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Summer Thyme PhD

TitleAssistant Professor
InstitutionUMass Chan Medical School
DepartmentBiochemistry and Molecular Biotechnology
AddressUniversity of Massachusetts Medical School
55 Lake Ave North
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBioinformatics and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentMillennium MD/PhD Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentNeuroscience

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentTranslational Science


    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Pluimer BR, Harrison DL, Boonyavairoje C, Prinssen EP, Rogers-Evans M, Peterson RT, Thyme SB, Nath AK. Behavioral analysis through the lifespan of disc1 mutant zebrafish identifies defects in sensorimotor transformation. iScience. 2023 Jul 21; 26(7):107099. PMID: 37416451.
      Citations:    
    2. Park JU, Petassi MT, Hsieh SC, Mehrotra E, Schuler G, Budhathoki J, Truong VH, Thyme SB, Ke A, Kellogg EH, Peters JE. Multiple adaptations underly co-option of a CRISPR surveillance complex for RNA-guided DNA transposition. Mol Cell. 2023 06 01; 83(11):1827-1838.e6. PMID: 37267904.
      Citations: 1     Fields:    
    3. Pandey S, Moyer AJ, Thyme SB. A single-cell transcriptome atlas of the maturing zebrafish telencephalon. Genome Res. 2023 04; 33(4):658-671. PMID: 37072188.
      Citations: 1     Fields:    Translation:AnimalsCells
    4. Campbell PD, Lee I, Thyme S, Granato M. Mitochondrial genes in the 22q11.2 deleted region regulate neural stem and progenitor cell proliferation. bioRxiv. 2023 Jan 03. PMID: 36711666.
      Citations:    
    5. Robens BK, Yang X, McGraw CM, Turner LH, Robens C, Thyme S, Rotenberg A, Poduri A. Mosaic and non-mosaic protocadherin 19 mutation leads to neuronal hyperexcitability in zebrafish. Neurobiol Dis. 2022 07; 169:105738. PMID: 35460869.
      Citations: 1     Fields:    Translation:Animals
    6. DeLaurier A, Howe DG, Ruzicka L, Carte AN, Mishoe Hernandez L, Wiggins KJ, Gallati MM, Vanpelt K, Loyo Rosado F, Pugh KG, Shabdue CJ, Jihad K, Thyme SB, Talbot JC. ZebraShare: a new venue for rapid dissemination of zebrafish mutant data. PeerJ. 2021; 9:e11007. PMID: 33954026.
      Citations:    Fields:    
    7. Joo W, Vivian MD, Graham BJ, Soucy ER, Thyme SB. A Customizable Low-Cost System for Massively Parallel Zebrafish Behavioral Phenotyping. Front Behav Neurosci. 2020; 14:606900. PMID: 33536882.
      Citations:    
    8. Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmstr?m L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, ?'Conch?ir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods. 2020 07; 17(7):665-680. PMID: 32483333.
      Citations: 201     Fields:    Translation:Cells
    9. Thyme SB, Pieper LM, Li EH, Pandey S, Wang Y, Morris NS, Sha C, Choi JW, Herrera KJ, Soucy ER, Zimmerman S, Randlett O, Greenwood J, McCarroll SA, Schier AF. Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions. Cell. 2019 04 04; 177(2):478-491.e20. PMID: 30929901.
      Citations: 73     Fields:    Translation:Animals
    10. Escamilla CO, Filonova I, Walker AK, Xuan ZX, Holehonnur R, Espinosa F, Liu S, Thyme SB, L?pez-Garc?a IA, Mendoza DB, Usui N, Ellegood J, Eisch AJ, Konopka G, Lerch JP, Schier AF, Speed HE, Powell CM. Kctd13 deletion reduces synaptic transmission via increased RhoA. Nature. 2017 11 09; 551(7679):227-231. PMID: 29088697.
      Citations: 67     Fields:    Translation:AnimalsCells
    11. Thyme SB, Akhmetova L, Montague TG, Valen E, Schier AF. Internal guide RNA interactions interfere with Cas9-mediated cleavage. Nat Commun. 2016 06 10; 7:11750. PMID: 27282953.
      Citations: 67     Fields:    Translation:AnimalsCells
    12. Thyme SB, Schier AF. Polq-Mediated End Joining Is Essential for Surviving DNA Double-Strand Breaks during Early Zebrafish Development. Cell Rep. 2016 05 17; 15(7):1611-1613. PMID: 27192698.
      Citations: 11     Fields:    
    13. Labun K, Montague TG, Gagnon JA, Thyme SB, Valen E. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res. 2016 07 08; 44(W1):W272-6. PMID: 27185894.
      Citations: 402     Fields:    Translation:HumansAnimalsCells
    14. Thyme SB, Schier AF. Polq-Mediated End Joining Is Essential for Surviving DNA Double-Strand Breaks during Early Zebrafish Development. Cell Rep. 2016 Apr 26; 15(4):707-714. PMID: 27149851.
      Citations: 23     Fields:    
    15. Thyme S, Song Y. Computational Design of DNA-Binding Proteins. Methods Mol Biol. 2016; 1414:265-83. PMID: 27094297.
      Citations:    Fields:    
    16. Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D. Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Res. 2014 Dec 16; 42(22):13839-52. PMID: 25389263.
      Citations: 5     Fields:    Translation:Cells
    17. Gagnon JA, Valen E, Thyme SB, Huang P, Akhmetova L, Ahkmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One. 2014; 9(5):e98186. PMID: 24873830.
      Citations: 451     Fields:    Translation:HumansAnimals
    18. Wang Y, Khan IF, Boissel S, Jarjour J, Pangallo J, Thyme S, Baker D, Scharenberg AM, Rawlings DJ. Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus. Nucleic Acids Res. 2014 Jun; 42(10):6463-75. PMID: 24682825.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    19. Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with Rosetta. Methods Mol Biol. 2014; 1123:265-82. PMID: 24510272.
      Citations: 7     Fields:    Translation:Cells
    20. Thyme SB, Boissel SJ, Arshiya Quadri S, Nolan T, Baker DA, Park RU, Kusak L, Ashworth J, Baker D. Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Res. 2014 Feb; 42(4):2564-76. PMID: 24270794.
      Citations: 18     Fields:    Translation:AnimalsCells
    21. Thyme SB, Baker D, Bradley P. Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design. J Mol Biol. 2012 Jun 08; 419(3-4):255-74. PMID: 22426128.
      Citations: 8     Fields:    Translation:Cells
    22. Szeto MD, Boissel SJ, Baker D, Thyme SB. Mining endonuclease cleavage determinants in genomic sequence data. J Biol Chem. 2011 Sep 16; 286(37):32617-27. PMID: 21778233.
      Citations: 10     Fields:    
    23. Windbichler N, Menichelli M, Papathanos PA, Thyme SB, Li H, Ulge UY, Hovde BT, Baker D, Monnat RJ, Burt A, Crisanti A. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature. 2011 May 12; 473(7346):212-5. PMID: 21508956.
      Citations: 154     Fields:    Translation:AnimalsPHPublic Health
    24. Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D. Exploitation of binding energy for catalysis and design. Nature. 2009 Oct 29; 461(7268):1300-4. PMID: 19865174.
      Citations: 52     Fields:    Translation:AnimalsCells
    25. Madison BL, Thyme SB, Keene S, Williams BS. Mechanistic study of competitive sp(3)-sp(3) and sp(2)-sp(3) carbon-carbon reductive elimination from a platinum (IV) center and the isolation of a C-C agostic complex. J Am Chem Soc. 2007 Aug 08; 129(31):9538-9. PMID: 17629265.
      Citations: 1     Fields:    Translation:Cells
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