† Indicates equal contributions § Indicates co-senior author Citations: 3600+ Google Scholar
51. Expression Pattern of Ultra-Conserved Noncoding RNAs in Head and Neck Cancer: The role of micro RNAs.
Chamala, S., Hakimjavadi, H., Jiang, J., Menefee,J. N., Dixit, P., & Fredenburg, K. Under Preparation.
50. Role of Genetic Factors in Determining Pancreas Weight in Type 1 Diabetes.
Chamala, S., Bacher, Rhonda., Perry, D. J., Williams, M., Wasserfall, C., Brusko, T. M., Atkinson, M. A., Haller, M. J., Campbell-Thompson, M., and Concannon, P. Under Preparation.
49. Endometrial Cancer Diagnosis and Cervical Microbiome.
†George, S., †Hakimjavadi, H., Taub, M., Dodds, L., Pearson, J. M., Huang, M., Kobetz, E., Gharaibeh, R., Sowamber, R., Pinto, A., §Chamala, S., & §Schlumbrecht, M. Submitted and under review at Frontiers in Oncology.
48. COMT and DRD3 haplotypes associated with pain intensity and acute care utilization in adults with sickle cell disease.
Powell-Roach, K.L., Yao, Y., Wallace, P., Chamala, S., Cruz-Almeida, Y., Jhun, E., Molokie, R.E., Wang, Z.J., & Wilkie, D.J. Submitted and under review at Journal of Pain.
47. Transcriptional Profile of Human Pancreatic Acinar Ductal Metaplasia.
39. Jiang J., *Hakimjavadi, H., Bray, J.K., Gosling, A., daSilva L., Bulut, G., Perkins, C., Ali, J., Setiawan, V.W., Campbell-Thompson, M., §Chamala, S., and §Schmittgen, T.D. Submitted and under review at Journal of Gastroenterology.
46. Unique Genetic Signatures Underlie Divergent Biology in Ethnically Diverse Patients with Pancreatic Cancer.
Cameron, M. E., Hakimjavadi, H., Riner, A. N., Herremans, K. M., Underwood, P. W., Judge, A. R., Odedina, F., Carpten, J. D., Wilkie, D. Reams, R. R., Han, B., Agyare, E., §Chamala, S., & §Trevino, J. G. Submitted and under review at Genomics.
45. Functionality of Apheresis Platelets Exposed to Lower than Standard Temperatures as Measured by Thromboeleastography (TEG) Analysis.
Duque, M.A., Aysola, A.E., Hakimjavadi, H., Mukhtar, F., Harris, N., Chamala, S., & Pelletier, P.R. Submitted and under review at Transfusion.
44. Implementation and Evaluation of Live Microscopy and Whole Slide Imaging Instruments.
Casler, V. L., & Chamala, S. Submitted and under review at Journal of Pathology Informatics.
43. Digital Pathology in Cameroon.
Gruber-Mösenbacher, U., Casler, V., Neier, E., Jean, B., & Chamala, S. (2021). Accepted at Journal of Global Oncology.
42. Wrong Tissue in Block: Grossing Gone Wrong can be Made Right with Tailored Informatics Solutions.
Weaver, K.D., De Los Santos, Y., Gaffar, M., Zona, M.C., Flax, S., Chamala, S., Seifert, R.P., & Esnakula, A.K. (2021). American Journal of Clinical Pathology
41. Pathology Informatics and Robotics Strategies for Improving Efficiency of COVID-19 Pooled Testing.
Balasubramani, B., Newsom, K., Martinez, K., Starostik, P., Clare-Salzler, M., & Chamala, S. (2021). Academic Pathology.
40. The Hologic Aptima SARS-CoV-2 Assay Enables High Ratio Pooling Saving Reagents and Improving Turnaround Time.
Newsom, K., Zhang, Y., Chamala, S., Martinez, K., Clare-Salzler, M., & Starostik. (2021). Journal of Clinical Laboratory Analysis.
39. vcf2fhir: A Utility to Convert VCF Files into HL7 FHIR Format for Genomics-EHR Integration.
Dolin, R.H., Gothi, S.R., Boxwala, A., Heale, B.S.E., Husami, A., Jones, J., Khangar, H., Londhe, S., Naeymi-Rad, F., Rao, S., Rapchak, B., Shalaby, J., Suraj, V., Xie, Ning., §Chamala, S., & §Alterovitz, G. (2021). BMC Bioinformatics.
38. Enrichment of the erythrocyte miR-451a in brain extracellular vesicles following impairment of the blood-brain barrier.
Koopaei, N. N., Chowdhury, E. A., Jiang, J., Noorani, B., da Silva, L., Bulut, G., Hakimjavadi, H., Chamala, S., Bickel, U., & Schmittgen, T. D. (2021). Neuroscience Letters.
37. Building a Precision Oncology Workforce by Multidisciplinary and Case-Based Learning.
†Chamala, S., †Maness, H. T. D., Brown, L., Adams, C. B., & Cogle, C.R. (2021). BMC Medical Education..
DOI: 10.1186/s12909-021-02500-6
36. Reverse plasticity underlies rapid evolution by clonal selection within populations of fibroblasts propagated on a novel soft substrate.
Purkayastha, P., Pendyala, K., Saxena, A.S., Hakimjavadi, H.,Chamala, S., Baer, C.F., & Lele, T.P. (2021). Mol Biol Evol.
35. Effect of Genetic Burden and Autoantibody Titers on the Probability of Detecting C-Peptide Following Type 1 Diabetes Diagnosis.
Williams, M.D., Bacher, B., Perry, D.J., Grace, C.R., McGrail, K.M., Posgai, A.L., Muir, A., Chamala, S., Haller, M.J., Schatz, D.A., Brusko, T.M., Atkinson, M.A., & Wasserfall, C.H. (2021). Diabetes Care.
DOI: 10.2337/db20-0937
34. Integrative Analyses of TEDDY Omics Data Reveal Lipid Metabolism Abnormalities, Increased Intracellular ROS and Heightened Inflammation Prior to Autoimmunity for Type 1 Diabetes.
Balzano-Nogueira L., Ramirez R., Zamkovaya T., Dailey J., Ardissone A.N., Chamala S., Serrano-Quílez J., Rubio T., Haller M.J., Concannon P., Atkinson M.A., Schatz D.A., Triplett E.W., & Conesa A. (2021). Genome Biology.
33. Indispensability of Clinical Bioinformatics for Effective Implementation of Genomic Medicine in Pathology Laboratories.
Chamala, S., Mishra, S.N., Newsom, K.J., Majety, S., Gothi, R.N., Dolin, R.H., Walton, N.A., and Starostik, P. (2020). Applied Clinical Informatics Open.
DOI: https://doi.org/10.1055/s-0040-1721480
32. Informatics Driven Quality Improvement in the Modern Histology Lab.
Casler, V. L., Seifert, R. P., Al Qaysi, N., Gothi, S.R., Williams, L., Christensen, P.R., Flax, S., & Chamala, S. (2020) JAMIA Open.
DOI: https://doi.org/10.1093/jamiaopen/ooaa066
31. Optimizing COVID-19 Testing Capabilities and Clinical Management Using Pathology Informatics.
Chamala, S., Flax, S., Starostik, Petr., Cherabuddi, K., Iovine, N.M., Majety, A., Newsom, K.J., Reeves, M., Joshi-Guske, M.J., Downey, M.M., Lele, T.P., & Clare-Salzler, M.J. (2020) JAMIA Open.
DOI: https://doi.org/10.1093/jamiaopen/ooaa055
30. Histological Validation of a Type 1 Diabetes Clinical Diagnostic Model for Classification of Diabetes.
Carr, A. L. J., Perry, D. J., Lynam, A. L., Chamala, S., Flaxman, C. S., Sharp, S. A., Ferrat, L. A., Jones, A. G., Beery, M. L., Jacobsen, L. M., Wasserfall, C. H., Campbell-Thompson, M. L., Kusmartseva, I., Posgai, A., Schatz, Desmond. A., Atkinson, M. A., Brusko, T. M., Richardson, S. J., Shields, B. M., & Oram, R. A. (2020) Diabetes Medicine
PUBMED: 32634859 | DOI: https://doi.org/10.1111/dme.14361
29. Informatics Training for Pathology Practice and Research in the Digital Era.
Maness, H. T. D., Behar-Horenstein, L. S., Clare-Salzler, M., & Chamala, S. (2020) Academic Pathology.
PUBMED: 32284963 | DOI: 10.1177/2374289520911179
28. Disparities in Pancreatic Ductal Adenocarcinoma—The Significance of Hispanic Ethnicity, Subgroup Analysis, and Treatment Facility on Clinical Outcomes.
Riner, A. N., Underwood, P. W., Yang, K., Herremans, K. M., Cameron, M. E., Chamala, S., Qiu, P., George, T.J., Permuth, J.B., Merchant, N.B., & Trevino, J. G. (2020) Cancer Medicine.
PUBMED: 32285629 | DOI: 10.1002/cam4.3042
27. Haplotype Analysis of COMT SNPs Associated with Pain Intensity and Acute Care Utilization in Adults with Sickle Cell Disease.
Roach, K., Yao, Y., Chamala, S., Black, V., Ahn, H., Fillingim, R., Ezenwa, M., Schlaeger, J., Suarez, M., Molokie, R., Wang, Z., & Wilkie, D. (2019) The Journal of Pain, 20(4), S8.
DOI: 10.1016/j.jpain.2019.01.047
26. The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen Influenced Gene Space Adaptation.
Rendon-Anaya, M., Ibarra-Laclette, E., Bravo, A. M., Lan, T., Zheng, C., Carretero-Paulet, L., Perez-Torres, C. A., Chacon-Lopez , A., Hernandez-Guzman, G., Chang, T., Farr, K., Barbazuk, W. B., Chamala, S., Mutwil, M., Shivhare, D., Alvarez-Ponce, D., Mitter, N., Hayward, A., Fletcher, S., Rozas, J., Gracia, A. S., Kuhn, D., Barrientos-Priego, A. F., Salojarvi, J., Librado, P., Sankoff, D., Herrera-Estrella, A., Albert, V. A., & Herrera-Estrella, L. (2019) Proceedings of the National Academy of Sciences, 201822129.
PUBMED: 31387975 | DOI: 10.1073/pnas.1822129116
25. Genomic Data in the Electronic Health Record.
Walton, N. A., Johnson, D. K., Person, T. N., & Chamala, S. (2019) Advances in Molecular Pathology, 2(1), 21-33.
24. Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae).
García, N., Folk, R.A., Meerow, A.W., Chamala, S., Gitzendanner, M.A., de Oliveira, R.S., Soltis, D.E., & Soltis, P.S. (2017) Molecular Phylogenetics and Evolution, 111, pp.231-247.
PUBMED: 28390909 | DOI: 10.1016/j.ympev.2017.04.003
23. Endometrial thickness as measured by transvaginal ultrasound and the corresponding histopathologic diagnosis in women with postmenopausal bleeding.
Patel, V., Wilkinson, E. J., Chamala, S., Lu, X., Costagno, J., and Rush D. (2016) International Journal of Gynecological Pathology, 36(4), 348-355.
PUBMED: 27801761 | DOI: 10.1097/PGP.0000000000000344
22. The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity.
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) Scientific Reports, 6:38063.
PUBMED: 27905489 | DOI: 10.1038/srep38063
21. A consensus genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two genotype-phenotype discovery populations of P. taeda.
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) G3: Genes| Genomes| Genetics, g3-115.3.
PUBMED: 26068575 | DOI: 10.1534/g3.115.019588
20. MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.
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) Applications in Plant Sciences, 3(4).
PUBMED: 25909041 | DOI: 10.3732/apps.1400115
19. Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants.
Chamala, S., Feng, G., Chavarro, C., & Barbazuk, W. B. (2015) Frontiers in Bioengineering and Biotechnology, 3, 33.
PUBMED: 25859541 | DOI: 10.3389/fbioe.2015.00033
18. Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae.
Pillon, Y., Johansen, J., Sakishima, T., Chamala, S., Barbazuk, W. B., & Stacy, E. A. (2014) Applications in Plant Sciences, 2(10).
PUBMED: 25309837 | DOI: 10.3732/apps.1400049
17. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
†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) Science, 342(6165), 1516–1517.
PUBMED: 24357320 | DOI: 10.1126/science.1241130
16. The Amborella genome and the evolution of flowering plants.
Amborella Genome Consortium (Chamala, S. is listed as one of the four major contributors). (2013) Science, 342(6165), 1241089.
PUBMED: 24357323 | DOI: 10.1126/science.1241089
15. Validation of reference transcripts in strawberry (Fragaria spp.).
Clancy, M. A., Rosli, H. G., Chamala, S., Barbazuk, W. B., Civello, P. M., & Folta, K. M. (2013) Molecular Genetics and Genomics, 288(12), 671-681.
PUBMED: 24061528 | DOI: 10.1007/s00438-013-0780-6
14. Primers for Low-Copy Nuclear Genes in the Hawaiian Endemic Clermontia (Campanulaceae) and Cross-Amplification in Lobelioideae.
Pillon, Y., Johansen, J., Sakishima, T., Chamala, S., Barbazuk, W. B., & Stacy, E. A. (2013) Applications in Plant Sciences, 1(6).
PUBMED: 25202552 | DOI: 10.3732/apps.1200450
13. Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations.
Pillon, Y., Johansen, J., Sakishima, T., Chamala, S., Barbazuk, W. B., Roalson, E. H., Price, D.K., & Stacy, E. A. (2013) BMC Evolutionary Biology, 13(1), 35.
PUBMED: 23394592 | DOI: 10.1186/1471-2148-13-35
12. A genome-enabled, high-throughput, and multiplexed fingerprinting platform for
Chambers, A., Carle, S., Njuguna, W., Chamala, S., Bassil, N., Whitaker, V., Barbazuk, W. B., & Folta, K. (2013) Molecular Breeding, 1-15.
DOI: 10.1007/s11032-012-9819-3
11. The potential of genomics in plant systematics.
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) Taxon, 62(5), 886-898.
DOI: 10.12705/625.13
10. Inside arbuscular mycorrhizal roots – molecular probes to understand the symbiosis.
Ruzicka, D., Chamala, S., Barrios-Masias, F. H., Martin, F., Smith, S., Jackson, L. E., Barbazuk, W. B., & Schachtman, D. P. (2012) The Plant Genome, 6(0),1-13.
DOI: 10.3835/plantgenome2012.06.0007
9. The tomato genome sequence provides insights into fleshy fruit evolution.
Tomato Genome Consortium. (2012) Nature, 485(7400), 635-641.
PUBMED: 22660326 | DOI: 10.1038/nature11119
8. Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin.
Buggs, R. J., Chamala, S., Wu, W., Tate, J. A., Schnable, P. S., Soltis, D. E., Soltis, P. S., & Barbazuk, W. B. (2012) Current Biology, 22(3), 248-252.
PUBMED: 22264605 | DOI: 10.1016/j.cub.2011.12.027
7. Making next-generation sequencing work for you: approaches and practical considerations for marker development and phylogenetics.
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) Plant Ecology & Diversity, 5(4), 427-450.
DOI: 10.1080/17550874.2012.745909
6. The Early Stages of Polyploidy: Rapid and Repeated Evolution in Tragopogon.
Soltis, D. E., Buggs, R. J. A., Barbazuk, W. B., Chamala, S., Chester, M., Gallagher, J. P., Schnable, P. S., & Soltis, P. S. (2012) Polyploidy and Genome Evolution (pp. 271-292): Springer Berlin Heidelberg.
DOI: 10.1007/978-3-642-31442-1_14
5. Next-generation sequencing and genome evolution in allopolyploids.
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) American Journal of Botany, 99(2), 372-382.
PUBMED: 22268220 | DOI: 10.3732/ajb.1100395
4. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.
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) Genome Biology, 12(5), R48.
PUBMED: 21619600 | DOI: 10.1186/gb-2011-12-5-r48
3. A transcript accounting from diverse tissues of a cultivated strawberry.
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) The Plant Genome, 3(2), 90-105.
DOI: 10.3835/plantgenome2010.02.0003
2. Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping.
†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) Molecular ecology, 19 Suppl 1, 132-146.
PUBMED: 20331776 | DOI: 10.1111/j.1365-294X.2009.04469.x
1. Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians.
Chamala, S., Beckstead, W. A., Rowe, M. J., & McClellan, D. A. (2007) International Journal of Bioinformatics Research and Applications, 3(4), 504-522.
PUBMED: 18048316 | DOI :10.1504/IJBRA.2007.015418