Preprints and Papers


Brimacombe, C.A., Burke, J.E., Parsa, J.-Y., Witchley, J.N., S. Catania, O’Meara, T.L., Burrack, L., Madhani, H.D., Noble, S.M. (2019) A natural histone H2A variant lacking the Bub1 phosphorylation site and regulated depletion of centromeric histone CENP-A foster evolvability in Candida albicans. PLoS Biology 17(6): e3000331. [PDF]

Wallace, E.W.J., Maufrais, C., Sales-Lee, J., Tuck, L.R., de Oliviera, L., Feurbach, F., Moyrand, F., Madhani, H.D., Janbon, G. (2019) Start codon context controls translational initiation in fungi. [bioRxiv Preprint]

Burke, J.E., Longhurst, A.D., Natarajan, P., Rao, B., Liu, J., Sales-Lee, J., Morgensen, Y., Moresco, J.J., Diedrich, J.K., Yates, J.R.3rd, Madhani, H.D. (2019) A non-Dicer RNAse III and four other novel factors required for RNAi-mediated transposon suppression in the human pathogenic yeast Cryptococcus neoformans. G3: Genes, Genomes, Genetics g3.400330.2019. [PDF]


Burke, J.E., Longhurst, A.D., Merkurjev, D., Sales-Lee, J., Rao, B., Moresco, J.J., Yates, J.R. 3rd, Li, J.J., Madhani, H.D. (2018) Spliceosome profiling visualizes the operations of a dynamic RNP at nucleotide resolution.  Cell 173, 1014-1030 [PDF].

Harrigan, P., Madhani, H.D., El-Samad, H. (2018) Real time genetic compensation operationally defines the dynamic demands of feedback control. Cell 175, 877–886. [PDF]

Parsa, J.-Y., Boudoukha, S., Burke, J.E., Homer, C.M., Madhani, H.D. (2018) Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly.  Genes and Development 32, 953-964.  [PDF]

Allshire, R.C. and Madhani, H.D.  (2018) Ten Principles of heterochromatin formation and  function.  Nature Reviews Molecular Cell Biology, 19, 229-244. [PDF]

Brimacombe, C., Burke, J., Parsa, J., Witchley, J., Burrack, L., Madhani, H.D., Noble, S.M. (2018) Chromatin rewiring mediates programmed evolvability via aneuploidy. [bioRxiv Preprint]

Garcia-Santamarina S, Festa RA, Smith AD, Yu CH, Probst C, Ding C, Homer CM, Yin J, Noonan JP, Madhani H, Perfect JR Thiele DJ (2018) Genome-wide analysis of the regulation of Cu metabolism in Cryptococcus neoformans.  Molecular Microbiology 108, 473-494. [PDF]

Harrigan, P., Madhani, H.D., El-Samad, H. (2018) Real time genetic compensation operationally defines the dynamic demands of feedback control.  [bioRxiv Preprint]


Catania, S., Dumesic, P.A., Stoddard, C, Cooke, S., Burke, J., Cuomo, C.A., Narlikar, G.J., and Madhani, H.D. (2017) Epigenetic maintenance of DNA methylation after evolutionary loss of the de novo methyltransferase. [bioRxiv Preprint]

Parsa, J., Boudoukha, S., Burke, J., Homer, C. and Madhani, H.D. (2017)  Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly [bioRxiv Preprint]


Homer, C.M., Summers, D.K., Goranov, A.I., Clarke, S.C., Wiesner, D.L., Diedrich, J.K., Moresco, J.J., Toffaletti, D., Upadhya, R., Caradonna, I., et al. (2016). Intracellular Action of a Secreted Peptide Required for Fungal Virulence. Cell Host & Microbe 19, 849-864. [PDF]

Inada, M., Nichols, R.J., Parsa, J.Y., Homer, C.M., Benn, R.A., Hoxie, R.S., Madhani, H.D., Shuman, S., Schwer, B., and Pleiss, J.A. (2016). Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast. Nucleic Acids Research 44, 9180-9189. [PDF]

Clarke, S.C., Dumesic, P.A., Homer, C.M., O'Donoghue, A.J., La Greca, F., Pallova, L., Majer, P., Madhani, H.D., and Craik, C.S. (2016). Integrated Activity and Genetic Profiling of Secreted Peptidases in Cryptococcus neoformans Reveals an Aspartyl Peptidase Required for Low pH Survival and Virulence. PLoS Pathogens 12, e1006051. [PDF]

Al-Sady, B., Greenstein, R.A., El-Samad, H.J., Braun, S., and Madhani, H.D. (2016). Sensitive and Quantitative Three-Color Protein Imaging in Fission Yeast Using Spectrally Diverse, Recoded Fluorescent Proteins with Experimentally-Characterized In Vivo Maturation Kinetics.  Al-Sady B, Greenstein RA, El-Samad HJ, Braun S, Madhani HD (2016) PloS One 11, e0159292. [PDF]


Dumesic, P.A., Homer, C.M., Moresco, J.J., Pack, L.R., Shanle, E.K., Coyle, S.M., Strahl, B.D., Fujimori, D.G., Yates, J.R., Madhani, H.D. (2014) Product binding enforces the genomic specificity of a yeast Polycomb repressive complex. Cell 160(1-2):204-18. [PDF]

Garcia, J.F., Al-Sady, B., Madhani, H.D. (2015) Intrinsic Toxicity of Unchecked Heterochromatin Spread is Suppressed by Redundant Chromatin Boundary Functions in Schizosacchromyces pombe. Genes, Genomes, Genetics 5(7):1453-61. [PDF]

Desjardins, C.A., Sanscrainte, N.D., Goldberg, J.M., Heiman, D., Young, S., Zeng, Q., Madhani, H.D., Becnel, J.J., Cuomo, C.A. (2015) Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes. Nature Communications 6:7121. [PDF]

Dumesic, P.A., Rosenblad, M.A., Samuelsson, T., Nguyen, T., Moresco, J.J, Yates, J.R., Madhani, H.D. (2015) Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Research Aug 14. [Epub ahead of print] [PDF]


Brown, J.C.S., Nelson, J., VanderSluis, B., Deshpande, R., Butts, A., Kagan, S., Polacheck, I., Krysan, D.J., Myers, C.L., and Madhani, H.D. (2014) Unravelling the biology of a fungal meningitis pathogen using chemical genetics. Cell 159(5):1168-87. [PDF]

Butts A, Koselny K, Chabrier-Roselló Y, Semighini CP, Brown JC, Wang X, Annadurai S, Didone L, Tabroff J, Childers WE, Abou-Gharbia M, Wellington M, Cardenas ME, Madhani HD, Heitman J, Krysan DJ. (2014) Estrogen Receptor Antagonists Are Anti-Cryptococcal Agents That Directly Bind EF Hand Proteins and Synergize with Fluconazole In Vivo. MBio 5(1). [PDF]

Goranov and Madhani, H.D. (2014) Functional profiling of pathogen genomes. Cold Spring Harbor Perspectives in Medicine 5(3):a019596 . [PDF]


Dumesic, P.A., Natarajan, P., Chen, C., Drinnenberg, I.A., Schiller, B.J., Thompson, J., Moresco, J.J., Yates, J.R. III, Bartel, D.P. and Madhani, H.D. (2013). Stalled Spliceosomes Are a Signal for RNAi-Mediated Genome Defense. Cell 152: 957–968. [PDF]

Madhani, H.D. (2013) The frustrated gene: origins of eukaryotic gene expression. Cell 155:744-9. [PDF]

Dumesic, P.A. and Madhani, H.D. (2013) Recognizing the enemy within: licensing RNA-guided genome defense. Trends in Biochemical Sciences Nov. 23 Epub ahead of print. [PDF]

Dumesic, P.A. and Madhani, H.D. (2013) The spliceosome as a transposon sensor. RNA Biology 10: 1653-1660. [PDF]

Marina, D.B., Shankar, S., Natarajan, P., Finn, K., and Madhani, H.D. (2013) A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism. Genes and Development 27: 1851-1856. [PDF]

Canzio, D., Liao, M., Naber, N., Pate, E., Larson, A., Wu, S., Marina, D.B., Garcia, J.F., Madhani, H.D., Cooke, R., Schuck, P., Cheng, Y., Narlikar, G.J. (2013) A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly. Nature 496:377-81. [PDF]

Al-Sady, B., Madhani, H.D., Narlikar, G.J. (2013) Division of Labor between the Chromodomains of HP1 and Suv39 Methylase Enables Coordination of Heterochromatin Spread. Molecular Cell 51:80-91. [PDF]


Brown, J.C.S. and Madhani, H.D. (2012) Approaching the functional annotation of fungal virulence factors using cross-species genetic interaction profiling. PLoS Genetics 8:e1003168. [PDF]

Xu, M., Soloveychik M., Ranger M., Schertzberg, M., Shah, Z., Raisner, R., Venkatasubrahmanyan, S., Tsui, K., Gebbia, M., Hughes, T., van Bakel, H., Nislow, C., Madhani, H.D., Meneghini, M.D. (2012). Timing of transcriptional quiescence during gametogenesis is controlled by global histone H3K4 demethylation. Developmental Cell 23:1059-71. [PDF]

Braun, S., Madhani, H.D. (2012). Shaping the landscape: mechanistic consequences of ubiquitin modification of chromatin. EMBO Reports 13:619-30 [PDF]

Rougemaille, M., Braun, S., Coyle, S., Dumesic, P.A., Garcia, J.F., Isaac, R.S., Libri, D., Narlikar, G.J. and Madhani, H.D. (2012). Ers1 links HP1 to RNAi. Proceedings of the National Academy of Sciences, USA 109: 11258–11263. [PDF]


Braun, S., Garcia, J.F., Rowley, M., Rougemaille, M., Shankar, S., Madhani, H.D. (2011) The Cul4-Ddb1Cdt2 ubiquitin ligase inhibits the invasion of a boundary-associated anti-silencing factor into heterochromatin. Cell 144: 41-54. [PDF]

Madhani, H.D. (2011) Quorum sensing in fungi: Q&A. PLoS Pathogens 7:e1002301 [PDF]

El-Samad, H. and Madhani, H.D. (2011) Can a Systems Perspective Help Us Appreciate the Biological Meaning of Small Effects? Developmental Cell 21: 11–13. [PDF]

Kiely C.M., Marguerat S., Garcia J., Madhani, H.D., Bähler J, Winston F. (2011) Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Molecular and Cellular Biology 31: 4193-4204. [PDF]

Charles G.M., Chen C., Shih S.C., Collins S.R., Beltrao P., Zhang X., Sharma T., Tan S., Burlingame A.L., Krogan N.J., Madhani, H.D.,* Narlikar G.J* (2011) Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress. Proceedings of the National Academy of Sciences, USA 108:10620-5. *co-corresponding authors [PDF]

Chun, C.D.*, Brown, J.C.*, Madhani, H.D (2011). A Major Role for Capsule-Independent Phagocytosis-Inhibitory Mechanisms in Mammalian Infection by Cryptococcus neoformans. Cell Host and Microbe 9: 243-251. *co-first authors [PDF]

Canzio D., Chang E.Y., Shankar S., Kuchenbecker K.M., Simon M.D., Madhani, H.D., Narlikar G.J., Al-Sady B. (2011) Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly. Molecular Cell 41:67-81. [PDF]


McCullagh, E., Seshan, A., El-Samad, H., Madhani, H.D. (2010) Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nature Cell Biology, 12: 954–962. [PDF]

Garcia J.F., Dumesic P.A., Hartley P.D., El-Samad H., Madhani H.D. (2010) Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions. Genes and Development 15:1758-71. [PDF]

Chun C.D., Madhani H.D. (2010) Ctr2 Links Copper Homeostasis to Polysaccharide Capsule Formation and Phagocytosis Inhibition in the Human Fungal Pathogen Cryptococcus neoformans. PLoS One 5(9). pii: e12503. [PDF]

Chun, C.D. & Madhani, H.D. (2010). Applying Genetics and Molecular Biology to the Study of the Human Pathogen Cryptococcus neoformans, Methods in Enzymology 470:797-831. [PDF]

Bao, M.Z, Shock, T.R., Madhani, H.D. (2010) Multisite phosphorylation of the Saccharomyces cerevisiae filamentous growth regulator Tec1 is required for its recognition by the E3 ubiquitin ligase adaptor Cdc4 and its subsequent destruction in vivo. Eukaryotic Cell 9: 31-36 [PDF]


Hartley, P.D. & Madhani, H.D. (2009). Mechanisms that specify nucleosome location and identity Cell 137: 445-458. [PDF]

Madhani, H.D., Kasturi Haldar, Grant McFadden (2009). "Pearls": A New Type of Open-Access Educational Resource. PLoS Pathogens 5(6): e1000499. [PDF]

Hwang, W.W. & Madhani, H.D. (2009). Nonredundant Requirement for Multiple Histone Modifications for the Early Anaphase Release of the Mitotic Exit Regulator Cdc14 from Nucleolar Chromatin. PLoS Genetics 5:e1000588. [PDF]

Shock, T.R. & Madhani, H.D. (2009). Hog1 MAP kinase interrupts signal transduction between the Kss1 MAP kinase and the Tec1 transcription factor to maintain pathway specificity. Eukaryotic Cell 8: 606-616. [PDF]


Liu, O.W., Chun, C.D., Chow, E.D., Chen, C., Madhani, H.D.* & Noble, S.M. (2008). Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell 135: 174-188. [PDF] *Corresponding author

Breslow, D.K., Cameron, D.M., Collins, S.R., Schuldiner, M., Stewart-Ornstein, J., Newman, H.W., Braun, S., Madhani, H.D., Krogan, N.J. & Weissman, J.S. (2008). A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nature Methods 5: 711-718. [PDF]

Rougemaille, M., Shankar, S., Braun, S., Rowley, M. & Madhani, H.D. (2008). Ers1, a rapidly diverging protein essential for RNA interference-dependent heterochromatic silencing in Schizosaccharomyces pombe. Journal of Biological Chemistry. 283: 25770-25773. [PDF]

Raisner, R.M. & Madhani, H.D. (2008). Genomewide screen for negative regulators of sirtuin activity in S. cerevisiae reveals 40 loci and links to metabolism. Genetics 179: 1933-1944. [PDF]


Chun, C.D., Liu, O.W., Madhani, H.D. (2007). A Link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Crytococcus neoformans. PLoS Pathogens 3: e22. [PDF]

Chow, E.D., Liu, O.W., O’Brien, S & Madhani, H.D. (2007). Exploration of whole-genome responses of the human AIDS-associated yeast pathogen Cryptococcus neoformans var grubii: nitric oxide stress and body temperature. Current Genetics 57: 137-148. [PDF]

Cantin, G.T, Shock, T.R., Madhani, H.D., and Yates, J.R. IIIrd (2007) Optimizing TiO2-based phosphopeptide enrichment for automated multidimensional liquid chromatography coupled to tandem mass spectrometry. Analytical Chemistry 79: 4666-4673. [PDF]

Venkatasubrahmanyam, S., Hwang, W.W. Meneghini, M.D., Tong, A.H. & Madhani, H.D. (2007). Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. Proceedings of the National Academy of Sciences, USA 104: 16609-16614. [PDF]

Liu, O.W., Kelly, M.J., Chow, E.D., Madhani, H.D. (2007). Parallel beta-helix proteins required for accurate capsule polysaccharide synthesis and virulence in the yeast Cryptococcus neoformans. Eukaryotic Cell 6: 630-40. [PDF]

Tompa, R., Madhani, H.D. (2007). Histone H3 Lysine 36 Methylation Antagonizes Silencing in Saccharomyces cerevisiae Independently of the Rpd3S Histone Deacetylase Complex. Genetics 175: 585-93. [PDF]


Madhani, H.D. (2006). Functional analysis of protein kinase networks in living cells: beyond “knock-outs” and “knock-downs”. Methods 40: 251-4. [PDF]

Kung, C., Kenski, D.M., Krukenbeg, K., Madhani, H.D., and Shokat, K.M. (2006) Selective kinase inhibition by exploiting differential pathway sensitivity. Chemistry and Biology 13, 399-407. [PDF]

Schwartz, M.A. and Madhani, H.D. (2006) Control of MAPK signaling specificity by a conserved residue in the MEK-binding of the yeast scaffold protein Ste5. Current Genetics 49:351-363. [PDF]


Raisner, R.M., Hartley, P.D., Meneghini, M.D., Bao, M.Z., Liu, C.L., Schreiber, S.L., Rando, O.J., Madhani, H.D. (2005) Histone variant H2A.Z marks the 5’ ends of both active and inactive genes in euchromatin. Cell 123: 233-248. [PDF]

Kung C., Kenski, D.M., Dickerson, S.H., Howson, R.W., Kuyper, L.F., Madhani, H.D., Shokat, K.M. (2005) Chemical genomic profiling to identify intracellular targets of a multiplex kinase inhibitor. Proceedings of the National Academy of Sciences, USA 102: 3487-3592. [PDF]


Bao, M.Z., Schwartz, M.A., Cantin, G.T., Yates, J.R. 3rd, Madhani, H.D. (2004). Pheromone-dependent destruction of the Tec1 transcription factor is required for MAP kinase signaling specificity in yeast. Cell 119: 911-1000. [PDF]

Kobor, M.S., Venkatasubrahmanyam, S., Meneghini, M.D., Gin, J.W., Jennings, J.L., Link, A.J., Madhani, H.D.*, Rine, J.* (2004) A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biology 2: 587-599. *co-corresponding authors. [PDF]

Schwartz, M.A. and Madhani, H.D. (2004) Principles of MAP Kinase Signaling Specificity in Saccharomyces cerevisiae. Annual Review of Genetics 38:724-748. [PDF]


Meneghini, M.D., Wu., M, and Madhani, H.D. (2003) Conserved histone variant H2A.Z prevents the ectopic spread of silent heterochromatin. Cell 112: 725-736. [PDF]

Hwang, W., Venkatasubrahmanyam, S., Ianculescu, A.G., Tong, A., Boone, C., Madhani, H.D. (2003) A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. Molecular Cell 11: 261-266. Published online Dec. 28, 2002. [PDF]

2002 and earlier

Brugnera, E., Haney, L., Grimsley, C., Lu, M., Walk S.F., Tosello-Trampont, A.C., Macara I.G., Madhani, H.D., Fink G.R., Ravichandran K.S. (2002) Unconventional Rac-GEF activity is mediated through the Dock180-ELMO complex. Nature Cell Biology 4:574-82.

Madhani, H.D., Galitski, T., Lander, E.S., Fink, G.R. (1999) Effectors of a developmental MAP kinase cascade revealed by expression signatures of signaling mutants. Proceedings of the National Academy of Sciences, USA 96: 12530-12535.

Rupp, S., Summers, E., Lo, H., Madhani, H.D., Fink, G.R. (1999) MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene. EMBO J. 18: 1257-1269.

Madhani, H.D., Styles, C.A., Fink, G.R. (1997). MAP kinases with distinct inhibitory functions impart signaling specificity during yeast differentiation. Cell 91: 673-684.

Madhani, H.D., Fink, G.R. (1997). Combinatorial control required for the specificity of yeast MAPK signaling. Science 275: 1314-1317.

Madhani, H.D., Guthrie, C. (1994b). Genetic interactions between the yeast helicase homolog Prp16 and spliceosomal snRNAs identify candidate ligands for the Prp16 RNA-dependent ATPase. Genetics 137:677-687.

Madhani, H.D., Guthrie, C. (1994a). Randomization-selection analysis of snRNAs in vivo: Evidence for a tertiary interaction in the spliceosome. Genes and Development 8: 1071-1086.

Madhani, H.D., Guthrie, C. (1992). A Novel Base-Pairing Interaction Between U2 and U6 snRNAs Suggests a Mechanism for the Catalytic Activation of the Spliceosome. Cell 71: 803-817.

Madhani, H.D., Bordonné, R., Guthrie, C. (1990). Multiple Roles for U6 snRNA in the Splicing Pathway. Genes and Development 4:2274-2287.

Jacks, T., Madhani, H.D., Masiarz, F.R., Varmus, H.E. (1988). Signals for Ribosomal Frameshifting in the Rous Sarcoma Virus gag-pol Region. Cell 55:447-458.

Madhani, H.D., Bohr, V.A. and Hanawalt, P.C. (1986). Differential DNA Repair in Transcriptionally Active and Inactive Proto-oncogenes: c-abl and c-mos. Cell 45:417-423.

Madhani, H.D., Leadon, S.A., Smith, C.A., and Hanawalt, P.C. (1986). α-DNA in African Green Monkey Cells is Organized into Extremely Long Tandem Arrays. Journal of Biological Chemistry 261: 2314-2318.