Relating past and present diet to phenotypic and transcriptomic variation in the fruit fly.

abstract：BACKGROUND:Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequi...

journal_title：BMC genomics

authors： Schulte D,Ariyadasa R,Shi B,Fleury D,Saski C,Atkins M,deJong P,Wu CC,Graner A,Langridge P,Stein N

更新日期：2011-05-19 00:00:00

abstract：BACKGROUND:The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptos...

journal_title：BMC genomics

authors： Zhu W,Wang J,Zhu Y,Tang B,Zhang Y,He P,Zhang Y,Liu B,Guo X,Zhao G,Qin J

更新日期：2015-02-15 00:00:00

abstract：BACKGROUND:Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species ar...

journal_title：BMC genomics

authors： Luo H,Sun C,Sun Y,Wu Q,Li Y,Song J,Niu Y,Cheng X,Xu H,Li C,Liu J,Steinmetz A,Chen S

更新日期：2011-12-23 00:00:00

abstract：BACKGROUND:Rhesus monkeys (Macaca mulatta) are widely-used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as cynomolgus monkeys (Macaca fascicularis), and to humans, sharing a last common ancestor from about 25 million years ago. Although rhesus monkeys have be...

journal_title：BMC genomics

authors： Kim DS,Huh JW,Kim YH,Park SJ,Lee SR,Chang KT

更新日期：2010-07-12 00:00:00

abstract：BACKGROUND:Aggression is influenced by individual variation in temperament as well as behavioral plasticity in response to adversity. DNA methylation is stably maintained over time, but also reversible in response to specific environmental conditions, and may thus be a neuromolecular regulator of both of these processe...

journal_title：BMC genomics

authors： Herb BR,Shook MS,Fields CJ,Robinson GE

更新日期：2018-03-26 00:00:00

abstract：BACKGROUND:Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the most important oilseed crops. However, little is known on genes coding for LPAATs involved in oil biosy...

journal_title：BMC genomics

authors： Wang N,Ma J,Pei W,Wu M,Li H,Li X,Yu S,Zhang J,Yu J

更新日期：2017-03-01 00:00:00

abstract：BACKGROUND:Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age gro...

journal_title：BMC genomics

authors： Cowley LA,Beckett SJ,Chase-Topping M,Perry N,Dallman TJ,Gally DL,Jenkins C

更新日期：2015-04-08 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:The histone variant H2A.Z, which has been reported to have both activating and repressive effects on gene expression, is known to occupy nucleosomes at the 5' ends of protein-coding genes. RESULTS:We now find that H2A.Z is also significantly enriched in gene coding regions and at the 3' ends of genes in bud...

journal_title：BMC genomics

authors： Gu M,Naiyachit Y,Wood TJ,Millar CB

更新日期：2015-02-19 00:00:00

abstract：BACKGROUND:Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplas...

journal_title：BMC genomics

authors： Do TD,Vuong TD,Dunn D,Clubb M,Valliyodan B,Patil G,Chen P,Xu D,Nguyen HT,Shannon JG

更新日期：2019-04-25 00:00:00

abstract：BACKGROUND:The freshwater snail Lymnaea stagnalis (L. stagnalis) has served as a successful model for studies in the field of Neuroscience. However, a serious drawback in the molecular analysis of the nervous system of L. stagnalis has been the lack of large-scale genomic or neuronal transcriptome information, thereby ...

journal_title：BMC genomics

authors： Feng ZP,Zhang Z,van Kesteren RE,Straub VA,van Nierop P,Jin K,Nejatbakhsh N,Goldberg JI,Spencer GE,Yeoman MS,Wildering W,Coorssen JR,Croll RP,Buck LT,Syed NI,Smit AB

更新日期：2009-09-23 00:00:00

abstract：BACKGROUND:Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often th...

journal_title：BMC genomics

authors： Heng S,Wei C,Jing B,Wan Z,Wen J,Yi B,Ma C,Tu J,Fu T,Shen J

更新日期：2014-04-30 00:00:00

abstract：BACKGROUND:Pre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops. RESULTS:We identified orthologous...

journal_title：BMC genomics

authors： Onishi K,Yamane M,Yamaji N,Tokui M,Kanamori H,Wu J,Komatsuda T,Sato K

更新日期：2017-06-29 00:00:00

abstract：BACKGROUND:Circannual rhythms in vertebrates can influence a wide variety of physiological processes. Some notable examples include annual reproductive cycles and for poikilotherms, seasonal changes modulating growth. Increasing water temperature elevates growth rates in fishes, but increases in photoperiod regime can ...

journal_title：BMC genomics

authors： Danzmann RG,Kocmarek AL,Norman JD,Rexroad CE 3rd,Palti Y

更新日期：2016-01-15 00:00:00

abstract：BACKGROUND:One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing...

journal_title：BMC genomics

authors： Nguyen KD,Pan Y,Nong G

更新日期：2011-12-23 00:00:00

abstract：BACKGROUND:The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, Marburg virus is a member of the family Filoviridae that causes severe hemorrhagic fever disease i...

journal_title：BMC genomics

authors： Lee AK,Kulcsar KA,Elliott O,Khiabanian H,Nagle ER,Jones ME,Amman BR,Sanchez-Lockhart M,Towner JS,Palacios G,Rabadan R

更新日期：2015-12-07 00:00:00

abstract：BACKGROUND:A major goal of post-genomics research is the integrated analysis of genes, regulatory elements and the chromatin architecture on a genome-wide scale. Mapping DNase I hypersensitive sites within the nuclear chromatin is a powerful and well-established method of identifying regulatory element candidates. RES...

journal_title：BMC genomics

authors： Shi B,Guo X,Wu T,Sheng S,Wang J,Skogerbø G,Zhu X,Chen R

更新日期：2009-02-25 00:00:00

abstract：BACKGROUND:Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sorting and prioritization of the output data. Previously described methodologies have used functional pat...

journal_title：BMC genomics

authors： Schlicht M,Matysiak B,Brodzeller T,Wen X,Liu H,Zhou G,Dhir R,Hessner MJ,Tonellato P,Suckow M,Pollard M,Datta MW

更新日期：2004-08-20 00:00:00

abstract：BACKGROUND:The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and others have previously shown that binding sites of these two transcription factors show a high degr...

journal_title：BMC genomics

authors： Schmidt SF,Jørgensen M,Chen Y,Nielsen R,Sandelin A,Mandrup S

更新日期：2011-03-16 00:00:00

abstract：BACKGROUND:Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. This aflatoxigenic species is capable of secreting both B and G aflatoxins, similar to A. parasit...

journal_title：BMC genomics

authors： Moore GG,Mack BM,Beltz SB,Puel O

更新日期：2018-03-09 00:00:00

abstract：BACKGROUND:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was...

journal_title：BMC genomics

authors： Miao Y,Liu D,Li G,Li P,Xu Y,Shen Q,Zhang R

更新日期：2015-06-16 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:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongy...

journal_title：BMC genomics

authors： Pilkington SM,Crowhurst R,Hilario E,Nardozza S,Fraser L,Peng Y,Gunaseelan K,Simpson R,Tahir J,Deroles SC,Templeton K,Luo Z,Davy M,Cheng C,McNeilage M,Scaglione D,Liu Y,Zhang Q,Datson P,De Silva N,Gardiner SE,Bas

更新日期：2018-04-16 00:00:00

abstract：BACKGROUND:Burkholderia cenocepacia is an opportunistic pathogen causing life-threatening infections in patients with cystic fibrosis. The bacterium survives within macrophages by interfering with endocytic trafficking and delaying the maturation of the B. cenocepacia-containing phagosome. We hypothesize that B. cenoce...

journal_title：BMC genomics

authors： Tolman JS,Valvano MA

更新日期：2012-02-09 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: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: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:The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's...

journal_title：BMC genomics

authors： Krishna A,Biryukov M,Trefois C,Antony PM,Hussong R,Lin J,Heinäniemi M,Glusman G,Köglsberger S,Boyd O,van den Berg BH,Linke D,Huang D,Wang K,Hood L,Tholey A,Schneider R,Galas DJ,Balling R,May P

更新日期：2014-12-20 00:00:00

abstract：BACKGROUND:Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. In the pre...

journal_title：BMC genomics

authors： Vieira FA,Gregório SF,Ferraresso S,Thorne MA,Costa R,Milan M,Bargelloni L,Clark MS,Canario AV,Power DM

更新日期：2011-10-07 00:00:00

abstract：UNLABELLED:Transcription-induced chimerism, a mechanism involving the transcription and intergenic splicing of two consecutive genes, has recently been estimated to account for approximately 5% of the human transcriptome. Despite this prevalence, the regulation and function of these fused transcripts remains largely un...

journal_title：BMC genomics

authors： Wang K,Ubriaco G,Sutherland LC

更新日期：2007-10-01 00:00:00