Srikar Chamala, Ph.D.

Clinical Assistant Professor
Director of Biomedical Informatics

Dept. of Pathology, Immunology and Laboratory Medicine
Dept. of Health Outcomes and Policy
UF Health Pathology Laboratories
University of Florida College of Medicine

Contact Information

Physical Address :
UF Health Pathology Laboratories
4800 SW 35 Drive
Room # 1140.a
Gainesville, FL 32608

Mailing Address: P.O. Box 100275, Gainesville, FL 32610

Office: 352.265.9900, ext. 72272

Cell: 801.404.3165

Fax: 352.265.9901

E-mail: schamala@ufl.edu

Srikar Chamala, Ph.D., work primarily focus on developing informatics strategies and methodologies for effective implementation of precision cancer medicine. I have been leading clinical bioinformatics and biomedical informatics efforts at UF Health in developing custom next-generation sequencing (NGS) clinical assays, bioinformatics data analysis & management workflows, and solutions for integrating genomic data into health information systems. He also performs research in understating genetic basis for cancer and type 1 diabetes using genotype and clinical metadata. Dr. Chamala’s scientific contributions have been published in high-impact journals, including Science, Nature, and Genome Biology, and highlighted by news outlets across the globe.

Curriculum Vitae

Education

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

Research

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

Teaching

Spring 2018: GMS 5905 – Section 25G1 : Informatics for Pathology Practice and Research I

Spring 2018: GMS 5905 – Section 264E : Informatics for Pathology Practice and Research II

Publications

  • [24] García, N., Folk, R.A., Meerow, A.W., Chamala, S., Gitzendanner, M.A., de Oliveira, R.S., Soltis, D.E., & Soltis, P.S. (2017). Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Molecular Phylogenetics and Evolution, 111, pp.231-247. PMID: 28390909
  • [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