AIMC Topic: Genome, Human
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Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.
American journal of human genetics
Feb 9, 2017
The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or contaminated or if they include unintended individuals. Unfortunately, the potential for such errors is...
A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes.
Journal of integrative bioinformatics
Dec 22, 2016
Identification of microRNA (miRNA) precursors has seen increased efforts in recent years. The difficulty in experimental detection of pre-miRNAs increased the usage of computational approaches. Most of these approaches rely on machine learning especi...
Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology.
BioMed research international
Aug 22, 2016
Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference ...
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Nucleic acids research
May 3, 2016
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gen...
S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning.
PLoS genetics
Mar 15, 2016
Detecting the targets of adaptive natural selection from whole genome sequencing data is a central problem for population genetics. However, to date most methods have shown sub-optimal performance under realistic demographic scenarios. Moreover, over...
A knowledgebase of the human Alu repetitive elements.
Journal of biomedical informatics
Jan 28, 2016
Alu elements are the most abundant retrotransposons in the human genome with more than one million copies. Alu repeats have been reported to participate in multiple processes related with genome regulation and compartmentalization. Moreover, they hav...
Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.
BMC bioinformatics
Jan 11, 2016
BACKGROUND: Understanding the mechanisms by which transcription factors (TF) are recruited to their physiological target sites is crucial for understanding gene regulation. DNA sequence intrinsic features such as predicted binding affinity are often ...
Machine-Learning-Based Analysis in Genome-Edited Cells Reveals the Efficiency of Clathrin-Mediated Endocytosis.
Cell reports
Sep 17, 2015
Cells internalize various molecules through clathrin-mediated endocytosis (CME). Previous live-cell imaging studies suggested that CME is inefficient, with about half of the events terminated. These CME efficiency estimates may have been confounded b...
Genome Modeling System: A Knowledge Management Platform for Genomics.
PLoS computational biology
Jul 9, 2015
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled...
PaPI: pseudo amino acid composition to score human protein-coding variants.
BMC bioinformatics
Apr 19, 2015
BACKGROUND: High throughput sequencing technologies are able to identify the whole genomic variation of an individual. Gene-targeted and whole-exome experiments are mainly focused on coding sequence variants related to a single or multiple nucleotide...
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