Deep learning methods improve linear B-cell epitope prediction
B-cell epitopes play important roles in vaccine design, clinical diagnosis, and antibody production. Although some models have been developed to predict linear or conformational B-cell epitopes, their performa... (Source: BioData Mining)
Source: BioData Mining - April 17, 2020 Category: Bioinformatics Authors: Tao Liu, Kaiwen Shi and Wuju Li Tags: Methodology Source Type: research
Correction to: Investigating the parameter space of evolutionary algorithms
Following publication of the original article [1], an error was reported in one of the experiments. (Source: BioData Mining)
Source: BioData Mining - November 18, 2019 Category: Bioinformatics Authors: Moshe Sipper, Weixuan Fu, Karuna Ahuja and Jason H. Moore Tags: Correction Source Type: research
SEQdata-BEACON: a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500
The sequencing platform BGISEQ-500 is based on DNBSEQ technology and provides high throughput with low costs. This sequencer has been widely used in various areas of scientific and clinical research. A better ... (Source: BioData Mining)
Source: BioData Mining - November 15, 2019 Category: Bioinformatics Authors: Yanqiu Zhou, Chen Liu, Rongfang Zhou, Anzhi Lu, Biao Huang, Liling Liu, Ling Chen, Bei Luo, Jin Huang and Zhijian Tian Tags: Research Source Type: research
Screening for mouse genes lost in mammals with long lifespans
Gerontogenes include those that modulate life expectancy in various species and may be the actual longevity genes. We believe that a long (relative to body weight) lifespan in individual rodent and primate spe... (Source: BioData Mining)
Source: BioData Mining - November 9, 2019 Category: Bioinformatics Authors: Lev I. Rubanov, Andrey G. Zaraisky, Gregory A. Shilovsky, Alexandr V. Seliverstov, Oleg A. Zverkov and Vassily A. Lyubetsky Tags: Research Source Type: research
Predicting metabolite-disease associations based on KATZ model
Increasing numbers of evidences have illuminated that metabolites can respond to pathological changes. However, identifying the diseases-related metabolites is a magnificent challenge in the field of biology a... (Source: BioData Mining)
Source: BioData Mining - October 26, 2019 Category: Bioinformatics Authors: Xiujuan Lei and Cheng Zhang Tags: Research Source Type: research
Integrative analysis of genetic and epigenetic profiling of lung squamous cell carcinoma (LSCC) patients to identify smoking level relevant biomarkers
Incidence and mortality of lung cancer have dramatically decreased during the last decades, yet still approximately 160,000 deaths per year occurred in United States. Smoking intensity, duration, starting age,... (Source: BioData Mining)
Source: BioData Mining - October 21, 2019 Category: Bioinformatics Authors: Bidong Ma, Zhiyou Huang, Qian Wang, Jizhou Zhang, Bin Zhou and Jiaohong Wu Tags: Research Source Type: research
RNSCLC-PRSP software to predict the prognostic risk and survival in patients with resected T1-3N0 –2 M0 non-small cell lung cancer
The clinical outcomes of patients with resected T1-3N0 –2M0 non-small cell lung cancer (NSCLC) with the same tumor-node-metastasis (TNM) stage are diverse. Although other prognostic factors and prognostic predicti... (Source: BioData Mining)
Source: BioData Mining - August 23, 2019 Category: Bioinformatics Authors: Yunkui Zhang, YaoChen Li, Rongsheng Zhang, Yujie Zhang and Haitao Ma Tags: Software article Source Type: research
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontolog... (Source: BioData Mining)
Source: BioData Mining - August 6, 2019 Category: Bioinformatics Authors: Aur élien Brionne, Amélie Juanchich and Christelle Hennequet-Antier Tags: Short report Source Type: research
Disease associations depend on visit type: results from a visit-wide association study
Widespread adoption of Electronic Health Records (EHR) increased the number of reported disease association studies, or Phenome-Wide Association Studies (PheWAS). Traditional PheWAS studies ignore visit type (i.e... (Source: BioData Mining)
Source: BioData Mining - July 11, 2019 Category: Bioinformatics Authors: Mary Regina Boland, Snigdha Alur-Gupta, Lisa Levine, Peter Gabriel and Graciela Gonzalez-Hernandez Tags: Short report Source Type: research
Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies
The principal line of investigation in Genome Wide Association Studies (GWAS) is the identification of main effects, that is individual Single Nucleotide Polymorphisms (SNPs) which are associated with the trai... (Source: BioData Mining)
Source: BioData Mining - July 9, 2019 Category: Bioinformatics Authors: Elisabetta Manduchi, Patryk R. Orzechowski, Marylyn D. Ritchie and Jason H. Moore Tags: Research Source Type: research
On the utilization of deep and ensemble learning to detect milk adulteration
Fraudulent milk adulteration is a dangerous practice in the dairy industry that is harmful to consumers since milk is one of the most consumed food products. Milk quality can be assessed by Fourier Transformed... (Source: BioData Mining)
Source: BioData Mining - July 8, 2019 Category: Bioinformatics Authors: Habib Asseiss Neto, Wanessa L.F. Tavares, Daniela C.S.Z. Ribeiro, Ronnie C.O. Alves, Leorges M. Fonseca and S érgio V.A. Campos Tags: Methodology Source Type: research
ClickGene: an open cloud-based platform for big pan-cancer data genome-wide association study, visualization and exploration
Tremendous amount of whole-genome sequencing data have been provided by large consortium projects such as TCGA (The Cancer Genome Atlas), COSMIC and so on, which creates incredible opportunities for functional... (Source: BioData Mining)
Source: BioData Mining - June 26, 2019 Category: Bioinformatics Authors: Jia-Hao Bi, Yi-Fan Tong, Zhe-Wei Qiu, Xing-Feng Yang, John Minna, Adi F. Gazdar and Kai Song Tags: Software article Source Type: research
Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies
In Genome-Wide Association Studies (GWAS), the concept of linkage disequilibrium is important as it allows identifying genetic markers that tag the actual causal variants. In Genome-Wide Association Interactio... (Source: BioData Mining)
Source: BioData Mining - June 10, 2019 Category: Bioinformatics Authors: Marc Joiret, Jestinah M. Mahachie John, Elena S. Gusareva and Kristel Van Steen Tags: Research Source Type: research
Innovative strategies for annotating the “relationSNP” between variants and molecular phenotypes
Characterizing how variation at the level of individual nucleotides contributes to traits and diseases has been an area of growing interest since the completion of sequencing the first human genome. Our unders... (Source: BioData Mining)
Source: BioData Mining - May 14, 2019 Category: Bioinformatics Authors: Jason E. Miller, Yogasudha Veturi and Marylyn D. Ritchie Tags: Review Source Type: research
Within-sample co-methylation patterns in normal tissues
DNA methylation is an epigenetic event that may regulate gene expression. Because of this regulation role, aberrant DNA methylation is often associated with many diseases. Within-sample DNA co-methylation is t... (Source: BioData Mining)
Source: BioData Mining - May 9, 2019 Category: Bioinformatics Authors: Lillian Sun and Shuying Sun Tags: Research Source Type: research
