Dr. Martin Steffen, Ph.D.

photo of Dr. Steffen

Assistant Professor, Biomedical Engineering
Assistant Professor, Pathology and Laboratory Medicine
Director, Proteomics Core Facility
Department of Pathology, Boston University School of Medicine

Primary appointment, BUSM
Steffen Laboratory
Ph.D., Chemistry, Stanford University
M.D., Stanford University
B.A., Chemistry, Dartmouth College
Phone: (617) 414-7935
Email: steffen@bu.edu
Office: 36 Cummington Mall, Room 305; Office hours: By appointment

Research Interests

My lab works on developing the tools of systems biology for mammalian cells. Currently we are emphasizing the technique of mass spectrometry. Using mass spec, one can currently identify a few thousand proteins in a single experiment, as well as many important post-translational modifications (PTMs). Our guiding biological focus is cancer biology, and our interests are both at the level of basic research and clinical application. Specifically, we wish to characterize proteomic differences (identities, amounts, PTMs, splice forms) between normal and diseased tissue. We will also examine serum samples from donors with and without cancer as part of an effort to identify proteins that behave as early indicators of tumor development.

Current Research

Our efforts in the area of technology development aim at identifying protein interactions using mass spectrometry. We are developing two methods: (1) for identifying strong, stable interactions in complexes, such as those that might be found in a ribosome, polymerase or other multi-subunit complex; (2) for identifying weak, transient interactions, such as those that are involved in signal transduction. Our efforts in bioinformatics revolve around pathway and network identification. We have developed an algorithm for automated modeling of pathways in yeast, based only on two-hybrid protein interaction and microarray data. No prior knowledge of the pathway is needed. We now wish to extend this method to C. elegans and drosophila, and will explore application of this algorithm to mouse and human. Other computational efforts involve integrating known pathway and network data with proteomic and microarray experiments.

Selected Recent Publications

Kasif S, Steffen M.Biochemical networks: The evolution of gene annotationNat Chem Biol. 6(1):4-5 (2010 Jan)

Wu CJ, Cai T, Rikova K, Merberg D, Kasif S, Steffen M. “A predictive phosphorylation signature of lung cancerPLoS One. 4(11):e7994 (2009 Nov 25)

Bushkin GG, Ratner DM, Cui J, Banerjee S, Duraisingh MT, Jennings CV, Dvorin JD, Gubbels MJ, Robertson SD, Steffen M, O’Keefe BR, Robbins PW, Samuelson J. “Suggestive evidence for Darwinian selection against asparagine-linked glycans of Plasmodium and Toxoplasma” Eukaryot Cell. (2009 Oct 16)

Chatterjee A, Banerjee S, Steffen M, O’Connor RM, Ward HD, Robbins PW, Samuelson J. Evidence for mucin-like glycoproteins that tether sporozoites of Cryptosporidium parvum to the inner surface of the oocyst wallEukaryot Cell. (2009 Nov 30)

K. Steiling, A. Y. Kadar, A. Bergerat, J. Flanigon, S. Sridhar, V. Shah, Q. R. Ahmad, J. S. Brody, M. E. Lenburg, M. Steffen, A. Spira Comparison of proteomic and transcriptomic profiles in the bronchial airway epithelium of current and never smokersPLoS ONE. 4, e5043 (2009)

Herrera VL, Decano JL, Steffen M, Ruiz-Opazo N. “Autophagy: insights from DEspR-deficiency and haploinsufficiencyAutophagy. 5: 259-62 (2009)

Herrera VL, Decano JL, Bagamasbad P, Kufahl T, Steffen M, Ruiz-Opazo N. “Sex-Specific, Hippocampal-Dependent Cognitive Deficits and Increased Neuronal Autophagy in DEspR Haploinsufficiency in Mice” Physiol Genomics. (2008 Sep 9)

Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED “Integration of Relational and Hierarchical Network Information for Protein Function Prediction” BMC Bioinformatics. 9: 350 (2008 Aug 22)

Saharia A, Guittat L, Crocker S, Lim A, Steffen M, Kulkarni S, Stewart SA “Flap Endonuclease 1 Contributes to Telomere Stability” Curr Biol. 18 (7): 496-500 (2008 Apr 8)

Van Dellen KL, Chatterjee A, Ratner DM, Magnelli PE, Cipollo JF, Steffen MA, Robbins PW, Samuelson J “Unique Posttranslational Modifications of Chitin-Binding Lectins of Entamoeba Invadens Cyst Walls” Eukaryot Cell 5 (5): 836-48 (2006 May)

Ahmad QR, Nguyen D, Wingerd MA, Church GM, and Steffen MA “Molecular Weight Determination of Proteins in Total Proteome Profiles Using 1D-PAGE and LC/MS/MS” Proteome Sci. 3 (1): 6 (2005 Jun 8)