for Integrative Genomics Lewis-Sigler Institute

Off screen link: Skip to content Off screen link: Skip to search
Princeton University
Home
for Integrative Genomics
Lewis-Sigler Institute

Main Menu

  • Research
    Research
    • Research Overview
    • Research Areas
      • Biophysics: Theory and Experiment
      • Computational Genomics
      • Evolutionary and Population Genomics
      • Experimental Genomics
      • Statistical Genomics
      • Systems Biology: Development/Aging
      • Systems Biology: Metabolomics/Proteomics
    • Faculty Research Labs
    • Research Facilities & Resources
      • Genomics Computing Resources
      • LSI Media Facility
      • Genomics Core Facility
        • Instructions
        • RNA-Seq
        • Microarray
        • Contacts
    • Research Centers
      • Center for Quantitative Biology
      • Glenn Laboratories For Aging Research
    • Faculty Publications
  • People
    People
    • Faculty
    • Associated Faculty
    • Faculty Emeriti
    • Lewis-Sigler Scholars
    • Graduate Students
    • Staff
  • Education
    Education
    • Education Overview
    • Quantitative & Computational Biology Graduate Program
      • Ph.D. Program Requirements
      • How to Apply
      • Financial Support
      • Faculty & Research
      • Graduate Students
      • Student Committees
      • Peer Mentoring Program
    • Graduate Program in Biophysics
      • Program Requirements
      • Faculty and Research
      • Graduate Students
    • Undergraduate Minor in Quantitative & Computational Biology
      • Minor Requirements
      • Application
      • Program Committee
      • Frequently Asked Questions
    • Integrated Science Curriculum
      • Course details
      • Paths from ISC
      • Student perspectives
      • Instructor perspectives
      • ISC Revitalization
    • NIH NHGRI Training Program
    • QCB Scholars Program
  • Seminars & Events
  • News
  • Diversity & Inclusion
  • About
    About
    • Founding Donors
    • History
    • Opportunities
  • Contact Us
  • Visitor Information

Search

  1. Home
  2. Research
  3. Faculty Publications

Models, Statistical

Section Menu

  • Research Overview
  • Research Areas
  • Faculty Research Labs
  • Research Facilities & Resources
  • Research Centers
  • Faculty Publications
  • Lee, Young-suk, Arjun Krishnan, Qian Zhu, and Olga G Troyanskaya. (2013) 2013. “Ontology-Aware Classification of Tissue and Cell-Type Signals in Gene Expression Profiles across Platforms and Technologies.”. Bioinformatics 29 (23): 3036-44.
    Reference Link
  • Chen, Kathleen M, Evan M Cofer, Jian Zhou, and Olga G Troyanskaya. (2019) 2019. “Selene: A PyTorch-Based Deep Learning Library for Sequence Data.”. Nat Methods 16 (4): 315-18. doi:10.1038/s41592-019-0360-8.
    Reference Link
  • Troyanskaya, Olga G, Mitchell E Garber, Patrick O Brown, David Botstein, and Russ B Altman. (2002) 2002. “Nonparametric Methods for Identifying Differentially Expressed Genes in Microarray Data.”. Bioinformatics 18 (11): 1454-61.
    Reference Link
  • Segal, Eran, Michael Shapira, Aviv Regev, Dana Pe’er, David Botstein, Daphne Koller, and Nir Friedman. (2003) 2003. “Module Networks: Identifying Regulatory Modules and Their Condition-Specific Regulators from Gene Expression Data.”. Nat Genet 34 (2): 166-76.
    Reference Link
  • Tkačik, Gašper, Curtis G Callan, and William Bialek. (2008) 2008. “Information Capacity of Genetic Regulatory Elements.”. Phys Rev E Stat Nonlin Soft Matter Phys 78 (1 Pt 1): 011910.
    Reference Link
  • Straile, Dietmar, Reiner Eckmann, Tobias Jüngling, Gregor Thomas, and Herbert Löffler. (2007) 2007. “Influence of Climate Variability on Whitefish (Coregonus Lavaretus) Year-Class Strength in a Deep, Warm Monomictic Lake.”. Oecologia 151 (3): 521-9.
    Reference Link
  • Nabieva, Elena, Kam Jim, Amit Agarwal, Bernard Chazelle, and Mona Singh. (2005) 2005. “Whole-Proteome Prediction of Protein Function via Graph-Theoretic Analysis of Interaction Maps.”. Bioinformatics 21 Suppl 1.
    Reference Link
  • Huelsenbeck, John P, and Peter Andolfatto. (2007) 2007. “Inference of Population Structure under a Dirichlet Process Model.”. Genetics 175 (4): 1787-802.
    Reference Link
  • Hibbs, Matthew A, Nathaniel C Dirksen, Kai Li, and Olga G Troyanskaya. 2005. “Visualization Methods for Statistical Analysis of Microarray Clusters.”. BMC Bioinformatics 6: 115.
    Reference Link
  • Emberly, Eldon, and Ned S Wingreen. (2006) 2006. “Hourglass Model for a Protein-Based Circadian Oscillator.”. Phys Rev Lett 96 (3): 038303.
    Reference Link
  • Stephens, Greg J, Thierry Mora, Gašper Tkačik, and William Bialek. (2013) 2013. “Statistical Thermodynamics of Natural Images.”. Phys Rev Lett 110 (1): 018701.
    Reference Link
  • Zhou, Jian, and Olga G Troyanskaya. (2014) 2014. “Global Quantitative Modeling of Chromatin Factor Interactions.”. PLoS Comput Biol 10 (3): e1003525.
    Reference Link
  • Brenner, Naama, Oded Agam, William Bialek, and Rob de Ruyter van Steveninck. (2002) 2002. “Statistical Properties of Spike Trains: Universal and Stimulus-Dependent Aspects.”. Phys Rev E Stat Nonlin Soft Matter Phys 66 (3 Pt 1): 031907.
    Reference Link
  • Guan, Yuanfang, Chad L Myers, Rong Lu, Ihor R Lemischka, Carol J Bult, and Olga G Troyanskaya. 2008. “A Genomewide Functional Network for the Laboratory Mouse.”. PLoS Comput Biol 4 (9): e1000165.
    Reference Link
  • Mukhopadhyay, Ranjan, Eldon Emberly, Chao Tang, and Ned S Wingreen. (2003) 2003. “Statistical Mechanics of RNA Folding: Importance of Alphabet Size.”. Phys Rev E Stat Nonlin Soft Matter Phys 68 (4 Pt 1): 041904.
    Reference Link
  • Park, Christopher Y, Aaron K Wong, Casey S Greene, Jessica Rowland, Yuanfang Guan, Lars A Bongo, Rebecca Burdine, and Olga G Troyanskaya. 2013. “Functional Knowledge Transfer for High-Accuracy Prediction of under-Studied Biological Processes.”. PLoS Comput Biol 9 (3): e1002957.
    Reference Link
  • Bialek, William, Andrea Cavagna, Irene Giardina, Thierry Mora, Edmondo Silvestri, Massimiliano Viale, and Aleksandra M Walczak. (2012) 2012. “Statistical Mechanics for Natural Flocks of Birds.”. Proc Natl Acad Sci U S A 109 (13): 4786-91.
    Reference Link
  • Abouchar, Laurent, Mariela D Petkova, Cynthia R Steinhardt, and Thomas Gregor. (2014) 2014. “Fly Wing Vein Patterns Have Spatial Reproducibility of a Single Cell.”. J R Soc Interface 11 (97): 20140443.
    Reference Link
  • Shaevitz, Joshua W, Steven M Block, and Mark J Schnitzer. (2005) 2005. “Statistical Kinetics of Macromolecular Dynamics.”. Biophys J 89 (4): 2277-85.
    Reference Link
  • Chen, Lin S, and John D Storey. (2008) 2008. “Eigen-R2 for Dissecting Variation in High-Dimensional Studies.”. Bioinformatics 24 (19): 2260-2.
    Reference Link
  • Tkačik, Gašper, Thomas Gregor, and William Bialek. 2008. “The Role of Input Noise in Transcriptional Regulation.”. PLoS One 3 (7): e2774.
    Reference Link
  • Rabinowitz, Joshua D, Jennifer J Hsiao, Kimberly R Gryncel, Evan R Kantrowitz, Xiao-Jiang Feng, Genyuan Li, and Herschel Rabitz. (2008) 2008. “Dissecting Enzyme Regulation by Multiple Allosteric Effectors: Nucleotide Regulation of Aspartate Transcarbamoylase.”. Biochemistry 47 (21): 5881-8.
    Reference Link
  • Lossos, Izidore S, Debra K Czerwinski, Ash A Alizadeh, Mark A Wechser, Rob Tibshirani, David Botstein, and Ronald Levy. (2004) 2004. “Prediction of Survival in Diffuse Large-B-Cell Lymphoma Based on the Expression of Six Genes.”. N Engl J Med 350 (18): 1828-37.
    Reference Link
  • Tkačik, Gašper, and William Bialek. (2009) 2009. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.”. Phys Rev E Stat Nonlin Soft Matter Phys 79 (5 Pt 1): 051901.
    Reference Link
  • Halligan, Daniel L, Adam Eyre-Walker, Peter Andolfatto, and Peter D Keightley. (2004) 2004. “Patterns of Evolutionary Constraints in Intronic and Intergenic DNA of Drosophila.”. Genome Res 14 (2): 273-9.
    Reference Link
  • Huttenhower, Curtis, and Olga G Troyanskaya. 2006. “Bayesian Data Integration: A Functional Perspective.”. Comput Syst Bioinformatics Conf, 341-51.
    Reference Link
  • Kulkarni, Rahul, V, Kerwyn Casey Huang, Morten Kloster, and Ned S Wingreen. (2004) 2004. “Pattern Formation Within Escherichia Coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules.”. Phys Rev Lett 93 (22): 228103.
    Reference Link
  • Jensen, Jeffrey D, Kevin R Thornton, and Peter Andolfatto. 2008. “An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila.”. PLoS Genet 4 (9): e1000198.
    Reference Link

Footer

Lewis-Sigler Institute for Integrative Genomics
South Drive, Carl Icahn Laboratory
Princeton University
Princeton, NJ 08544 USA

General Information:  [email protected]

  • Diversity & Non-Discrimination
  • Accessibility Help

© 2025 The Trustees of Princeton University

Princeton University