Gustavo A Stolovitzky

Manager, Functional Genomics and Systems Biology

IBM Computational Biology Center
IBM T.J. Watson Research Center

Research lab: Watson Research Center (Yorktown)

Current Position:

Manager, IBM Functional Genomics and Systems Biology Group
IBM Computational Biology Center, IBM TJ Watson Research Center

Contact Information:

(914) 945-1292
(914) 945-4217 (fax)
e-mail: gustavo@us.ibm.com

Education:

B.A., M. Sc. (with Honors), University of Buenos Aires, Argentina, Physics, 1987
M.Phil, Ph.D. (with Honors), Yale University, New Haven, Mechanical Engineering, 1994
Post Doctoral Fellowship, The Rockefeller University, New York, Biophysics and Genomics, 1994-1997
Post Doctoral Fellowship, NEC Research Institute, Princeton, Computational Biology, 1997-1998

Work Experience:

The Rockefeller University, Postdoctoral Fellow; Magnasco Lab., 1994-1997
NEC Research Institute, Postdoctoral Research Associate; Lab.,1997-1998
IBM T.J. Watson Research Center, Manager, IBM Functional Genomics and Systems Biology Group, Feb 1998-present

Other Professional Activities:

Member of the American Physical Society.
Member of the American Association for the Advancement of Science.

Member of the New York Academy of Sciences.

Conference Organization

Co-organizer: DIMACS workshop on "Analysis of Gene Expression Array Data", October 25-27, 2001, Piscataway, NJ.
Co-organizer: Second Blue Gene Conference, "Workshop on Protein Science", March 15-16, 2002, Edinburgh.

Steering committe member: "Premiere Systems Biology in Drug Discovery Conference", Institute for International Research, 2003.

Session Chair: IEEE conference: Computer Society Bioinformatics Conference. Aug 11-14, 2003.

Program committee Member: IEEE conference: Computer Society Bioinformatics Conference, Aug 11-14, 2003
Co-organizer: Third Blue Gene Conference, "Computing for Biology", Brookhaven National Lab, July 31-Aug 1, 2003.
Session Chair: Third Blue Gene Conference, Brookhaven National Lab, July 31-Aug 1, 2003.
Session Moderator, Workshop on Information Processing in the Bio Organism (A systems Bio approach), Bethesda, Nov 4-5, 2003.

Program committee Member: IEEE conference: Computer Society Bioinformatics Conference, Aug, 2004.

Steering Committee Member: Systems Biology Discussion Group of the New York Academy of Sciences, 2004.

Honors and Awards:

Honors Diploma, M. Sc. in Physics, University of Buenos Aires, Argentina, (1987).

Initiation Fellowship for Doctoral Studies, CONICET (equivalent to NSF), Argentina (1988-1990).

Yale University Graduate Fellowship (1990-1994).

The Henry Prentiss Becton Prize, awarded by The Faculty of Engineering at Yale University for Excellence in Engineering and Applied Science (1995).

Joliot Invited Professor, at Laboratoire de Mecanique de Fluides, ESPCI, Paris, France (October-November 1996).

Visiting Scholar at the Physics Department of The Chinese University of Hong Kong (May 1997).

Guest Investigator at The Rockefeller University, (1997-1998)

Genes@Work project chosen as an" IBM Research Technology accomplishment", (2002).

Steering Committee Member: Systems Biology Discussion Group of the New York Academy of Sciences, (2004).

Elected Permanent Member of DIMACS (Center for Discrete Math and Computer Science), (2004).

Patents:

A. Floratos, I. Rigoutsos, G. Stolovitzky, "Tandem Repeat Detection Using Pattern Discovery", US Patent 6,446,011, September 3 2002. (USPTO)

A. Califano, G. Stolovitzky, Y. Tu, "Characterization of phenotypes by gene expression patterns and classification of samples based thereon", US Patent Application 20020042681, April 11 2002. (USPTO)

Publications:

J. Lepre, R. Mushlin, A. Kershenbaum, K. Basso, U. Klein, N.E. Kay, A. Califano and G. Stolovitzky, Function-centric mining of gene expression data: application to functional profiling distinctions between CLL subtypes, submitted (2005)

G. Alexe, G. Bhanot, A.J. Levine and G. Stolovitzky, Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories, submitted (2005).

J.J. Rice, A. Kershenbaum and G. Stolovitzky, Lasting impressions: Motifs in protein-protein maps may provide footprints of evolutionary events, submitted (2005).

K. Basso, A. Margolin, I. Nemenman, U. Klein, C. Wiggins, G. Stolovitzky, R. Dalla Favera, and A. Califano, Reverse engineering of regulatory networks in human B cells. submitted (2005).

A. Margolin, I. Nemenman, K. Basso, U. Klein, C. Wiggins, G. Stolovitzky, R. Dalla Favera, and A. Califano. ARACNE: An algorithm for reconstruction of genetic networks in a mammalian cellular context. arXiv: q-bio.MN/0410037, submitted (2005).

G. A. Held, G. Stolovitzky, Y. Tu, Global Gene Expression Assays: Quantitative Noise Analysis, submitted (2005).

A. Ma’ayan, S. L. Jenkins, S. Neves, A. Hasseldine, E. Grace, B. Dubin-Thaler, N. J. Eungdamrong, G. Weng, P. Ram, J. J. Rice, A. Kershenbaum, G. Stolovitzky, R. D. Blitzer and R. Iyengar, Emergence of regulatory patterns during propagation of signal induced connectivity in a mammalian neuronal cellular network, submitted (2005).

L. Ma, J. Wagner, J.J. Rice, W. Hu, A. Levine and G. Stolovitzky, A plausible model for the digital response of p53 to DNA damage, submitted (2005).

J.J. Rice, A. Kershenbaum and G. Stolovitzky. Analyzing and reconstructing gene regulatory networks. “Specialist review” to The Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Jorde, Little, Dunn and Subramaniam, eds. John Wiley & Sons, Ltd:Chichester, in press (2005).

G. Stolovitzky, A. Kundaje, G.A. Held, K. Duggar, C. Haudenschild, D. Zhou, T. Vasicek, K. Smith, A. Aderem and J. Roach, Statistical analysis of MPSS measurements: application to the study of LPS activated macrophage gene expression, Proc. Natl. Acad. Sci. USA in press, (2005).

G. Stolovitzky, Gene Selection Strategies in microarray expression data: applications to case-control studies, Book Chapter in "Complex Systems Science in BioMedicine", J.Y. Kresh and T. Deisboeck, editors. Kluwer, in press (2005) (online toc)

A. Margolin, I. Nemenman, C. Wiggins, G. Stolovitzky, and A. Califano, On the reconstruction of interaction networks with applications to transcriptional regulation. In G Chechik, C Leslie, G Ratsch, and K Tsuda, editors, NIPS'04 Computational Biology Workshop. arXiv: q-bio.MN/0410036. (2004). (pdf)

J.J. Rice, Y. Tu and G. Stolovitzky, Reconstructing synthetic biological networks using conditional correlation analysis, Bioinformatics, Oct 14; (2004). (Pubmed)

J. Hussan, K. Krishnamoorthy and G. Stolovitzky, Identifying Mechanisms Associated with Diseases Using Classification Techniques, WSEAS Transactions on Information Science and Applications, 1, 1, 118, July (2004). (pdf)

J.J. RIce and G. Stolovitzky, Making the most of it: Pathway reconstruction and integrative simulation using the data at hand, Biosilico 2(2):70-7 (2004).
Note: Biosilico is currently available with a free subscription but is not yet online. Please contact us if you need a copy of this article.

J. Lepre, J.J. Rice, Y. Tu, and G. Stolovitzky, Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data, Bioinformatics 20(7):1033-44 (2004). (Pubmed).

K. Basso, U. Klein, H. Niu, G. Stolovitzky, Y. Tu, A. Califano, G. Cattoretti, R. Dalla Favera, Tracking CD40 signaling during normal germinal center development, Blood 104(13):4088-96 (2004). (Pubmed)

N. Shah, J. Lepre, Y. Tu, G. Stolovitzky, Can we identify cellular pathways implicated in cancer using gene expression data?, Proceedings of the 2nd IEEE Computational Systems Bioinformatics Conference, pp. 94-103, (2003). (pdf)

D.F. Jelinek, R.C. Tschumper, G. Stolovitzky, S.J. Iturria, Y. Tu, J. Lepre, N. Shah, and N.E. Kay, Identification of a global Gene Expression Signature of B-Chronic-Lymphocytic Leukemia, Molecular Cancer Research, 1 (5) :346-61 (2003). (full text)

A.H. Liu, X. Zhang, G. Stolovitzky, A. Califano and S.J. Firestein, Motif-based construction of a functional map for mammalian olfactory receptors, Genomics, 81(5):443-56 (2003).

K. Basso, U. Klein, H. Niu, G. Stolovitzky, Y. Tu, A. Califano, G. Cattoretti, R. Dalla Favera, Tracking CD40 Signaling during Normal Germinal Center Development by Gene Expression Profiling, Ann. NY Acad. Sci. 987:288-290 (2003).

U. Klein, Y. Tu, G. Stolovitzky, J.L. Keller, J. Haddad Jr., V. Miljkovic, G. Cattoretti, A. Califano, R. Dalla Favera, Gene Expression Dynamics during Germinal Center Transit in B Cells, Ann. NY Acad. Sci. 987:166-172 (2003).

U. Klein, Y. Tu, G. Stolovitzky, J.L. Keller, J. Haddad Jr., V. Miljkovic, G. Cattoretti, A. Califano, and R. Dalla Favera, Transcriptional analysis of the germinal-center reaction, Proc. Nat. Acad. Sci. USA, 100(5):2639-44, (2003). (full text)

G. Stolovitzky, Gene selection in microarray data: the elephant, the blind men and our algorithms. Current Opinion in Structural Biology, 13:370–376 (2003). (Pubmed)

R. Kuppers, U. Klein, I. Schwering, V. Distler, A. Brauninger, G. Cattoretti, Y. Tu, G. Stolovitzky, A. Califano, M.L. Hansmann, R. Dalla Favera, Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling. J Clin Invest. 111(4):529-37 (2003). (Pubmed)

J.J. Rice, G. Stolovitzky, Y. Tu, and P.P. de Tombe, Ising Model of cardiac thin filament activation with nearest neighbor interactions, Biophys. Journal, 84(2), 897-909, (2003). (Pubmed)

S.L. Pomeroy, P. Tamayo, M. Gaasenbeek, L.M. Sturla, M. Angelo, M.E. McLaughlin, J.Y. Kim, L.C. Goumnerova, P.M. Black, C. Lau, J.C. Allen, D. Zagzag, J.M. Olson, T. Curran, C. Wetmore, J.A. Biegel, T. Poggio, S. Mukherjee, R. Rifkin, A. Califano, G. Stolovitzky, D.N. Louis, J.P. Mesirov, E.S. Lander, T.R. Golub, Prediction of central nervous system embryonal tumour outcome based on gene expression, Nature, Jan 24;415(6870):436-42 (2002). (Pubmed)

Y. Tu, G. Stolovitzky and U. Klein, Quantitative noise analysis for gene expression microarray experiments, Proc. Natl. Acad. Sci. USA 99, 14031-6 (2002). (full text)

A. Mateos, J. Dopazo, R. Jansen, Y. Tu, M. Gerstein and G. Stolovitzky, Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons, Genome Research 12, 1703-15 (2002). (Pubmed)

U. Klein, Y. Tu, G. Stolovitzky, M. Mattioli, G. Cattoretti, H. Husson, A. Freedman, G. Inghirami, L. Cro, L. Baldini, A. Neri, A. Califano and R. Dalla-Favera, Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells, J Exp Med. Dec 3;194(11):1625-38 (2001). (Pubmed)

G. Stolovitzky and B.J. Berne, Catalytic Tempering: A Method for Sampling Rough Energy Landscapes by Monte Carlo, Proc. Natl. Acad. Sci. USA. 97 (21): 11164-9 (2000). (pdf)

R. Hart, A.K.Royyuru, G.Stolovitzky and A. Califano, Systematic and Fully Automated Discovery of Patterns in PROSITE Families , Proccedings 4th Annual ACM International Conference on Computational Molecular Biology (RECOMB 2000), (2000). In extended form in: Journal of Computational Biology, 7(3-4) : 585-600 (2000). (pdf)

A. Califano, G. Stolovitzky and Y. Tu, Analysis of Gene Expression Microarrays for Phenotype Classification , Proceedings of the 8th Annual Intelligent Systems in Molecular Biology (ISMB) 2000; 8:75-85 (2000). (pdf)

A. Floratos, I. Rigoutsos, L. Parida, G. Stolovitzky and Y. Gao, Sequence Homology Detection Through Large Scale Pattern Discovery , in Proccedings 3rd Annual ACM International Conference on Computational Molecular Biology (RECOMB 99), (1999).

G. Stolovitzky, Y. Gao, A. Floratos and I. Rigoutsos, Tandem Repeat Detection using Pattern Discovery, with Applications to the Identification of Yeast Satellites , IBM Research Report, RC21508 (1999). (pdf). See also: patent issued. (USPTO)

G. Stolovitzky and E.S.C. Ching, Characterization of Stationary Distributions Using Conditional Expectations , Physics Letters A, 255 11-16, (1999).

N. Rudin, K. Inman, G. Stolovitzky and I. Rigoutsos, DNA Based Identification , Book Chapter in: Biometrics, Personal Identification in Networked Society , A. Jain, R. Bolle and S. Pankanti eds, Kluwer Acad. Publishers, Boston (1999).

G. Stolovitzky and A. Califano, Pattern Relevance in Biological Datasets (abstract only) , Microbial and Comparative Genomics, C-31 (1998), also IBM Research Report. (pdf)

W. Li, G. Stolovitzky, P. Bernaola-Galvan and J.L. Oliver, Compositional Heterogeneity Within, and Uniformity Between, DNA Sequences of Yeast Chromosomes. Genome Research, 8, 916-928, (1998).

G.V. Shivashankar, G. Stolovitzky and A. Libchaber, Backscattering from a Tethered Bead as a Probe of DNA Flexibility , Applied Physics Letters, 73, 291-293, (1998).

M.O.Magnasco and G. Stolovitzky, Feynman s Ratchet and Pawl, Journal of Statistical Physics 93, 615-632, (1998).

E.S.C. Ching, C.S. Pang and G. Stolovitzky, Effects of a Large Scale Mean Circulating Flow on Passive Scalar Statistics in a Model of Random Advection, Physical Review E, 58, 1948-1954, (1998).

G. Stolovitzky, Nonisothermal Inertial Brownian motion , Physics Letters A, 241, 240-256, (1998).

G. Stolovitzky, C. Meneveau and K.R. Sreenivasan, Comment on "Isotropic Turbulence: Important differences between True Dissipation Rate and Its One-Dimensional Surrogate", Physical Review Letters 80, 3883 (1998).

G. Stolovitzky, J.L. Aider and J.E. Wesfreid, Conditional statistics and coherent structures in inhomogeneous turbulent mixing , Physical Review Letters 23, 78, (1997).

D. Brunner, S. Fairhurst, G. Stolovitzky and J. Gibbon, Mnemonics for variability: Remembering food delay , J. Exp. Psych.: Animal Behavior Processes, 23 1, 68-83 (1997).

G. Stolovitzky and G. Cecchi, Efficiency of DNA replication in the Polymarase Chain Reaction , Proc. Natl. Acad. Sci. USA, 93, 12947-12952, (1996). (full text)

M. Nelkin and G. Stolovitzky, Limitations of random multipliers in describing turbulent energy dissipation Physical Review E, 54, 5100-5106 (1996).

K. R. Sreenivasan and G. Stolovitzky, Statistical dependence of inertial range properties on the large scale in high-Reynolds-number shear flows, Physical Review Letters, 77, 2218-2221, (1996).

G. Stolovitzky, T. Kapper and L. Sirovich, A simple model for chaotic advection and scattering, Chaos, 5, 671-686 (1995).

G. Stolovitzky and K. R. Sreenivasan, Intermittency, the second order structure function, and the turbulent energy dissipation rate, Physical Review E, 52, 3242-3244, (1995).

G. Stolovitzky, K. R. Sreenivasan, Refined similarity hypotheses for passive scalars mixed by turbulence, Journal of Fluid Mechanics, 297, 275-291 (1995).

L. Faucheux, G. Stolovitzky and A. Libchaber, Periodic forcing of a Brownian particle, Physical Review E, 51, 5239-5250 (1995).

K. R. Sreenivasan and G. Stolovitzky, Turbulent cascades, Journal of Statistical Physics, 78, Nos 1/2, 311 (1995).

A. Juneja, D. P. Lathrop, K. R. Sreenivasan and G. Stolovitzky, Synthetic turbulence , Physical Review E, 49, 5179-5194 (1994).

G. Stolovitzky and K. R. Sreenivasan, Kolmogorov s refined similarity hypotheses for turbulence and general stochastic processes , Reviews of Modern Physics, 66, 229 (1994).

K. R. Sreenivasan and G. Stolovitzky, Multiplicative models for turbulent energy dissipation, Acta Mechanica, Suppl., 4, 113 (1994).

G. Stolovitzky and K. R. Sreenivasan, Independent velocity increments and Kolmogorov s refined similarity hypotheses , Procceedings of the 2nd ONR/NUWC technical conference: Nonlinear dynamics (chaos) and full spectrum processing, AIP Conference Proceedings 296, (R. Katz, ed), 97 (1993).

G. Stolovitzky, K. R. Sreenivasan and A. Juneja, Scaling functions and scaling exponents in turbulence, Physical Review E, 48, R3217 (1993).

G. Stolovitzky and K. R. Sreenivasan, Scaling of structure functions, Physical Review E, 48, R33 (1993).

G. Stolovitzky, P. Kailasnath, and K. R. Sreenivasan, Kolmogorov's refined similarity hypotheses, Physical Review Letters, 69, 1178 (1992).

P. Kailasnath, K. R. Sreenivasan and G. Stolovitzky, Probability density of velocity increments in turbulent flows, Physical Review Letters, 68, 2766 (1992).

G. Stolovitzky and J. Hernando, Intermittency, ergodicity and spectral analysis in classical Hamiltonian dynamics , Physical Review A, 43, 2774 (1991).

G. Stolovitzky and J. Hernando, Attractive and repulsive interactions in a two dimensional billiardlike system: The Lennard-Jones stadium , Physical Review A, 41, 6716 (1990).

G. Stolovitzky and J. Hernando, A study on the resonant structure of integrable and near-integrable two dimensional systems, Physical Review A, 41, 3026 (1990).

J. Talpe, G. Stolovitzky and V. Bekeris, Cryogenic thermometry and level detection with common diodes, Cryogenics, 27, 693 (1987).

] Attached files: JPG007.jpg, Gus_11_small.JPG Last updated 21 May 2007