Rebecca Elyanow

PhD Candidate in Computer Science
and Computational Biology

relyanow @

About Me

I will receive my PhD in Computer Science and Computational Biology from Brown University in May 2020. I relocated to Princeton in 2017 to continue work with my advisor Ben Raphael. My research is broadly focused on developing algorithms to analyze RNA-seq data using knowledge of gene and cell relationships to produce biologically interprable results. Recent projects include netNMF-sc, a matrix factorization method which incorporates prior knowledge in the form a gene interaction network to assist in clustering and imputation of cells from sparse single-cell RNA-seq data and NetMix, a method for identifying differentially expressed genes connected on a biological interaction network.


Brown University (Visiting Scholar at Princeton University)

2015 - May 2020

PhD in Computer Science and Computational Biology

Brown University

2015 - 2018

Master of Computer Science

Carnegie Mellon University

2010 - 2014

Bachelor of Computer Science and Computational Biology

Research Experience

Brown University

PhD Candidate

I work with advisor Ben Raphael to develop algorithms for understanding tumor heterogeneity. Recent projects include developing a probabilistic method to identify structural variants from whole-genome linked-read sequencing data and using machine learning to cluster cells from high-throughput single-cell RNA-seq data.

Sage Bionetworks

Research Intern

I work with the Neurodegenerative Disease team to develop algorithms for identifying genes and pathways correlated with the progression of Alzheimer's disease.

Brown University


I am collaborating with ecologists to assemble a high-quality genome and transcriptome for the barnacle species S. balanoides and to characterize allele frequencies and microbiome composition differences across the upper and lower extremes of the intertidal zone. 

École Polytechnique Fédérale de Lausanne (EPFL)

Blue Brain Project Intern

I developed software to synthesize neuron morphologies of different cell types for the Blue Brain Project. The software uses diffusive particle dynamics to “grow” a population of neurons in parallel, allowing growing neurons to interact with each other and create realistic neuronal arbors.

Carnegie Mellon University

Undergraduate Researcher

I worked under Dr. Robert Murphy to develop algorithms to create generative models of neuron shape as part of the CellOrganizer tool.

Teaching Experience

Prison Teaching Initiative

Math Instructor

I taught Elementary Algebra and Basic Math to inmates at Garden State Youth Correctional Facility and Albert C. Wagner Youth Correctional Facility. The courses are accredited through Raritan Valley Community College.

Princeton University

Student Supervisor, Laboratory Learning Program

I designed a research project and supervised a high school intern as part of the Laboratory Learning Program.

Princeton University

Undergraduate Research Mentor

I mentored junior independent work for COS397

Princeton University

Programming mentor

I mentored Princeton undergraduates in website and app development as part of Princeton Summer Programming Experiences


Elyanow, Rebecca and Dumitrascu, Bianca and Engelhardt, Barbara E and Raphael, Benjamin J (2019). netNMF-sc: Leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis. bioRxiv.

We present netNMF-sc, an algorithm which combines network-regularized non-negative matrix factorization with a specialized procedure to handle the large fraction of zero entries in the transcript count matrix obtained from scRNA-seq. Accepted to RECOMB 2019.

Nunez J.C.B., Elyanow R.G., Ferranti D.A., Rand D.M. (2018). Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches. Population Genomics: Marine Organisms. Springer, Cham.

Text-book chapter describing genome assembly approaches using pooled-sequencing data. I contributed computational bioinformatics approaches as part of the IGERT fellowship in reverse ecology.

Elyanow, R., Wu, H.T., & Raphael, B.J. (2017). Identifying structural variants using linked-read sequencing data. Bioinformatics

Method for identifying structural variants, accepted to RECOMB-CCB 2017.

Invited Talks

RECOMB, Washington, D.C.

May 2019

netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data

Brown Bag Seminar Series, Brown University

November 2017

From tides to nucleotides: Ecological genomics of Semibalanus balanoides

RECOMB-CCB, Los Angeles, CA

July 2017

Identifying structural variants using linked-read sequencing data

Poster Presentations

New York Area Meeting in Quantitative Biology, Cold Spring Harbor

August 2017

Identifying structural variants using linked-read sequencing data

Evolution, Austin, TX

June 2016

Hybrid genome assembly of the northern acorn barnacle, Semibalanus balanoides

RECOMB, Los Angeles, CA

April 2016

Identifying structural variants using linked-read sequencing data

RECOMB, Pittsburgh, PA

April 2014

Generative Models of the Spatial Organization of Neurons

Honors & Awards

Bloomberg Data for Good Exchange Immersion Fellowship


Bloomberg L.P.

NSF IGERT Fellowship in Reverse Ecology

2015 - 2017

Brown University

Scholarship of Excellence in Research

Spring 2014

École Polytechnique Fédérale de Lausanne (EPFL)

Holleran Scholar


Carnegie Mellon University


President, Princeton Citizen Scientists

2017 - Present

Princeton University

Princeton Citizen Scientists is a graduate organization aimed at promoting effective science communication and evidence-based policy making. I am one of four executive board members.

Event Organizer, Science and Intersectionality Workshop

Fall 2018

Princeton University

Co-organized a series of talks and teach-ins with Princeton Citizen Scientists, taking an intersectional look at the relation of the sciences to society in the form of advocacy, science culture, and inclusivity.

Volunteer Computer Science Instructor

Spring 2017

Hopewell Elementary School

Volunteer Computer Science Instructor


Nathaniel Bishop Middle School



netNMF-sc is a network regularization algorithm for dimensionality reduction and imputation of single-cell expression data.

View Project

Billion Oyster Project Digital Platform data visualizations

I was partnered with the Billion Oyster Project through the Bloomberg Data for Good Exchange Immersion Fellowship. I created a web application for generating plots and figures for visualization of oyster measurement data on the digital platform.

View Project


NAIBR (Novel Adjacency Identifying with Barcoded Reads) is a probabilistic method for identifying novel adjacencies created by structural variants. NAIBR utilizes barcoded reads produced by 10X Genomics' whole genome sequencing pipeline to probabalistically model and rank candidate novel adjacencies.

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Single Cell Geometries

Software to simulate single cell count matrices from several canonical geometries. Created with members of the Cell Types working group at the Chan Zuckerberg Initiative (CZI) investigator meeting Collaborative Computational Tools for the Human Cell Atlas.

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The Octduino is an octopus plush that has 12 programmable buttons sewn to its tentacles with conductive thread. We have programmed the buttons to play the 12 notes of an octave so that the Octduino can be played like a piano. The user can also program the Octduino to be a general purpose USB controller, allowing the user use the Octduino to control all types of video games. Octduino placed 3rd at HackPrinceton as well as winning 'Best Hardware' and 'Made My Day'.

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