Gustavo A. Stolovitzky  Gustavo A. Stolovitzky photo       

contact information

Program Director, Translational Systems Biology and Nanobiotechnology
Thomas J. Watson Research Center, Yorktown Heights, NY USA
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2016

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease
Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, and others
Alzheimers Dement. 12(6), 645-53, 2016
Abstract

Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data
Guinney, Justin and Wang, Tao and Laajala, Teemu D and Winner, Kimberly Kanigel and Bare, J Christopher and Neto, Elias Chaibub and Khan, Suleiman A and Peddinti, Gopal and Airola, Antti and Pahikkala, Tapio and others
The Lancet Oncology, Elsevier, 2016
Abstract

Reverse-engineering human olfactory perception from chemical features of odor molecules
Keller, Andreas and Gerkin, Richard C and Guan, Yuanfang and Dhurandhar, Amit and Turu, Gabor and Szalai, Bence and Mainland, Joel D and Ihara, Yusuke and Yu, Chung Wen and Wolfinger, Russ and others
bioRxiv, 082495, Cold Spring Harbor Labs Journals, 2016
Abstract

Reducing overfitting in challenge-based competitions
Neto, Elias Chaibub and Hoff, Bruce R and Bare, Chris and Bot, Brian M and Yu, Thomas and Magravite, Lara and Trister, Andrew D and Norman, Thea and Meyer, Pablo and Saez-Rodrigues, Julio and others
arXiv preprint arXiv:1607.00091, 2016
Abstract

Crowdsourcing biomedical research: leveraging communities as innovation engines
Saez-Rodriguez, Julio and Costello, James C and Friend, Stephen H and Kellen, Michael R and Mangravite, Lara and Meyer, Pablo and Norman, Thea and Stolovitzky, Gustavo
Nature Reviews Genetics 17(8), 470--486, Nature Publishing Group, 2016
Abstract

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin
Patro, Rob and Norel, Raquel and Prill, Robert J and Saez-Rodriguez, Julio and Lorenz, Peter and Steinbeck, Felix and Ziems, Bjoern and Lu{v{s}}trek, Mitja and Barbarini, Nicola and Tiengo, Alessandra and others
BMC bioinformatics 17(1), 1, BioMed Central, 2016
Abstract

Nanoscale lateral displacement arrays for the separation of exosomes and colloids down to 20 nm
Wunsch, Benjamin H and Smith, Joshua T and Gifford, Stacey M and Wang, Chao and Brink, Markus and Bruce, Robert L and Austin, Robert H and Stolovitzky, Gustavo and Astier, Yann
Nature Nanotechnology, Nature Research, 2016
Abstract

Inferring causal molecular networks: empirical assessment through a community-based effort
Hill, Steven M and Heiser, Laura M and Cokelaer, Thomas and Unger, Michael and Nesser, Nicole K and Carlin, Daniel E and Zhang, Yang and Sokolov, Artem and Paull, Evan O and Wong, Chris K and others
Nature methods 13(4), 310--318, Nature Publishing Group, 2016
Abstract

A community-based collaboration to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer patients
Seyednasrollah, Fatemeh and Koestler, Devin C and Wang, Tao and Piccolo, Stephen R and Vega, Roberto and Greiner, Russ and Fuchs, Christiane and Gofer, Eyal and Kumar, Luke and Wolfinger, Russel D and others
bioRxiv, 087809, Cold Spring Harbor Labs Journals, 2016
Abstract

Voices of biotech.
Amit, Ido and Baker, David and Barker, Roger and Berger, Bonnie and Bertozzi, Carolyn and Bhatia, Sangeeta and Biffi, Alessandra and Demichelis, Francesca and Doudna, Jennifer and Dowdy, Steven F and others
Nature biotechnology 34(3), 270, 2016
Abstract

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
Sieberts, Solveig K and Zhu, Fan and Garc{'i}a-Garc{'i}a, Javier and Stahl, Eli and Pratap, Abhishek and Pandey, Gaurav and Pappas, Dimitrios and Aguilar, Daniel and Anton, Bernat and Bonet, Jaume and others
Nature communications7, Nature Research, 2016
Abstract

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis
Noren, David P and Long, Byron L and Norel, Raquel and Rrhissorrakrai, Kahn and Hess, Kenneth and Hu, Chenyue Wendy and Bisberg, Alex J and Schultz, Andre and Engquist, Erik and Liu, Li and others
PLoS Comput Biol 12(6), e1004890, Public Library of Science, 2016
Abstract


2015

DREAMTools: a Python package for scoring collaborative challenges
Cokelaer, Thomas and Bansal, Mukesh and Bare, Christopher and Bilal, Erhan and Bot, Brian M and Neto, Elias Chaibub and Eduati, Federica and de la Fuente, Alberto and G{"o}nen, Mehmet and Hill, Steven M and others
F1000Research4, Faculty of 1000 Ltd, 2015
Abstract

Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression
K{"u}ffner, Robert and Zach, Neta and Norel, Raquel and Hawe, Johann and Schoenfeld, David and Wang, Liuxia and Li, Guang and Fang, Lilly and Mackey, Lester and Hardiman, Orla and others
Nature biotechnology 33(1), 51--57, Nature Publishing Group, 2015
Abstract

DREAMTools: a Python package for scoring collaborative challenges [version 1; referees: awaiting peer review]
Cokelaer, Thomas and Bansal, Mukesh and Bare, Christopher and Bilal, Erhan and Bot, Brian M and Neto, Elias Chaibub and Eduati, Federica and G{"o}nen, Mehmet and Hill, Steven M and Hoff, Bruce and others
2015 - karrlab.org
Abstract

Noise-Driven Causal Inference in Biomolecular Networks
Prill, Robert J and Vogel, Robert and Cecchi, Guillermo A and Altan-Bonnet, Gr{'e}goire and Stolovitzky, Gustavo
PloS one 10(6), e0125777, Public Library of Science, 2015
Abstract

Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels
Wang, Chao and Bruce, Robert L and Duch, Elizabeth A and Patel, Jyotica V and Smith, Joshua T and Astier, Yann and Wunsch, Benjamin H and Meshram, Siddharth and Galan, Armand and Scerbo, Chris and others
ACS nano 9(2), 1206--1218, ACS Publications, 2015
Abstract

The Prostate Cancer DREAM Challenge: A community-wide effort to use open clinical trial data for the quantitative prediction of outcomes in metastatic prostate cancer
Abdallah, Kald and Hugh-Jones, Charles and Norman, Thea and Friend, Stephen and Stolovitzky, Gustavo
The oncologist 20(5), 459--460, AlphaMed Press, 2015

Summary of the DREAM8 parameter estimation challenge: toward parameter identification for whole-cell models
Karr, Jonathan R and Williams, Alex H and Zucker, Jeremy D and Raue, Andreas and Steiert, Bernhard and Timmer, Jens and Kreutz, Clemens and Wilkinson, Simon and Allgood, Brandon A and Bot, Brian M and others
PLoS Comput Biol 11(5), e1004096, Public Library of Science, 2015
Abstract


2014

The species translation challenge--A systems biology perspective on human and rat bronchial epithelial cells
Poussin, Carine and Mathis, Carole and Alexopoulos, Leonidas G and Messinis, Dimitris E and Dulize, R{'e}mi HJ and Belcastro, Vincenzo and Melas, Ioannis N and Sakellaropoulos, Theodore and Rhrissorrakrai, Kahn and Bilal, Erhan and others
Scientific Data1, 140009, Nature Publishing Group, 2014
Abstract

Global optimization of somatic variant identification in cancer genomes with a global community challenge
Boutros, Paul C and Ewing, Adam D and Ellrott, Kyle and Norman, Thea C and Dang, Kristen K and Hu, Yin and Kellen, Michael R and Suver, Christine and Bare, J Christopher and Stein, Lincoln D and others
Nature genetics 46(4), 318, NIH Public Access, 2014
Abstract

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach
Meyer, Pablo and Cokelaer, Thomas and Chandran, Deepak and Kim, Kyung Hyuk and Loh, Po-Ru and Tucker, George and Lipson, Mark and Berger, Bonnie and Kreutz, Clemens and Raue, Andreas and others
BMC systems biology 8(1), 1, BioMed Central, 2014
Abstract

Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria
Meyer, Pablo and Cecchi, Guillermo and Stolovitzky, Gustavo
BMC systems biology 8(1), 1, BioMed Central, 2014
Abstract

Toward better benchmarking: challenge-based methods assessment in cancer genomics
Boutros, Paul C and Margolin, Adam A and Stuart, Joshua M and Califano, Andrea and Stolovitzky, Gustavo
Genome biology 15(9), 1, BioMed Central, 2014
Abstract

A community computational challenge to predict the activity of pairs of compounds
Bansal, Mukesh and Yang, Jichen and Karan, Charles and Menden, Michael P and Costello, James C and Tang, Hao and Xiao, Guanghua and Li, Yajuan and Allen, Jeffrey and Zhong, Rui and others
Nature biotechnology 32(12), 1213--1222, Nature Publishing Group, 2014
Abstract

Controlling Motion of DNA in a Nanochannel with Transverse Alternating-Electric-Voltages
Luan, Binquan and Wang, Chao and Royyuru, Ajay and Stolovitzky, Gustavo
Biophysical Journal 106(2), 212a, Elsevier, 2014
Abstract

A community effort to assess and improve drug sensitivity prediction algorithms
Costello, James C and Heiser, Laura M and Georgii, Elisabeth and G{"o}nen, Mehmet and Menden, Michael P and Wang, Nicholas J and Bansal, Mukesh and Hintsanen, Petteri and Khan, Suleiman A and Mpindi, John-Patrick and others
Nature biotechnology 32(12), 1202--1212, Nature Publishing Group, 2014
Abstract

RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue
Califano, Andrea and Kellis, Manolis and Stolovitzky, Gustavo
Journal of Computational Biology 21(5), 371--372, Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA, 2014
Abstract

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge
Rhrissorrakrai, Kahn and Belcastro, Vincenzo and Bilal, Erhan and Norel, Raquel and Poussin, Carine and Mathis, Carole and Dulize, R{'e}mi HJ and Ivanov, Nikolai V and Alexopoulos, Leonidas and Rice, J Jeremy and others
Bioinformatics, btu611, Oxford Univ Press, 2014
Abstract

A crowd-sourcing approach for the construction of species-specific cell signaling networks
Bilal, Erhan and Sakellaropoulos, Theodore and Participants, Challenge and Melas, Ioannis N and Messinis, Dimitris E and Belcastro, Vincenzo and Rhrissorrakrai, Kahn and Meyer, Pablo and Norel, Raquel and Iskandar, Anita and others
Bioinformatics, btu659, Oxford Univ Press, 2014
Abstract

Fixed-gap tunnel junction for reading DNA nucleotides
Pang, Pei and Ashcroft, Brian Alan and Song, Weisi and Zhang, Peiming and Biswas, Sovan and Qing, Quan and Yang, Jialing and Nemanich, Robert J and Bai, Jingwei and Smith, Joshua T and others
ACS nano 8(12), 11994--12003, ACS Publications, 2014
Abstract

Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages
Luan, Binquan and Wang, Chao and Royyuru, Ajay and Stolovitzky, Gustavo
Nanotechnology 25(26), 265101, IOP Publishing, 2014
Abstract

Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales
Bai, Jingwei and Wang, Deqiang and Nam, Sung-wook and Peng, Hongbo and Bruce, Robert and Gignac, Lynn and Brink, Markus and Kratschmer, Ernst and Rossnagel, Stephen and Waggoner, Phil and others
Nanoscale 6(15), 8900--8906, Royal Society of Chemistry, 2014
Abstract


2013

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
Meyer, Pablo and Siwo, Geoffrey and Zeevi, Danny and Sharon, Eilon and Norel, Raquel and Segal, Eran and Stolovitzky, Gustavo and Rider, Andrew K and Tan, Asako and Pinapati, Richard S and others
Genome research 23(11), 1928--1937, Cold Spring Harbor Lab, 2013
Abstract

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue
Califano, Andrea and Kellis, Manolis and Stolovitzky, Gustavo
Journal of Computational Biology 20(5), 373--374, Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA, 2013
Abstract

Fabricatable nanopore sensors with an atomic thickness
Luan, Binquan and Bai, Jingwei and Stolovitzky, Gustavo
Applied Physics Letters 103(18), 183501, AIP Publishing, 2013
Abstract

Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge
Plenge, Robert M and Greenberg, Jeffrey D and Mangravite, Lara M and Derry, Jonathan MJ and Stahl, Eli A and Coenen, Marieke JH and Barton, Anne and Padyukov, Leonid and Klareskog, Lars and Gregersen, Peter K and others
Nature genetics 45(5), 468--469, Nature Publishing Group, 2013
Abstract

sbv IMPROVER Diagnostic Signature Challenge: Scoring strategies
Norel, Raquel and Bilal, Erhan and Conrad-Chemineau, Nathalie and Bonneau, Richard and de la Fuente, Alberto and Jurisica, Igor and Marbach, Daniel and Meyer, Pablo and Rice, J Jeremy and Tuller, Tamir and others
Systems Biomedicine 1(4), 208--216, Taylor & Francis, 2013
Abstract

sbv IMPROVER Diagnostic Signature Challenge: Preface to this special issue
Hoeng, Julia and Stolovitzky, Gustavo and Peitsch, Manuel C
Systems Biomedicine 1(4), 193--195, Taylor & Francis, 2013
Abstract

sbv IMPROVER diagnostic signature challenge: design and results
Rhrissorrakrai, Kahn and Rice, J Jeremy and Boue, Stephanie and Talikka, Marja and Bilal, Erhan and Martin, Florian and Meyer, Pablo and Norel, Raquel and Xiang, Yang and Stolovitzky, Gustavo and others
Systems Biomedicine 1(4), 196--207, Taylor & Francis, 2013
Abstract

An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation
Luan, Binquan and Stolovitzky, Gustavo
Nanotechnology 24(19), 195702, IOP Publishing, 2013
Abstract

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer
Margolin, Adam A and Bilal, Erhan and Huang, Erich and Norman, Thea C and Ottestad, Lars and Mecham, Brigham H and Sauerwine, Ben and Kellen, Michael R and Mangravite, Lara M and Furia, Matthew D and others
Science translational medicine 5(181), 181re1--181re1, American Association for the Advancement of Science, 2013
Abstract

Improving breast cancer survival analysis through competition-based multidimensional modeling
Bilal, Erhan and Dutkowski, Janusz and Guinney, Justin and Jang, In Sock and Logsdon, Benjamin A and Pandey, Gaurav and Sauerwine, Benjamin A and Shimoni, Yishai and Vollan, Hans Kristian Moen and Mecham, Brigham H and others
PLoS Comput Biol 9(5), e1003047, Public Library of Science, 2013
Abstract

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge
Tarca, Adi L and Lauria, Mario and Unger, Michael and Bilal, Erhan and Boue, Stephanie and Dey, Kushal Kumar and Hoeng, Julia and Koeppl, Heinz and Martin, Florian and Meyer, Pablo and others
Bioinformatics 29(22), 2892--2899, Oxford Univ Press, 2013
Abstract


2012

News FeATURe
Stolovitzky, Gustavo
Nature Biotechnology 30(4), 335, 2012
Abstract

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue
Califano, Andrea and Kellis, Manolis and Stolovitzky, Gustavo
Journal of Computational Biology 19(2), 101--101, Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA, 2012
Abstract

Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol
B. Luan, D. Wang, R. Zhou, S. Harrer, H. Peng, G. Stolovitzky
Nanotechnology 23(45), 455102, IOP Publishing, 2012

Wisdom of crowds for robust gene network inference
D. Marbach, J.C. Costello, R. Kuffner, N.M. Vega, R.J. Prill, D.M. Camacho, K.R. Allison, The DREAM5 Consortium, M. Kellis, J.J. Collins, G. Stolovitzky
Nature Methods, Nature Publishing Group, 2012

Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis
M. Rodriguez Martinez, A. Corradin, U. Klein, M.J. Alvarez, G.M. Toffolo, B. di Camillo, A. Califano, G.A. Stolovitzky
Proceedings of the National Academy of Sciences 109(7), 2672-2677, 2012

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification
P. Meyer, J. Hoeng, J. J. Rice, R. Norel, J. Sprengel, K. Stolle, T. Bonk, S. Corthesy, A. Royyuru, M. C. Peitsch, G. Stolovitzky
Bioinformatics 28(9), 1193--1201, 2012

Slowing and controlling the translocation of DNA in a solid-state nanopore
B. Luan, G Stolovitzky, G Martyna
Nanoscale 4(4), 1068-1077, The Royal Society of Chemistry, 2012


2011

Setting the standards for signal transduction research
Saez-Rodriguez, Julio and Alexopoulos, Leonidas G and Stolovitzky, Gustavo
Sci. Signal. 4(160), pe10--pe10, American Association for the Advancement of Science, 2011
Abstract

Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore
B. Luan, G. Stolovitzky, H. Peng, S. Harrer, P. Waggoner, S. Polonsky, S. Rossnagel, and G. Martyna
Biophysical Journal 100(3), 168, Elsevier, 2011

The self-assessment trap: can we all be better than average?
R. Norel, J.J. Rice, G. Stolovitzky
Molecular Systems Biology 7(1), Nature Publishing Group, 2011

Electrochemical Protection of Thin Film Electrodes in Solid State Nanopores
S. Harrer, P. S. Waggoner, B. Luan, A. Afzali-Ardakani, D. L. Goldfarb, H. Peng, G. Martyna, S. M. Rossnagel, G. A. Stolovitzky
Nanotechnology 22(27), 275304, IOP Publishing, 2011

Verification of systems biology research in the age of collaborative competition
P. Meyer, L. G. Alexopoulos, T. Bonk, A. Califano, C. R. Cho, A. de la Fuente, D. de Graaf, A. J. Hartemink, J. Hoeng, N. V. Ivanov, H. Koeppl, R. Linding, D. Marbach, R. Norel, M. C. Peitsch, J. J. Rice, A. Royyuru, F. Schacherer, J. Sprengel, K. Stolle,
Nat. Biotechnol. 29(9), 811--815, 2011

Setting the standards for signal transduction research.
J Saez-Rodriguez, L G Alexopoulos, G Stolovitzky
Sci Signal, 4(160) pe10, pe10, 2011

Nanopore-Based DNA Sequencing and DNA Motion Control
H Peng, B Luan, G Stolovitzky
Nanopores: Sensing and Fundamental Biological Interactions; Iqbal, Samir M. and Bashir, Rashid (Eds.) , pp. 255, Springer Verlag, 2011

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge
Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G
Sci Signal ,Sep 6;4(189):mr7 4(189), mr7, NIH Public Access, 2011


2010

When the optimal is not the best: parameter estimation in complex biological models (Supplemental Material)
Slezak, Diego Fern{'a}ndez and Su{'a}rez, Cecilia and Cecchi, Guillermo A and Marshall, Guillermo and Stolovitzky, Gustavo
2010 - Citeseer, Citeseer
Abstract

When the optimal is not the best: parameter estimation in complex biological models
Slezak, Diego Fern{'a}ndez and Su{'a}rez, Cecilia and Cecchi, Guillermo A and Marshall, Guillermo and Stolovitzky, Gustavo
PloS one 5(10), e13283, Public Library of Science, 2010
Abstract

Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer
Binquan Luan, Ali Afzali, Stefan Harrer, Hongbo Peng, Philip Waggoner, Stas Polonsky, Gustavo Stolovitzky, Glenn Martyna
The Journal of Physical Chemistry B 114(51), 17172 17176, ACS Publications, 2010
Abstract

Electrochemical Characterization of Thin Film Electrodes Toward Developing a DNA Transistor
S. Harrer, S. Ahmed, A. Afzali-Ardakani, B. Luan, P. S. Waggoner, X. Shao, H. Peng, D. L. Goldfarb, G. J Martyna, S. M. Rossnagel, L. Deligianni, G. A. Stolovitzky
Langmuir 26(24), 153103--153103, ACS Publications, 2010

When the optimal is not the best: parameter estimation in complex biological models.
Fernandez Slezak D, Suarez C, Cecchi GA, Marshall G, Stolovitzky G.
PLoS One. 2010 Oct 25;5(10):e13283

Characterize and Control the Motion of DNA in a Solid-State Nanopore
B Luan, G Stolovitzky, G Martyna
Bulletin of the American Physical Society55, APS, 2010

Base-By-Base Ratcheting of Single Stranded DNA through a Solid-State Nanopore
B Luan, H Peng, S Polonsky, S Rossnagel, G Stolovitzky, G Martyna
Physical Review Letters 104(23), 238103, APS, 2010
Abstract   Copyright (C) 2010 The American Physical SocietyPlease report any problems to prola@aps.orgPRL

Towards a rigorous assessment of systems biology models: The DREAM3 challenges
R J Prill, D Marbach, J Saez-Rodriguez, P K Sorger, L G Alexopoulos, X Xue, N D Clarke, G Altan-Bonnet, G Stolovitzky
PLoS ONE 5(2), e9202, Public Library of Science, 2010

Revealing strengths and weaknesses of methods for gene network inference
D Marbach, R J Prill, T Schaffter, C Mattiussi, D Floreano, G Stolovitzky
Proc Natl Acad Sci U S A 107(14), 6286, 2010


2009

Distal Tumors Elicit Distinctive Gene Expression Changes in Mouse Brain, Different from Those Induced by Arthritis
M J Alvarez, M C Salibe, G Stolovitzky, M Rubinstein, F J Pitossi, O L Podhajcer
Open Neuroscience Journal3, 13--25, 2009


The challenges of systems biology. Preface.
G Stolovitzky, P Kahlem, A Califano
Annals of the New York Academy of Sciences 1158(Annals of the New York Academy o), 2009

Distal Tumors Elicit Distinctive Gene Expression Changes in Mouse Brain Different from Those Induced by Arthritis
M.J. Alvarez, M.C. Salibe, G. Stolovitzky, M. Rubinstein, F.J.Pitossi and O.L. Podhajcer
The Open Neuroscience Journal3, 13-25, 2009

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes
A A Margolin, T Palomero, P Sumazin, A Califano, A Ferrando, G A Stolovitzky
Proc Natl Acad Sci U S A. 6(106), 244-9 , BioMed Central Ltd, 2009

Lessons from the DREAM2 Challenges
G Stolovitzky, R J Prill, A Califano
Annals of the New York Academy of Sciences 1158(1), 159--195, Wiley Online Library, 2009


2008

Stability and Time-Delay Modeling of Negative Feedback Loops
J Wagner, G Stolovitzky
Proceedings of the IEEE 96(8), 1398--1410, Institute of Electrical and Electronics Engineers, 2008

Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks
Avi Ma'ayan, Guillermo A. Cecchi, John Wagner, A. Ravi Rao, Ravi Iyengar, and Gustavo Stolovitzky
Proc Natl Acad Sci U S A 105(49), 19235-19240, National Acad Sciences, 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.


2007

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding
Margolin, Adam A and Palomero, Teresa and Ferrando, Adolfo A and Califano, Andrea and Stolovitzky, Gustavo
BMC Bioinformatics 8(Suppl 8), S2, BioMed Central Ltd, 2007
Abstract

Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference.
Stolovitzky, Gustavo and Monroe, DON and Califano, Andrea
Annals of the New York Academy of Sciences1115, 1, 2007
Abstract

Dialogue on Reverse-Engineering Assessment and Methods
Stolovitzky, Gustavo and Monroe, DON and Califano, Andrea
Annals of the New York Academy of Sciences 1115(1), 1--22, Wiley Online Library, 2007
Abstract

Preface
Stolovitzky, Gustavo and Califano, Andrea
Annals of the New York Academy of Sciences 1115(1), xi--xiv, Wiley Online Library, 2007
Abstract

Dialogue on Reverse-Engineering Assessment and Methods
Stolovitzky, Gustavo and Monroe, DON and Califano, Andrea
Annals of the New York Academy of Sciences 1115(1), 1--22, Wiley Online Library, 2007
Abstract

Experimental test of specific predictions of a model for the oscillatory response of p53 to DNA damage.
G Stolovitzky, J Wagner, J J Rice, L Ma, W Hu, Z Feng, A Levine
Bulletin of the American Physical Society52, APS, 2007

Nanopore in metal-dielectric sandwich for DNA position control
S Polonsky, S Rossnagel, G Stolovitzky
Applied Physics Letters 91(15), 153103, 2007
Abstract


Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells
J C Roach, K D Smith, K L Strobe, S M Nissen, C D Haudenschild, D Zhou, T J Vasicek, GA Held, G A Stolovitzky, L E Hood, A Aderem
Proc Natl Acad Sci U S A 104(41), 16245, 2007

A single nucleotide polymorphism in the MDM2 gene disrupts the oscillation of p53 and MDM2 levels in cells
W Hu, Z Feng, L Ma, J Wagner, J J Rice, G Stolovitzky, A J Levine
Cancer research 67(6), 2757, AACR, 2007

Dialogue on Reverse-Engineering Assessment and Methods: The DREAM of High-Throughput Pathway Inference
G Stolovitzky, D Monroe, A Califano
Annals of the New York Academy of Sciences 1115(1), 1--22, Wiley Online Library, 2007


2006

Genomica funcional: En busca de la funci{'o}n de los genes
Fern{'a}ndez, E and Alvarez, M and Podhajcer, O and Stolovitzky, GUSTAVO
Proceedings of the Argentinian Academy of Sciences, Acta13, 2006
Abstract

Global gene expression assays: quantitative noise analysis
G A Held, G Stolovitzky, Y Tu
Systems Biology Vol II: Networks, Models and Applications (I. Rigoutsos and G. Stephanopoulos, eds., Oxford University Press), pp. 103--136, 2006

Genomica Funcional: En busca de la function de los Genes
E. Fernandez, M. Alvarez, O. Podhajcer and G. Stolovitzky
Proceedings of the Argentinean Academy of Sciences13, 2006

Tracking CD40 signaling during normal germinal center development by gene expression profiling
K Basso, U Klein, H Niu, G A Stolovitzky, Y Tu, A Califano, G Cattoretti, R Dalla-Favera
Annals of the New York Academy of Sciences987, 288--290, 2006

Comparison of Amersham and Agilent microarray technologies through quantitative noise analysis
GA Held, K Duggar, G Stolovitzky
OMICS: A Journal of Integrative Biology 10(4), 532--544, 2006

Gene selection strategies in microarray expression data: applications to case-control studies
G Stolovitzky
Complex Systems Science in Biomedicine (J.Y. Kresh and T. Deisboeck, editors), 679--699, Springer, 2006

Gene expression dynamics during germinal center transit in B cells
U Klein, Y Tu, G A Stolovitzky, J L Keller, J Haddad Jr, V Miljkovic, G Cattoretti, A Califano, R Dalla-Favera
Annals of the New York Academy of Sciences987, 166--172, 2006

ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
A Margolin, I Nemenman, K Basso, C Wiggins, G Stolovitzky, R Dalla Favera, A Califano
BMC bioinformatics 7(Suppl 1), S7, 2006


2005

Lasting impressions: motifs in protein--protein maps may provide footprints of evolutionary events
Rice, J Jeremy and Kershenbaum, Aaron and Stolovitzky, Gustavo
Proceedings of the National Academy of Sciences of the United States of America 102(9), 3173--3174, National Acad Sciences, 2005
Abstract

Lasting impressions: motifs in protein--protein maps may provide footprints of evolutionary events
Rice, J Jeremy and Kershenbaum, Aaron and Stolovitzky, Gustavo
Proceedings of the National Academy of Sciences of the United States of America 102(9), 3173--3174, National Acad Sciences, 2005
Abstract

Report: workshop on mediastinal grey zone lymphoma
S Poppema, J L Kluiver, C Atayar, A Berg, A Rosenwald, M Hummel, D Lenze, H Lammert, H Stein, S Joos, others
European Journal of Haematology75, 45--52, Wiley Online Library, 2005

p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback
J. Wagner, L. Ma, J. J. Rice, W. Hu, A. J. Levine, G. A. Stolovitzky
Syst Biol (Stevenage) 152(3), 109--118, 2005

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

Formation of regulatory patterns during signal propagation in a Mammalian cellular network
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
Science 309(5737), 1078-83, American Association for the Advancement of Science, 2005


Statistical analysis of MPSS measurements: Application to the study of LPS-activated macrophage gene expression
G Stolovitzky, A Kundaje, GA Held, KH Duggar, CD Haudenschild, D Zhou, TJ Vasicek, KD Smith, A Aderem, JC Roach
Proc. Natl. Acad. Sci. U S A 102(5), 1402, 2005

A plausible model for the digital response of p53 to DNA damage
L. Ma, J. Wagner, J. J. Rice, W. Hu, A. J. Levine, G. A. Stolovitzky
Proc. Natl. Acad. Sci. U.S.A. 102(40), 14266--14271, 2005

A robust meta-classification strategy for cancer diagnosis from gene expression data
G Alexe, G Bhanot, B Venkataraghavan, R Ramaswamy, J Lepre, AJ Levine, G Stolovitzky
IEEE Computational Systems Bioinformatics Conference, pp. 322--325, 2005

Lasting impressions: Motifs in protein--protein maps may provide footprints of evolutionary events
J J Rice, A Kershenbaum, G Stolovitzky
Proc. Natl. Acad. Sci. U S A 102(9), 3173, National Acad Sciences, 2005

Reverse engineering of regulatory networks in human B cells
K Basso, A A Margolin, G Stolovitzky, U Klein, R Dalla-Favera, A Califano
Nature Genetics 37(4), 382--390, 2005

Reconstructing biological networks using conditional correlation analysis
J. J. Rice, Y. Tu, G. Stolovitzky
Bioinformatics 21(6), 765--773, 2005


2004

Identifying Mechanisms Associated with Diseases Using Classification techniques
J R Hussan, K G Krishnamoorthy, G Stolovitzky
WSEAS Transactions on Information Science and Applications, 2004

On the reconstruction of interaction networks with applications to transcriptional regulation
A A Margolin, I Nemenman, C Wiggins, G Stolovitzky, A Califano
NIPS'04 Computational Biology Workshop (G Chechik, C Leslie, G Ratsch, and K Tsuda, editors), 2004


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



2003

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


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

Motif-based construction of a functional map for mammalian olfactory receptors
A H Liu, X Zhang, G A Stolovitzky, A Califano, S J Firestein
Genomics 81(5), 443--456, 2003

Gene selection in microarray data: the elephant, the blind men and our algorithms
G Stolovitzky
Current opinion in structural biology 13(3), 370--376, 2003

Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling
R. Kuppers, U. Klein, I. Schwering, V. Distler, A. Brauninger, G. Cattoretti, Y. Tu, G. Stolovitzky, A. Califano, M.L. Hansmann, R. Dalla Favera,
Journal of Clinical Investigation 111(4), 529--537, 2003

Transcriptional analysis of the B cell germinal center reaction
U Klein, Y Tu, G A Stolovitzky, J L Keller, J Haddad, V Miljkovic, G Cattoretti, A Califano, R Dalla-Favera
Proc. Nat. Acad. Sci. U S A 100(5), 2639, 2003


2002

Bioinformatics: The Machine Learning Approach
P Baldi, S Brunak, G A Stolovitzky
Physics Today 55(12), 57--58, 2002


Quantitative noise analysis for gene expression microarray experiments
Y Tu, G Stolovitzky, U Klein
Proc. Natl. Acad. Sci. U S A 99(22), 14031, 2002

Prediction of central nervous system embryonal tumour outcome based on gene expression
37. 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.
Nature 415(6870), 436--442, 2002


2001

Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells
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,
Journal of Experimental Medicine 194(11), 1625, 2001


2000

Analysis of gene expression microarrays for phenotype classification.
Califano, Andrea and Stolovitzky, Gustavo and Tu, Yuhai and others
Ismb, pp. 75--85, 2000
Abstract

Systematic and automated discovery of patterns in PROSITE families
Hart, Reece and Royyuru, Ajay K and Stolovitzky, Gustavo and Califano, Andrea
Proceedings of the fourth annual international conference on Computational molecular biology, pp. 147--154, 2000
Abstract

Analysis of gene expression microarrays for phenotype classification
A Califano, G Stolovitzky, Y Tu
Proceedings of the 8th Annual Intelligent Systems in Molecular Biology (ISMB) , pp. 75--85, 2000

Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo
G Stolovitzky, B J Berne
Proc. Natl. Acad. Sci. U S A 97(21), 11164, 2000

Systematic and fully automated identification of protein sequence patterns
R K Hart, A K Royyuru, G Stolovitzky, A Califano
Journal of Computational Biology 7(3-4), 585--600, 2000


1999


DNA Based Identification
N Rudin, K Inman, G Stolovitzky, I Rigoutsos
Biometrics: Personal Identification in Networked Society (A. Jain, R. Bolle and S. Pankanti eds) , pp. 287--309, Kluwer Acad. Publishers, 1999

Tandem repeat detection using pattern discovery with application to the identification of yeast satellites
G Stolovitzky, Y Gao, A Floratos, I Rigoutsos
IBM TJ Watson Research Center, Research Report, 1999

Sequence homology detection through large scale pattern discovery
A Floratos, I Rigoutsos, L Parida, G Stolovitzky, Y Gao
Proceedings of the third annual international conference on Computational Molecular Biology (RECOMB), pp. 164--173, 1999


1998

Unsupervised Hierarchical Motif Discovery In the Sequence Space Of Natural Proteins
I Rigoutsos, A Floratos, C Ouzounis, L Parida, G Stolovitzky, Y Gao
Technical Report, 1998

Pattern statistics in biological datasets
G Stolovitzky, A Califano
IBM RC, 1998


Non-isothermal inertial Brownian motion
G Stolovitzky
Physics Letters A 241(4-5), 240--256, 1998

Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes
W Li, G Stolovitzky, P Bernaola-Galvan, J L Oliver
Genome Research 8(9), 916, 1998

Feynman's Ratchet and Pawl
M O Magnasco, G Stolovitzky
Journal of Statistical Physics 93(3), 615--632, 1998

Backscattering from a Tethered Bead as a Probe of DNA Flexibility
G.V. Shivashankar, G. Stolovitzky and A. Libchaber
Applied Physics Letters73, , 291-293, 1998


Statistical Significance of Patterns in Biosequences
G Stolovitzky, A Califano
IBM TJ Watson Research Center, Research Report, Citeseer, 1998


1997

Coherent structures and conditional statistics in inhomogeneous turbulent mixing
G Stolovitzky, J L Aider, J E Wesfreid
Physical Review Letters 78(23), 4398--4401, APS, 1997

Mnemonics for variability: Remembering food delay
D Brunner, S Fairhurst, G Stolovitzky, J Gibbon
JOURNAL OF EXPERIMENTAL PSYCHOLOGY ANIMAL BEHAVIOR PROCESSES23, 68--83, 1997


1996

Limitations of random multipliers in describing turbulent energy dissipation
M Nelkin, G Stolovitzky
Physical Review E 54(5), 5100--5106, APS, 1996


Efficiency of DNA replication in the polymerase chain reaction
G Stolovitzky, G Cecchi
Proceedings of the National Academy of Sciences of the United States of America 93(23), 12947, National Acad Sciences, 1996


1995

Turbulent cascades
K R Sreenivasan, G Stolovitzky
Journal of Statistical Physics 78(1), 311--333, Springer, 1995

Refined similarity hypotheses for passive scalars mixed by turbulence
G Stolovitzky, P Kailasnath, KR Sreenivasan
Journal of Fluid Mechanics297, 275--291, 1995

A simple model of chaotic advection and scattering
G Stolovitzky, T J Kaper, L Sirovich
Chaos An Interdisciplinary Journal of Nonlinear Science 5(4), 671, 1995

Periodic forcing of a Brownian particle
L P Faucheux, G Stolovitzky, A Libchaber
Physical Review E 51(6), 5239--5250, APS, 1995



1994

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

Synthetic turbulence
A Juneja, DP Lathrop, KR Sreenivasan, G Stolovitzky
Physical Review E 49(6), 5179--5194, APS, 1994

Kolmogorov's refined similarity hypotheses for turbulence and general stochastic processes
G Stolovitzky, KR Sreenivasan
Reviews of Modern Physics 66(1), 229--240, APS, 1994



1993

Independent Velocity Increments and Kolmogorov's Refined Similarity Hypotheses
G Stolovitzky, KR Sreenivasan
Procceedings of the 2nd ONR/NUWC technical conference: Nonlinear dynamics (chaos) and full spectrum processing, AIP Conference Proceedings (R. Katz, ed), pp. 97--97, 1993

Scaling of structure functions
G Stolovitzky, KR Sreenivasan
Physical Review E 48(1), 33--36, APS, 1993

Scaling functions and scaling exponents in turbulence
G Stolovitzky, KR Sreenivasan, A Juneja
Physical Review E 48(5), 3217--3220, APS, 1993


1992

Kolmogorov’s refined similarity hypotheses
G Stolovitzky, P Kailasnath, KR Sreenivasan
Physical review letters 69(8), 1178--1181, APS, 1992

Probability density of velocity increments in turbulent flows
P Kailasnath, KR Sreenivasan, G Stolovitzky
Physical review letters 68(18), 2766--2769, APS, 1992


1991



1990

Resonant structure of integrable and near-integrable two-dimensional systems
G Stolovitzky, JA Hernando
Physical Review A 41(6), 3026--3037, APS, 1990



1987

Cryogenic thermometry and level detection with common diodes
J Talpe, G Stolovitzky, V Bekeris
Cryogenics 27(12), 693--695, Elsevier, 1987


Year Unknown

Robust meta-analysis of genomic data for cancer diagnosis
Bhanot, Gyan and Alexe, Gabriela and Vengataraghavan, Babu and Ramaswamy, Ramakrishna and Lepre, Jorge and Levine, Arnold J and Stolovitzky, Gustavo
broad.mit.edu, 0
Abstract