2018 – Present:

Sunder, S., Bauman, J.S., Decker, S.J., Lifton, A.R., and Kumar, A. (2023). The yeast AMP-activated protein kinase Snf1 phosphorylates the inositol polyphosphate kinase Kcs1. J. Biol. Chem., in press.  PubMed Link

Beckwith, J.K., Ganesan, M., VanEpps, J.S., Kumar, A., and Solomon, M.J. (2022). Rheology of Candida albicans fungal biofilms. J. Rheology, 66:683-697.  Article Link

Kumar, A.  (2021).  The Complex Genetic Basis and Multilayered Regulatory Control of Yeast Pseudohyphal Growth.  Ann. Rev. Genetics, 55:1-21. PMID: 34280314.  PubMed Link

Klionsky, D.J. et al. (2021). Guidelines For the Use and Interpretation of Assays For Monitoring Autophagy (4th Edition). Autophagy, 17:1-382. PMID: 33634751.  PubMed Link

Wakade, R.S., Ristow, L.C., Stamnes, M.A., Kumar, A., and Krysan, D.J.  (2020).  The Ndr/LATS kinase Cbk1 regulates a specific subset of Ace2 functions and suppresses the hyphae-to-yeast transition in Candida albicansmBio, 11:e01900-20.  PMID: 32817109.  PubMed Link

Kumar, A.  (2020).  Jump around: transposons in and out of the laboratory.  F1000Res, 9:F1000 Faculty Rev-135.  PMCID:PMC7043111.  PubMed Link

Mutlu, N.*, Sheidy, D.T.*, Hsu, A., Jeong, H., Wozniak, K.J., and Kumar, A.  (2019).  The Yeast  Stress-responsive Ksp1p Kinase Signaling Network Is Required for Pseudohyphal Growth and Wild-Type Ribonucleoprotein Granule Abundance.  Genetics, 213:705-720.  (*, These authors contributed equally to this work).  PubMed Link

Chow, J., Starr, I., Jamalzadeh, S., Muniz, O., Kumar, A., Gokcumen, O., Ferkey, D., and Cullen, P.J. (2019). Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast.  Genetics, 212:667-690.  PubMed Link

Mutlu, N., and Kumar, A.  (2018).  Messengers for morphogenesis: inositol polyphosphate signaling and yeast pseudohyphal growth.  Curr. Genetics65:119-25.  PubMed Link

Norman, K.L., Shively, C.A., De La Rocha, A.J., Mutlu, N., Basu, S., Cullen, P.J., and Kumar, A.  (2018).  Inositol Polyphosphates Regulate and Predict Yeast Pseudohyphal Growth Phenotypes.  PLoS Genetics, 14:e1007493.  PubMed Link

Koselny, K., Mutlu, N., Minard, A.Y., Kumar, A., Krysan, D.J., and Wellington, M.  (2018).  A Genome-Wide Screen of Deletion Mutants in the Filamentous Saccharomyces cerevisiae Background Identifies Ergosterol as a Direct Trigger of Macrophage Pyroptosis.  mBio, 9:e01204-18.  PubMed Link

Kumar, A.  (2018).  A fungus among us: The emerging opportunistic pathogen Candida tropicalis and PKA signaling.  Virulence, 9:659-661.  PubMed Link

Glazier, V.E., Murante, T., Koselny, K., Murante, D., Esqueda, M., Wall, G.A., Wellington, M., Hung, C.Y., Kumar, A., and Krysan, D.J.  (2018).  Systematic Complex Haploinsufficiency-Based Genetic Analysis of Candida albicans Transcription Factors: Tools and Applications to Virulence-Associated Phenotypes.  G3 (Bethesda), 8:1299-1314.  PubMed Link

Phadke, S.S., Maclean, C.J., Zhao, S.Y., Mueller, E.A., Michelotti, L.A., Norman, K.L., Kumar, A., and James, T.Y.  (2018).  Genome-Wide Screen for Saccharomyces cerevisiae Genes Contributing to Opportunistic Pathogenicity in an Invertebrate Model Host.  G3 (Bethesda), 8:63-78.  PubMed Link


Klionsky, D.J. et al.  (2016).  Guidelines For the Use and Interpretation of Assays For Monitoring Autophagy (3rd Edition).  Autophagy12:1-222.  PubMed Link

Mutlu, N., and Kumar, A.  (2016).  Mapping Paths: New Approaches to Dissect Eukaryotic Signaling Circuitry.  F1000 Research, 5(F1000 Faculty Rev):1853.  PubMed Link

Saputo, S., Norman, K.L., Murante, T., Horton, B.N., De La Cruz Diaz, J., DiDone, L., Colquhoun, J., Schroeder, J.W., Simmons, L.A., Kumar, A., and Krysan, D.J.  (2016).  Complex Haploinsufficiency-Based genetic Analysis of the NDR/Lats Kinase Cbk1 Provides Insight into Its Multiple Functions in Candida albicans.  Genetics, 203:1217-1233.  PubMed Link

Kumar, A.  (2016).  New Day Rising: State of the Art in Yeast Functional Genomics.  Brief. Funct. Genomics15: 73-74.  Pubmed Link

Norman, K.L., and Kumar, A.  (2016).  Mutant Power: Using Mutant Allele Collections for Yeast Functional Genomics.  Brief. Funct. Genomics15: 75-84.  PubMed Link

Kumar, A.  (2016).  Multipurpose Transposon-Insertion Libraries in Yeast.  In Cold Spring Harbor Protocols, Budding Yeast: A Laboratory Manual, ed. Andrews, B., Boone, C., Davis, T.N., Fields, S., p. 161-164.  PubMed Link

Kumar, A.  (2016).  Using yeast transposon-insertion libraries for phenotypic screening and protein localization.  In Cold Spring Harbor Protocols, Budding Yeast: A Laboratory Manual, ed. Andrews, B., Boone, C., Davis, T.N., Fields, S., p. 165-172.  PubMed Link

Shively, C.A., Kweon, H.K., Norman, K.L., Mellacheruvu, D., Xu, T., Sheidy, D.T., Dobry, C.J., Sabath, I., Cosky, E.E.P., Tran, E.J., Nesvizhskii, A., Andrews, P.C., and Kumar, A.  (2015).  Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules.  PLoS Genetics11: e1005564.  PubMed Link  (Selected as being of special significance in its field by the Faculty of 1000)   

Horton, B.N., and Kumar, A.  (2015).  Genome-Wide Synthetic Genetic Screening by Transposon Mutagenesis in Candida albicans.  Methods Mol. Biol.1279: 125-35.  PubMed Link

Song, Q., Johnson, C., Wilson, T.E., and Kumar, A.  (2014).  Pooled Segregant Sequencing Reveals genetic Determinants of Yeast Pseudohyphal Growth.  PLoS Genetics10: e1004570. (Featured on the PLoS Genetics website) Pubmed Link

Johnson, C., Kweon, H.K., Sheidy, D., Shively, C.A., Mellacheruvu, D., Nesvizhskii, A.I., Andrews, P.C., and Kumar, A.  (2014).  The Yeast Sks1p Kinase Signaling Network Regulates Pseudohyphal Growth and Glucose Response.  PLoS Genetics, 10: e1004183. PubMed Link (Selected as being of special significance in its field by the Faculty of 1000)   badgef1000

Saputo, S., Kumar, A., and Krysan, D.J.  (2014).  Efg1 directly regulates ACE2 expression to mediate cross-talk between the cAMP/PKA and RAM pathways during Candida albicans morphogenesis.  Eukaryotic Cell, 13: 1169-80.  PubMed Link


Zhang, Y., Kweon, H.K., Shively, C.A., Kumar, A., and Andrews, P.C.  (2013).  Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data.  PLoS Comput. Biol., 9: e1003077. PubMed Link

Shively, C.A., Eckwahl, M.J., Dobry, C.J., Mellacheruvu, D., Nesvizhskii, A., and Kumar, A.  (2013).  Genetic Networks Inducing Invasive Growth in Saccharomyces cerevisiae Identified Through Systematic Genome-Wide Overexpression.  Genetics, 193: 1297-1310. PubMed Link

Judeh, T., Johnson, C., Kumar, A.*, and Xu, D.* (2013).  TEAK: Topology enrichment analysis framework for detecting activated biological subpathways.  Nucleic Acids Res., 41: 1425-37. (*Corresponding authors). PubMed Link

Song, Q. and Kumar, A.  (2012).  An Overview of Autophagy and Yeast Pseudohyphal Growth: Integration of Signaling Pathways During Nitrogen Stress.  Cells, 1: 263-283. Pubmed Link

Saputo, S., Chabrier-Rosello, Y., Luca, F.C., Kumar, A., and Krysan, D.J.  (2012). The RAM Network in Pathogenic Fungi.  Eukaryotic Cell, 11: 708-717. PubMed Link

Chabrier-Rosello, Y., Kumar, A., and Krysan, D.J. (2012). Large Scale Genetic Interaction Screening in C. albicans. In Candida and Candidiasis, 3rd edition, eds. R.C. Calderone and C.J. Clancy, ASM Press, Washington, DC (in press).

Walter, G. M., Smith, M. C., Wisen, S., Basrur, V., Elenitoba-Johnson, K. S. J., Duennwald, M. L., Kumar, A., Gestwicki, J. E. (2011) Ordered assembly of heat shock proteins, Hsp26, Hsp70, Hsp90 and Hsp104, on expanded polyglutamine fragments revealed by chemical probes.   J. Biol. Chem286: 40486-93.PubMed link

Bharucha, N., Chabrier-Rosello, Y., Xu, T., Johnson, C., Sobczynski, S., Song, Q., Dobry, C.J., Eckwahl, M.J., Anderson, C.P., Benjamin, A.J., Kumar, A.* and Krysan, D.J.* (2011). A large-scale complex haploinsufficiency-based genetic interaction screen in C. albicans: analysis of the RAM network during morphogenesis.  PLoS Genetics7: e1002058. (*Corresponding authors) PubMed link   badgef1000

Xu, T., Bharucha, N., and Kumar, A. (2011). Genome-Wide Transposon Mutagenesis in Saccharomyces cerevisiae and Candida albicans.  Methods Mol. Biol.,765: 207-224. PubMed link

Xu, T., Johnson, C., Gestwicki, J.E., and Kumar, A. (2010). Conditionally Controlling Nuclear Trafficking in Yeast by Chemical-Induced Protein Dimerization.  Nature Protocols5: 1831-1843. PubMed link

Xu, T., Shively, C.A., Jin, R., Eckwahl, M.J., Dobry, C.J., Song, Q., and Kumar, A. (2010). A Profile of Differentially Abundant Proteins at the Yeast Cell Periphery During Pseudohyphal Growth.   J. Biol. Chem.285: 15476-15488. PubMed link

2003 – 2009:

Kumar, A. (2009). An overview of nested genes in eukaryotic genomes.  Eukaryotic Cell8: 1321-1329. PubMed link

Patury, S., Geda, P., Dobry, C.J., Kumar, A., and Gestwicki, J.E. (2009). Conditional Nuclear Import and Export of Yeast Proteins Using a Chemical Inducer of Dimerization.  Cell Biochem. Biophys53: 127-134. PubMed link

Geda, P., Patury, S., Ma, J., Bharucha, N., Dobry, C.J., Lawson, S.K., Gestwicki, J.E., and Kumar, A. (2008). A small molecule-directed approach to control protein localization and function in yeast.  Yeast25: 577-594. PubMed link

Gestwicki, J.E., and Kumar, A. (2008). Two and three hybrid systems. In Encyclopedia of Chemical Biology, ed. T. Begley. Wiley-VCH.

Jin, R., and Kumar, A. (2008). Might as well jump: Transposons as tools for functional genomics. In DNA Transposable Elements, eds. K. Yoshida and M. Aoki. Nova Science Publishers.

Kumar, A. (2008) Multipurpose Transposon-Insertion Libraries for Large-Scale Analysis of Gene Function in Yeast.  Methods Mol. Biol. 416: 117-129.PubMed link

Ma, J., Bharucha, N., Dobry, C.J., Frisch, R.L., Lawson, S., and Kumar, A. (2008). Localization of autophagy-related proteins in yeast using a versatile plasmid-based resource of fluorescent protein fusions.  Autophagy4: 792-800. PubMed link

Bharucha, N., Ma, J., Dobry, C.J., Lawson, S.K., Yang, Z., and Kumar, A. (2008). Analysis of the yeast kinome reveals a network of regulated protein localization during filamentous growth.  Mol. Biol. Cell19: 2708-2717. PubMed link

Ma, J., Dobry, C.J., Krysan, D.J., and Kumar, A. (2008). An unconventional genomic architecture in the budding yeast Saccharomyces cerevisiae masks the nested antisense gene NAG1.  Eukaryotic Cell7: 1289-1298. PubMed link

Jin, R., Dobry, C.J., McCown, P.J., and Kumar, A. (2008). Large-Scale Analysis of Yeast Filamentous Growth by Systematic Gene Disruption and Overexpression.  Mol. Biol. Cell19: 284-296. PubMed link

Ma, J., Jin, R., Dobry, C.J., Lawson, S.K., and Kumar, A. (2007). Overexpression of autophagy-related genes inhibits yeast filamentous growth.  Autophagy3: 604-9. PubMed link

Kumar, A. (2007). Chemical genomics.  Comb. Chem. High Throughput Screen.10: 617.

Bharucha, N. and Kumar, A. (2007). Yeast genomics and drug target identification.  Comb. Chem. High Throughput Screen.10: 618-634. PubMed link

Ma, J., Jin, R., Jia, X., Dobry, C.J., Wang, L., Reggiori, F., Zhu, J., and Kumar, A. (2007). An Interrelationship Between Autophagy and Filamentous Growth in Budding Yeast.  Genetics177: 205-14. PubMed link

Wiwatwattana, N., Landau, C.M., Cope, J.G., Harp, G.A., and Kumar, A. (2007). Organelle DB: an updated resource of eukaryotic protein localization and function.  Nucleic Acids Res.35: D810-814. PubMed link

Seringhaus, M., Kumar, A., Hartigan, J., Snyder, M., and Gerstein, M. (2006). Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.  Nucleic Acids Res.34(8): e57.

Wiwatwattana, N. and Kumar, A. (2005). OrganelleDB: a cross-species database of protein localization and function.  Nucleic Acids Res. 33: D598-604.PubMed link

Kumar, A.*, Seringhaus, M., Biery, M.C., Sarnovsky, R.J., Umansky, L., Piccirillo, S., Heidtman, M., Cheung, K.-H., Dobry, C.J., Gerstein, M.B., Craig, N.L., and Snyder, M. (2004). Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon.  Genome Res. 14: 1975-1986 (* corresponding author).

Kumar, A. (2003). Where do all the proteins go?  Drug Discovery Today, TARGETS: Innovations in Genomics and Proteomics 2: 237-244.

Teaching Publications:

Mirel, B., Kumar, A., Nong, P., Su, G., and Meng, F. (2016). Using Interactive Data Visualizations for Exploratory Analysis in Undergraduate Genomics Coursework: Field Study Findings and Guidelines. J. Sci. Educ. Technol., 25:91-110. PMID:26877625.

Klionsky, D.J. and Kumar, A. (2006). A Systems Biology Approach to Learning Autophagy.  Autophagy2: 12-23. PubMed link

Kumar, A. (2005). Teaching Systems Biology: An Active Learning Approach.  Cell Biology Education 4: 323-329. PubMed link

Selected Prior Work:

Kumar, A., and Snyder, M. (2003). Large-scale protein localization in yeast. In Cell Biology: A Laboratory Handbook, Third Edition, Elsevier Science, London, UK.

Snyder, M., and Kumar, A. (2002). Yeast genomics: past, present, and future promise.  Funct. Integr. Genomics 2: 135-137.

Kumar, A., Agarwal, S., Heyman, J.A., Matson, S., Heidtman, M., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R., Liu, Y., Cheung, K.-H., Miller, P., Gerstein, M., Roeder, G.S., and Snyder, M. (2002). Subcellular localization of the yeast proteome.  Genes & Dev16: 707-719.

Kumar, A., Harrison, P.M., Cheung, K.-H., Lan, N., Echols, N., Bertone, P., Miller, P., Gerstein, M.B., and Snyder, M. (2002). An integrated approach for finding overlooked genes in yeast.  Nature Biotech. 20: 58-63.

Kumar, A., Cheung, K.-H., Tosches, N., Masiar, P., Liu, Y., Miller, P., and Snyder, M. (2002). The TRIPLES database: a community resource for yeast molecular biology.  Nucleic Acids Res. 30: 73-75.

Coelho, P.S.R., Bryan, A.C., Kumar, A., Shadel, G.S., and Snyder, M. (2002). A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA.  Genes & Dev. 16: 2755-2760.

Harrison, P.M., Kumar, A., Lan, N., Snyder, M., and Gerstein, M.B. (2002). A question of size: the eukaryotic proteome and the problems in defining it.  Nucleic Acids Res. 30: 1083-1090.

Kumar, A. and Snyder, M. (2002). Protein complexes take the bait.  Nature 415: 123-124.

Harrison, P.M., Kumar, A., Lan, N., Echols, N., Snyder, M., and Gerstein, M.B. (2002). A small reservoir of disabled ORFs in the Saccharomyces cerevisiae genome and its implications for the dynamics of proteome evolution.  J. Mol. Biol. 316: 409-419.

Kumar, A., Vidan, S., and Snyder, M. (2002). Insertional mutagenesis: transposon-insertion libraries as mutagens in yeast.  Methods Enzymol. 350: 219-229.

Kumar, A. and Snyder, M. (2001). Emerging technologies in yeast genomics.  Nature Rev. Genet. 2: 302-312.

Kumar, A., and Snyder, M. (2000). Genome-wide transposon mutagenesis in yeast. In Current Protocols in Molecular Biology (ed, Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D., Seidman, J.G., Smith, J.A., and Struhl, K.), Unit 13.3, John Wiley and Sons, New York, NY.

Kumar, A., Cheung, K.-H., Ross-Macdonald, P., Coelho, P.S.R., Miller, P., and Snyder, M. (2000). TRIPLES: a database of gene function in Saccharomyces cerevisiae.  Nucleic Acids Res. 28: 81-84.

Kumar, A., des Etages, S.A., Coelho, P.S.R., Roeder, G.S. and Snyder, M. (2000). High-throughput methods for the large-scale analysis of gene function by transposon tagging.  Methods Enzymol. 328: 550-574.

Ross-Macdonald, P., Coelho, P., Roemer, T., Agarwal, S., Kumar, A., Cheung, K.-H., Jansen, R., Symoniatis, D., Umansky, L., Nelson, K., Iwasaki, H., Hager, K., Gerstein, M., Miller, P., Roeder, G.S., and Snyder, M. (1999). Large-scale analysis of the yeast genome by transposon tagging and gene disruption.  Nature 402: 413-418.

Kumar, A. and Paietta, J.V. (1998). A new role for the F-Box motif: gene regulation within the Neurospora crassa sulfur control network.  Proc. Natl. Acad. Sci. USA 95: 2417-2422.

Kumar, A. and Paietta, J.V. (1995). The sulfur controller-2 negative regulatory gene of Neurospora crassa encodes a protein with β-transducin repeats.  Proc. Natl. Acad. Sci. USA 92: 3343-3347.