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

Reproducibility of Results

Section Menu

  • Research Overview
  • Research Areas
  • Faculty Research Labs
  • Research Facilities & Resources
  • Research Centers
  • Faculty Publications
  • Novoradovskaya, Natalia, Michael L Whitfield, Lee S Basehore, Alexey Novoradovsky, Robert Pesich, Jerry Usary, Mehmet Karaca, et al. (2004) 2004. “Universal Reference RNA As a Standard for Microarray Experiments.”. BMC Genomics 5 (1): 20.
    Reference Link
  • Myers, Chad L, Daniel R Barrett, Matthew A Hibbs, Curtis Huttenhower, and Olga G Troyanskaya. 2006. “Finding Function: Evaluation Methods for Functional Genomic Data.”. BMC Genomics 7: 187.
    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
  • Hibbs, Matthew A, David C Hess, Chad L Myers, Curtis Huttenhower, Kai Li, and Olga G Troyanskaya. (2007) 2007. “Exploring the Functional Landscape of Gene Expression: Directed Search of Large Microarray Compendia.”. Bioinformatics 23 (20): 2692-9.
    Reference Link
  • Park, Christopher Y, David C Hess, Curtis Huttenhower, and Olga G Troyanskaya. 2010. “Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components.”. PLoS Comput Biol 6 (11): e1001009.
    Reference Link
  • Myers, Chad L, Drew Robson, Adam Wible, Matthew A Hibbs, Camelia Chiriac, Chandra L Theesfeld, Kara Dolinski, and Olga G Troyanskaya. 2005. “Discovery of Biological Networks from Diverse Functional Genomic Data.”. Genome Biol 6 (13): R114.
    Reference Link
  • Bajad, Sunil U, Wenyun Lu, Elizabeth H Kimball, Jie Yuan, Celeste Peterson, and Joshua D Rabinowitz. (2006) 2006. “Separation and Quantitation of Water Soluble Cellular Metabolites by Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry.”. J Chromatogr A 1125 (1): 76-88.
    Reference Link
  • Huttenhower, Curtis, and Olga G Troyanskaya. 2006. “Bayesian Data Integration: A Functional Perspective.”. Comput Syst Bioinformatics Conf, 341-51.
    Reference Link
  • Gregor, Thomas, David W Tank, Eric F Wieschaus, and William Bialek. (2007) 2007. “Probing the Limits to Positional Information.”. Cell 130 (1): 153-64.
    Reference Link
  • Morozova, Tatiana, V, Julien Ayroles, Katherine W Jordan, Laura Duncan, Mary Anna Carbone, Richard F Lyman, Eric A Stone, et al. (2009) 2009. “Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics.”. Genetics 183 (2): 733-45, 1SI.
    Reference Link
  • Fong, Jessica H, Amy E Keating, and Mona Singh. 2004. “Predicting Specificity in BZIP Coiled-Coil Protein Interactions.”. Genome Biol 5 (2): R11.
    Reference Link
  • Dubuis, Julien, Reba Samanta, and Thomas Gregor. 2013. “Accurate Measurements of Dynamics and Reproducibility in Small Genetic Networks.”. Mol Syst Biol 9: 639.
    Reference Link
  • Persikov, Anton, V, Robert Osada, and Mona Singh. (2009) 2009. “Predicting DNA Recognition by Cys2His2 Zinc Finger Proteins.”. Bioinformatics 25 (1): 22-9.
    Reference Link
  • Greene, Casey S, and Olga G Troyanskaya. (2012) 2012. “Accurate Evaluation and Analysis of Functional Genomics Data and Methods.”. Ann N Y Acad Sci 1260: 95-100.
    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
  • Myers, Chad L, Maitreya Dunham, S Y Kung, and Olga G Troyanskaya. (2004) 2004. “Accurate Detection of Aneuploidies in Array CGH and Gene Expression Microarray Data.”. Bioinformatics 20 (18): 3533-43.
    Reference Link
  • Kristensen, Vessela N, Charles J Vaske, Josie Ursini-Siegel, Peter Van Loo, Silje H Nordgard, Ravi Sachidanandam, Therese Sørlie, et al. (2012) 2012. “Integrated Molecular Profiles of Invasive Breast Tumors and Ductal Carcinoma in Situ (DCIS) Reveal Differential Vascular and Interleukin Signaling.”. Proc Natl Acad Sci U S A 109 (8): 2802-7.
    Reference Link
  • Gorenshteyn, Dmitriy, Elena Zaslavsky, Miguel Fribourg, Christopher Y Park, Aaron K Wong, Alicja Tadych, Boris M Hartmann, et al. (2015) 2015. “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”. Immunity 43 (3): 605-14.
    Reference Link
  • Pop, Ana, Curtis Huttenhower, Anjali Iyer-Pascuzzi, Philip N Benfey, and Olga G Troyanskaya. 2010. “Integrated Functional Networks of Process, Tissue, and Developmental Stage Specific Interactions in Arabidopsis Thaliana.”. BMC Syst Biol 4: 180.
    Reference Link
  • Vizcarra, Christina L, Naigong Zhang, Shannon A Marshall, Ned S Wingreen, Chen Zeng, and Stephen L Mayo. (2008) 2008. “An Improved Pairwise Decomposable Finite-Difference Poisson-Boltzmann Method for Computational Protein Design.”. J Comput Chem 29 (7): 1153-62.
    Reference Link
  • Lu, Wenyun, Elizabeth Kimball, and Joshua D Rabinowitz. (2006) 2006. “A High-Performance Liquid Chromatography-Tandem Mass Spectrometry Method for Quantitation of Nitrogen-Containing Intracellular Metabolites.”. J Am Soc Mass Spectrom 17 (1): 37-50.
    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
  • Chikina, Maria D, Curtis Huttenhower, Coleen T Murphy, and Olga G Troyanskaya. (2009) 2009. “Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis Elegans.”. PLoS Comput Biol 5 (6): e1000417.
    Reference Link
  • Guan, Yuanfang, Cheryl L Ackert-Bicknell, Braden Kell, Olga G Troyanskaya, and Matthew A Hibbs. 2010. “Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations.”. PLoS Comput Biol 6 (11): e1000991.
    Reference Link
  • Endres, Robert G, Olga Oleksiuk, Clinton H Hansen, Yigal Meir, Victor Sourjik, and Ned S Wingreen. 2008. “Variable Sizes of Escherichia Coli Chemoreceptor Signaling Teams.”. Mol Syst Biol 4: 211.
    Reference Link
  • Ayroles, Julien, Brooke A Laflamme, Eric A Stone, Mariana F Wolfner, and Trudy F C Mackay. (2011) 2011. “Functional Genome Annotation of Drosophila Seminal Fluid Proteins Using Transcriptional Genetic Networks.”. Genet Res (Camb) 93 (6): 387-95.
    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