ACEP: improving antimicrobial peptides recognition through automatic feature fusion and amino acid embedding.

abstract：BACKGROUND:The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda w...

journal_title：BMC genomics

authors： Liu W,Zhao Y,Liu Z,Zhang Y,Lian Z,Li N

更新日期：2006-11-17 00:00:00

abstract：BACKGROUND:The capacity of European pear fruit (Pyrus communis L.) to ripen after harvest develops during the final stages of growth on the tree. The objective of this study was to characterize changes in 'Bartlett' pear fruit physico-chemical properties and transcription profiles during fruit maturation leading to att...

journal_title：BMC genomics

authors： Nham NT,de Freitas ST,Macnish AJ,Carr KM,Kietikul T,Guilatco AJ,Jiang CZ,Zakharov F,Mitcham EJ

更新日期：2015-10-09 00:00:00

abstract：BACKGROUND:Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species. RESULTS:Aiming at characterizing SDs across the genomes ...

journal_title：BMC genomics

authors： Feng X,Jiang J,Padhi A,Ning C,Fu J,Wang A,Mrode R,Liu JF

更新日期：2017-04-12 00:00:00

abstract：BACKGROUND:Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and...

journal_title：BMC genomics

authors： Xu F,Bao J,He Q,Park YJ

更新日期：2016-08-20 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in...

journal_title：BMC genomics

authors： Wang B,Ye N,Cao SJ,Wen XT,Huang Y,Yan QG

更新日期：2016-11-08 00:00:00

abstract：BACKGROUND:V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. RESULTS:We prop...

journal_title：BMC genomics

authors： Giraud M,Salson M,Duez M,Villenet C,Quief S,Caillault A,Grardel N,Roumier C,Preudhomme C,Figeac M

更新日期：2014-05-28 00:00:00

abstract：BACKGROUND:Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometr...

journal_title：BMC genomics

authors： Jhamat N,Niazi A,Guo Y,Chanrot M,Ivanova E,Kelsey G,Bongcam-Rudloff E,Andersson G,Humblot P

更新日期：2020-06-03 00:00:00

abstract：BACKGROUND:Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IP...

journal_title：BMC genomics

authors： Ma X,Zhao X,Wang K,Tang X,Guo J,Mi M,Qi Y,Chang L,Huang Y,Tong D

更新日期：2019-11-04 00:00:00

abstract：BACKGROUND:Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata) transcriptome using 454 sequence reads, and ...

journal_title：BMC genomics

authors： Fraser BA,Weadick CJ,Janowitz I,Rodd FH,Hughes KA

更新日期：2011-04-20 00:00:00

abstract：BACKGROUND:Dictyostelium discoideum is frequently subjected to environmental changes in its natural habitat, the forest soil. In order to survive, the organism had to develop effective mechanisms to sense and respond to such changes. When cells are faced with a hypertonic environment a complex response is triggered. It...

journal_title：BMC genomics

authors： Na J,Tunggal B,Eichinger L

更新日期：2007-05-21 00:00:00

abstract：MOTIVATION:With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree estimation is difficult in the presence of gene tree discordance, which is often due to incomplete l...

journal_title：BMC genomics

authors： Bayzid MS,Hunt T,Warnow T

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or very low temperatures. Being able to accurately predict this based on a genomic sequence, would thu...

journal_title：BMC genomics

authors： Jensen DB,Vesth TC,Hallin PF,Pedersen AG,Ussery DW

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...

journal_title：BMC genomics

authors： Zhang X,Liu X,Li L,Wei G,Zhang D,Liang Y,Miao B

更新日期：2019-05-30 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:Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane va...

journal_title：BMC genomics

authors： Yang H,Wang T,Yu X,Yang Y,Wang C,Yang Q,Wang X

更新日期：2020-07-22 00:00:00

abstract：BACKGROUND:Frontotemporal lobar degeneration (FTLD) is a progressive neurodegenerative disorder that can be triggered through genetic or sporadic mechanisms. MicroRNAs (miRNAs) have become a major therapeutic focus as their pervasive expression and powerful regulatory roles in disease pathogenesis become increasingly a...

journal_title：BMC genomics

authors： Kocerha J,Kouri N,Baker M,Finch N,DeJesus-Hernandez M,Gonzalez J,Chidamparam K,Josephs KA,Boeve BF,Graff-Radford NR,Crook J,Dickson DW,Rademakers R

更新日期：2011-10-27 00:00:00

abstract：BACKGROUND:The complex genome of rapeseed (Brassica napus) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence gen...

journal_title：BMC genomics

authors： Bus A,Hecht J,Huettel B,Reinhardt R,Stich B

更新日期：2012-06-24 00:00:00

abstract：BACKGROUND:In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However,...

journal_title：BMC genomics

authors： Qiu H,Hildebrand F,Kuraku S,Meyer A

更新日期：2011-06-23 00:00:00

abstract：BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of i...

journal_title：BMC genomics

authors： Cho YB,Lee EJ,Cho S,Kim TY,Park JH,Cho BK

更新日期：2016-02-29 00:00:00

abstract：BACKGROUND:The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inference...

journal_title：BMC genomics

authors： Yang W,Rosenstiel PC,Schulenburg H

更新日期：2016-08-04 00:00:00

abstract：BACKGROUND:Streptococcus infantarius subsp. infantarius (Sii) belongs to the Streptococcus bovis/Streptococcus equinus complex associated with several human and animal infections. Sii is a predominant bacterium in spontaneously fermented milk products in Africa. The genome sequence of Sii strain CJ18 was compared with ...

journal_title：BMC genomics

authors： Jans C,Follador R,Hochstrasser M,Lacroix C,Meile L,Stevens MJ

更新日期：2013-03-22 00:00:00

abstract：BACKGROUND:RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kits. To date there has been no analysis of the effect of these choices on identifying differentially e...

journal_title：BMC genomics

authors： Corley SM,MacKenzie KL,Beverdam A,Roddam LF,Wilkins MR

更新日期：2017-05-23 00:00:00

abstract：BACKGROUND:An estimated 15,000 children and adolescents under the age of 19 years are diagnosed with leukemia, lymphoma and other tumors in the USA every year. All children and adolescent acute leukemia patients will undergo chemotherapy as part of their treatment regimen. Fortunately, survival rates for most pediatric...

journal_title：BMC genomics

authors： Rajagopala SV,Yooseph S,Harkins DM,Moncera KJ,Zabokrtsky KB,Torralba MG,Tovchigrechko A,Highlander SK,Pieper R,Sender L,Nelson KE

更新日期：2016-08-15 00:00:00

abstract：BACKGROUND:Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown...

journal_title：BMC genomics

authors： Zhang L,Zuo K,Zhang F,Cao Y,Wang J,Zhang Y,Sun X,Tang K

更新日期：2006-12-25 00:00:00

abstract：BACKGROUND:At sexual maturity, the liver of laying hens undergoes many metabolic changes to support vitellogenesis. In published transcriptomic approaches, hundreds of genes were reported to be overexpressed in laying hens and functional gene annotation using gene ontology tools have essentially revealed an enrichment ...

journal_title：BMC genomics

authors： Gloux A,Duclos MJ,Brionne A,Bourin M,Nys Y,Réhault-Godbert S

更新日期：2019-11-07 00:00:00

abstract：BACKGROUND:Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq...

journal_title：BMC genomics

authors： Zepeda-Mendoza CJ,Mukhopadhyay S,Wong ES,Harder N,Splinter E,de Wit E,Eckersley-Maslin MA,Ried T,Eils R,Rohr K,Mills A,de Laat W,Flicek P,Sengupta AM,Spector DL

更新日期：2015-11-21 00:00:00

abstract：BACKGROUND:GLV-1h68 is an attenuated recombinant vaccinia virus (VACV) that selectively colonizes established human xenografts inducing their complete regression. RESULTS:Here, we explored xenograft/VACV/host interactions in vivo adopting organism-specific expression arrays and tumor cell/VACV in vitro comparing VACV ...

journal_title：BMC genomics

authors： Worschech A,Chen N,Yu YA,Zhang Q,Pos Z,Weibel S,Raab V,Sabatino M,Monaco A,Liu H,Monsurró V,Buller RM,Stroncek DF,Wang E,Szalay AA,Marincola FM

更新日期：2009-07-07 00:00:00

abstract：BACKGROUND:Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the pre...

journal_title：BMC genomics

authors： Chen J,Dong X,Li Q,Zhou X,Gao S,Chen R,Sun L,Zhang L,Chen W

更新日期：2013-12-05 00:00:00

abstract：BACKGROUND:RNA editing is an important mechanism that expands the diversity and complexity of genetic codes. The conversions of adenosine (A) to inosine (I) and cytosine (C) to uridine (U) are two prominent types of RNA editing in animals. The roles of RNA editing events have been implicated in important biological pat...

journal_title：BMC genomics

authors： Cao Y,Cao R,Huang Y,Zhou H,Liu Y,Li X,Zhong W,Hao P

更新日期：2018-01-19 00:00:00

abstract：BACKGROUND:Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptation contribute to the formation of ecotypically differentiated groups of plants is just beginning to b...

journal_title：BMC genomics

authors： Gould BA,Palacio-Mejia JD,Jenkins J,Mamidi S,Barry K,Schmutz J,Juenger TE,Lowry DB

更新日期：2018-11-01 00:00:00