Genetics

Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier.

BACKGROUND: BRCA1-mutated cancers exhibit deficient homologous recombination (HR) DNA repair, resulting in extensive copy number alterations and genome instability. HR deficiency can also arise in tumors without a BRCA1 mutation. Compared with other breast tumors, HR-deficient, BRCA1-like tumors exhibit worse prognosis but selective chemotherapeutic sensitivity. Presently, patients with triple neg...

tRNA-DL: A Deep Learning Approach to Improve tRNAscan-SE Prediction Results.

BACKGROUND: tRNAscan-SE is the leading tool for transfer RNA (tRNA) annotation, which has been widely used in the field. However, tRNAscan-SE can return a significant number of false positives when applied to large sequences. Recently, conventional machine learning methods have been proposed to address this issue, but their efficiency can be still limited due to their dependency on handcrafted fea...

Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis.

PURPOSE: Despite the successful progress next-generation sequencing technologies has achieved in diagnosing the genetic cause of rare Mendelian diseas...

Learning from Longitudinal Data in Electronic Health Record and Genetic Data to Improve Cardiovascular Event Prediction.

Current approaches to predicting a cardiovascular disease (CVD) event rely on conventional risk factors and cross-sectional data. In this study, we ap...

A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

A key challenge for the diagnosis and treatment of complex human diseases is identifying their molecular basis. Here, we developed a unified computati...

De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms.

Agave, monocotyledonous succulent plants, is endemic to arid regions of North America, exhibiting exceptional tolerance to their xeric environments. T...

Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters.

Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement pro...

Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives.

In the field of cancer genomics, the broad availability of genetic information offered by next-generation sequencing technologies and rapid growth in ...

TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning.

Accurately identifying DNA-binding proteins (DBPs) from protein sequence information is an important but challenging task for protein function annotat...

EPAI-NC: Enhanced prediction of adenosine to inosine RNA editing sites using nucleotide compositions.

RNA editing process like Adenosine to Intosine (A-to-I) often influences basic functions like splicing stability and most importantly the translation....

An Efficient Population Density Method for Modeling Neural Networks with Synaptic Dynamics Manifesting Finite Relaxation Time and Short-Term Plasticity.

When incorporating more realistic synaptic dynamics, the computational efficiency of population density methods (PDMs) declines sharply due to the inc...

Aflatoxin B Degradation and Detoxification by CG1061 Isolated From Chicken Cecum.

Aflatoxin B (AFB) is one of the most hazardous mycotoxins contamination in food and feed products, which leads to hepatocellular carcinoma in humans a...

A Recursive Approach to Quantized H State Estimation for Genetic Regulatory Networks Under Stochastic Communication Protocols.

This paper deals with the finite-horizon quantized H state estimation problem for a class of discrete time-varying genetic regulatory networks with qu...

Machine learning framework for assessment of microbial factory performance.

Metabolic models can estimate intrinsic product yields for microbial factories, but such frameworks struggle to predict cell performance (including pr...

Bacteria Associated With a Commercial Mycorrhizal Inoculum: Community Composition and Multifunctional Activity as Assessed by Illumina Sequencing and Culture-Dependent Tools.

The implementation of sustainable agriculture encompasses practices enhancing the activity of beneficial soil microorganisms, able to modulate biogeoc...

Developmental Dioxin Exposure Alters the Methylome of Adult Male Zebrafish Gonads.

2,3,7,8-Tetrachlorodibenzo--dioxin (TCDD) is a persistent environmental toxicant and endocrine disrupting compound with reproductive and developmental...

Elevated Serum Growth Differentiation Factor 15 Levels in Hyperthyroid Patients.

Recent studies have shown that growth differentiation factor 15 (GDF15), a member of the transforming growth factor-β (TGF-β)/bone morphogenetic prot...

Genomic Selection and Use of Molecular Tools in Breeding Programs for Indigenous and Crossbred Cattle in Developing Countries: Current Status and Future Prospects.

Genomic selection (GS) has resulted in rapid rates of genetic gains especially in dairy cattle in developed countries resulting in a higher proportion...

DCDE: An Efficient Deep Convolutional Divergence Encoding Method for Human Promoter Recognition.

Efficient human promoter feature extraction is still a major challenge in genome analysis as it can better understand human gene regulation and will b...

OMeta: an ontology-based, data-driven metadata tracking system.

BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metageno...