Nilah Ioannidis

Timeline

1. 2005–2013

   Chemistry and biophysics degrees

   She earns an MPhil in chemistry at the University of Cambridge in 2005 and a PhD in biophysics at Harvard University in 2013. During her doctoral studies, she works in MIT’s Department of Biological Engineering, developing methods that use hidden Markov modeling and Bayesian inference to analyze the movement of particles inside cells.

2. 2013–2014

   A Stanford postdoctoral fellowship

   In 2013–2014, she is a postdoctoral fellow at Stanford’s Center for Computational, Evolutionary and Human Genomics, with Carlos Bustamante as her faculty advisor.

3. July 2019

   Joining Berkeley’s computer science faculty

   In July 2019, she joins UC Berkeley as an assistant professor with a joint appointment in computer science and the Center for Computational Biology. Her previous work in Stanford’s Department of Biomedical Data Science includes REVEL, an ensemble predictor of whether missense genetic variants cause disease. Her earlier roles also include research director at the Jain Foundation, which focuses on the rare genetic disease dysferlinopathy.

4. 2022

   A Biohub investigator award

   In 2022, she becomes a Chan Zuckerberg Biohub Investigator. The award provides $1 million in unrestricted research funds over five years.

5. November 2023

   Testing genomic deep learning

   In November 2023, she coauthors “Personal transcriptome variation is poorly explained by current genomic deep learning models” in Nature Genetics. She conceives and supervises the study, which tests four models and finds limited ability to explain differences in gene expression between individuals.

6. 2024

   Designing promoters for specific cells

   In 2024, she coauthors “Designing Cell-Type-Specific Promoter Sequences Using Conservative Model-Based Optimization” at NeurIPS. The team uses conservative objective models to design regulatory DNA sequences and experimentally validates new promoters in three leukemia cell lines: Jurkat, K562 and THP1.

7. September 2025

   UC Santa Cruz faculty report

   A September 2025 UC Santa Cruz report introduces her as an assistant professor in Applied Mathematics at the Baskin School of Engineering, coming from UC Berkeley. Her group develops machine learning and AI methods to interpret individual genomes and model differences in gene expression and other molecular and cellular traits.

8. As of October 2026

   Faculty roles at both campuses

   As of October 2026, she is an assistant professor in UC Santa Cruz’s Applied Mathematics department and Genomics Institute, and an adjunct assistant professor in UC Berkeley’s Department of Electrical Engineering and Computer Sciences with a joint appointment in the Center for Computational Biology. She also participates in Berkeley’s Center for Targeted Machine Learning and Causal Inference.