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- Overview of Chaperone Networks
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1. Mapping the molecular chaperone interaction network in yeast
- Prof. Walid A. Houry
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2. The interaction network of the GroEL chaperonin
- Prof. Dr. F. Ulrich Hartl
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3. Human heat shock protein families
- Prof. Herman Kampinga
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4. Extracellular proteostasis: an emerging field
- Prof. Mark Wilson
- Proteasome Networks
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6. Biogenesis of the eukaryotic proteasome
- Prof. Mark Hochstrasser
- Understanding Intrinsically Disordered Proteins in Protein Homeostasis
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7. Intrinsically unstructured proteins: regulation and disease
- Dr. M. Madan Babu
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8. The roles of intrinsic disorder in protein interaction networks
- Prof. Vladimir N. Uversky
- Gene Regulatory Networks and their Role in Protein Homeostasis
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10. Structure, evolution and dynamics of gene regulatory networks
- Dr. M. Madan Babu
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12. Protein-protein interaction networks
- Prof. Peter Csermely
- Protein Homeostasis in the Endoplasmic Reticulum
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13. Role of calnexin and calreticulin in protein homeostasis within the endoplasmic reticulum
- Prof. David B. Williams
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14. The unfolded protein response
- Prof. Kazutoshi Mori
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15. Role of ER stress in cystic fibrosis airway inflammation
- Dr. Carla Maria Pedrosa Ribeiro
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16. The recognition of misfolded glycoproteins in the endoplasmic reticulum
- Dr. David Y. Thomas
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17. Chaperone systems of the endoplasmic reticulum
- Prof. Linda M. Hendershot
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18. The ERAD network
- Prof. Daniel Hebert
- Protein Homeostasis in the Mitochondria
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19. Protein homeostasis in mitochondria: AAA+ chaperones & proteases
- Dr. David A. Dougan
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21. Mitochondrial chaperonin Hsp60: locations, functions and pathology
- Prof. Francesco Cappello
- Prof. Alberto J. L. Macario
- Protein Homeostasis in the Nucleus
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22. Nuclear protein quality control degradation
- Dr. Richard G. Gardner
- Protein Homeostasis in Aging Disease
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23. Protein homeostasis during ageing: C. elegans as a model organism
- Prof. Nektarios Tavernarakis
- Protein Homeostasis in Neurodegeneration
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24. Endoplasmic reticulum stress in neurodegenerative diseases
- Prof. Claudio Soto
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25. Roles for Hsp40 molecular chaperones in protein misfolding disease
- Prof. Douglas M. Cyr
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26. Protein folding in vivo
- Prof. James Bardwell
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27. Protein degradation and defense against neurodegenerative disease 1
- Prof. Alfred Goldberg
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28. Protein degradation and defense against neurodegenerative disease 2
- Prof. Alfred Goldberg
Printable Handouts
Navigable Slide Index
- Introduction
- Outline
- Finding regulatory motifs
- Motif discovery: the two-step strategy
- Amadeus
- Motif search algorithm
- Scoring over-represented motifs
- Metazoan motif discovery benchmark
- Comparing Amadeus to 5 popular motifs
- Amadeus - global spatial analysis
- Global analyses
- Chromosomal preference in C. elegans
- Finding transcriptional programs
- Goal (1)
- Our goal: bypass the two-step approach
- Yeast osmotic shock pathway
- 3' UTR analysis: human stem cells
- Human stem cells: results using binned score
- A new regulatory motif pair in C. elegans
- Pair occurs in 154 promoters
- Motif across the C. rhabditis genus
- Testing the motif experimentally
- User interface of Amadeus
- Analysis of gene expression profiles + a network
- Overall gene interaction network
- Goal (2)
- Matisse algorithm development
- Probabilistic model
- Front vs. back nodes
- Test case: yeast osmotic shock
- Pheromone response subnetwork
- Performance comparison
- GO and promoter analysis
- Application to stem cells
- Network found using Matisse
- Accounting for PPI confidence
- DNA damage response in S. cerevisiae
- DNA damage response modules
- Comparison with prior work
- Conclusion (1)
- Conclusion (2)
- Thanks (1)
- Thanks (2)
Topics Covered
- Finding regulatory motifs
- Finding motifs using target sets of promoters
- Problem definition
- The Amadeus motif finding algorithm
- Architecture, benchmark results and global analysis
- Finding transcriptional programs and their regulatory motifs
- Problem definition
- The Allegro software for recovering transcriptional program
- Results on yeast osmotic shock expression profiles
- Recovering microRNA binding motifs from 3' UTRs using stem cell expression profiles
- Discovering a novel motif pair in C. elegans
- Utilizing network information
- Using expression and protein interaction data
- Problem definition and the Matisse algorithm
- Demonstration of Matisse on yeast osmotic shock data
- Comparison of Matisse to other algorithms
- Demonstration of Matisse on human stem cell data
- The pluripotency network
- Using expression and protein interaction data with interaction confidence
- The Cezanne algorithm
- DNA damage response in yeast
Talk Citation
Shamir, R. (2020, October 19). Computational methods in analysis of gene regulation and protein interactions [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved March 21, 2025, from https://doi.org/10.69645/WTDF6649.Export Citation (RIS)
Publication History
Financial Disclosures
- Prof. Ron Shamir has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.
Computational methods in analysis of gene regulation and protein interactions
A selection of talks on Methods
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