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Srikar Chamala, Ph.D.

Faculty

UF Department of Pathology, Immunology and Laboratory Medicine
College of Medicine
P.O. Box 100275
Gainesville, FL 32610

Office Location
UF Health Pathology Laboratories
4800 SW 35 Drive

Gainesville, FL 32608

  • Office: 352.265.9900, ext. 72272
  • Cell: 801.404.3165
  • Fax: 352.265.9901
  • E-mail: schamala@ufl.edu

Srikar Chamala, Ph.D., leads the clinical bioinformatics and biomedical informatics efforts at the University of Florida Health Pathology Laboratories Molecular & Genomic Pathology Laboratory in developing next-generation sequencing clinical assays and data management for precision medicine. He also performs research in understating genetic basis for cancer and type 1 diabetes, using sequencing and array-based genomics technologies. Dr. Chamala’s research in genomics and bioinformatics has been published in high-impact journals, including Science, Nature, and Genome Biology, and he has also been highlighted by news outlets across the globe.

Curriculum Vitae

Education

  • 2011 – 14 | Ph.D: Department of Biology, University of Florida
  • 2007 – 08 | Master of Science, Bioinformatics: Department of Computer Science, University of Illinois at Urbana-Champaign
  • 2002 – 06 | Bachelor of Science with Honors. Bioinformatics: Department of Integrative Biology, Brigham Young University

Publications

  • [23] Patel, V., Wilkinson, E. J., Chamala, S., Lu, X., Costagno, J., and Rush D. (2016). Endometrial thickness as measured by transvaginal ultrasound and the corresponding histopathologic diagnosis in women with postmenopausal bleeding. International Journal of Gynecological Pathology.  PMID: 27801761
  • [22] Alam, S. G., Zhang, Q., Prasad, G., Li, Yuan., Chamala, S., Kuchibhotla, R., Birendra, K.C., Aggarwal, V., Shrestha, S., Jones, A., Levy S., Roux, K., Nickerson, J., & Lele, T. P. (2016). The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity. Scientific Reports, 6:38063. PMID: 27905489
  • [21] Westbrook, J. W., Chhatre, V. E., Wu, L. S., Chamala, S., Neves, L. G., Muñoz, P., Martínez-García. P. J., Neale, D.B.,  Kirst, M.,  Mockaitis, K., Nelson, C.D., Peter, G.F., Davis, J. M., & Echt, C. S. (2015).  A consensus genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two genotype-phenotype discovery populations of P. taedaG3: Genes| Genomes| Genetics, g3-115.3.  PMID: 26068575
  • [20] Chamala, S., García, N., Godden, G. T., Krishnakumar, V., Jordon-Thaden, I. E., De Smet, R., Barbazuk, W. B., Soltis, D. E., &  Soltis, P. S. (2015). MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.  Applications in Plant Sciences, 3(4). PMID: 25909041
  • [19] Chamala, S., Feng, G., Chavarro, C., & Barbazuk, W. B. (2015). Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants. Frontiers in Bioengineering and Biotechnology, 3, 33. PMID: 25859541
  • [18] Pillon, Y., Johansen, J., Sakishima, T., Chamala, S., Barbazuk, W. B., & Stacy, E. A. (2014). Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae. Applications in Plant Sciences, 2(10). PMID: 25309837
  •  [17] Chamala, S., Chanderbali, A. S., Der, J. P., Lan, T., Walts, B., Albert, V. A., dePamphilis, C. W., Leebens-Mack, J., Rounsley, S., Schuster, S., Wing, R. A., Xiao, N., Moore, R., Soltis, P. S., Soltis, D. E., & Barbazuk, W. B (2013). Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science, 342(6165), 1516–1517. PMID: 24357320
  • [16] Amborella Genome Consortium (Chamala, S. is listed as one of the four major contributors) (2013). The Amborella genome and the evolution of flowering plants. Science, 342(6165), 1241089. PMID: 24357323
  • [15] Clancy, M. A., Rosli, H. G., Chamala, S., Barbazuk, W. B., Civello, P. M., & Folta, K. M. (2013). Validation of reference transcripts in strawberry (Fragaria spp.). Molecular Genetics and Genomics, 288(12), 671-681. PMID: 24061528
  • [14] Pillon, Y., Johansen, J., Sakishima, T., Chamala, S., Barbazuk, W. B., & Stacy, E. A. (2013). Primers for Low-Copy Nuclear Genes in the Hawaiian Endemic Clermontia (Campanulaceae) and Cross-Amplification in Lobelioideae. Applications in Plant Sciences, 1(6). PMID: 25202552
  • [13] Pillon, Y., Johansen, J., Sakishima, T., Chamala, S., Barbazuk, W. B., Roalson, E. H., Price, D.K., & Stacy, E. A. (2013). Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations. BMC Evolutionary Biology, 13(1), 35. PMID: 23394592
  • [12] Chambers, A., Carle, S., Njuguna, W., Chamala, S., Bassil, N., Whitaker, V., Barbazuk, W. B., & Folta, K. (2013). A genome-enabled, high-throughput, and multiplexed fingerprinting platform for strawberry (Fragaria L.). Molecular Breeding, 1-15. Publisher
  • [11] Soltis, D. E., Gitzendanner, M. A., Stull, G., Chester, M., Chanderbali, A., Chamala, S., Jordon-Thaden, I., Soltis, P. S., Schnable, P. S., & Barbazuk, W. B. (2013). The potential of genomics in plant systematics. Taxon, 62(5), 886-898. Publisher
  • [10] Ruzicka, D., Chamala, S., Barrios-Masias, F. H., Martin, F., Smith, S., Jackson, L. E., Barbazuk, W. B., & Schachtman, D. P. (2012). Inside arbuscular mycorrhizal roots – molecular probes to understand the symbiosis. The Plant Genome, 6(0),1-13. Publisher
  • [9] Tomato Genome Consortium. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), 635-641. PMID: 22660326
  • [8] Buggs, R. J., Renny-Byfield, S., Chester, M., Jordon-Thaden, I. E., Viccini, L. F., Chamala, S., Leitch, A. R., Schnable, P. S., Barbazuk, W. B., Soltis, P. S., & Soltis, D. E. (2012). Next-generation sequencing and genome evolution in allopolyploids. American Journal of Botany, 99(2), 372-382. PMID: 22268220
  • [7] Soltis, D. E., Buggs, R. J. A., Barbazuk, W. B., Chamala, S., Chester, M., Gallagher, J. P., Schnable, P. S., & Soltis, P. S. (2012). The Early Stages of Polyploidy: Rapid and Repeated Evolution in Tragopogon. Polyploidy and Genome Evolution (pp. 271-292): Springer Berlin Heidelberg. Publisher
  • [6] Godden, G. T., Jordon-Thaden, I. E., Chamala, S., Crowl, A. A., García, N., Germain-Aubrey, C. C., Heaney, J. M., Latvis, M., Qi, X., & Gitzendanner, M. A. (2012). Making next-generation sequencing work for you: approaches and practical considerations for marker development and phylogenetics. Plant Ecology & Diversity, 5(4), 427-450. Publisher
  • [5] Buggs, R. J., Chamala, S., Wu, W., Tate, J. A., Schnable, P. S., Soltis, D. E., Soltis, P. S., & Barbazuk, W. B. (2012). Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin.  Current Biology, 22(3), 248-252. PMID: 22264605
  • [4] Zuccolo, A., Bowers, J. E., Estill, J. C., Xiong, Z., Luo, M., Sebastian, A., Goicoechea, J. L., Collura, K., Yu, Y., Jiao, Y., Duarte, J., Tang, H., Ayyampalayam, S., Rounsley, S., Kudrna, D., Paterson, A. H., Pires, J. C., Chanderbali, A., Soltis, D. E., Chamala, S., Barbazuk, B., Soltis, P. S., Albert, V. A., Ma, H., Mandoli, D., Banks, J., Carlson, J. E., Tomkins, J., dePamphilis, C. W., Wing, R. A., & Leebens-Mack, J. (2011). A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biology, 12(5), R48. PMID: 21619600
  • [3] Folta, K. M., Clancy, M. A., Chamala, S., Brunings, A. M., Dhingra, A., Gomide, L., Kulathinal, R. J., Peres, N., Davis, T. M., & Barbazuk, W. B. (2010). A transcript accounting from diverse tissues of a cultivated strawberry. The Plant Genome, 3(2), 90-105. Publisher
  • [2] Buggs, R. J., Chamala, S., Wu, W., Gao, L., May, G. D., Schnable, P. S., Soltis, D. E., Soltis, P. S., & Barbazuk, W. B. (2010). Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular ecology, 19 Suppl 1, 132-146. PMID: 20331776
  •  [1] Chamala, S., Beckstead, W. A., Rowe, M. J., & McClellan, D. A. (2007). Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians. International Journal of Bioinformatics Research and Applications, 3(4), 504-522. PMID: 18048316

Research

  • Biomedical informatics
  • Clinical bioinformatics
  • Comparative genomics
  • Genetic and phenotypic associations
  • Genetic marker development
  • Precision or genomic medicine