A fast-linear mixed model for genome-wide haplotype association analysis: application to agronomic traits in maize.

abstract：BACKGROUND:The technological revolution in next-generation sequencing has brought unprecedented opportunities to study any organism of interest at the genomic or transcriptomic level. Transcriptome assembly is a crucial first step for studying the molecular basis of phenotypes of interest using RNA-Sequencing (RNA-Seq)...

journal_title：BMC genomics

authors： Huang X,Chen XG,Armbruster PA

更新日期：2016-07-27 00:00:00

abstract：BACKGROUND:Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory single nucleotide variants (SNVs). Here, we present an alternative QTL-related approach applicable to transcribed SNV loci from scRNA-seq data: ...

journal_title：BMC genomics

authors： Liu H,Prashant NM,Spurr LF,Bousounis P,Alomran N,Ibeawuchi H,Sein J,Słowiński P,Tsaneva-Atanasova K,Horvath A

更新日期：2021-01-08 00:00:00

abstract：BACKGROUND:Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In area...

journal_title：BMC genomics

authors： Jacob CG,Tan JC,Miller BA,Tan A,Takala-Harrison S,Ferdig MT,Plowe CV

更新日期：2014-08-26 00:00:00

abstract：BACKGROUND:In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) a...

journal_title：BMC genomics

authors： Liang C,Liu X,Sun Y,Yiu SM,Lim BL

更新日期：2014-02-10 00:00:00

abstract：BACKGROUND:Accurate de novo genome assembly has become reality with the advancements in sequencing technology. With the ever-increasing number of de novo genome assembly tools, assessing the quality of assemblies has become of great importance in genome research. Although many quality metrics have been proposed and sof...

journal_title：BMC genomics

authors： Yavas G,Hong H,Xiao W

更新日期：2019-09-11 00:00:00

abstract：BACKGROUND:Evolutionary theory indicates that the dynamics of aging in the soma and reproductive tissues may be distinct. This difference arises from the fact that only the germline lineage establishes future generations. In the soma, changes in the landscape of heterochromatin have been proposed to have an important r...

journal_title：BMC genomics

authors： Erwin AA,Blumenstiel JP

更新日期：2019-04-23 00:00:00

abstract：BACKGROUND:The reconstruction of gene regulatory networks from high-throughput "omics" data has become a major goal in the modelling of living systems. Numerous approaches have been proposed, most of which attempt only "one-shot" reconstruction of the whole network with no intervention from the user, or offer only simp...

journal_title：BMC genomics

authors： Kadupitige SR,Leung KC,Sellmeier J,Sivieng J,Catchpoole DR,Bain ME,Gaëta BA

更新日期：2009-12-03 00:00:00

abstract：BACKGROUND:Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamica...

journal_title：BMC genomics

authors： Li S,Dong X,Su Z

更新日期：2013-07-30 00:00:00

abstract：BACKGROUND:The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis). While classical microbial taxonomy proposed these organisms as distinct species, newer molecular phylogenies and comparative genome sequencing s...

journal_title：BMC genomics

authors： Schmidt TR,Scott EJ 2nd,Dyer DW

更新日期：2011-08-24 00:00:00

abstract：UNLABELLED:AB BACKGROUND: MicroRNAs (miRNAs) are small, non-coding 21-25 nt RNA molecules that play an important role in regulating gene expression. Little is known about the expression profiles and functions of miRNAs in skin and their role in pigmentation. Alpacas have more than 22 natural coat colors, more than any ...

journal_title：BMC genomics

authors： Tian X,Jiang J,Fan R,Wang H,Meng X,He X,He J,Li H,Geng J,Yu X,Song Y,Zhang D,Yao J,Smith GW,Dong C

更新日期：2012-10-16 00:00:00

abstract：BACKGROUND:Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity....

journal_title：BMC genomics

authors： Cantu D,Segovia V,MacLean D,Bayles R,Chen X,Kamoun S,Dubcovsky J,Saunders DG,Uauy C

更新日期：2013-04-22 00:00:00

abstract：BACKGROUND:Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy langu...

journal_title：BMC genomics

authors： Kusuma P,Cox MP,Pierron D,Razafindrazaka H,Brucato N,Tonasso L,Suryadi HL,Letellier T,Sudoyo H,Ricaut FX

更新日期：2015-03-17 00:00:00

abstract：BACKGROUND:Ultrasound imaging technology has wide applications in cattle reproduction and has been used to monitor individual follicles and determine the patterns of follicular development. However, the speckles in ultrasound images affect the post-processing, such as follicle segmentation and finally affect the measur...

journal_title：BMC genomics

authors： Tang J,Guo S,Sun Q,Deng Y,Zhou D

更新日期：2010-11-02 00:00:00

abstract：BACKGROUND:Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfort, chronic keratitis, and corneal ulceration, potentially impacting vision due to corneal fibrosis, ...

journal_title：BMC genomics

authors： Hisey EA,Hermans H,Lounsberry ZT,Avila F,Grahn RA,Knickelbein KE,Duward-Akhurst SA,McCue ME,Kalbfleisch TS,Lassaline ME,Back W,Bellone RR

更新日期：2020-11-30 00:00:00

abstract：BACKGROUND:During embryogenesis the liver is derived from endodermal cells lining the digestive tract. These endodermal progenitor cells contribute to forming the parenchyma of a number of organs including the liver and pancreas. Early in organogenesis the fetal liver is populated by hematopoietic stem cells, the sourc...

journal_title：BMC genomics

authors： Lee JS,Ward WO,Knapp G,Ren H,Vallanat B,Abbott B,Ho K,Karp SJ,Corton JC

更新日期：2012-01-19 00:00:00

abstract：BACKGROUND:Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated...

journal_title：BMC genomics

authors： Luo P,Yun L,Li Y,Tian Y,Liu Q,Huang W,Hu C

更新日期：2018-10-11 00:00:00

abstract：BACKGROUND:Increased focus surrounds identifying patients with advanced non-small cell lung cancer (NSCLC) who will benefit from treatment with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI). EGFR mutation, gene copy number, coexpression of ErbB proteins and ligands, and epithelial to mesenchy...

journal_title：BMC genomics

authors： Balko JM,Potti A,Saunders C,Stromberg A,Haura EB,Black EP

更新日期：2006-11-10 00:00:00

abstract：BACKGROUND:Oxidative stress caused by ground level ozone is a contributor to yield loss in a number of important crop plants. Soybean (Glycine max) is considered to be ozone sensitive, and current research into its response to oxidative stress is limited. To better understand the genetic response in soybean to oxidativ...

journal_title：BMC genomics

authors： Whaley A,Sheridan J,Safari S,Burton A,Burkey K,Schlueter J

更新日期：2015-06-04 00:00:00

abstract：BACKGROUND:Hop (Humulus lupulus L.) is an economically important plant forming organogenic nodules which can be used for genetic transformation and micropropagation. We are interested in the mechanisms underlying reprogramming of cells through stress and hormone treatments. RESULTS:An integrated molecular and metabolo...

journal_title：BMC genomics

authors： Fortes AM,Santos F,Choi YH,Silva MS,Figueiredo A,Sousa L,Pessoa F,Santos BA,Sebastiana M,Palme K,Malhó R,Verpoorte R,Pais MS

更新日期：2008-09-29 00:00:00

abstract：BACKGROUND:Microsatellites (repeated subsequences based on motifs of one to six nucleotides) are widely used as codominant genetic markers because of their frequent polymorphism and relative selective neutrality. Minisatellites are repeats of motifs having seven or more nucleotides. The large number of EST sequences no...

journal_title：BMC genomics

authors： Crane CF

更新日期：2007-06-15 00:00:00

abstract：BACKGROUND:The cellular proteome and metabolome are underlying dynamic regulation allowing rapid adaptation to changes in the environment. System-wide analysis of these dynamics will provide novel insights into mechanisms of stress adaptation for higher photosynthetic organisms. We applied pulsed-SILAC labeling to a ph...

journal_title：BMC genomics

authors： Mastrobuoni G,Irgang S,Pietzke M,Assmus HE,Wenzel M,Schulze WX,Kempa S

更新日期：2012-05-31 00:00:00

abstract：BACKGROUND:Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers to express and study complete proteomes in a high-throughput fashion. RESULTS:We have constructed an...

journal_title：BMC genomics

authors： Rajagopala SV,Yamamoto N,Zweifel AE,Nakamichi T,Huang HK,Mendez-Rios JD,Franca-Koh J,Boorgula MP,Fujita K,Suzuki K,Hu JC,Wanner BL,Mori H,Uetz P

更新日期：2010-08-11 00:00:00

abstract：BACKGROUND:Gene duplication is an important biological phenomenon associated with genomic redundancy, degeneration, specialization, innovation, and speciation. After duplication, both copies continue functioning when natural selection favors duplicated protein function or expression, or when mutations make them functio...

journal_title：BMC genomics

authors： Chain FJ,Dushoff J,Evans BJ

更新日期：2011-12-12 00:00:00

abstract：BACKGROUND:The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus c...

journal_title：BMC genomics

authors： Lang AS,Austin SH,Harris RM,Calisi RM,MacManes MD

更新日期：2020-03-23 00:00:00

abstract：BACKGROUND:A high caloric diet, in conjunction with low levels of physical activity, promotes obesity. Many studies are available regarding the relation between dietary saturated fats and the etiology of obesity, but most focus on liver, muscle and white adipose tissue. Furthermore, the majority of transcriptomic studi...

journal_title：BMC genomics

authors： Nyima T,Müller M,Hooiveld GJ,Morine MJ,Scotti M

更新日期：2016-02-09 00:00:00

abstract：BACKGROUND:Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, de...

journal_title：BMC genomics

authors： Powell AJ,Conant GC,Brown DE,Carbone I,Dean RA

更新日期：2008-03-28 00:00:00

abstract：BACKGROUND:Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a n...

journal_title：BMC genomics

authors： Dang X,Xie Z,Liu W,Sun Y,Liu X,Zhu Y,Staehelin C

更新日期：2019-08-12 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:Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great...

journal_title：BMC genomics

authors： Velie BD,Lillie M,Fegraeus KJ,Rosengren MK,Solé M,Wiklund M,Ihler CF,Strand E,Lindgren G

更新日期：2019-02-04 00:00:00

abstract：BACKGROUND:Controlling and managing the breeding of bluefin tuna (Thunnus spp.) in captivity is an imperative step towards obtaining a sustainable supply of these fish in aquaculture production systems. Germ cell transplantation (GCT) is an innovative technology for the production of inter-species surrogates, by transp...

journal_title：BMC genomics

authors： Bar I,Cummins S,Elizur A

更新日期：2016-03-10 00:00:00