Henry E Miller

Researcher, ML Team, Shift Bioscience

Joined

May 2025

Names

Henry E Miller (Preferred)

Henry Miller

Henry E. Miller

H. E. Miller

Emails

****@gmail.com (Confirmed)

****@shiftbioscience.com (Confirmed)

Personal Links

Google Scholar

ORCID

Career & Education History

Researcher

ML Team, Shift Bioscience (shiftbioscience.com)

2024 – Present

Researcher

Institute of Science, Altos Labs, Inc. (altoslabs.com)

2022 – 2024

PhD student

Barshop Institute, UT Health San Antonio (uthscsa.edu)

2018 – 2022

Advisors, Relations & Conflicts

PhD Advisor

Alex Bishop

2018 – 2022

Expertise

No areas of expertise listed

Publications

Deep Learning-Based Genetic Perturbation Models Do Outperform Uninformative Baselines on Well-Calibrated Metrics
Henry E. Miller, Gabriel M. Mejia, Francis J. A. Leblanc, Bo Wang, Brendan Swain, Lucas Paulo de Lima Camillo
- Crossref
- Readers: Everyone
BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML
Henry E. Miller, Matthew Greenig, Benjamin Tenmann, Bo Wang
- Crossref
- Readers: Everyone
A single factor for safer cellular rejuvenation
Lucas Paulo de Lima Camillo, Rihab Gam, Katsiaryna Maskalenka, Francis J. A. LeBlanc, Gustavo Antonio Urrutia, Gabriel M. Mejia, Henry E. Miller, Christopher P. Wardlaw, Adam Pickles, Laura Everton, Ringaile Zaksauskaite, Rejina B. Khan, Andreas Welsh, Samira Gambo, Stephany Gallardo, Zoryana Oliynyk, Sagar S. Varankar, Alexander E. Epstein, Adam Bendall, Jonathan Mowatt et al. (2 additional authors not shown)
- Crossref
- Readers: Everyone
Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics
Gabriel Mateo Mejia, Henry E Miller, Francis J.A. Leblanc, BO WANG, Brendan Swain, Lucas Paulo de Lima Camillo
- GenBio 2025 Poster
- Readers: Everyone
scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth T Gao, Akram Baharlouei, Kyra Thrush-Evensen, Nina Riehs, Amy F Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry E Miller, Ashley Mae Conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P Amini, Alex Xijie Lu et al. (4 additional authors not shown)
- NeurIPS 2025 Datasets and Benchmarks Track poster
- Readers: Everyone
CpGPT: a Foundation Model for DNA Methylation
Lucas Paulo de Lima Camillo, Raghav Sehgal, Jenel Armstrong, Henry E. Miller, Jessica A. Lasky-Su, Albert T. Higgins-Chen, Steve Horvath, Bo Wang
- Crossref
- Readers: Everyone
Multi-omics analyses reveal novel effects of PLCγ2 deficiency in the mouse brain
Sarah C. Hopp, Juliet Garcia Rogers, Sabrina Smith, Gabriela Campos, Henry Miller, Savannah Barannikov, Eduardo Gutierrez Kuri, Hu Wang, Xianlin Han, Kevin F. Bieniek, Susan T. Weintraub, Juan Pablo Palavicini
- Crossref
- Readers: Everyone
Exploration and analysis of R-loop mapping data with RLBase
Henry E Miller, Daniel Montemayor, Janet Li, Simon A Levy, Roshan Pawar, Stella Hartono, Kumar Sharma, Bess Frost, Frédéric Chedin, Alexander J R Bishop
- Nucleic Acids Research
- Readers: Everyone
Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease
Mirolyuba Ilieva, James Dao, Henry E. Miller, Jens Hedelund Madsen, Alexander J. R. Bishop, Sakari Kauppinen, Shizuka Uchida
- Non-Coding RNA
- Readers: Everyone
RLSuite: An integrative R-loop bioinformatics framework
H. E. Miller, D. Montemayor, S. Levy, K. Sharma, B. Frost, A. J. R. Bishop
- Crossref
- Readers: Everyone

View all 13 publications

Co-Authors

View all 95 co-authors