The biorepository portal toolkit: an honest brokered, modular service oriented software tool set for biospecimen-driven translational research.

abstract：BACKGROUND:Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animals. RESULTS:T...

journal_title：BMC genomics

authors： Ren L,Yan X,Gao X,Cui J,Yan P,Wu C,Li W,Liu S

更新日期：2020-07-02 00:00:00

abstract：:An amendment to this paper has been published and can be accessed via the original article. ...

journal_title：BMC genomics

authors： Assefa AT,Vandesompele J,Thas O

更新日期：2020-06-03 00:00:00

abstract：BACKGROUND:The activity of the yeast activator protein 1 (Yap1p) increases under stress conditions, which leads to enhanced transcription of a number of genes encoding protective enzymes or other proteins. To obtain a global overview of changes in expression of Yap1p-targeted proteins, we compared a Yap1p-overexpressin...

journal_title：BMC genomics

authors： Jun H,Kieselbach T,Jönsson LJ

更新日期：2012-06-09 00:00:00

abstract：BACKGROUND:The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is dependent on an intricate gene regulatory program coordinated by a number of transcription factors and m...

journal_title：BMC genomics

authors： Chang LW,Viader A,Varghese N,Payton JE,Milbrandt J,Nagarajan R

更新日期：2013-02-06 00:00:00

abstract：BACKGROUND:Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-chara...

journal_title：BMC genomics

authors： Olender T,Keydar I,Pinto JM,Tatarskyy P,Alkelai A,Chien MS,Fishilevich S,Restrepo D,Matsunami H,Gilad Y,Lancet D

更新日期：2016-08-11 00:00:00

abstract：BACKGROUND:Although primarily known as the site of ribosome subunit production, the nucleolus is involved in numerous and diverse cellular processes. Recent large-scale proteomics projects have identified thousands of human proteins that associate with the nucleolus. However, in most cases, we know neither the fraction...

journal_title：BMC genomics

authors： Scott MS,Boisvert FM,Lamond AI,Barton GJ

更新日期：2011-01-27 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:Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuti...

journal_title：BMC genomics

authors： Deng CH,Plummer KM,Jones DAB,Mesarich CH,Shiller J,Taranto AP,Robinson AJ,Kastner P,Hall NE,Templeton MD,Bowen JK

更新日期：2017-05-02 00:00:00

abstract：BACKGROUND:Regulatory networks often employ the model that attributes changes in gene expression levels, as observed across different cellular conditions, to changes in the activity of transcription factors (TFs). Although the actual conditions that trigger a change in TF activity should form an integral part of the ge...

journal_title：BMC genomics

authors： Knijnenburg TA,de Winde JH,Daran JM,Daran-Lapujade P,Pronk JT,Reinders MJ,Wessels LF

更新日期：2007-01-22 00:00:00

abstract：BACKGROUND:RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kits. To date there has been no analysis of the effect of these choices on identifying differentially e...

journal_title：BMC genomics

authors： Corley SM,MacKenzie KL,Beverdam A,Roddam LF,Wilkins MR

更新日期：2017-05-23 00:00:00

abstract：BACKGROUND:Functional analysis of the catfish genome will be useful for the identification of genes controlling traits of economic importance, especially innate disease resistance. However, this species lacks a platform for global gene expression profiling, so we designed a first generation high-density oligonucleotide...

journal_title：BMC genomics

authors： Li RW,Waldbieser GC

更新日期：2006-06-01 00:00:00

abstract：BACKGROUND:The pathogenesis-related (PR) group of proteins are operationally defined as polypeptides that increase in concentration in plant tissues upon contact with a pathogen. To date, 17 classes of highly divergent proteins have been described that act through multiple mechanisms of pathogen resistance. Characteriz...

journal_title：BMC genomics

authors： Fister AS,Mejia LC,Zhang Y,Herre EA,Maximova SN,Guiltinan MJ

更新日期：2016-05-17 00:00:00

abstract：BACKGROUND:The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequen...

journal_title：BMC genomics

authors： Kazakov AE,Rajeev L,Chen A,Luning EG,Dubchak I,Mukhopadhyay A,Novichkov PS

更新日期：2015-11-10 00:00:00

abstract：BACKGROUND:Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of t...

journal_title：BMC genomics

authors： Huang X,Otecko NO,Peng M,Weng Z,Li W,Chen J,Zhong M,Zhong F,Jin S,Geng Z,Luo W,He D,Ma C,Han J,Ommeh SC,Zhang Y,Zhang X,Du B

更新日期：2020-04-20 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:Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were ...

journal_title：BMC genomics

authors： Cordoni G,Woodward MJ,Wu H,Alanazi M,Wallis T,La Ragione RM

更新日期：2016-11-22 00:00:00

abstract：BACKGROUND:The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a ...

journal_title：BMC genomics

authors： Ishii K,Washio T,Uechi T,Yoshihama M,Kenmochi N,Tomita M

更新日期：2006-02-28 00:00:00

abstract：BACKGROUND:Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measu...

journal_title：BMC genomics

authors： Rodriguez BA,Frankhouser D,Murphy M,Trimarchi M,Tam HH,Curfman J,Huang R,Chan MW,Lai HC,Parikh D,Ball B,Schwind S,Blum W,Marcucci G,Yan P,Bundschuh R

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Aberrant DNA methylation is a hallmark of many cancers. Classically there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I, and uterine papillary serous carcinoma (UPSC), or Type II. However, the whole genome DNA methylation changes in these two classical types of endometrial...

journal_title：BMC genomics

authors： Zhang B,Xing X,Li J,Lowdon RF,Zhou Y,Lin N,Zhang B,Sundaram V,Chiappinelli KB,Hagemann IS,Mutch DG,Goodfellow PJ,Wang T

更新日期：2014-10-06 00:00:00

abstract：BACKGROUND:Incilaria (= Meghimatium) fruhstorferi is an air-breathing land slug found in restricted habitats of Japan, Taiwan and selected provinces of South Korea (Jeju, Chuncheon, Busan, and Deokjeokdo). The species is on a decline due to depletion of forest cover, predation by natural enemies, and collection. To fac...

journal_title：BMC genomics

authors： Patnaik BB,Chung JM,Hwang HJ,Sang MK,Park JE,Min HR,Cho HC,Dewangan N,Baliarsingh S,Kang SW,Park SY,Jo YH,Park HS,Kim WJ,Han YS,Lee JS,Lee YS

更新日期：2019-02-26 00:00:00

abstract：BACKGROUND:GLV-1h68 is an attenuated recombinant vaccinia virus (VACV) that selectively colonizes established human xenografts inducing their complete regression. RESULTS:Here, we explored xenograft/VACV/host interactions in vivo adopting organism-specific expression arrays and tumor cell/VACV in vitro comparing VACV ...

journal_title：BMC genomics

authors： Worschech A,Chen N,Yu YA,Zhang Q,Pos Z,Weibel S,Raab V,Sabatino M,Monaco A,Liu H,Monsurró V,Buller RM,Stroncek DF,Wang E,Szalay AA,Marincola FM

更新日期：2009-07-07 00:00:00

abstract：BACKGROUND:Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure a...

journal_title：BMC genomics

authors： Ling Z,Kong J,Liu F,Zhu H,Chen X,Wang Y,Li L,Nelson KE,Xia Y,Xiang C

更新日期：2010-09-07 00:00:00

abstract：BACKGROUND:Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The...

journal_title：BMC genomics

authors： Mulley JF,Hargreaves AD,Hegarty MJ,Heller RS,Swain MT

更新日期：2014-12-06 00:00:00

abstract：BACKGROUND:Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasit...

journal_title：BMC genomics

authors： Vincent B,Kaeslin M,Roth T,Heller M,Poulain J,Cousserans F,Schaller J,Poirié M,Lanzrein B,Drezen JM,Moreau SJ

更新日期：2010-12-07 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 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:Phanerochaete chrysosporium, the model white rot basidiomycetous fungus, has the extraordinary ability to mineralize (to CO2) lignin and detoxify a variety of chemical pollutants. Its cytochrome P450 monooxygenases have recently been implied in several of these biotransformations. Our initial P450 cloning ef...

journal_title：BMC genomics

authors： Doddapaneni H,Chakraborty R,Yadav JS

更新日期：2005-06-14 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:Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression system...

journal_title：BMC genomics

authors： Moshonov S,Elfakess R,Golan-Mashiach M,Sinvani H,Dikstein R

更新日期：2008-02-25 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