May Institute ONLINE: Computation and statistics for mass spectrometry and proteomics

May 9 – May 20, 2022, Northeastern University, Boston MA via Zoom
Organizer: Olga Vitek

Speakers

Susan Abbatiello

Susan Abbatiello Susan is currently Principal Consulting Scientist at Waters Corporation. Prior to that she was the executive director of the MS Core Facility at the Barnett Institute at Northeastern University, a Product Manager at Thermo Fisher Scientific, and a scientist in the Proteomics Platform at the Broad Institute of MIT and Harvard. Susan received her Ph.D. in analytical chemistry at the University of Florida, and completed a postdoc at the University of Pittsburgh’s Hillman Cancer Center. Susan’s research focuses on the development of experiments to measure potential protein biomarkers in cell lines and blood for diseases such as cancer. Susan has co-chaired a committee that is part of the National Cancer Institute’s Clinical Proteomic Technology Assessment for Cancer (CPTAC).

Nuno Bandeira

Nuno Bandeira Nuno is Associate Professor with joint appointments in Computer Science and Engineering and in the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego. He is an executive director in Center for Computational Mass Spectrometry. Nuno obtained his Ph.D. in Computer Science and Engineering from the University of California, San Diego. His research focuses on the development of algorithms for interpretation of proteomics and metabolomics mass spectrometry data from endogenous and digested peptides, discovery and localization of post-translational modifications, protein-protein interactions, sequencing of non-linear peptides with unknown amino acids and characterization of microbial, marine, reptile and plant natural products. As Executive Director of UCSD’s Center for Computational Mass Spectrometry, Nuno’s research further extends to distributed algorithms for large scale data analysis (ProteoSAFe), data sharing (MassIVE) and crowdsourced, community-wide interpretation (GnPS) of all publicly available mass spectrometry data. Nuno is the recipient of the 2021 Biemann Medal of the American Society for Mass Spectrometry and of the 2021 Gilbert S. Omenn Computational Proteomics Award of the US Human Proteome Organization

Kylie Bemis

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. She is the recipient of the 2015 John M. Chambers Statistical Software Award of the American Statistical Association.

Ryan Benz

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.

Meena Choi

Meena is Bioinformatics Scientist at Genentech. Prior to that she was Associate Research Scientist in the lab of Olga Vitek at Northeastern University. She holds a PhD in Statistics from Purdue University, and a B.S. in Biology from the Korea Advanced Institute for Science and Technology. Meena’s work focuses on statistical methods for quantitative proteomics. She is the original lead developer and maintainer of MSstats. In 2021 Meena was named one of the rising stars in proteomics and metabolomics by Journal of Proteome Research

Felipe Da Veiga Leprevost

Felipe Da Veiga Leprevost Felipe is a Biological Data Scientist at University of Michigan Medical School. He holds a PhD in Bioinformatics and Computational Biology, and an M.Sc. in Molecular and Cell Biology. The computational methods and tools previously developed by Felipe and his colleagues, such as PepExplorer, MSFragger, Philosopher, and PatternLab for Proteomics, are among the most referred proteome informatics tools and are used by hundreds of laboratories worldwide. Felipe is also a Proteogenomics Data Analysis Center (UM-PGDAC) member as part of the NCI’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative for processing and analyzing hundreds of cancer proteomics samples.

Ting Huang

Ting Huang Ting is a Data Scientist at Seer. She received her PhD from Northeastern University College of Computer Information and Science in the lab of Olga Vitek. She received her B.S. and M.S. degree in Software Engineering from Dalian University of Technology, China. Ting’s research focuses on experimental design and statistical analysis of mass spectrometry-based protein quantification experiments. Ting is the lead author and developer of MSstatsTMT.

Brendan MacLean

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

Alexey Nesvizhskii

Alexey Nesvizhskii Alexey is Professor with joint appointments in the Computational Medicine and Bioinformatics, and Pathology departments at University of Michigan. Alexey’s research interest is in the field of quantitative proteomics, with a focus on the development of computational methods for processing and extracting biological information from complex proteomic datasets. One of the aims of Alexey’s research is to close the critical gap between the development of high throughput quantitative proteomics methods and the ability to deal with the resulting data deluge and to convert it into new biological knowledge or to develop new disease biomarkers. Alexey was the recipient of the 2017 Gilbert S. Omenn Computational Proteomics Award of the US Human Proteome Organization

Yasset Perez-Riverol

Yasset Perez-Riverol Yasset is a Technical Lead at European Bioinformatics Institute (EMBL-EBI), and Proteomics Team Coordinator, including PRIDE Archive, PRIDE Cluster and Proteogenomics resources. Yasset has led the development of Omics Discovery Index, an open source platform to facilitate the access and dissemination of omics datasets coming from multiple omics studies. In addition, he has lead the BioContainers, a community for bioinformatics software containers. Between 2006-2014, he worked at the Center for Genetic Engineering and Biotechnology (CIGB), Havana, Cuba, as a Group Leader in the Proteomics Department. During this period, he developed new machine learning algorithms and tools for peptide and protein identification using mass spectrometry data. Yasset holds a PhD in Biochemistry and a BSc degree in Software Engineering from Havana University.

Lindsay K. Pino

Lindsay Pino Lindsay is the co-founder and chief technology officer at Talus Bio. With over a decade’s experience in analytical chemistry and computational biology, she develops technologies for quantitative proteomics. In particular, at Talus, she is working on the challenges associated with scaling-up quantitative proteomics experiments, and is directly involved in a variety of research projects spanning cancer drug discovery, molecular mechanisms of aging, epigenetics, and spatiotemporal proteomics. Lindsay has trained at the Broad Institute, the University of Washington, and the University of Pennsylvania, where she has focused on developing techniques for quantitative proteomics. In 2021 Lindsay was named one of the rising stars in proteomics and metabolomics by Journal of Proteome Research

Vagisha Sharma

Vagisha Sharma Vagisha got involved with proteomics at UC San Diego where she worked with Prof. Vineet Bafna. During that time she built her first tools for visualizing Mass Spectrometry data while working at ActivX Biosciences. Since moving to Seattle Vagisha has worked on Mass Spectrometry pipelines for the Aebersold group at the Institute for Systems Biology, and developed a data management system while at the University of Washington Proteomics Resource and the Yeast Resource Center. She joined the Skyline team in October, 2011. Vagisha enjoys developing tools that help researchers get stuff done.

Charles Tapley Hoyt

Charles Tapley Hoyt Charlie is a Postdoctoral Research Fellow in the Laboratory of Systems Pharmacology at Harvard Medical School based out of Germany. He received his Ph.D. in Computational Life Sciences from the University of Bonn. His research interests cover the interface of biocuration, knowledge graphs, and machine learning with systems biology, networks biology, and drug discovery. 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 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 a Senior Member of the International Society for Computational Biology, and an Elected Member of the Council of HUPO and of the Board of Directors of USHUPO. She is Associate Editor of the journal Bioinformatics. Olga is an elected Fellow of the American Statistical Association, and a recipient of the 2021 Gilbert S. Omenn Computational Proteomics Award of the US Human Proteome Organization

Administrative Support

Roger Donaghy

Roger Donaghy Web Developer

Northeastern University