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John Irwin, PhD

Title(s)Adjunct Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address1700 4th St
San Francisco CA 94158
Phone415-878-1705
ORCID ORCID Icon0000-0002-1195-6417 Additional info
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    Collapse Research 
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    Ultra-large library docking for ligand discovery
    NIH R01GM133836Sep 27, 2019 - Aug 31, 2023
    Role: Principal Investigator
    A Web-Based Automatic Virtual Screening System
    NIH R01GM071896Aug 1, 2004 - Jul 31, 2016
    Role: Co-Principal Investigator

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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. Property-Unmatched Decoys in Docking Benchmarks. J Chem Inf Model. 2021 Jan 25. Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ. PMID: 33494610.
      View in: PubMed   Mentions:    Fields:    
    2. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv. 2020 Nov 24. PMID: 33269349.
      View in: PubMed   Mentions:
    3. ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery. J Chem Inf Model. 2020 Dec 28; 60(12):6065-6073. Irwin JJ, Tang KG, Young J, Dandarchuluun C, Wong BR, Khurelbaatar M, Moroz YS, Mayfield J, Sayle RA. PMID: 33118813.
      View in: PubMed   Mentions: 1     Fields:    
    4. The activities of drug inactive ingredients on biological targets. Science. 2020 07 24; 369(6502):403-413. Pottel J, Armstrong D, Zou L, Fekete A, Huang XP, Torosyan H, Bednarczyk D, Whitebread S, Bhhatarai B, Liang G, Jin H, Ghaemi SN, Slocum S, Lukacs KV, Irwin JJ, Berg EL, Giacomini KM, Roth BL, Shoichet BK, Urban L. PMID: 32703874.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    5. In vivo Efficacy of Novel Type Preferring MT1 Melatonin Receptor Inverse Agonists in C3H/HeN Mouse Models of Chronobiological Behavior. The FASEB Journal. 2020 Apr 1; 34(S1):1-1. Grant Glatfelter, Reed Stein, Hye Jin Kang, Anthony Jones, John Irwin, Bryan Roth, Brian Shoichet, Margarita Dubocovich. .
      View in: Publisher Site   Mentions:
    6. Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking. J Am Chem Soc. 2020 03 18; 142(11):4960-4964. Wan X, Yang T, Cuesta A, Pang X, Balius TE, Irwin JJ, Shoichet BK, Taunton J. PMID: 32105459.
      View in: PubMed   Mentions: 3     Fields:    
    7. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature. 2020 03; 579(7800):609-614. Stein RM, Kang HJ, McCorvy JD, Glatfelter GC, Jones AJ, Che T, Slocum S, Huang XP, Savych O, Moroz YS, Stauch B, Johansson LC, Cherezov V, Kenakin T, Irwin JJ, Shoichet BK, Roth BL, Dubocovich ML. PMID: 32040955.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    8. Docking Finds GPCR Ligands in Dark Chemical Matter. J Med Chem. 2020 01 23; 63(2):613-620. Ballante F, Rudling A, Zeifman A, Luttens A, Vo DD, Irwin JJ, Kihlberg J, Brea J, Loza MI, Carlsson J. PMID: 31846328.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    9. Ultra-large library docking for discovering new chemotypes. Nature. 2019 02; 566(7743):224-229. Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O'Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ. PMID: 30728502.
      View in: PubMed   Mentions: 42     Fields:    Translation:Humans
    10. Predicted Biological Activity of Purchasable Chemical Space. J Chem Inf Model. 2018 01 22; 58(1):148-164. Irwin JJ, Gaskins G, Sterling T, Mysinger MM, Keiser MJ. PMID: 29193970.
      View in: PubMed   Mentions: 2     Fields:    
    11. Discovery of new GPCR ligands to illuminate new biology. Nat Chem Biol. 2017 Nov; 13(11):1143-1151. Roth BL, Irwin JJ, Shoichet BK. PMID: 29045379.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    12. Identification of Novel Smoothened Ligands Using Structure-Based Docking. PLoS One. 2016; 11(8):e0160365. PMID: 27490099.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    13. Docking Screens for Novel Ligands Conferring New Biology. J Med Chem. 2016 05 12; 59(9):4103-20. PMID: 26913380.
      View in: PubMed   Mentions: 47     Fields:    
    14. ZINC 15--Ligand Discovery for Everyone. J Chem Inf Model. 2015 Nov 23; 55(11):2324-37. PMID: 26479676.
      View in: PubMed   Mentions: 219     Fields:    Translation:HumansAnimals
    15. An Aggregation Advisor for Ligand Discovery. J Med Chem. 2015 Sep 10; 58(17):7076-87. PMID: 26295373.
      View in: PubMed   Mentions: 64     Fields:    
    16. Erratum: Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2015 Mar; 11(3):235. PMID: 25689339.
      View in: PubMed   Mentions:    Fields:    
    17. Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2014 Dec; 10(12):1066-72. PMID: 25344815.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    18. Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol. 2014 Jul 18; 9(7):1528-35. PMID: 24807704.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    19. Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells. Bioorg Med Chem. 2014 Mar 15; 22(6):1960-72. PMID: 24530226.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    20. Covalent Docking of Large Libraries for the Discovery of Chemical Probes. Biophysical Journal. 2014 Jan 1; 106(2):264a. Nir London, Rand M. Miller, John J. Irwin, Oliv Eidam, Lucie Gibold, Richard Bonnet, Brian K. Shoichet, Jack Taunton. .
      View in: Publisher Site   Mentions:
    21. Ligand pose and orientational sampling in molecular docking. PLoS One. 2013; 8(10):e75992. PMID: 24098414.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    22. Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells. Bioorg Med Chem. 2013 Dec 15; 21(24):7999-8012. PMID: 24183589.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    23. Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem. 2013 Jul 05; 288(27):19830-44. PMID: 23667258.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    24. Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proc Natl Acad Sci U S A. 2013 Apr 02; 110(14):5480-5. PMID: 23509259.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    25. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem. 2012 Jul 26; 55(14):6582-94. PMID: 22716043.
      View in: PubMed   Mentions: 284     Fields:    Translation:HumansCells
    26. Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A. 2012 Jul 10; 109(28):11178-83. PMID: 22711801.
      View in: PubMed   Mentions: 44     Fields:    Translation:Humans
    27. ZINC: a free tool to discover chemistry for biology. J Chem Inf Model. 2012 Jul 23; 52(7):1757-68. PMID: 22587354.
      View in: PubMed   Mentions: 493     Fields:    
    28. Virtual ligand screening against comparative protein structure models. Methods Mol Biol. 2012; 819:105-26. PMID: 22183533.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    29. Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol. 2011 Dec 18; 8(2):144-6. PMID: 22179068.
      View in: PubMed   Mentions: 44     Fields:    Translation:Animals
    30. Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 2011 Dec 27; 51(12):3078-92. PMID: 22014038.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    31. Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol. 2011 Sep 18; 7(11):769-78. PMID: 21926995.
      View in: PubMed   Mentions: 103     Fields:    Translation:Cells
    32. Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET. Proc Natl Acad Sci U S A. 2011 Sep 20; 108(38):15810-5. PMID: 21885739.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansCells
    33. The chemical basis of pharmacology. Biochemistry. 2010 Dec 07; 49(48):10267-76. Keiser MJ, Irwin JJ, Shoichet BK. PMID: 21058655.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    34. The presynaptic component of the serotonergic system is required for clozapine's efficacy. Neuropsychopharmacology. 2011 Feb; 36(3):638-51. Yadav PN, Abbas AI, Farrell MS, Setola V, Sciaky N, Huang XP, Kroeze WK, Crawford LK, Piel DA, Keiser MJ, Irwin JJ, Shoichet BK, Deneris ES, Gingrich J, Beck SG, Roth BL. PMID: 21048700.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    35. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem. 2010 Jul 08; 53(13):4891-905. Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK. PMID: 20540517.
      View in: PubMed   Mentions: 45     Fields:    Translation:Humans
    36. Structure-based discovery of A2A adenosine receptor ligands. J Med Chem. 2010 May 13; 53(9):3748-55. Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA. PMID: 20405927.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansCells
    37. A FRAMEWORK FOR EVALUATING REGIONAL-SCALE NUMERICAL PHOTOCHEMICAL MODELING SYSTEMS. Environ Fluid Mech (Dordr). 2010; 10(4):471-489. Dennis R, Fox T, Fuentes M, Gilliland A, Hanna S, Hogrefe C, Irwin J, Rao ST, Scheffe R, Schere K, Steyn D, Venkatram A. PMID: 21461126.
      View in: PubMed   Mentions:
    38. Molecular docking screens using comparative models of proteins. J Chem Inf Model. 2009 Nov; 49(11):2512-27. Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. PMID: 19845314.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    39. Predicting new molecular targets for known drugs. Nature. 2009 Nov 12; 462(7270):175-81. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KL, Edwards DD, Shoichet BK, Roth BL. PMID: 19881490.
      View in: PubMed   Mentions: 456     Fields:    Translation:HumansAnimals
    40. Automated docking screens: a feasibility study. J Med Chem. 2009 Sep 24; 52(18):5712-20. Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y. PMID: 19719084.
      View in: PubMed   Mentions: 72     Fields:    Translation:Cells
    41. Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol. 2009 Aug; 20(4):429-36. Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. PMID: 19733475.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    42. Staring off into chemical space. Nat Chem Biol. 2009 Aug; 5(8):536-7. Irwin JJ. PMID: 19620992.
      View in: PubMed   Mentions: 1     Fields:    
    43. Quantifying biogenic bias in screening libraries. Nat Chem Biol. 2009 Jul; 5(7):479-83. Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK. PMID: 19483698.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    44. Structure-based discovery of beta2-adrenergic receptor ligands. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6843-8. Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK. PMID: 19342484.
      View in: PubMed   Mentions: 98     Fields:    Translation:Cells
    45. Docking screens: right for the right reasons? Curr Top Med Chem. 2009; 9(9):755-70. Kolb P, Irwin JJ. PMID: 19754393.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    46. ChemInform Abstract: Quantifying the Relationships among Drug Classes. ChemInform. 2008 Jul 15; 39(29). Jerome Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet. .
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    47. A procedure for inter-comparing the skill of regional-scale air quality model simulations of daily maximum 8-h ozone concentrations. Atmospheric Environment. 2008 Jul 1; 42(21):5403-5412. John S. Irwin, Kevin Civerolo, Christian Hogrefe, Wyat Appel, Kristen Foley, Jenise Swall. .
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    48. Using ZINC to acquire a virtual screening library. Curr Protoc Bioinformatics. 2008 Jun; Chapter 14:Unit 14.6. Irwin JJ. PMID: 18551414.
      View in: PubMed   Mentions: 6     Fields:    
    49. Quantifying the relationships among drug classes. J Chem Inf Model. 2008 Apr; 48(4):755-65. Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. PMID: 18335977.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
    50. Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem. 2008 Apr 24; 51(8):2502-11. Babaoglu K, Simeonov A, Irwin JJ, Nelson ME, Feng B, Thomas CJ, Cancian L, Costi MP, Maltby DA, Jadhav A, Inglese J, Austin CP, Shoichet BK. PMID: 18333608.
      View in: PubMed   Mentions: 56     Fields:    
    51. Community benchmarks for virtual screening. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):193-9. Irwin JJ. PMID: 18273555.
      View in: PubMed   Mentions: 38     Fields:    
    52. Has the Performance of Regional-Scale Photochemical Modelling Systems Changed over the Past Decade?. . 2008 Jan 1; 394-403. C. Hogrefe, J. -Y. Ku, G. Sistla, A. Gilliland, J. S. Irwin, P. S. Porter, E. Gégo, P. Kasibhatla, S. T. Rao. .
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    53. Chemistry in cancer research: a vital partnership. Cancer Res. 2007 Jul 15; 67(14):6539-43. Sturla SJ, Irwin JJ, Loeppky RN, Mulvihill MJ, Searcey M. PMID: 17621609.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    54. Chemistry in cancer research: a vital partnership. ACS Chem Biol. 2007 May 22; 2(5):286-92. Sturla SJ, Irwin JJ, Loeppky RN, Mulvihill MJ, Searcey M. PMID: 17518428.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    55. Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 2007 Feb; 25(2):197-206. Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. PMID: 17287757.
      View in: PubMed   Mentions: 389     Fields:    Translation:Cells
    56. Objective Reduction of the Space-Time Domain Dimensionality for Evaluating Model Performance. . 2007 Jan 1; 543-552. Edith Gégo, P. Steven Porter, Christian Hogrefe, R. Gilliam, A. Gilliland, J. Swall, J. Irwin, S. T. Rao. .
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    57. Temporal Signatures of Observations and Model Outputs: Do Time Series Decomposition Methods Capture Relevant Time Scales?. . 2007 Jan 1; 421-429. P. S. Porter, J. Swall, R. Gillian, E. L. Gego, Christian Hogrefe, A. Gilliland, J. S. Irwin, T. Rao. .
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    58. Evaluation of an Annual Simulation of Ozone and Fine Particulate Matter over the Continental United States – Which Temporal Features are Captured?. . 2007 Jan 1; 562-570. Christian Hogrefe, J. M. Jones, A. Gilliland, P. Steven Porter, Edith Gégo, R. Gilliam, J. Swall, J. Irwin, S. T. Rao. .
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    59. Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc. 2006 Dec 13; 128(49):15882-91. Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK. PMID: 17147401.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    60. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801. Huang N, Shoichet BK, Irwin JJ. PMID: 17154509.
      View in: PubMed   Mentions: 319     Fields:    Translation:Cells
    61. Temporal features in observed and simulated meteorology and air quality over the Eastern United States. Atmospheric Environment. 2006 Aug 1; 40(26):5041-5055. C. Hogrefe, P.S. Porter, E. Gego, A. Gilliland, R. Gilliam, J. Swall, J. Irwin, S.T. Rao. .
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    62. An objective comparison of CMAQ and REMSAD performances. Atmospheric Environment. 2006 Aug 1; 40(26):4920-4934. Edith Gégo, P. Steven Porter, Christian Hogrefe, John S. Irwin. .
      View in: Publisher Site   Mentions:
    63. How good is your screening library? Curr Opin Chem Biol. 2006 Aug; 10(4):352-6. Irwin JJ. PMID: 16797220.
      View in: PubMed   Mentions: 4     Fields:    
    64. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model. 2006 Jan-Feb; 46(1):243-53. Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. PMID: 16426060.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    65. Assessing the Comparability of Ammonium, Nitrate and Sulfate Concentrations Measured by Three Air Quality Monitoring Networks. Pure and Applied Geophysics. 2005 Oct 1; 162(10):1919-1939. Edith L Gego, P. Steven Porter, John S. Irwin, Christian Hogrefe, S. Trivikrama Rao. .
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    66. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry. 2005 Sep 20; 44(37):12316-28. Irwin JJ, Raushel FM, Shoichet BK. PMID: 16156645.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    67. Here be dragons: docking and screening in an uncharted region of chemical space. J Biomol Screen. 2005 Oct; 10(7):667-74. Brenk R, Irwin JJ, Shoichet BK. PMID: 16170052.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    68. ZINC — A Free Database of Commercially Available Compounds for Virtual Screening. ChemInform. 2005 Apr 19; 36(16). John J. Irwin, Brian K. Shoichet. .
      View in: Publisher Site   Mentions:
    69. Examination of model predictions at different horizontal grid resolutions. Environmental Fluid Mechanics. 2005 Apr 1; 5(1-2):63-85. Edith Gego, Christian Hogrefe, George Kallos, Antigoni Voudouri, John S. Irwin, S. Trivikrama Rao. .
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    70. Assessing the Comparability of Ammonium, Nitrate and Sulfate Concentrations Measured by Three Air Quality Monitoring Networks. . 2005 Jan 1; 1919-1939. Edith L. Gego, P. Steven Porter, John S. Irwin, Christian Hogrefe, S. Trivikrama Rao. .
      View in: Publisher Site   Mentions:
    71. ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model. 2005 Jan-Feb; 45(1):177-82. Irwin JJ, Shoichet BK. PMID: 15667143.
      View in: PubMed   Mentions: 819     Fields:    Translation:Cells
    72. Comparison of the Space-Time Signatures of Air Quality Data From Different Monitoring Networks. . 2004 Jan 1; 481-490. Edith L. Gego, Christian Hogrefe, P. Steven Porter, John S. Irwin, S. Trivikrama Rao. .
      View in: Publisher Site   Mentions:
    73. A molecular docking strategy identifies Eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase. J Biol Chem. 2003 Apr 18; 278(16):14092-100. Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, Anderson KS. PMID: 12556445.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    74. Lead discovery using molecular docking. Curr Opin Chem Biol. 2002 Aug; 6(4):439-46. Shoichet BK, McGovern SL, Wei B, Irwin JJ. PMID: 12133718.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansAnimalsCells
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