Speakers

May Institute: Computation and statistics for mass spectrometry and proteomics

April 29–May 10, 2019, Northeastern University, Boston MA
Organizers : Meena Choi, Brendan MacLean, and Olga Vitek

Susan Abbatiello
	Susan received a Ph.D. in analytical chemistry at the University of Florida, and completed a postdoc at the University of Pittsburgh’s Hillman Cancer Center. Susan is currently the executive director of the MS Core Facility at the Barnett Institute at Northeastern University, and a visiting scientist in the Proteomics Platform at the Broad Institute of MIT and Harvard. 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).
Ruedi Aebersold
	Ruedi is a professor at ETH Zurich. His research has focused on the development of new technologies for quantitative proteomics and on applying them to challenging questions of contemporary life science research. In this area, the group has a worldwide standing and has pioneered many of concepts and technologies that have transformed proteomics. These include the introduction of relative and absolute proteome quantification, the development of open source computational tools for the objective, statistically supported analysis of large proteomic datasets, the development of a method for the determination of the spatial organization of protein complexes and the development of targeted proteomic techniques such as Selected Reaction Monitoring and SWATH-MS.The concept of targeted proteomics has been selected Method of the Year 2012 by the journal Nature Methods.
Nuno Bandeira
	Nuno Bandeira obtained his Ph.D. in Computer Science and Engineering from the University of California, San Diego, where he is now a associate professor with joint appointments in Computer Science and Engineering and in the Skaggs School of Pharmacy and Pharmaceutical Sciences and an executive director in Center for Computational Mass Spectrometry. 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, Dr. Bandeira’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.
Gabriel Becker
	Gabe is a statistical computing researcher with interests in reproducibility, discoverability, and related meta-computing topics, and in improving and advancing the R computing language. He proposed the ALTREP framework recently added to R’s internals – representing one of the largest conceptual changes in R’s history to how vector data is fundamentally modeled internally – and collaborated closely with R-core members on the design and implementation of the framework. Previously, Gabe was a Scientist at Genentech Research, where he performed novel research on how to improve the reproducibility, comparability, and ultimate usefulness of computational results in multi-analyst industrial research settings. He is currently taking time to focus on open source projects. Gabe received his PhD in Statistics from the University of California at Davis.
Kylie Bemis
	Kylie Bemis is a Postdoctoral Future Faculty Fellow in the College of Computer and Information Science 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.
Steven Braun
	Steven Braun is the Data Analytics and Visualization Specialist in the Snell Library Digital Scholarship Group and a creative developer who works in data visualization, digital humanities, and web and graphic design. He often speaks on the theoretical and philosophical dimensions of information design, and through his visualization projects he endeavors to capture different facets of human experience across creative, physical, and epistemological domains. Prior to joining the Northeastern University Libraries, Steven served as the Informatics Specialist in the Health Sciences Libraries at the University of Minnesota. He received his M.S. in molecular biophysics and biochemistry from Yale University, and he holds a B.A. in chemistry and Asian studies from St. Olaf College in Northfield, MN. He is the past recipient of a Fulbright Fellowship from the U.S. Department of State, during which he spent time living in Kyoto, Japan studying computational models of protein folding at Kyoto University.
Vincent Carey
	Vincent Carey is Professor of Medicine (Biostatistics) in the Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School. As a Fulbright Specialist and as an invited lecturer, he has given short courses in statistical genomics on four continents. He was an inaugural faculty member in the Cold Spring Harbor Laboratory Summer Course on statistical analysis of genome-scale data, and is former Editor-in-Chief of The R Journal. He is Scientific Director of Bioinformatics in the National Institute of Allergy and Infectious Diseases Immune Tolerance Network, and is a member of the Scientific Advisory Board of the Vaccine and Immunology Statistical Center of the Collaboration for AIDS Vaccine Discovery. Vince is a co-founder of the Bioconductor project.
Meena Choi
	Meena is an associate research scientist in the lab of Olga Vitek at Northeastern University. She holds a B.S. in Biology from the Korea Advanced Institute for Science and Technology, and a PhD in Statistics from Purdue University. Meena’s work focuses on statistical methods for quantitative proteomics. She is the lead developer and maintainer of MSstats.
Laurent Gatto
	Laurent is an associate professor of Bioinformatics at the UCLouvain, in Belgium, and director of the Computational Biology and Bioinformatics (CBIO) group, since September 2018. He is located in the de Duve Institute, on the medical campus in Brussels, where he runs a research group and teaches at the faculty of pharmacy and biomedical sciences (FASB). Prior to joining UCLouvain, he worked in the Cambridge Centre for Proteomics on various aspects of quantitative and spatial proteomics, developing new methods and implementing computational tools with a strong emphasis on rigorous and reproducible data analysis. He is also a visiting scientist in the PRIDE team at the European Bioinformatics Institute, affiliated member of the Bioconductor project, a fellow of the Software Sustainability Institute, a Software and Data Carpentry instructor and an affiliate teaching staff at the Cambridge Computational Biology Institute.
Nils Gehlenborg
	Nils is an assistant professor in the Department of Biomedical Informatics at Harvard Medical School. He received his PhD from the University of Cambridge and was a predoctoral fellow at the European Bioinformatics Institute (EMBL-EBI). Currently, Nils is researching and developing novel tools to visualize heterogeneous data from large-scale cancer genomics studies such as The Cancer Genome Atlas (TCGA), integration of visual and computational approaches to support sense-making in biology, and software to support reproducible collaborative research in epigenomics and genomics. He is also a co-founder and former General Chair of BioVis, the Symposium on Biological Data Visualization, and co-founder of VIZBI, the annual Workshop on Visualizing Biological Data. Occasionally, he contributes to the Points of View data visualization column in Nature Methods.
Andy Hoofnagle
	Andy is an Associate Professor in the Department of Laboratory Medicine at the University of Washington. His laboratory focuses on developing CLIA-certified assays for small molecules using mass spectrometry. They also investigate the function of high density lipoproteins in patients at increased risk for cardiovascular disease and the translation of proteomics technologies into the clinical laboratory.
Oliver Kohlbacher
	Oliver is the chair for Applied Bioinformatics at University of Tübingen and a fellow at the Max Planck Institute for Developmental Biology in Tübingen. Besides research in structural bioinformatics and computational immunology, his group has been developing algorithms and software tools for computational mass spectrometry, including the software library and tool box OpenMS (www.OpenMS.org) for the analysis of proteomics and metabolomics data.
Alexander Lex
	Alexander Lex is an Assistant Professor of Computer Science at the Scientific Computing and Imaging Institute and the School of Computing at the University of Utah. Alex co-directs the Visualization Design Lab and conducts research on visualization methods and systems to help solve today’s data analysis problems in the biomedical sciences. Alex is a co-founder of datavisyn, a company developing visual analytics solutions for the pharmaceutical industry, and a member of the Huntsman Cancer Institute. Before joining the University of Utah, he was a lecturer and post-doctoral researcher at Harvard University. He received his PhD, master’s, and undergraduate degrees from the Graz University of Technology, and was a visiting researcher at the Department for Biomedical Informatics at Harvard Medical School. Alex is the recipient of an NSF CAREER award and multiple best paper awards or honorable mentions at IEEE VIS, ACM CHI, BioVis, and other conferences. He also received a best dissertation award from his alma mater.
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.
Michael J. MacCoss
	Mike became interested in biomedical applications of mass spectrometry while working in Dr. Patrick Griffin’s protein mass spectrometry lab at Merck Research Laboratories. He obtained a Ph.D. with Professor Dwight Matthews and pursued a postdoc with Professor John R. Yates III. In 2004 he started the MacCoss lab at the University of Washington and it became obvious that while mass spectrometry data could be collected quickly and robustly, the lack of computational tools for the visualization and analysis of these data was a stumbling block. In 2009 he recruited Brendan MacLean with the goal of developing professional quality software tools for quantitative proteomics. Mike has worked closely with the Skyline development team and our outstanding group of laboratory scientists and collaborators to ensure that our software uses analytical approaches that have been thoroughly vetted by the mass spectrometry community.
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.
Lindsay K. Pino
	Lindsay K. Pino is a Ph.D. candidate at the University of Washington’s Department of Genome Sciences in the MacCoss lab. Her research interests include the development of large-scale proteomics assays using data independent acquisition-MS to investigate complex mixtures and applying computational techniques to mine the resulting high-dimensional data. Prior to joining the MacCoss lab, she worked as a research associate at the Broad Institute of MIT and Harvard in Dr. Steve Carr’s Proteomics Platform, where she worked under Dr. Susan Abbatiello to improve the speed and selectivity of targeted proteomics assays using high-field asymmetric waveform ion mobility spectrometry (FAIMS).
Barret Schloerke
	`hello()`! Dr. Barret Schloerke is a Software Engineer on the Shiny Dev Team at RStudio. He currently maintains and creates many R packages surrounding the Shiny ecosystem, including reactlog, plumber, leaflet, learnr, and shinyloadtest. Dr. Schloerke received his PhD in Statistics from Purdue University under the direction of Dr. Ryan Hafen and Dr. William Cleveland, specializing in Large Data Visualization.
Brian Searle
	Brian is a Translational Research Fellow at the Institute for Systems Biology. Brian received his chemistry BA at Reed College in 2001. In 2004, he co-founded Proteome Software with Mark Turner and Dr. Ashley McCormack to produce and distribute cutting-edge data analysis software for proteomicists. In 2014, he returned to academia to earn his PhD with Dr. Michael MacCoss at University of Washington, where he developed methods to detect and quantify proteins and phosphosites using mass spectrometry. In 2018, he joined the Institute for Systems Biology as an independent fellow to build a research program that spans the intersection of proteomics, mass spectrometry, bioinformatics, and technology development to study human genetic variation.
Tsung-Heng Tsai
	Tsung-Heng is a postdoctoral research associate in the lab of Olga Vitek at Northeastern University. He is a co-developer of MSstats, an open-source software package for statistical analysis of quantitative proteomic experiments. Tsung-Heng holds a PhD in Electrical Engineering from Virginia Tech. His current research focuses on developing statistical and computational methods for mass spectrometry-based proteomics.
Olga Vitek
	Olga is Associate Professor in the College of Science and the College of Computer and Information Science at Northeastern University. Olga holds a PhD in Statistics from Purdue University. Her group develops statistical methods and algorithms for quantitative proteomics. The methods optimize the experimental design, and ensure accurate and objective interpretation of the resulting large and complex datasets. The tools developed by her group include MSstats, an open-source software for statistical analysis of quantitative shotgun, targeted and data-independent proteomic experiments, and Cardinal, an open-source software for analysis of mass spectrometry-based imaging experiments.
Alicia Williams
	Alicia holds a PhD in English literature from Rutgers University, where she is postdoctoral lecturer teaching in both undergraduate and graduate writing programs. She studies nineteenth-century British fiction and the history of reading, and her work has appeared in Victorian Poetry and is forthcoming in NOVEL: A Forum on Fiction—literary equivalents of JASMS and Nature Methods. In the past, Alicia worked as a manuscript editor and writing mentor in the area of mass spectrometry and proteomics in the group of Joshua Coon at University of Wisconsin-Madison.

Course Instructors

Oliver Alka
	Oliver obtained his BSc in Biology and MSc in Biochemistry and Biophysics from the University of Freiburg. He is currently doing his PhD studies in the lab of Oliver Kohlbacher at the University of Tübingen. Here, he is working on improving identification and quantification of targeted SWATH analysis for Metabolomics. As part of these efforts, he is strongly involved in the development and maintenance of OpenMS.
Dan Guo
	Dan is a PhD student from Northeastern University College of Computer Information and Science in the lab of Olga Vitek. She holds a B.S. in Biological Engineering and a M.S. in Chemical Engineering and Technology from Beijing Institute of Technology, China. Dan’s research focuses on Mass spectrometry imaging data mining and statistical analysis.
Ting Huang
	Ting Huang is a PhD student 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.
Julianus Pfeuffer
	Julianus obtained his BSc and MSc undergraduate degree in Bioinformatics from the University of Tuübingen. He has a background in cheminformatics and computer-aided drug design and now pursues improving protein identification and quantitation algorithms for mass spectrometry data analysis during his PhD studies in the lab of Oliver Kohlbacher at the University of Tübingen. As part of these efforts, he is strongly involved in the development and maintenance of OpenMS.
Timo Sachsenberg
	Timo is Ph.D. students in the lab of Oliver Kohlbacher at the University of Tübingen. He is a lead developer of OpenMS. During his Ph.D., he developed novel methods for the identification of protein-RNA interactions and quantitative metaproteomics.
Sara Taheri
	Sara is a Ph.D student in the College of Computer and Information Science at Northeastern University. She received her B.S. and M.S. degree in Applied Mathematics from Sharif University of Technology, Iran. She is the main developer of MSstatsQC, an open-source web-based software which provides longitudinal system suitability monitoring tools for proteomic experiments. Sara’s current research focus on causal inference of bimolecular networks for experiments that quantify molecular abundance with multiple biotechnological platforms, and differ in the amounts of technological artifacts.