Frank Suits

Research Staff Member, Proteomics

Research lab: Watson Research Center (Yorktown)

Current Position:

Research Staff Member, Functional Genomics and Systems Biology Group
Analysis of Liquid-Chromatography/Mass-Spectrometry data for Proteomic Biomarker Discovery
IBM T. J. Watson Research Center

Adjunct Associate Professor, Columbia University, Department of Electrical Engineering

Contact Information:

suits@us.ibm.com
914-945-1294 (work)
914-945-4104 (fax)
862/1294 (tie-line)

Education:

Ph.D. Optical Sciences, Optical Sciences Center, University of Arizona, 1988
M. Sc. Physics, University of Arizona, (DuNuoy fellow) 1985
B. A. Math and Physics, with distinction in each, Carleton College 1983

Work Experience:

1988 – present: IBM T. J. Watson Research Center
2005 – present: Liquid-Chromatography/Mass-Spectrometry analysis for discovery of proteomic biomarkers
2000 – 2005: Analysis of large scale biomolecular simulations on the Blue Gene supercomputer with Blue Matter
1997 – 1999: Computational geometry for 3D CAD and network graphics
1993 – 1996: Scientific visualization with Data Explorer on SMP/Distributed/PC architectures
1988 – 1992: Magneto-optic studies of thin films related to storage materials and inductive heads
1983: Oak Ridge National Laboratory: Optical properties of a simulated atmosphere of Saturn’s moon, Titan

Patents:

Suits, F., J. T. Klosowski and W. P. Horn (2003). Dynamic view-dependent texture mapping. US6525731

Suits, F., J. T. Klosowski, W. P. Horn and G. Lecina (2003). Apparatus, system, and method for simplifying annotations on a geometric surface. US6518964

Klosowski, J. T., F. Suits, W. P. Horn and G. Lecina (2003). Apparatus, system, and method for draping annotations on to a geometric surface. US6978230

Horn, W. P., J. A. Valuyeva, J. T. Klosowski, F. Suits and G. Lecina (2003). System and method for the coordinated simplification of surface and wire-frame descriptions of a geometric model. US6570568

Borrel, P., S. Hall, W. P. Horn, J. T. Klosowski, W. L. Luken, I. M. Martin and F. Suits (2002). Method and apparatus for delivering 3D graphics in a networked environment using transparent video. US6384821

Borrel, P., S. Hall, W. P. Horn, J. T. Klosowski, W. L. Luken, I. M. Martin and F. Suits (2002). Methods and apparatus for delivering 3D graphics in a networked environment. US6377257

Publications:

Suits, F., J. Lepre, P. Du, R. Bischoff and P. Horvatovich (2008). "Two-dimensional method for time aligning liquid chromatography-mass spectrometry data." Analytical Chemistry 80(9)3095-104.

Christin, C., A. K. Smilde, H. C. J. Hoefsloot, F. Suits, R. Bischoff and P. L. Horvatovich (2008)."Optimized Time Alignment Algorithm for LC-MS Data: Correlation Optimized Warping using Component Detection Algorithm-Selected Mass Chromatograms." Analytical Chemistry In press.

Du, P., G. Stolovitzky, P. Horvatovich, R. Bischoff, J. Lim, F. Suits (2008). "A noise model for mass spectrometry based proteomics." Bioinformatics 24(8):1070-7.

Horvatovich, P., N. I. Govurukhina, T. H. Reijmers, A. G. van der Zee, F. Suits, R. Bischoff (2007). "Chip-LC-MS for label-free profiling of human serum." Electrophoresis 28(23):4493-505.

Lahankar S. A., S. D. Chambreau, D. Townsend, F. Suits, J. Farnum, X. Zhang, J. M. Bowman , A. G. Suits (2006)."The roaming atom pathway in formaldehyde decomposition." J. Chem. Phys. 125(4):44303

Zhou, R., A. Royyuru, P. Athma, F. Suits and B. D. Silverman (2006). "Magnitude and Spatial Orientation of the Hydrophobic Moments of Multi-Domain Proteins." Int. J. Bioinform. Res. Appl. 2(2):161-76.

Suits, F., M. C. Pitman and S. E. Feller (2005). "Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers." J Chem Phys 122(24): 244714.

Suits, F., M. C. Pitman, J. W. Pitera, W. C. Swope and R. S. Germain (2005). "Overview of molecular dynamics techniques and early scientific results from the Blue Gene project." IBM Journal of Research and Development 49(2/3): 475-87.

Germain, R. S., B. Fitch, A. Rayshubskiy, M. Eleftheriou, M. C. Pitman, F. Suits, M. Giampapa and T. J. C. Ward (2005). "Blue matter on blue gene/L: massively parallel computation for biomolecular simulation." Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis Jersey City, NJ, USA ACM Press: 207-212

Pitman, M. C., A. Grossfield, F. Suits and S. E. Feller (2005). "Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment." J Am Chem Soc 127(13): 4576-7.

Pitman, M. C., F. Suits, K. Gawrisch and S. E. Feller (2005). "Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers." J Chem Phys 122(24): 244715.

Germain, R. S., Y. Zhestkov, M. Eleftheriou, A. Rayshubskiy, F. Suits, T. J. C. Ward and B. G. Fitch (2005). "Early performance data on the Blue Matter molecular simulation framework." IBM Journal of Research and Development 49(2/3): 447-55.

Fitch, B. G., A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. Giampapa, Y. Zhestkov, M. C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. Zhou, R. S. Germain and S. Feller (2005). "Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L." IBM Research Report(RC23688).

Enenkel, R. F., B. G. Fitch, R. S. Germain, F. G. Gustavson, A. Martin, M. Mendell, J. W. Pitera, M. C. Pitman, A. Rayshubskiy, F. Suits, W. C. Swope and T. J. C. Ward (2005). "Custom math functions for molecular dynamics." IBM Journal of Research and Development 49(2/3): 465-74.

Almasi, G., G. Bhanot, D. Chen, M. Eleftheriou, B. Fitch, A. Gara, R. Germain, J. Gunnels, M. Gupta, P. Heidelberg, M. Pitman, A. Rayshubskiy, J. Sexton, F. Suits, P. Vranas, B. Walkup, C. Ward, Y. Zhestkov, A. Curioni, W. Andreoni, C. Archer, J. Moreira, R. Loft, H. Tufo, T. Voran and K. Riley (2005). "Early Experience with Scientific Applications on the Blue Gene/L Supercomputer." Lecture Notes in Computer Science, Volume 3648, Aug 2005, Pages 560 - 570 3648: 560-70.

Suits, F. (2004). "Astronomical Lengths with Simple Instruments." Sky and Telescope: 93-4.

Swope, W. C., J. W. Pitera and F. Suits (2004). "Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory." J. Phys. Chem. B 108: 6571-6581.

Swope, W. C., J. W. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. G. Fitch, R. S. Germain, A. Rayshubski, T. J. C. Ward, Y. Zhestkov and R. Zhou (2004). "Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a Beta-Hairpin Peptide." J. Phys. Chem. B 108: 6582-6594.

Pitman, M. C., F. Suits, A. D. Mackerell, Jr. and S. E. Feller (2004). "Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol." Biochemistry 43(49): 15318-28.

Fitch, B. G., R. S. Germain, M. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Sham, F. Suits, W. Swope, T. J. C. Ward, Y. Zhestkov and R. Zhou (2003). "Blue Matter, an application framework for molecular simulation on Blue Gene." Journal of Parallel and Distributed Computing vol.63, no.7-8: 759-773.

Sham, Y. Y., R. H. Zhou, F. Suits and R. Germain (2002). "Effect of ion binding on the conformational dynamics of calmodulin." Abstracts of Papers of the American Chemical Society 224: U509-U509.

Gresh, D., F. Suits and Y. Sham (2001). Case Study: An Environment for Understanding Protein Simulations Using Game Graphics. IEEE Visualization 2001, San Diego, CA.

Allen, F., G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, C. Cascaval, J. Castanos, P. Coteus, P. Crumley, A. Curioni, M. Denneau, W. Donath, M. Eleftheriou, B. Fitch, B. Fleischer, C. J. Georgiou, R. Germain, M. Giampapa, D. Gresh, M. Gupta, R. Haring, H. Ho, P. Hochschild, S. Hummel, T. Jonas, D. Lieber, G. Martyna, K. Maturu, J. Moreira, D. Newns, M. Newton, R. Philhower, T. Picunko, J. Pitera, M. Pitman, R. Rand, A. Royyuru, V. Salapura, A. Sanomiya, R. Shah, Y. Sham, S. Singh, M. Snir, F. Suits, R. Swetz, W. C. Swope, N. Vishnumurthy, T. J. C. Ward, H. Warren and R. Zhou (2001). "Blue Gene: a vision for protein science using a petaflop supercomputer." IBM Systems Journal vol.40, no.2: 310-327.

Trouilloud, P. L., F. Suits, C. V. Jahnes, M. A. Russak, E. J. Spada and J. W. Chang (1994). "Magnetoresistive Characterization of Thin-Film Structures by a Gradient-Field Method." Journal of Applied Physics 75(10): 5923-5923.

Suits, F. (1992). "Poincare Sphere Interpretation of Kerr-Effect Measurements Using a Photoelastic Modulator." Ieee Transactions on Magnetics 28(5): 2976-2978.

Suits, F. (1990). "Bilayer Permalloy-Films Grown in Orthogonal Applied Fields." Ieee Transactions on Magnetics 26(5): 2353-2355.

Hwangbo, C. K., L. J. Lingg, J. P. Lehan, H. A. Macleod and F. Suits (1989). "Reactive Ion Assisted Deposition of Aluminum Oxynitride Thin-Films." Applied Optics 28(14): 2779-2784.

Argyle, B. E., B. Petek, M. E. Re, F. Suits and D. A. Herman (1988). "Bloch Line Influence on Wall Motion Response in Thin-Film Heads." Journal of Applied Physics 64(11): 6595-6597.

Mizrahi, V., F. Suits, J. E. Sipe, U. J. Gibson and G. I. Stegeman (1987). "New probe of thin-film microstructure." Applied Physics Letters vol.51, no.6: 427-429.

Khare, B. N., C. Sagan, W. R. Thompson, E. T. Arakawa, F. Suits, T. A. Callcott, M. W. Williams, S. Shrader, H. Ogino, T. O. Willingham and B. Nagy (1984). "The organic aerosols of Titan." Adv Space Res 4(12): 59-68.

Khare, B. N., C. Sagan, E. T. Arakawa, F. Suits, T. A. Callcott and M. W. Williams (1984). "Optical constants of organic tholins produced in a simulated Titanian Atmosphere: from soft X-ray to microwave frequencies." Icarus vol.60, no.1: 127-137.

Last updated 14 Aug 2008