Date:
Time:
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Event Description:
The Computational and Systems Biology Ph.D. Program will hold our annual retreat at the Colony Hotel in picturesque Kennebunkport, ME. from Sunday, October 13th - Monday, October 14h 2024. Our retreat will feature a poster session, lobster buffet, and talks from CSB students, MIT Faculty, and invited speakers.
We are pleased to announce our lineup of speakers:
Guest Speakers :
Sunday, October 13, 2024 11:15 - 11:45 AM
Dr. Kristin Knouse, MIT Biology Department Whitehead Career Development Professor; Intramural Faculty, Koch Institute
Title of Talk: Understanding how the organism monitors liver function to properly time regeneration
Bio:
Kristin is the Whitehead Career Development Professor in the MIT Department of Biology and the Koch Institute for Integrative Cancer Research. She received a B.S. in biology from Duke University in 2010 and then enrolled in the Harvard and Massachusetts Institute of Technology (MIT) M.D.-Ph.D. Program, where she earned a Ph.D. through the MIT Department of Biology in 2016 and an M.D. through the Harvard-MIT Division of Health Sciences and Technology in 2018. She conducted her doctoral research in the laboratory of Angelika Amon, where she developed tools to characterize large-scale somatic copy number alterations in mammalian tissues and then used diverse approaches to reveal the importance of tissue architecture for chromosome segregation fidelity in epithelia. In 2018, she established her laboratory as a Whitehead Fellow at the Whitehead Institute for Biomedical Research and was honored with the NIH Director’s Early Independence Award. In July 2021, she joined the MIT Department of Biology and Koch Institute for Integrative Cancer Research as an Assistant Professor. Her lab develops high-throughput functional genomics approaches to understand and modulate organ injury and regeneration.
Sunday, October 13, 2024, 11:45 am - 12:00 pm
Mack Litz, CSB student in the lab of Prof. Pulin Li
Title of Talk: Mesenchyme developmental stage impacts the lung morphogenesis clock
Bio:
Mack is a 5th year PhD Candidate in Pulin Li's Lab studying lung branching morphogenesis in the developing mouse embryo. In her spare time, Mack has recently started woodworking at the MIT hobby shop.
Sunday, October 13, 2024, 12:00 - 12:15 pm
Ivy Liu, CSB student in the lab of Prof. Alex Shalek
Title of Talk: Scalable, compressed phenotypic screening using pooled perturbations
Bio:
Ivy Liu is a 5th year CSB student in the lab of Alex Shalek at the Institute of Medical Engineering and Science (IMES), Broad Institute, and Ragon Institute. Her PhD research has focused on using single-cell technologies to understand different disease mechanisms and enable better therapeutic discovery. In this talk, Ivy will highlight her work on developing a broadly applicable method for overcoming barriers to scaling-up high-content phenotypic discovery efforts.
Sunday, October 13, 2024, 1:30 - 2:00 pm
Dr. Marian Walhout, Professor & Chair- Department of Systems Biology; Maroun Semaan Chair in Biomedical Research; University of Massachusetts Chan Medical School
Title of Talk: Genome-scale models of metabolic wiring and rewiring
Bio:
Dr. Marian Walhout, PhD, is the founding Chair of the Department of Systems Biology, and Maroun Semaan Chair in Biomedical Research at the University of Massachusetts Chan Medical School (UMass Chan). She joined UMass Chan in the spring of 2003 and co-directed the Program in Systems Biology since its establishment in 2011 until the elevation to full department status in 2021.
How do organisms deal with metabolic perturbations that occur due to genetics, diet, environment, or therapeutics? Dr. Walhout aims to answer this question by studying the interplay between metabolism and gene regulation at a systems, or network, level. Most of her work uses a powerful interspecies model system of the nematode C. elegans and its bacterial diet. Her work already provides both broad, systems-level, and deep, mechanistic, insights into biology related to both rare and common human diseases.
Dr. Walhout is keen on mentoring trainees and strives to bring out the best in each and every one of them. She welcomes applications for positions in her lab.
Sunday, October 13, 2024, 2:00 - 2:30 pm
Dr. Job Dekker, Investigator, Howard Hughes Medical Institute; Joseph J. Byrne Chair in Biomedical Research; Professor, Department of Systems Biology; University of Massachusetts Chan Medical School
Title of Talk: Mitotic inheritance of chromosome folding programs
Bio:
Job Dekker received his undergraduate and graduate training at Utrecht University in The Netherlands. As a post-doctoral fellow in the laboratory of Nancy Kleckner at Harvard University, he developed chromosome conformation capture methodology. He is currently an Investigator of the Howard Hughes Medical Institute and Professor in the Department of Systems Biology at the University of Massachusetts Chan Medical School. His laboratory studies how genomes are folded in three dimensions. His work has led to insights into the formation of chromatin loops involved in long-range gene regulation, the organization of the interphase nucleus, the structure of mitotic chromosomes, and general folding principles of genomes. His group pioneered the use of genome folding data for genome assembly. Recently, his lab started exploring chromosome folding mechanisms in organisms with unusual genome organizations, such as dinoflagellates.
Sunday, October 13, 2024, 5:30 -6:00 pm
Dr. Danny Lew, MIT Professor of Biology
Title of Talk: Orienting cell polarity in response to chemical cues
Bio:
Daniel Lew joined the Department of Biology as a Professor in the Spring of 2023. Professor Lew completed a PhD in Molecular Biology from Rockefeller University in 1990 and then did postdoctoral work at the Scripps Research Institute, where he investigated the cell cycle control in the model yeast Saccharomyces cerevisiae. His research focuses on the study of cell polarity and the spatial decoding of chemical signals by cells, which are critical for many biological phenomena. His lab applies, genetic, cell biological, and computational approaches to address these questions.
Sunday, October 13, 2024, 7:30 - 7:45 pm
Diep Nguyen, CSB Student in the lab of Prof. Pulin Li
Title of Talk: Tiered threat-assessment from tissue topology balances immune tolerance and resistance
Bio:
Diep Nguyen is a graduate student in Dr. Pulin Li’s lab at Whitehead Institute. Her work combines quantitative imaging, spatial transcriptomics, and mathematical modeling to understand how multicellular systems perceive and respond to diverse environmental changes, and how the spatial organization of a tissue influences its physiology. Outside of the lab, Diep enjoys baking, photography, and listening to podcasts.
Sunday, October 13, 2024, 7:45 - 8:00 pm
Allison Keys, CSB Student in the lab of Prof. Laura Kiessling and Prof. Heather Kulik
Title of Talk: The energetic landscape of CH-pi interactions in protein carbohydrate binding
Bio:
Alli is a fifth-year PhD student in the CSB program. She graduated from Stanford with a BS in chemistry and an MS in computer science, where she worked on research projects ranging from an experimental study of yeast transcription factors to a computational analysis of protein-small molecule binding. At MIT, she is co-advised by Heather Kulik and Laura Kiessling. For her research, she studies protein carbohydrate binding interactions using classical and quantum physics-based modeling. Outside of the lab, she enjoys playing volleyball, reading, skiing, and hiking.
Sunday, October 13, 2024, 8:00 - 8:30 pm
Dr. Brian Cleary, Shibulal Family Career Development Professor in the Faculty of Computing and Data Sciences, the Department of Biology, and the Department of Biological Engineering,Boston University
Title of Talk: Fundamental organizing units in cells and tissues: theory, tools, and algorithmic experimental design
Bio:
Brian Cleary is a Shibulal Family Career Development Professor in the Faculty of Computing and Data Sciences, the Department of Biology, and the Department of Biological Engineering at Boston University. He received his PhD in Computational and Systems Biology from MIT and was an Independent Broad Fellow at the Broad Institute.
Monday, October 14, 2024, 9:00-9:30 am
Dr. Nezar Abdennur, Assistant Professor, Genomics and Computational Biology, University of Massachusetts Chan Medical School
Title of Talk: On composition and composability
Bio:
Nezar received training in biochemistry, mathematics, and bioinformatics at the University of Ottawa in Canada, where he was born and raised. He completed his PhD in Computational and Systems Biology at MIT in Leonid Mirny's lab, dissecting the biophysical processes that fold and shape the genome from the data generated by 3D genomic (3C/Hi-C) technologies. He is a contributor and a passionate advocate for open-source scientific software, and has also dabbled (lightly) in biotech, venture capital, and quantitative finance. In 2022, Nezar joined UMass Chan Medical School as an Assistant Professor in the Department of Genomics and Computational Biology and the Department of Systems Biology, where he leads a computational research group with a dual mandate. His group's investigatory research focuses on the relationship of the 3D genome to the epigenome, and the resulting influences on cellular fate, differentiation, aging, and disease. His group's open-source interests are in supporting foundational software infrastructure to improve genomic data science, making it more interoperable and composable with the wider AI/ML ecosystem.
Monday, October 14, 2024, 9:30 - 9:45 am
Alex LeNail, CSB Student in the lab of Prof. Myriam Heiman
Title of Talk: Charting the Cellular Rejuvenation Landscape in Aging Neurons
Bio:
Alex did his undergrad at Tufts in Computer Science. He was a research tech in Ernest Fraenkel's lab from 2016-2019 where he worked on ALS. He started his CSB PhD in 2019, and joined the labs of Jonathan Weissman and Alan Edelman before shifting into Myriam Heiman's lab, where he is now.
Alex is insulted by the characterization of a PhD as "it's not a sprint it's a marathon", as he has completed 10 ultramarathons during his PhD and can attest that they're all shorter than PhDs.
(more info about Alex can be found on his CV linked to his website)
Studen Posters:
Poster Session Sunday, October 13, 2024, 8:30 - 10:00 pm
|
Student |
Year |
Advisor |
Poster Title |
|
Athreya, Advait |
2020 |
Zhang, Bin |
Epigenetic control of chromatin phase separation regulates stem cell plasticity |
|
Birnbaum, Foster |
2021 |
Keating, Amy |
Jointly Embedding Protein Structures and Sequences through Residue Level Alignment |
|
Chen, Yi |
2020 |
Weissman, Jonathan |
Functional annotation of uncharacterized small viral proteins |
|
Chitayat, Liyam |
2023 |
Boyden, Ed |
Building cells inside cells |
|
Colgan, William |
2022 |
Weissman, Jonathan |
Spatially-resolved cell state and lineage maps of cancer |
|
DeWeirdt, Peter |
2021 |
Laub Michael |
Machine Learning to Identify Novel Anti-Phage Defense Systems |
|
Di Bernardo, Matteo |
2022 |
Cheeseman, Iain |
Deep learning approaches to uncover perturbation-level heterogeneity of cell morphologies |
|
Gai, Eric |
2022 |
Wong, Harikesh |
Multicellular control of T cell response initiation |
|
Guan, Lindsey |
2022 |
Keating, Amy |
Toward interpretability of AlphaFold2 for protein-peptide complexes |
|
Kozareva, Velina |
2020 |
Fraenkel, Ernest |
Quantitative proteomics in ALS patient- and control-derived iPSC motor neuron lines reveals significant covariates and disease-related changes |
|
LeNail, Alex |
2019 |
Heiman, Myriam |
Charting the Rejuvenation Landscape in Aging Neurons |
|
Maher, Kamal |
2020 |
Wang, Xiao |
Harmonic representations of regions and interactions in spatial transcriptomics |
|
Owen, Erik |
2022 |
Page, David |
Interplay of NPX-NPY homolog genes reveals degrees of haploinsufficiency in vitro |
|
Pagane, Nicole |
2021 |
Wong, Harikesh |
Tissue-specific optimization of T cell activation in draining lymph nodes |
|
Prabhu, Gautam |
2021 |
Reddien, Peter |
Dynamic Pattern Formation in the Planarian Blastema |
| Ramcharan, Hannah | 2021 | Corradin, Olivia |
Enhancers Enriched in Six Different Brain Regions Play an Important Role in Neurological Traits |
|
Reveiz, Mateo |
2022 |
Barzilay, Regina |
MiniFold: Simple, Fast, and Accurate Protein Structure Prediction |
|
Rodriguez, Chris |
2019 |
Reddien, Peter |
Genetic Decay in Asexual Fissioning Organisms |
|
Skalnik, Chris |
2022 |
Wong, Harikesh |
Spatiotemporal segregation of functionally opposing immune responses during infection |
| Torrillo, Paul | 2021 | Lieberman, Tami | Predicting genome dependent gene gain and loss in Staphyloccus aureus with residual neural networks |