MINER: exploratory analysis of gene interaction networks by machine learning from expression data.

abstract：BACKGROUND:The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or very low temperatures. Being able to accurately predict this based on a genomic sequence, would thu...

journal_title：BMC genomics

authors： Jensen DB,Vesth TC,Hallin PF,Pedersen AG,Ussery DW

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:The AP2/ERF transcription factor, one of the largest gene families in plants, plays a crucial role in the regulation of growth and development, metabolism, and responses to biotic and abiotic stresses. Castor bean (Ricinus communis L., Euphobiaceae) is one of most important non-edible oilseed crops and its s...

journal_title：BMC genomics

authors： Xu W,Li F,Ling L,Liu A

更新日期：2013-11-13 00:00:00

abstract：BACKGROUND:Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus) using Illumina short-read sequencing data, by comparing our lab data for 38 goats from three Chi...

journal_title：BMC genomics

authors： Guo J,Zhong J,Liu GE,Yang L,Li L,Chen G,Song T,Zhang H

更新日期：2020-11-27 00:00:00

abstract：BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...

journal_title：BMC genomics

authors： Zhang X,Liu X,Li L,Wei G,Zhang D,Liang Y,Miao B

更新日期：2019-05-30 00:00:00

abstract：BACKGROUND:Triptolide is a therapeutic diterpenoid derived from the Chinese herb Tripterygium wilfordii Hook f. Triptolide has been shown to induce apoptosis by activation of pro-apoptotic proteins, inhibiting NFkB and c-KIT pathways, suppressing the Jak2 transcription, activating MAPK8/JNK signaling and modulating the...

journal_title：BMC genomics

authors： Chauhan L,Jenkins GD,Bhise N,Feldberg T,Mitra-Ghosh T,Fridley BL,Lamba JK

更新日期：2015-06-30 00:00:00

abstract：BACKGROUND:As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+...

journal_title：BMC genomics

authors： Yu N,Guo X,Zelikovsky A,Pan Y

更新日期：2017-05-24 00:00:00

abstract：BACKGROUND:Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpre...

journal_title：BMC genomics

authors： Field MA,Burgio G,Chuah A,Al Shekaili J,Hassan B,Al Sukaiti N,Foote SJ,Cook MC,Andrews TD

更新日期：2019-07-16 00:00:00

abstract：BACKGROUND:microRNA (miRNA) expression plays an influential role in cancer classification and malignancy, and miRNAs are feasible as alternative diagnostic markers for pancreatic cancer, a highly aggressive neoplasm with silent early symptoms, high metastatic potential, and resistance to conventional therapies. METHOD...

journal_title：BMC genomics

authors： Kwon MS,Kim Y,Lee S,Namkung J,Yun T,Yi SG,Han S,Kang M,Kim SW,Jang JY,Park T

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Human interfollicular epidermis is sustained by the proliferation of stem cells and their progeny, transient amplifying cells. Molecular characterization of these two cell populations is essential for better understanding of self renewal, differentiation and mechanisms of skin pathogenesis. The purpose of th...

journal_title：BMC genomics

authors： Koçer SS,Djurić PM,Bugallo MF,Simon SR,Matic M

更新日期：2008-07-30 00:00:00

abstract：BACKGROUND:Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classi...

journal_title：BMC genomics

authors： Thybert D,Avner S,Lucchetti-Miganeh C,Chéron A,Barloy-Hubler F

更新日期：2008-12-31 00:00:00

abstract：BACKGROUND:The variability in gene organization and architecture of green algal mitochondrial genomes is only recently being studied on a finer taxonomic scale. Sequenced mt genomes from the chlorophycean orders Volvocales and Sphaeropleales exhibit considerable variation in size, content, and structure, even among clo...

journal_title：BMC genomics

authors： Farwagi AA,Fučíková K,McManus HA

更新日期：2015-10-21 00:00:00

abstract：BACKGROUND:Auxin plays a critical role in inducing adventitious rooting in many plants. Indole-3-butyric acid (IBA) is the most widely employed auxin for adventitious rooting. However, the molecular mechanisms by which auxin regulate the process of adventitious rooting are less well known. RESULTS:The RNA-Seq data ana...

journal_title：BMC genomics

authors： Li SW,Shi RF,Leng Y,Zhou Y

更新日期：2016-01-12 00:00:00

abstract：BACKGROUND:Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices based on phenomics methods, especially in China. This study aimed to apply phenomics to systematically e...

journal_title：BMC genomics

authors： Hu Y,Tan A,Yu L,Hou C,Kuang H,Wu Q,Su J,Zhou Q,Zhu Y,Zhang C,Wei W,Li L,Li W,Huang Y,Huang H,Xie X,Lu T,Zhang H,Yang X,Gao Y,Li T,Jiang Y,Mo Z

更新日期：2019-12-16 00:00:00

abstract：BACKGROUND:Despite the known importance of somatic cells for oocyte developmental competence acquisition, the overall mechanisms underlying the acquisition of full developmental competence are far from being understood, especially in non-mammalian species. The present work aimed at identifying key molecular signals fro...

journal_title：BMC genomics

authors： Charlier C,Montfort J,Chabrol O,Brisard D,Nguyen T,Le Cam A,Richard-Parpaillon L,Moreews F,Pontarotti P,Uzbekova S,Chesnel F,Bobe J

更新日期：2012-10-19 00:00:00

abstract：BACKGROUND:Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey o...

journal_title：BMC genomics

authors： Bi YM,Meyer A,Downs GS,Shi X,El-Kereamy A,Lukens L,Rothstein SJ

更新日期：2014-01-28 00:00:00

abstract：BACKGROUND:The recently developed RNA interference (RNAi) technology has created an unprecedented opportunity which allows the function of individual genes in whole organisms or cell lines to be interrogated at genome-wide scale. However, multiple issues, such as off-target effects or low efficacies in knocking down ce...

journal_title：BMC genomics

authors： Wang L,Tu Z,Sun F

更新日期：2009-05-12 00:00:00

abstract：BACKGROUND:Obesity and phenotypic traits associated with this condition exhibit significant heritability in natural populations of most organisms. While a number of genes and genetic pathways have been implicated to play a role in obesity associated traits, the genetic architecture that underlies the natural variation ...

journal_title：BMC genomics

authors： Jumbo-Lucioni P,Ayroles JF,Chambers MM,Jordan KW,Leips J,Mackay TF,De Luca M

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:Two fifths of the world's population is at risk from dengue. The absence of effective drugs and vaccines leaves vector control as the primary intervention tool. Understanding dengue virus (DENV) host interactions is essential for the development of novel control strategies. The availability of genome sequenc...

journal_title：BMC genomics

authors： Guo X,Xu Y,Bian G,Pike AD,Xie Y,Xi Z

更新日期：2010-06-16 00:00:00

abstract：BACKGROUND:Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f., an evergreen broadleaf legume shrub, is distributed in Mid-Asia where the temperature can be as low as -30°C during the winter. Although A. mongolicus is an ideal model to study the plant response to cold stress, insufficient genomic resources for this spe...

journal_title：BMC genomics

authors： Pang T,Ye CY,Xia X,Yin W

更新日期：2013-07-18 00:00:00

abstract：BACKGROUND:Little is known about the genome sequences of Euphausiacea (krill) although these crustaceans are abundant components of the pelagic ecosystems in all oceans and used for aquaculture and pharmaceutical industry. This study reports the results of an expressed sequence tag (EST) sequencing project from differe...

journal_title：BMC genomics

authors： De Pittà C,Bertolucci C,Mazzotta GM,Bernante F,Rizzo G,De Nardi B,Pallavicini A,Lanfranchi G,Costa R

更新日期：2008-01-28 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:The capacity of European pear fruit (Pyrus communis L.) to ripen after harvest develops during the final stages of growth on the tree. The objective of this study was to characterize changes in 'Bartlett' pear fruit physico-chemical properties and transcription profiles during fruit maturation leading to att...

journal_title：BMC genomics

authors： Nham NT,de Freitas ST,Macnish AJ,Carr KM,Kietikul T,Guilatco AJ,Jiang CZ,Zakharov F,Mitcham EJ

更新日期：2015-10-09 00:00:00

abstract：BACKGROUND:Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visuali...

journal_title：BMC genomics

authors： Miller CA,McMichael J,Dang HX,Maher CA,Ding L,Ley TJ,Mardis ER,Wilson RK

更新日期：2016-11-07 00:00:00

abstract：BACKGROUND:Tumor genomes are often highly heterogeneous, consisting of genomes from multiple subclonal types. Complete characterization of all subclonal types is a fundamental need in tumor genome analysis. With the advancement of next-generation sequencing, computational methods have recently been developed to infer t...

journal_title：BMC genomics

authors： Li Y,Xie X

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Rice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world. However, the genomic information for this fungal pathogen is limited and the pathogenic mechanism of this disease is still not clear. To facilitate genetic, molecular...

journal_title：BMC genomics

authors： Wang X,Liu Q,Wang H,Luo CX,Wang G,Luo M

更新日期：2013-12-16 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 bulldog calf syndrome is a lethal form of the inherited congenital chondrodysplasias. Among the progeny of the polled Holstein bull Energy P cases of lethal chondrodysplasia were observed. Pedigrees of the cases and the frequency of 3/8 cases among the offspring of Energy P at our teaching and experiment...

journal_title：BMC genomics

authors： Reinartz S,Mohwinkel H,Sürie C,Hellige M,Feige K,Eikelberg D,Beineke A,Metzger J,Distl O

更新日期：2017-10-10 00:00:00

abstract：BACKGROUND:Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in rec...

journal_title：BMC genomics

authors： Jiao Y,Jia HM,Li XW,Chai ML,Jia HJ,Chen Z,Wang GY,Chai CY,van de Weg E,Gao ZS

更新日期：2012-05-23 00:00:00

abstract：BACKGROUND:Molecular characterization is important for efficient utilization of germplasm and development of improved varieties. In the present study, we investigated the genetic purity, relatedness and population structure of 265 maize inbred lines from the Ethiopian Institute of Agricultural Research (EIAR), the Inte...

journal_title：BMC genomics

authors： Ertiro BT,Semagn K,Das B,Olsen M,Labuschagne M,Worku M,Wegary D,Azmach G,Ogugo V,Keno T,Abebe B,Chibsa T,Menkir A

更新日期：2017-10-12 00:00:00

abstract：BACKGROUND:Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infection with the destructive bacterial pathogen Xanthomonas oryzae pv. oryzae(Xoo) in both resistant and s...

journal_title：BMC genomics

authors： Narsai R,Wang C,Chen J,Wu J,Shou H,Whelan J

更新日期：2013-02-12 00:00:00