Michael J. Steinbaugh, PhD
Director, Data, AI & Genome Sciences (DAGS)
Merck Research Laboratories (MRL)
320 Bent Street, Cambridge, MA 02141
mike@steinbaugh.com

Research scientist and team builder specializing in small molecule drug discovery, RNA biology, and genomics, with extensive experience in clinical development from target identification through patient selection. Active participant in open-source software development at Acid Genomics.

Experience

• Merck, Cambridge, MA
  Director, Data, AI & Genome Sciences (DAGS) — 2024-pres.
• Redona Therapeutics, Watertown, MA
  Pre-clinical development of small molecules targeting RNA splicing and stability.
  • Director of Translational Science — 2021-24
    • Lead bioinformatics and translational teams for CLK and TUT4/7 inhibitors.
    • Engaged in licensing efforts related to lead CLK program.
    • Contributed to Investigational New Drug (IND) application for CLK inhibitor.
    • Deployed cloud-based genomics workflows on AWS and LatchBio platforms.
  • Principal Scientist — 2020-21
    • Bioinformatics support for TUT4/7, PAPD5/7, and new target discovery.
    • Deployed cloud infrastructure on Amazon Web Services (AWS).
• Acid Genomics, Quechee, VT
  Startup biotech consulting and bioinformatics software development.
  • Founder — 2019-pres.
    • Developed Python and R packages for bioinformatics workflows.
    • Managed sequencing data submissions to NIH GEO/SRA.
• Constellation Pharmaceuticals, Cambridge, MA
  Pre-clinical development of small molecules targeting chromatin regulation and transcriptional control.
  • Scientist II — 2018-20
    • Contributed to development of Pelabresib (BET inhibitor) and Tulmimetostat (EZH2/1 inhibitor), currently in clinical trials.
    • Analyzed RNA-seq and epigenomics data (ChIP-seq, ATAC-seq, PRO-seq) of small molecule chromatin modifiers in primary tumors and cancer cell lines.
    • Migrated bioinformatics cloud infrastructure from Microsoft Azure to AWS.
• Harvard T.H. Chan School of Public Health, Boston, MA
  Single-cell genomics research support and bioinformatics software development.
  • Research Associate — 2017‑18
    
    • Provided bioinformatics consulting and training for Harvard Medical School.
    • Contributed to open-source genomics toolkit software development.
    • Optimized single-cell RNA-seq analysis workflow using R and Python: quality control, dimensional reduction, clustering, and differential expression.
    • Developed R packages for RNA-seq: bcbioRNASeq and bcbioSingleCell.
• Joslin Diabetes Center and Harvard Medical School, Boston, MA
  Research on the role of Nrf transcription factors in aging and disease.
  • Research Fellow — 2012-17
    
    • Discovered that the reproductive system regulates aging in C. elegans via the SKN-1/Nrf transcription factor, a key regulator of intracellular detoxification and lipid homeostasis.
    • Identified new SKN-1 target genes through transcriptomic analysis with RNA-seq.
    • Conducted a genome-wide GFP reporter RNAi screen for novel SKN-1 effectors.
    • Performed targeted lipidomics using GC-MS and LC-MS/MS.
    • Developed R packages for C. elegans functional genomics analyses.

Education

• PhD, University of Michigan, Ann Arbor
  Cellular and Molecular Biology
• BS, University of California, Los Angeles
  Microbiology, Immunology and Molecular Genetics; Spanish Minor

Publications

• Triboulet R, Sadykov K, Harvey DM, Wilson DM, Steinbaugh MJ, Mayo CB, Hawley D, Madanjian A, Fyfe C, Bracken C, Rivera-Rivera I, Ericsson A, Snyder AR, Knutson SK, Stein RL, Gibaja V, Ghosh S, Campbell RM. (2024). Targeting the synthetic lethal relationship between FOCAD and TUT7 represents a potential therapeutic opportunity for TUT4/7 small molecule inhibitors in cancer. Molecular Cancer Therapeutics. PDF.
• Vicidomini C, Goode TD, McAvoy KM, Yu R, Beveridge CH, Iyer SN, Victor MB, Leary N, Evans L, Steinbaugh MJ, Lai ZW, Lyon MC, Silvestre MRFS, Bonilla G, Sadreyev RI, Walther TC, Ho Sui S, Saido T, Yamamoto K, Murakami M, Tsai LH, Chopra G, Sahay A. (2024). An aging-sensitive compensatory secretory phospholipase that confers neuroprotection and cognitive resilience. bioRxiv 2024.07.26.605338. PDF.
• Castillo-Quan JI, Steinbaugh MJ, Fernández-Cárdenas LP, Pohl NK, Wu Z, Zhu F, Moroz N, Teixeira V, Bland MS, Lehrbach NJ, Moronetti Mazzeo LE, Teufl M, Blackwell TK. (2023). An anti-steatosis response regulated by oleic acid through lipid droplet-mediated ERAD enhancement. Science Advances 9(1):eadc891. PDF.
• Bommi-Reddy A, Park-Chouinard S, Mayhew DN, Terzo E, Hingway A, Steinbaugh MJ, Wilson JE, Sims RJ, Conery AR. (2022). CREBBP/EP300 acetyltransferase inhibition disrupts FOXA1-bound enhancers to inhibit the proliferation of ER+ breast cancer cells. PLoS ONE 17(3):e0262378. PDF.
• Li CM, Shapiro H, Tsiobikas C, Selfors LM, Chen H, Rosenbluth J, Moore K, Gupta KP, Gray GK, Oren Y, Steinbaugh MJ, Guerriero JL, Pinello L, Regev A, Brugge JS. (2020). Aging-associated alterations in mammary epithelia and stroma revealed by single-cell RNA sequencing. Cell Reports 33(13):108566. PDF.
• Ha CWY, Martin A, Sepich-Poore GD, Shi B, Wang Y, Gouin K, Humphrey G, Sanders K, Ratnayake Y, Chan KSL, Hendrick G, Caldera JR, Arias C, Moskowitz JE, Ho Sui SJ, Yang S, Underhill D, Brady MJ, Knott S, Kaihara K, Steinbaugh MJ, Li H, McGovern DPB, Knight R, Fleshner P, Devkota S. (2020). Translocation of viable gut microbiota to mesenteric adipose drives formation of creeping fat in humans. Cell 183(3):666-683. PDF. Code.
• Burkewitz K, Feng G, Dutta S, Kelley CA, Steinbaugh MJ, Cram E, Mair WB. (2020). Atf-6 regulates lifespan through ER-mitochondrial calcium homeostasis. Cell Reports 32(10):108125. PDF. Code.
• Tattikota SG, Cho B, Liu Y, Hu Y, Barrera V, Steinbaugh MJ, Yoon S, Comjean A, Li F, Dervis F, Hung R, Nam J, Ho Sui S, Shim J, Perrimon N. (2020). A single-cell survey of Drosophila blood. eLife 9:e54818. PDF. Code.
• Ghazizadeh Z, Kiviniemi T, Olafsson S, Plotnick D, Beerens ME, Zhang K, Gillon L, Steinbaugh MJ, Barrera V, Ho Sui S, Werdich AA, Kapur S, Eranti A, Gunn J, Jalkanen J, Airaksinen J, Kleber AG, Hollmén M, MacRae CA. (2019). A metastable atrial state underlies the primary genetic substrate for MYL4 mutation-associated atrial fibrillation. Circulation 141(4):301-312. PDF. Code.
• Wu Z, Isik M, Moroz N, Steinbaugh MJ, Zhang P, Blackwell TK. (2019). Dietary restriction extends lifespan through metabolic regulation of innate immunity. Cell Metabolism 29(5):1192-1205. PDF.
• Klim JR, Williams LA, Limone F, Guerra San Juan I, Davis-Dusenbery BN, Mordes DA, Burberry A, Steinbaugh MJ, Gamage KK, Kirchner R, Moccia R, Cassel SH, Chen K, Wainger BJ, Woolf CJ, Eggan K. (2019). ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair. Nature Neuroscience 22(2):167-179. PDF. Code.
• Steinbaugh MJ, Pantano L, Kirchner RD, Barrera V, Chapman BA, Piper ME, Mistry M, Khetani RS, Rutherford KD, Hoffman O, Hutchinson JN, Ho Sui SJ. (2017). bcbioRNASeq: R package for bcbio RNA-seq analysis. F1000Research 2017(6):1976. PDF. Code.
• Blackwell TK, Steinbaugh MJ, Hourihan JM, Ewald CY, Isik M. (2015). SKN‑1/Nrf, stress responses, and aging in Caenorhabditis elegans. Free Radical Biology and Medicine 88:290-301. Review. PDF.
• Steinbaugh MJ, Narasimhan SD, Robida-Stubbs S, Moronetti Mazzeo LE, Dreyfuss JM, Hourihan JM, Raghavan P, Operaña TN, Esmaillie R, Blackwell TK. (2015). Lipid-mediated regulation of SKN‑1/Nrf in response to germ cell absence. eLife 4:e07836. PDF.
• Yoon JC, Ling AJ, Isik M, Lee DY, Steinbaugh MJ, Sack LM, Boduch AN, Blackwell TK, Sinclair DA, Elledge SJ. (2014). GLTSCR2/PICT1 links mitochondrial stress and Myc signaling. Proceedings of the National Academy of Sciences of the United States of America 111(10):3781-3786. PDF.
• Steinbaugh MJ, Sun LY, Bartke A, Miller RA. (2012). Activation of genes involved in xenobiotic metabolism is a shared signature of mouse models with extended lifespan. American Journal of Physiology-Endocrinology and Metabolism 303:E488-E495. PDF.
• Sun LY, Steinbaugh MJ, Masternak MM, Bartke A, Miller RA. (2009). Fibroblasts from long-lived Snell and GHRKO mutant mice show diminished ERK phosphorylation but exaggerated induction of immediate early genes. Free Radical Biology and Medicine 47(12):1753-1761. PDF.