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  1. Selenium (Se) and sulfur (S) are closely related elements that exhibit similar chemical properties. Some genes related to S metabolism are also involved in Se utilization in many organisms. However, the evolut...

    Authors: Gao-Peng Li, Liang Jiang, Jia-Zuan Ni, Qiong Liu and Yan Zhang
    Citation: BMC Genomics 2014 15:908
    Content type: Research article Published on:

  2. (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed ...

    Authors: Kelly Houston, Joanne Russell, Miriam Schreiber, Claire Halpin, Helena Oakey, Jennifer M Washington, Allan Booth, Neil Shirley, Rachel A Burton, Geoffrey B Fincher and Robbie Waugh
    Citation: BMC Genomics 2014 15:907
    Content type: Research article Published on:

  3. The human pathogen Trichomonas vaginalis is a parabasalian flagellate that is estimated to infect 3% of the world’s population annually. With a 160 megabase genome and up to 60,000 genes residing in six chromosom...

    Authors: Christian Woehle, Gary Kusdian, Claudia Radine, Dan Graur, Giddy Landan and Sven B Gould
    Citation: BMC Genomics 2014 15:906
    Content type: Research article Published on:

  5. Bone destruction is a feature of multiple myeloma, characterised by osteolytic bone destruction due to increased osteoclast activity and suppressed or absent osteoblast activity. Almost all multiple myeloma pa...

    Authors: Paul Dowling, Catriona Hayes, Kay Reen Ting, Abdul Hameed, Justine Meiller, Constantine Mitsiades, Kenneth C Anderson, Martin Clynes, Colin Clarke, Paul Richardson and Peter O’Gorman
    Citation: BMC Genomics 2014 15:904
    Content type: Research article Published on:

  7. Reed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy grass of the temperate regions of the world. Despite its economic importance, it is lacking in public genomic data. We ex...

    Authors: Niina Haiminen, Manfred Klaas, Zeyu Zhou, Filippo Utro, Paul Cormican, Thomas Didion, Christian Sig Jensen, Christopher E Mason, Susanne Barth and Laxmi Parida
    Citation: BMC Genomics 2014 15(Suppl 6):S18
    Content type: Research Published on:

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

  8. In comparative genomics, orthologs are used to transfer annotation from genes already characterized to newly sequenced genomes. Many methods have been developed for finding orthologs in sets of genomes. Howeve...

    Authors: Cécile Pereira, Alain Denise and Olivier Lespinet
    Citation: BMC Genomics 2014 15(Suppl 6):S16
    Content type: Research Published on:

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

  10. Because prokaryotic genomes experience a rapid flux of genes, selection may act at a higher level than an individual genome. We explore a quantitative model of the distributed genome whereby groups of genomes ...

    Authors: Alexander E Lobkovsky, Yuri I Wolf and Eugene V Koonin
    Citation: BMC Genomics 2014 15(Suppl 6):S14
    Content type: Research Published on:

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

  11. Codon decoding time is a fundamental property of mRNA translation believed to affect the abundance, function, and properties of proteins. Recently, a novel experimental technology--ribosome profiling--was deve...

    Authors: Alexandra Dana and Tamir Tuller
    Citation: BMC Genomics 2014 15(Suppl 6):S13
    Content type: Research Published on:

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

  13. Species tree estimation can be challenging in the presence of gene tree conflict due to incomplete lineage sorting (ILS), which can occur when the time between speciation events is short relative to the popula...

    Authors: Théo Zimmermann, Siavash Mirarab and Tandy Warnow
    Citation: BMC Genomics 2014 15(Suppl 6):S11
    Content type: Research Published on:

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

  14. The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for examp...

    Authors: Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova and Gabriella Trucco
    Citation: BMC Genomics 2014 15(Suppl 6):S10
    Content type: Research Published on:

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

  15. Phylogenetic birth-death models are opening a new window on the processes of genome evolution in studies of the evolution of gene and protein families, protein-protein interaction networks, microRNAs, and copy...

    Authors: Maureen Stolzer, Larry Wasserman and Dannie Durand
    Citation: BMC Genomics 2014 15(Suppl 6):S9
    Content type: Research Published on:

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

  17. With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree ...

    Authors: Md Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow
    Citation: BMC Genomics 2014 15(Suppl 6):S7
    Content type: Research Published on:

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

  19. The evolution of a cancer genome has traditionally been described as a sequential accumulation of mutations - including chromosomal rearrangements - over a period of time. Recent research suggests, however, th...

    Authors: Caleb Weinreb, Layla Oesper and Benjamin J Raphael
    Citation: BMC Genomics 2014 15(Suppl 6):S4
    Content type: Research Published on:

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

  20. Comparative analyses of chromosomal gene orders are successfully used to predict gene clusters in bacterial and fungal genomes. Present models for detecting sets of co-localized genes in chromosomal sequences ...

    Authors: Daniel Doerr, Jens Stoye, Sebastian Böcker and Katharina Jahn
    Citation: BMC Genomics 2014 15(Suppl 6):S2
    Content type: Research Published on:

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

  21. Common bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common...

    Authors: Marco H Bello, Samira M Moghaddam, Mark Massoudi, Phillip E McClean, Perry B Cregan and Phillip N Miklas
    Citation: BMC Genomics 2014 15:903
    Content type: Research article Published on:

  23. Metatranscriptome sequence data can contain highly redundant sequences from diverse populations of microbes and so data reduction techniques are often applied before taxonomic and functional annotation. For me...

    Authors: Andrew Toseland, Simon Moxon, Thomas Mock and Vincent Moulton
    Citation: BMC Genomics 2014 15:901
    Content type: Research article Published on:

  25. Seasonal estrus is a critical limiting factor of animal fecundity, and it involves changes in both ovarian biology and hormone secretion in different seasons. Previous studies indicate that two classes of smal...

    Authors: Ran Di, Jianning He, Shuhui Song, Dongmei Tian, Qiuyue Liu, Xiaojun Liang, Qing Ma, Min Sun, Jiandong Wang, Wenming Zhao, Guiling Cao, Jinxin Wang, Zhimin Yang, Ying Ge and Mingxing Chu
    Citation: BMC Genomics 2014 15:899
    Content type: Research article Published on:

  26. Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Similar mechanisms and gene transcr...

    Authors: Hong Zhang, Yongzheng Yang, Changyou Wang, Min Liu, Hao Li, Ying Fu, Yajuan Wang, Yingbin Nie, Xinlun Liu and Wanquan Ji
    Citation: BMC Genomics 2014 15:898
    Content type: Research article Published on:

  27. Mammalian spermatozoa must undergo capacitation, before becoming competent for fertilization. Despite its importance, the fundamental molecular mechanisms of capacitation are poorly understood. Therefore, in t...

    Authors: Woo-Sung Kwon, Md Saidur Rahman, June-Sub Lee, Jin Kim, Sung-Jae Yoon, Yoo-Jin Park, Young-Ah You, Seongsoo Hwang and Myung-Geol Pang
    Citation: BMC Genomics 2014 15:897
    Content type: Research article Published on:

  28. The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the ...

    Authors: Fabio Cericola, Ezio Portis, Sergio Lanteri, Laura Toppino, Lorenzo Barchi, Nazzareno Acciarri, Laura Pulcini, Tea Sala and Giuseppe Leonardo Rotino
    Citation: BMC Genomics 2014 15:896
    Content type: Research article Published on:

  29. Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified gen...

    Authors: Jun Rong, Youri Lammers, Jared L Strasburg, Natasha S Schidlo, Yavuz Ariyurek, Tom J de Jong, Peter G L Klinkhamer, Marinus J M Smulders and Klaas Vrieling
    Citation: BMC Genomics 2014 15:895
    Content type: Research article Published on:

  30. Aspergillus fumigatus produces a number of secondary metabolites, one of which, gliotoxin, has been shown to exhibit anti-fungal activity. Thus, A. fumigatus must be able to protect itself against gliotoxin. Inde...

    Authors: Grainne O’Keeffe, Stephen Hammel, Rebecca A Owens, Thomas M Keane, David A Fitzpatrick, Gary W Jones and Sean Doyle
    Citation: BMC Genomics 2014 15:894
    Content type: Research article Published on:

  31. Cryptic prophages are genetically defective in their induction and propagation, and are simply regarded as genetic remnants. There are several putative cryptic WO prophages in the sequenced Wolbachia genomes. Whe...

    Authors: Guan-Hong Wang, Li-Ming Niu, Guang-Chang Ma, Jin-Hua Xiao and Da-Wei Huang
    Citation: BMC Genomics 2014 15:893
    Content type: Research article Published on:

  32. Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ,...

    Authors: Jin-Zhi Zhang, Kun Zhao, Xiao-Yan Ai and Chun-Gen Hu
    Citation: BMC Genomics 2014 15:892
    Content type: Research article Published on:

  33. Many plant-pathogenic fungi have a tendency towards genome size expansion, mostly driven by increasing content of transposable elements (TEs). Through comparative and evolutionary genomics, five members of the Le...

    Authors: Jonathan Grandaubert, Rohan GT Lowe, Jessica L Soyer, Conrad L Schoch, Angela P Van de Wouw, Isabelle Fudal, Barbara Robbertse, Nicolas Lapalu, Matthew G Links, Bénédicte Ollivier, Juliette Linglin, Valérie Barbe, Sophie Mangenot, Corinne Cruaud, Hossein Borhan, Barbara J Howlett…
    Citation: BMC Genomics 2014 15:891
    Content type: Research article Published on:

  34. Inherited developmental diseases can cause severe animal welfare and economic problems in dairy cattle. The use of a small number of bulls for artificial insemination (AI) carries a risk that recessive defects...

    Authors: Heli Venhoranta, Hubert Pausch, Krzysztof Flisikowski, Christine Wurmser, Juhani Taponen, Helena Rautala, Alexander Kind, Angelika Schnieke, Ruedi Fries, Hannes Lohi and Magnus Andersson
    Citation: BMC Genomics 2014 15:890
    Content type: Research article Published on:

  35. Genome-wide profiling of single-nucleotide polymorphisms is receiving increasing attention as a method of pre-implantation genetic diagnosis in humans and of commercial genotyping of pre-transfer embryos in ca...

    Authors: Habib A Shojaei Saadi, Christian Vigneault, Mehdi Sargolzaei, Dominic Gagné, Éric Fournier, Béatrice de Montera, Jacques Chesnais, Patrick Blondin and Claude Robert
    Citation: BMC Genomics 2014 15:889
    Content type: Methodology article Published on:

  37. We have recently developed several homozygous families of transgenic rainbow trout harbouring cecropin P1 transgene. These fish exhibit resistance characteristic to infection by Aeromonas salmonicida and infectio...

    Authors: Jay H Lo, Chun-Mean Lin, Maria J Chen and Thomas T Chen
    Citation: BMC Genomics 2014 15:887
    Content type: Research article Published on:

  39. Kutzneria is a representative of a rarely observed genus of the family Pseudonocardiaceae. Kutzneria species were initially placed in the Streptosporangiaceae genus and later reconsidered to be an independent gen...

    Authors: Yuriy Rebets, Bogdan Tokovenko, Igor Lushchyk, Christian Rückert, Nestor Zaburannyi, Andreas Bechthold, Jörn Kalinowski and Andriy Luzhetskyy
    Citation: BMC Genomics 2014 15:885
    Content type: Research article Published on:

  40. Atlantic salmon have been subject to domestication for approximately ten generations, beginning in the early 1970s. This process of artificial selection will have created various genetic differences between wi...

    Authors: Beatrix Bicskei, James E Bron, Kevin A Glover and John B Taggart
    Citation: BMC Genomics 2014 15:884
    Content type: Research article Published on:

  41. Neurons display a highly polarized architecture. Their ability to modify their features under intracellular and extracellular stimuli, known as synaptic plasticity, is a key component of the neurochemical basi...

    Authors: Chantal Francis, Shreedhar Natarajan, Miler T Lee, Mugdha Khaladkar, Peter T Buckley, Jai-Yoon Sul, James Eberwine and Junhyong Kim
    Citation: BMC Genomics 2014 15:883
    Content type: Research article Published on:

  43. High-throughput DNA sequencing produces vast amounts of data, with millions of short reads that usually have to be mapped to a reference genome or newly assembled. Both reference-based mapping and de novo assembl...

    Authors: Andreas Steiner, David Stucki, Mireia Coscolla, Sonia Borrell and Sebastien Gagneux
    Citation: BMC Genomics 2014 15:881
    Content type: Software Published on:

  44. Gene expression changes induced by carcinogens may identify differences in molecular function between target and non-target organs. Target organs for benzo[a]pyrene (BaP) carcinogenicity in mice (lung, spleen and...

    Authors: Jie Zuo, Daniel S Brewer, Volker M Arlt, Colin S Cooper and David H Phillips
    Citation: BMC Genomics 2014 15:880
    Content type: Research article Published on:

  45. Accurate analysis of whole-gene expression and individual-exon expression is essential to characterize different transcript isoforms and identify alternative splicing events in human genes. One of the omic techno...

    Authors: Alberto Risueño, Beatriz Roson-Burgo, Anna Dolnik, Jesus M Hernandez-Rivas, Lars Bullinger and Javier De Las Rivas
    Citation: BMC Genomics 2014 15:879
    Content type: Methodology article Published on:

  46. MicroRNAs (miRNAs) regulate gene expression by binding to mRNA transcripts in various biological processes. In mammals and birds, miRNAs are known to play vital parts in both host immune defense and viral infe...

    Authors: Bao-cun Zhang, Jian Zhang and Li Sun
    Citation: BMC Genomics 2014 15:878
    Content type: Research article Published on:

  47. It has been shown in a number of metagenomic studies that the addition and removal of specific genes have allowed microbiomes to adapt to specific environmental conditions by losing and gaining specific functi...

    Authors: Leyden Fernandez, Josep M Mercader, Mercè Planas-Fèlix and David Torrents
    Citation: BMC Genomics 2014 15:877
    Content type: Research article Published on:

  48. Molecular heterogeneity of tumors suggests the presence of multiple different subclones that may limit response to targeted therapies and contribute to acquisition of drug resistance, but its quantification ha...

    Authors: Tingting Jiang, Weiwei Shi, René Natowicz, Sophia N Ononye, Vikram B Wali, Yuval Kluger, Lajos Pusztai and Christos Hatzis
    Citation: BMC Genomics 2014 15:876
    Content type: Methodology article Published on:

  50. A great number of studies have investigated changes induced by morphine exposure in gene expression using several experimental models. In this study, we examined gene expression changes during chronic exposure...

    Authors: M Javier Herrero-Turrión, Iván Rodríguez-Martín, Roger López-Bellido and Raquel E Rodríguez
    Citation: BMC Genomics 2014 15:874
    Content type: Research article Published on:

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