Daniel Segrè, PI, Professor, Bioinformatics Program, Department of Biology, Department of Biomedical Engineering, Department of Physics

Director, BU Microbiome Initiative, Co-Director, BU ARC on Systems Biology of Microbiomes

Ph.D., Life Sciences, Weizmann Institute of Science, Israel
M.Sc., Physics, University of Trieste, Italy


Marisol Dothard | Molecular Biology, Cell Biology & Biochemistry ProgramMarisol Dothard, Ph.D. Student, MCBB (jointly with the Finnerty Lab)

Microbiomes are sum-total communities of viruses, microbes, and fungi in and on organisms/environments. My interests lie in improving the understanding of these communities in corals, who are massively affected by ocean acidification and rising global temperatures, in the hopes to elucidate advantages these communities may relay to their coral hosts in the context of mangrove corals. 



Ilija Dukovski, Research Scientist

Ph.D. Physics, University of Massachusetts, Amherst

B.S. Theoretical Physics, Belgrade University, Serbia

Ilija got his undergraduate degree from Belgrade University, Serbia in 1995. His diploma work was on quantum information and teleportation. He continued his education as a Ph.D. student at the Physics Department at Umass, Amherst from 1996 to 2001, when he defended his thesis in statistical physics, focusing on the development of cluster Monte Carlo methods for studies of critical phenomena. After that he joined the Polymer Science and Engineering Department at Umass, and worked on molecular dynamics simulations of polymer crystallization. He spent the next nine years in industry, working on charge transport in semiconductors utilizing Monte Carlo and ab-initio Density Functional Theory methods. He joined the lab in 2013 as a research scientist. His current focus is the development and maintaining of the COMETS software package. His research interests are primarily focused on the biophysics of pattern/morphology formation in bacterial colonies, human gut microbiome, and metabolism and biophysics of cancerous tumors.

ELENAElena Forchielli, Ph.D. Student, MCBB

I use models, experiments and field work to map metabolic interactions in synthetic and natural marine bacterial ecosystems.





Ziwei Huang, Ph.D. Student, Physics






Dileep Kishore, Ph.D. Student, Bioinformatics Program

Dileep obtained his B.Tech and M.Tech in Biotechnology with a minor in Operations Research from the Indian Institute of Techonology Madras (May 2016) and is currently pursuing his Ph.D. in Bioinformatics. He is interested in modeling microbial interactions and their interactions with their hosts. In the Segre lab, he works on building a database of microbial interactions and a tool to explore them through networks, a kinetic model of the effect of microbial metabolites on the human AHR pathway, and a reinforcement learning model exploring microbial interactions and their dynamics in a community. His other interests include algorithm development, quantified-self, and artificial intelligence.
In his spare time, Dileep loves working on open-source software, reading, hacking his window manager and text editor, reading, and exploring productivity tools.

Devlin Moyer, Ph.D. Student, Bioinformatics Program (jointly with the Fuxman-Bas Lab)

Devlin got a B.S. in Biochemistry from Case Western Reserve University. During his undergraduate studies, he worked in a lab at the Cleveland Clinic studying the role of disruptions in pre-mRNA splicing in human diseases. He started out in the wet-lab, but eventually switched to exclusively computational work, helping graduate students in the lab with some analyses of RNA-seq data and independently creating a database of introns in many species to study the evolution of the two classes of spliceosomal introns in eukaryotes. At BU, Devlin is co-advised by Juan Fuxman Bass and Daniel Segrè and his thesis project is about creating a new framework for incorporating expression data into genome-scale metabolic models, with the end goal of building more robust and realistic metabolic models of human cancers. Devlin’s rotation project in the Segrè lab was about combining artificial chemistry and Flux-Balance Analysis to study the general principles governing the structural features of metabolic networks.

osborne_idMelisa Osborne, Research Scientist & Lab Manager

Melisa joined the Segre lab in 2016 as a research scientist and wet lab manager.  She began her career as a biochemist, with a B.A. in Biochemistry and Molecular Biology from the College of Wooster and a doctorate degree in Biochemistry from Brandeis University.  After completing her graduate thesis on the single molecule kinetics of bacterial transcription factors in the lab of Jeff Gelles, she expanded her expertise to include in vivo molecular biology and microbiology in the labs of Simon Dove (Boston Children’s Hospital and Harvard Medical School) and Alvaro Sanchez (currently of Yale University).  Melisa has a passion for teaching, which has been evident since her days as an undergraduate.  She spent a formative year with her colleagues at the College of Wooster teaching chemistry and biochemistry, and in her current role at Boston University teaches BF751 Biochemistry and Molecular Biology for Bioinformatics.  Outside of the lab, Melisa enjoys playing the flute and listening to records and exploring the outdoors with her family.

Michael S

Michael Silverstein, Ph.D. Candidate, Graduate Program in Bioinformatics (jointly with the Bhatnagar Lab)

Michael is a PhD student in the Bioinformatics program and he is interested in the role that soil microbial interactions play in regulating climate change. He got his start in studying microbial communities while working at Finch Therapeutics where he helped to design a microbial consortia for the treatment of Ulcerative Colitis using gut microbiome derived strains. While his hands and mind aren’t in the dirt he enjoys rock climbing, cooking, reading, biking, playing music, gardening, and camping (so, some dirt still included…). He is co-advised by Jennifer Bhatnagar.


Jing Zhang, Ph.D. Candidate, Graduate Program in Bioinformatics

My research interest lies at the interface of synthetic biology and microbial ecology. I’m passionate about innovating solutions for environmental challenges. In my spare time, I lead a nature conservation and animal welfare thinktank in China. 






Former Lab Members


Name Past position in the lab Position after leaving the lab or Current Position
Qasim Beg Research Scientist Microbiology Lecturer
David Bernstein PhD student, Biomedical Engineering Postdoc, Arkin Lab, UC Berkeley
Emma Briars Research Assistant, BU Biology (UROP) Ph.D. Student, BU Bioinformatics
David Byrne Ph.D. Student, BU  Bioinformatics
Hsuan-Chao Chiu Ph.D. Student, BU Bioinformatics Senior Software Engineer at MediaTek
Sara Baldwin Collins Ph.D. Student, BU Bioinformatics Bioinformatics Specialist at MIT
Demetrius Dimucci Ph.D. Student, BU Bioinformatics Postdoctoral Fellow, Forsyth Institute, Harvard
Lina Faller Ph.D. Student, BU Bioinformatics Computational Biologist, Ginkgo Bioworks
Francesco Gatto Exchange Student, University of Padova, Italy Chief Scientific Officer at Elypta
Lili Ge Master Student, BU Bioinformatics
Keegan Go BU Summer Research Internship Program for High School Students Undergrad at Stanford U.
Josh Goldford Ph.D. Student, BU Bioinformatics Associate Scientist, Agios Pharmaceuticals
Brian Granger Ph.D. Student, BU Bioinformatics Postdoctoral Researcher at AstraZeneca
Lan Hu Ph.D. Student, BU Bioinformatics Sr. Scientist at Bio-Rad Laboratories
Christopher Jacobs Ph.D. Student, BU Bioinformatics
Anu Jayaraman M.Sc. Student, BU Bioinformatics Senior Software Developer, Biobase
Charles Jo Masters Student, Biomedical Engineering PhD Student, BU
Amrita Kar Ph.D. Student, BU Bioinformatics Bioinformatics Analyst, New York Genome Center
Yasin Kaymaz M.Sc. Student, Bioinformatics Program Graduate Student, U Mass Worcester
Niels Klitgord Ph.D. student, Bioinformatics Program Bioinformatics Staff Scientist, Viome
Wesley Marrero SURF Student (winner of 3rd Place Poster Award at UROP symposium) Student at Universidad del Turabo
Varun Mazumdar Ph.D. student, Bioinformatics Program Computational Scientist, Seres Therapeutics
Shany Ofaim Postdoctoral Fellow Postdoctoral fellow, Barabasi Lab
Alan Pacheco Ph.D. student, Bioinformatics Program, HHMI Gilliam fellow, Ford Fellow Postdoctoral McDonnell fellow, Vorholt Lab, ETH
Paimon Pakzad BU Summer Research Internship Program for High School Students Undergraduate Student, Princeton
Elisabetta Panizzoni Exchange Student, University of Padova, Italy
Michael Quintin Ph.D. student, Bioinformatics Program
Ed Reznik Ph.D. Student, Biomedical Engineering Research Fellow and Manager of Biocomputing at Memorial Sloan Kettering Cancer Center
William Riehl Ph.D. Student and Posdoctoral Fellow,
Bioinformatics Program
Software Developer at Lawrence Berkeley National Laboratory
Moritz Schuette Visiting Student, Max Planck Institute
William Erik Sherwood Postdoctoral Fellow, Center for BioDynamics and Dept. of Mathematics and Statistics Chief Scientist at Cypher Corporation
Maddalena Silli Visiting Student, Univ. of Trieste, Italy
Evan Snitkin Ph.D. Student, BU Bioinformatics Assistant Professor, U. Michigan
Arion Stettner Ph.D. Student, BU BME Postdoctoral Fellow, ETH, Zurich
Meghan Thommes Ph.D. Student, BU BME Data Scientist, Joyn Bio
Adam Wolberg Undergraduate Student, Biochemistry
Mattia Zampieri Visiting Ph.D. Student, SISSA, Trieste, Italy Postdoctoral Fellow, ETH, Zurich
Jin Zhao Visiting graduate student
Summer Zhuang Postdoctoral Fellow
Ali Zomorrodi Postdoctoral Fellow Computational and Systems Biology Lead at Mass General Hospital & Instructor of Pediatrics at Harvard Medical School