Speakers

April 29 – May 10, 2024, Northeastern University, Boston MA in person

Organizer: Olga Vitek

Sponsor: Barnett Institute for Chemical and Biological Analysis, Northeastern University

Kylie Bemis
	Kylie is Assistant Teaching Professor in the Khoury College of Computer Sciences at Northeastern University. She holds a B.S. degree in Statistics and Mathematics, a M.S. degree in Applied Statistics, and a Ph.D. in Statistics from Purdue University. In 2013, she interned at the Canary Center at Stanford for Cancer Early Detection, where she developed the Cardinal software package for statistical analysis of mass spectrometry imaging experiments. In 2015, she was awarded the John M. Chambers Statistical Software Award by the American Statistical Association for her work on Cardinal. In 2016, she joined the Olga Vitek lab for Statistical Methods for Studies of Biomolecular Systems at Northeastern University as a postdoctoral fellow. In 2019, she joined Northeastern as faculty, where she now teaches data science and develops curriculum for the M.S. in Data Science program. Her research interests include machine learning and large-scale statistical computing for bioinformatics..
Ryan Benz
	Ryan is a Data Scientist at Seer, working in the fields of Bioinformatics and Proteomics. He holds a Ph.D. in Chemistry from the Univeristy of California, Irvine. Prior to joining Seer, Ryan worked at Applied Proteomics as a Bioinformatics Scientist working on a wide range of Proteomics-based biomarker discovery projects and blood-based tests for cancer. Ryan is an avid R user with over 15 years of experience, and is a certified RStudio trainer.
Benjamin Gyori
	Ben is Associate professor in the Khoury College of Computer Sciences at Northeastern University. His research combines computational modeling, machine learning, natural language processing, and human–machine interaction to improve our understanding of human biology. Ben’s lab creates computational frameworks that combine high-throughput data with the biological mechanisms that govern health. Since joining Khoury College in 2023, Ben has been leading several research projects focused on artificial intelligence approaches to complex systems modeling, biomedical data integration, and accelerating vaccine development. Ben is a recipient of a DARPA Young Faculty Award, the DARPA Director’s Fellowship Award, is supported by DARPA, DTRA, and the Chan-Zuckerberg Initiative. He is an advocate for open science and open-source scientific software.
Devon Kohler
	Devon is a PhD student at Northeastern University’s Khoury College of Computer Science in Olga Vitek’s lab. His research interests are in developing computational methods for mass spectrometry (MS)-based proteomics, specifically focused on the application of statistical and causal inference techniques. He is one of the lead developers of the MSstats family of R packages. He is the creator of a number packages, including MSstatsPTM and MSstatsLiP packages, as well as the R shiny-based GUI MSstatsShiny. He is currently researching applications of causal inference to biochemical systems; leveraging observational MS-based proteomics data and estimating the effect of perturbations on the downstream system.
Christina Ludwig
	Tina is the Head of Proteomics section at the Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) at the Technical University Munich (www.baybioms.wzw.tum.de). Her current research interests are focused on technical development projects related to targeted and data-independent mass spectrometry, including Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and SWATH-MS. During her postdoc in the laboratory of Professor Ruedi Aebersold at the ETH Zürich Christina was involved in projects aiming for specific site-localization of post-translational modifications and estimation of absolute protein abundances from label-free, targeted mass spectrometric data.
Brendan MacLean
	Brendan worked at Microsoft for 8 years in the 1990s where he was a lead developer and development manager for the Visual C++/Developer Studio Project. Since leaving Microsoft, Brendan has been the Vice President of Engineering for Westside Corporation, Director of Engineering for BEA Systems, Inc., Sr. Software Engineer at the Fred Hutchinson Cancer Research Center, and a founding partner of LabKey Software. In this last position he was one of the key programmers responsible for the Computational Proteomics Analysis System (CPAS), made significant contributions to the development of X!Tandem and the Trans Proteomic Pipeline, and created the LabKey Enterprise Pipeline. Since August, 2008 he has worked as a Sr. Software Engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics Environment and its growing worldwide user community. Brendan was the inaugural recipient of the 2016 Gilbert S. Omenn Computational Proteomics Award of the US Human Proteome Organization
Lindsay Pino
	Lindsay is the co-founder and CTO of Talus Bio. She leads the development of Talus’s screening platform, guiding and coordinating scientific efforts across automated proteomics sample preparation and high-throughput mass spectrometry data acquisition and analysis. She has built and leads a team of multi-disciplinary scientists encompassing the breadth of scientific work at Talus, including chemical biologists, protein chemists, and computational biologists. Lindsay holds a Ph.D. from the University of Washington’s Department of Genome Sciences in the MacCoss lab. Prior to that, she worked at the Broad Institute of MIT and Harvard.
Charles Tapley Hoyt
	Charlie received a Ph.D. in Computational Life Sciences from the University of Bonn in 2019. His research interests cover the interface of biocuration, knowledge graphs, and machine learning with systems biology, networks biology, and drug discovery. He currently works remotely from Germany as a Senior Scientist in the Gyori Lab at Northeastern University. He is an advocate of open source software, reproducibility, and open science. His open source projects such as PyBEL and PyKEEN are used by several academic and industrial groups.
Olga Vitek
	Olga is Professor in the Khoury College of Computer Sciences at Northeastern University, and was previously a Faculty and a University Faculty Scholar at Purdue. She holds a PhD in Statistics from Purdue University. Her research intersects statistical science, machine learning, mass spectrometry and systems biology. Statistical methods and open-source software MSstats and Cardinal developed in her lab are widely used in academia and industry. Olga is an elected Fellow of the American Statistical Association, a recipient of the 2021 Gilbert S. Omenn Computational Proteomics Award of the US Human Proteome Organization, and of the Indigo BioAutomation Females in Mass Spectrometry Distinguished Contribution Award. She is a recipient of the CAREER award of the National Science Foundation, and of the Essential Open-source Software Award of the Chan-Zuckerberg foundation.
Alicia Williams
	Alicia is an in-house science editor at the Morgridge Institute for Research, a private biomedical research institute affiliated with the University of Wisconsin–Madison. She has been working with science writers on grants and publications for a decade, having started out as an editor in a mass spectrometry lab at UW–Madison. She also holds a PhD in English literature from Rutgers University, where her research focused on the relationship between nineteenth-century novels and an increasingly literate public.