A kingdom-specific protein domain HMM library for improved annotation of fungal genomes.

abstract：BACKGROUND:Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited...

journal_title：BMC genomics

authors： Machida RJ,Hashiguchi Y,Nishida M,Nishida S

更新日期：2009-09-17 00:00:00

abstract：BACKGROUND:Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily spec...

journal_title：BMC genomics

authors： Yusuf D,Marz M,Stadler PF,Hofacker IL

更新日期：2010-07-13 00:00:00

abstract：BACKGROUND:Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21) is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB) disease in many cereals. Understanding the interaction between mycoviruses and plant pathogenic fungi is necessa...

journal_title：BMC genomics

authors： Cho WK,Yu J,Lee KM,Son M,Min K,Lee YW,Kim KH

更新日期：2012-05-06 00:00:00

abstract：BACKGROUND:Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a population. We previously identified a chromosomally encoded hok-sok type I TA system in Erwinia am...

journal_title：BMC genomics

authors： Peng J,Triplett LR,Sundin GW

更新日期：2021-01-22 00:00:00

abstract：BACKGROUND:The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constrain...

journal_title：BMC genomics

authors： Alam MT,Merlo ME,STREAM Consortium.,Hodgson DA,Wellington EM,Takano E,Breitling R

更新日期：2010-03-26 00:00:00

abstract：BACKGROUND:DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between...

journal_title：BMC genomics

authors： Sharifi-Zarchi A,Gerovska D,Adachi K,Totonchi M,Pezeshk H,Taft RJ,Schöler HR,Chitsaz H,Sadeghi M,Baharvand H,Araúzo-Bravo MJ

更新日期：2017-12-12 00:00:00

abstract：BACKGROUND:Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even after a short exposure to maternal obesity around the time of conception. The hypothesis of this work ...

journal_title：BMC genomics

authors： McCoski SR,Vailes MT,Owens CE,Cockrum RR,Ealy AD

更新日期：2018-10-11 00:00:00

abstract：BACKGROUND:Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon mobility in Drosophila somatic cells by poorly understood mechanisms. 21 nucleotide esiRNAs are primarily generated from retrotransposons and two inverted repeat (hairpin) loci in Drosophila culture cells in a Dicer2 dependent man...

journal_title：BMC genomics

authors： Harrington AW,McKain MR,Michalski D,Bauer KM,Daugherty JM,Steiniger M

更新日期：2017-04-17 00:00:00

abstract：BACKGROUND:The eutherian fibroblast growth factors were implicated as key regulators in developmental processes. However, there were major disagreements in descriptions of comprehensive eutherian fibroblast growth factors gene data sets including either 18 or 22 homologues. The present analysis attempted to revise and ...

journal_title：BMC genomics

authors： Premzl M

更新日期：2020-08-05 00:00:00

abstract：BACKGROUND:Copy neutral loss of heterozygosity (CN-LOH) refers to a special case of LOH occurring without any resulting loss in copy number. These alterations is sometimes seen in tumors as a way to inactivate a tumor suppressor gene and have been found to be important in several types of cancer. RESULTS:We have used ...

journal_title：BMC genomics

authors： Kryh H,Carén H,Erichsen J,Sjöberg RM,Abrahamsson J,Kogner P,Martinsson T

更新日期：2011-09-07 00:00:00

abstract：BACKGROUND:Tubulin isotypes and expression patterns are highly regulated in diverse organisms. The genome sequence of the protozoan parasite Leishmania major contains three distinct beta-tubulin loci. To investigate the diversity of beta-tubulin genes, we have compared the published genome sequence to draft genome sequ...

journal_title：BMC genomics

authors： Jackson AP,Vaughan S,Gull K

更新日期：2006-06-06 00:00:00

abstract：BACKGROUND:Human genetic variation produces the wide range of phenotypic differences that make us individual. However, little is known about the distribution of variation in the most conserved functional regions of the human genome. We examined whether different subsets of the conserved human genome have been subjected...

journal_title：BMC genomics

authors： Davidson S,Starkey A,MacKenzie A

更新日期：2009-12-16 00:00:00

abstract：BACKGROUND:The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly anal...

journal_title：BMC genomics

authors： Williams D,Trimble WL,Shilts M,Meyer F,Ochman H

更新日期：2013-08-08 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. ME...

journal_title：BMC genomics

authors： Wake C,Labadorf A,Dumitriu A,Hoss AG,Bregu J,Albrecht KH,DeStefano AL,Myers RH

更新日期：2016-10-04 00:00:00

abstract：BACKGROUND:Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Sho...

journal_title：BMC genomics

authors： Lu S,Le S,Tan Y,Li M,Liu C,Zhang K,Huang J,Chen H,Rao X,Zhu J,Zou L,Ni Q,Li S,Wang J,Jin X,Hu Q,Yao X,Zhao X,Zhang L,Huang G,Hu F

更新日期：2014-09-19 00:00:00

abstract：BACKGROUND:Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that chang...

journal_title：BMC genomics

authors： De Wit P,Durland E,Ventura A,Langdon CJ

更新日期：2018-02-22 00:00:00

abstract：BACKGROUND:Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneo...

journal_title：BMC genomics

authors： Li W,Wang X,Li C,Sun J,Li S,Peng M

更新日期：2019-06-24 00:00:00

abstract：BACKGROUND:Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA typing at high resolution is challenging even with whole-genome sequencing data. RESULTS:We have d...

journal_title：BMC genomics

authors： Nariai N,Kojima K,Saito S,Mimori T,Sato Y,Kawai Y,Yamaguchi-Kabata Y,Yasuda J,Nagasaki M

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina Methylation...

journal_title：BMC genomics

authors： Lee Y,Haftorn KL,Denault WRP,Nustad HE,Page CM,Lyle R,Lee-Ødegård S,Moen GH,Prasad RB,Groop LC,Sletner L,Sommer C,Magnus MC,Gjessing HK,Harris JR,Magnus P,Håberg SE,Jugessur A,Bohlin J

更新日期：2020-10-27 00:00:00

abstract：BACKGROUND:Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for s...

journal_title：BMC genomics

authors： Ma L,Wiggans GR,Wang S,Sonstegard TS,Yang J,Crooker BA,Cole JB,Van Tassell CP,Lawlor TJ,Da Y

更新日期：2012-10-06 00:00:00

abstract：BACKGROUND:Chronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinical complications of this pathological condition. Several reports have focused on the identification o...

journal_title：BMC genomics

authors： Granata S,Zaza G,Simone S,Villani G,Latorre D,Pontrelli P,Carella M,Schena FP,Grandaliano G,Pertosa G

更新日期：2009-08-21 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:Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objective...

journal_title：BMC genomics

authors： Leung WY,Marschall T,Paudel Y,Falquet L,Mei H,Schönhuth A,Maoz Moss TY

更新日期：2015-03-25 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:Anthocyanins are a group of flavonoid compounds. As a group of important secondary metabolites, they perform several key biological functions in plants. Anthocyanins also play beneficial health roles as potentially protective factors against cancer and heart disease. To elucidate the anthocyanin biosynthetic...

journal_title：BMC genomics

authors： Guo N,Cheng F,Wu J,Liu B,Zheng S,Liang J,Wang X

更新日期：2014-06-04 00:00:00

abstract：BACKGROUND:The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular path...

journal_title：BMC genomics

authors： Go JT,Belisle SE,Tchitchek N,Tumpey TM,Ma W,Richt JA,Safronetz D,Feldmann H,Katze MG

更新日期：2012-11-15 00:00:00

abstract：BACKGROUND:The Brassicaceae family is an exemplary model for studying plant polyploidy. The Brassicaceae knowledge-base includes the well-annotated Arabidopsis thaliana reference sequence; well-established evidence for three rounds of whole genome duplication (WGD); and the conservation of genomic structure, with 24 co...

journal_title：BMC genomics

authors： Kim J,Lee J,Choi JP,Park I,Yang K,Kim MK,Lee YH,Nou IS,Kim DS,Min SR,Park SU,Kim H

更新日期：2014-07-18 00:00:00

abstract：BACKGROUND:The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, Marburg virus is a member of the family Filoviridae that causes severe hemorrhagic fever disease i...

journal_title：BMC genomics

authors： Lee AK,Kulcsar KA,Elliott O,Khiabanian H,Nagle ER,Jones ME,Amman BR,Sanchez-Lockhart M,Towner JS,Palacios G,Rabadan R

更新日期：2015-12-07 00:00:00

abstract：BACKGROUND:Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal re...

journal_title：BMC genomics

authors： Pornsukarom S,van Vliet AHM,Thakur S

更新日期：2018-11-06 00:00:00

abstract：BACKGROUND:Bayesian mixture models in which the effects of SNP are assumed to come from normal distributions with different variances are attractive for simultaneous genomic prediction and QTL mapping. These models are usually implemented with Monte Carlo Markov Chain (MCMC) sampling, which requires long compute times ...

journal_title：BMC genomics

authors： Wang T,Chen YP,Bowman PJ,Goddard ME,Hayes BJ

更新日期：2016-09-21 00:00:00