mouse retina+optic nerve×conditions
Discover new targets for
vision restoration.
I use computational biology to discover therapeutic targets for vision restoration, combining retinal and optic-nerve atlas assembly, machine-learning-enabled integration, quantitative cell-state modeling, multi-omics, and scientific software development.
01
North star
Eye1k
A pan-conditional mouse atlas of the retina and optic nerve
A unified reference to resolve retinal and optic-nerve cell types and states across development, homeostasis, injury, and neurodegeneration.
Eye1k currently integrates 13 single-cell atlases and is being developed with a consortium-based annotation strategy. The long-term goal is to use cross-condition maps to identify molecular programs and candidate therapeutic targets relevant to vision restoration.
Download, process, integrate & harmonize
In-house pipelines standardize public and collaborative datasets, scale analysis to millions of cells, use GPU acceleration, and apply machine-learning integration where it adds value.
Assemble the atlas ecosystem
Individual studies become one connected reference rather than isolated datasets — spanning retina and optic nerve, ages, perturbations, disease models, and experimental conditions.
Complete systematic annotation
I established and coordinate a consortium of wet-lab and domain experts who work with my bioinformatics team to resolve cell classes and subtypes consistently across the collection.
Ask downstream biological questions
The unified atlas enables analyses of aging, optic-nerve-crush responses, neurodegeneration, model-to-model differences, cross-species conservation, and recurrent molecular programs relevant to vision restoration.
02
In parallel
Other ongoing projects
METHOD2026 →
scCS
single-cell Commitment Scores
A computational framework for quantitative assessment of cell-fate commitment from single-cell transcriptomic data, designed to describe commitment as a continuous property rather than only a discrete cell label.
Preprint ↗
ATLASongoing
HROCA
Human Retinal Organoid Cell Atlas
Ongoing development of a high-resolution single-cell reference for human retinal organoids, with cross-system comparison to in vivo human retinal development and a focus on transcriptional states that emerge or diverge in vitro.
Preprint ↗ACTIVE PAPER2026
NF1 optic glioma
Systems-level single-cell dissection
A systems-level single-cell dissection of a preclinical murine model of NF1 optic glioma, focused on tumor-associated cellular states, microenvironmental changes, and candidate vulnerabilities.
ACTIVE PAPER2026
Human optic nerve atlas
Integrated single-cell multi-omics
Contributing to an integrated single-cell multi-omics reference of the human optic nerve to resolve cell types, molecular programs, and tissue organization across complementary modalities.
03
Trajectory
Positions, questions, papers
2026 — present
CURRENT
Lead Bioinformatician
University of Pittsburgh
Leading Eye1k, developing scCS, coordinating a five-member bioinformatics team, and supporting computational work across internal and collaborative studies.
Eye1k — pan-conditional mouse atlas of retina and optic nerveongoing flagship atlas project
HROCA — Human Retinal Organoid Cell Atlasongoing atlas project
Quantitative assessment of cell-fate commitment using scCSbioRxiv · 2026 ↗
NF1 optic glioma at single-cell resolutionCommunications Biology · in review, 2026
Human optic nerve multi-omics atlasNature Genetics · in review, 2026
2022 — 2026
Lead Bioinformatician
Schepens Eye Research Institute of Mass Eye and Ear · Harvard Medical School
Built and analyzed large-scale single-cell atlases of retinal development across in vivo and in vitro systems, with emphasis on retinal ganglion cell specification and maturation. Developed workflows for integration, trajectories, and cross-system comparison across datasets totaling more than three million cells.
Human retinal organoid single-cell atlasbioRxiv · 2025 ↗
Developmental heterogeneity of human retinal ganglion cellsDevelopmental Biology · 2025 ↗
Retinal myeloid response to transplantation of human neuronsiScience · accepted 2026 ↗
Müller glia–microglia cross talk during retina regenerationPNAS · 2026 ↗
DNMT3a suppression and optic-nerve regenerationScience Translational Medicine · in revision, 2026 ↗
Neurotrophic factor co-treatment improves donor and host RGC survivalTVST · 2025 ↗
Improving donor retinal ganglion cell survival through microglia modulationbioRxiv · 2024 ↗
SOCS3 regulates pathological retinal angiogenesis through SPP1Molecular Therapy · 2024 ↗
Controlling donor and newborn neuron migration and maturation in the eyePNAS · 2023 ↗
IGFBPL1, microglia homeostasis, and neuroinflammation in glaucomaCell Reports · 2023 ↗
2021 — 2023
Research Intern
Laboratory of Bone and Cartilage Physiology · Karolinska Institutet
Studied the cartilage stem-cell niche in development and regeneration while developing expertise in light-sheet microscopy, single-cell transcriptomics, RNA velocity, and deep-learning models for microscopy.
2021
Research Intern
Center for Brain Research · Medical University of Vienna
Worked with spatial and single-cell approaches around Schwann-cell progenitor derivatives and adrenal development, including slide-seq2 / merFISH concepts, RNA Scope, advanced microscopy, visualization, and Seurat.
2020
Research Intern
Laboratory of Skeletal Tissues Regeneration · Sechenov University
Worked on mineralized-tissue analysis during regeneration and advanced microscopy, including Lambda, Airyscan, IHC modifications, and whole-mount IHC.
2019
Research Intern
Laboratory of Developmental Biology and Regenerative Medicine · Karolinska Institutet
Worked on neural-crest development and neuroblastoma biology while developing hands-on experience in confocal microscopy, cryotomy, and immunohistochemistry.
2019 — 2021
Student Researcher
Institute of Experimental Oncology and Biomedical Technologies · Nizhny Novgorod
Early research spanning tumor metabolism and chemoresistance, neural-crest derivatives, tumor stem cells, transplantation biology, and the regenerative potential and metabolism of the growth-plate stem-cell niche.
04
Teaching
Mentoring, courses, workshops
MENTORING2023 → present
Research mentoring
Computational biology training across career stages
I enjoy mentoring people at very different stages, from high-school students to postdocs, especially around single-cell analysis, computational thinking, and research design.
- Sergio Pestun — High School Student (2023)
- Sthavir Vinjamuri — College Student (2024–2025)
- Everett Labrecque — High School / College Student (2024–present)
- Chien-Yu Lin — Master’s Student (2025–present)
- Anil Upreti — Postdoc (2025–2026)
COURSES + WORKSHOPShands-on teaching
Lectures and training programs
From formal coursework to practical workshop teaching
- Lecturer at the Master’s program Bioinformatics: Single-cell multiomics — Tomsk National Research Medical Center
- Organized and hosted bioinformatics workshops on single-cell RNA-seq analysis at Belgrade University (14 people) and the Institute for Biological Research “Siniša Stanković” (5 people)
- Organiser of BNV Lab Summer School 2025
05
Side quests
Hobby projects
CURRENT BIOLOGY2023
The parasite story
Polymorphic parasitic larvae that cooperate as a swimming colony
A collaboration outside my main retinal work: two morphologically and functionally distinct cercarial forms cooperate to build a swimming aggregate proposed to aid host infection — a striking example of division of labor in a parasite.
Current Biology ↗
CELL2025
Axolotl regeneration
Body-wide and local responses to amputation
A large collaborative regeneration project showing that adrenergic signaling coordinates systemic stem-cell activation with local limb-regeneration responses after amputation in axolotl.
Cell ↗
06
Methods
Methods & technical toolkit
My work spans the full path from raw sequencing data to atlas-scale analysis, quantitative modeling, and experimental validation, with an emphasis on scalable omics workflows.
Next step
I am currently looking for a PhD student position.
I am happy to discuss PhD opportunities, research collaborations, atlas integration, single-cell methods, and computational approaches to vision restoration.