I am a postdoctoral researcher at the Eric and Wendy Schmidt Center of the Broad Institute of MIT and Harvard. My research is at the intersection of computer science, molecular biology, and statistics. I develop algorithms and machine learning models to integrate multi-modal genomic data, with a goal of understanding cellular dynamics in health and disease and assisting cell state engineering. I received my Ph.D. in computer science and computational biology from Brown University, under the advisement of Ritambhara Singh, Ph.D. (primary advisor) and Sorin Istrail, Ph.D. My doctoral dissertation was on optimal transport algorithms for integrated analysis of single-cell multi-omics data.

Since January 2024, I co-chair the Models, Inference, and Algorithms (MIA) seminar series at the Broad, where we host hybrid (in-person & online) talks by computational scientists in bio(medicine). You can check out our upcoming schedule and past talks.

Apart from research, I have had the opportunity to work on various fun projects that can be found here. Outside of research, I enjoy boardgames with friends, swimming, hiking, playing with my cat, and practicing the ukulele and violin.
Feel free to e-mail me if you’d like to talk.

Research Interests

Application areas
  • Representation learning
  • Optimal transport
  • Manifold learning
  • Bayesian statistics and inference
  • Variable selection
  • Deep learning
  • Causality
  • Graph algorithms
  • Regulatory genomics
  • Functional genomics
  • Single-cell sequencing & imaging
  • Multi-omics
  • 3D genome
  • Precision medicine
  • Structural biology


2018 - 2023 Ph.D. in Computer Science and Computational Biology (3.90/4.00)
M.Sc. in Computer Science (4.00/4.00)
Brown University (Providence, RI)
2013 - 2017 B.Sc. in Engineering (with concentration in Bioengineering) (3.67/4.00)
Olin College of Engineering (Needham, MA)
2008 - 2013 TEVITOL High School with IB Diploma (Gebze, Turkey)

Professional Experience

July 2023 - Present Broad Institute of MIT and Harvard, EWSC Postdoctoral Fellow (Cambridge, MA)
June 2022 - Aug 2022 Microsoft Research, Research Intern (Redmond, WA)
June 2020 - Sep 2020 Microsoft Research, Research Intern (Redmond, WA)
June 2017 - August 2018 Massachusetts Institute of Technology, Research Support Associate (Cambridge, MA)
Jan 2016 - Oct 2016 Design That Matters, Student Engineer (Salem, MA)
Jan 2015 - Dec 2015 Daktari Diagnostics, Student Engineer (Cambridge, MA)

Research Publications Google Scholar


Breaking isometric ties and introducing priors in Gromov-Wasserstein distances
P. Demetci, Q.H. Tran, I. Redko, R. Singh
Proceedings of the 27th International Conference on Artificial Intelligence and Statistics
(AISTATS 2024)
Proceedings of Machine Learning Research (PMLR) -- to appear
[11] [abstract] [paper] [code]


Unbalanced CO-Optimal Transport
Q.H. Tran, H. Janati, N. Courty, R. Flamary, I. Redko, P. Demetci, R Singh
Proceedings of the 37th AAAI Conference on Artificial Intelligence
(AAAI 2023)
[10] [abstract] [paper] [code]
Mammalian olfactory cortex neurons retain molecular signatures of ancestral cell types
S. Zeppilli, A. Ortega Gurrola, P. Demetci, DH. Brann, R. Attey, N. Zilkha, T. Kimchi, SR. Datta, R. Singh, MA. Tosches, A. Crombach, A. Fleischmann
bioRxiv (Under review at Nature Neuroscience)
[9] [abstract] [paper] [code]


Unsupervised Integration of Single-Cell Multi-omics Datasets with Disproportionate Cell-Type Representation
P. Demetci, R. Santorella, B. Sandstede, R. Singh
Proceedings of the 26th Annual Intl. Conference on Research in Computational Molecular Biology
(RECOMB 2022)
Springer Nature Lecture Notes in Bioinformatics (2022) pp 3-19
[8] [abstract] [paper] [code]


SCOT: Single-cell multi-omics integration with optimal transport
P. Demetci*, R. Santorella*, B. Sandstede, W. Stafford Noble and Ritambhara Singh#
*Equal Contribution, #Corresponding Author
Journal of Computational Biology, 2021
[7] [abstract] [paper] [code] [tutorial]
Gromov-Wasserstein Optimal Transport to Align Single-Cell Multi-Omics Data
P. Demetci*, R. Santorella*, B. Sandstede, W. Stafford Noble and Ritambhara Singh#
*Equal Contribution, #Corresponding Author
International Conference on Research in Computational Molecular Biology
(RECOMB 2021)
[6] [abstract] [paper] [code] [tutorial]
ICML WCB Best Poster Award
Multi-scale Inference of Genetic Trait Architecture using Biologically Annotated Neural Networks
P. Demetci,W. Cheng,Gregory Darnell, Xiang Zhou, Sohini Ramachandran, Lorin Crawford#
PLOS Genetics, 2021
[5] [abstract] [paper]


Unsupervised Manifold Alignment for Single-Cell Multi-Omics Data
R. Singh#, P. Demetci, G. Bonora, V. Ramani, C. Lee, H. Fang, Z. Duan, X. Deng, J. Shendure, C. Disteche and W. Stafford Noble#
#Corresponding Authors
Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
(ACM BCB 2020)
[4] [abstract] [paper] [code]
Combinatorial and statistical prediction of gene expression from haplotype sequence
B. Alpay*, P. Demetci* Sorin Istrail, and Derek Aguiar#
*Equal Contribution, #Corresponding Author
Bioinformatics (Oxford Press) vol.36, Supplement_1, p:i194-i202. 2020
Proceedings of the 27th International Conference on Intelligent Systems for Molecular Biology
(ISMB 2020)
[3] [abstract] [paper] [code]


Rapid accumulation of motility-activating mutations in resting liquid culture of Escherichia coli
D. Parker*, P.Demetci*, and G.W. Li#
*Equal Contribution, #Corresponding Author
Journal of Bacteriology, 2019
[2] [abstract] [paper]


Internalization and externalization in the classroom: How do they emerge and why is it important?
P.Demetci, C. Nichols, Y. V. Zastavker, J. D. Stolk, A. Dillon, M. D. Gross.
IEEE Frontiers in Education
(FIE 2016)
[1] [abstract] [paper]

Awards and Honors

2023 EWSC Postdoctoral Fellowship (up to three years)
2023 Harvard/DFCI Data Science Postdoctoral Fellowship (turned down)
2022 Selected to the Rising Stars in EECS cohort (by UT Austin)
2022 RECOMB Travel Fellowship
2020 ICML WCB Fellowship
2020 Microsoft Research Ph.D. Fellowship Nominee (by Brown CCMB)
2016 Meritorius Winner: 2016 MCM/ICM Interdisciplinary Contest in Mathematical Modeling
2015-2017 Olin Alumni Scholarship (towards expenses beyond tuition)
2013-2017 Sunlin Chou International Scholarship (50% tuition)
2013-2017 Olin Merit Scholarship (50% tuition)
2013 Honorable Mention (Instrumentation): 21st Intl. Competition of First Step to Nobel Prize in Physics
(by the Polish Academy of Sciences)
2013 First Place in Physics: 22nd MEF International Research Projects Contest (Turkiye)

Last updated on 23 Jan 2024. Template based on github.com/bamos/bamos.github.io