Comparative proteome analysis of Saccharomyces cerevisiae: a global overview of in vivo targets of the yeast activator protein 1.

abstract：BACKGROUND:The disease caused by Haemonchus contortus, a blood-feeding nematode of small ruminants, is of major economic importance worldwide. The infective third-stage larva (L3) of this gastric nematode is enclosed in a cuticle (sheath) and, once ingested with herbage by the host, undergoes an exsheathment process th...

journal_title：BMC genomics

authors： Cantacessi C,Campbell BE,Young ND,Jex AR,Hall RS,Presidente PJ,Zawadzki JL,Zhong W,Aleman-Meza B,Loukas A,Sternberg PW,Gasser RB

更新日期：2010-04-27 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:Previously, we could show that L-lactate affects cultured bovine granulosa cells (GC) in a specific manner driving the cells into an early pre-ovulatory phenotype. Here we studied genome wide effects in L-lactate-treated GC to further elucidate the underlying mechanisms that are responsible for the L-lactate...

journal_title：BMC genomics

authors： Baufeld A,Koczan D,Vanselow J

更新日期：2019-04-05 00:00:00

abstract：BACKGROUND:Flow cytometry has been widely used for the diagnosis of various hematopoietic diseases. Although there have been advances in the number of biomarkers that can be analyzed simultaneously and technologies that enable fast performance, the diagnostic data are still interpreted by a manual gating strategy. The ...

journal_title：BMC genomics

authors： Shih MC,Huang SH,Donohue R,Chang CC,Zu Y

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Cells transformed by human adenoviruses (Ad) exhibit differential capacities to induce tumours in immunocompetent rodents; for example, Ad12-transformed rodent cells are oncogenic whereas Ad5-transformed cells are not. The E1A gene determines oncogenic phenotype, is a transcriptional regulator and dysregulat...

journal_title：BMC genomics

authors： Strath J,Georgopoulos LJ,Kellam P,Blair GE

更新日期：2009-02-06 00:00:00

abstract：BACKGROUND:The recent advance of high-throughput sequencing makes it feasible to study entire transcriptomes through the application of de novo sequence assembly algorithms. While a popular strategy is to first construct an intermediate de Bruijn graph structure to represent the transcriptome, an additional step is nee...

journal_title：BMC genomics

authors： Sze SH,Tarone AM

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri ('Dangshansuli', an Asian pear) and Pyrus communis ('Bartlett', a European pear) genomes, but the patterns of ge...

journal_title：BMC genomics

authors： Sun M,Zhang M,Singh J,Song B,Tang Z,Liu Y,Wang R,Qin M,Li J,Khan A,Wu J

更新日期：2020-11-19 00:00:00

abstract：BACKGROUND:Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds...

journal_title：BMC genomics

authors： Calviño M,Bruggmann R,Messing J

更新日期：2011-07-08 00:00:00

abstract：BACKGROUND:DNA methylation is associated with aberrant gene expression in cancer, and has been shown to correlate with therapeutic response and disease prognosis in some types of cancer. We sought to investigate the biological significance of DNA methylation in lung cancer. RESULTS:We integrated the gene expression pr...

journal_title：BMC genomics

authors： Lin SH,Wang J,Saintigny P,Wu CC,Giri U,Zhang J,Menju T,Diao L,Byers L,Weinstein JN,Coombes KR,Girard L,Komaki R,Wistuba II,Date H,Minna JD,Heymach JV

更新日期：2014-12-08 00:00:00

abstract：BACKGROUND:Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequenc...

journal_title：BMC genomics

authors： Kochan KJ,Amaral ME,Agarwala R,Schäffer AA,Riggs PK

更新日期：2008-11-17 00:00:00

abstract：BACKGROUND:Chemosensory receptors including olfactory receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) play a central role in sensing chemical signals and guiding insect behaviours, and are potential target genes in insect pest control. The cotton bollworm Helicoverpa armigera is one of the mos...

journal_title：BMC genomics

authors： Liu NY,Xu W,Papanicolaou A,Dong SL,Anderson A

更新日期：2014-07-15 00:00:00

abstract：BACKGROUND:Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and th...

journal_title：BMC genomics

authors： Lopes-Ramos CM,Paulson JN,Chen CY,Kuijjer ML,Fagny M,Platig J,Sonawane AR,DeMeo DL,Quackenbush J,Glass K

更新日期：2017-09-12 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by targeting specific mRNA species for degradation or interfering with translation. Specific miRNAs are key regulators of adipogenesis, and are expressed at different levels in adipose tissue from lean and obese mice. The deg...

journal_title：BMC genomics

authors： Link JC,Hasin-Brumshtein Y,Cantor RM,Chen X,Arnold AP,Lusis AJ,Reue K

更新日期：2017-01-17 00:00:00

abstract：BACKGROUND:Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are composed of structural and/or functional domains, of which many appear in multiple proteins. Once a domain is characterized in on...

journal_title：BMC genomics

authors： Kemmer D,Podowski RM,Arenillas D,Lim J,Hodges E,Roth P,Sonnhammer EL,Höög C,Wasserman WW

更新日期：2006-03-13 00:00:00

abstract：BACKGROUND:Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5-245 gigabases) and produce structurally unique and biologically active polyketide secondary metabolites. Although polyketide biosynthesis is well studied in terrestrial and freshwater organisms, only rec...

journal_title：BMC genomics

authors： Beedessee G,Hisata K,Roy MC,Satoh N,Shoguchi E

更新日期：2015-11-14 00:00:00

abstract：BACKGROUND:Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recent...

journal_title：BMC genomics

authors： Rainer J,Meraviglia V,Blankenburg H,Piubelli C,Pramstaller PP,Paolin A,Cogliati E,Pompilio G,Sommariva E,Domingues FS,Rossini A

更新日期：2018-06-25 00:00:00

abstract：BACKGROUND:Leishmania (L) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex interplay then takes place between the macrophage (MPhi) striving to eliminate the pathogen and the pa...

journal_title：BMC genomics

authors： Guerfali FZ,Laouini D,Guizani-Tabbane L,Ottones F,Ben-Aissa K,Benkahla A,Manchon L,Piquemal D,Smandi S,Mghirbi O,Commes T,Marti J,Dellagi K

更新日期：2008-05-21 00:00:00

abstract：BACKGROUND:Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. RESULTS:In this study, we identified a...

journal_title：BMC genomics

authors： Liu YC,Chen WL,Kung WH,Huang HD

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:The papaya Y chromosome has undergone a degenerative expansion from its ancestral autosome, as a consequence of recombination suppression in the sex determining region of the sex chromosomes. The non-recombining feature led to the accumulation of repetitive sequences in the male- or hermaphrodite-specific re...

journal_title：BMC genomics

authors： Na JK,Wang J,Ming R

更新日期：2014-05-04 00:00:00

abstract：BACKGROUND:Sequencing of the approximately 1.7 billion bases of the zebrafish genome is currently underway. To date, few high resolution genetic maps exist for the zebrafish genome, based mainly on single nucleotide polymorphisms (SNPs) and short microsatellite repeats. The desire to construct a higher resolution genet...

journal_title：BMC genomics

authors： Rouchka EC

更新日期：2010-06-01 00:00:00

abstract：BACKGROUND:Macrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused by Macrobrachium rosenbergii nodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on ho...

journal_title：BMC genomics

authors： Pasookhush P,Hindmarch C,Sithigorngul P,Longyant S,Bendena WG,Chaivisuthangkura P

更新日期：2019-10-22 00:00:00

abstract：BACKGROUND:One of the key characters of social insects is the division of labor, in which different tasks are allocated to various castes. In termites, one of the representative groups of social insects, morphological differences as well as behavioral differences can be recognized among castes. However, very little is ...

journal_title：BMC genomics

authors： Ishikawa Y,Okada Y,Ishikawa A,Miyakawa H,Koshikawa S,Miura T

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese jujube (Ziziphus jujuba Mill.) is the largest type of dried fruit tree in China in terms of production,...

journal_title：BMC genomics

authors： Xue C,Li H,Liu Z,Wang L,Zhao Y,Wei X,Fang H,Liu M,Zhao J

更新日期：2019-06-07 00:00:00

abstract：BACKGROUND:Controlling gene expression is fundamental to biological complexity. The nematode Caenorhabditis elegans is an important model for studying principles of gene regulation in multi-cellular organisms. A comprehensive parts list of putative regulatory motifs was yet missing for this model system. In this study,...

journal_title：BMC genomics

authors： Dieterich C,Sommer RJ

更新日期：2008-01-23 00:00:00

abstract：BACKGROUND: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 recently described in these species, further sequencing efforts are required to establish a comple...

journal_title：BMC genomics

authors： Benzekri H,Armesto P,Cousin X,Rovira M,Crespo D,Merlo MA,Mazurais D,Bautista R,Guerrero-Fernández D,Fernandez-Pozo N,Ponce M,Infante C,Zambonino JL,Nidelet S,Gut M,Rebordinos L,Planas JV,Bégout ML,Claros MG,Manchado

更新日期：2014-11-03 00:00:00

abstract：MOTIVATION:Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to integrate various modules and evaluate them from a systems point of view. RESUL...

journal_title：BMC genomics

authors： Sun Y,Braga-Neto U,Dougherty ER

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Accurate identification of synteny blocks is an important step in comparative genomics towards the understanding of genome architecture and expression. Most computer programs developed in the last decade for identifying synteny blocks have limitations. To address these limitations, we recently developed a ro...

journal_title：BMC genomics

authors： Vergara IA,Chen N

更新日期：2010-09-24 00:00:00

abstract：BACKGROUND:Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicate...

journal_title：BMC genomics

authors： De Maayer P,Chan WY,Rubagotti E,Venter SN,Toth IK,Birch PR,Coutinho TA

更新日期：2014-05-27 00:00:00

abstract：BACKGROUND:Alternative σ factors are important transcriptional regulators in bacteria. While σ(B) has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σ(H) has not yet been well defined in Listeria, even though σ(H) c...

journal_title：BMC genomics

authors： Liu Y,Orsi RH,Boor KJ,Wiedmann M,Guariglia-Oropeza V

更新日期：2016-02-16 00:00:00

abstract：BACKGROUND:Identifying the genotypes underlying human disease phenotypes is a fundamental step in human genetics and medicine. High-throughput genomic technologies provide thousands of genetic variants per individual. The causal genes of a specific phenotype are usually expected to be functionally close to each other. ...

journal_title：BMC genomics

authors： Itan Y,Mazel M,Mazel B,Abhyankar A,Nitschke P,Quintana-Murci L,Boisson-Dupuis S,Boisson B,Abel L,Zhang SY,Casanova JL

更新日期：2014-04-03 00:00:00