Bayesian prediction of bacterial growth temperature range based on genome sequences.

abstract：BACKGROUND:Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. A...

journal_title：BMC genomics

authors： Ding Y,Chen M,Liu Z,Ding D,Ye Y,Zhang M,Kelly R,Guo L,Su Z,Harris SC,Qian F,Ge W,Fang H,Xu X,Tong W

更新日期：2012-07-20 00:00:00

abstract：BACKGROUND:Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and thre...

journal_title：BMC genomics

authors： Amiri Ghanatsaman Z,Wang GD,Asadollahpour Nanaei H,Asadi Fozi M,Peng MS,Esmailizadeh A,Zhang YP

更新日期：2020-03-04 00:00:00

abstract：BACKGROUND:In recent years, dozens of Arabidopsis and rice CCCH-type zinc finger genes have been functionally studied, many of which confer important traits, such as abiotic and biotic stress tolerance, delayed leaf senescence and improved plant architecture. Switchgrass (Panicum virgatum) is an important bioenergy cro...

journal_title：BMC genomics

authors： Yuan S,Xu B,Zhang J,Xie Z,Cheng Q,Yang Z,Cai Q,Huang B

更新日期：2015-02-25 00:00:00

abstract：BACKGROUND:Understanding the underlying genetic structure of human populations is of fundamental interest to both biological and social sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation. The most widely used methods for col...

journal_title：BMC genomics

authors： Maróti Z,Boldogkői Z,Tombácz D,Snyder M,Kalmár T

更新日期：2018-10-29 00:00:00

abstract：BACKGROUND:Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: elements of different families do not cooperate, but they independently fight for their survival in ...

journal_title：BMC genomics

authors： Marco A,Marín I

更新日期：2008-05-14 00:00:00

abstract：BACKGROUND:Cytochrome P450s (CYPs) in animals fall into two categories: those that synthesize or metabolize endogenous molecules and those that interact with exogenous chemicals from the diet or the environment. The latter form a critical component of detoxification systems. RESULTS:Data mining and manual curation of ...

journal_title：BMC genomics

authors： Baldwin WS,Marko PB,Nelson DR

更新日期：2009-04-21 00:00:00

abstract：BACKGROUND:Porcine circovirus type 2 (PCV2) is the causal agent of postweaning multisystemic wasting syndrome (PMWS), which has severely impacted the swine industry worldwide. PCV2 triggers a weak and atypical innate immune response, but the key genes and mechanisms by which the virus interferes with host innate immuni...

journal_title：BMC genomics

authors： Li W,Liu S,Wang Y,Deng F,Yan W,Yang K,Chen H,He Q,Charreyre C,Audoneet JC

更新日期：2013-05-27 00:00:00

abstract：BACKGROUND:Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. Francisella tularensis is a highly pathogenic Gram-negative bacterium that causes the disease tularaemia in humans and animals. Relatively little is known about the regulatory networks exi...

journal_title：BMC genomics

authors： Postic G,Frapy E,Dupuis M,Dubail I,Livny J,Charbit A,Meibom KL

更新日期：2010-11-10 00:00:00

abstract：BACKGROUND:Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species with large and highly repetitive genomes, the acquisition of whole genome...

journal_title：BMC genomics

authors： Morishige DT,Klein PE,Hilley JL,Sahraeian SM,Sharma A,Mullet JE

更新日期：2013-07-05 00:00:00

abstract：BACKGROUND:Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecula...

journal_title：BMC genomics

authors： Ma L,Ma Q,Li X,Cheng L,Li K,Li S

更新日期：2014-03-09 00:00:00

abstract：BACKGROUND:Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Mol...

journal_title：BMC genomics

authors： Ginolhac A,Vilstrup J,Stenderup J,Rasmussen M,Stiller M,Shapiro B,Zazula G,Froese D,Steinmann KE,Thompson JF,Al-Rasheid KA,Gilbert TM,Willerslev E,Orlando L

更新日期：2012-05-10 00:00:00

abstract：BACKGROUND:Tandemly arranged nuclear ribosomal DNA (rDNA), encoding 18S, 5.8S and 26S ribosomal RNA (rRNA), exhibit concerted evolution, a pattern thought to result from the homogenisation of rDNA arrays. However rDNA homogeneity at the single nucleotide polymorphism (SNP) level has not been detailed in organisms with ...

journal_title：BMC genomics

authors： Matyášek R,Renny-Byfield S,Fulneček J,Macas J,Grandbastien MA,Nichols R,Leitch A,Kovařík A

更新日期：2012-12-23 00:00:00

abstract：BACKGROUND:Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a criti...

journal_title：BMC genomics

authors： Xia Y,Luo W,Yuan S,Zheng Y,Zeng X

更新日期：2018-12-07 00:00:00

abstract：BACKGROUND:Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis w...

journal_title：BMC genomics

authors： Cheng D,Tan M,Yu H,Li L,Zhu D,Chen Y,Jiang M

更新日期：2018-09-26 00:00:00

abstract：BACKGROUND:Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage...

journal_title：BMC genomics

authors： Natali L,Cossu RM,Barghini E,Giordani T,Buti M,Mascagni F,Morgante M,Gill N,Kane NC,Rieseberg L,Cavallini A

更新日期：2013-10-06 00:00:00

abstract：BACKGROUND:Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable b...

journal_title：BMC genomics

authors： Christopherson MR,Dawson JA,Stevenson DM,Cunningham AC,Bramhacharya S,Weimer PJ,Kendziorski C,Suen G

更新日期：2014-12-04 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes at the post-transcriptional level in spatiotemporal manner. Several miRNAs are identified as prognostic and diagnostic markers in many human cancers. Estimation of the temporal activities of the miRNAs is an important step in the way to underst...

journal_title：BMC genomics

authors： Jayavelu ND,Bar N

更新日期：2015-12-18 00:00:00

abstract：BACKGROUND:Mytilisepta virgata is a marine mussel commonly found along the coasts of Japan. Although this species has been the subject of occasional studies concerning its ecological role, growth and reproduction, it has been so far almost completely neglected from a genetic and molecular point of view. In the present ...

journal_title：BMC genomics

authors： Gerdol M,Fujii Y,Hasan I,Koike T,Shimojo S,Spazzali F,Yamamoto K,Ozeki Y,Pallavicini A,Fujita H

更新日期：2017-08-08 00:00:00

abstract：BACKGROUND:Colon cancer occurrence is increasing worldwide, making it the third most frequent cancer. Although many therapeutic options are available and quite efficient at the early stages, survival is strongly decreased when the disease has spread to other organs. The identification of molecular markers of colon canc...

journal_title：BMC genomics

authors： Durand S,Trillet K,Uguen A,Saint-Pierre A,Le Jossic-Corcos C,Corcos L

更新日期：2017-09-30 00:00:00

abstract：BACKGROUND:There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in promising applications such as gaining insights into bacterial drug resistance. RESULTS:Here, we propos...

journal_title：BMC genomics

authors： Wozniak M,Wong L,Tiuryn J

更新日期：2011-01-01 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:Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work toget...

journal_title：BMC genomics

authors： Wei W,Mesquita ACO,Figueiró AA,Wu X,Manjunatha S,Wickland DP,Hudson ME,Juliatti FC,Clough SJ

更新日期：2017-11-07 00:00:00

abstract：BACKGROUND:Hop (Humulus lupulus L.) is an economically important plant forming organogenic nodules which can be used for genetic transformation and micropropagation. We are interested in the mechanisms underlying reprogramming of cells through stress and hormone treatments. RESULTS:An integrated molecular and metabolo...

journal_title：BMC genomics

authors： Fortes AM,Santos F,Choi YH,Silva MS,Figueiredo A,Sousa L,Pessoa F,Santos BA,Sebastiana M,Palme K,Malhó R,Verpoorte R,Pais MS

更新日期：2008-09-29 00:00:00

abstract：BACKGROUND:The cellular proteome and metabolome are underlying dynamic regulation allowing rapid adaptation to changes in the environment. System-wide analysis of these dynamics will provide novel insights into mechanisms of stress adaptation for higher photosynthetic organisms. We applied pulsed-SILAC labeling to a ph...

journal_title：BMC genomics

authors： Mastrobuoni G,Irgang S,Pietzke M,Assmus HE,Wenzel M,Schulze WX,Kempa S

更新日期：2012-05-31 00:00:00

abstract：BACKGROUND:With advances in next generation sequencing technology and analysis methods, single nucleotide variants (SNVs) and indels can be detected with high sensitivity and specificity in exome sequencing data. Recent studies have demonstrated the ability to detect disease-causing copy number variants (CNVs) in exome...

journal_title：BMC genomics

authors： Samarakoon PS,Sorte HS,Stray-Pedersen A,Rødningen OK,Rognes T,Lyle R

更新日期：2016-01-14 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:Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in rec...

journal_title：BMC genomics

authors： Jiao Y,Jia HM,Li XW,Chai ML,Jia HJ,Chen Z,Wang GY,Chai CY,van de Weg E,Gao ZS

更新日期：2012-05-23 00:00:00

abstract：BACKGROUND:The Spemann/Mangold organizer is a transient tissue critical for patterning the gastrula stage vertebrate embryo and formation of the three germ layers. Despite its important role during development, there are still relatively few genes with specific expression in the organizer and its derivatives. Foxa2 is ...

journal_title：BMC genomics

authors： Tamplin OJ,Kinzel D,Cox BJ,Bell CE,Rossant J,Lickert H

更新日期：2008-10-30 00:00:00

abstract：BACKGROUND:Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of ...

journal_title：BMC genomics

authors： Van Zee JP,Schlueter JA,Schlueter S,Dixon P,Sierra CA,Hill CA

更新日期：2016-03-16 00:00:00

abstract：BACKGROUND:Cultivated peanut (Arachis hypogaea L.) is an important oil and protein crop, but it has low disease resistance; therefore, it is important to reveal the number, sequence features, function, and evolution of genes that confer resistance. Nucleotide-binding site-leucine-rich repeats (NBS-LRRs) are resistance ...

journal_title：BMC genomics

authors： Song H,Guo Z,Hu X,Qian L,Miao F,Zhang X,Chen J

更新日期：2019-11-13 00:00:00