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Adam C. Searleman

dblp:170/9232 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2015
0000-0003-1084-2415ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › cancer genomics
cancer driver gene identification
0.212015
Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data · Bioinform. 2015
Bioinformatics and computational biology › cancer genomics
somatic mutation analysis
0.112015
Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data · Bioinform. 2015

Methods — techniques the papers use, named apart from their topics

statistical hypothesis testing · 0.2random forest · 0.2patient bias signal · 0.2
YearPublicationVenuePosition
2015 Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data
abstract
MOTIVATION: Several tools exist to identify cancer driver genes based on somatic mutation data. However, these tools do not account for subclasses of cancer genes: oncogenes, which undergo gain-of-function events, and tumor suppressor genes (TSGs) which undergo loss-of-function. A method which accounts for these subclasses could improve performance while also suggesting a mechanism of action for new putative cancer genes. RESULTS: We develop a panel of five complementary statistical tests and assess their performance against a curated set of 99 HiConf cancer genes using a pan-cancer dataset of 1.7 million mutations. We identify patient bias as a novel signal for cancer gene discovery, and use it to significantly improve detection of oncogenes over existing methods (AUROC = 0.894). Additionally, our test of truncation event rate separates oncogenes and TSGs from one another (AUROC = 0.922). Finally, a random forest integrating the five tests further improves performance and identifies new cancer genes, including CACNG3, HDAC2, HIST1H1E, NXF1, GPS2 and HLA-DRB1. AVAILABILITY AND IMPLEMENTATION: All mutation data, instructions, functions for computing the statistics and integrating them, as well as the HiConf gene panel, are available at www.github.com/Bose-Lab/Improved-Detection-of-Cancer-Genes. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Runjun D. Kumar, Adam C. Searleman, Sanjay Joshua Swamidass, Obi L. Griffith, Ron Bose
Bioinform.2