Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction.

abstract：BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of i...

journal_title：BMC genomics

authors： Cho YB,Lee EJ,Cho S,Kim TY,Park JH,Cho BK

更新日期：2016-02-29 00:00:00

abstract：BACKGROUND:Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant s...

journal_title：BMC genomics

authors： Li L,Briskine R,Schaefer R,Schnable PS,Myers CL,Flagel LE,Springer NM,Muehlbauer GJ

更新日期：2016-11-04 00:00:00

abstract：BACKGROUND:The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inference...

journal_title：BMC genomics

authors： Yang W,Rosenstiel PC,Schulenburg H

更新日期：2016-08-04 00:00:00

abstract：BACKGROUND:The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to...

journal_title：BMC genomics

authors： Sanchez-Alberola N,Campoy S,Barbé J,Erill I

更新日期：2012-02-03 00:00:00

abstract：BACKGROUND:Rhesus monkeys (Macaca mulatta) are widely-used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as cynomolgus monkeys (Macaca fascicularis), and to humans, sharing a last common ancestor from about 25 million years ago. Although rhesus monkeys have be...

journal_title：BMC genomics

authors： Kim DS,Huh JW,Kim YH,Park SJ,Lee SR,Chang KT

更新日期：2010-07-12 00:00:00

abstract：BACKGROUND:Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by the lack of a genome reference and the large computational requirements for analysing these data sets. RESULTS:DAWN (Diversity Among Wheat geNomes) integrates data from the T. aes...

journal_title：BMC genomics

authors： Watson-Haigh NS,Suchecki R,Kalashyan E,Garcia M,Baumann U

更新日期：2018-12-17 00:00:00

abstract：BACKGROUND:Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The...

journal_title：BMC genomics

authors： Mulley JF,Hargreaves AD,Hegarty MJ,Heller RS,Swain MT

更新日期：2014-12-06 00:00:00

abstract：BACKGROUND:The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies. RESULTS:We propose an intuitive and efficient algorithm, titled extreme MApping of OligoNucleotide (xMAN), to rapidly map millions of oligonucleotide fragments to a...

journal_title：BMC genomics

authors： Li W,Carroll JS,Brown M,Liu xS

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:A-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing ...

journal_title：BMC genomics

authors： Giacopuzzi E,Gennarelli M,Sacco C,Filippini A,Mingardi J,Magri C,Barbon A

更新日期：2018-12-27 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： Assefa AT,Vandesompele J,Thas O

更新日期：2020-06-03 00:00:00

abstract：BACKGROUND:We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS:By using simulated and real datasets we showed that our tool, based on read count approac...

journal_title：BMC genomics

authors： Magi A,Pippucci T,Sidore C

更新日期：2017-09-21 00:00:00

abstract：BACKGROUND:Fitness epistasis, the interaction effect of genes at different loci on fitness, makes an important contribution to adaptive evolution. Although fitness interaction evidence has been observed in model organisms, it is more difficult to detect and remains poorly understood in human populations as a result of ...

journal_title：BMC genomics

authors： Ni X,Zhou M,Wang H,He KY,Broeckel U,Hanis C,Kardia S,Redline S,Cooper RS,Tang H,Zhu X

更新日期：2020-07-11 00:00:00

abstract：:The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the billions of base-pairs of Archosaur sequence that have become available in the last few years. This editorial de...

journal_title：BMC genomics

authors： Bridges SM,Burgess SC,McCarthy FM

更新日期：2009-07-14 00:00:00

abstract：BACKGROUND:Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence T...

journal_title：BMC genomics

authors： Ponyared P,Ponsawat J,Tongsima S,Seresangtakul P,Akkasaeng C,Tantisuwichwong N

更新日期：2016-12-22 00:00:00

abstract：BACKGROUND:Short non-coding RNAs (ncRNAs) perform their cellular functions in ribonucleoprotein (RNP) complexes, which are also essential for maintaining the stability of the ncRNAs. Depletion of individual protein components of non-coding ribonucleoprotein (ncRNP) particles by RNA interference (RNAi) may therefore aff...

journal_title：BMC genomics

authors： Aftab MN,He H,Skogerbø G,Chen R

更新日期：2008-06-11 00:00:00

abstract：BACKGROUND:The androgen receptor plays a critical role throughout the progression of prostate cancer and is an important drug target for this disease. While chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) is becoming an essential tool for studying transcription and chromatin modifica...

journal_title：BMC genomics

authors： Zhu Z,Shi M,Hu W,Estrella H,Engebretsen J,Nichols T,Briere D,Hosea N,Los G,Rejto PA,Fanjul A

更新日期：2012-07-31 00:00:00

abstract：BACKGROUND:During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of genes in a genome. Our aim is to compute the evolutionary distance b...

journal_title：BMC genomics

authors： Cordonnier G,Lafond M

更新日期：2020-04-16 00:00:00

abstract：BACKGROUND:The desiccation-tolerant moss Bryum argenteum is an important component of the Biological Soil Crusts (BSCs) found in the Gurbantunggut desert. Desiccation tolerance is defined as the ability to revive from the air dried state. To elucidate the molecular mechanisms related to desiccation tolerance, we employ...

journal_title：BMC genomics

authors： Gao B,Zhang D,Li X,Yang H,Zhang Y,Wood AJ

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) worldwide. In spite of its agricultural importance, the genomics and genetics of the pathogen are poorly characterized. Pst transcripts from urediniospores and germinated ...

journal_title：BMC genomics

authors： Yin C,Chen X,Wang X,Han Q,Kang Z,Hulbert SH

更新日期：2009-12-23 00:00:00

abstract：BACKGROUND:Insertion sequences (ISs) are approximately 1 kbp long "jumping" genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I ("cut-and-paste") Mobile Genetic Elements. ISs are proposed to be involve...

journal_title：BMC genomics

authors： Vigil-Stenman T,Larsson J,Nylander JA,Bergman B

更新日期：2015-03-17 00:00:00

abstract：BACKGROUND:The reconstruction of gene regulatory networks from high-throughput "omics" data has become a major goal in the modelling of living systems. Numerous approaches have been proposed, most of which attempt only "one-shot" reconstruction of the whole network with no intervention from the user, or offer only simp...

journal_title：BMC genomics

authors： Kadupitige SR,Leung KC,Sellmeier J,Sivieng J,Catchpoole DR,Bain ME,Gaëta BA

更新日期：2009-12-03 00:00:00

abstract：BACKGROUND:Higher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Ma...

journal_title：BMC genomics

authors： Koyama T,Asakawa S,Katagiri T,Shimizu A,Fagutao FF,Mavichak R,Santos MD,Fuji K,Sakamoto T,Kitakado T,Kondo H,Shimizu N,Aoki T,Hirono I

更新日期：2010-02-26 00:00:00

abstract：BACKGROUND:Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effects on splicing of other sequence variations are difficult to predict. Loosely defined exonic and int...

journal_title：BMC genomics

authors： Lastella P,Surdo NC,Resta N,Guanti G,Stella A

更新日期：2006-09-22 00:00:00

abstract：BACKGROUND:Gene expression profiling is a promising approach to better estimate patient prognosis; however, there are still unresolved problems, including little overlap among similarly developed gene sets and poor performance of a developed gene set in other datasets. RESULTS:We applied a gene sets approach to develo...

journal_title：BMC genomics

authors： Kim SY,Kim YS

更新日期：2008-04-16 00:00:00

abstract：BACKGROUND:Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. RESULTS:This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, us...

journal_title：BMC genomics

authors： Jin L,Li G,Yu D,Huang W,Cheng C,Liao S,Wu Q,Zhang Y

更新日期：2017-02-06 00:00:00

abstract：BACKGROUND:Due to the high morbidity and mortality of fulminant hepatitis, early diagnosis followed by early effective treatment is the key for prognosis improvement. So far, little is known about the gene expression changes in the early stage of this serious illness. Identification of the genes related to the very ear...

journal_title：BMC genomics

authors： Chen F,Zhu HH,Zhou LF,Li J,Zhao LY,Wu SS,Wang J,Liu W,Chen Z

更新日期：2010-04-15 00:00:00

abstract：BACKGROUND:Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnan...

journal_title：BMC genomics

authors： Zheng J,Liu L,Wang J,Jin Q

更新日期：2013-11-11 00:00:00

abstract：BACKGROUND:As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+...

journal_title：BMC genomics

authors： Yu N,Guo X,Zelikovsky A,Pan Y

更新日期：2017-05-24 00:00:00

abstract：BACKGROUND:Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the pre...

journal_title：BMC genomics

authors： Chen J,Dong X,Li Q,Zhou X,Gao S,Chen R,Sun L,Zhang L,Chen W

更新日期：2013-12-05 00:00:00

abstract：BACKGROUND:There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limit...

journal_title：BMC genomics

authors： Garcia-Seco D,Zhang Y,Gutierrez-Mañero FJ,Martin C,Ramos-Solano B

更新日期：2015-01-22 00:00:00