Srikar Chamala, PhD

Srikar Chamala, PhD, is an Associate Professor of Clinical Pathology at the Keck School of Medicine of USC. He also serves as Director of the Center for Pathology Informatics and Data Science at Children’s Hospital Los Angeles. The major areas of research interest include clinical genome informatics, cancer disparity informatics, pathology informatics and data analytics, and translational bioinformatics.

• Assessment of the adequacy of the Fast Healthcare Interoperability Resources (FHIR) Genomics standard for the representation of somatic testing reports. JAMIA Open. 2026 Apr; 9(2):ooag022.. View in PubMed
• Genetic data normalization for genomic medicine: a Fast Healthcare Interoperability Resources Genomics reference implementation. J Am Med Inform Assoc. 2025 Oct 01; 32(10):1598-1608.. View in PubMed
• Algorithmic Fairness in Machine Learning Prediction of Autism Using Electronic Health Records. Stud Health Technol Inform. 2025 Aug 07; 329:1180-1184.. View in PubMed
• Achieving ACGME Clinical Informatics Fellowship Accreditation: A Chronicle of Our Institution’s Journey. Appl Clin Inform. 2025 08; 16(4):1171-1183.. View in PubMed
• Surveying the Efficacy of an Open Access Biomedical Informatics Boot Camp. Appl Clin Inform. 2025 05; 16(3):583-588.. View in PubMed
• Somatic Genomic Profiling of Pancreatic Ductal Adenocarcinomas From a Diverse Cohort of Patients. Pancreas. 2025 Mar 01; 54(3):e171-e178.. View in PubMed
• Fecal Microbiota Transplantation Induces Sustained Gut Microbiome Changes in Pediatric Ulcerative Colitis: A Combined Randomized and Open-Label Study. Gastro Hep Adv. 2025; 4(10):100741.. View in PubMed
• Evaluating utility of routine ferritin testing in blood donors: A hospital-based blood donor centre experience. Transfus Med. 2024 Dec; 34(6):491-498.. View in PubMed
• Analyzing the Efficacy of an Open Access Biomedical Informatics Boot Camp. Stud Health Technol Inform. 2024 08 22; 316:1545-1546.. View in PubMed
• Molecularly-Guided Cancer Clinical Trial Matching using FHIR and HL7 Clinical Quality Language: A Proof of Concept. AMIA Annu Symp Proc. 2024; 2024:359-367.. View in PubMed
• Sync for Genes Phase 5: Computable artifacts for sharing dynamically annotated FHIR-formatted genomic variants. Learn Health Syst. 2023 Oct; 7(4):e10385.. View in PubMed
• A genomic data archive from the Network for Pancreatic Organ donors with Diabetes. Sci Data. 2023 05 26; 10(1):323.. View in PubMed
• Introducing HL7 FHIR Genomics Operations: a developer-friendly approach to genomics-EHR integration. J Am Med Inform Assoc. 2023 02 16; 30(3):485-493.. View in PubMed
• Automated HL7v2 LRI informatics framework for streamlining genomics-EHR data integration. J Pathol Inform. 2023; 14:100330.. View in PubMed
• Transcriptional Profile of Human Pancreatic Acinar Ductal Metaplasia. Gastro Hep Adv. 2023; 2(4):532-543.. View in PubMed
• Development and application of a computable genotype model in the GA4GH Variation Representation Specification. Pac Symp Biocomput. 2023; 28:383-394.. View in PubMed
• Maintaining informatics training learning outcomes with a COVID-19 era shift to a fully online flipped course. J Pathol Inform. 2023; 14:100162.. View in PubMed
• Pharmacological inhibition and reversal of pancreatic acinar ductal metaplasia. Cell Death Discov. 2022 Sep 02; 8(1):378.. View in PubMed
• HUMAN STUDY COMT and DRD3 haplotype-associated pain intensity and acute care utilization in adult sickle cell disease. Exp Biol Med (Maywood). 2022 09; 247(17):1601-1608.. View in PubMed
• The vaginal microbiome is associated with endometrial cancer grade and histology. Cancer Res Commun. 2022 06; 2(6):447-455.. View in PubMed
• Analysis of AVPR1A, thermal and pressure pain thresholds, and stress in sickle cell disease. Front Pain Res (Lausanne). 2022; 3:1060245.. View in PubMed
• Wrong Tissue in Block. Am J Clin Pathol. 2021 Sep 08; 156(4):700-707.. View in PubMed
• The Hologic Aptima SARS-CoV-2 assay enables high ratio pooling saving reagents and improving turnaround time. J Clin Lab Anal. 2021 Sep; 35(9):e23888.. View in PubMed
• Digital Pathology in Cameroon. JCO Glob Oncol. 2021 08; 7:1380-1389.. View in PubMed
• Reverse Plasticity Underlies Rapid Evolution by Clonal Selection within Populations of Fibroblasts Propagated on a Novel Soft Substrate. Mol Biol Evol. 2021 07 29; 38(8):3279-3293.. View in PubMed
• Enrichment of the erythrocyte miR-451a in brain extracellular vesicles following impairment of the blood-brain barrier. Neurosci Lett. 2021 04 23; 751:135829.. View in PubMed
• Genetic Composition and Autoantibody Titers Model the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis. Diabetes. 2021 04; 70(4):932-943.. View in PubMed
• vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. BMC Bioinformatics. 2021 Mar 02; 22(1):104.. View in PubMed
• Building a precision oncology workforce by multidisciplinary and case-based learning. BMC Med Educ. 2021 Jan 26; 21(1):75.. View in PubMed
• Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes. Genome Biol. 2021 01 21; 22(1):39.. View in PubMed
• An Assessment of Ovarian Cancer Histotypes Across the African Diaspora. Front Oncol. 2021; 11:732443.. View in PubMed
• Pathology Informatics and Robotics Strategies for Improving Efficiency of COVID-19 Pooled Testing. Acad Pathol. 2021 Jan-Dec; 8:23742895211020485.. View in PubMed
• Optimizing COVID-19 testing capabilities and clinical management using pathology informatics. JAMIA Open. 2020 Dec; 3(4):523-529.. View in PubMed
• Informatics driven quality improvement in the modern histology lab. JAMIA Open. 2020 Dec; 3(4):530-535.. View in PubMed
• Histological validation of a type 1 diabetes clinical diagnostic model for classification of diabetes. Diabet Med. 2020 12; 37(12):2160-2168.. View in PubMed
• Disparities in Pancreatic Ductal Adenocarcinoma-The Significance of Hispanic Ethnicity, Subgroup Analysis, and Treatment Facility on Clinical Outcomes. Cancer Med. 2020 06; 9(12):4069-4082.. View in PubMed
• Informatics Training for Pathology Practice and Research in the Digital Era. Acad Pathol. 2020 Jan-Dec; 7:2374289520911179.. View in PubMed
• The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proc Natl Acad Sci U S A. 2019 08 20; 116(34):17081-17089.. View in PubMed
• Endometrial Thickness as Measured by Transvaginal Ultrasound and the Corresponding Histopathologic Diagnosis in Women With Postmenopausal Bleeding. Int J Gynecol Pathol. 2017 Jul; 36(4):348-355.. View in PubMed
• Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Mol Phylogenet Evol. 2017 06; 111:231-247.. View in PubMed
• The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity. Sci Rep. 2016 12 01; 6:38063.. View in PubMed
• 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). 2015 Jun 11; 5(8):1685-94.. View in PubMed
• MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. Appl Plant Sci. 2015 Apr; 3(4).. View in PubMed
• Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants. Front Bioeng Biotechnol. 2015; 3:33.. View in PubMed
• Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae. Appl Plant Sci. 2014 Oct; 2(10).. View in PubMed
• Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science. 2013 Dec 20; 342(6165):1516-7.. View in PubMed
• Validation of reference transcripts in strawberry (Fragaria spp.). Mol Genet Genomics. 2013 Dec; 288(12):671-81.. View in PubMed
• Primers for low-copy nuclear genes in the Hawaiian endemic Clermontia (Campanulaceae) and cross-amplification in Lobelioideae. Appl Plant Sci. 2013 Jun; 1(6).. View in PubMed
• Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations. BMC Evol Biol. 2013 Feb 09; 13:35.. View in PubMed
• Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr Biol. 2012 Feb 07; 22(3):248-52.. View in PubMed
• Next-generation sequencing and genome evolution in allopolyploids. Am J Bot. 2012 Feb; 99(2):372-82.. View in PubMed
• A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biol. 2011; 12(5):R48.. View in PubMed
• Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol Ecol. 2010 Mar; 19 Suppl 1:132-46.. View in PubMed
• Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians. Int J Bioinform Res Appl. 2007; 3(4):504-22.. View in PubMed

• Haiman, Christopher
• Peters, Anne
• Matsuo, Koji
• Lenz, Heinz-Josef
• Thomas, Paul