Gad Shaulsky, Ph.D.
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Positions
- Professor and Director of Graduate Studies
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Graduate Program in Genetics & Genomics
Baylor College of Medicine
- Professor
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Graduate Program in Immunology & Microbiology
Baylor College of Medicine
- Professor and Vice Chair for Graduate Education Affairs
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Molecular and Human Genetics
Department of Molecular and Human Genetics
Houston, Texas United States
Addresses
- BCM-Smith Medical Research Bldg (Lab)
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Room: BCMS-S930
Houston, TX 77030
United States
Phone: (713) 798-8082
gadi@bcm.edu
- BCM-Smith Medical Research Bldg (Office)
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Room: BCMS-S930
Houston, TX 77030
United States
Phone: (713) 798-8082
gadi@bcm.edu
Education
- BSc from Tel Aviv University
- 09/1985 - Tel Aviv, Israel
- MSc from Tel Aviv University
- 09/1986 - Tel Aviv, Israel
- PhD from Weizmann Institute of Science
- 05/1991 - Rehovot, Israel
- Post-Doctoral Fellowship at University Of California, San Diego
- 06/1997 - La Jolla, California United States
Honors & Awards
- Barbara & Corbin J. Robertson, Jr. Presidential Award for Excellence In Education
- Baylor College of Medicine (05/2020)
- Michael E. DeBakey, M.D., Excellence in Research Award
- Baylor College of Medicine (05/2011)
- Michael E. DeBakey, M.D., Excellence in Research Award
- Baylor College of Medicine (05/2006)
Professional Interests
- Functional Genomics and Transcriptome analysis
- The evolution of social behavior in Dictyostelium
- Allorecognition in Dictyostelium
- Developmental genetics in Dictyostelium
Professional Statement
Allorecognition: Dictyostelium cells preferentially cooperate with relatives (Ostrowski, 2008), and we are investigating the mechanisms that underlie this kin discrimination. We found two cell-cell adhesion genes, tgrB1 and tgrC1, that are highly polymorphic in natural populations and required for allorecognition (Benabentos, 2009), and showed that the sequence polymorphism in these genes is sufficient to explain allorecognition in Dictyostelium (Hirose, 2011). This kin-recognition system protects cooperators against cheaters (Ho, 2013) and is temporally regulated, which allows it to evolve despite its essential role in development (Ho, 2015). We are investigating the mechanisms that regulate allorecognition under the hypothesis that TgrB1 and TgrC1 function as a ligand-receptor pair (Hirose, 2017), which is at the top of a signal transduction cascade that regulates development and allorecognition. The TgrB1-C1 system replaces cAMP as the central signaling system during tissue integration (Hirose, 2021), and we are investigating the downstream signal transduction mechanisms that were initially found using a genetic suppressor screen (Li, 2016).The evolution of social behavior in Dictyostelium: Social organisms must deal with cheaters - individuals that reap the benefits of sociality without paying the costs. In Dictyostelium, some cells sacrifice themselves and benefit other cells that may be genetically different, providing a fertile ground for cheating. We have found over 100 genes that participate in social interactions (Santorelli, 2008) and used genetic tools to characterize mechanisms that determine social interactions and test how cooperators resist cheating (Khare and Shaulsky, 2006; Khare, 2009; Khare and Shaulsky, 2010). We are investigating the role of the TgrB1-C1 signaling system in cheating.
Functional Genomics: We have used transcriptomes to discover gene function in Dictyostelium (Booth, 2005; Van Driessche, 2007). We also showed that the transcriptome is a good phenotyping tool for discovering epistatic relationships (Van Driessche, 2005). Using RNA-seq, we compared the developmental transcriptomes of D. discoideum and D. purpureum, two species that diverged ~350MYA, but whose developmental morphologies are similar. We found vast similarities between the two transcriptomes (Parikh, 2010). We analyzed many mutants, and we developed a system for the analysis of transcription factors with RNA-seq and ChIP-seq (Santhanam, 2015). We found complex regulation of transcriptional activity during development (Rosengarten, 2015) and described the long-non-coding transcriptome (Rosengarten, 2017). We are analyzing the major transcriptional transitions that characterize Dictyostelium development using RNA-seq profiles of 20 mutants (Katoh-Kurasawa, 2021). We are also developing new tools for the exploration of the Dictyostelium genome, including a deep coverage genomic DNA library (Rosengarten, 2015), gene discovery by chemical mutagenesis at low level and whole-genome sequencing to identify mutations (Li, 2016) and an adaptation of GoldenBraid as a synthetic biology tool for Dictyostelium (Kundert, 2020).
Data Mining: We are collaborating with Dr. Zupan and his group at the University of Ljubljana, Slovenia to develop new concepts in genetic analysis. Previously we have developed a tool that performs automated epistasis analysis, GenePath (Demsar, 2001). We developed a gene function prediction system that relies on compressive data fusion and chaining and demonstrated its utility in predicting the function of bacterial-recognition genes in D. discoideum (Zitnik, 2015). We also developed dictyExpress, a web tool that can access and analyze our transcriptional profiling data (Stajdohar, 2017). Two of our recent collaborative projects include scOrange, a tool for analyzing single-cell RNA-seq data (Stražar, 2019) and an image analysis platform that utilizes deep models in a visual programming environment (Godec, 2019).
Websites
An interactive search and exploration tool for the BCM Dictyostelium gene expression database. Developed in collaboration with the Bioinformatics Laboratory, University of Ljubljana, Slovenia
GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks. Developed in collaboration with the Bioinformatics Laboratory, University of Ljubljana, Slovenia
Selected Publications
- Ho HI, Hirose S, Kuspa A, Shaulsky G "Kin Recognition Protects Cooperators against Cheaters.." Curr. Biol.. 2013 23 (16): 1590-1595. Pubmed PMID: 23910661
- Khare A, Santorelli LA, Strassmann JE, Queller DC, Kuspa A, Shaulsky G "Cheater-resistance is not futile.." Nature. 2009 October 15; 461 (7266): 980-2. Pubmed PMID: 19794414
- Santorelli LA, Thompson CR, Villegas E, Svetz J, Dinh C, Parikh A, Sucgang R, Kuspa A, Strassmann JE, Queller DC, Shaulsky G "Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae.." Nature. 2008 February 28; 451 (7182): 1107-10. Pubmed PMID: 18272966
- Benabentos R, Hirose S, Sucgang R, Curk T, Katoh M, Ostrowski EA, Strassmann JE, Queller DC, Zupan B, Shaulsky G, Kuspa A "Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium.." Curr. Biol.. 2009 April 14; 19 (7): 567-72. Pubmed PMID: 19285397
- Hirose S, Benabentos R, Ho HI, Kuspa A, Shaulsky G "Self-recognition in social amoebae is mediated by allelic pairs of tiger genes.." Science. 2011 July 22; 333 (6041): 467-70. Pubmed PMID: 21700835
- Rosengarten RD, Santhanam B, Fuller D, Katoh-Kurasawa M, Loomis WF, Zupan B, Shaulsky G "Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.." BMC Genomics. 2015 April 13; 16 (1): 294. Pubmed PMID: 25887420
- Cai, H. Katoh-Kurasawa, M. Muramoto, T. Santhanam, B. Long, Y. Li, L. Ueda, M. Iglesias, P. A. Shaulsky, G. Devreotes, P. N. "Nucleocytoplasmic shuttling of a GATA transcription factor functions as a development timer." Science. 2014 March ; 343 (6177): 1249531. Pubmed PMID: 24653039
- Ho HI, Shaulsky G "Temporal regulation of kin recognition maintains recognition-cue diversity and suppresses cheating." Nat Commun. 2015 May 28; 6 : 7144. Pubmed PMID: 4448137
- Santhanam B, Cai H, Devreotes PN, Shaulsky G, Katoh-Kurasawa M "The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium." Nat Commun.. 2015 July 6; 6 : 7551. Pubmed PMID: 26144553
- Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, Shaulsky G "Conserved developmental transcriptomes in evolutionarily divergent species.." Genome Biol.. 2010 11 (3): R35. Pubmed PMID: 20236529
- Kundert, P., Sarrion-Perdigones, A., Gonzalez, Y., Katoh-Kurasawa, M., Hirose, S., Lehmann, P., Venken, K.J.T., and Shaulsky, G "A GoldenBraid cloning system for synthetic biology in social amoebae.." Nucleic Acids Res. 2020 48 : 4139-4146.
- Kundert, P., and Shaulsky, G. "Cellular allorecognition and its roles in Dictyostelium development and social evolution.." Int J Dev Biol. 2019 63 : 383-393.
- 100. Godec, P., Pancur, M., Ilenic, N., Copar, A., Strazar, M., Erjavec, A., Pretnar, A., Demsar, J., Staric, A., Toplak, M., Zagar, L., Hartman, J., Wang, H., Bellazzi, R., Petrovic, U., Garagna, S., Zuccotti, M., Park, D., Shaulsky, G., Zupan, B. "Democratized image analytics by visual programming through integration of deep models and small-scale machine learning.." Nat Commun. 2019 10 : 4551.
- Stražar, M., Žagar, L., Kokošar, J., Tanko, V., Erjavec, A., Poličar, P.G., Starič, A., Demšar, J., Shaulsky, G., Menon, V., Lemire, A., Parikh, A., Zupan, B. "scOrange—a tool for hands-on training of concepts from single-cell data analytics.." Bioinformatics. 2019 35 : i4-i12.
- Hirose, S. Chen, G. Kuspa, A. Shaulsky, G. "The polymorphic proteins TgrB1 and TgrC1 function as a ligand-receptor pair in Dictyostelium allorecognition." J Cell Sci. 2017 130 (23): 4002-4012. Pubmed PMID: 5769593
- Hirose S, Katoh-Kurasawa M, Shaulsky G "Cyclic AMP is dispensable for allorecognition in Dictyostelium cells overexpressing PKA-C." J Cell Sci. 2021 134 : jcs258777.
- Katoh-Kurasawa M, Hrovatin K, Hirose S, Webb A, Ho HI, Zupan B, Shaulsky G "Transcriptional milestones in Dictyostelium development.." Genome Res. 2021 31 : 1498-1511.
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