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
Bipin RimalAndrew Patterson2023Multi-omics insights into microbial metabolism of bile acids
Jeremy SutherlandJesse Lasky and Terrence Bell2023The impact of genotype-by-environment interactions on switchgrass rhizosphere microbiome composition and insights for breeding in sustainable agriculture
Chachrit Khunsriraksakul (Ph.D)Dajiang Liu2022Integrating Genomic, Epigenomic, and 3D Genomic Date to Empower Discover, Risk Prediction, and Drug Repositioning
Ayaan Hossain (Ph.D)Howard Salis2022Advanced algorithms for the design and analysis of synthetic genetic parts
Jordan Hughey (Ph.D)Alexandros Vgontzas2022Inflammation in Obstructive Sleep Apnea: Its Mediating Role and Potential as a Marker of Severity
Ayaan HossainHoward Salis2021Advanced algorithms for the design and analysis of synthetic genetic partsMachine Learning Scientist, Tessera TherapeuticsMachine Learning Scientist, Tessera Therapeutics
Fan SongFeng Yue, Shaun Mahony2021Unveiling structural variation: detection, characterization, phasing and its role in 3D genome reorganization in cancerBioinformatics Scientist, IlluminaBioinformatics Scientist, Illumina
Jordan HugheyDajiang Liu2021In-silico modeling gene expression utilizing genomic activity and 3D contact informationComputational Biologist, GlaxoSmithKlineComputational Biologist, GlaxoSmithKline
Vijay KumarSanthosh Girirajan2021Computational methods for dissecting the genetic basis of neurodevelopmental disordersSenior Statistical Geneticist, RegeneronSenior Statistical Geneticist, Regeneron
Divyanshi SrivastavaShaun Mahony2021Computational methods for characterizing the sequence and chromatin determinants of transcription factor bindingMachine Learning Engineer, InvitaeMachine Learning Engineer, Invitae
Matthew JensenSanthosh Girirajan2021Complex genetic interaction patterns determine the phenotypic trajectory of neurodevelopmental disordersPostdoctoral Researcher, Yale UniversityPostdoctoral Researcher, Yale University
Mehreen MughalMichael DeGiorgio, Stephen Shaeffer2020Advanced statistical frameworks for evaluating evolutionary hypotheses from genomic dataPostdoctoral Fellow, Cold Spring Harbor LaboratoryPostdoctoral Fellow, Cold Spring Harbor Laboratory
Guanjue XiangRoss Hardison2020Computational tools for normalization, integration, and gene regulatory inference of multi-dimensional epigenomic and transcriptomic dataPostdoctoral Researcher, Dana-Faber Cancer InstitutePostdoctoral Researcher, Dana-Faber Cancer Institute
Lila RieberShaun Mahony2020Multidimensional scaling for three-dimensional modeling of chromosome conformationComputational Biologist, Element GenomicsComputational Biologist, Element Genomics
Tarik SalamehFeng Yue2020Chromatin loop detection via machine learning on genome-wide contact dataDoctor of Medicine, Pennsylvania State UniversityDoctor of Medicine, Pennsylvania State University
Naomi YamadaShaun Mahony2020Computational methods to characterize protein-DNA interactions in ChIP-exo dataComputational Biologist, GlaxoSmithKlineComputational Biologist, GlaxoSmithKline
Rahulsimham VegesnaPaul Medvedev, Kateryna Makova2020Evolution of Y chromosome ampliconic genes in great apesPostdoctoral Research Fellow, National Cancer InstitutePostdoctoral Research Fellow, National Cancer Institute
Wilfried GuibletKateryna Makova, Anton Nekrutenko2020Non-B DNA and evolution of the human genomePostdoctoral Research Fellow, National Cancer InstitutePostdoctoral Research Fellow, National Cancer Institute
Nicholas StolerAnton Nekrutenko2020Accurate measurement of variants with continuous ranges of frequencies with Next-Generation SequencingComputational Scientist, Pennsylvania State UniversityComputational Scientist, Pennsylvania State University
Bo ZhangFeng Yue2019Novel mechanisms of Ikaros' regulatory functions in leukemiaPrincipal Scientist of Bioinformatics, GomicsgeneBioinformatics Scientist, Illumina
Lin AnYu Zhang2019Understanding gene regulation at a fine-scale: zooming into 3D chromatin conformationData Scientist II, CAMP4 TherapeuticsComputational Biologist, Sanofi
Nabeel AhmedEdward O'Brien2019Physical bioinformatics methods to understand causes and consequences of variable codon translation RatesComputational Biologist, Resolution BiosciencesBioinformatics Scientist, Karius Diagnostics
Tao YangQunhua Li2018Statistical methods for comparing next-generation sequencing data reproducibility, similarity and differentiationAssociate Scientist - Bioinformatics, RegeneronSenior Scientist - Applied Bioinformatics, Bristol Myers Squibb
Di WuJohn Carlson2018Intraspecific variation in green ash response to an invasive insectResearch Bioinformatician, Cedars-SinaiResearch Bioinformatician, Cedars-Sinai
Yafei LyuQunhua Li2018Statistical integration of genomic data across labs, platforms and experimental conditionsPostdoctoral Researcher, University of PennsylvaniaInvestigator II, Bioinformatics and Data Science, Novartis Institutes for BioMedical Research
Samarth RangavittalKateryna Makova2018Assembly and analysis of great ape Y chromosomesResearch Scientist, 23andMeData Scientist, Apple
Anurag VermaMarylyn Ritchie2017PheWAS and beyond: Approaches to address challenges for identifying robust associations using clinical dataLead Bioinformatics Scientist, University of PennsylvaniaInstructor, Department of Medicine, University of Pennsylvania
Shefali Setia VermaMarylyn Ritchie2017Investigating computational methods to model the genotypic and phenotypic complexity of adverse health outcomes: Understanding undercover heritabilityLead Bioinformatics Scientist, University of PennsylvaniaInstructor, Department of Medicine, University of Pennsylvania
Akshay KakumanuShaun Mahony2017Computational modelling of sequence features driving transcription factor binding in neuronal reprogrammingAssociate Scientist, Computational Biology, Fulcrum TherapeuticsSenior Scientist, Computational Biology, Foundation Medicine
Yanli WangFeng Yue2017Identification and visualization of regulatory elements and 3D genome structureDoctor of Medicine, Pennsylvania State UniversityPediatrics-Medical Genetics, Children's Hospital of Philadelphia
Yin TangSarah Assmann2017Hidden RNA codes revealed from the plant in vivo rna structuromePostdoctoral Associate, Yale UniversityPostdoctoral Associate, Yale University
Akhil KumarCostas Maranas2017Elucidation and synthetic design of biochemical pathways using novoStoicMachine Learning Scientist, AmazonSenior Data Scientist, Discovery Inc
Juan Antonio Raygoza GaraySanthosh Girirajan2016Understanding the role of a hypermutator switch in the evolution of an extremely resistant Staphylococcus aureus infectionPostdoctoral Research Fellow, University of TorontoPostdoctoral Research Fellow, University of Toronto
Rohit RejaFrank Pugh2016Understanding molecular mechanisms of gene regulation using high resolution ChIP-exoBioinformatics Scientist, Seven Bridges GenomicsSenior Scientist Bioinformatis, Genentech
Ruowang LiMarylyn Ritchie2016Using large-scale genomics data to understand the genetic basis of complex traitsPostdoctoral Research Fellow, University of PennsylvaniaResearch Associate, University of Pennsylvania
Boris Rebolledo-JaramilloAnton Nekrutenko2016Understanding mitochondrial DNA and RNA variability in humansAssistant Professor, Universidad del DesarrolloAssistant Professor, Universidad del Desarrollo
Arkarachai FungtammasanKateryna Makova2016Genome and transcriptome architecture shaped by short tandem repeats: comparison of RNA-DNA differences, reverse transcription errors, and sequencing errors in short tandem repeatsScientist, DNAnexusPrincipal Scientist, DNAnexus
Qingyu WangWebb Miller, Ross Hardison, Naomi Altman2016Evaluating multiple sequence alignments using ENCODE dataResearch Scientist, Agilent TechnologiesResearch Scientist, Agilent Technologies
Tyler MalysCooduvalli Shashikant2015Microbiome and epigenetics: Two keys to the development of personalized medicineSenior Statistician, National Cancer InstituteAssistant Director, National Cancer Institute
Garam Celine HanFrank Pugh2015Transcriptional regulation of erythropoiesis via high resolution ChIP-exoPostdoctoral Research Fellow, Broad Institute of MIT and HarvardPrincipal Scientist, Bristol Myers Squibb
Oscar Bedoya ReinaWebb Miller2014Computational approaches to predict phenotype differences in populations from high-throughput sequencing dataPostdoctoral Fellow, University of EdinburghAssistant Professor, Karolinska Institute
Bongsoo ParkSeogchan Kang2013Cyber-infrastructure supporting fungal and oomycete phylogenetics and genomicsInstructor, Johns Hopkins UniversityBioinformatics Scientist, National Institutes of Health
Christapher MorrisseyRoss Hardison2013Understanding the epigenetics of erythroid differentiation through the power of deep sequencingPostdoctoral Fellow, Buck Institute for Research on AgingManager of Data Science, DNAnexus
Gue Su ChangFrank Pugh2013Integrated genomics approach to uncovering gene regulation and epigenetics across eukaryotesPostdoctoral Fellow, Yale UniversityPostdoctoral Fellow, Yale University
Jihye ParkEric Harvill2013Phylogenomic variations and host adaptations of the classical bordetellaePostdoctoral Research Fellow, Massachusetts General HospitalPostdoctoral Research Fellow, Dana-Faber Cancer Institute
Sushant Kumar MishraWilliam Noid2013Molecular principles of folding upon binding processes in disordered proteins: A computational case studyResearch Scientist, Yale UniversityResearch Scientist, Yale University
Venkatesh MoktaliSeogchan Kang2013A comparative genomic investigation of niche adaptation in fungiBioinformatics Scientist, University of California, RiversideSenior Product Manager, Twist Bioscience
Zhaorong MaMichael Axtell2013Functional and evolutionary genomics of plant small RNAsProgrammer, SoftGeneticsProgrammer, SoftGenetics
Ti-Cheng ChangWansheng Liu2011The genomic organization and gene repertoire of the male-specific region of the bovine Y chromosomeSenior Bioinformatics Research Scientist, St. Jude Children's HospitalGroup Lead Genomics, St. Jude Children's Hospital
Zhenhai ZhangFrank Pugh2011Datamining of genome-wide nucleosome data generated by Next-Generation SequencingResearch Associate Scientist, Columbia UniversityProfessor, Guangdong Academy of Medical Sciences
Guruprasad AnandaKateryna Makova2011Decoding the multifactorial nature of mutation rate variation in the human genome using computational and statistical approachesPostdoctoral Researcher, Pennsylvania State UniversityDirector, NGS Bioinformatics, Dana-Faber Cancer Institute
Sridhar RanganathanCostas Maranas2011Using computation to analyze and redesign metabolismStaff Scientist, Thermo Fisher ScientificDirector of Computational Biology, Jumpcode Genomics
Sunando RoyMary Poss2011Identifying structural changes in evolving viral proteinsORISE Fellow, Centers for Disease Control and PreventionResearch Associate, University College London
Melissa WilsonKateryna Makova2011Mammalian genome evolution through the lens of the sex chromosomesMiller Fellow, University of California, BerkeleyAssistant Professor, Arizona State University
Eric SamorodnitskyFrank Pugh2010Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms Using Chromatin Immunoprecipitation DataPostdoctoral Fellow, Boston UniversityPostdoctoral Fellow, Ohio State University
Song LiSarah Assmann2010Identification of Key Regulators of Guard Cell Functions Using Systems Biology ApproachesPostdoctoral Researcher, Duke UniversityAssociate Professor, Virginia Tech
Brian CanadaJames Wang2010Augmentation of the Zebrafish Phenomic Landscape by Histological Analysis and Content-Based Image RetrievalAssistant Professor, University of South Carolina, BeaufortChair, Department of Computer Science, University of South Carolina, Beaufort
Yogeshwar KelkarKateryna Makova2010Evolution of microsatellites in primate genomes: Definition of microsatellites, causes of variation, and the microsatellite life cyclePostdoctoral Associate, Yale UniversityDirector of Data Science, Finch Therapeutics
Kyung Dae KoRanden Patterson2009Quantitative functional measurement of a protein using phylogenetic profilesPostdoctoral Researcher, Georgetown UniversityStaff Scientist, National Institutes of Health
David KingRoss Hardison2009Phylogenetic conservation of cis-regulatory regions using sequence alignability and cladistic motifsBioinformatics Research Scientist, Colorado State UniversityBioinformatics Research Scientist, Colorado State University

NameAdvisorGraduating YearFirst PositionCurrent Position
Austin DiazSanthosh Girirajan2023
Saakshi S. DonthiSanthosh Girirajan2022
Sai Sruthi Amirtha GaneshSuzanne Gonzalez2022
Yuhuan ChengDajiang Liu2021Doctor of Philosophy, North Carolina State UniversityDoctor of Philosophy, North Carolina State University
Rachel CooperShaun Mahony2021NoneNone
Jui-Shan LinYifei Huang2021Data Science Associate, New York Genome CenterData 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 SuranaSanthosh Girirajan2020Doctor of Philosophy, Stony Brook UniversityDoctor of Philosophy, Stony Brook University
Natalie ZesatiShaun Mahony2020Bioinformatics Engineer, PeptilogicsBioinformatics Engineer, Peptilogics
Siddharth WekhandeShaun Mahony2019Associate Computational Biologist I, Broad Institute of MIT and HarvardAssociate Computational Biologist I, Broad Institute of MIT and Harvard
Nayeim KhanSanthosh Girirajan2019Product Owner, Bioinformatics, CosmosIDProduct Owner, Bioinformatics, CosmosID
Debmalya NandyFrancesca Chiaromonte2019Postdoctoral Fellow, Colorado School of Public HealthPostdoctoral Fellow, Colorado School of Public Health
Yinan WanIstvan Albert2014Product Manager, DNAnexusProduct Manager, DNAnexus
Neerja KatiyarMarylyn Ritchie2013
Bioinformatician, Jackson Laboratory
Bioinformatician, Jackson Laboratory
Bhargavi PanchangamNone2013Staff Bioinformatics Systems Software Engineer, Guardant HealthStaff Bioinformatics Systems Software Engineer, Guardant Health
Yuchen ZhangClaude Depamphilis2011Assistant Professor, Tulane UniversityAssistant Professor, Tulane University