Aging in the Drosophila ovary: contrasting changes in the expression of the piRNA machinery and mitochondria but no global release of transposable elements.

abstract：BACKGROUND:Wood formation affects the chemical and physical properties of wood, and thus affects its utility as a building material or a feedstock for biofuels, pulp and paper. To obtain genome-wide insights on the transcriptome changes and regulatory networks in wood formation, we used high-throughput RNA sequencing t...

journal_title：BMC genomics

authors： Chen J,Chen B,Zhang D

更新日期：2015-03-10 00:00:00

abstract：BACKGROUND:Effector proteins are translocated into host cells by plant-pathogens to undermine pattern-triggered immunity (PTI), the plant response to microbe-associated molecular patterns that interferes with the infection process. Individual effectors are found in variable repertoires where some constituents target th...

journal_title：BMC genomics

authors： Worley JN,Pombo MA,Zheng Y,Dunham DM,Myers CR,Fei Z,Martin GB

更新日期：2016-03-14 00:00:00

abstract：BACKGROUND:Three-dimensional (3D) multicellular spheroids of mesenchymal stem cells (MSCs) are generally regarded to have beneficial properties over MSCs in monolayer. Recent literatures have documented that MSCs can self-assemble into 3D spheroids with a greater capacity for differentiation into various cell types whe...

journal_title：BMC genomics

authors： Yeh HY,Liu BH,Sieber M,Hsu SH

更新日期：2014-01-05 00:00:00

abstract：BACKGROUND:Genome-wide expression profiles are altered during biological aging and can describe molecular regulation of tissue degeneration. Age-regulated mRNA expression trends from cross-sectional studies could describe how aging progresses. We developed a novel statistical methodology to identify age-regulated expre...

journal_title：BMC genomics

authors： Gheorghe M,Snoeck M,Emmerich M,Bäck T,Goeman JJ,Raz V

更新日期：2014-02-14 00:00:00

abstract：BACKGROUND:Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic i...

journal_title：BMC genomics

authors： Heitlinger E,Bridgett S,Montazam A,Taraschewski H,Blaxter M

更新日期：2013-02-08 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:Identification and classification of highly similar microbial strains is a challenging issue in microbiology, ecology and evolutionary biology. Among various available approaches, gene content analysis is also at the core of microbial taxonomy. However, no threshold has been determined for grouping microorgn...

journal_title：BMC genomics

authors： Tu Q,Lin L

更新日期：2016-08-17 00:00:00

abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. RESULTS:In this study, we investigated ...

journal_title：BMC genomics

authors： Liu S,An Y,Tong W,Qin X,Samarina L,Guo R,Xia X,Wei C

更新日期：2019-12-05 00:00:00

abstract：BACKGROUND:A disease-causing mutation refers to a heritable genetic change that is associated with a specific phenotype (disease). The detection of a mutation from a patient's sample is critical for the diagnosis, treatment, and prognosis of the disease. There are numerous databases and applications with which to archi...

journal_title：BMC genomics

authors： Jho S,Kim BC,Ghang H,Kim JH,Park D,Kim HM,Jung SY,Yoo KY,Kim HJ,Lee S,Bhak J

更新日期：2009-12-03 00:00:00

abstract：BACKGROUND:Fragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population. Based on the frequency of fragile site induction, they are categorized as common and rare fragile sites. Common fragile sites are sensitive to replication stress and often rearra...

journal_title：BMC genomics

authors： Kumar R,Nagpal G,Kumar V,Usmani SS,Agrawal P,Raghava GPS

更新日期：2019-04-18 00:00:00

abstract：BACKGROUND:ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher...

journal_title：BMC genomics

authors： Ou J,Liu H,Yu J,Kelliher MA,Castilla LH,Lawson ND,Zhu LJ

更新日期：2018-03-01 00:00:00

abstract：BACKGROUND:Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use ...

journal_title：BMC genomics

authors： Money D,Migicovsky Z,Gardner K,Myles S

更新日期：2017-07-10 00:00:00

abstract：BACKGROUND:In recent years, dozens of Arabidopsis and rice CCCH-type zinc finger genes have been functionally studied, many of which confer important traits, such as abiotic and biotic stress tolerance, delayed leaf senescence and improved plant architecture. Switchgrass (Panicum virgatum) is an important bioenergy cro...

journal_title：BMC genomics

authors： Yuan S,Xu B,Zhang J,Xie Z,Cheng Q,Yang Z,Cai Q,Huang B

更新日期：2015-02-25 00:00:00

abstract：BACKGROUND:Many bacteria can deliver pathogenic proteins (effectors) through type IV secretion systems (T4SSs) to eukaryotic cytoplasm, causing host diseases. The inherent property, such as sequence diversity and global scattering throughout the whole genome, makes it a big challenge to effectively identify the full se...

journal_title：BMC genomics

authors： Wang Y,Wei X,Bao H,Liu SL

更新日期：2014-01-21 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:The question of whether synonymous codon choice is affected by cellular tRNA abundance has been positively answered in many organisms. In some recent works, concerning the human genome, this relation has been studied, but no conclusive answers have been found. In the human genome, the variation in base compo...

journal_title：BMC genomics

authors： Kotlar D,Lavner Y

更新日期：2006-04-03 00:00:00

abstract：BACKGROUND:Soybean (Glycine max) is an important oil provider and ecosystem participant. The protein phosphatase 2C (PP2C) plays important roles in key biological processes. Molecular evolution and functional analysis of the PP2C family in soybean are yet to be reported. RESULTS:The present study identified 134 GmPP2C...

journal_title：BMC genomics

authors： Fan K,Chen Y,Mao Z,Fang Y,Li Z,Lin W,Zhang Y,Liu J,Huang J,Lin W

更新日期：2020-07-06 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:The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constrain...

journal_title：BMC genomics

authors： Alam MT,Merlo ME,STREAM Consortium.,Hodgson DA,Wellington EM,Takano E,Breitling R

更新日期：2010-03-26 00:00:00

abstract：BACKGROUND:The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a ...

journal_title：BMC genomics

authors： Ishii K,Washio T,Uechi T,Yoshihama M,Kenmochi N,Tomita M

更新日期：2006-02-28 00:00:00

abstract：BACKGROUND:In many microbial genomes, a strong preference for a small number of codons can be observed in genes whose products are needed by the cell in large quantities. This codon usage bias (CUB) improves translational accuracy and speed and is one of several factors optimizing cell growth. Whereas CUB and the overr...

journal_title：BMC genomics

authors： von Mandach C,Merkl R

更新日期：2010-11-04 00:00:00

abstract：BACKGROUND:Propionibacterium acnes and Staphylococcus epidermidis live in close proximity on human skin, and both bacterial species can be isolated from normal and acne vulgaris-affected skin sites. The antagonistic interactions between the two species are poorly understood, as well as the potential significance of bac...

journal_title：BMC genomics

authors： Christensen GJ,Scholz CF,Enghild J,Rohde H,Kilian M,Thürmer A,Brzuszkiewicz E,Lomholt HB,Brüggemann H

更新日期：2016-02-29 00:00:00

abstract：BACKGROUND:Dimension reduction is a critical issue in the analysis of microarray data, because the high dimensionality of gene expression microarray data set hurts generalization performance of classifiers. It consists of two types of methods, i.e. feature selection and feature extraction. Principle component analysis ...

journal_title：BMC genomics

authors： Li GZ,Bu HL,Yang MQ,Zeng XQ,Yang JY

更新日期：2008-09-16 00:00:00

abstract：BACKGROUND:The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative ana...

journal_title：BMC genomics

authors： Auvinet J,Graça P,Belkadi L,Petit L,Bonnivard E,Dettaï A,Detrich WH 3rd,Ozouf-Costaz C,Higuet D

更新日期：2018-05-09 00:00:00

abstract：BACKGROUND:Rhesus macaques serve a critical role in the study of human biomedical research. While both Indian and Chinese rhesus macaques are commonly used, genetic differences between these two subspecies affect aspects of their behavior and physiology, including response to simian immunodeficiency virus (SIV) infecti...

journal_title：BMC genomics

authors： Ferguson B,Street SL,Wright H,Pearson C,Jia Y,Thompson SL,Allibone P,Dubay CJ,Spindel E,Norgren RB Jr

更新日期：2007-02-07 00:00:00

abstract：BACKGROUND:Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the com...

journal_title：BMC genomics

authors： Wang JT,Li JT,Zhang XF,Sun XW

更新日期：2012-03-19 00:00:00

abstract：BACKGROUND:Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabol...

journal_title：BMC genomics

authors： Fonknechten N,Chaussonnerie S,Tricot S,Lajus A,Andreesen JR,Perchat N,Pelletier E,Gouyvenoux M,Barbe V,Salanoubat M,Le Paslier D,Weissenbach J,Cohen GN,Kreimeyer A

更新日期：2010-10-11 00:00:00

abstract：BACKGROUND:Non-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific importance in biological research. Several studies in recent years have reported a small number of non-c...

journal_title：BMC genomics

authors： Wang L,Yu X,Wang H,Lu YZ,de Ruiter M,Prins M,He YK

更新日期：2011-06-03 00:00:00

abstract：BACKGROUND:Mammalian genomes contain a large number (approximately 1000) of olfactory receptor (OR) genes, many of which (20 to 50%) are pseudogenes. OR gene transcription is not restricted to the olfactory epithelium, but is found in numerous tissues. Using microarray hybridization and RTqPCR, we analyzed the mRNA pro...

journal_title：BMC genomics

authors： Rimbault M,Robin S,Vaysse A,Galibert F

更新日期：2009-12-02 00:00:00

abstract：UNLABELLED:Little is known, either experimentally or computationally, about the genomic sequence features that regulate malaria genes. A sequence conservation analysis of the malaria species P. falciparum, P. berghei, P. yoelii, and P. chabaudi could significantly advance knowledge of malaria gene regulation. RESULTS:...

journal_title：BMC genomics

authors： Imamura H,Persampieri JH,Chuang JH

更新日期：2007-10-15 00:00:00