AIMC Topic: Computational Biology

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Anticancer drug synergy prediction in understudied tissues using transfer learning.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: Drug combination screening has advantages in identifying cancer treatment options with higher efficacy without degradation in terms of safety. A key challenge is that the accumulated number of observations in in-vitro drug responses varies...

The Human Phenotype Ontology in 2021.

Nucleic acids research
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for ...

UniProt: the universal protein knowledgebase in 2021.

Nucleic acids research
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over ...

canSAR: update to the cancer translational research and drug discovery knowledgebase.

Nucleic acids research
canSAR (http://cansar.icr.ac.uk) is the largest, public, freely available, integrative translational research and drug discovery knowledgebase for oncology. canSAR integrates vast multidisciplinary data from across genomic, protein, pharmacological, ...

FireProtDB: database of manually curated protein stability data.

Nucleic acids research
The majority of naturally occurring proteins have evolved to function under mild conditions inside the living organisms. One of the critical obstacles for the use of proteins in biotechnological applications is their insufficient stability at elevate...

Identification of Blood-Based Glycolysis Gene Associated with Alzheimer's Disease by Integrated Bioinformatics Analysis.

Journal of Alzheimer's disease : JAD
BACKGROUND: Alzheimer's disease (AD) is one of many common neurodegenerative diseases without ideal treatment, but early detection and intervention can prevent the disease progression.

Identification of Gene Regulatory Networks from Single-Cell Expression Data.

Methods in molecular biology (Clifton, N.J.)
Single-cell RNAseq is an emerging technology that allows the quantification of gene expression in individual cells. In plants, single-cell sequencing technology has been applied to generate root cell expression maps under many experimental conditions...

Machine and Deep Learning for Prediction of Subcellular Localization.

Methods in molecular biology (Clifton, N.J.)
Protein subcellular localization prediction (PSLP), which plays an important role in the field of computational biology, identifies the position and function of proteins in cells without expensive cost and laborious effort. In the past few decades, v...

Deep Learning Models for Gastric Signet Ring Cell Carcinoma Classification in Whole Slide Images.

Technology in cancer research & treatment
Signet ring cell carcinoma (SRCC) of the stomach is a rare type of cancer with a slowly rising incidence. It tends to be more difficult to detect by pathologists, mainly due to its cellular morphology and diffuse invasion manner, and it has poor prog...

Determining Cell Death Pathway and Regulation by Enrichment Analysis.

Methods in molecular biology (Clifton, N.J.)
Bioinformatics tools and resources are valuable for the analysis of data sets focusing on programmed cell death. This chapter discusses methods for the generation of gene sets as well as enrichment analysis using publicly available databases.