News

2021

3/21 May Institute on computation and statistics for mass spectrometry and proteomics IS OPEN FOR APPLICATIONS! It will take place online on May 3 – May 14, 2021. Find more information and apply at this link!

3/21 Congratulations to Ting, who was awarded the Northeastern University Dissertation Completion Fellowship award!

3/21 Our group was recognized with the 2021 Gilbert S. Omenn Computational Proteomics Award of the US Human Proteome Organization!

3/21 Join us in the USHUPO short course on “Statistical Design and Analysis of Quantitative Proteomics Experiments with TMT Labeling: Case Studies with MSstatsTMT”, led by Ting, Mateusz and Melanie. Devon and Mateusz also present posters related to MSstats.

1/21 Congratulations to Meena, who was named one of the rising stars in proteomics and metabolomics by Journal of Proteome Research!!! Way to go Meena, very much deserved! 

2020

12/20 At the end of the year, we are celebrating our milestones. Congratulations to Sai and Devon with successful completion of the MS program! Congratulations to Ting with the successful completion of the PhD preliminary exam. We are excited for the next steps.

12/20This professor rarely works alone” says the new profile of Olga’s work by the Khoury College of Computer Sciences at Northeastern University.

9/20 It is with mixed feelings that we celebrate Meena’s transition to the new position as Bioinformatics Scientist at Genentech! We are grateful for Meena’s contributions to the lab, and send her our best wishes for the next steps.

9/20 We welcome to the lab new members, Vartika Tewari and Ritwik Anand who joined the PhD in CS program, and research scientist Devon Kohler.  

8/20 Congratulations to Meena, Nuno Bandeira, and many of our collaborators, with the publication of their work on MassIVE.quant in a recent Nature Methods report! 

8/20 Check out the recent interview with Ting by EVOSEP, where Ting argues for the importance of biological replication in mass spectrometry-based experiments.

7/20 Congratulations to Ting and Meena, who’s manuscript “MSstatsTMT: Statistical detection of differentially abundant proteins in experiments with isobaric labeling and multiple mixtures” is accepted to Molecular & Cellular Proteomics! This was a lot of hard work, and we are very excited to finally see this in print.

5/20 May Institute on computation and statistics for mass spectrometry and proteomics online was a great success! Thank you all the presenters, and over 500 participants who registered for the talks! Take a look at the handouts and screencasts, and watch this space for the details of May Institute May 3 – May 14, 2021.

4/20 We present our work in several talks and posters (now online) at USHUPO, MSACL, ASMS and ISMB/CompMS. Please joins us if you can.

4/20 Olga was awarded an Excellence in Research and Creative Activity Award, given by Northeastern University to faculty conducting outstanding research and creative activity of national and international significance.

4/20 Olga is elected the next President of the Boston Chapter of the American Statistical Association starting January 2021.

3/20 We welcome to the lab new research scientists Melanie Föll and Mateusz Staniak. Welcome to the lab!

3/20 Congratulations to Tsung-Heng and Meena, who’s paper “Selection of features with consistent profiles improves relative protein quantification in mass spectrometry experiments” is accepted to Molecular & Cellular Proteomics! Many thanks to Tsung-Heng for putting a lot of energy and perseverance into this project.

3/20 Congratulations to Dan Guo and Melanie Föll, who’s paper “Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations” is accepted to ISMB 2020! Fantastic work.

2019

12/19 The 2020 May Institute on computation and statistics for mass spectrometry and proteomics, April 27 – May 8 2020 at Northeastern University in Boston is now accepting application! Take a look at the last year’s presentation screencasts, and the handouts.

12/19 Congratulations to Ting, and our colleagues from Biognosys, who’s paper “Combining precursor and fragment information for improved detection of differential abundance in data independent acquisition” is accepted to Molecular & Cellular Proteomics!

11/19 We are very excited to share that Chan Zuckerberg Initiative will support MSstats and Cardinal as part of the Essential Open Source Software for Science program. Thank you for recognizing the great work by Meena and Kylie, the contributions of multiple other developers, and by the hundreds of our users.

11/19 Olga was named Senior Member of the International Society for Computational Biology.

9/19 Join us at the OurCon Workshop on October 28 in San Malo, France, for an in-depth presentation of Cardinal. Led by Kylie and Dan!

9/19 Join us at the Asilomar MS Imaging Pre-Conference Workshop on October 11, for an in-depth look into statistical analyses enabled by the open-source software Cardinal. Led by Kylie!

10/19 Congratulations to Robert and Kaushal, who’s paper “Integrating mechanistic and structural causal models enables counterfactual inference in complex systems” is accepted to NeurIPS 2019!

8/19 Congratulations to Kaushal with the successful MS thesis defense! Best wishes for the new beginnings at Microsoft. 

8/19 Best wishes to Tsung-Heng, who is on to the position of Assistant Professor in the Department of Mathematical Sciences at Kent State University!

7/19 Check out the Khoury newsletter describing our experience with May Institute 2019.

7/19 Congratulations to our collaborator Ruth Hüttenhain and Meena, who’s paper “A targeted mass spectrometry strategy for developing proteomic biomarkers: a case study of epithelial ovarian cancer” appeared at MCP after many years of very hard work! Very well deserved!

5/19 Extensive materials from the 2019 May Institute on computation and statistics for mass spectrometry and proteomics are now posted! You can find the presentation screencasts, and the handouts. Please take a look.

12/19 Congratulations to Dan and Kylie, who’s paper “Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues” is accepted to ISMB/ECCB 2019!

2018

12/18 The May Institute on computation and statistics for mass spectrometry and proteomics 2019, taking place on April 29–May 10, 2019 at Northeastern University, Boston IS NOW ACCEPTING APPLICATIONS!

10/18 Congratulations to Eralp and Sara, who’s manuscript “MSstatsQC 2.0: R/Bioconductor package for statistical quality control of mass spectrometry-based proteomic experiments” is accepted to Journal of Proteome Research! Learn more about the software here.

10/18 An extension to MSstats, MSstatsTMT, is now available from Bioconductor. Great job Meena, Ting and Sicheng!

9/18 Olga was elected to the Council of the International Human Proteome Organization (HUPO).

9/18 Congratulations to Meena, who is promoted to the position of Associate Research Scientist @CCIS. Way to go Meena!

9/18 Ting, Tsung-Heng and Olga speak at the 2018 World Congress of the Human Proteome Organization. Join us if you can.

9/18 Congratulations to Kylie, a recipient of the Burroughs Wellcome Fund Postdoctoral Enrichment Program award! Very well deserved!

6/18 Busy summer for the entire lab! Kylie is invited to speak at the Purdue Symposium on Statistics and at the CompMS track of ISMB; Tsung-Heng participates at the ETH DIA/SWATH short course, and Sara interns at GNS Healthcare.

6/18 Multiple opportunities this year to learn more about statistical experimental design and analysis with MSstats. Join us at ETH ZürichUniversity of WashingtonUniversity of Wisconsin and CRG Barcelona! Come back to this page for more news.

6/18 Join us in a 2-day short course discussing case studies in quantitative mass spectrometry at the Annual Conference of the American Society for Mass Spectrometry (ASMS) on June 2 – 3, 2018!

5/18 Olga is elected Officer and Program Chair of the Boston Chapter of the American Statistical Association, starting January 2019.

5/18 Congratulations to Cyril, a new Fellow at Insight Data Science Boston. We wish Cyril great success as he advances his career!

5/18 Over 100 participants took part from the 2018 May Institute on computation and statistics for mass spectrometry and proteomics! Course materials are posted here and here.

5/18 The 2018 May Institute on computation and statistics for mass spectrometry and proteomics on April 30 – May 11, 2018 is now accepting applications! Submit your application here.

4/18 Meena speaks at the Annual Meeting of the Association of Biomedical Resource Facilities (ABRF).

3/18 Join us in a 2-day short course introducing MSstats at the Annual Conference of the US Human Proteome Organization (US HUPO) on March 10 – 11, 2018!

2/18 Congratulations to Cyril, who’s paper “Nonlinear regression improves accuracy of characterization of multiplexed mass spectrometric assays” in collaboration with the MacCoss and Hoofnagle labs at UW is accepted to Molecular and Cellular Proteomics

2/18 April is featured as a Rising Star on Mathematically Gifted and Black. Congratulations April!

2017

12/17 Congratulations to Cyril, who’s manuscript “Statistical inference of peroxisome dynamics” in collaboration with the Cristea lab is accepted to RECOMB 2018

12/17 Congratulations to April, who successfully defended her PhD dissertation “Design and statistical analysis of mass spectrometry imaging experiments”! April is on to the Insight Data Science Fellows program in Seattle.

10/17 Kylie and Olga organize an invited session on “Data Analysis and Quantitation” at the Imaging Mass Spectrometry Society Inaugural Meeting.

10/17 Kylie speaks at two panels at the Grace Hopper Women in Computing Conference 2017, discussing the work of Native women and diversity in computing. Way to go Kylie!

9/17 Kylie and Olga speak at OurCon V – Mass Spectrometry Imaging Conference. Congratulations to Kylie for receiving a travel award!

7/17 Congratulations to Tsung-Heng, who’s paper “Statistical characterization of therapeutic protein modifications” is accepted to Nature Scientific Reports!

6/17 Ting is spending her summer as an intern at Biognosis, and Sara as an intern at GNS Healthcare. Good luck to both!

6/17 Congratulations to April, who successfully passed her PhD preliminary exam!

6/17 Congratulations to Cyril, who was awarded a travel grant by the Burroghs Wellcome foundation, in support of a collaboration with the Cristea lab at Princeton University!

5/17 Kylie presents her work on Matter at the UseR! conference in Brussels. Watch the presentation here.

5/17 The 2017 May Institute on Computation and Statistics for Mass Spectrometry and Proteomics completed with success! Take a look at the course materials, and at the videos of the presentations

4/17 Olga gives a keynote presentation at Biomedical Computation at Stanford.

4/17 Congratulations to Eralp, who’s paper “MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experiments” is accepted to Molecular and Cellular Proteomics

4/17 Congratulations to Kylie, who’s paper “Matter: an R package for rapid prototyping with larger-than-memory datasets on disk” is accepted to Bioinformatics!

4/17 Meena, Ting, Tsung-Heng and Olga are co-teaching short courses introducing MSstats, in association with ABRF, US HUPO and ASMS. Look out for similar opportunities in 2018!

2016

12/16 “May Institute: Computation and Statistics for Mass Spectrometry and Proteomics” is now accepting applications. Register here.

12/16 Congratulations to Robert, who’s paper “A Bayesian active learning experimental design for inferring signaling networks” is accepted to RECOMB 2017!

12/16 Congratulations to Meena and Zeynep, who led the synthesis of the “ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments”. The manuscript is accepted to Journal of Proteome Research.

12/16 Congratulations to Robert, who successfully defended his dissertation “Bayesian causal inference of cell signal transaction”!

11/16 Eralp presents our research at VII Proteomics Workshop. The VII Proteomics Workshop will be held by the Brazilian Biosciences National Laboratory (LNBio) at the Brazilian Center.

10/16 Meena, April, Ting, Sara and Kylie are traveling to Grace Hopper Celebration of Women in Computing. The Grace Hopper Celebration of Women in Computing is the world’s largest gathering of women technologists. It is produced by the Anita Borg Institute and presented in partnership with ACM.

10/16 Olga and Meena are organizing a session on “Proteomics in the Era of Large Datasets” at Northeast Regional Life Sciences Core Directors(NERLSCD) conference.

08/16 Congratulations to Kylie, who successfully defended her dissertation “A framework for the statistical analysis of mass spectrometry imaging experiments”. Kylie is on to a Future Faculty Postdoctoral associate position at Northeastern University. Congratulations Kylie!

03/16 The special issue of Journal Proteome Research on Large-Scale Computational Mass Spectrometry and Multiomics edited by Olga is out! Take a look.

03/16 Congratulations to Ting, who was awarded the Wolfgang Goetzinger – Amgen Memorial Graduate scholar Award in Life Sciences. This Amgen-sponsored award covers travel and other research-related expenses. Congratulations Ting!

02/16 Congratulations to Robert, who’s perspective article “From correlation to causality: statistical approaches to learning regulatory relationships in large-scale biomolecular investigations” was named an ‘Editor’s choice’ manuscript by the American Chemical Society (ACS)!

01/16 Congratulations to Kyle, who’s manuscript “Probabilistic segmentation of mass spectrometry images helps select important ions and characterize confidence in the resulting segments” is accepted to Molecular and Cellular Proteomics!

01/16 Congratulations to Robert, who’s perspective article “From correlation to causality: statistical approaches to learning regulatory relationships in large-scale biomolecular investigations” is accepted to Journal of Proteome Research!

01/16 Join us at the annual conference of US HUPO, which will take place on March 13-16 in Boston. Olga is co-organizing the conference.