BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//Department of Computer Science - ECPv6.15.20//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
X-WR-CALNAME:Department of Computer Science
X-ORIGINAL-URL:https://www.cs.jhu.edu
X-WR-CALDESC:Events for Department of Computer Science
REFRESH-INTERVAL;VALUE=DURATION:PT1H
X-Robots-Tag:noindex
X-PUBLISHED-TTL:PT1H
BEGIN:VTIMEZONE
TZID:America/New_York
BEGIN:DAYLIGHT
TZOFFSETFROM:-0500
TZOFFSETTO:-0400
TZNAME:EDT
DTSTART:20250309T070000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0400
TZOFFSETTO:-0500
TZNAME:EST
DTSTART:20251102T060000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0500
TZOFFSETTO:-0400
TZNAME:EDT
DTSTART:20260308T070000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0400
TZOFFSETTO:-0500
TZNAME:EST
DTSTART:20261101T060000
END:STANDARD
BEGIN:DAYLIGHT
TZOFFSETFROM:-0500
TZOFFSETTO:-0400
TZNAME:EDT
DTSTART:20270314T070000
END:DAYLIGHT
BEGIN:STANDARD
TZOFFSETFROM:-0400
TZOFFSETTO:-0500
TZNAME:EST
DTSTART:20271107T060000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20260205T103000
DTEND;TZID=America/New_York:20260205T120000
DTSTAMP:20260420T001556
CREATED:20260202T172759Z
LAST-MODIFIED:20260202T172759Z
UID:1993227-1770287400-1770292800@www.cs.jhu.edu
SUMMARY:CS & BME Seminar Series: Proteomics at Genome Scale: Connecting Molecules to Systems with Biological Foundation Models
DESCRIPTION:Refreshments are available starting at 10:30 a.m. The seminar will begin at 10:45 a.m. \nAbstract\nUnderstanding the mechanisms linking genetic sequence to cellular function remains a central challenge in biology. Existing computational approaches are often computationally expensive or fail to generalize beyond well-studied model organisms and protein families. Samuel Sledzieski’s work leverages protein language models to connect molecular structure to systems biology at genome scale. He will highlight three applications where protein language modeling unlocks new capabilities: training on molecular dynamics simulations to predict protein conformational dynamics\, enabling an analysis of the allosteric behavior of KRAS; building de novo protein-protein interaction networks in non-model organisms\, revealing previously uncharacterized proteins involved in coral stress response; and high-throughput screening of massive small molecule libraries for drug-target interactions\, identifying novel kinase inhibitors with experimentally validated nanomolar affinity. Sledzieski will discuss how recent advances in contrastive learning\, parameter-efficient fine-tuning\, and multimodal representation learning address key computational barriers to effective genome-scale modeling. Finally\, he proposes a research plan to model heterogeneity in protein structure and molecular interactions across cellular contexts. \nSpeaker Biography\nSamuel Sledzieski is a Flatiron Research Fellow at the Flatiron Institute Center for Computational Biology and a visiting researcher at the Lewis-Sigler Institute for Integrative Genomics at Princeton University. His research uses protein language models to integrate molecular biophysics with systems genomics\, with the ultimate goal of mapping the mechanisms of cellular behavior and complex disease. He has developed and released several open-source machine learning models\, including D-SCRIPT\, ConPLex\, and RocketSHP\, and has held research positions at Microsoft Research\, Cellarity\, Serinus Biosciences\, and the Centre Scientifique de Monaco. A recipient of the NSF Graduate Research Fellowship\, Sledzieski received his PhD (2024) and MS (2021) in computer science from the Massachusetts Institute of Technology\, and his BS (2019) from the University of Connecticut. \nZoom link »
URL:https://www.cs.jhu.edu/event/cs-bme-seminar-series-proteomics-at-genome-scale-connecting-molecules-to-systems-with-biological-foundation-models/
LOCATION:228 Malone Hall
CATEGORIES:Seminars and Lectures
END:VEVENT
END:VCALENDAR