Machine learning applications in genetics and genomics

MW Libbrecht, WS Noble - Nature Reviews Genetics, 2015 - nature.com
The field of machine learning, which aims to develop computer algorithms that improve with
experience, holds promise to enable computers to assist humans in the analysis of large …

[HTML][HTML] A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

C Yang, D Chowdhury, Z Zhang, WK Cheung… - Computational and …, 2021 - Elsevier
Metagenomic sequencing provides a culture-independent avenue to investigate the
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

AD Rouillard, GW Gundersen, NF Fernandez… - Database, 2016 - academic.oup.com
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly
generate a plethora of data on the activity and levels of biomolecules within mammalian …

Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics

B Tang, L Feng, MT Hulin, P Ding, W Ma - Cell Host & Microbe, 2023 - cell.com
Pathogen infection is a dynamic process. Here, we employ single-cell transcriptomics to
investigate plant response heterogeneity. By generating an Arabidopsis thaliana leaf atlas …

A draft network of ligand–receptor-mediated multicellular signalling in human

JA Ramilowski, T Goldberg, J Harshbarger… - Nature …, 2015 - nature.com
Cell-to-cell communication across multiple cell types and tissues strictly governs proper
functioning of metazoans and extensively relies on interactions between secreted ligands …

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

EY Chen, CM Tan, Y Kou, Q Duan, Z Wang… - BMC …, 2013 - Springer
Background System-wide profiling of genes and proteins in mammalian cells produce lists of
differentially expressed genes/proteins that need to be further analyzed for their collective …

Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and …

PCY Woo, SKP Lau, CSF Lam, CCY Lau… - Journal of …, 2012 - journals.asm.org
Recently, we reported the discovery of three novel coronaviruses, bulbul coronavirus
HKU11, thrush coronavirus HKU12, and munia coronavirus HKU13, which were identified …

A large-scale evaluation of computational protein function prediction

P Radivojac, WT Clark, TR Oron, AM Schnoes… - Nature …, 2013 - nature.com
Automated annotation of protein function is challenging. As the number of sequenced
genomes rapidly grows, the overwhelming majority of protein products can only be …

Effector identification in plant pathogens

AH Lovelace, S Dorhmi, MT Hulin, Y Li… - …, 2023 - Am Phytopath Society
Effectors play a central role in determining the outcome of plant− pathogen interactions. As
key virulence proteins, effectors are collectively indispensable for disease development. By …

An efficient algorithm for large-scale detection of protein families

AJ Enright, S Van Dongen… - Nucleic acids research, 2002 - academic.oup.com
Detection of protein families in large databases is one of the principal research objectives in
structural and functional genomics. Protein family classification can significantly contribute to …