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


BACKGROUND:Antimicrobial resistance is one of our most serious health threats. Antimicrobial peptides (AMPs), effecter molecules of innate immune system, can defend host organisms against microbes and most have shown a lowered likelihood for bacteria to form resistance compared to many conventional drugs. Thus, AMPs are gaining popularity as better substitute to antibiotics. To aid researchers in novel AMPs discovery, we design computational approaches to screen promising candidates. RESULTS:In this work, we design a deep learning model that can learn amino acid embedding patterns, automatically extract sequence features, and fuse heterogeneous information. Results show that the proposed model outperforms state-of-the-art methods on recognition of AMPs. By visualizing data in some layers of the model, we overcome the black-box nature of deep learning, explain the working mechanism of the model, and find some import motifs in sequences. CONCLUSIONS:ACEP model can capture similarity between amino acids, calculate attention scores for different parts of a peptide sequence in order to spot important parts that significantly contribute to final predictions, and automatically fuse a variety of heterogeneous information or features. For high-throughput AMPs recognition, open source software and datasets are made freely available at .


BMC Genomics


BMC genomics


Fu H,Cao Z,Li M,Wang S




Has Abstract


2020-08-28 00:00:00












  • Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca).

    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

    pub_type: 杂志文章


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

    更新日期:2006-11-17 00:00:00

  • A transcriptome approach towards understanding the development of ripening capacity in 'Bartlett' pears (Pyrus communis L.).

    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

    pub_type: 杂志文章


    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

  • Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals.

    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

    pub_type: 杂志文章


    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

  • Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.).

    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

    pub_type: 杂志文章


    authors: Xu F,Bao J,He Q,Park YJ

    更新日期:2016-08-20 00:00:00

  • Identification of novel and differentially expressed MicroRNAs in goat enzootic nasal adenocarcinoma.

    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

    pub_type: 杂志文章


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

    更新日期:2016-11-08 00:00:00

  • Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.

    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

    pub_type: 杂志文章


    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

  • LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.

    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

    pub_type: 杂志文章


    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

  • Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection.

    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

    pub_type: 杂志文章


    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

  • Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome.

    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

    pub_type: 杂志文章


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

    更新日期:2011-04-20 00:00:00

  • STATc is a key regulator of the transcriptional response to hyperosmotic shock.

    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

    pub_type: 杂志文章


    authors: Na J,Tunggal B,Eichinger L

    更新日期:2007-05-21 00:00:00

  • Disk covering methods improve phylogenomic analyses.

    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

    pub_type: 杂志文章


    authors: Bayzid MS,Hunt T,Warnow T

    更新日期:2014-01-01 00:00:00

  • Bayesian prediction of bacterial growth temperature range based on genome sequences.

    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

    pub_type: 杂志文章


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

    更新日期:2012-01-01 00:00:00

  • Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations.

    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

    pub_type: 杂志文章


    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

  • Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures.

    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

    pub_type: 杂志文章


    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

  • Enhanced sugar accumulation and regulated plant hormone signalling genes contribute to cold tolerance in hypoploid Saccharum spontaneum.

    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

    pub_type: 杂志文章


    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

  • Altered microRNA expression in frontotemporal lobar degeneration with TDP-43 pathology caused by progranulin mutations.

    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

    pub_type: 杂志文章


    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

  • High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing.

    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

    pub_type: 杂志文章


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

    更新日期:2012-06-24 00:00:00

  • Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case.

    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

    pub_type: 杂志文章


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

    更新日期:2011-06-23 00:00:00

  • Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase.

    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

    pub_type: 杂志文章


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

    更新日期:2016-02-29 00:00:00

  • ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences.

    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

    pub_type: 杂志文章


    authors: Yang W,Rosenstiel PC,Schulenburg H

    更新日期:2016-08-04 00:00:00

  • Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment.

    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

    pub_type: 杂志文章


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

    更新日期:2013-03-22 00:00:00

  • Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols.

    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

    pub_type: 杂志文章


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

    更新日期:2017-05-23 00:00:00

  • Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.

    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

    pub_type: 杂志文章


    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

  • Conservation of noncoding microsatellites in plants: implication for gene regulation.

    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

    pub_type: 杂志文章


    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

  • Integrative analysis of transcriptomic data related to the liver of laying hens: from physiological basics to newly identified functions.

    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

    pub_type: 杂志文章


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

    更新日期:2019-11-07 00:00:00

  • Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.

    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

    pub_type: 杂志文章


    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

  • Systemic treatment of xenografts with vaccinia virus GLV-1h68 reveals the immunologic facet of oncolytic therapy.

    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

    pub_type: 杂志文章


    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

  • Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling.

    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

    pub_type: 杂志文章


    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

  • A comprehensive study on cellular RNA editing activity in response to infections with different subtypes of influenza a viruses.

    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

    pub_type: 杂志文章


    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

  • Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae).

    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

    pub_type: 杂志文章


    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