Publications

Recent Articles (2003 - Present) | Selected Articles (1995-2002)

Recent Articles (2003 - Present)

Bharucha, N., Ma, J., Dobry, C.J., Lawson, S.K., Yang, Z. & Kumar, A. (2008). Analysis of the Yeast Kinome Reveals a Network of Regulated Protein Localization During Filamentous Growth. Mol. Biol. Cell, 19, 2708-2717. PubMed Link

Geda, P., Patury, S., Ma, J., Bharucha, N., Dobry, C.J., Lawson, S.K., Gestwicki, J.E. & Kumar, A. (2008). A Small Molecule-Directed Approach to Control Protein Localization and Function. Yeast, 25, 577-594. PubMed Link

Ma, J., Bharucha, N., Dobry, C.J., Frisch, R.L., Lawson, S., & Kumar, A. (2008). Localization of Autophagy-Related Proteins in Yeast Using a Versatile Plasmid-Based Resource of Fluorescent Protein Fusions. Autophagy, 4, , 792-800. PubMed Link

Gestwicki, J.E. & Kumar, A. (2008). Two and Three Hybrid Systems. In Encyclopedia of Chemical Biology. Wiley-VCH: in press.

Jin, R. & Kumar, A. (2008). Might As Well Jump: Transposons As Tools For Functional Genomics. In DNA Transposable Elements. Nova Science Publishers: in press.

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

Bharucha, N. & Kumar, A. (2007). Yeast Genomics and Drug Target Identification. Comb. Chem. High Throughput Screen., 10, 618-634. PubMed Link

Ma, J., Dobry, C.J., Krysan, D.J., & Kumar, A. (2008). An Unconventional Genomic Architecture In the Budding Yeast Saccharomyces cerevisiae Masks the Nested Antisense Gene NAG1. Eukaryotic Cell, 7, 1289-1298 (featured on the cover and in the ASM newsletter Microbe). PubMed Link

Jin, R., Dobry, C.J., McCown, P.J., & Kumar, A. (2008). Large-Scale Analysis of Yeast Filamentous Growth by Systematic Gene Disruption and Overexpression. Mol. Biol. Cell, 19, 284-296. PubMed Link

Ma, J., Jin, R., Dobry, C.J., Lawson, S.K., & Kumar, A. (2007). Overexpression of Autophagy-Related Genes Inhibits Yeast Filamentous Growth. Autophagy, 3, 604-609. PubMed Link

Ma, J., Jin, R., Jia, X., Dobry, C.J., Wang, L., Reggiori, F., Zhu, J., & Kumar, A. (2007). An Interrelationship Between Autophagy and Filamentous Growth in Budding Yeast. Genetics, 177, 205-214. PubMed Link

Wiwatwattana, N., Landau, C.M., Cope, G.J., Harp, G.A., & Kumar, A. (2007). Organelle DB: an updated resource of eukaryotic protein localization and function. Nucleic Acids Research, 35, D810-D814. PubMed Link

Seringhaus, M., Kumar, A., Hartigan, J., Snyder, M., & Gerstein, M. (2006). Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucleic Acids Research, 34, E57. PubMed LInk

Klionsky, D.J., & Kumar, A. (2006). A systems biology approach to learning autophagy. Autophagy, 2, 12-23. PubMed Link

Kumar, A. (2005). Teaching systems biology: an active learning approach. Cell Biol. Education, 4, 323-329. PubMed Link

Wiwatwattana, N., & Kumar, A. (2005). Organelle DB: A cross-species database of protein localization and function. Nucleic Acids Research, 33, D598-D604. 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., & Snyder, M. (2004). Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Research, 14, 1975-1986.PubMed Link

Kumar, A., & Snyder, M. (2004). Large-scale protein localization in yeast. In Cell Biology: A Laboratory Handbook, Third Edition, Elsevier Science, London, UK.

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

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Selected Articles (1995-2002)

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., & Snyder, M. (2002). Subcellular localization of the yeast proteome. Genes & Development, 16, 707-719. PubMed Link

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

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

Harrison, P., Kumar, A., Lan, N., Echols, N., Snyder, M., & Gerstein, M. (2002). A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. Journal of Molecular Biology, 316, 409-419. PubMed Link

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

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

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

Harrison, P. M., Kumar, A., Lang, N., Snyder, M., & Gerstein, M. (2002). A question of size: The eukaryotic proteome and the problems in defining it. Nucleic Acids Research, 30, 1083-1090. PubMed Link

Cheung, K. H., Deshpande, A. M., Tosches, N., Nath, S., Agarwal, A., Miller, P., Kumar, A., & Snyder, M. (2001). A metadata framework for interoperating heterogenous genome data using XML. Journal of the American Medical Informatics Association, Suppl S, 110-114. PubMed Link

Kumar, A., & Snyder, M. (2001). Emerging technologies in yeast genomics. Nature Reviews Genetics, 2, 302-312.

Coelho, P. S. R., Kumar, A., & Snyder, M. (2000). Genome-wide mutant collections: Toolboxes for functional genomics. Current Opinion in Microbiology, 3, 309-315.

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

Cheung, K. H., Miller, P., Sherman, A., Weston, S., Stratmann, E., Schultz, M., Snyder, M., & Kumar, A. (2000). Graphically-enabled integration of bioinformatics tools allowing parallel execution. Journal of the American Medical Informatics Association, Suppl S, 141-145. PubMed Link

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

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

Kumar, A., & Paietta, J. V. (1998). An additional role for the F-box motif: Gene regulation within the Neurospora crassa sulfur control network. Proceedings of the National Academy of Sciences of the USA, 95, 2417-2422. PubMed Link

Kumar, A., & Paietta, J. V. (1995). The sulfur controller 2 negative regulatory gene of Neurospora crassa encodes a protein with beta-transducin repeats. Proceedings of the National Academy of Sciences of the USA, 92, 3343-3347. PubMed Link

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