Accumulation of CTCF-binding sites drives expression divergence between tandemly duplicated genes in humans.

abstract：BACKGROUND:Hypoxia Inducible Factor (HIF) regulates a cascade of transcriptional events in response to decreased oxygenation, acting from the cellular to the physiological level. This response is evolutionarily conserved, allowing the use of zebrafish (Danio rerio) as a model for studying the hypoxic response. Activati...

journal_title：BMC genomics

authors： Greenald D,Jeyakani J,Pelster B,Sealy I,Mathavan S,van Eeden FJ

更新日期：2015-11-11 00:00:00

abstract：BACKGROUND:Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use ...

journal_title：BMC genomics

authors： Money D,Migicovsky Z,Gardner K,Myles S

更新日期：2017-07-10 00:00:00

abstract：BACKGROUND:The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyse...

journal_title：BMC genomics

authors： Saatchi M,Beever JE,Decker JE,Faulkner DB,Freetly HC,Hansen SL,Yampara-Iquise H,Johnson KA,Kachman SD,Kerley MS,Kim J,Loy DD,Marques E,Neibergs HL,Pollak EJ,Schnabel RD,Seabury CM,Shike DW,Snelling WM,Spangler ML,

更新日期：2014-11-20 00:00:00

abstract：BACKGROUND:Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallani...

journal_title：BMC genomics

authors： Zou H,Jakovlić I,Chen R,Zhang D,Zhang J,Li WX,Wang GT

更新日期：2017-11-02 00:00:00

abstract：BACKGROUND:Bacteroides thetaiotaomicron, a predominant member of the human gut microbiota, is characterized by its ability to utilize a wide variety of polysaccharides using the extensive saccharolytic machinery that is controlled by an expanded repertoire of transcription factors (TFs). The availability of genomic seq...

journal_title：BMC genomics

authors： Ravcheev DA,Godzik A,Osterman AL,Rodionov DA

更新日期：2013-12-12 00:00:00

abstract：BACKGROUND:Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported...

journal_title：BMC genomics

authors： Zhu S,Tang S,Tan Z,Yu Y,Dai Q,Liu T

更新日期：2017-01-10 00:00:00

abstract：BACKGROUND:The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Comparisons between same- and cross-species hybridisations were also made. Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed...

journal_title：BMC genomics

authors： Moody DE,Zou Z,McIntyre L

更新日期：2002-09-27 00:00:00

abstract：BACKGROUND:Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In ...

journal_title：BMC genomics

authors： Lautwein T,Lerch S,Schäfer D,Schmidt ER

更新日期：2015-07-22 00:00:00

abstract：BACKGROUND:Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepatocellular carcinoma (HCC) recurrence for application in clinical purposes. To overcome the limitati...

journal_title：BMC genomics

authors： Kim BY,Choi DW,Woo SR,Park ER,Lee JG,Kim SH,Koo I,Park SH,Han CJ,Kim SB,Yeom YI,Yang SJ,Yu A,Lee JW,Jang JJ,Cho MH,Jeon WK,Park YN,Suh KS,Lee KH

更新日期：2015-04-10 00:00:00

abstract：BACKGROUND:Nucleosomes facilitate the packaging of the eukaryotic genome and modulate the access of regulators to DNA. A detailed description of the nucleosomal organization under different transcriptional programmes is essential to understand their contribution to genomic regulation. RESULTS:To visualize the dynamics...

journal_title：BMC genomics

authors： Soriano I,Quintales L,Antequera F

更新日期：2013-11-21 00:00:00

abstract：BACKGROUND:Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or Illumina short-read low-coverage ...

journal_title：BMC genomics

authors： Baeza JA

更新日期：2020-12-09 00:00:00

abstract：BACKGROUND:Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pathogenic potential. RESULTS:We selected 25 representative strains within 16 V. cholerae serogrou...

journal_title：BMC genomics

authors： Li Z,Lu X,Wang D,Liang WL,Zhang J,Li J,Xu J,Pang B,Kan B

更新日期：2019-03-25 00:00:00

abstract：BACKGROUND:Gene duplication is an important biological phenomenon associated with genomic redundancy, degeneration, specialization, innovation, and speciation. After duplication, both copies continue functioning when natural selection favors duplicated protein function or expression, or when mutations make them functio...

journal_title：BMC genomics

authors： Chain FJ,Dushoff J,Evans BJ

更新日期：2011-12-12 00:00:00

abstract：BACKGROUND:Bovine papillomavirus (BPV) belongs to the Papillomaviridae family and infects epithelial cells of bovines and closely related animals, causing hyperproliferative lesions known as warts or papillomas, which may regress or progress to form benign or malignant tumors. The virus enters the host cell and interac...

journal_title：BMC genomics

authors： Barreto DM,Barros GS,Santos LABO,Soares RC,Batista MVA

更新日期：2018-12-19 00:00:00

abstract：BACKGROUND:The steady-state behaviour of gene regulatory networks (GRNs) can provide crucial evidence for detecting disease-causing genes. However, monitoring the dynamics of GRNs is particularly difficult because biological data only reflects a snapshot of the dynamical behaviour of the living organism. Also most GRN ...

journal_title：BMC genomics

authors： Kim H,Gelenbe E

更新日期：2009-12-03 00:00:00

abstract：:Following the publication of this article [1], the authors reported that the original shading in columns 3 and 4 of Table 3, which indicated the presence or absence of viruses in each library, had been removed during typesetting. ...

journal_title：BMC genomics

authors： Belda E,Nanfack-Minkeu F,Eiglmeier K,Carissimo G,Holm I,Diallo M,Diallo D,Vantaux A,Kim S,Sharakhov IV,Vernick KD

更新日期：2019-09-05 00:00:00

abstract：BACKGROUND:Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation. RESULTS:The analyses show that neighbou...

journal_title：BMC genomics

authors： Ng YK,Wu W,Zhang L

更新日期：2009-01-22 00:00:00

abstract：BACKGROUND:An important subfamily of membrane proteins are the transmembrane alpha-helical proteins, in which the membrane-spanning regions are made up of alpha-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmem...

journal_title：BMC genomics

authors： Yang JY,Yang MQ,Dunker AK,Deng Y,Huang X

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large variety of species and contexts has created an urgent need for the development of easy, time- and cos...

journal_title：BMC genomics

authors： Köferle A,Worf K,Breunig C,Baumann V,Herrero J,Wiesbeck M,Hutter LH,Götz M,Fuchs C,Beck S,Stricker SH

更新日期：2016-11-14 00:00:00

abstract：BACKGROUND:Two strains of the silver fox (Vulpes vulpes), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain a...

journal_title：BMC genomics

authors： Kukekova AV,Johnson JL,Teiling C,Li L,Oskina IN,Kharlamova AV,Gulevich RG,Padte R,Dubreuil MM,Vladimirova AV,Shepeleva DV,Shikhevich SG,Sun Q,Ponnala L,Temnykh SV,Trut LN,Acland GM

更新日期：2011-10-03 00:00:00

abstract：BACKGROUND:CCCH type zinc finger proteins are RNA binding proteins with regulatory functions at all stages of mRNA metabolism. The best-characterized member, tritetraproline (TTP), binds to AU rich elements in 3' UTRs of unstable mRNAs, mediating their degradation. In kinetoplastids, CCCH type zinc finger proteins have...

journal_title：BMC genomics

authors： Kramer S,Kimblin NC,Carrington M

更新日期：2010-05-05 00:00:00

abstract：BACKGROUND:Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI), which could be re...

journal_title：BMC genomics

authors： Toussaint J,Sieuwerts AM,Haibe-Kains B,Desmedt C,Rouas G,Harris AL,Larsimont D,Piccart M,Foekens JA,Durbecq V,Sotiriou C

更新日期：2009-09-10 00:00:00

abstract：BACKGROUND:Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this deterioration. Eggshell formation is a highly complex process under precise regulation of genes and bio...

journal_title：BMC genomics

authors： Feng J,Zhang HJ,Wu SG,Qi GH,Wang J

更新日期：2020-11-09 00:00:00

abstract：BACKGROUND:Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity,...

journal_title：BMC genomics

authors： English AC,Salerno WJ,Hampton OA,Gonzaga-Jauregui C,Ambreth S,Ritter DI,Beck CR,Davis CF,Dahdouli M,Ma S,Carroll A,Veeraraghavan N,Bruestle J,Drees B,Hastie A,Lam ET,White S,Mishra P,Wang M,Han Y,Zhang F,Stankie

更新日期：2015-04-11 00:00:00

abstract：BACKGROUND:Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. scitamineum is a complex network system. However, to date, there is no report on the identificati...

journal_title：BMC genomics

authors： Su Y,Xiao X,Ling H,Huang N,Liu F,Su W,Zhang Y,Xu L,Muhammad K,Que Y

更新日期：2019-01-18 00:00:00

abstract：BACKGROUND:Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a recognized pathogen for humans, little is known about how its transcriptional pattern is related...

journal_title：BMC genomics

authors： Wang L,Ma L,Leng W,Liu T,Yu L,Yang J,Yang L,Zhang W,Zhang Q,Dong J,Xue Y,Zhu Y,Xu X,Wan Z,Ding G,Yu F,Tu K,Li Y,Li R,Shen Y,Jin Q

更新日期：2006-10-11 00:00:00

abstract：BACKGROUND:Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, t...

journal_title：BMC genomics

authors： Zamani N,Russell P,Lantz H,Hoeppner MP,Meadows JR,Vijay N,Mauceli E,di Palma F,Lindblad-Toh K,Jern P,Grabherr MG

更新日期：2013-05-24 00:00:00

abstract：BACKGROUND:Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model organisms including zebrafish. Recently, long single-stranded DNA (lssDNA) molecules have been developed...

journal_title：BMC genomics

authors： Bai H,Liu L,An K,Lu X,Harrison M,Zhao Y,Yan R,Lu Z,Li S,Lin S,Liang F,Qin W

更新日期：2020-01-21 00:00:00

abstract：BACKGROUND:It is unclear whether improving feed efficiency by selection for low residual feed intake (RFI) compromises pigs' immunocompetence. Here, we aimed at investigating whether pig lines divergently selected for RFI had different inflammatory responses to lipopolysaccharide (LPS) exposure, regarding to clinical p...

journal_title：BMC genomics

authors： Liu H,Feye KM,Nguyen YT,Rakhshandeh A,Loving CL,Dekkers JCM,Gabler NK,Tuggle CK

更新日期：2019-10-11 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNA molecules that downregulate gene expression by base pairing to the 3'-untranslated region (UTR) of target messenger RNAs (mRNAs). Up to now, rare information for the miRNAs is available in decapod crustaceans. Our previous studies showed that many miRNA-binding sit...

journal_title：BMC genomics

authors： Song YN,Shi LL,Liu ZQ,Qiu GF

更新日期：2014-07-01 00:00:00