Date:
Time:
Location:
Colony Hotel
140 Ocean Avenue, Kennebunkport, ME 04046
email address
reservations@thecolonyhotel.com
sales@thecolonyhotel.com
phone
207.967.3331
800.552.2363
Event Description:
The Computational and Systems Biology PhD Program will be traveling up to Kennebunkport, ME this fall! Mark your calendars and plan to join us for a day and half of student and faculty talks, an evening poster session, lobster buffet, a career panel, fun and more!
We will depart Sunday morning at 8:30AM Sunday October 8th 2017 from MIT and arrive at the beautiful Colony Hotel.
All student faculty and alumni invited!
Photo Credit: J. Teo
Guest Speakers :
Dr. Bree Aldridge 
Assistant Professor, Tufts University School of Medicine, Department of Molecular Biology and Microbiology
Adjunct Assistant Professor, Tufts University School of Engineering,Department of Biomedical Engineering
Bree Aldridge is an Assistant Professor in the Department of Molecular Biology and Microbiology and Department of Biomedical Engineering.
Her lab investigates tuberculosis infection and drug response at single-cell resolution. She specializes in combining live-cell microscopy and mathematical modeling to create intuitive descriptions of complex cell biology. She earned double B.S. degrees in computer engineering and molecular and cellular biology and the University of Arizona as a Flinn Scholar. She completed her PhD in Biological Engineering at MIT with Douglas Lauffenburger and Peter Sorger with the support of a DOE Computational Science Graduate Fellowship. She brought her interdisciplinary perspective to tuberculosis and infectious diseases during her postdoctoral training at the Harvard School of Public Health with Sarah Fortune. She is an Alfred P. Sloan Research Fellow and is the recipient of an NIH Director's New Innovator Award.
Email: bree [dot] aldridge [at] Tufts [dot] edu
Seminar
Date: Sunday October 8, 2017 5:30-6:00pm
Title: "Adding it up: mycobacterial growth, division, and drug susceptibility"
Dr. Joey Davis
Assistant Professor, Department of Biology, MIT 
While an undergraduate computer science and biological engineering student at UC Berkeley, Joey worked in the lab of Dr. Michael Marletta, studying bacterial gas sensing proteins. As a graduate student in Bob Sauer's lab, he applied biochemical and biophysical approaches to understand the assembly of bacterial proteases and to determine how these molecular machines function. From 2010-2012, he was the first employee at Ginkgo Bioworks, a Boston-based metabolic engineering startup company, before moving to The Scripps Research Institute to study ribosome biogenesis in Dr. Jamie Williamson’s group. There, Joey developed mass spectrometry and cryo-electron microscopy based techniques to determine how cells build large macromolecular assemblies such as ribosomes. This fall, Dr. Davis is starting his own lab in the Biology department at MIT where he will apply these techniques to understand the assembly of the autophagosome - a multi-subunit complex that is critical for maintaining cellular protein homeostasis through degradation of proteins, lipids, RNAs and, incredibly, other organelles.
Email: jhdavis [at] MIT [dot] EDU
Seminar
Date: Sunday October 8, 2017 11:30am-12:00pm
Title: "Biological assembly of macromolecular machines: insights into ribosome biogenesis"
Dr. Sean Eddy
HHMI Investigator and Professor, Dept of Molecular & Cellular Biology and of Applied Mathematics, Harvard University 
Sean Eddy is a computational biologist at Harvard University. Before moving to Harvard in 2015, he was a group leader at the Howard Hughes Medical Institute's Janelia Research Campus, and before that, a faculty member in the Genetics department at Washington University in St. Louis. He received a bachelor's degree from Caltech, a Ph.D. from the University of Colorado at Boulder, and did postdoctoral work at NeXagen in Boulder and at the MRC Laboratory of Molecular Biology in Cambridge, UK.
Email: seaneddy [at] fas[dot] Harvard [dot] edu
Seminar
Date: Sunday October 8, 2017 1:30 - 2:00 PM
Title: "Biological sequence homology searches: the future of deciphering the past”
Dr. Andrew Emili
Joint Full Professor, Departments of Biochemistry and Biology, Boston University
Faculty, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 
Andrew Emili is a Joint Full Professor in the Departments of Biology and Biochemistry at Boston University, and status only faculty at the Donnelly Centre for Cellular and Biomolecular Research and the Department of Molecular Genetics at the University of Toronto (UofT). Dr. Emili received his PhD in Molecular and Medical Genetics from the UofT. He then pursued post-doctoral studies as a Damon Runyon/Walter Winchell Cancer Research Fellow with the distinguished geneticist Leland Hartwell at the Fred Hutchison Cancer Research Center in Seattle, while learning protein mass spectrometry with John Yates III, a pioneer in the field, at the University of Washington. Prior to recently joining BU, Prof. Emili was a Principal Investigator (2000-2017) and founding member of the Donnelly Centre at the University of Toronto. Dr. Emili is an internationally recognized leader in protein interaction networks and the development of innovative technologies to systematically characterize protein complexes on a proteome-scale. He directs a multidisciplinary research laboratory with a track record in functional proteomics and systems biology. His group develops and applies innovative methods to characterize macromolecules of broad biomedical significance, publishing ‘global’ molecular interaction maps of unprecedented scope. In particular, his lab uses precision mass spectrometry to characterize protein networks in a comprehensive, high-throughput manner, with the long-term goal of translating basic knowledge into new diagnostics and therapeutics. Dr. Emili has published over 200 peer reviewed papers with >25,000 citations (h-index 68), including proteome-wide studies of soluble and membrane protein complexes in microbes, human cells, and other models, documenting hundreds of assemblies linked to disease. Dr. Emili was also lead editor of "Network Biology" and "Systems Analysis" books with >26,000 e-downloads, and he has given >150 talks at research conferences, international symposia and workshops.
Email: aemili [at] bu [dot] edu
Seminar
Date: Sunday October 8, 2017 5:00-5:30pm
Title: "Global Mapping of Protein Interaction Networks"
Dr. Lauren C. Foster
Associate Director, MIT Technology Licensing Office
Director of IP and Strategic Alliances at Koch Institute
Lauren C. Foster is the Assistant Director of M.I.T.'s Technology Licensing Office (TLO), focusing principally on licensing and commercialization of technologies in the biomedical, biotechnology and medical device fields. She also serves as Director of Intellectual Property and Strategic Alliances at the Koch Institute for Integrative Cancer Research at M.I.T. where she is involved in the strategic management of the Koch Institute’s industrial partnerships and intellectual property portfolio. Prior to joining M.I.T., Lauren was Senior Director, IP and Technology Acquisition at Antigenics, Inc., a public biotechnology company, where she played an integral role in envisioning and implementing the company’s business, intellectual property and technology strategies. Lauren was also a Technical Specialist at the law firm Lahive & Cockfield LLP where she focused on strategic development of intellectual property rights for biotechnology and pharmaceutical companies and universities. Ms. Foster holds a D.Sc. from Harvard University and a B.S. from Haverford College, and is a registered Patent Agent.
Email: lcfoster [at] mit [dot ]edu
Seminar
Date: Monday October 9, 2017 9:15 - 10:15 am
Dr. Becky Lamason
Assistant Professor, Department of Biology, MIT
Becky Lamason investigates the strategies used by diverse bacterial pathogens to reprogram host machinery during infection. Becky received a B.S. in Molecular Biology/Biotechnology from Millersville University and a Ph.D. in Immunology from the Johns Hopkins University School of Medicine. As a postdoctoral fellow in Matthew Welch’s lab at UC Berkeley, she received a fellowship with the Helen Hay Whitney Foundation, and an NIH Pathway to Independence Award. During her postdoctoral work, she discovered that intracellular bacterial pathogens spread throughout our tissues by targeting host intercellular communication pathways and manipulating different force-generating machinery, ultimately revealing exciting mechanisms of host-pathogen interactions. As a new member of the Biology Department, the Lamason lab will continue to investigate the process of bacterial cell-to-cell spread, combining genetic, cell biological, biochemical and biophysical approaches to reveal how bacteria manipulate host cells to promote pathogenesis.
Email: rlamason[at] mit [dot] edu
Seminar
Date: Sunday October 8, 2017 12:00 - 12:30 pm
Title: “Tension, trafficking, and translocation: how bacteria hijack host cell pathways during spread”
Dr. Tami Lieberman
Assistant Professor of Institute for Medical Engineering & Science, MIT (Starting January 2018)
Assistant Professor of Civil and Environmental Engineering, MIT (Starting January 2018)
Tami trained in molecular biology and mathematics at Northwestern University, where she conducted research in the laboratory of Jon Widom and was funded by a Barry M. Goldwater Scholarship. She then earned a PhD in Systems Biology from Harvard University, where she conducted research in Roy Kishony’s laboratory. During her graduate research, Tami developed new genomic approaches for understanding how bacteria evolve during infections of individual people. As a postdoc in Eric Alm’s lab at MIT, she further developed and applied these genomic approaches to understand the microbes that colonize us during health. Tami has also made contributions to our understanding of antibiotic resistance, including the co-invention of a new platform for visualizing evolution in real time. The Lieberman Lab, opening at MIT in January 2018, will use computational and experimental methods to uncover the principles governing colonization, niche range, and personalization in the human microbiome.
Email: tami [at] mit [dot] edu
Seminar
Date: Monday October 9, 2017 10:45 - 11:15 am
Title: "Adaptation and diversification of commensal bacteria within humans"
Dr. Elena Rivas
Senior Research Fellow and Lecturer, Department of Molecular and Cellular Biology, Harvard University 
Elena Rivas started her career as a theoretical physicist with a Ph.D. from the University of Zaragoza, Spain. After a postdoctoral position at UCLA in physics in 1997, she switched to computational biology, where she has been working ever since. As a Sloan Fellow at Washington University in St. Louis, Elena worked on computational algorithms for RNA structure prediction. She introduced one of the first exact algorithms to describe a particular type of RNA structure called pseudoknots. Later as a research associate, she developed one of the first RNA genefinding programs, which was applied to E.coli, yeast, and nematodes. As a Fellow at Janelia Research Campus, she put her efforts into mathematical models of evolution that could improve existing methods for homology detection, while continuing her work on RNA genes by extensively exploring a wide range of probabilistic method to improve existing methods based on thermodynamic parameters. Currently a Senior Research Fellow at Harvard, Elena is working on characterizing RNA base pair covariations that could identify conserved RNA structures. R-scape her new method is a statistical tool to find novel conserved structural RNAs.
Email: elenarivas [at] fas [dot] Harvard [dot] edu
Seminar
Date: Sunday October 8, 2017 2:00 - 2:30 pm
Title: "A statistical test of RNA base pair covariation applied to proposed long noncoding RNA structures”
Student Speakers & Posters:
Maria Alexis
5th Year MIT CSB Graduate Student 
Maria is originally from New York and got her B.S. in Biology from Stanford in 2013. She is currently a 5th year graduate student in Chris Burge's lab and is interested in how RNA binding-proteins select their targets in cells.
Seminar
Date: Sunday October 8, 2017 7:35 - 7:50 PM
Title: "Shared and distinct Sequence, Structure and Context Preferences of Human RNA Binding Proteins"
Jonathan Teo
5th Year MIT CSB Graduate Student
Jonathan is graduate student from Sarpeshkar Lab (Analog Circuits and Biological Systems Group). He enjoys building computational models of biological systems to deepen his understanding of how they work. After all, biological systems are complex machinery that often function in beautiful but mysterious ways. A good model not only captures these behaviors, but also provides a compelling story to help scientists understand the bigger picture. To achieve this goal, Jonathan has been applying design and analysis techniques from analog circuit design to guide his modeling efforts, with a particular focus on understanding how feedback and feedforward mechanisms improve or deteriorate the performance of biological circuits. To date, he has created models for chemotaxis in neutrophils, artificial tissue homeostasis in stem cells and is currently working on modeling the immune response against tumors. In his free time, Jonathan is an avid photographer with a passion for great food.
Seminar
Date: Sunday October 8, 2017 11:15 - 11:30 AM
Title: "Building an Artificial tissue homeostasis circuit design"
Jacob Witten
4th Year MIT CSB Graduate Student 
Jacob Witten grew up in Los Angeles and received his BA in Mathematics and Biophysics from Amherst College in 2014. In 2015, he joined Professor Katharina Ribbeck's group in the department of Biological Engineering at Massachusetts Institute of Technology. His current research combines computational and experimental techniques to study molecular transport in mucus, focusing on applications to drug delivery for treating diseases such as cystic fibrosis.
Seminar
Date: Sunday October 8, 2017 7:50 - 8:05 PM
Title:"Characterizing the chemical selectivity of the mucus barrier"
Joy Yang
5th Year MIT CSB Graduate Student
Joy is a 5th year graduate student in Martin Polz’s marine microbial ecology group at MIT. Her two main areas of focus are (1) predicting bacteriophage infection patterns using genomic sequences of the phage and their bacterial hosts (2) searching for the function of phage tRNA. Having majored in statistics as an undergraduate in Berkeley, she is interested in finding ways to cultivate statistical curiosity at an earlier age, and has been working on a statistical education project in her free time.
Seminar
Date: Sunday October 8, 2017 8:05 - 8:20 PM
Title: "Identifying mechanisms of phage-host infection"
Poster Session Sunday October 8th 8:30-10:30pm:
- Anastasiya Belyaeva (Uhler lab) Title: "Network Analysis Identifies Regions of Chromosome Interactions in the Genome"
- Tristan Bepler (Berger Lab) Title: "Semi-supervised convolutional neural networks for particle picking in cryo-electron microscopy images"
- Carles Boix (Kellis Lab) Title: "Genome-wide Characterization of Chromatin Regulation"
- Peter Freese (Burge Lab) Title:"Shared and Distinct Sequence, Structure, and Context Preferences of Human RNA Binding Proteins"
- Amanda Kedaigle (Fraenkel Lab) Title: "Comparing preclinical models of Huntington's Disease by integrating high-throughput data"
- Kathy Lin (Bartel Lab) Title: "Learning miRNA targeting rules from high-throughput binding and repression measurements"
- Kayla McCue (Burge Lab) Title: "Modeling RNA Splicing Kinetics"
- Colette Picard (Gehring Lab) Title:"Imprinting dynamics at the single-cell level in Arabidopsis"
- Cassandra Schaening (Gilbert & Li Lab) "Probing the structural specificity of the pseudouridine synthase Pus7"
- Max Shen (Gifford Lab) Title: "Random" CRISPR Editing Outcomes are Predictable
- Alvin Shi (Kellis Lab) Title: "Choose your adventure: (1) predicting and tracking checkpoint blockade immunotherapy response with peripheral-blood derived exosomal RNA or (2) dissecting motif-motif interactions in High Definition Reporter Assay (HiDRA) data"
- Jesse Tordoff (Weis Lab)Title: "Programming Self-Patterning 3D Shape Formation in Multicellular Mammalian Systems"
- Vincent Xue (Keating Lab) Title: "Mapping sequence landscape to design specificity with protein families"
- Grace Yeo (Gifford lab)Title: "Leveraging single-cell RNA-sequencing to study the combinatorial action of signaling pathways in directed differentiation"