AIMC Topic: Chromosome Mapping

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Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism.

Genetics in medicine : official journal of the American College of Medical Genetics
PurposeRecognizing individuals with inherited diseases can be difficult because signs and symptoms often overlap those of common medical conditions. Focusing on inborn errors of metabolism (IEMs), we present a method that brings the knowledge of high...

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

Nature biotechnology
We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strai...

GuideScan software for improved single and paired CRISPR guide RNA design.

Nature biotechnology
We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. We a...

Prediction of potent shRNAs with a sequential classification algorithm.

Nature biotechnology
We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel data sets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a give...

Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology.

BioMed research international
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 ...

The identification of cis-regulatory elements: A review from a machine learning perspective.

Bio Systems
The majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regions contain cis-regulatory elements, such as promoters, enhancers, silencers, insulators, etc. These ...

Genome-Wide Detection and Analysis of Multifunctional Genes.

PLoS computational biology
Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular...

Genome Modeling System: A Knowledge Management Platform for Genomics.

PLoS computational biology
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...

PsyGeNET: a knowledge platform on psychiatric disorders and their genes.

Bioinformatics (Oxford, England)
UNLABELLED: PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of a database and a web interface supporting data...

Mapping QTLs for PHS resistance and development of a deep learning model to measure PHS rate in japonica rice.

The plant genome
Rice (Oryza sativa L.) is a staple food for more than half of the global population. Preharvest sprouting (PHS), which reduces yield and grain quality, presents a major challenge for rice production. The development of PHS-resistant varieties is a ma...