Proteome Bioinformatics Lab
Our research interests are in the fields of bioinformatics and systems biology, with a focus on the development of computational methods and tools for
processing and extracting biological information from complex biological datasets. We are are particularly interested in computational and
statistical methods for mass spectrometry-based proteomics, interactome analysis using affinity purification mass spectrometry (AP-MS) technology, proteogenomics, metabolomics, global analysis of
RNA-Seq transcriptome and proteome profiles in cancer, and in multi-omics data integration (RNA-seq, proteomics, ribosomal profiling, ect) for reconstruction of pathways deregulated in cancer. We
continue developing many computational resources widely used by the proteomics community worldwide, described on our Software page. While we are a computational lab, we actively collaborate
with technology developers, biologists, and clinical scientists.
Bioinformatics resources we developed: SOFTWARE
Current and former lab members: MEMBERS
News in the lab or about the lab: NEWS
Recent NewsFor more news see: NEWS
We have post-doctoral positions available
The first version of our new software for visualization of raw mass spectrometry data is released. BatMass
New DIA-Umpire version 1.4 is released. Many improvements and one new key feature (external spectral library search option) added.
Welcome to new post-doctoral fellow Felipe Leprevost. Felipe joins us from the Oswaldo Cruz Foundation (known as Fiocruz) in Curitiba, Brazil. Felipe received his Ph.D. in Bioinformatics and Computational Biology working in Paulo Carvalho'lab at Fiocruz-PR.
Congratulations to Andy Kong and Dattatreya Mellacheruvu, who received travel awards to attend the US HUPO Conference in Tempe Arizona. Andy presented his work on GPU accelerated MS/MS database search, and Datta presented an update on our CRAPome resource for the analysis of protein-protein interaction data. At the same conference, Chih-Chiang Tsou presented an update on his DIA-Umpire tool for SWATH/DIA mass spectrometry data, Alexey taught a short course on protein interactions (with Ileana Christea) and presented on the subject of false discovery rates in large proteomics and proteogenomics datasets in an evening Characterizing Confidence in Complete Proteome Elucidation Workshop.
Congratulations to Chih-Chiang Tsou who was selected to receive a 2015 Graduate Student Award from the American Society for Mass Spectrometry (ASMS)! The ASMS Graduate Student Award recognizes graduate students whose academic achievements and current mass spectrometry research display a high level of excellence and distinction. The award will be presented during the ASMS business meeting on Wednesday, June 3, 2015.
"DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics" has been published in Nature Methods. You can find links to this and all other computational tools on our SOFTWARE page. News coverage: The publication was discussed in GenomeWeb (January 2015).
Congratulations to Dattatreya Mellacheruvu who successfully defended his Ph.D. thesis "A computational and informatics framework for the analysis of affinity purification mass spectrometry data and reconstruction of protein interaction network"!
We (with David Tabb, Vandervilt; Nuno Bandeira, UCSD) will again teach a two-day course "Bioinformatics for Protein Identifications" at the 2014 ASMS conference (May 30-31, 2015). As part of this couse, we offer a hands-on tutorial on PeptideProphet and ProteinProphet.
Congratulations to Avinash Shanmugam, Ph.D student in the lab, who received a poster award for his presentation on "Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS" at the 3rd Mass Spectrometry Special Interest Group (MS-SIG) workshop during the 2014 ISMB meeting in Boston, MA. The manuscript has now been published in the Journal of Proteome Research.
Congratulations to Dattatreya Mellacheruvu, Ph.D student in the lab, who received the 2014 Endowment for the Development of Graduate Education (EDGE) award from the University of Michigan.
Congratulations to Andy Kong, Ph.D. student in the lab, who received the Pre-doctororal Fellowship Award from the Natural Sciences and Engineering Research Council of Canada (NSERC).
- DIA-Umpire tool for data independent acquisition proteomics data in Nature Methods
- Comprehensive review on Proteogenomics in Nature Methods
- Utility of RNA-seq and GPMDB for improving protein identification in J Prot Research
- SAINTexpress software for AP-MS data in J Proteomics
- On reconstruction of cancer pathways using omics data integration in Nature Commun.
- CRAPome is published in Nature Methods
- iProphet method and software is published in Molecular & Cellular Proteomics
- Special issue of the journal Proteomics on Protein Complexes and Interaction Networks
- New manuscripts on joint analysis of proteomic and RNA-seq transcriptomic data
- SAINT-MS1 for intensity-based AP-MS published in J Prot Research
- SAINT 2.0 method for AP-MS data published in Nature Methods
- Abacus: software for label-free proteomics now available
- Comprehensive review on peptide/protein error rates in J. Proteomics
- Comprehensive review on scoring protein interactions in AP-MS data in Proteomics
- Global yeast protein kinase and phosphatase interaction network published in Science
- PeptideProphet and ProteinProphet manuscripts reach 2000 citations
- Proteome Informatics of Cancer Training Program at U Michigan
- Watch us talk about our research on YouTube