Gustavo Stolovitzky - Publications

1994-1997 IBM Thomas J. Watson Research Center, Yorktown Heights, NY, United States 

135 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, ... ... Stolovitzky G, et al. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Life Science Alliance. 3. PMID 32972997 DOI: 10.26508/lsa.202000867  0.56
2020 Ahsen ME, Vogel R, Stolovitzky GA. R/PY-SUMMA: An R/Python Package for Unsupervised Ensemble Learning for Binary Classification Problems in Bioinformatics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 31905016 DOI: 10.1089/cmb.2019.0348  0.4
2019 Davis S, Button-Simons K, Bensellak T, Ahsen EM, Checkley L, Foster GJ, Su X, Moussa A, Mapiye D, Khoo SK, Nosten F, Anderson TJC, Vendrely K, Bletz J, Yu T, ... ... Stolovitzky G, et al. Leveraging crowdsourcing to accelerate global health solutions. Nature Biotechnology. PMID 31324891 DOI: 10.1038/s41587-019-0180-5  0.56
2019 Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang IS, Ghazoui Z, ... ... Stolovitzky G, et al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. 10: 2674. PMID 31209238 DOI: 10.1038/s41467-019-09799-2  0.4
2019 Santos LC, Vogel R, Chipuk JE, Birtwistle MR, Stolovitzky G, Meyer P. Mitochondrial origins of fractional control in regulated cell death. Nature Communications. 10: 1313. PMID 30899020 DOI: 10.1038/s41467-019-09275-x  0.56
2017 Keller A, Gerkin RC, Guan Y, Dhurandhar A, Turu G, Szalai B, Mainland JD, Ihara Y, Yu CW, Wolfinger R, Vens C, Schietgat L, De Grave K, Norel R, ... Stolovitzky G, et al. Predicting human olfactory perception from chemical features of odor molecules. Science (New York, N.Y.). PMID 28219971 DOI: 10.1126/science.aal2014  0.56
2016 Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G. Crowdsourcing biomedical research: leveraging communities as innovation engines. Nature Reviews. Genetics. 17: 470-86. PMID 27418159 DOI: 10.1038/nrg.2016.69  1
2016 Noren DP, Long BL, Norel R, Rrhissorrakrai K, Hess K, Hu CW, Bisberg AJ, Schultz A, Engquist E, Liu L, Lin X, Chen GM, Xie H, Hunter GA, Boutros PC, ... ... Stolovitzky G, et al. A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis. Plos Computational Biology. 12: e1004890. PMID 27351836 DOI: 10.1371/journal.pcbi.1004890  1
2016 Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C. A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. Bmc Bioinformatics. 17: 155. PMID 27059896 DOI: 10.1186/s12859-016-1008-7  1
2016 Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, ... ... Stolovitzky G, et al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods. PMID 26901648 DOI: 10.1038/nmeth.3773  1
2015 Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, ... ... Stolovitzky G, et al. DREAMTools: a Python package for scoring collaborative challenges. F1000research. 4: 1030. PMID 27134723 DOI: 10.12688/f1000research.7118.1  1
2015 Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, et al. Prediction of human population responses to toxic compounds by a collaborative competition. Nature Biotechnology. PMID 26258538 DOI: 10.1038/nbt.3299  1
2015 Prill RJ, Vogel R, Cecchi GA, Altan-Bonnet G, Stolovitzky G. Noise-driven causal inference in biomolecular networks. Plos One. 10: e0125777. PMID 26030907 DOI: 10.1371/journal.pone.0125777  0.4
2015 Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, et al. Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. Plos Computational Biology. 11: e1004096. PMID 26020786 DOI: 10.1371/journal.pcbi.1004096  1
2015 Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY, Kellen MR, Norman TC, Haussler D, Friend SH, ... Stolovitzky G, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature Methods. PMID 25984700 DOI: 10.1038/nmeth.3407  1
2015 Califano A, Kellis M, Stolovitzky G. Preface: RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2014 Special Issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 251-2. PMID 25844665 DOI: 10.1089/cmb.2015.020P  1
2015 Abdallah K, Hugh-Jones C, Norman T, Friend S, Stolovitzky G. 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. The Oncologist. 20: 459-60. PMID 25777346 DOI: 10.1634/theoncologist.2015-0054  1
2015 Wang C, Bruce RL, Duch EA, Patel JV, Smith JT, Astier Y, Wunsch BH, Meshram S, Galan A, Scerbo C, Pereira MA, Wang D, Colgan EG, Lin Q, Stolovitzky G. Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels. Acs Nano. 9: 1206-18. PMID 25626162 DOI: 10.1021/nn507350e  1
2015 Küffner R, Zach N, Norel R, Hawe J, Schoenfeld D, Wang L, Li G, Fang L, Mackey L, Hardiman O, Cudkowicz M, Sherman A, Ertaylan G, Grosse-Wentrup M, Hothorn T, ... ... Stolovitzky G, et al. Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression. Nature Biotechnology. 33: 51-7. PMID 25362243 DOI: 10.1038/nbt.3051  1
2015 Bilal E, Sakellaropoulos T, Melas IN, Messinis DE, Belcastro V, Rhrissorrakrai K, Meyer P, Norel R, Iskandar A, Blaese E, Rice JJ, Peitsch MC, Hoeng J, Stolovitzky G, Alexopoulos LG, et al. A crowd-sourcing approach for the construction of species-specific cell signaling networks. Bioinformatics (Oxford, England). 31: 484-91. PMID 25294919 DOI: 10.1093/bioinformatics/btu659  1
2015 Rhrissorrakrai K, Belcastro V, Bilal E, Norel R, Poussin C, Mathis C, Dulize RH, Ivanov NV, Alexopoulos L, Rice JJ, Peitsch MC, Stolovitzky G, Meyer P, Hoeng J. Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge. Bioinformatics (Oxford, England). 31: 471-83. PMID 25236459 DOI: 10.1093/bioinformatics/btu611  1
2015 Prill RJ, Vogel R, Cecchi GA, Altan-Bonnet G, Stolovitzky G. Noise-driven causal inference in biomolecular networks Plos One. 10. DOI: 10.1371/journal.pone.0125777  1
2014 Poussin C, Mathis C, Alexopoulos LG, Messinis DE, Dulize RH, Belcastro V, Melas IN, Sakellaropoulos T, Rhrissorrakrai K, Bilal E, Meyer P, Talikka M, Boué S, Norel R, Rice JJ, ... Stolovitzky G, et al. The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells. Scientific Data. 1: 140009. PMID 25977767 DOI: 10.1038/sdata.2014.9  1
2014 Meyer P, Cecchi G, Stolovitzky G. Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria. Bmc Systems Biology. 8: 131. PMID 25495800 DOI: 10.1186/s12918-014-0131-1  1
2014 Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, ... ... Stolovitzky G, et al. A community computational challenge to predict the activity of pairs of compounds. Nature Biotechnology. 32: 1213-22. PMID 25419740 DOI: 10.1038/nbt.3052  1
2014 Pang P, Ashcroft BA, Song W, Zhang P, Biswas S, Qing Q, Yang J, Nemanich RJ, Bai J, Smith JT, Reuter K, Balagurusamy VS, Astier Y, Stolovitzky G, Lindsay S. Fixed-gap tunnel junction for reading DNA nucleotides. Acs Nano. 8: 11994-2003. PMID 25380505 DOI: 10.1021/nn505356g  1
2014 Bai J, Wang D, Nam SW, Peng H, Bruce R, Gignac L, Brink M, Kratschmer E, Rossnagel S, Waggoner P, Reuter K, Wang C, Astier Y, Balagurusamy V, Luan B, ... ... Stolovitzky G, et al. Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales. Nanoscale. 6: 8900-6. PMID 24964839 DOI: 10.1039/c3nr06723h  1
2014 Luan B, Wang C, Royyuru A, Stolovitzky G. Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages. Nanotechnology. 25: 265101. PMID 24920303 DOI: 10.1088/0957-4484/25/26/265101  1
2014 Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, ... ... Stolovitzky G, et al. A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology. 32: 1202-12. PMID 24880487 DOI: 10.1038/nbt.2877  1
2014 Califano A, Kellis M, Stolovitzky G. RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 21: 371-2. PMID 24784777 DOI: 10.1089/cmb.2014.009p  1
2014 Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM. Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nature Genetics. 46: 318-9. PMID 24675517 DOI: 10.1038/ng.2932  1
2014 Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Dream Six and Seven Parameter Estimation Consortium, Sauro HM, ... Stolovitzky G, et al. Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. Bmc Systems Biology. 8: 13. PMID 24507381 DOI: 10.1186/1752-0509-8-13  1
2014 Wang D, Harrer S, Luan B, Stolovitzky G, Peng H, Afzali-Ardakani A. Regulating the transport of DNA through biofriendly nanochannels in a thin solid membrane. Scientific Reports. 4: 3985. PMID 24496378 DOI: 10.1038/srep03985  1
2014 Wang C, Bruce RL, Duch EA, Patel JV, Smith JT, Astier Y, Colgan EG, Lin Q, Stolovitzky G. Clog-free translocation of long DNA in nanofluidic pillar arrays and 30 nm wide channels: A fabrication and hydrodynamic study 18th International Conference On Miniaturized Systems For Chemistry and Life Sciences, Microtas 2014. 1347-1349.  1
2013 Ansari S, Binder J, Boue S, Di Fabio A, Hayes W, Hoeng J, Iskandar A, Kleiman R, Norel R, O'Neel B, Peitsch MC, Poussin C, Pratt D, Rhrissorrakrai K, ... ... Stolovitzky G, et al. On Crowd-verification of Biological Networks. Bioinformatics and Biology Insights. 7: 307-25. PMID 24151423 DOI: 10.4137/BBI.S12932  1
2013 Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, Hoeng J, Koeppl H, Martin F, Meyer P, Nandy P, Norel R, Peitsch M, Rice JJ, Romero R, ... Stolovitzky G, et al. Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. Bioinformatics (Oxford, England). 29: 2892-9. PMID 23966112 DOI: 10.1093/bioinformatics/btt492  1
2013 Meyer P, Siwo G, Zeevi D, Sharon E, Norel R, Segal E, Stolovitzky G. Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Research. 23: 1928-37. PMID 23950146 DOI: 10.1101/gr.157420.113  1
2013 Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, ... ... Stolovitzky GA, et al. Improving breast cancer survival analysis through competition-based multidimensional modeling. Plos Computational Biology. 9: e1003047. PMID 23671412 DOI: 10.1371/journal.pcbi.1003047  1
2013 Califano A, Kellis M, Stolovitzky G. Preface: RECOMB systems biology, regulatory genomics, and DREAM 2012 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 373-4. PMID 23641866 DOI: 10.1089/cmb.2013.008p  1
2013 Plenge RM, Greenberg JD, Mangravite LM, Derry JM, Stahl EA, Coenen MJ, Barton A, Padyukov L, Klareskog L, Gregersen PK, Mariette X, Moreland LW, Bridges SL, de Vries N, Huizinga TW, ... ... Stolovitzky G, et al. Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge. Nature Genetics. 45: 468-9. PMID 23619782 DOI: 10.1038/ng.2623  1
2013 Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HK, Rueda OM, Guinney J, Deflaux NA, Hoff B, ... ... Stolovitzky G, et al. Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Science Translational Medicine. 5: 181re1. PMID 23596205 DOI: 10.1126/scitranslmed.3006112  1
2013 Luan B, Stolovitzky G. An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation. Nanotechnology. 24: 195702. PMID 23579206 DOI: 10.1088/0957-4484/24/19/195702  1
2013 Costello JC, Stolovitzky G. Seeking the wisdom of crowds through challenge-based competitions in biomedical research. Clinical Pharmacology and Therapeutics. 93: 396-8. PMID 23549146 DOI: 10.1038/clpt.2013.36  1
2013 Aghaeepour N, Finak G, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Critical assessment of automated flow cytometry data analysis techniques. Nature Methods. 10: 228-38. PMID 23396282 DOI: 10.1038/nmeth.2365  1
2013 Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31: 126-34. PMID 23354101 DOI: 10.1038/nbt.2486  1
2013 Wang C, Nam SW, Cotte JM, Peng H, Jahnes CV, Wang D, Bruce R, Guillorn M, Gignac LM, Advocate WH, Breslin CM, Brink M, Bucchignano J, Duch EA, Galan A, ... ... Stolovitzky GA, et al. 200 mm wafer-scale integration of sub-20 nm sacrificial nanofluidic channels for manipulating and imaging single DNA molecules Technical Digest - International Electron Devices Meeting, Iedm. 14.1.1-14.1.4. DOI: 10.1109/IEDM.2013.6724627  1
2013 Luan B, Bai J, Stolovitzky G. Fabricatable nanopore sensors with an atomic thickness Applied Physics Letters. 103. DOI: 10.1063/1.4826599  1
2012 Luan B, Wang D, Zhou R, Harrer S, Peng H, Stolovitzky G. Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol. Nanotechnology. 23: 455102. PMID 23064727 DOI: 10.1088/0957-4484/23/45/455102  1
2012 Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G. Wisdom of crowds for robust gene network inference. Nature Methods. 9: 796-804. PMID 22796662 DOI: 10.1038/nmeth.2016  1
2012 Meyer P, Hoeng J, Rice JJ, Norel R, Sprengel J, Stolle K, Bonk T, Corthesy S, Royyuru A, Peitsch MC, Stolovitzky G. Industrial methodology for process verification in research (IMPROVER): toward systems biology verification. Bioinformatics (Oxford, England). 28: 1193-201. PMID 22423044 DOI: 10.1093/bioinformatics/bts116  1
2012 Martínez MR, Corradin A, Klein U, Álvarez MJ, Toffolo GM, di Camillo B, Califano A, Stolovitzky GA. Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. Proceedings of the National Academy of Sciences of the United States of America. 109: 2672-7. PMID 22308355 DOI: 10.1073/pnas.1113019109  1
2012 Califano A, Kellis M, Stolovitzky G. Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 101. PMID 22300312 DOI: 10.1089/cmb.2012.010p  1
2012 Luan B, Stolovitzky G, Martyna G. Slowing and controlling the translocation of DNA in a solid-state nanopore. Nanoscale. 4: 1068-77. PMID 22081018 DOI: 10.1039/c1nr11201e  1
2011 Luan B, Martyna G, Stolovitzky G. Characterizing and controlling the motion of ssDNA in a solid-state nanopore. Biophysical Journal. 101: 2214-22. PMID 22067161 DOI: 10.1016/j.bpj.2011.08.038  1
2011 Norel R, Rice JJ, Stolovitzky G. The self-assessment trap: can we all be better than average? Molecular Systems Biology. 7: 537. PMID 21988833 DOI: 10.1038/msb.2011.70  1
2011 Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, ... ... Stolovitzky G, et al. Verification of systems biology research in the age of collaborative competition. Nature Biotechnology. 29: 811-5. PMID 21904331 DOI: 10.1038/nbt.1968  1
2011 Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G. Crowdsourcing network inference: the DREAM predictive signaling network challenge. Science Signaling. 4: mr7. PMID 21900204 DOI: 10.1126/scisignal.2002212  1
2011 Harrer S, Waggoner PS, Luan B, Afzali-Ardakani A, Goldfarb DL, Peng H, Martyna G, Rossnagel SM, Stolovitzky GA. Electrochemical protection of thin film electrodes in solid state nanopores. Nanotechnology. 22: 275304. PMID 21597142 DOI: 10.1088/0957-4484/22/27/275304  1
2011 Saez-Rodriguez J, Alexopoulos LG, Stolovitzky G. Setting the standards for signal transduction research. Science Signaling. 4: pe10. PMID 21325202 DOI: 10.1126/scisignal.2001844  1
2010 Luan B, Afzali A, Harrer S, Peng H, Waggoner P, Polonsky S, Stolovitzky G, Martyna G. Tribological effects on DNA translocation in a nanochannel coated with a self-assembled monolayer. The Journal of Physical Chemistry. B. 114: 17172-6. PMID 21128651 DOI: 10.1021/jp108865q  1
2010 Harrer S, Ahmed S, Afzali-Ardakani A, Luan B, Waggoner PS, Shao X, Peng H, Goldfarb DL, Martyna GJ, Rossnagel SM, Deligianni L, Stolovitzky GA. Electrochemical characterization of thin film electrodes toward developing a DNA transistor. Langmuir : the Acs Journal of Surfaces and Colloids. 26: 19191-8. PMID 21090688 DOI: 10.1021/la102671g  1
2010 Fernández Slezak D, Suárez C, Cecchi GA, Marshall G, Stolovitzky G. When the optimal is not the best: parameter estimation in complex biological models. Plos One. 5: e13283. PMID 21049094 DOI: 10.1371/journal.pone.0013283  1
2010 Luan B, Peng H, Polonsky S, Rossnagel S, Stolovitzky G, Martyna G. Base-by-base ratcheting of single stranded DNA through a solid-state nanopore. Physical Review Letters. 104: 238103. PMID 20867275 DOI: 10.1103/PhysRevLett.104.238103  1
2010 Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G. Revealing strengths and weaknesses of methods for gene network inference. Proceedings of the National Academy of Sciences of the United States of America. 107: 6286-91. PMID 20308593 DOI: 10.1073/pnas.0913357107  1
2010 Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. Plos One. 5: e9202. PMID 20186320 DOI: 10.1371/journal.pone.0009202  1
2009 Stolovitzky G, Prill RJ, Califano A. Lessons from the DREAM2 Challenges. Annals of the New York Academy of Sciences. 1158: 159-95. PMID 19348640 DOI: 10.1111/j.1749-6632.2009.04497.x  1
2009 Stolovitzky G, Kahlem P, Califano A. The challenges of systems biology. Preface. Annals of the New York Academy of Sciences. 1158: ix-xii. PMID 19348626 DOI: 10.1111/j.1749-6632.2009.04470.x  1
2009 Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proceedings of the National Academy of Sciences of the United States of America. 106: 244-9. PMID 19118200 DOI: 10.1073/pnas.0806445106  1
2008 Ma'ayan A, Cecchi GA, Wagner J, Rao AR, Iyengar R, Stolovitzky G. Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks. Proceedings of the National Academy of Sciences of the United States of America. 105: 19235-40. PMID 19033453 DOI: 10.1073/pnas.0805344105  1
2008 Du P, Stolovitzky G, Horvatovich P, Bischoff R, Lim J, Suits F. A noise model for mass spectrometry based proteomics. Bioinformatics (Oxford, England). 24: 1070-7. PMID 18353791 DOI: 10.1093/bioinformatics/btn078  1
2008 Wagner J, Stolovitzky G. Stability and time-delay modeling of negative feedback loops Proceedings of the Ieee. 96: 1398-1410. DOI: 10.1109/JPROC.2008.925427  1
2007 Stolovitzky G, Monroe D, Califano A. Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Annals of the New York Academy of Sciences. 1115: 1-22. PMID 17925349 DOI: 10.1196/annals.1407.021  1
2007 Roach JC, Smith KD, Strobe KL, Nissen SM, Haudenschild CD, Zhou D, Vasicek TJ, Held GA, Stolovitzky GA, Hood LE, Aderem A. Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. Proceedings of the National Academy of Sciences of the United States of America. 104: 16245-50. PMID 17913878 DOI: 10.1073/pnas.0707757104  1
2007 Yu H, Jansen R, Stolovitzky G, Gerstein M. Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. Bioinformatics (Oxford, England). 23: 2163-73. PMID 17540677 DOI: 10.1093/bioinformatics/btm291  1
2007 Hu W, Feng Z, Ma L, Wagner J, Rice JJ, Stolovitzky G, Levine AJ. A single nucleotide polymorphism in the MDM2 gene disrupts the oscillation of p53 and MDM2 levels in cells. Cancer Research. 67: 2757-65. PMID 17363597 DOI: 10.1158/0008-5472.CAN-06-2656  1
2007 Stolovitzky G, Califano A. Annals of the New York Academy of Sciences: Preface Annals of the New York Academy of Sciences. 1115: xi-xiv. DOI: 10.1196/annals.1407.022  1
2007 Margolin AA, Palomero T, Ferrando AA, Califano A, Stolovitzky G. ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S8-S2  1
2007 Polonsky S, Rossnagel S, Stolovitzky G. Nanopore in metal-dielectric sandwich for DNA position control Applied Physics Letters. 91. DOI: 10.1063/1.2798247  1
2006 Held GA, Duggar K, Stolovitzky G. Comparison of Amersham and Agilent microarray technologies through quantitative noise analysis. Omics : a Journal of Integrative Biology. 10: 532-44. PMID 17233562 DOI: 10.1089/omi.2006.10.532  1
2006 Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. Bmc Bioinformatics. 7: S7. PMID 16723010 DOI: 10.1186/1471-2105-7-S1-S7  1
2005 Wagner J, Ma L, Rice JJ, Hu W, Levine AJ, Stolovitzky GA. p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback. Systems Biology. 152: 109-18. PMID 16986275 DOI: 10.1049/ip-syb:20050025  1
2005 Alexe G, Bhanot G, Venkataraghavan B, Ramaswamy R, Lepre J, Levine AJ, Stolovitzky G. A robust meta-classification strategy for cancer diagnosis from gene expression data. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 322-5. PMID 16447989 DOI: 10.1109/CSB.2005.7  1
2005 Bhanot G, Alexe G, Levine AJ, Stolovitzky G. Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories. Genome Informatics. International Conference On Genome Informatics. 16: 233-44. PMID 16362926  1
2005 Ma L, Wagner J, Rice JJ, Hu W, Levine AJ, Stolovitzky GA. A plausible model for the digital response of p53 to DNA damage. Proceedings of the National Academy of Sciences of the United States of America. 102: 14266-71. PMID 16186499 DOI: 10.1073/pnas.0501352102  1
2005 Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R. Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science (New York, N.Y.). 309: 1078-83. PMID 16099987 DOI: 10.1126/science.1108876  1
2005 Poppema S, Kluiver JL, Atayar C, van den Berg A, Rosenwald A, Hummel M, Lenze D, Lammert H, Stein H, Joos S, Barth T, Dyer M, Lichter P, Klein U, Cattoretti G, ... ... Stolovitzky GA, et al. Report: workshop on mediastinal grey zone lymphoma. European Journal of Haematology. Supplementum. 45-52. PMID 16007868 DOI: 10.1111/j.1600-0609.2005.00454.x  1
2005 Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nature Genetics. 37: 382-90. PMID 15778709 DOI: 10.1038/ng1532  1
2005 Rice JJ, Kershenbaum A, Stolovitzky G. Lasting impressions: motifs in protein-protein maps may provide footprints of evolutionary events. Proceedings of the National Academy of Sciences of the United States of America. 102: 3173-4. PMID 15728355 DOI: 10.1073/pnas.0500130102  1
2005 Stolovitzky GA, Kundaje A, Held GA, Duggar KH, Haudenschild CD, Zhou D, Vasicek TJ, Smith KD, Aderem A, Roach JC. Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression. Proceedings of the National Academy of Sciences of the United States of America. 102: 1402-7. PMID 15668391 DOI: 10.1073/pnas.0406555102  1
2005 Rice JJ, Tu Y, Stolovitzky G. Reconstructing biological networks using conditional correlation analysis. Bioinformatics (Oxford, England). 21: 765-73. PMID 15486043 DOI: 10.1093/bioinformatics/bti064  1
2004 Basso K, Klein U, Niu H, Stolovitzky GA, Tu Y, Califano A, Cattoretti G, Dalla-Favera R. Tracking CD40 signaling during germinal center development. Blood. 104: 4088-96. PMID 15331443 DOI: 10.1182/blood-2003-12-4291  1
2004 Lepre J, Rice JJ, Tu Y, Stolovitzky G. Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data. Bioinformatics (Oxford, England). 20: 1033-44. PMID 14764572 DOI: 10.1093/bioinformatics/bth035  1
2004 Rice JJ, Stolovitzky G. Making the most of it: Pathway reconstruction and integrative simulation using the data at hand Drug Discovery Today: Biosilico. 2: 70-77. DOI: 10.1016/S1741-8364(04)02399-6  1
2003 Shah N, Lepre J, Tu Y, Stolovitzky G. Can we identify cellular pathways implicated in cancer using gene expression data? Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 2: 94-103. PMID 16452783 DOI: 10.1109/CSB.2003.1227308  1
2003 Stolovitzky G. Gene selection in microarray data: the elephant, the blind men and our algorithms. Current Opinion in Structural Biology. 13: 370-6. PMID 12831889 DOI: 10.1016/S0959-440X(03)00078-2  1
2003 Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R. Gene expression dynamics during germinal center transit in B cells. Annals of the New York Academy of Sciences. 987: 166-72. PMID 12727636  1
2003 Liu AH, Zhang X, Stolovitzky GA, Califano A, Firestein SJ. Motif-based construction of a functional map for mammalian olfactory receptors. Genomics. 81: 443-56. PMID 12706103 DOI: 10.1016/S0888-7543(03)00022-3  1
2003 Jelinek DF, Tschumper RC, Stolovitzky GA, Iturria SJ, Tu Y, Lepre J, Shah N, Kay NE. Identification of a global gene expression signature of B-chronic lymphocytic leukemia. Molecular Cancer Research : McR. 1: 346-61. PMID 12651908  1
2003 Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad J, Miljkovic V, Cattoretti G, Califano A, Dalla-Favera R. Transcriptional analysis of the B cell germinal center reaction. Proceedings of the National Academy of Sciences of the United States of America. 100: 2639-44. PMID 12604779 DOI: 10.1073/pnas.0437996100  1
2003 Küppers R, Klein U, Schwering I, Distler V, Bräuninger A, Cattoretti G, Tu Y, Stolovitzky GA, Califano A, Hansmann ML, Dalla-Favera R. Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling. The Journal of Clinical Investigation. 111: 529-37. PMID 12588891 DOI: 10.1172/JCI16624  1
2003 Rice JJ, Stolovitzky G, Tu Y, de Tombe PP. Ising model of cardiac thin filament activation with nearest-neighbor cooperative interactions. Biophysical Journal. 84: 897-909. PMID 12547772 DOI: 10.1016/S0006-3495(03)74907-8  1
2003 Basso K, Klein U, Niu H, Stolovitzky GA, Tu Y, Califano A, Cattoretti G, Dalla-Favera R. Tracking CD40 signaling during normal germinal center development gene expression profiling Annals of the New York Academy of Sciences. 987: 288-290.  1
2002 Mateos A, Dopazo J, Jansen R, Tu Y, Gerstein M, Stolovitzky G. Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Research. 12: 1703-15. PMID 12421757 DOI: 10.1101/gr.192502  1
2002 Tu Y, Stolovitzky G, Klein U. Quantitative noise analysis for gene expression microarray experiments. Proceedings of the National Academy of Sciences of the United States of America. 99: 14031-6. PMID 12388780 DOI: 10.1073/pnas.222164199  1
2002 Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, ... ... Stolovitzky G, et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 415: 436-42. PMID 11807556 DOI: 10.1038/415436a  1
2002 Stolovitzky GA, Rice JJ, Mello BA, Nowicki TJ, Martens M, Tresser C. Statistical and deterministic methods for reverse engineering biological pathways Annual International Conference of the Ieee Engineering in Medicine and Biology - Proceedings. 1: 720.  1
2001 Klein U, Tu Y, Stolovitzky GA, Mattioli M, Cattoretti G, Husson H, Freedman A, Inghirami G, Cro L, Baldini L, Neri A, Califano A, Dalla-Favera R. Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells Journal of Experimental Medicine. 194: 1625-1638. PMID 11733577 DOI: 10.1084/jem.194.11.1625  1
2000 Hart RK, Royyuru AK, Stolovitzky G, Califano A. Systematic and fully automated identification of protein sequence patterns. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 585-600. PMID 11108480 DOI: 10.1089/106652700750050952  1
2000 Stolovitzky G, Berne BJ. Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo. Proceedings of the National Academy of Sciences of the United States of America. 97: 11164-9. PMID 11027326 DOI: 10.1073/pnas.97.21.11164  1
2000 Califano A, Stolovitzky G, Tu Y. Analysis of gene expression microarrays for phenotype classification. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 75-85. PMID 10977068  1
1999 Stolovitzky G, Ching ESC. Characterization of stationary distributions using conditional expectations Physics Letters, Section a: General, Atomic and Solid State Physics. 255: 11-16.  1
1998 Li W, Stolovitzky G, Bernaola-Galván P, Oliver JL. Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes. Genome Research. 8: 916-28. PMID 9750191  1
1998 Shivashankar GV, Stolovitzky G, Libchaber A. Backscattering from a tethered bead as a probe of DNA flexibility Applied Physics Letters. 73: 291-293. DOI: 10.1063/1.121798  1
1998 Ching ESC, Pang CS, Stolovitzky G. Effects of a large-scale mean circulating flow on passive scalar statistics in a model of random advection Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 58: 1948-1954.  1
1998 Magnasco MO, Stolovitzky G. Feynman's ratchet and pawl Journal of Statistical Physics. 93: 615-632.  1
1998 Stolovitzky G. Non-isothermal inertial Brownian motion Physics Letters, Section a: General, Atomic and Solid State Physics. 241: 240-256.  1
1997 Brunner D, Fairhurst S, Stolovitzky G, Gibbon J. Mnemonics for variability: remembering food delay. Journal of Experimental Psychology. Animal Behavior Processes. 23: 68-83. PMID 9008863  1
1997 Stolovitzky G, Aider JL, Wesfreid JE. Coherent structures and conditional statistics in inhomogeneous turbulent mixing Physical Review Letters. 78: 4398-4401.  1
1996 Sreenivasan KR, Stolovitzky G. Statistical Dependence of Inertial Range Properties on Large Scales in a High-Reynolds-Number Shear Flow. Physical Review Letters. 77: 2218-2221. PMID 10061888  1
1996 Nelkin M, Stolovitzky G. Limitations of random multipliers in describing turbulent energy dissipation. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 54: 5100-5106. PMID 9965689  1
1996 Stolovitzky G, Cecchi G. Efficiency of DNA replication in the polymerase chain reaction. Proceedings of the National Academy of Sciences of the United States of America. 93: 12947-52. PMID 8917524 DOI: 10.1073/pnas.93.23.12947  1
1995 Stolovitzky G, Kaper TJ, Sirovich L. A simple model of chaotic advection and scattering. Chaos (Woodbury, N.Y.). 5: 671-686. PMID 12780224 DOI: 10.1063/1.166138  1
1995 Stolovitzky G, Sreenivasan KR. Intermittency, the second-order structure function, and the turbulent energy-dissipation rate. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 52: 3242-3244. PMID 9963776 DOI: 10.1103/PhysRevE.52.3242  1
1995 Faucheux LP, Stolovitzky G, Libchaber A. Periodic forcing of a Brownian particle. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 51: 5239-5250. PMID 9963256 DOI: 10.1103/PhysRevE.51.5239  1
1995 Sreenivasan KR, Stolovitzky G. Turbulent cascades Journal of Statistical Physics. 78: 311-333. DOI: 10.1007/BF02183351  1
1995 Stolovitzky G, Kailasnath P, Sreenivasan KR. Refined similarity hypotheses for passive scalars mixed by turbulence Journal of Fluid Mechanics. 297: 275-291.  1
1994 Juneja A, Lathrop DP, Sreenivasan KR, Stolovitzky G. Synthetic turbulence. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 49: 5179-5194. PMID 9961842 DOI: 10.1103/PhysRevE.49.5179  1
1994 Stolovitzky G, Sreenivasan KR. Kolmogorov's refined similarity hypotheses for turbulence and general stochastic processes Reviews of Modern Physics. 66: 229-240. DOI: 10.1103/RevModPhys.66.229  1
1993 Stolovitzky G, Sreenivasan KR, Juneja A. Scaling functions and scaling exponents in turbulence. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 48: R3217-R3220. PMID 9961088 DOI: 10.1103/PhysRevE.48.R3217  1
1993 Stolovitzky G, Sreenivasan KR. Scaling of structure functions. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 48: R33-R36. PMID 9960643 DOI: 10.1103/PhysRevE.48.R33  1
1992 Stolovitzky G, Kailasnath P, Sreenivasan KR. Kolmogorovs refined similarity hypotheses Physical Review Letters. 69: 1178-1181. DOI: 10.1103/PhysRevLett.69.1178  1
1992 Kailasnath P, Sreenivasan KR, Stolovitzky G. Probability density of velocity increments in turbulent flows Physical Review Letters. 68: 2766-2769. DOI: 10.1103/PhysRevLett.68.2766  1
1991 Stolovitzky G, Hernando JA. Intermittency, ergodicity, and spectral analysis in classical Hamiltonian dynamics Physical Review A. 43: 2774-2786. DOI: 10.1103/PhysRevA.43.2774  1
1990 Stolovitzky G, Hernando JA. Attractive and repulsive interactions in a two-dimensional billiardlike system: The Lennard-Jones stadium Physical Review A. 41: 6716-6726. DOI: 10.1103/PhysRevA.41.6716  1
1990 Stolovitzky G, Hernando JA. Resonant structure of integrable and near-integrable two-dimensional systems Physical Review A. 41: 3026-3037. DOI: 10.1103/PhysRevA.41.3026  1
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