Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure.

abstract：BACKGROUND:Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or stuck fermentations. Selection and development of new Saccharomyces cerevisiae strains well adapted a...

journal_title：BMC genomics

authors： López-Malo M,García-Rios E,Melgar B,Sanchez MR,Dunham MJ,Guillamón JM

更新日期：2015-07-22 00:00:00

abstract：BACKGROUND:The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent a...

journal_title：BMC genomics

authors： Canals R,Xia XQ,Fronick C,Clifton SW,Ahmer BM,Andrews-Polymenis HL,Porwollik S,McClelland M

更新日期：2012-05-30 00:00:00

abstract：BACKGROUND:The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to...

journal_title：BMC genomics

authors： McGuire AM,Weiner B,Park ST,Wapinski I,Raman S,Dolganov G,Peterson M,Riley R,Zucker J,Abeel T,White J,Sisk P,Stolte C,Koehrsen M,Yamamoto RT,Iacobelli-Martinez M,Kidd MJ,Maer AM,Schoolnik GK,Regev A,Galagan J

更新日期：2012-03-28 00:00:00

abstract：BACKGROUND:Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown...

journal_title：BMC genomics

authors： Zhang L,Zuo K,Zhang F,Cao Y,Wang J,Zhang Y,Sun X,Tang K

更新日期：2006-12-25 00:00:00

abstract：BACKGROUND:Many reptiles exhibit temperature-dependent sex determination (TSD). The initial cue in TSD is incubation temperature, unlike genotypic sex determination (GSD) where it is determined by the presence of specific alleles (or genetic loci). We used patterns of gene expression to identify candidates for genes wi...

journal_title：BMC genomics

authors： Chojnowski JL,Braun EL

更新日期：2012-07-15 00:00:00

abstract：BACKGROUND:Photorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strain P. luminescens subsp. laumondii TT01, which was originally isolated in Trinidad and Tobago, has...

journal_title：BMC genomics

authors： Zamora-Lagos MA,Eckstein S,Langer A,Gazanis A,Pfeiffer F,Habermann B,Heermann R

更新日期：2018-11-29 00:00:00

abstract：BACKGROUND:Designing sustainable animal production systems that better balance productivity and resistance to disease is a major concern. In order to address questions related to immunity and resistance to disease in pig, it is necessary to increase knowledge on its immune system and to produce efficient tools dedicate...

journal_title：BMC genomics

authors： Gao Y,Flori L,Lecardonnel J,Esquerré D,Hu ZL,Teillaud A,Lemonnier G,Lefèvre F,Oswald IP,Rogel-Gaillard C

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consistin...

journal_title：BMC genomics

authors： Jones SI,Gonzalez DO,Vodkin LO

更新日期：2010-02-24 00:00:00

abstract：BACKGROUND:Microsatellites (repeated subsequences based on motifs of one to six nucleotides) are widely used as codominant genetic markers because of their frequent polymorphism and relative selective neutrality. Minisatellites are repeats of motifs having seven or more nucleotides. The large number of EST sequences no...

journal_title：BMC genomics

authors： Crane CF

更新日期：2007-06-15 00:00:00

abstract：BACKGROUND:Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopoly...

journal_title：BMC genomics

authors： Ivády G,Madar L,Dzsudzsák E,Koczok K,Kappelmayer J,Krulisova V,Macek M Jr,Horváth A,Balogh I

更新日期：2018-02-21 00:00:00

abstract：BACKGROUND:In the model legume Medicago truncatula, the near saturation genome-wide Tnt1 insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified many Tnt1 mutants defective in nodule development and symbiotic nitrogen fixation (SNF). However...

journal_title：BMC genomics

authors： Veerappan V,Jani M,Kadel K,Troiani T,Gale R,Mayes T,Shulaev E,Wen J,Mysore KS,Azad RK,Dickstein R

更新日期：2016-02-27 00:00:00

abstract：BACKGROUND:Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ascomycetes associated with the adaptive radiation of the leotiom...

journal_title：BMC genomics

authors： McDonald TR,Mueller O,Dietrich FS,Lutzoni F

更新日期：2013-04-04 00:00:00

abstract：BACKGROUND:Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between...

journal_title：BMC genomics

authors： Yan J,Chuai G,Qi T,Shao F,Zhou C,Zhu C,Yang J,Yu Y,Shi C,Kang N,He Y,Liu Q

更新日期：2017-01-25 00:00:00

abstract：BACKGROUND:Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines ...

journal_title：BMC genomics

authors： Allan CW,Matzkin LM

更新日期：2019-10-12 00:00:00

abstract：:DpbCasX, also called Cas12e, is an RNA-guided DNA endonuclease isolated from Deltaproteobacteria. In this paper I characterized the CasX-compatible genome editing sites in the reference genomes of yeast (Saccharomyces cerevisiae), flatworms (Caenorhabditis elegans), flies (Drosophila melanogaster), zebrafish (Danio re...

journal_title：BMC genomics

authors： Roberson EDO

更新日期：2019-06-27 00:00:00

abstract：BACKGROUND:White spot syndrome (WSS) is a viral disease that affects most of the commercially important shrimps and causes serious economic losses to the shrimp farming industry worldwide. However, little information is available in terms of the molecular mechanisms of the host-virus interaction. In this study, we used...

journal_title：BMC genomics

authors： Leu JH,Chang CC,Wu JL,Hsu CW,Hirono I,Aoki T,Juan HF,Lo CF,Kou GH,Huang HC

更新日期：2007-05-16 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are mobile genetic sequences that randomly propagate within their host's genome. This mobility has the potential to affect gene transcription and cause disease. However, TEs are technically challenging to identify, which complicates efforts to assess the impact of TE insertions on...

journal_title：BMC genomics

authors： Kvikstad EM,Piazza P,Taylor JC,Lunter G

更新日期：2018-02-01 00:00:00

abstract：BACKGROUND:Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report ...

journal_title：BMC genomics

authors： Merrill BD,Grose JH,Breakwell DP,Burnett SH

更新日期：2014-08-30 00:00:00

abstract：BACKGROUND:Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex t...

journal_title：BMC genomics

authors： Freebern E,Santos DJA,Fang L,Jiang J,Parker Gaddis KL,Liu GE,VanRaden PM,Maltecca C,Cole JB,Ma L

更新日期：2020-01-13 00:00:00

abstract：BACKGROUND:Ras-related proteins in brain (Rab)-family proteins are key members of the membrane trafficking pathway in cells. In addition, these proteins have been identified to have diverse functions such as cross-talking with different kinases and playing a role in cellular signaling. However, only a few Rab proteins ...

journal_title：BMC genomics

authors： Kumar S,Lee HJ,Park HS,Lee K

更新日期：2016-10-10 00:00:00

abstract：BACKGROUND:Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserv...

journal_title：BMC genomics

authors： Tats A,Tenson T,Remm M

更新日期：2008-10-08 00:00:00

abstract：BACKGROUND:5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway, and is the target of the herbicide glyphosate. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous cop...

journal_title：BMC genomics

authors： Aramrak A,Kidwell KK,Steber CM,Burke IC

更新日期：2015-10-23 00:00:00

abstract：BACKGROUND:Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In area...

journal_title：BMC genomics

authors： Jacob CG,Tan JC,Miller BA,Tan A,Takala-Harrison S,Ferdig MT,Plowe CV

更新日期：2014-08-26 00:00:00

abstract：BACKGROUND:Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. ...

journal_title：BMC genomics

authors： Buongermino Pereira M,Österlund T,Eriksson KM,Backhaus T,Axelson-Fisk M,Kristiansson E

更新日期：2020-07-20 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 Pacific oyster Crassostrea gigas is an important fishery resource that is sensitive to temperature fluctuations. Thus, it has evolved a protection mechanism against heat stress by increasing the expression of the gene coding for heat shock protein (HSP) 70 under elevated temperatures. In other animals, h...

journal_title：BMC genomics

authors： Liu Y,Li L,Huang B,Wang W,Zhang G

更新日期：2019-08-08 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:Microarray-based Comparative Genomic Hybridisation (CGH) has been used to assess genetic variability between bacterial strains. Crucial for interpretation of microarray data is the availability of a reference to compare signal intensities to reliably determine presence or divergence each DNA fragment. Howeve...

journal_title：BMC genomics

authors： Carpaij N,Fluit AC,Lindsay JA,Bonten MJ,Willems RJ

更新日期：2009-11-13 00:00:00

abstract：BACKGROUND:Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which ...

journal_title：BMC genomics

authors： Brown CW,Sridhara V,Boutz DR,Person MD,Marcotte EM,Barrick JE,Wilke CO

更新日期：2017-04-17 00:00:00

abstract：BACKGROUND:Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the pa...

journal_title：BMC genomics

authors： Fletcher K,Klosterman SJ,Derevnina L,Martin F,Bertier LD,Koike S,Reyes-Chin-Wo S,Mou B,Michelmore R

更新日期：2018-11-29 00:00:00