AIMC Topic: Whole Genome Sequencing
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Identifying genetic determinants of complex phenotypes from whole genome sequence data.
BMC genomics
Jun 10, 2019
BACKGROUND: A critical goal in biology is to relate the phenotype to the genotype, that is, to find the genetic determinants of various traits. However, while simple monofactorial determinants are relatively easy to identify, the underpinnings of com...
NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans.
Genome biology
Feb 11, 2019
State-of-the-art methods assessing pathogenic non-coding variants have mostly been characterized on common disease-associated polymorphisms, yet with modest accuracy and strong positional biases. In this study, we curated 737 high-confidence pathogen...
OMeta: an ontology-based, data-driven metadata tracking system.
BMC bioinformatics
Jan 7, 2019
BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association stu...
Prognostic models in primary biliary cholangitis.
Journal of autoimmunity
Nov 9, 2018
Risk prediction modelling is important to better understand the determinants of the course and outcome of PBC and to inform the risk across the disease continuum in PBC enabling risk-stratified follow-up care and personalised therapy. Current prognos...
The first two mitochondrial genomes from Taeniopterygidae (Insecta: Plecoptera): Structural features and phylogenetic implications.
International journal of biological macromolecules
Dec 29, 2017
The complete mitochondrial genomes (mitogenomes) of Taeniopteryx ugola and Doddsia occidentalis (Plecoptera: Taeniopterygidae) were firstly sequenced from the family Taeniopterygidae. The 15,353-bp long mitogenome of T. ugola and the 16,020-bp long m...
HRProfiler Detects Homologous Recombination Deficiency in Breast and Ovarian Cancers Using Whole-Genome and Whole-Exome Sequencing Data.
Cancer research
Jul 2, 2025
UNLABELLED: Breast and ovarian cancers harboring homologous recombination deficiency (HRD) are sensitive to PARP inhibitors and platinum chemotherapy. Conventionally, detecting HRD involves screening for defects in BRCA1, BRCA2, and other relevant ge...
In-depth analysis of the risk factors for persistent severe acute respiratory syndrome coronavirus 2 infection and construction of predictive models: an exploratory research study.
BMC infectious diseases
May 14, 2025
BACKGROUND: Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection differs from long coronavirus disease (COVID-19) (acute symptoms ≥ 12 weeks post-clearance). The Omicron BA.5 variant has a shorter median clearance time (1...
Noninvasive fetal genotyping using deep neural networks.
Briefings in bioinformatics
Nov 22, 2024
Circulating cell-free DNA (cfDNA) is a powerful diagnostics tool that is widely studied in the context of liquid biopsy in oncology and other fields. In obstetrics, maternal plasma cfDNA have already proven its utility, enabling noninvasive prenatal ...
Prediction of Antibiotic Susceptibility in E. coli Isolates Using Machine Learning.
Studies in health technology and informatics
Sep 24, 2024
Antimicrobial resistance (AMR) poses a significant global health threat, resulting in 4.96 million deaths in 2019, with projections reaching 10 million by 2050. This resistance, primarily due to the overuse of antibiotics, complicates the treatment o...
Validation and depth evaluation of recurrent neural network-based ultra low-pass genome sequencing for the detection of absence of heterozygosity: A multi-centre study of 409 cases.
Clinical and translational medicine
Jul 1, 2024
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