List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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Transcriptional Activation
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
Transcription, Genetic
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
Transcription Factors
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
Time Factors
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Thermodynamics
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
Stress, Physiological
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Spores, Fungal
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Signal Transduction
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Sequence Analysis, Protein
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
Saccharomyces cerevisiae Proteins
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Saccharomyces cerevisiae
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
RNA, Helminth
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
RNA Interference
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Response Elements
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Repressor Proteins
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Regulatory Sequences, Nucleic Acid
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
Receptor, Insulin
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Proteins
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
Protein Folding
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
Protein Conformation
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
Promoter Regions, Genetic
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Phylogeny
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
Oligonucleotide Array Sequence Analysis
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Nuclear Proteins
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Molecular Sequence Data
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Models, Theoretical
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
Models, Genetic
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Longevity
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Insulin-Like Growth Factor I
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Insulin
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Hydrophobic and Hydrophilic Interactions
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
Humans
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
Genes, Helminth
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Gene Expression Regulation, Developmental
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Gene Expression Regulation
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
Gene Expression Profiling
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
Feedback, Physiological
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Drosophila melanogaster
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
DNA-Binding Proteins
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Databases, Genetic
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
Cluster Analysis
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Caenorhabditis elegans Proteins
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Caenorhabditis elegans
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Binding Sites
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Base Sequence
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Animals
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Amino Acids
H. Li, Tang, C., and Wingreen, N. S., “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
Algorithms
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
Aging
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
C. T. Murphy, McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H., and Kenyon, C., “Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.”, Nature, vol. 424, no. 6946, pp. 277-83, 2003.
Age Factors
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.