Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

OK Tørresen, B Star, P Mier… - Nucleic acids …, 2019 - academic.oup.com
The widespread occurrence of repetitive stretches of DNA in genomes of organisms across
the tree of life imposes fundamental challenges for sequencing, genome assembly, and …

A survey on computational models for predicting protein–protein interactions

L Hu, X Wang, YA Huang, P Hu… - Briefings in …, 2021 - academic.oup.com
Proteins interact with each other to play critical roles in many biological processes in cells.
Although promising, laboratory experiments usually suffer from the disadvantages of being …

[HTML][HTML] Phages and their satellites encode hotspots of antiviral systems

F Rousset, F Depardieu, S Miele, J Dowding… - Cell host & …, 2022 - cell.com
Bacteria carry diverse genetic systems to defend against viral infection, some of which are
found within prophages where they inhibit competing viruses. Phage satellites pose …

[HTML][HTML] Information fusion as an integrative cross-cutting enabler to achieve robust, explainable, and trustworthy medical artificial intelligence

A Holzinger, M Dehmer, F Emmert-Streib, R Cucchiara… - Information …, 2022 - Elsevier
Medical artificial intelligence (AI) systems have been remarkably successful, even
outperforming human performance at certain tasks. There is no doubt that AI is important to …

IMG/M v. 5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

IMA Chen, K Chu, K Palaniappan, M Pillay… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Integrated Microbial Genomes & Microbiomes system v. 5.0 (IMG/M: https://img.
jgi. doe. gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya …

IMG/M: integrated genome and metagenome comparative data analysis system

IMA Chen, VM Markowitz, K Chu… - Nucleic acids …, 2016 - academic.oup.com
Abstract The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.
jgi. doe. gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal …

Protein‐protein interaction detection: methods and analysis

VS Rao, K Srinivas, GN Su**i… - International journal of …, 2014 - Wiley Online Library
Protein‐protein interaction plays key role in predicting the protein function of target protein
and drug ability of molecules. The majority of genes and proteins realize resulting …

The STRING database in 2025: protein networks with directionality of regulation

D Szklarczyk, K Nastou, M Koutrouli… - Nucleic Acids …, 2025 - academic.oup.com
Proteins cooperate, regulate and bind each other to achieve their functions. Understanding
the complex network of their interactions is essential for a systems-level description of …

Predicting protein–protein interactions from the molecular to the proteome level

O Keskin, N Tuncbag, A Gursoy - Chemical reviews, 2016 - ACS Publications
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …

IMG: the integrated microbial genomes database and comparative analysis system

VM Markowitz, IMA Chen, K Palaniappan… - Nucleic acids …, 2012 - academic.oup.com
Abstract The Integrated Microbial Genomes (IMG) system serves as a community resource
for comparative analysis of publicly available genomes in a comprehensive integrated …