Alumni

Graduates of the Bioinformatics and Genomics program possess the knowledge and skills to successfully compete for top careers in academia, industry, government, and other arenas. In their current positions around the globe, our alumni are expanding the frontiers of discovery and making strides toward changing the world. A list of our alumni and their current positions is below.

NameAdvisorGraduating YearDissertationFirst PositionCurrent Position
Ayaan Hossain Howard Salis 2021 Advanced algorithms for the design and analysis of synthetic genetic parts Machine Learning Scientist, Tessera Therapeutics Machine Learning Scientist, Tessera Therapeutics
Fan Song Feng Yue, Shaun Mahony 2021 Unveiling structural variation: detection, characterization, phasing and its role in 3D genome reorganization in cancer Bioinformatics Scientist, Illumina Bioinformatics Scientist, Illumina
Jordan Hughey Dajiang Liu 2021 In-silico modeling gene expression utilizing genomic activity and 3D contact information Computational Biologist, GlaxoSmithKline Computational Biologist, GlaxoSmithKline
Vijay Kumar Santhosh Girirajan 2021 Computational methods for dissecting the genetic basis of neurodevelopmental disorders Senior Statistical Geneticist, Regeneron Senior Statistical Geneticist, Regeneron
Divyanshi Srivastava Shaun Mahony 2021 Computational methods for characterizing the sequence and chromatin determinants of transcription factor binding Machine Learning Engineer, Invitae Machine Learning Engineer, Invitae
Matthew Jensen Santhosh Girirajan 2021 Complex genetic interaction patterns determine the phenotypic trajectory of neurodevelopmental disorders Postdoctoral Researcher, Yale University Postdoctoral Researcher, Yale University
Mehreen Mughal Michael DeGiorgio, Stephen Shaeffer 2020 Advanced statistical frameworks for evaluating evolutionary hypotheses from genomic data Postdoctoral Fellow, Cold Spring Harbor Laboratory Postdoctoral Fellow, Cold Spring Harbor Laboratory
Guanjue Xiang Ross Hardison 2020 Computational tools for normalization, integration, and gene regulatory inference of multi-dimensional epigenomic and transcriptomic data Postdoctoral Researcher, Dana-Faber Cancer Institute Postdoctoral Researcher, Dana-Faber Cancer Institute
Lila Rieber Shaun Mahony 2020 Multidimensional scaling for three-dimensional modeling of chromosome conformation Computational Biologist, Element Genomics Computational Biologist, Element Genomics
Tarik Salameh Feng Yue 2020 Chromatin loop detection via machine learning on genome-wide contact data Doctor of Medicine, Pennsylvania State University Doctor of Medicine, Pennsylvania State University
Naomi Yamada Shaun Mahony 2020 Computational methods to characterize protein-DNA interactions in ChIP-exo data Computational Biologist, GlaxoSmithKline Computational Biologist, GlaxoSmithKline
Rahulsimham Vegesna Paul Medvedev, Kateryna Makova 2020 Evolution of Y chromosome ampliconic genes in great apes Postdoctoral Research Fellow, National Cancer Institute Postdoctoral Research Fellow, National Cancer Institute
Wilfried Guiblet Kateryna Makova, Anton Nekrutenko 2020 Non-B DNA and evolution of the human genome Postdoctoral Research Fellow, National Cancer Institute Postdoctoral Research Fellow, National Cancer Institute
Nicholas Stoler Anton Nekrutenko 2020 Accurate measurement of variants with continuous ranges of frequencies with Next-Generation Sequencing Computational Scientist, Pennsylvania State University Computational Scientist, Pennsylvania State University
Bo Zhang Feng Yue 2019 Novel mechanisms of Ikaros' regulatory functions in leukemia Principal Scientist of Bioinformatics, Gomicsgene Bioinformatics Scientist, Illumina
Lin An Yu Zhang 2019 Understanding gene regulation at a fine-scale: zooming into 3D chromatin conformation Data Scientist II, CAMP4 Therapeutics Computational Biologist, Sanofi
Nabeel Ahmed Edward O'Brien 2019 Physical bioinformatics methods to understand causes and consequences of variable codon translation Rates Computational Biologist, Resolution Biosciences Bioinformatics Scientist, Karius Diagnostics
Tao Yang Qunhua Li 2018 Statistical methods for comparing next-generation sequencing data reproducibility, similarity and differentiation Associate Scientist - Bioinformatics, Regeneron Senior Scientist - Applied Bioinformatics, Bristol Myers Squibb
Di Wu John Carlson 2018 Intraspecific variation in green ash response to an invasive insect Research Bioinformatician, Cedars-Sinai Research Bioinformatician, Cedars-Sinai
Yafei Lyu Qunhua Li 2018 Statistical integration of genomic data across labs, platforms and experimental conditions Postdoctoral Researcher, University of Pennsylvania Investigator II, Bioinformatics and Data Science, Novartis Institutes for BioMedical Research
Samarth Rangavittal Kateryna Makova 2018 Assembly and analysis of great ape Y chromosomes Research Scientist, 23andMe Data Scientist, Apple
Anurag Verma Marylyn Ritchie 2017 PheWAS and beyond: Approaches to address challenges for identifying robust associations using clinical data Lead Bioinformatics Scientist, University of Pennsylvania Instructor, Department of Medicine, University of Pennsylvania
Shefali Setia Verma Marylyn Ritchie 2017 Investigating computational methods to model the genotypic and phenotypic complexity of adverse health outcomes: Understanding undercover heritability Lead Bioinformatics Scientist, University of Pennsylvania Instructor, Department of Medicine, University of Pennsylvania
Akshay Kakumanu Shaun Mahony 2017 Computational modelling of sequence features driving transcription factor binding in neuronal reprogramming Associate Scientist, Computational Biology, Fulcrum Therapeutics Senior Scientist, Computational Biology, Foundation Medicine
Yanli Wang Feng Yue 2017 Identification and visualization of regulatory elements and 3D genome structure Doctor of Medicine, Pennsylvania State University Pediatrics-Medical Genetics, Children's Hospital of Philadelphia
Yin Tang Sarah Assmann 2017 Hidden RNA codes revealed from the plant in vivo rna structurome Postdoctoral Associate, Yale University Postdoctoral Associate, Yale University
Akhil Kumar Costas Maranas 2017 Elucidation and synthetic design of biochemical pathways using novoStoic Machine Learning Scientist, Amazon Senior Data Scientist, Discovery Inc
Juan Antonio Raygoza Garay Santhosh Girirajan 2016 Understanding the role of a hypermutator switch in the evolution of an extremely resistant Staphylococcus aureus infection Postdoctoral Research Fellow, University of Toronto Postdoctoral Research Fellow, University of Toronto
Rohit Reja Frank Pugh 2016 Understanding molecular mechanisms of gene regulation using high resolution ChIP-exo Bioinformatics Scientist, Seven Bridges Genomics Senior Scientist Bioinformatis, Genentech
Ruowang Li Marylyn Ritchie 2016 Using large-scale genomics data to understand the genetic basis of complex traits Postdoctoral Research Fellow, University of Pennsylvania Research Associate, University of Pennsylvania
Boris Rebolledo-Jaramillo Anton Nekrutenko 2016 Understanding mitochondrial DNA and RNA variability in humans Assistant Professor, Universidad del Desarrollo Assistant Professor, Universidad del Desarrollo
Arkarachai Fungtammasan Kateryna Makova 2016 Genome and transcriptome architecture shaped by short tandem repeats: comparison of RNA-DNA differences, reverse transcription errors, and sequencing errors in short tandem repeats Scientist, DNAnexus Principal Scientist, DNAnexus
Qingyu Wang Webb Miller, Ross Hardison, Naomi Altman 2016 Evaluating multiple sequence alignments using ENCODE data Research Scientist, Agilent Technologies Research Scientist, Agilent Technologies
Tyler Malys Cooduvalli Shashikant 2015 Microbiome and epigenetics: Two keys to the development of personalized medicine Senior Statistician, National Cancer Institute Assistant Director, National Cancer Institute
Garam Celine Han Frank Pugh 2015 Transcriptional regulation of erythropoiesis via high resolution ChIP-exo Postdoctoral Research Fellow, Broad Institute of MIT and Harvard Principal Scientist, Bristol Myers Squibb
Oscar Bedoya Reina Webb Miller 2014 Computational approaches to predict phenotype differences in populations from high-throughput sequencing data Postdoctoral Fellow, University of Edinburgh Assistant Professor, Karolinska Institute
Bongsoo Park Seogchan Kang 2013 Cyber-infrastructure supporting fungal and oomycete phylogenetics and genomics Instructor, Johns Hopkins University Bioinformatics Scientist, National Institutes of Health
Christapher Morrissey Ross Hardison 2013 Understanding the epigenetics of erythroid differentiation through the power of deep sequencing Postdoctoral Fellow, Buck Institute for Research on Aging Manager of Data Science, DNAnexus
Gue Su Chang Frank Pugh 2013 Integrated genomics approach to uncovering gene regulation and epigenetics across eukaryotes Postdoctoral Fellow, Yale University Postdoctoral Fellow, Yale University
Jihye Park Eric Harvill 2013 Phylogenomic variations and host adaptations of the classical bordetellae Postdoctoral Research Fellow, Massachusetts General Hospital Postdoctoral Research Fellow, Dana-Faber Cancer Institute
Sushant Kumar Mishra William Noid 2013 Molecular principles of folding upon binding processes in disordered proteins: A computational case study Research Scientist, Yale University Research Scientist, Yale University
Venkatesh Moktali Seogchan Kang 2013 A comparative genomic investigation of niche adaptation in fungi Bioinformatics Scientist, University of California, Riverside Senior Product Manager, Twist Bioscience
Zhaorong Ma Michael Axtell 2013 Functional and evolutionary genomics of plant small RNAs Programmer, SoftGenetics Programmer, SoftGenetics
Ti-Cheng Chang Wansheng Liu 2011 The genomic organization and gene repertoire of the male-specific region of the bovine Y chromosome Senior Bioinformatics Research Scientist, St. Jude Children's Hospital Group Lead Genomics, St. Jude Children's Hospital
Zhenhai Zhang Frank Pugh 2011 Datamining of genome-wide nucleosome data generated by Next-Generation Sequencing Research Associate Scientist, Columbia University Professor, Guangdong Academy of Medical Sciences
Guruprasad Ananda Kateryna Makova 2011 Decoding the multifactorial nature of mutation rate variation in the human genome using computational and statistical approaches Postdoctoral Researcher, Pennsylvania State University Director, NGS Bioinformatics, Dana-Faber Cancer Institute
Sridhar Ranganathan Costas Maranas 2011 Using computation to analyze and redesign metabolism Staff Scientist, Thermo Fisher Scientific Director of Computational Biology, Jumpcode Genomics
Sunando Roy Mary Poss 2011 Identifying structural changes in evolving viral proteins ORISE Fellow, Centers for Disease Control and Prevention Research Associate, University College London
Melissa Wilson Kateryna Makova 2011 Mammalian genome evolution through the lens of the sex chromosomes Miller Fellow, University of California, Berkeley Assistant Professor, Arizona State University
Eric Samorodnitsky Frank Pugh 2010 Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms Using Chromatin Immunoprecipitation Data Postdoctoral Fellow, Boston University Postdoctoral Fellow, Ohio State University
Song Li Sarah Assmann 2010 Identification of Key Regulators of Guard Cell Functions Using Systems Biology Approaches Postdoctoral Researcher, Duke University Associate Professor, Virginia Tech
Brian Canada James Wang 2010 Augmentation of the Zebrafish Phenomic Landscape by Histological Analysis and Content-Based Image Retrieval Assistant Professor, University of South Carolina, Beaufort Chair, Department of Computer Science, University of South Carolina, Beaufort
Yogeshwar Kelkar Kateryna Makova 2010 Evolution of microsatellites in primate genomes: Definition of microsatellites, causes of variation, and the microsatellite life cycle Postdoctoral Associate, Yale University Director of Data Science, Finch Therapeutics
Kyung Dae Ko Randen Patterson 2009 Quantitative functional measurement of a protein using phylogenetic profiles Postdoctoral Researcher, Georgetown University Staff Scientist, National Institutes of Health
David King Ross Hardison 2009 Phylogenetic conservation of cis-regulatory regions using sequence alignability and cladistic motifs Bioinformatics Research Scientist, Colorado State University Bioinformatics Research Scientist, Colorado State University

NameAdvisorGraduating YearFirst PositionCurrent Position
Yuhuan Cheng Dajiang Liu 2021 Doctor of Philosophy, North Carolina State University Doctor of Philosophy, North Carolina State University
Rachel Cooper Shaun Mahony 2021 NoneNone
Jui-Shan Lin Yifei Huang 2021 Data Science Associate, New York Genome Center Data Science Associate, New York Genome Center
Sage WrightSinisa Dovat2021Bioinformatician, Pennsylvania Department of HealthBioinformatician, Pennsylvania Department of Health
Karine MoussaDajiang Liu2021Test Conductor, National Aeronautics and Space AdministrationTest Conductor, National Aeronautics and Space Administration
Pallavi Surana Santhosh Girirajan 2020 Doctor of Philosophy, Stony Brook University Doctor of Philosophy, Stony Brook University
Natalie Zesati Shaun Mahony 2020 Bioinformatics Engineer, Peptilogics Bioinformatics Engineer, Peptilogics
Siddharth Wekhande Shaun Mahony 2019 Associate Computational Biologist I, Broad Institute of MIT and Harvard Associate Computational Biologist I, Broad Institute of MIT and Harvard
Nayeim Khan Santhosh Girirajan 2019 Product Owner, Bioinformatics, CosmosID Product Owner, Bioinformatics, CosmosID
Debmalya NandyFrancesca Chiaromonte2019Postdoctoral Fellow, Colorado School of Public HealthPostdoctoral Fellow, Colorado School of Public Health
Yinan Wan Istvan Albert 2014 Product Manager, DNAnexus Product Manager, DNAnexus
Neerja Katiyar
Marylyn Ritchie
2013
Bioinformatician, Jackson Laboratory
Bioinformatician, Jackson Laboratory
Bhargavi Panchangam None 2013 Staff Bioinformatics Systems Software Engineer, Guardant Health Staff Bioinformatics Systems Software Engineer, Guardant Health
Yuchen Zhang Claude Depamphilis 2011 Assistant Professor, Tulane University Assistant Professor, Tulane University