Anomaly detection in gene expression via stochastic models of gene regulatory networks.

abstract：BACKGROUND:The capsular polysaccharide is the principal virulence factor of Streptococcus pneumoniae and a target for current pneumococcal vaccines. However, some pathogenic pneumococci are serologically nontypeable [nontypeable pneumococci (NTPn)]. Due to their relative rarity, NTPn are poorly characterized, and, as s...

journal_title：BMC genomics

authors： Mohale T,Wolter N,Allam M,Ndlangisa K,Crowther-Gibson P,du Plessis M,von Gottberg A

更新日期：2016-06-22 00:00:00

abstract：BACKGROUND:Many plant genes have been identified through whole genome and deep transcriptome sequencing and other methods; yet our knowledge on the function of many of these genes remains limited. The integration and analysis of large gene-expression datasets gives researchers the ability to formalize hypotheses concer...

journal_title：BMC genomics

authors： Wilson TJ,Lai L,Ban Y,Ge SX

更新日期：2012-06-13 00:00:00

abstract：BACKGROUND:The pituitary is a critical neuroendocrine gland that is comprised of five hormone-secreting cell types, which develops in tandem during the embryonic stage. Some essential genes have been identified in the early stage of adenohypophysial development, such as PITX1, FGF8, BMP4 and SF-1. However, it is likely...

journal_title：BMC genomics

authors： Ma Y,Qi X,Du J,Song S,Feng D,Qi J,Zhu Z,Zhang X,Xiao H,Han Z,Hao X

更新日期：2009-03-15 00:00:00

abstract：BACKGROUND:Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequenc...

journal_title：BMC genomics

authors： Kochan KJ,Amaral ME,Agarwala R,Schäffer AA,Riggs PK

更新日期：2008-11-17 00:00:00

abstract：:Following the publication of the original article [1], the authors reported an error in Fig. 2 of the PDF version of their article. ...

journal_title：BMC genomics

authors： Maarsingh JD,Yang S,Park JG,Haydel SE

更新日期：2019-12-31 00:00:00

abstract：BACKGROUND:According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including Kañaris, a Quechua-speaking community located at the highlands of the Province of Ferreñafe, Lam...

journal_title：BMC genomics

authors： Sandoval JR,Lacerda DR,Jota MMS,Robles-Ruiz P,Danos P,Paz-Y-Miño C,Wells S,Santos FR,Fujita R

更新日期：2020-09-10 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes such as growth, development and stress responses. Chilling is a common abiotic stress that seriously ...

journal_title：BMC genomics

authors： Cao X,Wu Z,Jiang F,Zhou R,Yang Z

更新日期：2014-12-17 00:00:00

abstract：BACKGROUND:The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will fac...

journal_title：BMC genomics

authors： Xu J,Qian X,Wang X,Li R,Cheng X,Yang Y,Fu J,Zhang S,King GJ,Wu J,Liu K

更新日期：2010-10-22 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:There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in promising applications such as gaining insights into bacterial drug resistance. RESULTS:Here, we propos...

journal_title：BMC genomics

authors： Wozniak M,Wong L,Tiuryn J

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hyb...

journal_title：BMC genomics

authors： Dawson DA,Ball AD,Spurgin LG,Martín-Gálvez D,Stewart IR,Horsburgh GJ,Potter J,Molina-Morales M,Bicknell AW,Preston SA,Ekblom R,Slate J,Burke T

更新日期：2013-03-15 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:Protein-protein interaction (PPI) maps are useful tools for investigating the cellular functions of genes. Thus far, large-scale PPI mapping projects have not been implemented for the rice blast fungus Magnaporthe grisea, which is responsible for the most severe rice disease. Inspired by recent advances in P...

journal_title：BMC genomics

authors： He F,Zhang Y,Chen H,Zhang Z,Peng YL

更新日期：2008-11-02 00:00:00

abstract：BACKGROUND:The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the gen...

journal_title：BMC genomics

authors： Dia N,Lavie L,Faye N,Méténier G,Yeramian E,Duroure C,Toguebaye BS,Frutos R,Niang MN,Vivarès CP,Ben Mamoun C,Cornillot E

更新日期：2016-01-07 00:00:00

abstract：BACKGROUND:Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and perfo...

journal_title：BMC genomics

authors： Northcutt AJ,Lett KM,Garcia VB,Diester CM,Lane BJ,Marder E,Schulz DJ

更新日期：2016-11-04 00:00:00

abstract：BACKGROUND:S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, ...

journal_title：BMC genomics

authors： Li YY,Chang X,Yu WB,Li H,Ye ZQ,Yu H,Liu BH,Zhang Y,Zhang SL,Ye BC,Li YX

更新日期：2013-07-31 00:00:00

abstract：BACKGROUND:Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited...

journal_title：BMC genomics

authors： Machida RJ,Hashiguchi Y,Nishida M,Nishida S

更新日期：2009-09-17 00:00:00

abstract：BACKGROUND:Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to...

journal_title：BMC genomics

authors： Pedersen C,Ver Loren van Themaat E,McGuffin LJ,Abbott JC,Burgis TA,Barton G,Bindschedler LV,Lu X,Maekawa T,Wessling R,Cramer R,Thordal-Christensen H,Panstruga R,Spanu PD

更新日期：2012-12-11 00:00:00

abstract：BACKGROUND:Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, t...

journal_title：BMC genomics

authors： Zamani N,Russell P,Lantz H,Hoeppner MP,Meadows JR,Vijay N,Mauceli E,di Palma F,Lindblad-Toh K,Jern P,Grabherr MG

更新日期：2013-05-24 00:00:00

abstract：BACKGROUND:Gene expression profiling is a promising approach to better estimate patient prognosis; however, there are still unresolved problems, including little overlap among similarly developed gene sets and poor performance of a developed gene set in other datasets. RESULTS:We applied a gene sets approach to develo...

journal_title：BMC genomics

authors： Kim SY,Kim YS

更新日期：2008-04-16 00:00:00

abstract：BACKGROUND:The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to...

journal_title：BMC genomics

authors： McGuire AM,Weiner B,Park ST,Wapinski I,Raman S,Dolganov G,Peterson M,Riley R,Zucker J,Abeel T,White J,Sisk P,Stolte C,Koehrsen M,Yamamoto RT,Iacobelli-Martinez M,Kidd MJ,Maer AM,Schoolnik GK,Regev A,Galagan J

更新日期：2012-03-28 00:00:00

abstract：BACKGROUND:Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and thre...

journal_title：BMC genomics

authors： Amiri Ghanatsaman Z,Wang GD,Asadollahpour Nanaei H,Asadi Fozi M,Peng MS,Esmailizadeh A,Zhang YP

更新日期：2020-03-04 00:00:00

abstract：BACKGROUND:Xanthomonas citri pv. citri (Xcc) is a citrus canker causing Gram-negative bacteria. Currently, little is known about the biological and molecular responses of Xcc to low temperatures. RESULTS:Results depicted that low temperature significantly reduced growth and increased biofilm formation and unsaturated ...

journal_title：BMC genomics

authors： Liao JX,Li KH,Wang JP,Deng JR,Liu QG,Chang CQ

更新日期：2019-11-06 00:00:00

abstract：BACKGROUND:The purpose of this research was to develop a novel information theoretic method and an efficient algorithm for analyzing the gene-gene (GGI) and gene-environmental interactions (GEI) associated with quantitative traits (QT). The method is built on two information-theoretic metrics, the k-way interaction inf...

journal_title：BMC genomics

authors： Chanda P,Sucheston L,Liu S,Zhang A,Ramanathan M

更新日期：2009-11-04 00:00:00

abstract：BACKGROUND:Whole transcriptome analyses are an essential tool for understanding disease mechanisms. Approaches based on next-generation sequencing provide fast and affordable data but rely on the availability of annotated genomes. However, there are many areas in biomedical research that require non-standard animal mod...

journal_title：BMC genomics

authors： Schmucki R,Berrera M,Küng E,Lee S,Thasler WE,Grüner S,Ebeling M,Certa U

更新日期：2013-04-10 00:00:00

abstract：BACKGROUND:Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regressi...

journal_title：BMC genomics

authors： Gong P,Nan X,Barker ND,Boyd RE,Chen Y,Wilkins DE,Johnson DR,Suedel BC,Perkins EJ

更新日期：2016-03-08 00:00:00

abstract：BACKGROUND:Accurate identification of synteny blocks is an important step in comparative genomics towards the understanding of genome architecture and expression. Most computer programs developed in the last decade for identifying synteny blocks have limitations. To address these limitations, we recently developed a ro...

journal_title：BMC genomics

authors： Vergara IA,Chen N

更新日期：2010-09-24 00:00:00

abstract：BACKGROUND:Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer...

journal_title：BMC genomics

authors： Yin C,Li M,Hu J,Lang K,Chen Q,Liu J,Guo D,He K,Dong Y,Luo J,Song Z,Walters JR,Zhang W,Li F,Chen X

更新日期：2018-05-30 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 is true for many other antibiotic-resistant Gram-negative pathogens, members of the Burkholderia cepacia complex (BCC) are currently being assessed for their susceptibility to phage therapy as an antimicrobial treatment. The objective of this study was to perform genomic and limited functional characteriz...

journal_title：BMC genomics

authors： Lynch KH,Abdu AH,Schobert M,Dennis JJ

更新日期：2013-08-27 00:00:00