Genetics

Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations.

The distribution and composition of -regulatory modules composed of transcription factor (TF) binding site (TFBS) clusters in promoters substantially determine gene expression patterns and TF targets. TF knockdown experiments have revealed that TF binding profiles and gene expression levels are correlated. We use TFBS features within accessible promoter intervals to predict genes with similar tis...

Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring.

Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioindicator taxa. While prokaryotic and eukaryotic mi...

Identifying mouse developmental essential genes using machine learning.

The genes that are required for organismal survival are annotated as 'essential genes'. Identifying all the essential genes of an animal species can r...

Knowledge base toward understanding actionable alterations and realizing precision oncology.

In Japan, the National Cancer Center and university hospitals have initiated next-generation sequencing-based in vitro diagnostic testing for cancer p...

Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine.

Atopic dermatitis (AD) is a complex multifactorial inflammatory skin disease that affects ~280 million people worldwide. About 85% of AD cases begin i...

Biomarkers and polymorphisms in pancreatic neuroendocrine tumors treated with sunitinib.

Several circulating biomarkers and single nucleotide polymorphisms (SNPs) have been correlated with efficacy and tolerability to antiangiogenic agents...

Functional expression of porcine interferon-α using a combinational strategy in Pichia pastoris GS115.

Porcine interferon-α (pIFN-α) could be used as the vaccine adjuvant to enhance the antiviral ability of porcine in swine industry. In here, a combinat...

Multi-trait, Multi-environment Deep Learning Modeling for Genomic-Enabled Prediction of Plant Traits.

Multi-trait and multi-environment data are common in animal and plant breeding programs. However, what is lacking are more powerful statistical models...

Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology.

Identifying disease genes from a vast amount of genetic data is one of the most challenging tasks in the post-genomic era. Also, complex diseases pres...

Identification of tissue-specific tumor biomarker using different optimization algorithms.

BACKGROUND: Identification of differentially expressed genes, i.e., genes whose transcript abundance level differs across different biological or phys...

Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network.

The CRISPR-Cas9 system derived from adaptive immunity in bacteria and archaea has been developed into a powerful tool for genome engineering with wide...

Contrast enhancement is a prognostic factor in IDH1/2 mutant, but not in wild-type WHO grade II/III glioma as confirmed by machine learning.

BACKGROUND: Mutation of the isocitrate dehydrogenase (IDH) gene and co-deletion on chromosome 1p/19q is becoming increasingly relevant for the evaluat...

Distillation of the clinical algorithm improves prognosis by multi-task deep learning in high-risk Neuroblastoma.

We introduce the CDRP (Concatenated Diagnostic-Relapse Prognostic) architecture for multi-task deep learning that incorporates a clinical algorithm, e...

Effect of inter-individual variability in human liver cytochrome P450 isozymes on cyclophosphamide-induced micronucleus formation.

We investigated the relationship between metabolic activities of cytochrome P450 (CYP) isozymes present in microsomal fractions derived from the liver...

Improving the calling of non-invasive prenatal testing on 13-/18-/21-trisomy by support vector machine discrimination.

With the advance of next-generation sequencing (NGS) technologies, non-invasive prenatal testing (NIPT) has been developed and employed in fetal aneup...

A hybrid approach for automated mutation annotation of the extended human mutation landscape in scientific literature.

As the cost of DNA sequencing continues to fall, an increasing amount of information on human genetic variation is being produced that could help prog...

Setting Up a Surface-Enhanced Raman Scattering Database for Artificial-Intelligence-Based Label-Free Discrimination of Tumor Suppressor Genes.

The quality of input data in deep learning is tightly associated with the ultimate performance of the machine learner. Taking advantage of the unique ...

Porcine single nucleotide polymorphisms and their functional effect: an update.

OBJECTIVE: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were id...

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations.

Quantitative evaluation of binding affinity changes upon mutations is crucial for protein engineering and drug design. Machine learning-based methods ...

MSIpred: a python package for tumor microsatellite instability classification from tumor mutation annotation data using a support vector machine.

Microsatellite instability (MSI) is characterized by high degree of polymorphism in microsatellite lengths due to deficiency in mismatch repair (MMR) ...