Srikar Chamala, PhD

Title(s)Associate Professor of Clinical Pathology
SchoolKeck School of Medicine of Usc
Address4640 West Sunset Blvd
Off Campus
Los Angeles CA 90027
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    1. Sync for Genes Phase 5: Computable artifacts for sharing dynamically annotated FHIR-formatted genomic variants. Learn Health Syst. 2023 Oct; 7(4):e10385. Dolin R, Heale BSE, Gupta R, Alvarez C, Aronson J, Boxwala A, Gothi SR, Husami A, Shalaby J, Babb L, Wagner A, Chamala S. PMID: 37860057; PMCID: PMC10582236.
      View in: PubMed   Mentions:
    2. Automated HL7v2 LRI informatics framework for streamlining genomics-EHR data integration. J Pathol Inform. 2023; 14:100330. Dolin RH, Gupta R, Newsom K, Heale BSE, Gothi S, Starostik P, Chamala S. PMID: 37719179; PMCID: PMC10504540.
      View in: PubMed   Mentions:
    3. A genomic data archive from the Network for Pancreatic Organ donors with Diabetes. Sci Data. 2023 05 26; 10(1):323. Perry DJ, Shapiro MR, Chamberlain SW, Kusmartseva I, Chamala S, Balzano-Nogueira L, Yang M, Brant JO, Brusko M, Williams MD, McGrail KM, McNichols J, Peters LD, Posgai AL, Kaddis JS, Mathews CE, Wasserfall CH, Webb-Robertson BM, Campbell-Thompson M, Schatz D, Evans-Molina C, Pugliese A, Concannon P, Anderson MS, German MS, Chamberlain CE, Atkinson MA, Brusko TM. PMID: 37237059; PMCID: PMC10219990.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    4. 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. Dolin RH, Heale BSE, Alterovitz G, Gupta R, Aronson J, Boxwala A, Gothi SR, Haines D, Hermann A, Hongsermeier T, Husami A, Jones J, Naeymi-Rad F, Rapchak B, Ravishankar C, Shalaby J, Terry M, Xie N, Zhang P, Chamala S. PMID: 36548217; PMCID: PMC9933060.
      View in: PubMed   Mentions: 3     Fields:    
    5. Transcriptional Profile of Human Pancreatic Acinar Ductal Metaplasia. Gastro Hep Adv. 2023; 2(4):532-543. Jiang J, Hakimjavadi H, Bray JK, Perkins C, Gosling A, daSilva L, Bulut G, Ali J, Setiawan VW, Campbell-Thompson M, Chamala S, Schmittgen TD. PMID: 37425649; PMCID: PMC10328139.
      View in: PubMed   Mentions: 2  
    6. Analysis of AVPR1A, thermal and pressure pain thresholds, and stress in sickle cell disease. Front Pain Res (Lausanne). 2022; 3:1060245. Powell-Roach KL, Yao Y, Cao X, Chamala S, Wallace MR, Cruz-Almeida Y, Molokie RE, Wang ZJ, Wilkie DJ. PMID: 36688082; PMCID: PMC9845903.
      View in: PubMed   Mentions: 1  
    7. Development and application of a computable genotype model in the GA4GH Variation Representation Specification. Pac Symp Biocomput. 2023; 28:383-394. Goar W, Babb L, Chamala S, Cline M, Freimuth RR, Hart RK, Kuzma K, Lee J, Nelson T, Prlic A, Riehle K, Smith A, Stahl K, Yates AD, Rehm HL, Wagner AH. PMID: 36540993; PMCID: PMC9782714.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    8. Maintaining informatics training learning outcomes with a COVID-19 era shift to a fully online flipped course. J Pathol Inform. 2022 Dec 01; 100162. Maness HTD, Hakimjavadi H, Chamala S. PMID: 36471780; PMCID: PMC9714185.
      View in: PubMed   Mentions:
    9. Pharmacological inhibition and reversal of pancreatic acinar ductal metaplasia. Cell Death Discov. 2022 Sep 02; 8(1):378. da Silva L, Jiang J, Perkins C, Atanasova KR, Bray JK, Bulut G, Azevedo-Pouly A, Campbell-Thompson M, Yang X, Hakimjavadi H, Chamala S, Ratnayake R, Gharaibeh RZ, Li C, Luesch H, Schmittgen TD. PMID: 36055991; PMCID: PMC9440259.
      View in: PubMed   Mentions: 4  
    10. The vaginal microbiome is associated with endometrial cancer grade and histology. Cancer Res Commun. 2022 06; 2(6):447-455. Hakimjavadi H, George SH, Taub M, Dodds LV, Sanchez-Covarrubias AP, Huang M, Pearson JM, Slomovitz BM, Kobetz EN, Gharaibeh R, Sowamber R, Pinto A, Chamala S, Schlumbrecht MP. PMID: 35928983; PMCID: PMC9345414.
      View in: PubMed   Mentions: 4  Translation:Humans
    11. 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. Powell-Roach KL, Yao Y, Wallace MR, Chamala S, Cruz-Almeida Y, Jhun E, Molokie RE, Wang ZJ, Wilkie DJ. PMID: 35285297; PMCID: PMC9554168.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    12. An Assessment of Ovarian Cancer Histotypes Across the African Diaspora. Front Oncol. 2021; 11:732443. George SHL, Omotoso A, Pinto A, Mustapha A, Sanchez-Covarrubias AP, Umar UA, Umar AB, Oluwasola TA, Okolo CA, Anthony UU, Ukekwe FI, Bakari MA, Dahiru AMC, Abdullahi HI, Abimiku BA, Abdurrahman A, Usman A, Ahmed SA, Usman HA, Kabir A, Eleje GU, Chiemeka ME, Nzeribe E, Nweke I, Kadas S, Suleiman DE, Ekanem E, Uche UM, Paul J, Agwu UM, Edegbe FO, Anorlu RI, Banjo A, Ajenifuja KO, Fawole AA, Kazeem IOO, Magaji F, Silas O, Athanasius BP, Tamunomie NK, Bassey E, Abudu K, Ango IG, Abdullahi K, Lawal I, Kabir SA, Ekanem V, Ezeanochie M, Yahaya UR, Castillo MN, Bahall V, Chatrani V, Brambury I, Bowe S, Halliday D, Bruney G, Butler R, Ragin C, Odedina F, Chamala S, Schlumbrecht M, Audu B. PMID: 34900682; PMCID: PMC8662547.
      View in: PubMed   Mentions: 1  
    13. Wrong Tissue in Block. Am J Clin Pathol. 2021 Sep 08; 156(4):700-707. Weaver KD, De Los Santos Y, Gaffar M, Zona MC, Gennaro T, Shenoy A, Flax S, Chamala S, Seifert RP, Esnakula AK. PMID: 33940603.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. Digital Pathology in Cameroon. JCO Glob Oncol. 2021 08; 7:1380-1389. Gruber-Mösenbacher U, Katzell L, McNeely M, Neier E, Jean B, Kuran A, Chamala S. PMID: 34524835; PMCID: PMC8457846.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    15. 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. Purkayastha P, Pendyala K, Saxena AS, Hakimjavadi H, Chamala S, Dixit P, Baer CF, Lele TP. PMID: 33871606; PMCID: PMC8321517.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    16. 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. Newsom K, Zhang Y, Chamala S, Martinez K, Clare-Salzler M, Starostik P. PMID: 34213803; PMCID: PMC8418467.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCellsPHPublic Health
    17. Pathology Informatics and Robotics Strategies for Improving Efficiency of COVID-19 Pooled Testing. Acad Pathol. 2021 Jan-Dec; 8:23742895211020485. Balasubramani B, Newsom KJ, Martinez KA, Starostik P, Clare-Salzler M, Chamala S. PMID: 34189259; PMCID: PMC8209787.
      View in: PubMed   Mentions: 5  
    18. Enrichment of the erythrocyte miR-451a in brain extracellular vesicles following impairment of the blood-brain barrier. Neurosci Lett. 2021 04 23; 751:135829. Koopaei NN, Chowdhury EA, Jiang J, Noorani B, da Silva L, Bulut G, Hakimjavadi H, Chamala S, Bickel U, Schmittgen TD. PMID: 33727125.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    19. vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. BMC Bioinformatics. 2021 Mar 02; 22(1):104. Dolin RH, Gothi SR, Boxwala A, Heale BSE, Husami A, Jones J, Khangar H, Londhe S, Naeymi-Rad F, Rao S, Rapchak B, Shalaby J, Suraj V, Xie N, Chamala S, Alterovitz G. PMID: 33653260; PMCID: PMC7923512.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    20. Building a precision oncology workforce by multidisciplinary and case-based learning. BMC Med Educ. 2021 Jan 26; 21(1):75. Chamala S, Maness HTD, Brown L, Adams CB, Lamba JK, Cogle CR. PMID: 33499867; PMCID: PMC7836489.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    21. 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. Balzano-Nogueira L, Ramirez R, Zamkovaya T, Dailey J, Ardissone AN, Chamala S, Serrano-Quílez J, Rubio T, Haller MJ, Concannon P, Atkinson MA, Schatz DA, Triplett EW, Conesa A. PMID: 33478573; PMCID: PMC7818777.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    22. Genetic Composition and Autoantibody Titers Model the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis. Diabetes. 2021 04; 70(4):932-943. Williams MD, Bacher R, Perry DJ, Grace CR, McGrail KM, Posgai AL, Muir A, Chamala S, Haller MJ, Schatz DA, Brusko TM, Atkinson MA, Wasserfall CH. PMID: 33419759; PMCID: PMC7980194.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    23. Optimizing COVID-19 testing capabilities and clinical management using pathology informatics. JAMIA Open. 2020 Dec; 3(4):523-529. Chamala S, Flax S, Starostik P, Cherabuddi K, Iovine NM, Majety S, Newsom KJ, Reeves M, Joshi-Guske MJ, Downey MM, Lele TP, Clare-Salzler MJ. PMID: 33754137; PMCID: PMC7717304.
      View in: PubMed   Mentions: 1  
    24. Informatics driven quality improvement in the modern histology lab. JAMIA Open. 2020 Dec; 3(4):530-535. Seifert RP, Casler V, Al Qaysi N, Gothi SR, Williams L, Christensen PR, Flax S, Chamala S. PMID: 33623889; PMCID: PMC7886543.
      View in: PubMed   Mentions: 1  
    25. Histological validation of a type 1 diabetes clinical diagnostic model for classification of diabetes. Diabet Med. 2020 12; 37(12):2160-2168. Carr ALJ, Perry DJ, Lynam AL, Chamala S, Flaxman CS, Sharp SA, Ferrat LA, Jones AG, Beery ML, Jacobsen LM, Wasserfall CH, Campbell-Thompson ML, Kusmartseva I, Posgai A, Schatz DA, Atkinson MA, Brusko TM, Richardson SJ, Shields BM, Oram RA. PMID: 32634859; PMCID: PMC8086995.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    26. 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. Riner AN, Underwood PW, Yang K, Herremans KM, Cameron ME, Chamala S, Qiu P, George TJ, Permuth JB, Merchant NB, Trevino JG. PMID: 32285629; PMCID: PMC7300394.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    27. Informatics Training for Pathology Practice and Research in the Digital Era. Acad Pathol. 2020 Jan-Dec; 7:2374289520911179. Maness HTD, Behar-Horenstein LS, Clare-Salzler M, Chamala S. PMID: 32284963; PMCID: PMC7119238.
      View in: PubMed   Mentions: 6  
    28. 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. Rendón-Anaya M, Ibarra-Laclette E, Méndez-Bravo A, Lan T, Zheng C, Carretero-Paulet L, Perez-Torres CA, Chacón-López A, Hernandez-Guzmán G, Chang TH, Farr KM, Barbazuk WB, Chamala S, Mutwil M, Shivhare D, Alvarez-Ponce D, Mitter N, Hayward A, Fletcher S, Rozas J, Sánchez Gracia A, Kuhn D, Barrientos-Priego AF, Salojärvi J, Librado P, Sankoff D, Herrera-Estrella A, Albert VA, Herrera-Estrella L. PMID: 31387975; PMCID: PMC6708331.
      View in: PubMed   Mentions: 58     Fields:    Translation:Animals
    29. 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. Patel V, Wilkinson EJ, Chamala S, Lu X, Castagno J, Rush D. PMID: 27801761.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    30. 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. García N, Folk RA, Meerow AW, Chamala S, Gitzendanner MA, Oliveira RS, Soltis DE, Soltis PS. PMID: 28390909.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    31. The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity. Sci Rep. 2016 12 01; 6:38063. Alam SG, Zhang Q, Prasad N, Li Y, Chamala S, Kuchibhotla R, Kc B, Aggarwal V, Shrestha S, Jones AL, Levy SE, Roux KJ, Nickerson JA, Lele TP. PMID: 27905489; PMCID: PMC5131312.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
    32. 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. Westbrook JW, Chhatre VE, Wu LS, Chamala S, Neves LG, Muñoz P, Martínez-García PJ, Neale DB, Kirst M, Mockaitis K, Nelson CD, Peter GF, Davis JM, Echt CS. PMID: 26068575; PMCID: PMC4528325.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    33. MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. Appl Plant Sci. 2015 Apr; 3(4). Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, Barbazuk WB, Soltis DE, Soltis PS. PMID: 25909041; PMCID: PMC4406834.
      View in: PubMed   Mentions: 42  
    34. Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants. Front Bioeng Biotechnol. 2015; 3:33. Chamala S, Feng G, Chavarro C, Barbazuk WB. PMID: 25859541; PMCID: PMC4374538.
      View in: PubMed   Mentions: 57  
    35. Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae. Appl Plant Sci. 2014 Oct; 2(10). Pillon Y, Johansen J, Sakishima T, Chamala S, Barbazuk WB, Stacy EA. PMID: 25309837; PMCID: PMC4189496.
      View in: PubMed   Mentions: 1  
    36. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science. 2013 Dec 20; 342(6165):1516-7. Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB. PMID: 24357320.
      View in: PubMed   Mentions: 42     Fields:    Translation:Animals
    37. Validation of reference transcripts in strawberry (Fragaria spp.). Mol Genet Genomics. 2013 Dec; 288(12):671-81. Clancy MA, Rosli HG, Chamala S, Barbazuk WB, Civello PM, Folta KM. PMID: 24061528.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    38. Primers for low-copy nuclear genes in the Hawaiian endemic Clermontia (Campanulaceae) and cross-amplification in Lobelioideae. Appl Plant Sci. 2013 Jun; 1(6). Pillon Y, Johansen J, Sakishima T, Chamala S, Barbazuk WB, Stacy EA. PMID: 25202552; PMCID: PMC4105025.
      View in: PubMed   Mentions: 2  
    39. 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. Pillon Y, Johansen J, Sakishima T, Chamala S, Barbazuk WB, Roalson EH, Price DK, Stacy EA. PMID: 23394592; PMCID: PMC3605094.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    40. Next-generation sequencing and genome evolution in allopolyploids. Am J Bot. 2012 Feb; 99(2):372-82. Buggs RJ, Renny-Byfield S, Chester M, Jordon-Thaden IE, Viccini LF, Chamala S, Leitch AR, Schnable PS, Barbazuk WB, Soltis PS, Soltis DE. PMID: 22268220.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    41. Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr Biol. 2012 Feb 07; 22(3):248-52. Buggs RJ, Chamala S, Wu W, Tate JA, Schnable PS, Soltis DE, Soltis PS, Barbazuk WB. PMID: 22264605.
      View in: PubMed   Mentions: 62     Fields:    Translation:Animals
    42. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biol. 2011; 12(5):R48. Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D, Paterson AH, Pires JC, Chanderbali A, Soltis DE, Chamala S, Barbazuk B, Soltis PS, Albert VA, Ma H, Mandoli D, Banks J, Carlson JE, Tomkins J, dePamphilis CW, Wing RA, Leebens-Mack J. PMID: 21619600; PMCID: PMC3219971.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    43. 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. Buggs RJ, Chamala S, Wu W, Gao L, May GD, Schnable PS, Soltis DE, Soltis PS, Barbazuk WB. PMID: 20331776.
      View in: PubMed   Mentions: 51     Fields:    Translation:Animals
    44. 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. Chamala S, Beckstead WA, Rowe MJ, McClellan DA. PMID: 18048316.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
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