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Hire Holly S.

United States

USD 50 /hr

Computational Immunologist | expertise in immunology, machine learning, & single cell genomics

Profile Summary

I have worked for over 10 years as an immunologist and completed my PhD at Yale in Immunobiology studying the intersection of cell metabolism and immunity. I am currently a 3rd year Postdoc at Yale in Genetics conducting research on machine learning based computational methods for large biomedical data and single cell genomics. Extensive experience in python-based methods development, data analysis, and data visualization, as well as strong familiarity with R.

Subject Matter Expertise

• ☆ Computational Biology
• ☆ Microbiology
• ☆ Microbiome Research
• ☆ Biostatistics
• ☆ Biochemistry
• ☆ Immunoassay
• ☆ Biochemical Assays
• ☆ Apoptosis
• ☆ Oxidative Stress & Mitochondrial Function
• ☆ Enzyme Activity Assays
• ☆ Binding Assays
• ☆ Molecular Biology
• ☆ Genetics
• ☆ Omics
• ☆ Transcriptomics
• ☆ Lipidomics
• ☆ Metabolomics
• ☆ Epigenetics
• ☆ PCR
• ☆ Molecular Cloning
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ Gene Expression Analysis
• ☆ Recombinant DNA
• ☆ RNA Sequencing
• ☆ DNA/Gene Synthesis
• ☆ Oligonucleotide Synthesis
• ☆ Plasmid DNA
• ☆ ChIP-Seq
• ☆ Monoclonal Antibody Production
• ☆ Cell Biology
• ☆ Cell-Based Assays
• ☆ Cell Signaling Pathways
• ☆ Membrane Biology
• ☆ Gene Regulation
• ☆ Basic Immunology
• ☆ Adjuvant & Antigen Research
• ☆ Biotechnology & Bioengineering
• ☆ Recombinant Protein Expression
• ☆ Biomass & Bioenergy
• ☆ Data Analysis
• ☆ Image Processing
• ☆ Predictive Modeling & Analytics
• ☆ Data Processing
• ☆ Data Exploration
• ☆ Cluster Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Data Collection
• ☆ Data Management
• ☆ Data Manipulation
• ☆ Machine Learning
• ☆ Data Mining
• ☆ Data Cleaning
• ☆ Neural Networks
• ☆ Pattern Recognition
• ☆ Artificial Intelligence
• ☆ Deep Learning
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Applied Mathematics
• ☆ Mathematical Models
• ☆ Mathematical Optimization
• ☆ Mathematical Wavelets
• ☆ Computational Mathematics
• ☆ Pure Mathematics
• ☆ Geometry
• ☆ Graph Theory
• ☆ Biomarker Discovery
• ☆ Cell Culture
• ☆ Primary Cells
• ☆ Cell Surface Receptors
• ☆ Biomolecular Engineering
• ☆ Gene Editing/CRISPR
• ☆ Circadian Rhythm Research
• ☆ Cytometry

Services

• Writing

Writing Medical Writing, Technical Writing, Copywriting, Newswriting, Audio Transcription, General Proofreading & Editing

Work Experience

Postdoctoral Fellow

Krishnaswamy Lab Yale University

October 2021 - Present

Graduate Student (Co-Mentored: Drs. Richard Flavell & Joe Craft)

Yale University

August 2016 - September 2021

Research Technician

Taylor Lab Fred Hutchinson Cancer Research Center

June 2014 - June 2016

Research Assistant

Pepper Lab University of Washington

June 2013 - May 2014

Education

PhD in Immunology

Yale University

September 2016 - September 2021

B.S. (Biology)

University of Washington

September 2009 - 2014

Certifications

• Certification details not provided.

Publications

PREPRINT

Holly Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew Hirn, Michael Perlmutter, Smita Krishnaswamy (2023). Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning .

Esen Sefik, Rihao Qu, Caroline Junqueira, Eleanna Kaffe, Haris Mirza, Jun Zhao, J. Richard Brewer, Ailin Han, Holly R. Steach, Benjamin Israelow, et al.(2021). Inflammasome activation in infected macrophages drives COVID-19 pathology . Cold Spring Harbor Laboratory

JOURNAL ARTICLE

Carl A. Pierce, Lip Nam Loh, Holly R. Steach, Natalia Cheshenko, Paula Preston-Hurlburt, Fengrui Zhang, Stephanie Stransky, Leah Kravets, Simone Sidoli, William Philbrick, et al. (2023). HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal . Journal of Clinical Investigation.

Holly Steach, Irene Chernova, Wenzhi Song, Omeed Hafez, Jafar Al Souz, Ping-Min Chen, Nisha Chandra, Lloyd Cantley, Margaret Veselits, Marcus R. Clark, et al. (2023). The ion transporter Na + -K + -ATPase enables pathological B cell survival in the kidney microenvironment of lupus nephritis . Science Advances.

Holly Steach, Ian D. Odell, Stephen B. Gauld, Lauren Reinke-Breen, Jozsef Karman, Tracy L. Carr, Joseph B. Wetter, Lucy Phillips, Monique Hinchcliff, Richard A. Flavell (2022). Epiregulin is a dendritic cell–derived EGFR ligand that maintains skin and lung fibrosis . Science Immunology.

Esen Sefik, Rihao Qu, Caroline Junqueira, Eleanna Kaffe, Haris Mirza, Jun Zhao, J. Richard Brewer, Ailin Han, Holly R. Steach, Benjamin Israelow, et al.(2022). Inflammasome activation in infected macrophages drives COVID-19 pathology . Nature. Springer Science and Business Media {LLC}

Wenzhi Song, Olivia Q Antao, Emily Condiff, Sanchez GM, Chernova I, Zembrzuski K, Steach H, Rubtsova K, Davide Angeletti, Lemenze A, et al. (2022). Development of Tbet- and CD11c-expressing B cells in a viral infection requires T follicular helper cells outside of germinal centers . Immunity.

(2021). Skin-resident innate lymphoid cells converge on a pathogenic effector state . Nature.

(2021). An in vivo screen of noncoding loci reveals that <i>Daedalus</i> is a gatekeeper of an Ikaros-dependent checkpoint during haematopoiesis . Proceedings of the National Academy of Sciences of the United States of America.

Ping-Min Chen, Parker C. Wilson, Justin A. Shyer, Margaret Veselits, Holly R. Steach, Can Cui, Gilbert Moeckel, Marcus R. Clark, Joe Craft(2020). Kidney tissue hypoxia dictates T cell–mediated injury in murine lupus nephritis . Science Translational Medicine. 12. (538). American Association for the Advancement of Science ({AAAS})

(2019). Cross-Reactivity with Self-Antigen Tunes the Functional Potential of Naive B Cells Specific for Foreign Antigens . Journal of immunology (Baltimore, Md. : 1950).

(2019). Mechanosensation of cyclical force by PIEZO1 is essential for innate immunity . Nature.

(2019). Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes . The Journal of experimental medicine.

(2019). Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function . Nature.

(2018). The translation of non-canonical open reading frames controls mucosal immunity . Nature.

(2018). Nutrition and Food Science . The Yale journal of biology and medicine.

Hondowicz BD, An D, Schenkel JM, Kim KS, Steach HR, Krishnamurty AT, Keitany GJ, Garza EN, Fraser KA, Moon JJ, Altemeier WA, Masopust D, Pepper M, Immunity, 2016, vol. 44, no. 1, pp. 155-166 .

Taylor JJ, Pape KA, Steach HR, Jenkins MK, Science (New York, N.Y.), 2015, vol. 347, no. 6223, pp. 784-787 .

OTHER

Piotr Bielecki, Samantha J. Riesenfeld, Monika S. Kowalczyk, Maria C. Amezcua Vesely, Lina Kroehling, Parastou Yaghoubi, Danielle Dionne, Abigail Jarret, Holly R. Steach, Heather M. McGee, et al.(2018). Skin inflammation driven by differentiation of quiescent tissue-resident ILCs into a spectrum of pathogenic effectors . Cold Spring Harbor Laboratory

SUPERVISED STUDENT PUBLICATION

(2018). Nutrition and Food Science . The Yale journal of biology and medicine.