Nikita Kotlov
Burlington
Summary
Computational oncology and multi-omics data leader with deep expertise in tumor microenvironment biology, cancer immunology, biomarker discovery, and translational research. Author of 100+ peer-reviewed publications with an h-index of 18+, focused on translating genomic, transcriptomic, blood-based, and immune profiling data into clinically relevant insights across oncology and immune-mediated diseases.
Expertise includes RNA-seq, WES, blood-based molecular testing, AI-enabled omics interpretation, patient stratification, and multi-modal data integration across scRNA-seq, flow cytometry, and multiplex immunofluorescence. Proven experience leading cross-functional scientific teams, external collaborations, and research-to-product initiatives in precision oncology.
Overview
11
11
years of professional experience
Work History
Sr. Director Data Analysis
BostonGene
Waltham, MA
01.2024 - 06.2026
- Led data analysis programs across translational oncology, autoimmune disease research, and multi-omics initiatives, focusing on tumor microenvironment biology, cancer immunology, biomarker discovery, AI-enabled omics interpretation, and personalized medicine.
- Oversaw analytical strategy and resource allocation across projects involving blood-based tests, RNA-seq, WES, and other multi-omics data. Partnered with clinical, scientific, product, and business teams to deliver biologically interpretable and clinically relevant insights across solid tumors, hematologic malignancies including lymphomas, and immune-mediated diseases.
- Presented results and scientific strategy to internal stakeholders, external collaborators, and prospective partners, supporting research programs, product development, and clinically oriented molecular profiling.
Director Data Analysis
BostonGene
Waltham, MA
01.2023 - 12.2023
- Directed client-facing data analysis and project delivery across translational oncology, clinical reporting, product development, and external research collaborations.
- Led scientific discussions with clients and collaborators to define project goals, assess feasibility, develop analytical scope, and translate biological questions into executable multi-omics analysis plans. Coordinated cross-functional teams across bioinformatics, data analysis, clinical, scientific, product, and business functions to deliver scoped projects involving RNA-seq, WES, blood-based testing, tumor microenvironment profiling, and related molecular assays.
- Presented project updates, analytical findings, biological interpretation, and final deliverables to external clients, collaborators, prospective partners, and internal stakeholders. Work supported biomarker discovery, patient stratification, therapy-response analysis, clinical molecular profiling, and translational research across oncology and immune-mediated disease programs.
Senior Bioinformatics Scientist, Team lead
BostonGene
Moscow, Russia - Yerevan, Armenia - Waltham, MA
01.2018 - 12.2022
- Led a bioinformatics team supporting clinical reporting, translational oncology research, product development, and external collaborations.
- Managed up to 40 team members and up to 50 concurrent projects across internal R&D, customer-facing studies, and clinical report development.
- Developed bioinformatics methods for report QC, molecular data interpretation, and standardized analytical review across RNA-seq, WES, and related profiling workflows.
- Built internal education programs and delivered 100+ hours of training in bioinformatics, statistics, molecular biology, cancer biology, therapy mechanisms, pathways, research analytics, and clinical interpretation.
- Contributed to 14 peer-reviewed publications, including 10 produced under my management or supervision, and supported 25+ conference abstracts at AACR, ASCO, ASH, and SITC.
- Developed deep domain expertise in B-cell and T-cell lymphomas, solid tumors, immunotherapy, biomarker discovery, and clinically oriented molecular profiling.
Bioinformatics Specialist
BostonGene
Moscow, Russia
01.2017 - 01.2018
- Expanded into R&D-focused translational oncology analytics, contributing to the development of BostonGene’s early tumor microenvironment, DNA/RNA interpretation, and patient-level molecular profiling capabilities.
- Developed methods for projecting individual patient expression profiles onto reference cohorts; prototyped tumor microenvironment classification approaches for solid tumors; and built sequencing QC and analysis tools for RNA-seq, DNA alterations, tumor content estimation, CNA analysis, mutation interpretation, and genetic event prioritization.
- Worked extensively with public and controlled-access cohorts, including TCGA, GTEx, ENA/SRA, and dbGaP, applying differential expression analysis, survival modeling, multivariable statistics, pathway inference, clustering, and dimensionality reduction to oncology research questions. Supported external collaborations, personalized vaccine-related projects, and presented analytical findings to scientific partners.
- Managed up to five concurrent projects and supervised up to five team members.
Bioinformatician, software engineer
BostonGene
Moscow, Russia
09.2015 - 01.2017
- Supported the early development of BostonGene’s computational oncology platform through bioinformatics software engineering, cloud-based pipeline development, and cancer transcriptomics analysis.
- Built an asynchronous cloud pipeline engine for large-scale parallel execution of analytical tools; integrated Dockerized RNA-seq fusion-calling workflows; and analyzed public cancer expression datasets from TCGA, SRA, GEO, and related repositories. Developed RNA-seq QC and batch/sample classification approaches, introduced relative gene signature scoring methods used in downstream publications, and contributed to a patented machine learning model for melanoma immunotherapy-response prediction.
Summer Internship
Leiden University Medical Center
Leiden
07.2015 - 08.2015
- Performed computational analysis for a CYP2D6 genotyping project using single-molecule real-time PacBio RS II sequencing at Leiden University Medical Center.
- Responsibilities included long-read alignment, CYP2D6 genotype interpretation, activity classification, and prediction of functional effects for isoforms not represented in reference databases.
Education
Ph.D. - Molecular Biology
Institute of Molecular Biology National Academy of Science
Yerevan, Armenia12-2025
Master of Science - Bioinformatics And Bioengineering
Lomonosov Moscow State University (MSU)
Moscow, Russia08-2018
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Kaspersky antivirus school
01-2012
Computer Programming
Summer school of informatics
01-2012
High School Diploma - Mathematics and Computer Science
AESC MSU — Kolmogorov Boarding School
01-2012
Skills
- Scientific & Data Strategy
- Translational Oncology
- Multi-omics Product Development
- Biomarker Discovery & Strategy
- Blood-based Molecular Testing
- Clinical Genomics & Transcriptomics
- Tumor Microenvironment Profiling
- Cancer Immunology & Immune Profiling
- Multi-modal Omics Integration
- AI-enabled Omics Interpretation
- Cross-functional Team Leadership
- External Partner Engagement
Languages
English
Full Professional
Russian
Native or Bilingual
Japanese (N5)
Elementary
Scientific profile links
- Orchid https://orcid.org/0000-0002-6393-7357
- Web of Science https://www.webofscience.com/wos/author/record/976800
- Google Scholar https://scholar.google.com/citations?user=-1ERLBMAAAAJ
Timeline
Sr. Director Data Analysis
BostonGene
01.2024 - 06.2026
Director Data Analysis
BostonGene
01.2023 - 12.2023
Senior Bioinformatics Scientist, Team lead
BostonGene
01.2018 - 12.2022
Bioinformatics Specialist
BostonGene
01.2017 - 01.2018
Bioinformatician, software engineer
BostonGene
09.2015 - 01.2017
Summer Internship
Leiden University Medical Center
07.2015 - 08.2015
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Kaspersky antivirus school
Computer Programming
Summer school of informatics
High School Diploma - Mathematics and Computer Science
AESC MSU — Kolmogorov Boarding School
Ph.D. - Molecular Biology
Institute of Molecular Biology National Academy of Science
Master of Science - Bioinformatics And Bioengineering
Lomonosov Moscow State University (MSU)