I am a third year Ph.D. student in computational biology, working with professors Ritambhara Singh, Ph.D. and Sorin Istrail, Ph.D. at Brown University Department of Computer Science. My research is at the intersection of computer science, statistics, and molecular biology. Types of research problems I currently work on include (1) interpretable (sometimes Bayesian) machine learning models for the analysis of genomics data, with a goal to understand regulatory mechanisms behind complex traits and diseases, and (2) manifold alignment algorithms for multi-omic data integration.

Before joining Brown University, I received my bachelor’s degree in bioengineering from Olin College of Engineering. There, I worked with Jean J. Huang, Ph.D. and John Geddes, Ph.D. on bioinformatic analyses and dynamical modeling of microbial communities under various environmental perturbations. Then, I worked in Quantitative Biology Lab with Gene-Wei Li. Ph.D. at Massachusetts Institute of Technology (MIT) as a research support associate and lab manager, researching gene regulatory network rewiring in bacteria. In summer of 2020, I completed an internship with the Genomics team at Microsoft Research

Apart from computational biology, I have had the pleasure of working on different STEM projects, which can be found here. Outside of research, I enjoy holding boardgame nights with friends, feeding birds, playing ukulele and violin, and swimming (hopefully post-pandemic). Feel free to e-mail me if you’d like to talk.

Education

2018 - 2022 (Expected) Ph.D. in Computer Science and Computational Biology (3.90/4.00)
Brown University (Providence, RI)
2018 - 2020 (Expected) M.Sc. in Computer Science (4.00/4.00)
Brown University (Providence, RI)
2013 - 2017 B.Sc. in Bioengineering (3.67/4.00)
Olin College of Engineering (Needham, MA)
2008 - 2013 TEVITOL High School + IB Diploma (Gebze, Turkey)

Professional Experience

June 2020 - Sep 2020 Microsoft Research: Genomics, 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 2016 - Oct 2016 Daktari Diagnostics, Student Engineer (Cambridge, MA)

Research Projects and Publications

Google Scholar

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
bioRxiv, 2020
[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
bioRxiv, 2020
[4] [abstract] [paper]
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), 2020
ISMB Proceedings, 2020
[3] [abstract] [paper]
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, 2016
FIE Conference, 2016
[1] [abstract] [paper]

Invited Talks, Conferences, Oral and Poster Presentations

Presenters emphasized/italicized, Equal contribution denoted with:*

</table> ## Teaching Experience
2020 ICML Workshop on Computational Biology (Poster & Spotlight Presentation) [Acceptance Rate: 21%]
Gromov-Wasserstein Optimal Transport to Align Single-Cell Multi-Omics Data
P Demetci*, R Santorella*, B Sandstede, W Stafford Noble, R Singh
2020 ISMB Proceedings (Oral Presentation) [Acceptance Rate: 19%]
Combinatorial and statistical prediction of gene expression from haplotype sequence
B Alpay*, P Demetci*, S Istrail, D Aguiar
2020 ISMB (Oral & Poster Presentation) [Acceptance Rate: 25%]
Gromov-Wasserstein Optimal Transport to Align Single-Cell Multi-Omics Data
P Demetci , R Santorella*, B Sandstede, W Stafford Noble, R Singh
2020 ACM-BCB: Oral Presentation [Acceptance Rate: 27%]
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, W Stafford Noble.
2020 Brown Unconference on Computational Intelligence and Applications (Invited Talk)
Gromov-Wasserstein Optimal Transport to Align Single-Cell Multi-Omics Data
P Demetci*, R Santorella*, B Sandstede, W Stafford Noble, R Singh
2019 CCV-Con (Invited Talk @ Brown University)
Biologically Annotated Neural Networks for Multi-scale Genomic Association Discovery
P Demetci, W Cheng, G Darnell, S Ramachandran, L Crawford
2016 FIE (Oral Presentation) [Acceptance Rate: 48%]
Internalization and externalization: How do they emerge and why is it important?
P Demetci, C Nichols, Y V Zastavker, J D Stolk, A Dillon, M D Gross
2016 NEMPET (Poster Presentation)
Bioinformatic Comparison of Phototrophic Communitiesthat Degrade Cellulose and Fix Nitrogen
P Demetci, M Sheets, A Knapp, Linda Amaral-Zettler, Jean Huang
2015 Closing the Gap (Oral Presentation)
Project EyeHelper: Assistive Navigation for Blind Shopping
P Demetci, A Johnnson, M Ruehle, P Ruvolo
Spring 2019 Advanced Algorithms in Computational Biology and Medical Bioinformatics (CSCI 2820 @ Brown U.)
Teaching Assistant: wrote and graded assignments, held recitations and office hours, lectured a few times.
Fall 2016 Designing Better Drugs (SCI1240 @ Olin College)
Teaching and Laboratory Assistant: graded assignments, assisted students in the laboratory.
## Awards
2020 ICML WCB Fellowship
2016 Meritorius Winner: 2016 MCM/ICM Interdisciplinary Contest in Mathematical Modeling
2015-2017 Olin Alumni Scholarship
2013-2017 Sunlin Chou International Scholarship (50% tuition)
2013-2017 Olin Merit Scholarship (50% tuition)
2013 Honorable Mention (Instrumentation): First Step to Nobel Prize in Physics
## Professional Service and Community Memberships
2020 - Present Society for Industrial and Applied Mathematics (SIAM)
2018 - Present International Society for Computational Biology (ISCB)
2018 - Present Models, Inference, and Algorithms (MIA) at Broad Institute
Member Graduate Women in Science and Engineering @ Brown University
## Skills
Programming Languages More experienced: Python, R, MATLAB -- Less experienced: Java, C++
Frameworks NumPy, Pandas, SciPy, PyTorch, Pyro, TensorFlow, Tensorflow-Probability, HDF5, Bioconductor, Seurat
Systems Linux, OSX, High Performance Cluster Computing, slurm, Google Cloud Computing, Microsoft Azure
Bioinformatics Tools GATK, VCFtools, BCFtools, BEDtools, PLINK, Cromwell, Cytoscape, QIIME, VAMPS, JGI
Laboratory DNA & RNA Extraction, PCR & RT-qPCR, Electrophoresis & PAGE, Western blotting, Molecular transformation, Transfection, HPLC, Rheology, Scanning Electron Microscopy
Natural Languages English (Proficient), Turkish (Native Language), French (A2-Level proficiency)
--- Last updated on 2020-06-23