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UF Health University of Florida

Department of Pathology, Immunology and Laboratory Medicine

College of Medicine

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Srikar Chamala

Srikar Chamala, Ph.D.

Director Of Biomedical Informatics

Department: MD-PATHOLOGY-GENERAL
Business Phone: (352) 627-2272
Business Email: schamala@ufl.edu
CV: View Curriculum Vitae

About Srikar Chamala

Srikar Chamala, Ph.D., is the Director of Biomedical Informatics and Assistant Professor who leads the bioinformatics, genomics, and pathology informatics efforts at the University of Florida Department of Pathology, Immunology and Laboratory Medicine. Dr. Chamala’s research applies bioinformatics and genomics to investigate the genetic basis for human cancers and type 1 diabetes. Additionally, his work involves machine learning and other data analytic techniques to discover and improve clinical outcomes and diagnosis. Dr. Chamala has successfully collaborated and organized multiple international and inter-institutional projects focusing on global health disparities.

In addition to research, Dr. Chamala leads clinical bioinformatics and pathology informatics efforts at UF Health Pathology Laboratories in developing clinical genomic or precision medicine tests (in cancer, germline, and pharmacogenomics), clinical bioinformatics data analysis & management workflows, clinical genomic variant data interpretation, solutions for integrating genomic data into health information systems, pathology analytics and quality assurance (e.g., CAP Cancer Reporting Protocols).

Complementing clinical and basic research efforts, Dr. Chamala has been actively involved in teaching informatics courses – creating and implementing an Informatics for Pathology Practice and Research course series at the University of Florida. The goal of this course series is to build informatics skills among pathology students, residents, fellows, staff, and faculty in both clinical and experimental divisions.

Research Profile

In the area of Bioinformatics and Genomics, Dr. Chamala has made several original contributions in the areas of alternative splicing, comparative genomics, genome sequencing and annotation, genome evolution, genetic marker development, and genetic variant calling. The current focus of his research is in global health equity, specifically understanding the genetic basis for human cancers using genomics technologies. At the same time, Dr. Chamala is pursuing the application of machine learning and other data analytic techniques to discover and improve clinical outcomes and diagnosis using clinical, pathological, and digital imaging datasets. Currently at University of Florida (UF), Dr. Chamala leads informatics efforts in type 1 diabetes (PO1 Award # AI042288), and NCI-supported grants, Florida-California CaRE2 Health Equity Center (U54 Award # CA233444) and NCI-EGRP supported Prostate Cancer Transatlantic Consortium (CaPTC) (http://epi.grants.cancer.gov/captc/).

Open Researcher and Contributor ID (ORCID)

0000-0001-6367-7615

Publications

2021
Building a precision oncology workforce by multidisciplinary and case-based learning.
BMC medical education. 21(1) [DOI] 10.1186/s12909-021-02500-6. [PMID] 33499867.
View on: PubMed Publisher’s Site
2021
Enrichment of the erythrocyte miR-451a in brain extracellular vesicles following impairment of the blood-brain barrier.
Neuroscience letters. 751 [DOI] 10.1016/j.neulet.2021.135829. [PMID] 33727125.
View on: PubMed Publisher’s Site
2021
Genetic Composition and Autoantibody Titers Model the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis.
Diabetes. 70(4):932-943 [DOI] 10.2337/db20-0937. [PMID] 33419759.
View on: PubMed Publisher’s Site
2021
Informatics driven quality improvement in the modern histology lab
JAMIA Open. 3(4):530-535 [DOI] 10.1093/jamiaopen/ooaa066. [PMID] 33623889.
View on: PubMed Publisher’s Site
2021
Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes.
Genome biology. 22(1) [DOI] 10.1186/s13059-021-02262-w. [PMID] 33478573.
View on: PubMed Publisher’s Site
2021
Optimizing COVID-19 testing capabilities and clinical management using pathology informatics
JAMIA Open. 3(4):523-529 [DOI] 10.1093/jamiaopen/ooaa055. [PMID] 33754137.
View on: PubMed Publisher’s Site
2021
Pathology Informatics and Robotics Strategies for Improving Efficiency of COVID-19 Pooled Testing.
Academic pathology. 8 [DOI] 10.1177/23742895211020485. [PMID] 34189259.
View on: PubMed Publisher’s Site
2021
Reverse Plasticity Underlies Rapid Evolution by Clonal Selection within Populations of Fibroblasts Propagated on a Novel Soft Substrate.
Molecular biology and evolution. 38(8):3279-3293 [DOI] 10.1093/molbev/msab102. [PMID] 33871606.
View on: PubMed Publisher’s Site
2021
The Hologic Aptima SARS-CoV-2 assay enables high ratio pooling saving reagents and improving turnaround time.
Journal of clinical laboratory analysis. 35(9) [DOI] 10.1002/jcla.23888. [PMID] 34213803.
View on: PubMed Publisher’s Site
2021
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration.
BMC bioinformatics. 22(1) [DOI] 10.1186/s12859-021-04039-1. [PMID] 33653260.
View on: PubMed Publisher’s Site
2021
Wrong Tissue in Block.
American journal of clinical pathology. [DOI] 10.1093/ajcp/aqab011. [PMID] 33940603.
View on: PubMed Publisher’s Site
2020
Disparities in Pancreatic Ductal Adenocarcinoma-The Significance of Hispanic Ethnicity, Subgroup Analysis, and Treatment Facility on Clinical Outcomes.
Cancer medicine. 9(12):4069-4082 [DOI] 10.1002/cam4.3042. [PMID] 32285629.
View on: PubMed Publisher’s Site
2020
Histological validation of a type 1 diabetes clinical diagnostic model for classification of diabetes.
Diabetic medicine : a journal of the British Diabetic Association. 37(12):2160-2168 [DOI] 10.1111/dme.14361. [PMID] 32634859.
View on: PubMed Publisher’s Site
2020
Informatics Training for Pathology Practice and Research in the Digital Era.
Academic pathology. 7 [DOI] 10.1177/2374289520911179. [PMID] 32284963.
View on: PubMed Publisher’s Site
2019
Targeted amplicon sequencing of 40 nuclear genes supports a single introduction and rapid radiation of Hawaiian Metrosideros (Myrtaceae)
Plant Systematics and Evolution. 305(10):961-974 [DOI] 10.1007/s00606-019-01615-0.
View on: Publisher’s Site
2019
The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation.
Proceedings of the National Academy of Sciences of the United States of America. 116(34):17081-17089 [DOI] 10.1073/pnas.1822129116. [PMID] 31387975.
View on: PubMed Publisher’s Site
2017
Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae).
Molecular phylogenetics and evolution. 111:231-247 [DOI] 10.1016/j.ympev.2017.04.003. [PMID] 28390909.
View on: PubMed Publisher’s Site
2017
Endometrial Thickness as Measured by Transvaginal Ultrasound and the Corresponding Histopathologic Diagnosis in Women With Postmenopausal Bleeding.
International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists. 36(4):348-355 [DOI] 10.1097/PGP.0000000000000344. [PMID] 27801761.
View on: PubMed Publisher’s Site
2016
The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity.
Scientific reports. 6 [DOI] 10.1038/srep38063. [PMID] 27905489.
View on: PubMed Publisher’s Site
2015
A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda.
G3 (Bethesda, Md.). 5(8):1685-94 [DOI] 10.1534/g3.115.019588. [PMID] 26068575.
View on: PubMed Publisher’s Site
2015
Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants.
Frontiers in bioengineering and biotechnology. 3 [DOI] 10.3389/fbioe.2015.00033. [PMID] 25859541.
View on: PubMed Publisher’s Site
2015
MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.
Applications in plant sciences. 3(4) [DOI] 10.3732/apps.1400115. [PMID] 25909041.
View on: PubMed Publisher’s Site
2014
Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae.
Applications in plant sciences. 2(10) [DOI] 10.3732/apps.1400049. [PMID] 25309837.
View on: PubMed Publisher’s Site
2013
A Genome-Enabled, High-Throughput, and Multiplexed Fingerprinting Platform for Strawberry (Fragaria L.)
Molecular Breeding. 31(3):615-629 [DOI] 10.1007/s11032-012-9819-3.
View on: Publisher’s Site
2013
Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
Science (New York, N.Y.). 342(6165):1516-7 [DOI] 10.1126/science.1241130. [PMID] 24357320.
View on: PubMed Publisher’s Site
2013
Inside Arbuscular Mycorrhizal Roots – Molecular Probes To Understand the Symbiosis
Plant Genome. 6(2) [DOI] 10.3835/plantgenome2012.06.0007.
View on: Publisher’s Site
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 [DOI] 10.1186/1471-2148-13-35. [PMID] 23394592.
View on: PubMed Publisher’s Site
2013
Primers for low-copy nuclear genes in the Hawaiian endemic Clermontia (Campanulaceae) and cross-amplification in Lobelioideae.
Applications in plant sciences. 1(6) [DOI] 10.3732/apps.1200450. [PMID] 25202552.
View on: PubMed Publisher’s Site
2013
The Amborella genome and the evolution of flowering plants.
Science (New York, N.Y.). 342(6165) [DOI] 10.1126/science.1241089. [PMID] 24357323.
View on: PubMed Publisher’s Site
2013
The Potential of Genomics in Plant Systematics
. 62(5):886-898
2013
Validation of reference transcripts in strawberry (Fragaria spp.).
Molecular genetics and genomics : MGG. 288(12):671-81 [DOI] 10.1007/s00438-013-0780-6. [PMID] 24061528.
View on: PubMed Publisher’s Site
2012
Making Next-Generation Sequencing Work for You: Approaches and Practical Considerations for Marker Development and Phylogenetics
Plant Ecology and Diversity. 5(4):427-450 [DOI] 10.1080/17550874.2012.745909.
View on: Publisher’s Site
2012
Next-generation sequencing and genome evolution in allopolyploids.
American journal of botany. 99(2):372-82 [DOI] 10.3732/ajb.1100395. [PMID] 22268220.
View on: PubMed Publisher’s Site
2012
Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin.
Current biology : CB. 22(3):248-52 [DOI] 10.1016/j.cub.2011.12.027. [PMID] 22264605.
View on: PubMed Publisher’s Site
2011
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.
Genome biology. 12(5) [DOI] 10.1186/gb-2011-12-5-r48. [PMID] 21619600.
View on: PubMed Publisher’s Site
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 1:132-46 [DOI] 10.1111/j.1365-294X.2009.04469.x. [PMID] 20331776.
View on: PubMed Publisher’s Site
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):504-22 [PMID] 18048316.
View on: PubMed

Grants

Sep 2018 ACTIVE
2/3 Florida-California Cancer Research, Education & Engagement (CaRE2) Health Equity Center
Role: Co-Investigator
Funding: NATL INST OF HLTH NCI
Aug 2018 – Jun 2020
RoL:FELS:EAGER Rules for cellular adaptation to the mechanical properties of their environment
Role: Co-Investigator
Funding: NATL SCIENCE FOU
Jun 2018 ACTIVE
Immune Function and the Progression to Type 1 Diabetes
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAID

Education

Doctor of Philosophy (PH.D)
2014 · University of Florida (UF), Gainesville, FL, USA
Master of Science in Bioinformatics
2008 · University of Illinois at Urbana-Champaign (UIUC), IL, USA
Bachelor of Science with Honors in Bioinformatics
2006 · Brigham Young University (BYU), Provo, UT, USA

Teaching Profile

Courses Taught
2018-2021
GMS5905 Special Topics in Biomedical Sciences
2011,2013
PCB3063 Genetics

Contact Details

Phones:
Business:
(352) 627-2272
Emails:
Business:
schamala@ufl.edu