Pleiotrope

Deniz C. Aksel, PhD

contact@pleiotrope.xyz
Experience
Cellino Biotech Cambridge, MA
Head of Bioengineering Jan 2025 — Mar 2026
  • Lead all Bioengineering R&D for Cellino's optical iPSC manufacturing bioprocess; manage a 10-person cross-functional team spanning biology, engineering, and computation
  • Led program transferring the bioprocess onto the ARPA-H-backed Nebula platform
  • Presented as technical expert at FDA & EMA meetings and authored technical reports, enabling FDA Advanced Manufacturing Technology (AMT) designation
  • Authored multiple white papers and 5+ patents on imaging-based cell profiling and biomanufacturing methods
Manager of Bioengineering & Lead Bioalgorithm Engineer Nov 2023 — Jan 2025
  • Technical lead for the AI pipeline driving Cellino's optical iPSC bioprocess; achieved fully remote system management and increase in clone throughput per operator
  • Led team building AI models predicting cell viability, density, and state from label-free microscopy, from dataset generation through model training and evaluation
  • First demonstration of predicting genomic stability from time-resolved label-free microscopy of iPSCs
  • Defined technical strategy for extending the platform into directed differentiation, clonal gene editing, and iPSC-derived therapies
Senior Bioengineer Apr 2022 — Nov 2023
  • Developed scalable data generation methods integrating gene-edited cells, automated imaging, and image processing pipelines
  • Translated iPSC culture operations to Cellino's first integrated automation system; produced high-quality clones across multiple donors
Harvard University Cambridge, MA
Graduate Researcher, Ramanathan Lab Apr 2017 — Jan 2022
  • Studied cell fate decisions and tissue morphology in 2D & 3D stem cell models of early human embryonic development
  • Developed optogenetic tools for spatiotemporal control of developmental signaling pathways (Nodal, BMP, FGF) in human pluripotent stem cells
  • Applied dimensionality reduction on multi-omic data to map cell state transitions during early human gastrulation; translated into hPSC reporter lines for directed differentiation
Graduate Researcher / Collaborator, Schier Lab Feb 2017 — Jan 2022
  • Built a 4D image analysis pipeline for lightsheet microscopy of annual killifish embryogenesis, revealing Nodal-dependent axis formation — published in Science (2024)
MIT Synthetic Neurobiology Group (Boyden Lab) Cambridge, MA
Undergraduate Research Assistant Feb 2013 — Jun 2016
  • Designed and built a custom imaging-guided automated patch clamp system; demonstrated reliable automated patching of HEK cells and cultured primary neurons
Education
Harvard University 2022
PhD in Biophysics
Coordination of Patterning and Morphogenesis: Illuminating Principles of Early Embryonic Development Using Annual Killifish and Human Stem Cell Models
Massachusetts Institute of Technology 2016
SB in Biological Engineering  ·  Minor in Mechanical Engineering
Technical Skills
Biology  —  Cell culture (hPSCs, mammalian lines), iPSC reprogramming, directed differentiation & protocol development, tissue engineering & organoids, CRISPR gene editing (KO, HDR, CRISPRa/i), optogenetics, quantitative microscopy, immunocytochemistry, RNA-seq, flow cytometry, patch clamping
Engineering  —  Bioinstrumentation prototyping, lab automation (liquid handlers, microscopes, integrated workcells), signal processing & control theory, optics, fluidics, physics-based modeling
Computation  —  Statistical & deep learning, Bayesian optimization, image processing, high-dimensional data analysis, data visualization, scRNA-seq & ATAC-seq, bioinformatics, dashboard generation, Python (PyTorch, JAX), SQL, Apache Superset, Google Cloud Platform
Leadership  —  Cross-functional team building & management, multi-year program roadmapping, regulatory & investor communication, mentorship & talent development

Pleiotrope Consulting LLC