbourne
    Citation: BMC Genomics 2013 14:100
    Content type: Research article Published on:

  46. The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipi...

    Authors: Milos Pjanic, Christoph D Schmid, Armelle Gaussin, Giovanna Ambrosini, Jozef Adamcik, Petar Pjanic, Genta Plasari, Jan Kerschgens, Giovani Dietler, Philipp Bucher and Nicolas Mermod
    Citation: BMC Genomics 2013 14:99
    Content type: Research article Published on:

  47. Most studies on the origin and evolution of microRNA in the human genome have been focused on its relationship with repetitive elements and segmental duplications. However, duplication events at a smaller scal...

    Authors: Zhi-Qiang Du, Cai-Xia Yang, Max F Rothschild and Jason W Ross
    Citation: BMC Genomics 2013 14:98
    Content type: Research article Published on:

  48. Cotton (Gossypium hirsutum) anther development involves a diverse range of gene interactions between sporophytic and gametophytic tissues. However, only a small number of genes are known to be specifically involv...

    Authors: Mingming Wei, Meizhen Song, Shuli Fan and Shuxun Yu
    Citation: BMC Genomics 2013 14:97
    Content type: Research article Published on:

  49. A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive rad...

    Authors: Chris M Rands, Aaron Darling, Matthew Fujita, Lesheng Kong, Matthew T Webster, Céline Clabaut, Richard D Emes, Andreas Heger, Stephen Meader, Michael Brent Hawkins, Michael B Eisen, Clotilde Teiling, Jason Affourtit, Benjamin Boese, Peter R Grant, Barbara Rosemary Grant…
    Citation: BMC Genomics 2013 14:95
    Content type: Research article Published on:

  50. Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infectio...

    Authors: Reena Narsai, Chuang Wang, Jie Chen, Jianli Wu, Huixia Shou and James Whelan
    Citation: BMC Genomics 2013 14:93
    Content type: Research article Published on:

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BMC Genomics

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