Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum.

abstract：BACKGROUND:Regions of the genome that are under evolutionary constraint across multiple species have previously been used to identify functional sequences in the human genome. Furthermore, it is known that there is an inverse relationship between evolutionary constraint and the allele frequency of a mutation segregatin...

journal_title：BMC genomics

authors： Hodgkinson A,Casals F,Idaghdour Y,Grenier JC,Hernandez RD,Awadalla P

更新日期：2013-07-23 00:00:00

abstract：BACKGROUND:Copy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contribute to these methods by using sequence read depth, which takes the number of reads that map to a gi...

journal_title：BMC genomics

authors： Forni D,Martin D,Abujaber R,Sharp AJ,Sironi M,Hollox EJ

更新日期：2015-11-02 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:It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown. RESULTS:Choanoflagellates are phagotrophs and the closest living relatives ...

journal_title：BMC genomics

authors： Yue J,Sun G,Hu X,Huang J

更新日期：2013-10-25 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:Fasting induces specific molecular and metabolic adaptions in most organisms. In biomedical research fasting is used in metabolic studies to synchronize nutritional states of study subjects. Because there is a lack of standardization for this procedure, we need a deeper understanding of the dynamics and the ...

journal_title：BMC genomics

authors： Schupp M,Chen F,Briggs ER,Rao S,Pelzmann HJ,Pessentheiner AR,Bogner-Strauss JG,Lazar MA,Baldwin D,Prokesch A

更新日期：2013-11-05 00:00:00

abstract：BACKGROUND:Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. In the pre...

journal_title：BMC genomics

authors： Vieira FA,Gregório SF,Ferraresso S,Thorne MA,Costa R,Milan M,Bargelloni L,Clark MS,Canario AV,Power DM

更新日期：2011-10-07 00:00:00

abstract：BACKGROUND:Comparative genomics approaches have facilitated the discovery of many novel non-coding and structured RNAs (ncRNAs). The increasing availability of related genomes now makes it possible to systematically search for compensatory base changes - and thus for conserved secondary structures - even in genomic reg...

journal_title：BMC genomics

authors： Kirsch R,Seemann SE,Ruzzo WL,Cohen SM,Stadler PF,Gorodkin J

更新日期：2018-12-11 00:00:00

abstract：BACKGROUND:Inferring the microbial interaction networks (MINs) and modeling their dynamics are critical in understanding the mechanisms of the bacterial ecosystem and designing antibiotic and/or probiotic therapies. Recently, several approaches were proposed to infer MINs using the generalized Lotka-Volterra (gLV) mode...

journal_title：BMC genomics

authors： Alshawaqfeh M,Serpedin E,Younes AB

更新日期：2017-03-27 00:00:00

abstract：BACKGROUND:For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. RESULTS:Here, we used a combination of ...

journal_title：BMC genomics

authors： Dubois A,Carrere S,Raymond O,Pouvreau B,Cottret L,Roccia A,Onesto JP,Sakr S,Atanassova R,Baudino S,Foucher F,Le Bris M,Gouzy J,Bendahmane M

更新日期：2012-11-20 00:00:00

abstract：BACKGROUND:Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primaril...

journal_title：BMC genomics

authors： Grusz AL,Rothfels CJ,Schuettpelz E

更新日期：2016-08-30 00:00:00

abstract：BACKGROUND:Hepatitis C virus (HCV) is a rapidly evolving RNA virus that has been classified into seven genotypes. All HCV genotypes cause chronic hepatitis, which ultimately leads to liver diseases such as cirrhosis. The genotypes are unevenly distributed across the globe, with genotypes 1 and 3 being the most prevalen...

journal_title：BMC genomics

authors： Bull RA,Eltahla AA,Rodrigo C,Koekkoek SM,Walker M,Pirozyan MR,Betz-Stablein B,Toepfer A,Laird M,Oh S,Heiner C,Maher L,Schinkel J,Lloyd AR,Luciani F

更新日期：2016-03-17 00:00:00

abstract：BACKGROUND:Functional analysis of the catfish genome will be useful for the identification of genes controlling traits of economic importance, especially innate disease resistance. However, this species lacks a platform for global gene expression profiling, so we designed a first generation high-density oligonucleotide...

journal_title：BMC genomics

authors： Li RW,Waldbieser GC

更新日期：2006-06-01 00:00:00

abstract：BACKGROUND:Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; th...

journal_title：BMC genomics

authors： Xia X,Zhang S,Zhang H,Zhang Z,Chen N,Li Z,Sun H,Liu X,Lyu S,Wang X,Li Z,Yang P,Xu J,Ding X,Shi Q,Wang E,Ru B,Xu Z,Lei C,Chen H,Huang Y

更新日期：2021-01-09 00:00:00

abstract：BACKGROUND:Microarray gene expression (MAGE) signatures allow insights into the transcriptional processes of leukemias and may evolve as a molecular diagnostic test. Introduction of MAGE into clinical practice of leukemia diagnosis will require comprehensive assessment of variation due to the methodologies. Here we sys...

journal_title：BMC genomics

authors： Campo Dell'Orto M,Zangrando A,Trentin L,Li R,Liu WM,te Kronnie G,Basso G,Kohlmann A

更新日期：2007-06-22 00:00:00

abstract：BACKGROUND:Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model organisms including zebrafish. Recently, long single-stranded DNA (lssDNA) molecules have been developed...

journal_title：BMC genomics

authors： Bai H,Liu L,An K,Lu X,Harrison M,Zhao Y,Yan R,Lu Z,Li S,Lin S,Liang F,Qin W

更新日期：2020-01-21 00:00:00

abstract：BACKGROUND:Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mechanisms remain largely unknown. In this study, to better understand mechanisms underlying gametogenesi...

journal_title：BMC genomics

authors： Chiu YL,Shikina S,Yoshioka Y,Shinzato C,Chang CF

更新日期：2020-10-21 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:Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis w...

journal_title：BMC genomics

authors： Cheng D,Tan M,Yu H,Li L,Zhu D,Chen Y,Jiang M

更新日期：2018-09-26 00:00:00

abstract：BACKGROUND:Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the n...

journal_title：BMC genomics

authors： Pooyaei Mehr SF,DeSalle R,Kao HT,Narechania A,Han Z,Tchernov D,Pieribone V,Gruber DF

更新日期：2013-08-12 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:Adaptations to a new environment, such as a polluted one, often involve large modifications of the existing phenotypes. Changes in gene expression and regulation during critical developmental stages may explain these phenotypic changes. Embryos from a population of the teleost fish, Fundulus heteroclitus, in...

journal_title：BMC genomics

authors： Bozinovic G,Sit TL,Di Giulio R,Wills LF,Oleksiak MF

更新日期：2013-11-11 00:00:00

abstract：BACKGROUND:Aedes aegypti is the principle vector of many arboviruses, including dengue virus and Zika virus, which are transmitted when an infected female mosquito takes a blood meal in order to initiate vitellogenesis. During blood digestion, ~ 10 mM heme-iron is ingested into the midgut lumen. While heme acts as both...

journal_title：BMC genomics

authors： Eggleston H,Adelman ZN

更新日期：2020-08-31 00:00:00

abstract：BACKGROUND:Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have b...

journal_title：BMC genomics

authors： Tran Vdu T,Chassignet P,Sheikh S,Steyaert JM

更新日期：2012-04-12 00:00:00

abstract：BACKGROUND:Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI), which could be re...

journal_title：BMC genomics

authors： Toussaint J,Sieuwerts AM,Haibe-Kains B,Desmedt C,Rouas G,Harris AL,Larsimont D,Piccart M,Foekens JA,Durbecq V,Sotiriou C

更新日期：2009-09-10 00:00:00

abstract：BACKGROUND:Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not annotated) variation, is problematic for follow up analyses. Polymorphisms result in a high inciden...

journal_title：BMC genomics

authors： Walter NA,Bottomly D,Laderas T,Mooney MA,Darakjian P,Searles RP,Harrington CA,McWeeney SK,Hitzemann R,Buck KJ

更新日期：2009-08-17 00:00:00

abstract：BACKGROUND:Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale...

journal_title：BMC genomics

authors： Lescot M,Piffanelli P,Ciampi AY,Ruiz M,Blanc G,Leebens-Mack J,da Silva FR,Santos CM,D'Hont A,Garsmeur O,Vilarinhos AD,Kanamori H,Matsumoto T,Ronning CM,Cheung F,Haas BJ,Althoff R,Arbogast T,Hine E,Pappas GJ Jr,Sas

更新日期：2008-01-30 00:00:00

abstract：BACKGROUND:MECP2, the gene mutated in the majority of Rett syndrome cases, is a transcriptional regulator that can activate or repress transcription. Although the transcription regulatory function of MECP2 has been known for over a decade, it remains unclear how transcriptional dysregulation leads to the neurodevelopme...

journal_title：BMC genomics

authors： Lin P,Nicholls L,Assareh H,Fang Z,Amos TG,Edwards RJ,Assareh AA,Voineagu I

更新日期：2016-06-06 00:00:00

abstract：BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi...

journal_title：BMC genomics

authors： McKinlay JB,Laivenieks M,Schindler BD,McKinlay AA,Siddaramappa S,Challacombe JF,Lowry SR,Clum A,Lapidus AL,Burkhart KB,Harkins V,Vieille C

更新日期：2010-11-30 00:00:00

abstract：BACKGROUND:Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or stuck fermentations. Selection and development of new Saccharomyces cerevisiae strains well adapted a...

journal_title：BMC genomics

authors： López-Malo M,García-Rios E,Melgar B,Sanchez MR,Dunham MJ,Guillamón JM

更新日期：2015-07-22 00:00:00