Carnegie Mellon University

Ph.D Alumni

Seojin Bang

Seojin Bang

Ph.D. in Computational Biology
September 2015 - July 2020

Advisor: Dr. Wei Wu
Thesis: Development of trustworthy machine learning methods for integrating and analyzing biomedical data

 

 

 

 Salim Chowdhury

Ph.D. in Computational Biology
August 2010 - February 2015
Research Analyst, Millennium Management
Advisor: Dr. Russell Schwartz
Thesis: Algorithms to Reconstruct Evolutionary Models of Tumor Progression

 

Luis Pedro Coelho

Ph.D. in Computational Biology
August 2007 - September 2011
Junior Principal Investigator, Fudan University
Advisor: Dr. Robert Murphy
ThesisModeling the space of subcellular location patterns using images and other sources of information
Website

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Ross E. Curtis

 Ph.D. in Computational Biology
August 2008 - December 2011
Computational Biologist, AncestryDNA
Advisor: Dr. Eric Xing
ThesisUsing Visualization and Automation to Accelerate Genetics Discovery

 

Geet Duggal 

Ph.D. in Computational Biology
August 2012 - December 2014
Director of Engineering, DNANexus
Advisor: Dr. Carl Kingsford
Thesis: Algorithms for Determining the Higher Order Three-Dimensional Structure of DNA and its Relationship to Gene Regulation

 

David Farrow 

Ph.D. in Computational Biology
August 2012 - June 2016
Software Engineer, Google
Advisor: Dr. Roni Rosenfeld
Thesis: Modeling the Past, Present, and Future of Influenza

 

Darya Filippova

Ph.D. in Computational Biology
September 2010 - July 2015
Engineer, BetterOmics
Advisor: Dr. Carl Kingsford
Thesis: Algorithms for identification, visualization, and compression of prominent substructures in biological data
 Website

 

Gregory R. Johnson 

Ph.D. in Computational Biology
August 2012 - January 2016
Senior Applied Machine Learning Specialist, Amazon Web Services
Advisor: Dr. Robert F. Murphy
Thesis: Image-derived Models of the Organization of Cellular Components

 

 

Jacob Joseph

Ph.D. in Computational Biology
August 2006 - August 2012
Forensic Analyst, Software Engineering Institute, Carnegie Mellon University
Advisor: Dr. Dannie Durand
Thesis: On the Identification and Investigation of Homologous Gene Families, with Particular Emphasis on the Accuracy of Multidomain Families
Website

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Sabah Kadri

Ph.D. in Computational Biology
August 2007 - January 2012
Director of Bioinformatics and Assistant Professor of Pathology, Lurie Children's Hospital, Northwestern University Feinberg School of Medicine
Advisors:  Drs. Veronica Hinman and Panayiotis (Takis) Benos
Thesis: miRNA Regulation in Development
Website

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John Kang

Ph.D. in Computational Biology
August 2009 - August 2013
Radiation Oncologist, University of Rochester Medical Center
Advisors: Drs. Philip LeDuc and Russell Schwartz
Thesis: Spatiotemporal modeling of actin cytoskeletal mechanics linked to morphology and mechanotransduction

 

Joshua Kangas 

Ph.D. in Computational Biology
August 2008 - January 2013
Assistant Teaching Professor, Computational Biology Department, Carnegie Mellon University
Advisor: Dr. Robert F. Murphy
Thesis: Active Learning for Drug Discovery

Byoungkoo Lee 

Ph.D. in Computational Biology
August 2005 - August 2009
Associate Research Scientist, The Jackson Laboratory
Advisor: Dr. Russell Schwartz
Thesis: Stochastic Off-Lattice Simulations of Binding Chemistry in Crowded Conditions

Cong Ma

Cong Ma

Ph.D. in Computational Biology
August 2015 - October 2020
Postdoctoral Fellow, Princeton University
Advisor: Dr. Carl Kingsford
Thesis: Anomaly detection in RNA-seq alignment and quantification

 

Jun Ma

Ph.D. in Computational Biology
August 2008-May 2014
Senior Applied Scientist, Amazon
Advisors: Dr. Joel Stiles, Dr. Nathan Urban
Thesis: Quantitative simulation of synaptic vesicle release at the neuromuscular junction

 

Suvrajit Maji

Ph.D. in Computational BiologyAugust 2006 - August 2012
Associate Research Scientist, Columbia University
Advisor: Dr. Marcel Bruchez
Thesis: Generative Models for Super-Resolution Single Molecule Microscopy Images of Biological Structures

 

Armaghan Naik

Ph.D. in Computational Biology
August 2008 - August 2013
AVP R&D and Scientific Digital Hed, Sanofi Pasteur
Advisor: Dr. Robert F. Murphy
Thesis: Efficient Modeling and Active Learning of Biological Responses: Learning without Prior Knowledge
Website
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Arvind Ramanathan

Ph.D. in Computational Biology
August 2005 -  May 2010
Computational Biologist, Argonne National Laboratory
Advisor: Dr. Christopher Langmead
Thesis:  Internal Dynamics and Energetics During Enzyme Catalysis

 

Theodore Roman

Ph.D. in Computational Biology
August 2011 - May 2017
Engagement Manager, Highmark Health
Advisor: Dr. Russell Schwartz
Thesis: Understanding Tumor Composition and Evolution Through Geometric Models

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Xiongtao Ruan

Ph.D. in Computational Biology
August 2014 - May 2019
Postdoctoral Research Fellow, University of California, Berkeley
Advisor: Dr. Robert F. Murphy
Thesis: Computational Methods for Image-derived Modeling of Cell Shape and Organization Dynamics

Natalie Sauerwald

Natalie Sauerwald

Ph.D. in Computational Biology
August 2015 - September 2020
Postdoctoral Fellow, Flatiron Institute
Advisor: Dr. Carl Kingsford
Thesis: Algorithms for the study of chromosomal structure variability

Emre Sefer

Ph.D. in Computational Biology
August 2008 - August 2012 (University of Maryland)
August 2012 - February 2015 (Carnegie Mellon University)
Assistant Professor, Computer Science, Ozyegin University
Advisor: Dr. Carl Kingsford
Thesis: Inferring and Analyzing the Present and the Past of Networks from Limited Information

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Aabid Shariff

Ph.D. in Computational Biology
August 2005 - January 2012
Director of Data Science, Pairwise Plants
Advisors: Drs. Robert F. Murphy and Gustavo Rohde
Thesis: Learning Generative Models of Microtubule Distribution
Website

 

Bradley Solomon

Ph.D. in Computational Biology
August 2013 - July 2018
Teaching Assistant Professor,  University of Illinois at Urbana-Champaign
Advisor: Dr. Carl Kingsford
Thesis: Computational Methods for enabling sequence search on 100-terabase RNA-seq datasets

 

Devin Sullivan

Ph.D. in Computational Biology
August 2010 - February 2015
Senior Bioinformatics Scientist, Encodia, Inc. 
Advisor: Dr. Robert F. Murphy
Thesis: Image-derived generative modeling of complex cellular organization in both space and time
Website

 

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Ming-Chi Tsai

Ph.D. in Computational Biology August 2007 - September 2013
Software Engineer, Google
Advisor: Dr. Russell Schwartz
Thesis: Computational Methods for Learning Population History from Large Scale Genetic Variation Datasets

 

Hao Wang

Ph.D. in Computational Biology
August 2012 - May 2017
Bioinformatics Scientist II, Guardant Health
Advisor: Dr. Carl Kingsford
Thesis: Computational methods for exploring gene regulation mechanisms using high-throughput sequencing data

 

Chuang "Chris" Wu

Ph.D. in Computational Biology
August 2005 - July 2014
Engineering Manager, Facebook
Advisor: Dr. Roni Rosenfeld
Thesis: Phenotype Inference from Genotype in RNA Viruses

 

Lu Xie

Ph.D. in Computational Biology
August 2009 - February 2015
Software Engineer, Google
Advisor: Dr. Russell Schwartz
Thesis: Inferring Viral Capsid Self-Assembly Pathway from Bulk Experiment Measurement via Parameter Fitting Methods

 

Shan Zhong

Ph.D. in Computational Biology
August 2008 - May 2013
Principal Scientist, Translational Computational Biology, GSK
Advisor: Dr. Ziv Bar-Joseph
Thesis: Computational Study of Transcriptional Regulation – From Sequence to Expression

 

Guy Zinman

Ph.D. in Computational Biology
August 2007 - May 2012
General Manager of Solutions, Spark Beyond
Advisor: Dr. Ziv Bar-Joseph
Thesis: Analysis of High Throughput Genomic Datasets Across Species