Mark Kelly, PhD

Title(s)Professional Researcher, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address600 16th Street, #S126F
San Francisco CA 94158
Phone415-476-8143
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details 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. AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid. bioRxiv. 2024 Aug 26. Chen DF, Roe LT, Li Y, Borges AL, Zhang JY, Babbar P, Maji S, Stevens MGV, Correy GJ, Diolaiti ME, Smith DH, Ashworth A, Stroud RM, Kelly MJS, Bondy-Denomy J, Fraser JS. PMID: 39253479; PMCID: PMC11383003.
      View in: PubMed   Mentions:
    2. Deep learning guided design of dynamic proteins. bioRxiv. 2024 Jul 19. Guo AB, Akpinaroglu D, Kelly MJS, Kortemme T. PMID: 39071443; PMCID: PMC11275770.
      View in: PubMed   Mentions:
    3. Identifying ligands for the PHD1 finger of KDM5A through high-throughput screening. RSC Chem Biol. 2024 Mar 06; 5(3):209-215. Ortiz G, Longbotham JE, Qin SL, Zhang MY, Lee GM, Neitz RJ, Kelly MJS, Arkin MR, Fujimori DG. PMID: 38456036; PMCID: PMC10915964.
      View in: PubMed   Mentions:
    4. Chromatin Sensing by the Auxiliary Domains of KDM5C Regulates Its Demethylase Activity and Is Disrupted by X-linked Intellectual Disability Mutations. J Mol Biol. 2023 01 30; 435(2):167913. Ugur FS, Kelly MJS, Fujimori DG. PMID: 36495919; PMCID: PMC10247153.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    5. Probing the KRas Switch II Groove by Fluorine NMR Spectroscopy. ACS Chem Biol. 2022 10 21; 17(10):2710-2715. Peacock DM, Kelly MJS, Shokat KM. PMID: 36166818; PMCID: PMC9594042.
      View in: PubMed   Mentions: 1     Fields:    
    6. Systems-level effects of allosteric perturbations to a model molecular switch. Nature. 2021 11; 599(7883):152-157. Perica T, Mathy CJP, Xu J, Jang G?, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T. PMID: 34646016; PMCID: PMC8571063.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    7. Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A. ACS Chem Biol. 2023 09 15; 18(9):1915-1925. Longbotham JE, Kelly MJS, Fujimori DG. PMID: 33621062; PMCID: PMC8380758.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    8. Expanding the space of protein geometries by computational design of de novo fold families. Science. 2020 08 28; 369(6507):1132-1136. Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. PMID: 32855341; PMCID: PMC7787817.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    9. Computational design of a modular protein sense-response system. Science. 2019 11 22; 366(6468):1024-1028. Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. PMID: 31754004; PMCID: PMC7343396.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    10. Neural JNK3 regulates blood flow recovery after hindlimb ischemia in mice via an Egr1/Creb1 axis. Nat Commun. 2019 09 17; 10(1):4223. Kant S, Craige SM, Chen K, Reif MM, Learnard H, Kelly M, Caliz AD, Tran KV, Ramo K, Peters OM, Freeman M, Davis RJ, Keaney JF. PMID: 31530804; PMCID: PMC6748991.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    11. A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain. Cell. 2019 09 05; 178(6):1362-1374.e16. Lin King JV, Emrick JJ, Kelly MJS, Herzig V, King GF, Medzihradszky KF, Julius D. PMID: 31447178; PMCID: PMC6731142.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    12. HDAC inhibition in glioblastoma monitored by hyperpolarized 13 C MRSI. NMR Biomed. 2019 02; 32(2):e4044. Radoul M, Najac C, Viswanath P, Mukherjee J, Kelly M, Gillespie AM, Chaumeil MM, Eriksson P, Delos Santos R, Pieper RO, Ronen SM. PMID: 30561869; PMCID: PMC6545173.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    13. The centrosomin CM2 domain is a multi-functional binding domain with distinct cell cycle roles. PLoS One. 2018; 13(1):e0190530. Citron YR, Fagerstrom CJ, Keszthelyi B, Huang B, Rusan NM, Kelly MJS, Agard DA. PMID: 29315319; PMCID: PMC5760045.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    14. A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells. Nat Chem. 2017 09; 9(9):874-881. Stöhr J, Wu H, Nick M, Wu Y, Bhate M, Condello C, Johnson N, Rodgers J, Lemmin T, Acharya S, Becker J, Robinson K, Kelly MJS, Gai F, Stubbs G, Prusiner SB, DeGrado WF. PMID: 28837163; PMCID: PMC5759337.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    15. Allosteric Indole Amide Inhibitors of p97: Identification of a Novel Probe of the Ubiquitin Pathway. ACS Med Chem Lett. 2016 Feb 11; 7(2):182-7. Alverez C, Bulfer SL, Chakrasali R, Chimenti MS, Deshaies RJ, Green N, Kelly M, LaPorte MG, Lewis TS, Liang M, Moore WJ, Neitz RJ, Peshkov VA, Walters MA, Zhang F, Arkin MR, Wipf P, Huryn DM. PMID: 26985295; PMCID: PMC4753542.
      View in: PubMed   Mentions: 15  
    16. Allosteric N-WASP activation by an inter-SH3 domain linker in Nck. Proc Natl Acad Sci U S A. 2015 Nov 24; 112(47):E6436-45. Okrut J, Prakash S, Wu Q, Kelly MJ, Taunton J. PMID: 26554011; PMCID: PMC4664294.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    17. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. J Biomol Screen. 2015 Jul; 20(6):788-800. Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJ. PMID: 25690569.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    18. Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism. Nat Commun. 2015 Feb 17; 6:6204. Torres IO, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJ, Fujimori DG. PMID: 25686748; PMCID: PMC5080983.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansAnimalsCells
    19. Biophysical methods for identifying fragment-based inhibitors of protein-protein interactions. Methods Mol Biol. 2015; 1278:587-613. Pfaff SJ, Chimenti MS, Kelly MJ, Arkin MR. PMID: 25859978.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    20. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone. J Mol Biol. 2014 Jun 12; 426(12):2393-404. Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA. PMID: 24726919; PMCID: PMC5322795.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    21. 13C NMR metabolomic evaluation of immediate and delayed mild hypothermia in cerebrocortical slices after oxygen-glucose deprivation. Anesthesiology. 2013 Nov; 119(5):1120-36. Liu J, Segal MR, Kelly MJ, Pelton JG, Kim M, James TL, Litt L. PMID: 23748856; PMCID: PMC3890426.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    22. 1H nuclear magnetic resonance brain metabolomics in neonatal mice after hypoxia-ischemia distinguished normothermic recovery from mild hypothermia recoveries. Pediatr Res. 2013 Aug; 74(2):170-9. Liu J, Sheldon RA, Segal MR, Kelly MJ, Pelton JG, Ferriero DM, James TL, Litt L. PMID: 23708689; PMCID: PMC3734529.
      View in: PubMed   Mentions: 23     Fields:    Translation:Animals
    23. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure. 2013 Jan 08; 21(1):54-64. Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T. PMID: 23159126.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    24. Metabolomics of oxidative stress in recent studies of endogenous and exogenously administered intermediate metabolites. Int J Mol Sci. 2011; 12(10):6469-501. Liu J, Litt L, Segal MR, Kelly MJ, Pelton JG, Kim M. PMID: 22072900; PMCID: PMC3210991.
      View in: PubMed   Mentions: 25     Fields:    Translation:Humans
    25. Radically different amyloid conformations dictate the seeding specificity of a chimeric Sup35 prion. J Mol Biol. 2011 Apr 22; 408(1):1-8. Foo CK, Ohhashi Y, Kelly MJ, Tanaka M, Weissman JS. PMID: 21333653; PMCID: PMC3070826.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    26. Outcome-related metabolomic patterns from 1H/31P NMR after mild hypothermia treatments of oxygen-glucose deprivation in a neonatal brain slice model of asphyxia. J Cereb Blood Flow Metab. 2011 Feb; 31(2):547-59. Liu J, Litt L, Segal MR, Kelly MJ, Yoshihara HA, James TL. PMID: 20717124; PMCID: PMC3010526.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    27. Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding. J Cell Biol. 2008 Dec 01; 183(5):865-79. Frantz C, Barreiro G, Dominguez L, Chen X, Eddy R, Condeelis J, Kelly MJ, Jacobson MP, Barber DL. PMID: 19029335; PMCID: PMC2592832.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansAnimalsCells
    28. Exogenous ethyl pyruvate versus pyruvate during metabolic recovery after oxidative stress in neonatal rat cerebrocortical slices. Anesthesiology. 2007 Oct; 107(4):630-40. Zeng J, Liu J, Yang GY, Kelly MJ, James TL, Litt L. PMID: 17893460.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    29. The structural basis of yeast prion strain variants. Nature. 2007 Sep 13; 449(7159):233-7. Toyama BH, Kelly MJ, Gross JD, Weissman JS. PMID: 17767153.
      View in: PubMed   Mentions: 196     Fields:    Translation:AnimalsCells
    30. Parallel beta-helix proteins required for accurate capsule polysaccharide synthesis and virulence in the yeast Cryptococcus neoformans. Eukaryot Cell. 2007 Apr; 6(4):630-40. Liu OW, Kelly MJ, Chow ED, Madhani HD. PMID: 17337638; PMCID: PMC1865648.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    31. Pyruvate improves recovery after PARP-1-associated energy failure induced by oxidative stress in neonatal rat cerebrocortical slices. J Cereb Blood Flow Metab. 2007 Feb; 27(2):304-15. Zeng J, Yang GY, Ying W, Kelly M, Hirai K, James TL, Swanson RA, Litt L. PMID: 16736046.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    32. Using 31P NMR spectroscopy at 14.1 Tesla to investigate PARP-1 associated energy failure and metabolic rescue in cerebrocortical slices. J Bioenerg Biomembr. 2004 Aug; 36(4):415-9. Zeng J, Hirai K, Yang GY, Ying W, Swanson RA, Kelly M, Mayer M, James TL, Litt L. PMID: 15377881.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
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