Preprints and Papers

2024

Madhani, H.D. (2024). Mechanisms of inheritance of chromatin states: from yeast to human. Annual Review of Biophysics, in press [PDF].

Boucher, M.J., Banerjee, S., Joshi, M.B., Wei, A.L., Huang, M.Y., Lei, S., Ciranni, M., Condon, A., Langen, A., Goddard, T.D., Caradonna, I., Goranov, A.I., Homer, C.M., Mortensen, Y., Petnic, S., Reilly, M.C., Xiong, Y., Susa, K.J., Pastore, V.P., Zaro, B.W., Madhani, H.D. (2024) Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology. bioRxiv preprint [PDF]

Huang, M.Y., Nalley, M.J., Hecht, P., Madhani, H.D. (2024) An auxin-inducible degron system for conditional mutation in the fungal meningitis pathogen Cryptococcus neoformans. bioRxiv preprint [PDF]

Madhani, H.D. (2024) Deep learning meets histones at the replication fork. Cell 187, 4824-4826 [PDF]

Beusch, I., and Madhani, H.D. (2024) Understanding the dynamic design of the spliceosome. Trends in Biochemical Sciences 49(7):583-595 [PDF]

Boucher, M.J., and Madhani, H.D. (2024) Convergent evolution of innate immune-modulating effectors in invasive fungal pathogens. Trends in Microbiology doi.org/10.1016/j.tim.2023.10.011 [PDF]

2023

Beusch, I., Rao, B., Studer, M.K., Luhovska, T., Sukyte, V., Lei, S., Oses-Prieto, J., SeGraves, E., Burlingame, A., Jonas, S., Madhani, H.D. (2023) Targeted high-throughput mutagenesis of the human spliceosome reveals its in vivo operating principles. Molecular Cell 83,2578–2594 [PDF]

Lee S., Abini-Agbomson S., Perry, D.S., Goodman, A., Rao, B., Huang, M.Yl, Diedrich, J.K., Moresco, J.J., Yates, J.R., Armache, K.-J., Madhani, H.D. (2023) Intrinsic mesoscale properties of a Polycomb protein underpin heterochromatin fidelity. Nature Structural and Molecular Biology doi.org/10.1038/s41594-023-01000-z [PDF]

De Giovanni M, Dang EV, Chen KY, An J, Madhani HD, Cyster JG. (2023) Platelets and mast cells promote pathogenic eosinophil recruitment during invasive fungal infection via the 5-HIAA-GPR35 ligand-receptor system. Immunity S1074-7613(23)00223-6. [PDF]

2022

Beusch, I., Rao, B., Studer, M., Luhovska, T., Sukyte, V., Lei, S., Oses-Prieto, J., SeGaves, Em, Burlingame, A., Jonas, S., Madhani, H.D. (2022) Targeted high throughput mutagenesis of the human spliceosome reveals its in vivo operating principles. bioRxiv preprint [PDF]

Dang, E.V., Lei, S., Radkov, A., Volk, R.F., Zaro, B.W., Madhani, H.D. (2022) Secreted fungal virulence effector triggers allergic inflammation via TLR4. Nature 608, 161-167 [PDF]

Basso, P., Dang, E.V., Urisman, A., Cowen, L.E., Madhani, H.D., and Noble, S.M. (2022) Deep tissue infection by an invasive human fungal pathogen requires novel lipid-based suppression of the IL-17 response. Cell Host and Microbe 30, 1589-1601. [PDF]

Wang, J., Catania, S., Wang. C., de la Cruz, M.J., Rao, B., Madhani, H.D., Patel, D.J. (2022) Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance. Molecular Cell 82, 1186-1198. [PDF]

Huang, M., Joshi M.B., Boucher, M.J., Lee, S., Loza, L.C., Gaylord, E.A., Doering, T.L., Madhani, H.D. (2022) Short homology-directed repair using optimized Cas9 in the pathogen Cryptococcus neoformans enables rapid gene deletion and tagging. Genetics 220, iyab18. [PDF]

Basso, P., Dang, E.V., Urisman, A., Cowen, L.E., Madhani, H.D., and Noble, S.M. (2022) Deep tissue infection by an invasive human fungal pathogen requires novel lipid-based suppression of the IL-17 response. bioRxiv preprint [PDF]

Huang, M.Y and Madhani, H.D. (2022) Telomere transposon takeover in Cryptococcus. Nature Microbiology 7, 1108-1109, [PDF]

Bellen, H.J., Hubbard, E.J.A., Lehmann, R., Madhani, H.D., Solnica-Krezel, L., Southward-Smith, E.M. (2022) Model organism databases are in jeopardy. Development 149, dev200193. [PDF]

Mayerle, M., Madhani, H.D., and Maeder, C. (2022) Christine Guthrie (1945-2022): a tribute from her trainees. RNA 30, ix-xvii. [PDF]

Brow, D.A., and Madhani, H.D. (2022) Christine Guthrie (1945-2022) Cell 185, 3639-3643. [PDF]

2021

Madhani, H.D. (2020) Unbelievable but true: epigenetics and chromatin in fungi. Trends in Genetics, 37, 12-20. [PDF]

Sales-Lee, J., Perry, D.S., Bowser, B.A., Diedrich, J.K., Rao, B., Beusch, I. ,Yates, J.R. III, Roy, S.W., and Madhani, H.D. (2021) Coupling of spliceosome complexity to intron diversity. Current Biology 31, 4898-4910.e4 [PDF]

Krustufek, R. et al. (2021) Re-emerging protease targets: examining Cryptococcus neoformans Major Aspartyl Protease 1 as a target for antifungal drug discovery. J. Med. Chem. 64, 6706-6719. [PDF]

Dang, E.V., Lei, S., Radkov, A., Madhani, H.D. (2021) Mechanism of innate immune reprogramming by a fungal meningitis pathogen. bioRxiv preprint [PDF]

2020

Catania, S., Dumesic, P.A., Pimentel, H., Nasif, A., Stoddard, C.I., Burke, J.E., Diedrich, J.K., Cooke, S., Shea, T., Gieniger, E., Lintner, R., Yates, J.R., Hajkova, P., Narlikar, G.J., Cuomo, C.A., Pritchard, J.K., and Madhani, H.D. (2020) Evolutionary persistance of DNA methylation for millions of years after ancient loss of a de novo methyltransferase. Cell 180, 1-15. [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.* (2020) Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom. Nucleic Acids Research doi: 10.1093/nar/gkaa060 *co-corresponding authors [PDF]

Dumesic, P.A., Stoddard, C.I., Catania, S., Narlikar, G.J., Madhani, H.D. (2020) ATP hydrolysis by the SNF domain of Dnmt5 is coupled to both specific recognition and modification of hemimethylated DNA. Molecular Cell 79. 129-139. [PDF]

Dang, E.V., Madhani, H.D. and Vance, R.E. (2020) Cholesterol in quarantine. Nature Immunology 21, 716-717. [PDF]

Summers, D.K., Perry, D.S., Rao, B., and Madhani, H.D. (2020) Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans. PLoS Genetics, 16, e1008744. [PDF]

2019

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]

2018

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]

2017

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]

2016

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]

2015

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]

2014

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]

2013

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]

2012

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]

2011

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]

2010

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]

2009

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]

2008

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]

2007

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]

2006

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]

2005

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]

2004

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]

2003

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.