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

May 3 – May 14, 2021, Northeastern University, Boston MA via Zoom
Organizer: Olga Vitek


Nuno Bandeira

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. 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 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. 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.

Isabell Bludau

Isabell Bludau Isabell is a postdoctoral fellow in the lab of Prof. Matthias Mann at the Max Planck Institute of Biochemistry near Munich. During her PhD with Prof. Ruedi Aebersold at the Institute of Molecular Systems Biology, ETH Zurich, Isabell contributed to the development of software for analyzing large-scale data-independent acquisition (DIA) mass spectrometry datasets. She specifically focused on computational strategies for detecting and quantifying protein complexes from data generated by native co-fractionation coupled to DIA. Recently, Isabell’s work focuses on proteoforms including post-translational modifications and their crosstalk.

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 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 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

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.

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 a 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 Dr. Nesvizhskii’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

Lindsay K. Pino

Lindsay Pino Lindsay has over a decade of experience in developing mass spectrometry proteomics methods for studying human disease. She 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 particular, she is interested in the challenges associated with scaling-up quantitative proteomics experiments. Recently, she has been working on expanding these techniques to target dynamic systems including protein turnover, epigenetics, and protein interactions. In 2021 Lindsay was named one of the rising stars in proteomics and metabolomics by Journal of Proteome Research

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. In 2021 Brian was named one of the rising stars in proteomics and metabolomics by Journal of Proteome Research

Mateusz Staniak

Mateusz Staniak Mateusz is a PhD student from University of Wrocław, Poland, where he obtained his M.S. and B.S. in Mathematics. Mateusz is the current lead developer and maintainer of the MSstats package. His research focuses on statistical modeling in protein inference and quantification.

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. Olga is the 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