Information-theoretic gene-gene and gene-environment interaction analysis of quantitative traits.

abstract：BACKGROUND:Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received l...

journal_title：BMC genomics

authors： Huang X,Wang F,Singh R,Reinert JA,Engelke MC,Genovesi AD,Chandra A,Yu Q

更新日期：2016-08-08 00:00:00

abstract：BACKGROUND:The antitumor drug daunorubicin exerts some of its cytotoxic effects by binding to DNA and inhibiting the transcription of different genes. We analysed this effect in vivo at the transcriptome level using the budding yeast Saccharomyces cerevisiae as a model and sublethal (IC40) concentrations of the drug to...

journal_title：BMC genomics

authors： Rojas M,Casado M,Portugal J,Piña B

更新日期：2008-07-30 00:00:00

abstract：BACKGROUND:The histone variant H2A.Z, which has been reported to have both activating and repressive effects on gene expression, is known to occupy nucleosomes at the 5' ends of protein-coding genes. RESULTS:We now find that H2A.Z is also significantly enriched in gene coding regions and at the 3' ends of genes in bud...

journal_title：BMC genomics

authors： Gu M,Naiyachit Y,Wood TJ,Millar CB

更新日期：2015-02-19 00:00:00

abstract：BACKGROUND:Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a n...

journal_title：BMC genomics

authors： Dang X,Xie Z,Liu W,Sun Y,Liu X,Zhu Y,Staehelin C

更新日期：2019-08-12 00:00:00

abstract：BACKGROUND:Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species ar...

journal_title：BMC genomics

authors： Luo H,Sun C,Sun Y,Wu Q,Li Y,Song J,Niu Y,Cheng X,Xu H,Li C,Liu J,Steinmetz A,Chen S

更新日期：2011-12-23 00:00:00

abstract：BACKGROUND:Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Mol...

journal_title：BMC genomics

authors： Ginolhac A,Vilstrup J,Stenderup J,Rasmussen M,Stiller M,Shapiro B,Zazula G,Froese D,Steinmann KE,Thompson JF,Al-Rasheid KA,Gilbert TM,Willerslev E,Orlando L

更新日期：2012-05-10 00:00:00

abstract：BACKGROUND:HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate ...

journal_title：BMC genomics

authors： Chen B,Zhong D,Monteiro A

更新日期：2006-06-17 00:00:00

abstract：:An amendment to this paper has been published and can be accessed via the original article. ...

journal_title：BMC genomics

authors： Levin M,Scheibe M,Butter F

更新日期：2020-11-12 00:00:00

abstract：BACKGROUND:Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit crops, including those...

journal_title：BMC genomics

authors： Kang C,Liu Z

更新日期：2015-10-19 00:00:00

abstract：BACKGROUND:Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to...

journal_title：BMC genomics

authors： Olohan L,Gardiner LJ,Lucaci A,Steuernagel B,Wulff B,Kenny J,Hall N,Hall A

更新日期：2018-04-13 00:00:00

abstract：BACKGROUND:The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyse...

journal_title：BMC genomics

authors： Saatchi M,Beever JE,Decker JE,Faulkner DB,Freetly HC,Hansen SL,Yampara-Iquise H,Johnson KA,Kachman SD,Kerley MS,Kim J,Loy DD,Marques E,Neibergs HL,Pollak EJ,Schnabel RD,Seabury CM,Shike DW,Snelling WM,Spangler ML,

更新日期：2014-11-20 00:00:00

abstract：BACKGROUND:The Bacillus cereus sensu lato group currently includes seven species (B. cereus, B. anthracis, B. mycoides, B. pseudomycoides, B. thuringiensis, B. weihenstephanensis and B. cytotoxicus) that recent phylogenetic and phylogenomic analyses suggest are likely a single species, despite their varied phenotypes. ...

journal_title：BMC genomics

authors： Scott E 2nd,Dyer DW

更新日期：2012-10-22 00:00:00

abstract：BACKGROUND:In clinical and basic research custom panels for transcript profiling are gaining importance because only project specific informative genes are interrogated. This approach reduces costs and complexity of data analysis and allows multiplexing of samples. Polymerase-chain-reaction (PCR) based TaqMan assays ha...

journal_title：BMC genomics

authors： Zhang JD,Schindler T,Küng E,Ebeling M,Certa U

更新日期：2014-07-05 00:00:00

abstract：BACKGROUND:Obesity and phenotypic traits associated with this condition exhibit significant heritability in natural populations of most organisms. While a number of genes and genetic pathways have been implicated to play a role in obesity associated traits, the genetic architecture that underlies the natural variation ...

journal_title：BMC genomics

authors： Jumbo-Lucioni P,Ayroles JF,Chambers MM,Jordan KW,Leips J,Mackay TF,De Luca M

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:Two fifths of the world's population is at risk from dengue. The absence of effective drugs and vaccines leaves vector control as the primary intervention tool. Understanding dengue virus (DENV) host interactions is essential for the development of novel control strategies. The availability of genome sequenc...

journal_title：BMC genomics

authors： Guo X,Xu Y,Bian G,Pike AD,Xie Y,Xi Z

更新日期：2010-06-16 00:00:00

abstract：BACKGROUND:The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is dependent on an intricate gene regulatory program coordinated by a number of transcription factors and m...

journal_title：BMC genomics

authors： Chang LW,Viader A,Varghese N,Payton JE,Milbrandt J,Nagarajan R

更新日期：2013-02-06 00:00:00

abstract：BACKGROUND:Mitochondria are organelles that fulfill a fundamental role in cell bioenergetics, as well as in other processes like cell signaling and death. Small non-coding RNAs (sncRNA) are now being considered as pivotal post-transcriptional regulators, widening the landscape of their diversity and functions. In mamma...

journal_title：BMC genomics

authors： Larriba E,Rial E,Del Mazo J

更新日期：2018-08-28 00:00:00

abstract：BACKGROUND:Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) w...

journal_title：BMC genomics

authors： Bera BC,Virmani N,Kumar N,Anand T,Pavulraj S,Rash A,Elton D,Rash N,Bhatia S,Sood R,Singh RK,Tripathi BN

更新日期：2017-08-23 00:00:00

abstract：BACKGROUND:Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. scitamineum is a complex network system. However, to date, there is no report on the identificati...

journal_title：BMC genomics

authors： Su Y,Xiao X,Ling H,Huang N,Liu F,Su W,Zhang Y,Xu L,Muhammad K,Que Y

更新日期：2019-01-18 00:00:00

abstract：BACKGROUND:Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental...

journal_title：BMC genomics

authors： Dueck A,Evers M,Henz SR,Unger K,Eichner N,Merkl R,Berezikov E,Engelmann JC,Weigel D,Wenzl S,Meister G

更新日期：2016-11-02 00:00:00

abstract：BACKGROUND:Venomous animals incapacitate their prey using complex venoms that can contain hundreds of unique protein toxins. The realisation that many of these toxins may have pharmaceutical and insecticidal potential due to their remarkable potency and selectivity against target receptors has led to an explosion in th...

journal_title：BMC genomics

authors： Wood DL,Miljenović T,Cai S,Raven RJ,Kaas Q,Escoubas P,Herzig V,Wilson D,King GF

更新日期：2009-08-13 00:00:00

abstract：BACKGROUND:Mammalian genomes contain a large number (approximately 1000) of olfactory receptor (OR) genes, many of which (20 to 50%) are pseudogenes. OR gene transcription is not restricted to the olfactory epithelium, but is found in numerous tissues. Using microarray hybridization and RTqPCR, we analyzed the mRNA pro...

journal_title：BMC genomics

authors： Rimbault M,Robin S,Vaysse A,Galibert F

更新日期：2009-12-02 00:00:00

abstract：BACKGROUND:Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed ...

journal_title：BMC genomics

authors： Santana MF,Silva JC,Batista AD,Ribeiro LE,da Silva GF,de Araújo EF,de Queiroz MV

更新日期：2012-12-22 00:00:00

abstract：BACKGROUND:Toxigenic Vibrio cholerae serogroup O1 is the causative pathogen in the sixth and seventh cholera pandemics. Cholera toxin is the major virulent factor but other virulence and virulence-related factors play certain roles in the pathogenesis and survival in the host. Along with the evolution of the epidemic s...

journal_title：BMC genomics

authors： Li Z,Pang B,Wang D,Li J,Xu J,Fang Y,Lu X,Kan B

更新日期：2019-05-09 00:00:00

abstract：BACKGROUND:New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can...

journal_title：BMC genomics

authors： Stubben CJ,Duffield ML,Cooper IA,Ford DC,Gans JD,Karlyshev AV,Lingard B,Oyston PC,de Rochefort A,Song J,Wren BW,Titball RW,Wolinsky M

更新日期：2009-10-29 00:00:00

abstract：BACKGROUND:One member of the W family of human endogenous retroviruses (HERV) appears to have been functionally adopted by the human host. Nevertheless, a highly diversified and regulated transcription from a range of HERV-W elements has been observed in human tissues and cells. Aberrant expression of members of this f...

journal_title：BMC genomics

authors： Li F,Nellåker C,Yolken RH,Karlsson H

更新日期：2011-01-12 00:00:00

abstract：BACKGROUND: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, and nematodes. In this study, a comprehensive analysis of NBS-encoding genes within the whole cucumber...

journal_title：BMC genomics

authors： Wan H,Yuan W,Bo K,Shen J,Pang X,Chen J

更新日期：2013-02-19 00:00:00

abstract：BACKGROUND:Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of t...

journal_title：BMC genomics

authors： Huang X,Otecko NO,Peng M,Weng Z,Li W,Chen J,Zhong M,Zhong F,Jin S,Geng Z,Luo W,He D,Ma C,Han J,Ommeh SC,Zhang Y,Zhang X,Du B

更新日期：2020-04-20 00:00:00

abstract：BACKGROUND:Microarray gene expression (MAGE) signatures allow insights into the transcriptional processes of leukemias and may evolve as a molecular diagnostic test. Introduction of MAGE into clinical practice of leukemia diagnosis will require comprehensive assessment of variation due to the methodologies. Here we sys...

journal_title：BMC genomics

authors： Campo Dell'Orto M,Zangrando A,Trentin L,Li R,Liu WM,te Kronnie G,Basso G,Kohlmann A

更新日期：2007-06-22 00:00:00

abstract：BACKGROUND:Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measu...

journal_title：BMC genomics

authors： Rodriguez BA,Frankhouser D,Murphy M,Trimarchi M,Tam HH,Curfman J,Huang R,Chan MW,Lai HC,Parikh D,Ball B,Schwind S,Blum W,Marcucci G,Yan P,Bundschuh R

更新日期：2012-01-01 00:00:00