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

April 27–May 8, 2020, Northeastern University, Boston MA
Organizers : Meena Choi and Olga Vitek

Speakers

Ruedi Aebersold

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.

Kylie Bemis

Kylie Bemis Kylie is a Lecturer 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.

Meena Choi

Meena is 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 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.

Ting Huang

Ting Huang Ting 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.

Bernhard Kuster

Bernhard Kuster Bernhard conducts research in the field of chemical and functional proteomics. This research focuses on how proteins interact with each other and with active pharmaceutical ingredients, which molecular mechanisms play a role in cancer and how these can be used for individual approaches to clinical treatment. He uses chemical and biochemical methods as well as spectroscopic and bioinformatic high throughput technologies. After studying chemistry at the University of Cologne, Professor Küster obtained his doctorate in biochemistry at the University of Oxford. He worked as a postdoctoral researcher in Heidelberg, Germany, and Odense, Denmark. Prior to becoming a full professor at TUM and until 2007 he was Vice President of Cellzome AG. Professor Küster is the Chair of the TUM Department of Biosciences and a member of the Graduate School Experimental Medicine. His research is funded by the Center for integrated Protein Science Munich (CiPSM), the German Consortium for Translational Cancer Research (DKTK) and the pharmaceutical industry. Professor Küster is one of the founders of the biotech company OmicScouts GmbH.

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.

Lindsay K. Pino

Lindsay Pino Lindsay is a postdoctoral researcher in Dr. Ben Garcia’s lab at the University of Pennsylvania, where she uses quantitative mass spectrometry to study epigenetics. She earned her PhD from the University of Washington Genome Sciences program under the joint advisorship of Drs. Michael J. MacCoss and William Stafford Noble. There, she developed techniques for data independent acquisition mass spectrometry, tackling the challenges associated with scaling up quantitative mass spectrometry experiments. Before graduate school, she spent two years in South Korea as a Fulbright scholar and then three years working as a research associate in Dr. Steve Carr’s Proteomics Platform at the Broad Institute of MIT and Harvard.

Brian Searle

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.

Olga Vitek

Olga Vitek Dr. Olga Vitek holds a PhD in Statistics from Purdue University. She is Professor in the Khoury College of Computer Sciences at Northeastern University, and was previously a Faculty and a University Faculty Scholar at Purdue. 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. Dr. Vitek 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 a member of the Editorial advisory board of Molecular and Cellular Proteomics and of Journal of Proteome Research.

Alicia Williams

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.

Administrative Support

Roger Donaghy

Roger Donaghy Web Developer

Northeastern University