Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins.

abstract：BACKGROUND:Streptococcus infantarius subsp. infantarius (Sii) belongs to the Streptococcus bovis/Streptococcus equinus complex associated with several human and animal infections. Sii is a predominant bacterium in spontaneously fermented milk products in Africa. The genome sequence of Sii strain CJ18 was compared with ...

journal_title：BMC genomics

authors： Jans C,Follador R,Hochstrasser M,Lacroix C,Meile L,Stevens MJ

更新日期：2013-03-22 00:00:00

abstract：BACKGROUND:Genome-wide disease-gene finding approaches may sometimes provide us with a long list of candidate genes. Since using pure experimental approaches to verify all candidates could be expensive, a number of network-based methods have been developed to prioritize candidates. Such tools usually have a set of para...

journal_title：BMC genomics

authors： Hsu CL,Huang YH,Hsu CT,Yang UC

更新日期：2011-11-30 00:00:00

abstract：BACKGROUND:Detoxification in the liver involves activation of nuclear receptors, such as the constitutive androstane receptor (CAR), which regulate downstream genes of xenobiotic metabolism. Frequently, the metabolism of endobiotics is also modulated, resulting in potentially harmful effects. We therefore used 1,4-Bis ...

journal_title：BMC genomics

authors： Rezen T,Tamasi V,Lövgren-Sandblom A,Björkhem I,Meyer UA,Rozman D

更新日期：2009-08-19 00:00:00

abstract：BACKGROUND:In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective val...

journal_title：BMC genomics

authors： van Hijum SA,de Jong A,Baerends RJ,Karsens HA,Kramer NE,Larsen R,den Hengst CD,Albers CJ,Kok J,Kuipers OP

更新日期：2005-05-20 00:00:00

abstract：BACKGROUND:The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes efficiently. RESULTS:This work focuses on providing a tool for dis...

journal_title：BMC genomics

authors： Dziadkiewicz P,Dojer N

更新日期：2020-04-16 00:00:00

abstract：BACKGROUND:It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene m...

journal_title：BMC genomics

authors： López-Barragán MJ,Lemieux J,Quiñones M,Williamson KC,Molina-Cruz A,Cui K,Barillas-Mury C,Zhao K,Su XZ

更新日期：2011-11-30 00:00:00

abstract：BACKGROUND:Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid) and this bipartite genome structure is characteristic for most R. solanacearum strains. To determine whether the megaplasmid was acquired...

journal_title：BMC genomics

authors： Coenye T,Vandamme P

更新日期：2003-03-17 00:00:00

abstract：BACKGROUND:Cotton, one of the world's leading crops, is important to the world's textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction of a plant-transformation-competent binary bacterial artificial ...

journal_title：BMC genomics

authors： Lee MK,Zhang Y,Zhang M,Goebel M,Kim HJ,Triplett BA,Stelly DM,Zhang HB

更新日期：2013-03-28 00:00:00

abstract：BACKGROUND:The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar h...

journal_title：BMC genomics

authors： Ralph SG,Chun HJ,Cooper D,Kirkpatrick R,Kolosova N,Gunter L,Tuskan GA,Douglas CJ,Holt RA,Jones SJ,Marra MA,Bohlmann J

更新日期：2008-01-29 00:00:00

abstract：BACKGROUND:Developing effective strategies to reveal modular structures in protein interaction networks is crucial for better understanding of molecular mechanisms of underlying biological processes. In this paper, we propose a new density-based algorithm (ADHOC) for clustering vertices of a protein interaction network...

journal_title：BMC genomics

authors： Liu C,Li J,Zhao Y

更新日期：2010-12-02 00:00:00

abstract：BACKGROUND:Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model organisms including zebrafish. Recently, long single-stranded DNA (lssDNA) molecules have been developed...

journal_title：BMC genomics

authors： Bai H,Liu L,An K,Lu X,Harrison M,Zhao Y,Yan R,Lu Z,Li S,Lin S,Liang F,Qin W

更新日期：2020-01-21 00:00:00

abstract：BACKGROUND:To generate specific transcript profiles, one must isolate homogenous cell populations using techniques that often yield small amounts of RNA, requiring researchers to employ RNA amplification methods. The data generated by using these methods must be extensively evaluated to determine any technique dependen...

journal_title：BMC genomics

authors： Gold D,Coombes K,Medhane D,Ramaswamy A,Ju Z,Strong L,Koo JS,Kapoor M

更新日期：2004-01-06 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:The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's...

journal_title：BMC genomics

authors： Krishna A,Biryukov M,Trefois C,Antony PM,Hussong R,Lin J,Heinäniemi M,Glusman G,Köglsberger S,Boyd O,van den Berg BH,Linke D,Huang D,Wang K,Hood L,Tholey A,Schneider R,Galas DJ,Balling R,May P

更新日期：2014-12-20 00:00:00

abstract：BACKGROUND:With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal r...

journal_title：BMC genomics

authors： Dharmawardhana P,Brunner AM,Strauss SH

更新日期：2010-03-04 00:00:00

abstract：BACKGROUND:About 6 million Americans suffer from heart failure and 70% of heart failure cases are caused by myocardial infarction (MI). Following myocardial infarction, increased cytokines induce two major types of macrophages: classically activated macrophages which contribute to extracellular matrix destruction and a...

journal_title：BMC genomics

authors： Wang Y,Yang T,Ma Y,Halade GV,Zhang J,Lindsey ML,Jin YF

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the m...

journal_title：BMC genomics

authors： Shen Y,Wang L,Fu J,Xu X,Yue GH,Li J

更新日期：2019-06-07 00:00:00

abstract：BACKGROUND:Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a criti...

journal_title：BMC genomics

authors： Xia Y,Luo W,Yuan S,Zheng Y,Zeng X

更新日期：2018-12-07 00:00:00

abstract：BACKGROUND:The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression and defence against exogenous and endogenous genetic elements (viruses and transposable elements). The vast majority of endogenous small RNAs produced by the siRNA and piRNA pathways originate from repet...

journal_title：BMC genomics

authors： Biryukova I,Ye T

更新日期：2015-04-10 00:00:00

abstract：BACKGROUND:Finger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, and sulphur containing amino acids. In addition, it has C4 photosynthetic carbon assimilation mech...

journal_title：BMC genomics

authors： Hittalmani S,Mahesh HB,Shirke MD,Biradar H,Uday G,Aruna YR,Lohithaswa HC,Mohanrao A

更新日期：2017-06-15 00:00:00

abstract：BACKGROUND:Oomycetes are a group of filamentous microorganisms that includes both animal and plant pathogens and causes major agricultural losses. Phytophthora species can infect most crops and plants from natural ecosystems. Despite their tremendous economic and ecologic importance, few effective methods exist for lim...

journal_title：BMC genomics

authors： Attard A,Evangelisti E,Kebdani-Minet N,Panabières F,Deleury E,Maggio C,Ponchet M,Gourgues M

更新日期：2014-06-29 00:00:00

abstract：BACKGROUND:Human Malaria is transmitted by mosquitoes of the genus Anopheles. Transmission is a complex phenomenon involving biological and environmental factors of humans, parasites and mosquitoes. Among more than 500 anopheline species, only a few species from different branches of the mosquito evolutionary tree tran...

journal_title：BMC genomics

authors： Martínez-Barnetche J,Gómez-Barreto RE,Ovilla-Muñoz M,Téllez-Sosa J,García López DE,Dinglasan RR,Ubaida Mohien C,MacCallum RM,Redmond SN,Gibbons JG,Rokas A,Machado CA,Cazares-Raga FE,González-Cerón L,Hernández-Martínez S,Rod

更新日期：2012-05-30 00:00:00

abstract：BACKGROUND:Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking environment-friendly and cost-effective green methods in agricultural production becomes crucial nowaday...

journal_title：BMC genomics

authors： Zhou L,Song C,Li Z,Kuipers OP

更新日期：2021-01-07 00:00:00

abstract：BACKGROUND:The ascomycete fungus Zymoseptoria tritici (synonyms: Mycosphaerella graminicola, Septoria tritici) is a major pathogen of wheat that causes the economically important foliar disease Septoria tritici blotch. Despite its importance as a pathogen, little is known about the reaction of this fungus to light. To ...

journal_title：BMC genomics

authors： McCorison CB,Goodwin SB

更新日期：2020-07-25 00:00:00

abstract：BACKGROUND:The tetraploid durum wheat (Triticum turgidum L. ssp. durum Desf. Husnot) is an important crop which provides the raw material for pasta production and a valuable source of genetic diversity for breeding hexaploid wheat (Triticum aestivum L.). Future breeding efforts to enhance yield potential and climate re...

journal_title：BMC genomics

authors： Vendramin V,Ormanbekova D,Scalabrin S,Scaglione D,Maccaferri M,Martelli P,Salvi S,Jurman I,Casadio R,Cattonaro F,Tuberosa R,Massi A,Morgante M

更新日期：2019-04-10 00:00:00

abstract：BACKGROUND:Previous studies show that galanin neurons in ventrolateral preoptic nucleus (VLPO-Gal) are essential for sleep regulation. Here, we explored the transcriptional regulation of the VLPO-Gal neurons in sleep by comparing their transcriptional responses between sleeping mice and those kept awake, sacrificed at ...

journal_title：BMC genomics

authors： Guo X,Gao X,Keenan BT,Zhu J,Sarantopoulou D,Lian J,Galante RJ,Grant GR,Pack AI

更新日期：2020-09-14 00:00:00

abstract：BACKGROUND:Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the com...

journal_title：BMC genomics

authors： Wang JT,Li JT,Zhang XF,Sun XW

更新日期：2012-03-19 00:00:00

abstract：BACKGROUND:Nitrogen (N) is a key macronutrient required for plant growth and development. In this study, watermelon plants were grown under hydroponic conditions at 0.2 mM N, 4.5 mM N, and 9 mM N for 14 days. RESULTS:Dry weight and photosynthetic assimilation at low N (0.2 mM) was reduced by 29 and 74% compared with h...

journal_title：BMC genomics

authors： Nawaz MA,Chen C,Shireen F,Zheng Z,Sohail H,Afzal M,Ali MA,Bie Z,Huang Y

更新日期：2018-06-13 00:00:00

abstract：BACKGROUND:RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular i...

journal_title：BMC genomics

authors： Fu Y,Wu PH,Beane T,Zamore PD,Weng Z

更新日期：2018-07-13 00:00:00

abstract：BACKGROUND:Genomic imprinting is an evolutionary conserved mechanism of epigenetic gene regulation in placental mammals that results in silencing of one of the parental alleles. In order to decipher interactions between allele-specific DNA methylation of imprinted genes and evolutionary conservation, we performed a gen...

journal_title：BMC genomics

authors： Hutter B,Bieg M,Helms V,Paulsen M

更新日期：2010-11-22 00:00:00