Comparative genomics of downy mildews reveals potential adaptations to biotrophy.

abstract：BACKGROUND:Essential genes are indispensable for the survival of living entities. They are the cornerstones of synthetic biology, and are potential candidate targets for antimicrobial and vaccine design. DESCRIPTION:Here we describe the Cluster of Essential Genes (CEG) database, which contains clusters of orthologous ...

journal_title：BMC genomics

authors： Ye YN,Hua ZG,Huang J,Rao N,Guo FB

更新日期：2013-11-09 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: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:Sugarcane is an economically important crop contributing to about 80% of the world sugar production. Increasing efforts in molecular biological studies have been performed for improving the sugar yield and other relevant important agronomic traits. However, due to sugarcane's complicated genomes, it is still...

journal_title：BMC genomics

authors： Zhang Q,Hu W,Zhu F,Wang L,Yu Q,Ming R,Zhang J

更新日期：2016-02-01 00:00:00

abstract：BACKGROUND:The capsular polysaccharide is the principal virulence factor of Streptococcus pneumoniae and a target for current pneumococcal vaccines. However, some pathogenic pneumococci are serologically nontypeable [nontypeable pneumococci (NTPn)]. Due to their relative rarity, NTPn are poorly characterized, and, as s...

journal_title：BMC genomics

authors： Mohale T,Wolter N,Allam M,Ndlangisa K,Crowther-Gibson P,du Plessis M,von Gottberg A

更新日期：2016-06-22 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:Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousa...

journal_title：BMC genomics

authors： Toplak M,Curk T,Demsar J,Zupan B

更新日期：2010-01-22 00:00:00

abstract：BACKGROUND:The MYB superfamily is one of the most abundant transcription factor (TF) families in plants. MYB proteins include highly conserved N-terminal MYB repeats (1R, R2R3, 3R, and atypical) and various C-terminal sequences that confer extensive functions. However, the functions of most MYB genes are unknown, and h...

journal_title：BMC genomics

authors： Wang Z,Tang J,Hu R,Wu P,Hou XL,Song XM,Xiong AS

更新日期：2015-01-23 00:00:00

abstract：MOTIVATION:With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree estimation is difficult in the presence of gene tree discordance, which is often due to incomplete l...

journal_title：BMC genomics

authors： Bayzid MS,Hunt T,Warnow T

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized...

journal_title：BMC genomics

authors： Buiate EAS,Xavier KV,Moore N,Torres MF,Farman ML,Schardl CL,Vaillancourt LJ

更新日期：2017-01-10 00:00:00

abstract：BACKGROUND:Drosophila melanogaster females show changes in behavior and physiology after mating that are thought to maximize the number of progeny resulting from the most recent copulation. Sperm and seminal fluid proteins induce post-mating changes in females, however, very little is known about the resulting gene exp...

journal_title：BMC genomics

authors： Dalton JE,Kacheria TS,Knott SR,Lebo MS,Nishitani A,Sanders LE,Stirling EJ,Winbush A,Arbeitman MN

更新日期：2010-10-06 00:00:00

abstract：BACKGROUND:Sweet sorghum is an annual C4 crop considered to be one of the most promising bio-energy crops due to its high sugar content in stem, yet it is poorly understood how this plant increases its sugar content in response to salt stress. In response to high NaCl, many of its major processes, such as photosynthesi...

journal_title：BMC genomics

authors： Sui N,Yang Z,Liu M,Wang B

更新日期：2015-07-19 00:00:00

abstract：BACKGROUND:Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by f...

journal_title：BMC genomics

authors： Miao Z,Li D,Zhang Z,Dong J,Su Z,Wang T

更新日期：2012-02-06 00:00:00

abstract：BACKGROUND:Bacillus pumilus is a Gram-positive and endospore-forming bacterium broadly existing in a variety of environmental niches. Because it produces and secrets many industrially useful enzymes, a lot of studies have been done to understand the underlying mechanisms. Among them, scoC was originally identified as a...

journal_title：BMC genomics

authors： Han LL,Liu YC,Miao CC,Feng H

更新日期：2019-04-30 00:00:00

abstract：BACKGROUND:The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus c...

journal_title：BMC genomics

authors： Lang AS,Austin SH,Harris RM,Calisi RM,MacManes MD

更新日期：2020-03-23 00:00:00

abstract：BACKGROUND:Computational methods for the prediction of Major Histocompatibility Complex (MHC) class II binding peptides play an important role in facilitating the understanding of immune recognition and the process of epitope discovery. To develop an effective computational method, we need to consider two important cha...

journal_title：BMC genomics

authors： Guo L,Luo C,Zhu S

更新日期：2013-01-01 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 challenge of systems biology is the integration of new data into the preexisting, and then re-interpretation of the integrated data. Here we use readily available metaanalysis computational methods to integrate new data on the transcriptomic effects of EGF in primary human epidermal keratinocytes with pr...

journal_title：BMC genomics

authors： Blumenberg M

更新日期：2013-02-08 00:00:00

abstract：BACKGROUND:Laminitis, the structural failure of interdigitated tissue that suspends the distal skeleton within the hoof capsule, is a devastating disease that is the second leading cause of both lameness and euthanasia in the horse. Current transcriptomic research focuses on the expression of known genes. However, as t...

journal_title：BMC genomics

authors： Holl HM,Gao S,Fei Z,Andrews C,Brooks SA

更新日期：2015-10-03 00:00:00

abstract：BACKGROUND:Ophiocordyceps sinensis is an important traditional Chinese medicine for its comprehensive active ingredients, such as cordycepin, cordycepic acid, and Cordyceps polysaccharide. O. sinensis zjut, a special strain isolated from O. sinensis, has similar pharmacological functions to wild O. sinensis. Currently,...

journal_title：BMC genomics

authors： Zhang B,Li B,Men XH,Xu ZW,Wu H,Qin XT,Xu F,Teng Y,Yuan SJ,Jin LQ,Liu ZQ,Zheng YG

更新日期：2020-12-11 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:Miniature inverted repeat transposable element (MITE) is one type of transposable element (TE), which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only few MITEs were proved to be currently active and their physiological function remains largely unknown...

journal_title：BMC genomics

authors： Dong HT,Zhang L,Zheng KL,Yao HG,Chen J,Yu FC,Yu XX,Mao BZ,Zhao D,Yao J,Li DB

更新日期：2012-04-13 00:00:00

abstract：BACKGROUND:Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers as external clinical signs. However, there is no information about the changes produced by the wounds...

journal_title：BMC genomics

authors： Cordero H,Brinchmann MF,Cuesta A,Esteban MA

更新日期：2017-12-02 00:00:00

abstract：BACKGROUND:Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction endonucleases. We have proposed a method of restriction analysis of Alu repeats sequences in silico....

journal_title：BMC genomics

authors： Abdurashitov MA,Tomilov VN,Chernukhin VA,Degtyarev SKh

更新日期：2008-06-26 00:00:00

abstract：BACKGROUND:Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic anal...

journal_title：BMC genomics

authors： Dias O,Gombert AK,Ferreira EC,Rocha I

更新日期：2012-10-01 00:00:00

abstract：BACKGROUND:Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. RESULTS:In the current work, we carried out a bioinformatics analysis of...

journal_title：BMC genomics

authors： Iida K,Jin H,Zhu JK

更新日期：2009-04-09 00:00:00

abstract：BACKGROUND:Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomi...

journal_title：BMC genomics

authors： Butler JB,Vaillancourt RE,Potts BM,Lee DJ,King GJ,Baten A,Shepherd M,Freeman JS

更新日期：2017-05-22 00:00:00

abstract：BACKGROUND:Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is adapted to subtropical/temperate areas and is considered a source of high-quality cellulose; E. gr...

journal_title：BMC genomics

authors： Salazar MM,Nascimento LC,Camargo EL,Gonçalves DC,Lepikson Neto J,Marques WL,Teixeira PJ,Mieczkowski P,Mondego JM,Carazzolle MF,Deckmann AC,Pereira GA

更新日期：2013-03-22 00:00:00

abstract：BACKGROUND:Glycine max is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of G. max (domesticated soybean) as well as G. soja (wild soybean), both became available in 2010. This opened the door for comprehensive comparative genomic...

journal_title：BMC genomics

authors： Joshi T,Valliyodan B,Wu JH,Lee SH,Xu D,Nguyen HT

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Current ChIP-seq studies are interested in comparing multiple epigenetic profiles across several cell types and tissues simultaneously for studying constitutive and differential regulation. Simultaneous analysis of multiple epigenetic features in many samples can gain substantial power and specificity than a...

journal_title：BMC genomics

authors： Chen KB,Hardison R,Zhang Y

更新日期：2014-01-01 00:00:00