RNA-Seq quantification of the human small airway epithelium transcriptome.

abstract：BACKGROUND:Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model inference based on such data still manifests significant uncertainty. RE...

journal_title：BMC genomics

authors： Hajiramezanali E,Imani M,Braga-Neto U,Qian X,Dougherty ER

更新日期：2019-06-13 00:00:00

abstract：BACKGROUND:Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias. RESULTS:In this study we have sampled over 800 unrelated individuals from the population of Spain,...

journal_title：BMC genomics

authors： Gayán J,Galan JJ,González-Pérez A,Sáez ME,Martínez-Larrad MT,Zabena C,Rivero MC,Salinas A,Ramírez-Lorca R,Morón FJ,Royo JL,Moreno-Rey C,Velasco J,Carrasco JM,Molero E,Ochoa C,Ochoa MD,Gutiérrez M,Reina M,Pascual R,

更新日期：2010-05-25 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:Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.In order to evaluate the potential of these technologies in pea, we selected a ...

journal_title：BMC genomics

authors： Deulvot C,Charrel H,Marty A,Jacquin F,Donnadieu C,Lejeune-Hénaut I,Burstin J,Aubert G

更新日期：2010-08-11 00:00:00

abstract：BACKGROUND:Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcin...

journal_title：BMC genomics

authors： Brogaard L,Klitgaard K,Heegaard PM,Hansen MS,Jensen TK,Skovgaard K

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immun...

journal_title：BMC genomics

authors： Kucukural A,Yukselen O,Ozata DM,Moore MJ,Garber M

更新日期：2019-01-05 00:00:00

abstract：BACKGROUND:Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses. This sophisticated biotrophic parasite infiltrates wheat leaves and develops infection structures inside host cells, appropriating nutrients while sup...

journal_title：BMC genomics

authors： Mueth NA,Ramachandran SR,Hulbert SH

更新日期：2015-09-21 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:Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs) map each mutant to a specific locus within the genome. In maize, FSTs have...

journal_title：BMC genomics

authors： Settles AM,Holding DR,Tan BC,Latshaw SP,Liu J,Suzuki M,Li L,O'Brien BA,Fajardo DS,Wroclawska E,Tseung CW,Lai J,Hunter CT 3rd,Avigne WT,Baier J,Messing J,Hannah LC,Koch KE,Becraft PW,Larkins BA,McCarty DR

更新日期：2007-05-09 00:00:00

abstract：BACKGROUND:Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants a...

journal_title：BMC genomics

authors： Gowda M,Venu RC,Raghupathy MB,Nobuta K,Li H,Wing R,Stahlberg E,Couglan S,Haudenschild CD,Dean R,Nahm BH,Meyers BC,Wang GL

更新日期：2006-12-08 00:00:00

abstract：BACKGROUND:Ubiquitination is an important post-translational modification involved in diverse biological processes. Therefore, genomewide representation of the ubiquitination system for a species is important. DESCRIPTION:SCUD is a web-based database for the ubiquitination system in Saccharomyces cerevisiae (Baker's y...

journal_title：BMC genomics

authors： Lee WC,Lee M,Jung JW,Kim KP,Kim D

更新日期：2008-09-24 00:00:00

abstract：BACKGROUND:Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) tes...

journal_title：BMC genomics

authors： Chiniquy J,Garber ME,Mukhopadhyay A,Hillson NJ

更新日期：2020-01-28 00:00:00

abstract：BACKGROUND:Rich in genetic information and cost-effective to genotype, the Insertion-Deletion (InDel) molecular marker system is an important tool for studies in genetics, genomics and for marker-assisted breeding. Advent of next-generation sequencing (NGS) revolutionized the speed and throughput of sequence data gener...

journal_title：BMC genomics

authors： Lv Y,Liu Y,Zhao H

更新日期：2016-04-14 00:00:00

abstract：MOTIVATION:Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to integrate various modules and evaluate them from a systems point of view. RESUL...

journal_title：BMC genomics

authors： Sun Y,Braga-Neto U,Dougherty ER

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Skeletal muscle mass can be markedly reduced through a process called atrophy, as a consequence of many diseases or critical physiological and environmental situations. Atrophy is characterised by loss of contractile proteins and reduction of fiber volume. Although in the last decade the molecular aspects un...

journal_title：BMC genomics

authors： Calura E,Cagnin S,Raffaello A,Laveder P,Lanfranchi G,Romualdi C

更新日期：2008-12-23 00:00:00

abstract：BACKGROUND:Sugarcane is a major sugar and biofuel crop, but genomic research and molecular breeding have lagged behind other major crops due to the complexity of auto-allopolyploid genomes. Sugarcane cultivars are frequently aneuploid with chromosome number ranging from 100 to 130, consisting of 70-80 % S. officinarum,...

journal_title：BMC genomics

authors： Zhang J,Sharma A,Yu Q,Wang J,Li L,Zhu L,Zhang X,Chen Y,Ming R

更新日期：2016-06-10 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

abstract：BACKGROUND:Toxoplasmosis is caused by the apicomplexan parasite Toxoplasma gondii and can be acquired either congenitally or via the oral route. In the latter case, transmission is mediated by two distinct invasive stages, i.e., bradyzoites residing in tissue cysts or sporozoites contained in environmentally resistant ...

journal_title：BMC genomics

authors： Possenti A,Fratini F,Fantozzi L,Pozio E,Dubey JP,Ponzi M,Pizzi E,Spano F

更新日期：2013-03-15 00:00:00

abstract：BACKGROUND:The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM's reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting inserti...

journal_title：BMC genomics

authors： Yeo ZX,Wong JC,Rozen SG,Lee AS

更新日期：2014-06-24 00:00:00

abstract：BACKGROUND:Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work toget...

journal_title：BMC genomics

authors： Wei W,Mesquita ACO,Figueiró AA,Wu X,Manjunatha S,Wickland DP,Hudson ME,Juliatti FC,Clough SJ

更新日期：2017-11-07 00:00:00

abstract：BACKGROUND:In the model legume Medicago truncatula, the near saturation genome-wide Tnt1 insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified many Tnt1 mutants defective in nodule development and symbiotic nitrogen fixation (SNF). However...

journal_title：BMC genomics

authors： Veerappan V,Jani M,Kadel K,Troiani T,Gale R,Mayes T,Shulaev E,Wen J,Mysore KS,Azad RK,Dickstein R

更新日期：2016-02-27 00:00:00

abstract：BACKGROUND:Genomic imprinting is an evolutionary conserved mechanism of epigenetic gene regulation in placental mammals that results in silencing of one of the parental alleles. In order to decipher interactions between allele-specific DNA methylation of imprinted genes and evolutionary conservation, we performed a gen...

journal_title：BMC genomics

authors： Hutter B,Bieg M,Helms V,Paulsen M

更新日期：2010-11-22 00:00:00

abstract：BACKGROUND:Infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) infection causes high mortality and huge economic losses in the poultry industry. To protect chickens against ILTV infection, chicken-embryo origin (CEO) and tissue-culture origin (TCO) vaccines have been used. However, the transmission of vacci...

journal_title：BMC genomics

authors： Lee J,Bottje WG,Kong BW

更新日期：2012-04-24 00:00:00

abstract：BACKGROUND:Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, cl...

journal_title：BMC genomics

authors： Orsini L,Jansen M,Souche EL,Geldof S,De Meester L

更新日期：2011-06-13 00:00:00

abstract：BACKGROUND:Quercetin is a polyphenol of great interest given its antioxidant activity and involvement in the immune response. Although quercetin has been well studied at the molecular level as a gene regulator and an activator of specific cellular pathways, not much attention has been given to its mechanism of action a...

journal_title：BMC genomics

authors： Atrahimovich D,Samson AO,Barsheshet Y,Vaya J,Khatib S,Reuveni E

更新日期：2019-07-23 00:00:00

abstract：BACKGROUND:Parasites employ proteases to evade host immune systems, feed and replicate and are often the target of anti-parasite strategies to disrupt these interactions. Myxozoans are obligate cnidarian parasites, alternating between invertebrate and fish hosts. Their genes are highly divergent from other metazoans, a...

journal_title：BMC genomics

authors： Hartigan A,Kosakyan A,Pecková H,Eszterbauer E,Holzer AS

更新日期：2020-06-16 00:00:00

abstract：BACKGROUND:Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes der...

journal_title：BMC genomics

authors： Park KD,Park J,Ko J,Kim BC,Kim HS,Ahn K,Do KT,Choi H,Kim HM,Song S,Lee S,Jho S,Kong HS,Yang YM,Jhun BH,Kim C,Kim TH,Hwang S,Bhak J,Lee HK,Cho BW

更新日期：2012-09-12 00:00:00

abstract：BACKGROUND:High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequenc...

journal_title：BMC genomics

authors： Greminger MP,Stölting KN,Nater A,Goossens B,Arora N,Bruggmann R,Patrignani A,Nussberger B,Sharma R,Kraus RH,Ambu LN,Singleton I,Chikhi L,van Schaik CP,Krützen M

更新日期：2014-01-10 00:00:00

abstract：BACKGROUND:Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; however the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood. In this study, global transcriptome profiles of trifoliate orange under cold conditions (4 °C) ...

journal_title：BMC genomics

authors： Wang M,Zhang X,Liu JH

更新日期：2015-07-29 00:00:00

abstract：BACKGROUND:Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound ada...

journal_title：BMC genomics

authors： Wang MQ,Bai ZY,Xiao YF,Li Y,Liu QL,Zhang L,Pan YZ,Jiang BB,Zhang F

更新日期：2019-11-20 00:00:00