May Institute: Computation and statistics for mass spectrometry and proteomics

April 30–May 11, 2018, Northeastern University, Boston MA
Organizers : Meena Choi and Olga Vitek
 

Keynote Speakers

Susan Abbatiello

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 now a product specialist at ThermoFisher, and a research scientist in the Proteomics Platform at the Broad Institute of MIT and Harvard. Susan’s research focuses on the development of tests to measure potential protein biomarkers in the 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 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.

Joseph J. (J.J) Allaire

Joseph J. (J.J) Allaire J.J. is a software engineer and Internet entrepreneur. He created the ColdFusion programming language and web application server and founded Allaire Corporation, OnFolio, and RStudio. Allaire created LoseIt! and Windows Live Writers. He is currently the founder and CEO of statistical computing company RStudio.

Naomi Altman

Naomi Altman Naomi is a professor in department of statistics at the Pennsylvania State University. She is one of the authors for Points of Significance, a monthly column on statistics, in Nature Method. Her interest in statistics stems from her broad interests in the application of the mathematical sciences to problems in other disciplines – in particular, medical and biological sciences, earth and environmental sciences, and social sciences. Her statistical interests include bioinformatics, high dimensional data, nonparametric smoothing, model selection and analysis of functional and longitudinal data. Dr. Altman’s current research is in bioinformatics and dimension reduction.

Michelle Borkin

Michelle Borkin Michelle is an assistant professor in the College of Computer and Information Science at Northeastern University, and also an affiliated research at Brigham & women’s hospital. Her main research interests include information and scientific visualization, hierarchical and multidimensional data representations, network visualization, visualization cognition, user interface design, human computer interaction (HCI), and evaluation methodologies. Prior to joining Northeastern, she was a Postdoctoral Research Fellow in Computer Science at the University of British Columbia, as well as Associate in Computer Science at Harvard and Research Fellow at Brigham & Women’s Hospital. She received her Ph.D. in Applied Physics at Harvard’s School of Engineering and Applied Sciences (SEAS) in 2014. She also has an MS in Applied Physics and a BA in Astronomy and Astrophysics & Physics from Harvard University.

Jarrett Egertson

Jarrett Egertson Jarrett is a postdoctoral researcher at the University of Washington Department of Genome Sciences. He works in the MacCoss Lab and primarily focuses on developing new data acquisition methods and software in support of these methods. Jarrett earned his undergraduate degree (B.S. in Molecular, Cell, and Developmental Biology) from UCLA in 2008. While earning his undergraduate degree, Jarrett researched at the Spielberg Family Center for Applied Proteomics at the Cedars-Sinai Medical Center.

Laurent Gatto

Laurent Gatto Laurent works 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. He currently leads the Computational Proteomics Unit.

Nils Gehlenborg

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.

Jacob D. Jaffe

Jacob D. Jaffe Jake is the Assistant Director of the Proteomics Platform at the Broad Institute. He obtained his B.A. in Biochemistry from the University of Pennsylvania and his Ph.D. from Harvard University where he studied with George Church and Howard Berg. Dr. Jaffe has pioneered diverse problems in modern proteomics including large-scale mapping of proteomic data onto genomes, thus allowing their de novo annotation from proteomic evidence, pattern recognition for quantitative proteomics, determination and quantification of epigenetic marks on histone proteins, and high-throughput targeted phosphoproteomics.

Oliver Kohlbacher

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.

Michael J. MacCoss

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 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.

Olga Vitek

Olga Vitek Olga is a Sy and Laurie Sternberg 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.

Course Instructors

Kylie Bemis

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 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.

Meena Choi

Meena Choi Meena is a post-doctoral associate 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.

April Harry

April Harry April Harry is a PhD Candidate from Purdue University Department of Statistics and a member of Olga Vitek Lab at Northeastern University. She is an alum of Xavier University of Louisiana (BS in Mathematics, ’10) and Purdue (MS in Applied Statistics ’12). April’s dissertation research explores experimental design and statistical analysis of mass spectrometry imaging experiments.

Ting Huang

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.

Lindsay K. Pino

Lindsay 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).

Julianus Pfeuffer

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 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.

Tsung-heng Tsai

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.

Administrative Support

Roger Donaghy

Roger Donaghy Web Developer

Shan Li