Frank Suits  Frank Suits photo       

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Predictive Resource Optimization
Thomas J. Watson Research Center, Yorktown Heights, NY USA

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More information:  Computational Biology Center


2014

Parallelisation study of a three-dimensional environmental flow model
Fearghal O'donncha, Emanuele Ragnoli, Frank Suits
Computers \& Geosciences64, 96--103, Elsevier, 2014

Queries of MALDI-MSI Global Datasets Identifying Ion Mass Signatures Associated With Tissue Compartments
Fehniger, T. E., Suits, F., Vegvari, A., Horvatovich, P., Foster, M., Marko-Varga G.
PROTEOMICS, n/a-n/a, 2014


2013

Correlation Queries for Mass Spectrometry Imaging
Suits, F., Fehniger, T. E., Vegari, A., Marko-Varga, G., Horvatovich, P.
Analytical Chemistry 85(9), 4398-4404, 2013

A 3D Optimal Interpolation Assimilation Scheme of HF Radar Current Data into a Numerical Ocean Model
Emanuele Ragnoli, Sergiy Zhuk, Fearghal O'Donncha, Frank Suits, Michael Hartnett
EGU General Assembly Conference Abstracts, pp. 7267, 2013

CHAPTER 7 Bioinformatics and Statistics: LC-MS(/MS) Data Preprocessing for Biomarker Discovery
Horvatovich, P., Suits, F., Hoekman, B., Bischoff, R.
Comprehensive Biomarker Discovery and Validation for Clinical Application, pp. 199-225, The Royal Society of Chemistry, 2013

Uncertainty analysis of numerical model simulations and HFR measurements during high energy events
Fearghal O'Donncha, Emanuele Ragnoli, Frank Suits, Teresa Updyke, Hugh Roarty
EGU General Assembly Conference Abstracts, pp. 7665, 2013

A critical assessment of feature selection methods for biomarker discovery in clinical proteomics
C. Christin, H.C.J. Hoefsloot, A.K. Smilde, B. Hoekman, F. Suits, R. Bischoff, P. Horvatovich
Molecular & Cellular Proteomics 12(1), 263-276, ASBMB, 2013


2012

An optimal interpolation scheme for assimilation of HF radar current data into a numerical ocean model
Emanuele Ragnoli, Sergiy Zhuk, Fearghal O'Donncha, Frank Suits, Michael Hartnett
Oceans, 2012, pp. 1--5

Surface flow dynamics within an exposed wind-driven bay: Combined HF radar observations and model simulations
Fearghal O Donncha, Emanuele Ragnoli, Sergiy Zhuk, Frank Suits, Michael Hartnett
Oceans, 2012, pp. 1--8

Profiling and identification of cerebrospinal fluid proteins in a rat EAE model of multiple sclerosis
T. Rosenling, M.P. Stoop, A. Attali, H. Aken, E. Suidgeest, C. Christin, C. Stingl, F. Suits, P. Horvatovich, R.Q. Hintzen, others
Journal of Proteome Research 11(4), 2048--2060, ACS Publications, 2012

msCompare: A Framework for Quantitative Analysis of Label-free LC-MS Data for Comparative Candidate Biomarker Studies
B. Hoekman, R. Breitling, F. Suits, R. Bischoff, P. Horvatovich
Molecular \& Cellular Proteomics 11(6), ASBMB, 2012


2011

Threshold-Avoiding Proteomics Pipeline
F. Suits, B. Hoekman, T. Rosenling, R. Bischoff, P. Horvatovich
Analytical chemistry 83(20), 7786--7794, ACS Publications, 2011

A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data
I. Ahmad, F. Suits, B. Hoekman, M.A. Swertz, H. Byelas, M. Dijkstra, R. Hooft, D. Katsubo, B. van Breukelen, R. Bischoff, others
Bioinformatics 27(8), 1176--1178, Oxford Univ Press, 2011

The impact of delayed storage on the measured proteome and metabolome of human cerebrospinal fluid
T. Rosenling, M.P. Stoop, A. Smolinska, B. Muilwijk, L. Coulier, S. Shi, A. Dane, C. Christin, F. Suits, P.L. Horvatovich, others
Clinical chemistry 57(12), 1703--1711, Am Assoc Clin Chem, 2011


2010

Time alignment algorithms based on selected mass traces for complex LC-MS data
C Christin, H C Hoefsloot, A K Smilde, F Suits, R Bischoff, P L Horvatovich
J Proteome Res 9(3), 1483-95, 2010
Abstract   Christin, Christin Hoefsloot, Huub C J Smilde, Age K Suits, Frank Bischoff, Rainer Horvatovich, Peter L Research Support, Non-U.S. Gov't United States Journal of proteome research J Proteome Res. 2010 Mar 5;9(3):1483-95.


2009

Multiple Alignment of LC-MS Runs by Solving a Sparse System of Linear Equations
P Du, F Suits
Patent pp. YOR820081036, 2009

The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF)
T Rosenling, C L Slim, C Christin, L Coulier, S Shi, M P Stoop, J Bosman, F Suits, P L Horvatovich, N Stockhofe-Zurwieden, R Vreeken, T Hankemeier, A J Gool van, T M Luider, R Bischoff
J Proteome Res 8(12), 5511-22, 2009
Abstract   Rosenling, Therese Slim, Christiaan L Christin, Christin Coulier, Leon Shi, Shanna Stoop, Marcel P Bosman, Jan Suits, Frank Horvatovich, Peter L Stockhofe-Zurwieden, Norbert Vreeken, Rob Hankemeier, Thomas van Gool, Alain J Luider, Theo M Bischoff, Rainer

Precision Peak Matching in Liquid Chromatography Mass Spectrometry
P Du, F Suits
Patent pp. YOR9-2009-0122


2008

A noise model for mass spectrometry based proteomics
P Du, G Stolovitzky, P Horvatovich, R Bischoff, J Lim, F Suits
Bioinformatics 24(8), 1070-7, Oxford Univ Press, 2008
Abstract   Du, Peicheng Stolovitzky, Gustavo Horvatovich, Peter Bischoff, Rainer Lim, Jihyeon Suits, Frank Research Support, Non-U.S. Gov't England Bioinformatics (Oxford, England) Bioinformatics. 2008 Apr 15;24(8):1070-7. Epub 2008 Mar 18.

Optimized time alignment algorithm for LC-MS data: correlation optimized warping using component detection algorithm-selected mass chromatograms
C Christin, A K Smilde, H C Hoefsloot, F Suits, R Bischoff, P L Horvatovich
Anal Chem 80(18), 7012-21, 2008
Abstract   Christin, Christin Smilde, Age K Hoefsloot, Huub C J Suits, Frank Bischoff, Rainer Horvatovich, Peter L Research Support, Non-U.S. Gov't United States Analytical chemistry Anal Chem. 2008 Sep 15;80(18):7012-21. Epub 2008 Aug 21.

Two-dimensional method for time aligning liquid chromatography-mass spectrometry data
F Suits, J Lepre, P Du, R Bischoff, P Horvatovich
Anal Chem 80(9), 3095-104, 2008
Abstract   Suits, Frank Lepre, Jorge Du, Peicheng Bischoff, Rainer Horvatovich, Peter Research Support, Non-U.S. Gov't United States Analytical chemistry Anal Chem. 2008 May 1;80(9):3095-104. Epub 2008 Apr 9.


Further aspects of the roaming mechanism in formaldehyde dissociation
SA Lahankar, V Goncharov, F Suits, JD Farnum, JM Bowman, AG Suits
Chemical Physics 347(1-3), 288-299, 2008

Optimized Time Alignment Algorithm for LC- MS Data: Correlation Optimized Warping Using Component Detection Algorithm-Selected Mass Chromatograms
C. Christin, A.K. Smilde, H.C.J. Hoefsloot, F. Suits, R. Bischoff, P.L. Horvatovich
Analytical chemistry 80(18), 7012--7021, ACS Publications, 2008


2007

Chip-LC-MS for label-free profiling of human serum
P. Horvatovich, N.I. Govorukhina, T.H. Reijmers, A.G.J. van der Zee, F. Suits, R. Bischoff
Electrophoresis 28(23), 4493--4505, Wiley Online Library, 2007
Horvatovich, Peter Govorukhina, Natalia I Reijmers, Theo H van der Zee, Ate G J Suits, Frank Bischoff, Rainer Comparative Study Evaluation Studies Research Support, Non-U.S. Gov't Germany Electrophoresis Electrophoresis. 2007 Dec;28(23):4493-505.


2006

Second International Workshop on Bioinformatics Research and Applications (IWBRA06)-Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L
B.G. Fitch, A. Rayshubskiy, M. Eleftheriou, T.J.C. Ward, M. Giampapa, Y. Zhestkov, M.C. Pitman, F. Suits, A. Grossfield, J. Pitera, others
Lecture Notes in Computer Science3992, 846--854, Berlin: Springer-Verlag, 1973-, 2006

Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins
R. Zhou, A. Royyuru, P. Athma, F. Suits
Int J Bioinform Res Appl 2(2), 161--176, 2006

Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L
B Fitch, A Rayshubskiy, M Eleftheriou, TJ Ward, M Giampapa, Y Zhestkov, M Pitman, F Suits, A Grossfield, J Pitera
Computational Science–ICCS 20063992, 846-854, Springer

The roaming atom pathway in formaldehyde decomposition
S A Lahankar, S D Chambreau, D Townsend, F Suits, J Farnum, X Zhang, J M Bowman, A G Suits
J Chem Phys 125(4), 44303, 2006
Abstract   Lahankar, Sridhar A Chambreau, Steven D Townsend, Dave Suits, Frank Farnum, John Zhang, Xiubin Bowman, Joel M Suits, Arthur G Research Support, U.S. Gov't, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2006 Jul 28;125(4):44303.


2005

Early performance data on the blue matter molecular simulation framework by rs germain
Y. Zhestkov, M. Eleftheriou, A. Rayshubskiy, F. Suits, TJC Ward, BG Fitch
IBM Journal of Research and Development 49(2/3), 2005

Molecular dynamics investigation of dark-adapted rhodopsin in an explicit 2: 2: 1 SDPE/SDPC/cholesterol environment: Membrane structure and dynamics
MC Pitman, F. Suits, A. Grossfield, SE Feller
Biophys. J 88(1), 579A, 2005

Overview of molecular dynamics techniques and early scientific results from the Blue Gene project
F. Suits, MC Pitman, JW Pitera, W.C. Swope, R.S. Germain
IBM journal of research and development 49(2.3), 475--487, IBM, 2005

Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
F. Suits, M. Eleftheriou, M. Giampapa, A. Rayshubskiy, B. Fitch, MC Pitman, TJC Ward, RS Germain
Hardware/Software Codesign and System Synthesis, 2005. CODES+ ISSS'05. Third IEEE/ACM/IFIP International Conference on, pp. 207--212

Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers
F Suits, M C Pitman, S E Feller
J Chem Phys 122(24), 244714, 2005
Abstract   Suits, Frank Pitman, Michael C Feller, Scott E Research Support, U.S. Gov't, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2005 Jun 22;122(24):244714.

Overview of molecular dynamics techniques and early scientific results from the Blue Gene project
F Suits, MC Pitman, JW Pitera, WC Swope, RS Germain
IBM Journal of Research and Development 49(2), 475-487, 2005

Early Experience with Scientific Applications on the Blue Gene/L Supercomputer
G. Almasi, G. Bhanot, D. Chen, M. Eleftheriou, B. Fitch, A. Gara, R. Germain, J. Gunnels, M. Gupta, P. Heidelberg, M. Pitman, J. Sexton, F. Suits, P. Vranas, B. Walkup, Y. Zhestkov, A. Curioni, W. Andreoni, et al.
Euro-Par 2005 Parallel Processing, pp. 560-570
CiteSeerX - Scientific Literature Digital Library and Search Engine [http://citeseerx.ist.psu.edu/oai2] (United States) ER

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers
M C Pitman, F Suits, K Gawrisch, S E Feller
J Chem Phys 122(24), 244715, 2005
Abstract   Pitman, Michael C Suits, Frank Gawrisch, Klaus Feller, Scott E Comparative Study Research Support, U.S. Gov't, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2005 Jun 22;122(24):244715.

Early performance data on the Blue Matter molecular simulation framework
RS Germain, Y Zhestkov, M Eleftheriou, A Rayshubskiy, F Suits, TJC Ward, BG Fitch
IBM Journal of Research and Development 49(2), 447-455, Citeseer, 2005

Blue Matter on Blue Gene/L: Massively Parallel Computation for Biomolecular Simulation
R S Germain, B G Fitch, A Rayshubski, M Eleftheriou, M C Pitman, F Suits, M Giampapa, T J C Ward
Proceedings of the 3rd IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis, pp. 207-212, ACM Press, 2005

Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment
M C Pitman, A Grossfield, F Suits, S E Feller
J Am Chem Soc 127(13), 4576-7, [Washington, DC: American Chemical Society], 1879-, 2005
Abstract   Pitman, Michael C Grossfield, Alan Suits, Frank Feller, Scott E Research Support, U.S. Gov't, Non-P.H.S. United States Journal of the American Chemical Society J Am Chem Soc. 2005 Apr 6;127(13):4576-7.

Custom Math Functions for Molecular Dynamics
R F Enenkel, B G Fitch, R S Germain, FG Gustavson, A Martin, M Mendell, J Pitera, M C Pitman, A Rayshubski, F Suits, W Swope, T J C Ward
IBM Journal of Research and Development 49(2/3), 465-74, IBM Corp., 2005


2004

Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a [beta]-Hairpin Peptide†
WC Swope, JW Pitera, F Suits, M Pitman, M Eleftheriou, BG Fitch, RS Germain, A Rayshubski, TJC Ward, Y Zhestkov
J. Phys. Chem. B 108(21), 6582-6594, ACS Publications, 2004

Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory
WC Swope, JW Pitera, F Suits
J. Phys. Chem. B 108(21), 6571-6581, 2004

Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol
M C Pitman, F Suits, Jr. Mackerell A. D., S E Feller
Biochemistry 43(49), 15318-28, ACS Publications, 2004
Abstract   Pitman, Michael C Suits, Frank Mackerell, Alexander D Jr Feller, Scott E GM515001/GM/NIGMS NIH HHS/United States MCB-0091508/CB/NCI NIH HHS/United States Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. United States Biochemis

Astronomical Lengths with Simple Instruments
F Suits
Sky and Telescope 108(3), 93, 2004

Describing protein folding kinetics by molecular dynamics simulations. 2. example applications to alanine dipeptide and a $\beta$-hairpin peptide
W.C. Swope, J.W. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B.G. Fitch, R.S. Germain, A. Rayshubski, T.J.C. Ward, Y. Zhestkov, others
The Journal of Physical Chemistry B 108(21), 6582--6594, ACS Publications, 2004


2003

Dynamic View-Dependent Texture Mapping
F Suits, J T Klosowski, W P Horn, G Lecina
Patent, 2003
US Patent 6,525,731

Apparatus, System, and Method for Simplifying Annotations on a Geometric Surface
F Suits, J T Klosowski, W P Horn, G Lecina
Patent, 2003
US6518964

System and Method for the Coordinated Simplification of Surface and Wire-Frame Descriptions of a Geometric Model
W P Horn, J A Valuyeva, J T Klosowski, F Suits, G Lecina
Patent, 2003
US Patent 6,570,568

Blue Matter, an application framework for molecular simulation on Blue Gene
BG Fitch, RS Germain, M Mendell, J Pitera, M Pitman, A Rayshubskiy, Y Sham, F Suits, W Swope, TJC Ward
Journal of Parallel and Distributed Computing 63(7-8), 759-773, Elsevier, 2003

Apparatus, System, and Method for Draping Annotations on to a Geometric Surface
J T Klosowski, F Suits, W P Horn, G Lecina
Patent, 2003
US6978230


2002

Method and apparatus for delivering 3D graphics in a networked environment
P Borrel, S Hall, W P Horn, J T Klosowski, WL Luken, IM Martin, F Suits
Patent, 2002
US Patent 6,377,257

Method and apparatus for delivering 3D graphics in a networked environment using transparent video
P Borrel, S Hall, W P Horn, J T Klosowski, WL Luken, IM Martin, F Suits
Patent, 2002
US Patent 6,384,821

Effect of Ion Binding on the Conformational Dynamics of Calmodulin
Y Y Sham, R H Zhou, F Suits, R S Germain
Abstracts of Papers of the American Chemical Society224, U509-U509, 2002


2001

Blue Gene: a vision for protein science using a petaflop supercomputer
Frances Allen, G Almasi, Wanda Andreoni, D Beece, Bruce J. Berne, A Bright, Jose Brunheroto, Calin Cascaval, J Castanos, Paul Coteus
IBM Systems Journal 40(2), 310-327, IBM, 2001

Case study: an environment for understanding protein simulations using game graphics
D Gresh, F Suits, YY Sham
Proceedings of the conference on Visualization'01, pp. 445-448, 2001


2000

Simplification of surface annotations
F Suits, JT Klosowski, WP Horn, G Lecina
IEEE Visualization 2000, pp. 235-242, IEEE Computer Society Press


1994

Magnetoresistive characterization of thin-film structures by a gradient-field method
PL Trouilloud, F. Suits, CV Jahnes, MA Russak, EJ Spada, JW Chang
Journal of Applied Physics 75(10), 5923--5923, AIP, 1994

Magnetoresistive characterization of thin film structures by a gradient field method (abstract)
PL Trouilloud, F Suits, CV Jahnes, MA Russak, EJ Spada, JW Chang
Journal of Applied Physics75, 5923, 1994


1993

Gradient Field Method for the Magnetoresistive Characterization of Thin Film Structures
PL Trouilloud, F Suits, C Jahnes, M Russak
Magnetic Materials, Processes, and Devices, 75-86, 1993


1992

Poincare sphere interpretation of Kerr-effect measurements using a photoelastic modulator
F. Suits
Magnetics, IEEE Transactions on 28(5), 2976--2978, IEEE, 1992

Poincare sphere interpretation of Kerr-effect measurements using aphotoelastic modulator
F Suits
IEEE Transactions on Magnetics 28(5 Part 2), 2976-2978, 1992


1990

Bi-layer permalloy films with orthogonal easy-axes
F. Suits
Magnetics Conference, 1990. 1990 Digests of INTERMAG'90. International, pp. FC--FC

Bilayer Permalloy films grown in orthogonal applied fields
F Suits
IEEE Transactions on Magnetics 26(5), 2353-2355, 1990


1989

Reactive ion assisted deposition of aluminum oxynitride thin films
CK Hwangbo, LJ Lingg, JP Lehan, HA Macleod, F Suits
Appl. Opt28, 2779-2784, 1989


1988

Bloch line influence on wall motion response in thin-film heads
BE Argyle, B. Petek, ME Re, F. Suits, DA Herman
Journal of Applied Physics 63(8), 4033--4035, AIP, 1988

Bloch line influence on wall motion response in thin film heads
BE Argyle, B Petek, ME Re, F Suits, DA Herman
Journal of Applied Physics63, 4033, 1988


1987

Metal-dielectric composites studied by second harmonic generation (A)
V. Mizrahi, F. Suits, U.J. Gibson, C.T. Seaton, G.I. Stegeman, J.E. Sipe
J. Opt. Soc. Am. B, vol. 4, page P1364, 136, 1987

New probe of thin-film microstructure
V. Mizrahi, F. Suits, JE Sipe, UJ Gibson, GI Stegeman
Applied physics letters51, 427, 1987

New probe of thin film microstructure
V Mizrahi, F Suits, JE Sipe, UJ Gibson, GI Stegeman
Applied Physics Letters51, 427, 1987


1984

Optical constants of organic tholins produced in a simulated titanian atmosphere: from soft X-ray to microwave frequencies
BN Khare, C Sagan, ET Arakawa, F Suits, TA Callcott, MW Williams
Icarus 60(1), 127-137, 1984

The organic aerosols of Titan
B N Khare, C Sagan, W R Thompson, E T Arakawa, F Suits, T A Callcott, M W Williams, S Shrader, H Ogino, T O Willingham, B Nagy
Adv Space Res 4(12), 59-68, 1984
Abstract   Khare, B N Sagan, C Thompson, W R Arakawa, E T Suits, F Callcott, T A Williams, M W Shrader, S Ogino, H Willingham, T O Nagy, B DE-AC05-84-OR21400/DE/NIDCR NIH HHS/United States Research Support, U.S. Gov't, Non-P.H.S. England Advances in space research :


1983

Optical Constants of Titan Tholin Aerosols
BN Khare, C. Sagan, ET Arakawa, F. Suits, TA Callicott, MW Williams
Bulletin of the American Astronomical Society, pp. 842, 1983


Year Unknown


Evaluation of a biomarker discovery platform for low-molecular weight urinary compounds
R.F.J. Kemperman, P.L. Horvatovich, F. Suits, I.P. Kema, F.A.J. Muskiet, R. Bischoff
dissertations.ub.rug.nl, 0

COMPARATIVE ANALYSIS OF SERUM FROM CERVICAL CANCER PATIENTS AT DIFFERENT STAGES OF DISEASE
N. Govorukhina, P. Horvatovich, F. Suits, I. Sobczak-Elbourne, S. Smit, H.C.J. Hoefsloot, A.K. Smilde, A.G.J. van der Zee, R. Bischoff
eupa.org, 0