Author

Michelle T. Dow

University of California San Diego

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Genomics· 2 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Research Focus:variant calling· 3 Assay:whole-genome sequencing· 3 Approach:experimental assay· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell signaling & trafficking· 1

Frequent Co-Authors

Hannah K. CarteriD· 3 shared Adam KlieiD· 2 shared Brian TsuiiD· 2 shared Dylan SkolaiD· 2 shared Adam P. Butler· 1 shared Ahmed HasaniD· 1 shared Aleksandra OlowiD· 1 shared Alex Buchanan· 1 shared

Activity by Year

2017-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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3 shared papersBioinformatics

Hannah K. CarterORCID

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Author profile →

5 papers

Recent·Most cited

YAP/TEAD4-regulated placental alkaline phosphatases ALPP and ALPPL2 are immunosuppressive ectonucleotidases modulated by MAPK inhibitors

J MARTIN, Bruce Huang, Tobias Ehrenberger, Ahmed Hasan, Michelle T. Dow, Weng Hua Khoo, Romain Pacaud, Essam Metwally, Katherine Porth, Gukhan Kim, Sawyer McKenna, Cindy Li, Nicholas Ho, Khoa Nguyen, Spencer Hahn, , David Bauché

This study identifies YAP/TEAD4 as a regulator of ALPP/L2 expression and shows that MAPK inhibitors enhance their expression, improving ADC efficacy through immunomodulation.

bioRxiv · Oct 15, 2025 · PreprintCancer Biology

Target deconvolution using in vitro evolution in haploid human cells

Juan Carlos Jado, Michelle T. Dow, Krypton Carolino, Adam Klie, Gregory J. Fonseca, Trey E. Ideker, Hannah K. Carter, Elizabeth A. Winzeler

The paper uses in vitro evolution in haploid human cells to identify drug resistance mechanisms and validates them through gene expression experiments.

Scientific Reports · Jun 17, 2024Peer-reviewedGenomics

Increasing metadata coverage of SRA BioSample entries using deep learning based Named Entity Recognition

Adam Klie, Brian Tsui, Shamim Ara Mollah, Dylan Skola, Michelle T. Dow, Chun-Nan Hsu, Hannah K. Carter

The paper uses deep learning for Named Entity Recognition to predict missing metadata in SRA BioSample entries, achieving high accuracy for species, condition, and strain categories.

Database · Jan 1, 2021Peer-reviewedBioinformatics

Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive

Brian Tsui, Michelle T. Dow, Dylan Skola, Hannah K. Carter

The paper reprocesses 250,000 human sequencing runs to extract allelic read counts for 300,000 variants, enabling variant detection across different sequencing strategies.

Pacific Symposium on Biocomputing (PSB) · Nov 1, 2018Peer-reviewedBioinformatics

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

Christina K. Yung, Brian D. O’Connor, Sergei Yakneen, Junjun Zhang, Kyle Ellrott, Kortine Kleinheinz, Naoki Miyoshi, Keiran M. Raine, Romina Royo, Gordon Saksena, Matthias Schlesner, Solomon I. Shorser, Miguel Vazquez, Joachim Weischenfeldt, Denis Yuen, , Charles L. Short

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.

bioRxiv · Jul 10, 2017 · PreprintGenomics