Research Funding

  • June 6, 2025 - May 31, 2030 - Exploiting a high-precision phenotypic map to illuminate environmental sensing by a fungal meningitis pathogen , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI187603
  • July 8, 2024 - May 31, 2029 - Deciphering the significance of pathogen genetic variation and evolution , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI185204
  • June 23, 2022 - May 31, 2027 - Manipulation of macrophage polarization by a fungal meningitis pathogen , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI165541
  • May 1, 2012 - May 31, 2027 - Cryptococcus genomic resources , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI100272
  • April 1, 2005 - December 31, 2026 - Mechanisms of Gene Expression , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM071801
  • May 23, 2023 - April 30, 2025 - Deciphering a novel lipid-based mechanism of innate immune modulation , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R21AI178231
  • January 22, 2020 - December 31, 2021 - Intracellular Recognition of Fungi by the Innate Immune System , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R21AI150083
  • July 1, 2015 - June 30, 2021 - Epigenetic control of virulence in a fungal meningitis pathogen , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI120464
  • May 1, 2017 - April 30, 2019 - Peptide-based signaling and virulence in Cryptococcus neoformans , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R56AI126726
  • April 1, 2012 - March 31, 2018 - Chemical-genetic functional annotation of the genome of a meningitis pathogen , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI099206
  • November 4, 2011 - October 31, 2016 - Regulation of Virulence of Cryptococcus neoformans , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI096869
  • September 30, 1996 - June 30, 2016 - Comprehensive Biology: Exploiting the Yeast Genome , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P41RR011823
  • May 1, 2009 - June 28, 2013 - Systems Biology of Molecular Noise in Yeast , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM086379
  • June 1, 2001 - February 28, 2011 - Mechanisms of Signal Transduction Specificity in Yeast , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM063670
  • July 1, 2005 - March 31, 2010 - Systematic Genetic Analysis of Fungal Virulence , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI065519

Education

Stanford University, Stanford, California, B.S., M.S., 1986, Biological Sciences
University of California, San Francisco, Ph.D., 1993, Genetics
University of California, San Francisco, M.D., 1995, Medicine
Whitehead Institute, Cambridge, Massachusetts, Postdoctoral, 1995-1999, Signal Transduction

Honors & Awards

  • 1987
    Dean's Prize for Student Research, University of California, San Francisco
  • 1988
    Dean's Prize for Student Research, University of California, San Francisco
  • 1991-1992
    Chancellor's Fellowship, University of California, San Francisco
  • 1996
    Finalist, Pharmacia-Science Prize
  • 1995-1998
    Helen Hay Whitney Foundation Postdoctoral Research Fellowship
  • 1998-1999
    Burroughs-Wellcome Fund Career Development Award
  • 2000-2005
    David and Lucile Packard Foundation Fellowship for Scientists and Engineers
  • 1999-2002
    Burroughs-Wellcome Fund Career Development Award
  • 2005-2010
    Leukemia and Lymphoma Society Scholar
  • 2017
    Named to first cohort of Chan Zuckerberg Biohub Investigators

Selected Publications

  1. Ayers CB, Nalley MJ, Madhani HD, Potts WK, McClelland EE, Seipelt-Thiemann RL. Mammalian-evolved strains of the fungal pathogen Cryptococcus neoformans show adaptation via heritable transcript level differences specific to mouse MHC haplotype. BMC Genomics. 2026 Jul 21. View on PubMed
  2. Sethiya P, Desmarini D, Bowring BG, Cesar K, Boucher MJ, Wei AL, Madhani HD, Crossett B, Connelly A, Halliday CL, Chen SC-A, Lai J, Wong KH, Djordjevic JT. Functional insight into cyclin-dependent kinase (CDK)7 via chemical inhibition of the priority fungal pathogen Cryptococcus neoformans. mBio. 2025 12 10; 16(12):e0289825. View on PubMed
  3. Boucher MJ, Madhani HD. CRISPR/Cas9-compatible plasmids enabling seven dominant genetic selection methods for the human fungal pathogen Cryptococcus neoformans. Microbiol Spectr. 2025 11 04; 13(11):e0193525. View on PubMed
  4. Nalley MJ, Banerjee S, Huang MY, Madhani HD. Near 100% efficient homology-dependent genome engineering in the human fungal pathogen Cryptococcus neoformans. G3 (Bethesda). 2025 08 06; 15(8). View on PubMed
  5. Boucher MJ, Banerjee S, Joshi MB, Wei AL, Nalley MJ, Huang MY, Lei S, Ciranni M, Condon A, Langen A, Goddard TD, Caradonna I, Goranov AI, Homer CM, Mortensen Y, Petnic S, Reilly MC, Xiong Y, Susa KJ, Pastore VP, Zaro BW, Madhani HD. Phenotypic landscape of an invasive fungal pathogen reveals its unique biology. Cell. 2025 07 24; 188(15):4003-4024.e24. View on PubMed
  6. Huang MY, Nalley MJ, Hecht PC, Madhani HD. An auxin-inducible degron system for conditional mutation in the fungal meningitis pathogen Cryptococcus neoformans. G3 (Bethesda). 2025 06 04; 15(6). View on PubMed
  7. Kryštufek R, Verner V, Šácha P, Hadzima M, Trajhan F, Starková J, Tloušt'ová E, Dvoráková A, Pecina A, Brynda J, Chalupský K, Hájek M, Boucher MJ, Majer P, Rezác J, Madhani HD, Craik CS, Konvalinka J. On-Resin Assembly of Macrocyclic Inhibitors of Cryptococcus neoformans May1: A Pathway to Potent Antifungal Agents. J Med Chem. 2025 May 08; 68(9):9623-9637. View on PubMed
  8. Madhani HD. Mechanisms of Inheritance of Chromatin States: From Yeast to Human. Annu Rev Biophys. 2025 05; 54(1):59-79. View on PubMed
  9. Huang MY, Nalley MJ, Hecht P, Madhani HD. An auxin-inducible degron system for conditional mutation in the fungal meningitis pathogen Cryptococcus neoformans. bioRxiv. 2024 Nov 18. View on PubMed
  10. Boucher MJ, Banerjee S, Joshi MB, Wei AL, Huang MY, Lei S, Ciranni M, Condon A, Langen A, Goddard TD, Caradonna I, Goranov AI, Homer CM, Mortensen Y, Petnic S, Reilly MC, Xiong Y, Susa KJ, Pastore VP, Zaro BW, Madhani HD. Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology. bioRxiv. 2024 Oct 29. View on PubMed
  11. Madhani HD. Deep learning meets histones at the replication fork. Cell. 2024 Sep 05; 187(18):4824-4826. View on PubMed
  12. Beusch I, Madhani HD. Understanding the dynamic design of the spliceosome. Trends Biochem Sci. 2024 07; 49(7):583-595. View on PubMed
  13. Hiten Madhani. Abstract 2289 Understanding the dynamic design of the human spliceosome. Journal of Biological Chemistry. 2024 Mar 1; 300(3):106661. View on PubMed
  14. Boucher MJ, Madhani HD. Convergent evolution of innate immune-modulating effectors in invasive fungal pathogens. Trends Microbiol. 2024 05; 32(5):435-447. View on PubMed
  15. Beusch I, Madhani H. Meet the authors: Irene Beusch and Hiten Madhani. Mol Cell. 2023 07 20; 83(14):2387-2389. View on PubMed
  16. Beusch I, Rao B, Studer MK, Luhovska T, Šukyte V, Lei S, Oses-Prieto J, SeGraves E, Burlingame A, Jonas S, Madhani HD. Targeted high-throughput mutagenesis of the human spliceosome reveals its in vivo operating principles. Mol Cell. 2023 07 20; 83(14):2578-2594.e9. View on PubMed
  17. De Giovanni M, Dang EV, Chen KY, An J, Madhani HD, Cyster JG. Platelets and mast cells promote pathogenic eosinophil recruitment during invasive fungal infection via the 5-HIAA-GPR35 ligand-receptor system. Immunity. 2023 07 11; 56(7):1548-1560.e5. View on PubMed
  18. Lee S, Abini-Agbomson S, Perry DS, Goodman A, Rao B, Huang MY, Diedrich JK, Moresco JJ, Yates JR, Armache KJ, Madhani HD. Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity. Nat Struct Mol Biol. 2023 07; 30(7):891-901. View on PubMed
  19. Basso P, Dang EV, Urisman A, Cowen LE, Madhani HD, Noble SM. Deep tissue infection by an invasive human fungal pathogen requires lipid-based suppression of the IL-17 response. Cell Host Microbe. 2022 11 09; 30(11):1589-1601.e5. View on PubMed
  20. David A. Brow, Hiten D. Madhani. Christine Guthrie (1945–2022). Cell. 2022 Sep 1; 185(20):3639-3642. View on PubMed

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