Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs.

abstract：BACKGROUND:Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contexts such as developmental stages and tissue types. Experimental methods to study in vivo binding, inc...

journal_title：BMC genomics

authors： Zhong S,He X,Bar-Joseph Z

更新日期：2013-11-15 00:00:00

abstract：BACKGROUND:Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Singl...

journal_title：BMC genomics

authors： Childs LH,Witucka-Wall H,Günther T,Sulpice R,Korff MV,Stitt M,Walther D,Schmid KJ,Altmann T

更新日期：2010-03-20 00:00:00

abstract：BACKGROUND:Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease f...

journal_title：BMC genomics

authors： Tremblay DC,Alexander G Jr,Moseley S,Chadwick BP

更新日期：2010-11-15 00:00:00

abstract：BACKGROUND:While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gen...

journal_title：BMC genomics

authors： Tulpan D,Leger S,Tchagang A,Pan Y

更新日期：2015-04-15 00:00:00

abstract：BACKGROUND:Nucleosome positioning has an important role in gene regulation. However, dynamic positioning in vivo casts doubt on the reliability of predictions based on DNA sequence characteristics. What role does sequence-dependent positioning play? In this paper, using a curvature profile model, nucleosomes are predic...

journal_title：BMC genomics

authors： Liu H,Duan X,Yu S,Sun X

更新日期：2011-01-27 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:On a single strand of genomic DNA the number of As is usually about equal to the number of Ts (and similarly for Gs and Cs), but deviations have been noted for transcribed regions and origins of replication. RESULTS:The mouse genome is shown to have a segmented structure defined by strand bias. Transcriptio...

journal_title：BMC genomics

authors： Evans KJ

更新日期：2008-01-14 00:00:00

abstract：BACKGROUND:Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel t...

journal_title：BMC genomics

authors： Garg G,Ranganathan S

更新日期：2011-11-30 00:00:00

abstract：BACKGROUND:Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received l...

journal_title：BMC genomics

authors： Huang X,Wang F,Singh R,Reinert JA,Engelke MC,Genovesi AD,Chandra A,Yu Q

更新日期：2016-08-08 00:00:00

abstract：BACKGROUND:Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transcriptome (RNA-Seq) and metabolome analysis (UPLC-MS/MS) to identify structural and regulatory genes a...

journal_title：BMC genomics

authors： Zhou Z,Gao H,Ming J,Ding Z,Lin X,Zhan R

更新日期：2020-10-22 00:00:00

abstract：BACKGROUND:Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamica...

journal_title：BMC genomics

authors： Li S,Dong X,Su Z

更新日期：2013-07-30 00:00:00

abstract：BACKGROUND:Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, de...

journal_title：BMC genomics

authors： Powell AJ,Conant GC,Brown DE,Carbone I,Dean RA

更新日期：2008-03-28 00:00:00

abstract：BACKGROUND:Cadmium (Cd) is a severe detrimental environmental pollutant. To adapt to Cd-induced deleterious effects, plants have evolved sophisticated defence mechanisms. In this study, a genome-wide transcriptome analysis was performed to identify the mechanisms of Cd tolerance using two barley genotypes with distinct...

journal_title：BMC genomics

authors： Cao F,Chen F,Sun H,Zhang G,Chen ZH,Wu F

更新日期：2014-07-19 00:00:00

abstract：BACKGROUND:In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can ...

journal_title：BMC genomics

authors： Teran Hidalgo SJ,Wu M,Ma S

更新日期：2017-08-16 00:00:00

abstract：BACKGROUND:Genome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic variances, leaving a substantial portion of genetic heritability unexplained. As a result, searches for "m...

journal_title：BMC genomics

authors： Chen Q,Sun F

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:The milk fat profile of the Danish Holstein (DH) and Danish Jersey (DJ) show clear differences. Identification of the genomic regions, genes and biological pathways underlying the milk fat biosynthesis will improve the understanding of the biology underlying bovine milk fat production and may provide new pos...

journal_title：BMC genomics

authors： Buitenhuis B,Janss LL,Poulsen NA,Larsen LB,Larsen MK,Sørensen P

更新日期：2014-12-15 00:00:00

abstract：BACKGROUND:Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of word embedding. RESULTS:From a pure data-driven fashion, we trained a 200-dimension vector represe...

journal_title：BMC genomics

authors： Du J,Jia P,Dai Y,Tao C,Zhao Z,Zhi D

更新日期：2019-02-04 00:00:00

abstract：BACKGROUND:Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction betwe...

journal_title：BMC genomics

authors： Omotajo D,Tate T,Cho H,Choudhary M

更新日期：2015-08-14 00:00:00

abstract：BACKGROUND:Accurate identification of synteny blocks is an important step in comparative genomics towards the understanding of genome architecture and expression. Most computer programs developed in the last decade for identifying synteny blocks have limitations. To address these limitations, we recently developed a ro...

journal_title：BMC genomics

authors： Vergara IA,Chen N

更新日期：2010-09-24 00:00:00

abstract：BACKGROUND:Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ, which suggests its cells have distinctive molecular regulation. Although several studies have looke...

journal_title：BMC genomics

authors： Zhang JZ,Zhao K,Ai XY,Hu CG

更新日期：2014-10-13 00:00:00

abstract：BACKGROUND:Three-dimensional (3D) multicellular spheroids of mesenchymal stem cells (MSCs) are generally regarded to have beneficial properties over MSCs in monolayer. Recent literatures have documented that MSCs can self-assemble into 3D spheroids with a greater capacity for differentiation into various cell types whe...

journal_title：BMC genomics

authors： Yeh HY,Liu BH,Sieber M,Hsu SH

更新日期：2014-01-05 00:00:00

abstract：BACKGROUND:The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. Its persistence in the stomach mucosa is facilitated by several mechanisms of immune evasion and immune modulation, but also by an unusual genetic variability which might account for the capability to adapt to chan...

journal_title：BMC genomics

authors： Fischer W,Breithaupt U,Kern B,Smith SI,Spicher C,Haas R

更新日期：2014-04-27 00:00:00

abstract：BACKGROUND:Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone...

journal_title：BMC genomics

authors： Bhagwate AV,Liu Y,Winham SJ,McDonough SJ,Stallings-Mann ML,Heinzen EP,Davila JI,Vierkant RA,Hoskin TL,Frost M,Carter JM,Radisky DC,Cunningham JM,Degnim AC,Wang C

更新日期：2019-09-02 00:00:00

abstract：BACKGROUND:The use of dispersants can be an effective way to deal with acute oil spills to limit environmental damage, however very little is known about whether chemically dispersed oil have the same toxic effect on marine organisms as mechanically dispersed oil. We exposed Atlantic cod larvae to chemically and mechan...

journal_title：BMC genomics

authors： Olsvik PA,Lie KK,Nordtug T,Hansen BH

更新日期：2012-12-14 00:00:00

abstract：BACKGROUND:High-throughput genotyping platforms play important roles in plant genomic studies. Cotton (Gossypium spp.) is the world's important natural textile fiber and oil crop. Upland cotton accounts for more than 90% of the world's cotton production, however, modern upland cotton cultivars have narrow genetic diver...

journal_title：BMC genomics

authors： Cai C,Zhu G,Zhang T,Guo W

更新日期：2017-08-23 00:00:00

abstract：BACKGROUND:Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the div...

journal_title：BMC genomics

authors： Wang S,Yang C,Zhao X,Chen S,Qu GZ

更新日期：2018-12-20 00:00:00

abstract：BACKGROUND:The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the gen...

journal_title：BMC genomics

authors： Dia N,Lavie L,Faye N,Méténier G,Yeramian E,Duroure C,Toguebaye BS,Frutos R,Niang MN,Vivarès CP,Ben Mamoun C,Cornillot E

更新日期：2016-01-07 00:00:00

abstract：BACKGROUND:Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primaril...

journal_title：BMC genomics

authors： Grusz AL,Rothfels CJ,Schuettpelz E

更新日期：2016-08-30 00:00:00

abstract：BACKGROUND:Human Malaria is transmitted by mosquitoes of the genus Anopheles. Transmission is a complex phenomenon involving biological and environmental factors of humans, parasites and mosquitoes. Among more than 500 anopheline species, only a few species from different branches of the mosquito evolutionary tree tran...

journal_title：BMC genomics

authors： Martínez-Barnetche J,Gómez-Barreto RE,Ovilla-Muñoz M,Téllez-Sosa J,García López DE,Dinglasan RR,Ubaida Mohien C,MacCallum RM,Redmond SN,Gibbons JG,Rokas A,Machado CA,Cazares-Raga FE,González-Cerón L,Hernández-Martínez S,Rod

更新日期：2012-05-30 00:00:00

abstract：BACKGROUND:Magnesium (Mg)-deficiency is frequently observed in Citrus plantations and is responsible for the loss of productivity and poor fruit quality. Knowledge on the effects of Mg-deficiency on upstream targets is scarce. Seedlings of 'Xuegan' [Citrus sinensis (L.) Osbeck] were irrigated with Mg-deficient (0 mM Mg...

journal_title：BMC genomics

authors： Peng HY,Qi YP,Lee J,Yang LT,Guo P,Jiang HX,Chen LS

更新日期：2015-03-31 00:00:00