A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation.

abstract：BACKGROUND:Dystonia1 (DYT1) dystonia is caused by a glutamic acid deletion (ΔE) mutation in the gene encoding Torsin A in humans (HTorA). To investigate the unknown molecular and cellular mechanisms underlying DYT1 dystonia, we performed an unbiased proteomic analysis. RESULTS:We found that the amount of proteins and ...

journal_title：BMC genomics

authors： Kim AY,Seo JB,Kim WT,Choi HJ,Kim SY,Morrow G,Tanguay RM,Steller H,Koh YH

更新日期：2015-04-23 00:00:00

abstract：BACKGROUND:Genome-scale metabolic models (GSMM) integrating transcriptomics have been widely used to study cancer metabolism. This integration is achieved through logical rules that describe the association between genes, proteins, and reactions (GPRs). However, current gene-to-reaction formulation lacks the stoichiome...

journal_title：BMC genomics

authors： Marín de Mas I,Torrents L,Bedia C,Nielsen LK,Cascante M,Tauler R

更新日期：2019-08-15 00:00:00

abstract：BACKGROUND:Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneo...

journal_title：BMC genomics

authors： Li W,Wang X,Li C,Sun J,Li S,Peng M

更新日期：2019-06-24 00:00:00

abstract：BACKGROUND:Hepatitis C virus (HCV) is a rapidly evolving RNA virus that has been classified into seven genotypes. All HCV genotypes cause chronic hepatitis, which ultimately leads to liver diseases such as cirrhosis. The genotypes are unevenly distributed across the globe, with genotypes 1 and 3 being the most prevalen...

journal_title：BMC genomics

authors： Bull RA,Eltahla AA,Rodrigo C,Koekkoek SM,Walker M,Pirozyan MR,Betz-Stablein B,Toepfer A,Laird M,Oh S,Heiner C,Maher L,Schinkel J,Lloyd AR,Luciani F

更新日期：2016-03-17 00:00:00

abstract：BACKGROUND:Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recent...

journal_title：BMC genomics

authors： Rainer J,Meraviglia V,Blankenburg H,Piubelli C,Pramstaller PP,Paolin A,Cogliati E,Pompilio G,Sommariva E,Domingues FS,Rossini A

更新日期：2018-06-25 00:00:00

abstract：BACKGROUND:Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induce...

journal_title：BMC genomics

authors： Cohen D,Bogeat-Triboulot MB,Tisserant E,Balzergue S,Martin-Magniette ML,Lelandais G,Ningre N,Renou JP,Tamby JP,Le Thiec D,Hummel I

更新日期：2010-11-12 00:00:00

abstract：BACKGROUND:Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights into common disease mechanisms shared among tumors, which is important for guiding treatment and pr...

journal_title：BMC genomics

authors： Chen V,Paisley J,Lu X

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear how different waves of human migrations in South America contributed to the evolution of strain d...

journal_title：BMC genomics

authors： Devi SM,Ahmed I,Khan AA,Rahman SA,Alvi A,Sechi LA,Ahmed N

更新日期：2006-07-27 00:00:00

abstract：BACKGROUND:Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regio...

journal_title：BMC genomics

authors： Ramos E,Levinson BT,Chasnoff S,Hughes A,Young AL,Thornton K,Li A,Vallania FL,Province M,Druley TE

更新日期：2012-12-06 00:00:00

abstract：BACKGROUND:Venomous animals incapacitate their prey using complex venoms that can contain hundreds of unique protein toxins. The realisation that many of these toxins may have pharmaceutical and insecticidal potential due to their remarkable potency and selectivity against target receptors has led to an explosion in th...

journal_title：BMC genomics

authors： Wood DL,Miljenović T,Cai S,Raven RJ,Kaas Q,Escoubas P,Herzig V,Wilson D,King GF

更新日期：2009-08-13 00:00:00

abstract：BACKGROUND:Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insigh...

journal_title：BMC genomics

authors： Parmakelis A,Kotsakiozi P,Kontos CK,Adamopoulos PG,Scorilas A

更新日期：2017-06-28 00:00:00

abstract：BACKGROUND:Despite substantial progress in mosquito genomic and genetic research, few cis-regulatory elements (CREs), DNA sequences that control gene expression, have been identified in mosquitoes or other non-model insects. Formaldehyde-assisted isolation of regulatory elements paired with DNA sequencing, FAIRE-seq, i...

journal_title：BMC genomics

authors： Behura SK,Sarro J,Li P,Mysore K,Severson DW,Emrich SJ,Duman-Scheel M

更新日期：2016-05-10 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:Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene d...

journal_title：BMC genomics

authors： Jiang J,Gu J,Zhang L,Zhang C,Deng X,Dou T,Zhao G,Zhou Y

更新日期：2015-02-14 00:00:00

abstract：BACKGROUND:Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of severa...

journal_title：BMC genomics

authors： Boschiero C,Gheyas AA,Ralph HK,Eory L,Paton B,Kuo R,Fulton J,Preisinger R,Kaiser P,Burt DW

更新日期：2015-07-31 00:00:00

abstract：BACKGROUND:Sub-optimal developmental diets often have adverse effects on long-term fitness and health. One hypothesis is that such effects are caused by mismatches between the developmental and adult environment, and may be mediated by persistent changes in gene expression. However, there are few experimental tests of ...

journal_title：BMC genomics

authors： May CM,Zwaan BJ

更新日期：2017-08-22 00:00:00

abstract：BACKGROUND:Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA) from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been ide...

journal_title：BMC genomics

authors： Siqueira FM,de Morais GL,Higashi S,Beier LS,Breyer GM,de Sá Godinho CP,Sagot MF,Schrank IS,Zaha A,de Vasconcelos AT

更新日期：2016-10-25 00:00:00

abstract：BACKGROUND:The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular path...

journal_title：BMC genomics

authors： Go JT,Belisle SE,Tchitchek N,Tumpey TM,Ma W,Richt JA,Safronetz D,Feldmann H,Katze MG

更新日期：2012-11-15 00:00:00

abstract：BACKGROUND:Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 is also involved in vascular redox cell signaling. PDIA1 is coded by the P4HB gene. While forced chan...

journal_title：BMC genomics

authors： Kajihara D,Hon CC,Abdullah AN,Wosniak J Jr,Moretti AIS,Poloni JF,Bonatto D,Hashimoto K,Carninci P,Laurindo FRM

更新日期：2020-11-04 00:00:00

abstract：BACKGROUND:Prostaglandin E2 (PGE2) is involved in several chronic inflammatory diseases including periodontitis, which causes loss of the gingival tissue and alveolar bone supporting the teeth. We have previously shown that tumor necrosis factor alpha (TNFalpha) induces PGE2 synthesis in gingival fibroblasts. In this s...

journal_title：BMC genomics

authors： Båge T,Lindberg J,Lundeberg J,Modéer T,Yucel-Lindberg T

更新日期：2010-04-15 00:00:00

abstract：BACKGROUND:Aquaculture is the quickest growing sector in agriculture. However, QTL for important traits have been only identified in a few aquaculture species. We conducted QTL mapping for growth traits in an Asian seabass F(2) family with 359 individuals using 123 microsatellites and 22 SNPs, and performed association...

journal_title：BMC genomics

authors： Xia JH,Lin G,He X,Liu P,Liu F,Sun F,Tu R,Yue GH

更新日期：2013-05-01 00:00:00

abstract：BACKGROUND:Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and...

journal_title：BMC genomics

authors： Jiang P,Lai S,Wu S,Zhao XM,Chen WH

更新日期：2020-05-11 00:00:00

abstract：BACKGROUND:The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genom...

journal_title：BMC genomics

authors： Scaglione D,Acquadro A,Portis E,Taylor CA,Lanteri S,Knapp SJ

更新日期：2009-09-28 00:00:00

abstract：BACKGROUND:Simple sequence repeats (SSRs) are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that ca...

journal_title：BMC genomics

authors： Ellison CK,Shaw KL

更新日期：2010-07-12 00:00:00

abstract：BACKGROUND:Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to...

journal_title：BMC genomics

authors： Olohan L,Gardiner LJ,Lucaci A,Steuernagel B,Wulff B,Kenny J,Hall N,Hall A

更新日期：2018-04-13 00:00:00

abstract：BACKGROUND:Fasting induces specific molecular and metabolic adaptions in most organisms. In biomedical research fasting is used in metabolic studies to synchronize nutritional states of study subjects. Because there is a lack of standardization for this procedure, we need a deeper understanding of the dynamics and the ...

journal_title：BMC genomics

authors： Schupp M,Chen F,Briggs ER,Rao S,Pelzmann HJ,Pessentheiner AR,Bogner-Strauss JG,Lazar MA,Baldwin D,Prokesch A

更新日期：2013-11-05 00:00:00

abstract：BACKGROUND:Obesity affects quality of life and life expectancy and is associated with cardiovascular disorders, cancer, diabetes, reproductive disorders in women, prostate diseases in men, and congenital anomalies in children. The use of single nucleotide polymorphism (SNP) markers of diseases and drug responses (i.e.,...

journal_title：BMC genomics

authors： Arkova OV,Ponomarenko MP,Rasskazov DA,Drachkova IA,Arshinova TV,Ponomarenko PM,Savinkova LK,Kolchanov NA

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornis...

journal_title：BMC genomics

authors： Wang Q,Jia Y,Wang Y,Jiang Z,Zhou X,Zhang Z,Nie C,Li J,Yang N,Qu L

更新日期：2019-12-05 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:Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. RESULTS:In this study, 48 CIPK genes (SsCIPKs) were identifi...

journal_title：BMC genomics

authors： Su W,Ren Y,Wang D,Huang L,Fu X,Ling H,Su Y,Huang N,Tang H,Xu L,Que Y

更新日期：2020-12-07 00:00:00