Curriculum Vitae

Summary

Computational biologist and PhD candidate with seven years of experience in single-cell genomics, computational virology, and population-scale sequence analysis. Experienced in conducting petabyte-scale analyses on cloud and HPC infrastructure and translating them into novel insights leading to publications. Co-author on 10 peer-reviewed papers, including first-author work and studies in Nature, Nature Genetics, and PNAS.

Qualifications

• Petabyte-scale sequence analysis across biorepository and public sequencing archives using cloud and HPC infrastructure.

• Broad background spanning molecular genetics, computational virology, single-cell multi-omics, and population genetics.

• Proficient in R, Python, C++, and MATLAB, working within Unix-based systems and containerized, workflow-orchestrated pipelines.

• Experience and formal training in Machine Learning using R and Python, and Deep Learning using the PyTorch library.

• Wet bench experience performing molecular biology and stem cell culture.

• Excellent organizational and communication skills working in collaborative, cross-institutional projects.

• Independent and goal oriented, quickly learning new skills to become self sufficient within a working group.

Education

2023 - 2027 [anticipated]

PhD, Gerstner Sloan Kettering

Degree: Cancer Biology

2018 - 2021

MS, Oregon Health & Science University

Degree: Bioinformatics and Computational Biomedicine

2013 - 2016

BA, Lewis & Clark College

Degree: Biochemistry and Molecular Biology

Academic Experience

Jun 2023 - present Graduate Researcher

Memorial Sloan Kettering Cancer Center. Lareau Lab, Computational & Systems Biology. New York, NY

Principal Investigator: Caleb Lareau, PhD

• Conduct analysis of petabyte-scale biorepository datasets using cloud compute infrastructure for viral sequence detection and discovery, to derive insight into the genetic architecture of viral persistence at the population scale.
• Developed independent virology projects from cross-institutional training at The Rockefeller University lead by Nobel Laureate Charles Rice, PhD.
• Analysis of in-house single cell datasets generated from novel technology development projects.
• Provide broad bioinformatics support ranging from experimental design, data processing, and interpretation of diverse genomics and virology projects both in house and with collaborators.

Sep 2018 - Jun 2021 Research Assistant II

Oregon Health & Science University. Maslen Lab, Division of Cardiovascular Medicine. Portland, OR

Principal Investigator: Cheryl Maslen, PhD

• Main technician responsible for lab maintenance and ongoing cell culture experiments on patient derived stem cell lines.
• Review of clinical records identifying age matched controls powering study design for NGS targeted bisulfite sequencing experiment studying Genetically Triggered Aortic Aneurysms in patients with Turner Syndrome.
• Conducted data analysis on generated data for the Master’s thesis requirement leveraging rigorous and innovating analytics approaches leading to first author publication.

Professional Experience

Oct 2021 - Jun 2023 Life Science Research Professional I

Stanford University. Ansuman Satpathy MD PhD, Department of Pathology. Stanford, CA

• Leverage large scale single-cell datasets to derive novel insights in normal health and disease.
• Provide computational and analytics support to lab members to assist in a variety of data types and research questions.
• Specific focus on analysis of mtscATAC data and perform/develop mitochondrial lineage tracing analyses.
• Independent analysis of novel large scale datasets to investigate the cell type of origin for tubal-ovarian cancer in a collaborative setting.

May - August 2016 Manufacturing Scientist Intern II

One Lambda (ThermoFisher Scientific). Manufacturing Department. Canoga Park, CA

• Assembly and testing of clinical grade molecular based HLA allele typing devices (PCR, Sanger).
• Trained on manufacturing of 4 independent HLA typing products.
• Weekly maintenance of Thermo Fisher 96-capillary 3730xl DNA Analyzer.

Awards & Honors

2025 - 2026 T32 Cancer Engineering Training Program, Gerstner Sloan Kettering

2024 - 2025 Harold Varmus Fellowship, Gerstner Sloan Kettering

2014 - 2016 E. Victor Creed Scholarship, Lewis & Clark College

2014 - 2016 Faculty Scholarship, Lewis & Clark College

Publications

A list is also available online

Submitted & In Preparation

Gutierrez JC, Chen Y, Babaian A, Dhindsa RS, Lareau CA. Resolving human neuronal herpesvirus reactivation via petabase-scale association studies. bioRxiv [Preprint]. 2026 May 1:2026.04.29.721769. In Revision at Genome Biology. doi:10.64898/2026.04.29.721769

Gutierrez JC, Ali TA, Honeycutt CC, Neo JH, Helmsauer K, Nyeo SS, Le A, Vela A, Kida LC, Varela A, Ardy R, Metzner E, Ulirsch JC, Dhindsa RS, Fiziev PP, Chikhi R, Norman TM, Dey KK, Lareau CA. Host control and regulation of human anellovirus persistence. In Preparation.

Published Journal Articles

2026

Chu H, Hollyer M, Borden BA, Reilly CR, Gómez Tejeda Zañudo J, Thomas BS, Phelps K, Pimenta EM, Han S, Camp SY, Gillani R, Gutierrez J, Lareau CA, Nagy M, Johnson J, Alao O, Grundman H, Sterlin L, Terzi W, Sosa D, Small IK, McGillicuddy M, Alharbi N, Anastasio E, Chastain P, Bhakhri P, Hornick JL, Choudhry H, Diehl DM, Van Allen EM, Wagle N, Painter CA, AlDubayan S. Patient-partnered multiomics reveals the molecular architecture of angiosarcoma. Nat Commun. 2026;17(1):9032. doi:10.1038/s41467-026-75810-2

Liu V, Sandor K, Yan PK, Miao Z, Yin Y, Stickels RR, Chen AY, Hiam-Galvez K, Gutierrez J, Zhang W, Sajjath SM, Valbuena R, Wang S, Daniel B, Ludwig LS, Howitt BE, Lareau CA, Satpathy AT. Clonal lineage tracing of innate immune cells in human cancer. Cancer Cell. 2026;44(7):1509-1521.e4. doi:10.1016/j.ccell.2026.05.006

Nyeo SS, Cumming EM, Burren OS, Pagadala MS, Gutierrez JC, Ali TA, Kida LC, Chen Y, Chu H, Hu F, Zou XZ, Hollis B, Fabre MA, MacArthur S, Wang Q, Ludwig LS, Dey KK, Petrovski S, Dhindsa RS, Lareau CA. Population-scale sequencing resolves determinants of persistent EBV DNA. Nature. 2026;650(8102):664-672. doi:10.1038/s41586-025-10020-2

2025

Lareau CA, Maschmeyer P, Yin Y, Gutierrez JC, Dhindsa RS, Gribling-Burrer AS, Zielinski S, Hsieh YH, Nitsch L, Dimitrova V, Nalbant B, Buquicchio FA, Abay T, Stickels RR, Ulirsch JC, Yan P, Wang F, Miao Z, Sandor K, Daniel B, Liu V, Mendez PL, Knaus P, Meyer M, Greenleaf WJ, Kundaje A, Smyth RP, Munschauer M, Ludwig LS, Satpathy AT. Cell type-specific purifying selection of synonymous mitochondrial DNA variation. Proc Natl Acad Sci U S A. 2025;122(30):e2505704122. doi:10.1073/pnas.2505704122

2024

Buquicchio FA, Fonseca R, Yan PK, Wang F, Evrard M, Obers A, Gutierrez JC, Raposo CJ, Belk JA, Daniel B, Zareie P, Yost KE, Qi Y, Yin Y, Nico KF, Tierney FM, Howitt MR, Lareau CA, Satpathy AT, Mackay LK. Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation. Immunity. 2024;57(9):2202-2215.e6. doi:10.1016/j.immuni.2024.06.014

2023

Lareau CA, Yin Y, Maurer K, Sandor KD, Daniel B, Yagnik G, Peña J, Crawford JC, Spanjaart AM, Gutierrez JC, Haradhvala NJ, Riberdy JM, Abay T, Stickels RR, Verboon JM, Liu V, Buquicchio FA, Wang F, Southard J, Song R, Li W, Shrestha A, Parida L, Getz G, Maus MV, Li S, Moore A, Roberts ZJ, Ludwig LS, Talleur AC, Thomas PG, Dehghani H, Pertel T, Kundaje A, Gottschalk S, Roth TL, Kersten MJ, Wu CJ, Majzner RG, Satpathy AT. Latent human herpesvirus 6 is reactivated in CAR T cells. Nature. 2023;623(7987):608-615. doi:10.1038/s41586-023-06704-2

Lareau CA, Dubois SM, Buquicchio FA, Hsieh YH, Garg K, Kautz P, Nitsch L, Praktiknjo SD, Maschmeyer P, Verboon JM, Gutierrez JC, Yin Y, Fiskin E, Luo W, Mimitou EP, Muus C, Malhotra R, Parikh S, Fleming MD, Oevermann L, Schulte J, Eckert C, Kundaje A, Smibert P, Vardhana SA, Satpathy AT, Regev A, Sankaran VG, Agarwal S, Ludwig LS. Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nat Genet. 2023;55(7):1198-1209. doi:10.1038/s41588-023-01433-8

Lareau CA, Liu V, Muus C, Praktiknjo SD, Nitsch L, Kautz P, Sandor K, Yin Y, Gutierrez JC, Pelka K, Satpathy AT, Regev A, Sankaran VG, Ludwig LS. Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nat Protoc. 2023;18(5):1416-1440. doi:10.1038/s41596-022-00795-3

2022

Gutierrez JC, Davis BA, Nevonen KA, Ward S, Carbone L, Maslen CL. DNA Methylation Analysis of Turner Syndrome BAV. Front Genet. 2022;13:872750. doi:10.3389/fgene.2022.872750

2019

Corbitt H, Gutierrez JC, Silberbach M, Maslen CL. The genetic basis of Turner syndrome aortopathy. Am J Med Genet C Semin Med Genet. 2019;181(1):117-125. doi:10.1002/ajmg.c.31686

Technical Strengths

Computational Skills

R, Python, C++, MATLAB, Git, Unix (Debian), Bash, Docker, Singularity, Nextflow

High Performance Compute

Slurm, Google Cloud Compute, TerraBio, AWS

Bioinformatics Proficiencies

WGS, WXS, 10x Flex, sc-RNA/ATAC-seq, mtscATAC-seq, CITE-seq, ASAP-seq, scRNA+ATAC multiome, Nanostring CosMX Spatial Transcriptomics, bulk RNA/ATAC-seq, ChIP-seq, Bisulfite-seq

Software Expertise

• Alignment & Quantification: Samtools, bbmap, BWA, STAR, bowtie2, Minimap2, Kallisto, Bustools, Kraken2, Cellranger
• Genome Wide Variant Association Testing: Plink, GATK, REGENIE
• Sequencing Data Retrieval & De Novo Assembly: NCBI datasets, entrezdirect, sratoolkit, SPADES, Flye, PenguiN
• De Novo Protein Design & Structure: BindCraft, Alphafold3, ESMfold2, Dali, FoldSeek, FoldMason

Leadership & Service

Oct 2025 - Nov 2026 President

Gerstner Sloan Kettering Student Council. New York, NY

• Responsible for coordinating budgeting decisions for social events and student clubs, planning and leading the program retreat, and representing the student body in cross-institutional stakeholder meetings between Weill Cornell and Rockefeller University.

Sep 2026 Exhibitor

Science Saturday at The Rockefeller University. New York, NY

• Led an exhibit with hands-on demonstration of principles of single cell sequencing to elementary-middle school students and their families from across New York City.

May 2026 Exhibitor

Bronx STEM Expo. New York, NY

• Led an exhibit with hands-on demonstration of principles of single cell sequencing to elementary-high school students and their families from the greater Bronx area.

May 2017 - Jun 2022 Mentor

Minds Matter. Portland, OR

• Mentor low-income high-achieving high school students to prepare them for higher education.

Relevant Coursework

• Clinical Research Informatics

• Public Health Informatics

• Epigenetics

• Deep Learning

• Computational Genetics

• Network Biology