Spring 2022 Schedule

Thursday, March 24, 2022 - 4:00-5:00pm EST

Georg K. Gerber, MD, PhD, MPH presents

Novel machine learning methods for gaining insights into complex and dynamic host-microbial ecosystems

Zoom webinar registration HERE

Abstract The human gut microbiome is highly temporally dynamic. Some of the most profound changes over time occur during infancy and early childhood when the microbiome is first becoming established. Although the gut microbiome is more stable in adulthood, it continues to undergo significant changes over time due to diet, travel, antibiotic use, infection, gut inflammation, and a variety of other factors. Microbial dynamics, particularly early in life, have been linked to many human diseases including necrotizing enterocolitis, diabetes, food allergies, obesity, and inflammatory bowel diseases. Given the complexity of complex and dynamic host-microbial ecosystems, sophisticated computational methods are essential for analyzing data from these systems and ultimately deriving experimentally testable hypotheses. In this talk, I will first introduce the challenges of analyzing dynamic microbiomes. Then, I will present intuitive descriptions of some of the novel machine learning methods we have developed to address different problems, including: (a) forecasting microbiome dynamics and quantitating the “keystoneness” of individual microbes or groups of microbes, (b) finding groups of microbes that respond consistently to introduced perturbations, and (c) predicting the status of the human host (e.g., disease onset) given past changes in the microbiome. Throughout, I will give examples of biomedical applications of our work, including developing microbial consortia to treat or prevent Clostridioides difficile infection or food allergies. I will gear the talk to a broad audience, focusing on the intuition behind machine learning approaches rather than technical details.

Bio George Gerber is Associate Professor at Harvard Medical School; Member of the Faulty  at the Harvard-MIT Health Sciences & Technology, Chief, Division of Computational Pathology, Co-Director, Massachusetts Host-Microbiome Center, and affiliate of the Department of Pathology, Brigham and Women’s Hospital. Dr. Gerber is a computer scientist, microbiologist and physician who heads a research lab focused on creating novel machine learning methods and high-throughput experimental systems to understand the role of the microbiota in human diseases and applying these findings to develop new diagnostic tests and therapeutic interventions to improve patient care. He also serves as Chief of the Division of Computational Pathology and co-directs the MA Host-Microbiome Center. Dr. Gerber holds a PhD in Computer Science from MIT (statistical machine learning) and an MD from Harvard Medical School. Prior to his academic career, he was an executive in the film and computer graphics industry.

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Recent Past Talks:

• Thursday, Nov 18, 2021 - 5:00-6:00pm EST
  • Dr. Isaac Chiu, co-hosted by the Harvard Brain Sciences Initiative
  • Zoom webinar registration HERE
  • Title Bacterial interactions with neurons in pain and itch
  • Abstract The mammalian sensory nervous system densely innervates barrier tissues including the skin and gut that are exposed to microbes. Nociceptors are specialized neurons that mediate pain and itch. These unpleasant sensations are critical to protect organisms from danger. We find that nociceptors actively participate in host defense by detecting bacterial pathogens and signaling to the immune system. We will explore how bacteria interact with neurons to drive pain and itch, and how this crosstalk could regulate host defense.
  • Bio Isaac Chiu is Associate Professor in the Department of Immunology at Harvard Medical School. He received his undergraduate training in Biochemistry at Harvard College, working with Dr. Jack Strominger on MHC molecules in immune synapses. He then received a PhD in Immunology at Harvard Medical School under the mentorship of Dr. Michael Carroll, working on immune responses in neurodegeneration. He then trained in Dr. Tom Maniatis’s lab as a postdoctoral fellow on ALS. He did his second postdoctoral fellowship on the neurobiology of pain at Boston Children’s Hospital under Dr. Clifford Woolf. He started his lab at Harvard medical school in 2014. His research focuses on interactions between the nervous system, immune system, and microbes in host defense and inflammation. He has found that nociceptor neurons directly sense bacteria and immune mediators to produce pain. These neurons signal to the immune system via neuropeptides and neurotransmitters to mediate immunity in the skin, gut, and lungs. Recent work has shown that immune modulators also regulate itch during allergic inflammation. Defining neuroimmune crosstalk could lead to novel treatments for allergic diseases, infection, and pain. Dr. Chiu has received the NIH Director’s New Innovator Award, Chan-Zuckerberg Initiative Ben Barres Award, and Burroughs Wellcome Fund Investigators in the Pathogenesis of Infectious Disease Award.

• Thursday, Sept. 23, 2021 - 5:00-6:00pm EST
  • Dr. William Hanage
  • Zoom webinar registration HERE
  • Title Covid-19: What we've learned about the pandemic and what we keep forgetting
  • Abstract The Covid-19 pandemic has been the most acute global infectious disease emergency in living memory. While it has upended societies and led to more than 600,000 deaths (and counting) in the United States alone, much of the potential impact could be anticipated by epidemiologists as early as February or March 2020. Dr Hanage will discuss how infectious disease epidemiology informs pandemic response from vaccines to handwashing, what we have learned about the virus and what it can do, as well as how we can best manage it. As we enter the second fall and winter of the pandemic in the northern hemisphere, we should learn the lessons the virus has taught, and not forget their cost.
  • Bio Dr. William Hanage is an Associate Professor of Epidemiology in the department of Epidemiology, and a faculty member in the Center for Communicable Disease Dynamics. He employs a mix of theoretical and laboratory work to research the evolution and epidemiology of infectious disease. After his PhD, he did post doctoral study at the University of Oxford and Imperial College London, before being awarded a Royal Society University Research Fellowship. Prior to joining the Center for Communicable Disease Dynamics, he was a Reader in the department of Infectious Disease Epidemiology at Imperial College London. There he worked extensively developing multilocus sequence typing (MLST; www.mlst.net) and analysis (MLSA) for the study of bacterial pathogens and species, as well as means of analyzing data developed using this method. He is particularly interested in using an evolutionary framework such as methods derived from population genetics to inform epidemiology. In 2012 he received the Fleming Prize for research in Microbiology and was the recipient of a 2012 ICAAC Young Investigator Award from the American Society for Microbiology.

More seminar recordings are available on the MSI YouTube channel.