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, 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.
Elena 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 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.
Melisa 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 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,
|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|