A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions

U Seroussi, A Lugowski, L Wadi, RX Lao, AR Willis… - Elife, 2023 - elifesciences.org
Argonaute (AGO) proteins associate with small RNAs to direct their effector function on
complementary transcripts. The nematode Caenorhabditis elegans contains an expanded family …

[HTML][HTML] Evolution of microsporidia: An extremely successful group of eukaryotic intracellular parasites

L Wadi, AW Reinke - PLoS pathogens, 2020 - journals.plos.org
Microsporidia are obligate intracellular parasites that can infect a wide range of hosts. They
cause death and disease in both humans and agriculturally important animals. They have …

Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap

…, M Kucera, C Tannus-Lopes, A Rostamianfar, L Wadi… - Nature protocols, 2019 - nature.com
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological pathways …

[HTML][HTML] Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

…, HM Umer, L Uusküla-Reimand, C Wadelius, L Wadi… - Nature, 2020 - nature.com
The discovery of drivers of cancer has traditionally focused on protein-coding genes 1 , 2 , 3
– 4 . Here we present analyses of driver point mutations and structural variants in non-…

Impact of outdated gene annotations on pathway enrichment analysis

L Wadi, M Meyer, J Weiser, LD Stein, J Reimand - Nature methods, 2016 - nature.com
To the Editor: Pathway enrichment analysis is a common technique for interpreting gene
lists derived from high-throughput experiments1. Its success depends on the quality of gene …

[HTML][HTML] Pathway and network analysis of more than 2500 whole cancer genomes

…, S Pulido-Tamayo, J Barenboim, L Wadi… - Nature …, 2020 - nature.com
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the
past decade. However, non-coding cancer driver mutations are less well-characterized and …

[PDF][PDF] Candidate cancer driver mutations in distal regulatory elements and long-range chromatin interaction networks

H Zhu, L Uusküla-Reimand, K Isaev, L Wadi, A Alizada… - Molecular cell, 2020 - cell.com
A comprehensive catalog of cancer driver mutations is essential for understanding tumorigenesis
and developing therapies. Exome-sequencing studies have mapped many protein-…

A parental transcriptional response to microsporidia infection induces inherited immunity in offspring

AR Willis, W Zhao, R Sukhdeo, L Wadi… - Science …, 2021 - science.org
Parental infection can result in the production of offspring with enhanced immunity phenotypes.
Critically, the mechanisms underlying inherited immunity are poorly understood. Here, …

[HTML][HTML] Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma

…, J Theruvath, G Hutter, TD Azad, L Wadi… - Nature …, 2018 - nature.com
Medulloblastoma is the most common malignant brain tumor of childhood. Group 3
medulloblastoma, the most aggressive molecular subtype, frequently disseminates through the …

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

…, HM Umer, L Uusküla-Reimand, C Wadelius, L Wadi… - BioRxiv, 2017 - biorxiv.org
Discovery of cancer drivers has traditionally focused on the identification of protein-coding
genes. Here we present a comprehensive analysis of putative cancer driver mutations in both …