Trupti Joshi, PhD

Trupti Joshi, PhD

Health Management and Informatics

Trupti Joshi, MBBS, ADB, MS, PhD
Assistant Professor
Director of Translational Bioinformatics



Dr. Trupti Joshi is the Director of Translational Bioinformatics at the School of Medicine Medical Research Office and Assistant Professor in the Department of Health Management and Informatics at the University of Missouri-Columbia. She has appointments as Core Faculty with MU Informatics Institute (MUII), Interdisciplinary Plant Group (IPG) and Department of Computer Science. Her expertise is in the areas of bioinformatics and its application to plants sciences, animal sciences, biomedical sciences and health informatics fields. She obtained her Bachelor’s degree in Medicine and Surgery, followed by Advanced degree in Bioinformatics, both from highly reputable universities in India. Following this she obtained her MS degree in Bioinformatics from University of Tennessee and her Ph.D. degree in Bioinformatics from University of Missouri. She has published more than 70 journal publications including NAR, Nature, BMC Genomics, Bioinformatics, OMICS, PLOS One, etc. and Book Chapters in Knowledge Discovery in Bioinformatics: Techniques, Methods and Application and Genomics Protocols volume of Methods in Molecular Biology.

Academic Information

Trupti Joshi, MBBS, ADB, MS, PhD
Assistant Professor
Director of Translational Bioinformatics


NW502 Med Sci Bldg
1 Hospital Drive
Columbia, MO 65212
United States

P. 573-884-5963

Research Interests

  • Development of knowledge bases for genomics and multi-omics data integration
  • Development of computational methodologies and data analysis pipelines using HPC resources and hybrid cloud
  • Application of translational bioinformatics techniques towards advances in precision medicine, veterinary medicine and crop development
  • Genotype to phenotype inferences

Areas of Expertise

  • Translational bioinformatics
  • Computational Biology
  • Genomics and Systems Biology
  • Multi-Omics data integration
  • Software and Bioinformatics tool development


Peer-Reviewed Journal Publications

  • Du JianChao, Liang Zhu, Xu JianTao, Zhao Yan, Li XiaoYun, Zhang YanLi, Zhao DanDan, Chen RuXuan, Liu Yang, Joshi Trupti, Chang JiaHui, Wang ZhiQing, Zhang YanXu, Zhu JinDong, Liu Qiang, Xu Dong, Jiang ChengYu. Plant derivative phosphocholine could facilitate cellular uptake of anti-pulmonary fibrotic HJT-sRNA-m7. Sci China Life Sci. 2017 Mar 31. doi: 10.1007/s11427-017-9026-7.
  • Hossain MS, Kawakatsu T, Kim KD, Zhang N, Nguyen CT, Khan SM, Batek JM, Joshi T, Schmutz J, Grimwood J, Schmitz RJ, Xu D, Jackson SA, Ecker JR, Stacey G.Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. New Phytologist. 2017 Apr;214(2):808-819. doi: 10.1111/nph.14421.
  • Seeve CM, Cho IJ, Hearne LB, Srivastava GP, Joshi T, Smith DO, Sharp RE, Oliver MJ. Water deficit-induced changes in transcription factor expression in maize seedlings. Plant Cell Environment. 2016 Dec 31. doi: 10.1111/pce.12891.
  • Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Trupti Joshi, Dong Xu. End-to-End Security Formalization and Alignment for Federated Workflow Management. IEEE CLOUD 2016. 59-67.
  • Liu Y, Khan SM, Wang J, Rynge M, Zhang Y, Zeng S, Chen S, Maldonado dos Santos JV, Valliyodan B, Calyam PP, Merchant N, Nguyen HT, Xu D, Joshi T. PGen: Large-Scale Pegasus Workflow for Genomic Variation Analysis in SoyKB. BMC Bioinformatics. 2016. 17(Suppl 13):337. doi 10.1186/s12859-016-1227-y
  • Valdes-Lopez O, Batek J, Gomez-Hernandez N, Nguyen CT, Isidra-Arellano MC, Zhang N, Joshi T, Xu D, Hixson KK, Weitz KK, Aldrisch JT, Paša-Tolic L, Stacey G. Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles. Front Plant Science. 2016 Apr 25; 7:517. doi: 10.3389/fpls.2016.00517. eCollection 2016.
  • Valliyodan, B., Q. Dan, G. Patil, P. Zeng, J. Huang, L. Dai, C. Chen, Y. Li, T. Joshi, L. Song, T.D. Vuong, T.A. Musket, D. Xu, J.G. Shannon, C. Shifeng, X. Liu, and H.T. Nguyen, Landscape of genomic diversity and trait discovery in soybean. Scientific Reports, 2016. 6: p. 23598.
  • João Vitor Maldonado dos Santos, Babu Valliyodan, Trupti Joshi, Saad M. Khan, Yang Liu, Juexin Wang, Tri D. Vuong, Francismar Corrêa Marcelino-Guimarães, Marcelo Fernandes de Oliveira, Dong Xu, Henry T. Nguyen, Ricardo Vilela Abdelnoor. Evaluation of the genetic variation and population structure of Brazilian soybean cultivars by genome resequencing. BMC Genomics 2016. 17:110. doi: 10.1186/s12864-016-2431-x
  • Song L, Prince S, Valliyodan B, Joshi T, Maldonado Dos Santos JV, Wang J, Lin L, Wan J, Wang Y, Xu D, Nguyen HT. Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. BMC Genomics. 2016 Jan 15;17(1):57. doi: 10.1186/s12864-016-2378-y.
  • Bazan Antequera, Ronny; Calyam, Prasad; Debroy, Saptarshi; Cui, Longhai; Seetharam, Sripriya; Dickinson, Matthew; Joshi, Trupti; Xu, Dong; Beyene, Tsege. ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science. IEEE Transactions on Cloud Computing. 2015. Volume:PP Issue:99. DOI: 10.1109/TCC.2015.2511753
  • Wang J, Joshi T, Valliyodan B, Shi H, Liang Y, Nguyen HT, Zhang J, Xu D. A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. BMC Genomics. 2015 Nov 25;16(1):1011. doi: 10.1186/s12864-015-2217-6.
  • Syed NH, Prince SJ, Mutava RN, Patil G, Li S, Chen W, Babu V, Joshi T, Khan S and Nguyen HT. Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. Journal of Experimental Botany. 2015. doi:10.1093/jxb/erv407.
  • Patil G, Valliyodan B, Deshmukh R, Prince S, Nicander B, Zhao M, Sonah H, Song L, Lin L, Chaudhary J, Liu Y, Joshi T, Xu D and Nguyen HT. Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. BMC Genomics 2015, 16:520.
  • Chai C, Wang Y, Joshi T, Valliyodan B, Michel L, Xu D, Nguyen HT. Soybean Transcription Factor ORFeome: valuable resource to accelerate research on abiotic stress resistance. BMC Genomics. 2015 Aug 13;16(1):596. doi: 10.1186/s12864-015-1743-6.
  • Jiao Y, Vuong TD, Liu Y, Li Z, Noe J, Robbins RT, Joshi T, Xu D, Shannon JG, Nguyen HT. Identification of quantitative trait loci underlying resistance to southern root-knot and reniform nematodes in soybean accession PI 567516C. Mol Breed. 2015;35(6):131. Epub 2015 May 23.
  • Tanaka K, Cho SH, Lee H, Pham AQ, Batek JM, Cui S, Qiu J, Khan SM, Joshi T, Zhang ZJ, Xu D, Stacey G. Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings. J Exp Bot. 2015 Jun 6. pii: erv260.
  • Hossain MS, Joshi T, Stacey G. System approaches to study root hairs as a single cell plant model: current status and future perspectives. Front Plant Sci. 2015 May 19;6:363. doi: 10.3389/fpls.2015.00363. eCollection 2015.
  • Yan Z, Hossain MS, Valdés-López O, Hoang NT, Zhai J, Wang J, Libault M, Brechenmacher L, Findley S, Joshi T, Qiu L, Sherrier DJ, Ji T, Meyers BC, Xu D, Stacey G. Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Journal of Plant Biotechnology. 2015. Plant Biotechnology Journal (2015), pp. 1-10. doi: 10.1111/pbi.12387.
  • Prince SJ, Li S, Qiu D, Maldonado dos santos JV, Chai C, Joshi T, Patil G, Valliyodan B, Vuong T, Murphy M, Krampis K, Tucker DM, Biyashev R, Dorrance AE, Maroof MAS, Xu D, Shannon G, NguyenHT. Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC Genomics. 2015 Feb 25;16:132. doi: 10.1186/s12864-015-1334-6.
  • Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Cui S, Qiu J, Xu D, and Nguyen HT. Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating the interactions of soybean with cyst nematode (Heterodera glycines Ichinohe). BMC Genomics 2015, 16:148. doi:10.1186/s12864-015-1316-8.
  • Quach TN, Nguyen HTM, Valliyodan B, Joshi T, Xu D and Nguyen HT. Genome-Wide Expression Analysis of Soybean NF-Y Genes Reveal Potential Function in the Development and Drought Response. Mol Genet Genomics. 2015 Jun;290(3):1095-115. doi: 10.1007/s00438-014-0978-2. Epub 2014 Dec 27.
  • Appel, Heidi M., Fescemyer, H., Ehlting, J., Weston, D., Rehrig, E., Joshi, T., Xu, D., Bohlmann, J., and Schultz, Jack. Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores. Front Plant Sci. 2014 Nov 14;5:565. doi: 10.3389/fpls.2014.00565. eCollection 2014.
  • Joshi T, Williamson R, Patil K, Viyanon S, Li S, Zhang Y, Qi W, Li D, Zimmer J, Illindala U, Foley S, Campbell R, Duan Y, Xu D. Virtual Physical Examination (VPE): A Multimedia System for Education in Medicine. International Journal of Functional Informatics and Personalised Medicine. 2014. Vol 4, Issue 3-4. doi:
  • C Xu, X Ju, D Song, F Huang, D Tang, Z Zou, C Zhang, T Joshi, L Jia, W Xu, K-F Xu, Q Wang, Y Xiong, Z Guo, X Chen, F Huang, J Xu, Y Zhong, Y Zhu, Y Peng, L Wang, X Zhang, R Jiang, D Li, T Jiang, D Xu and C Jiang. An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus. Molecular Psychiatry. 2014. 1-8. In Press.
  • Valdes-Lopez O, Khan SM, Schmitz RJ, Cui S, Qiu J, Zhu M, Cheng JJ, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. Genotypic variation of gene expression during the soybean innate immunity response. Plant Genetic Resources. 2014. Plant Genetic Resources: Characterization and Utilization (2014) 12(S1); S27-S30. doi:10.1017/S1479262114000197.
  • Langewisch T, Zhang H, Vincent R, Joshi T, Xu D, Bilyeu K. Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes. PLoS One. 2014 Apr 11;9(4):e94150. doi: 10.1371/journal.pone.0094150. eCollection 2014.
  • Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D. Soybean Knowledge Base (SoyKB): A web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Research. 2014. Jan;42(Database issue):D1245-52. doi: 10.1093/nar/gkt905.
  • Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Ecker. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 2013 Oct;23(10):1663-74. doi: 10.1101/gr.152538.112.
  • Joshi T, Valliyodan B, Wu JH, Lee SH, Xu D, Nguyen HT. Genomic differences between cultivated soybean, G. max and its wild relative G. soja. BMC Genomics. 2013, 14(Suppl 1):S5.
  • Zhu M, Deng X, Joshi T, Xu D, Stacey G, Cheng J. Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. BMC Genomics. 2012, 13:437.
  • Roeseler DA, Sachdev S, Buckley DM, Joshi T, Wu DK, Xu D, Hannink M, Waters ST. Waters. Elongation Factor 1 alpha1 and genes associated with Usher syndromes are down-stream targets of GBX2. Plos One. 2012; 7(11).
  • Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, Wu X, Cheng J, Stacey G, Nguyen HT, Xu D. Soybean Knowledge Base (SoyKB): A Web Resource for Soybean Translational Genomics. BMC Genomics 2012, 13(Suppl 1):S15.
  • Lee EJ, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi JH, Robertson KD, Wang X, Colbourne JK, Zhang L, Schroth GP, Xu D, Zhang K, Shi H. Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Research 2011;39(19).
  • Liang Y, Zhang F, Wang J, Joshi T, Wang Y, Xu D. Prediction of Drought-Resistant Genes in Arabidopsis thaliana Using SVM-RFE. PLoS ONE. 2011;6(7):e21750. doi: 10.1371/journal.pone.0021750.
  • Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics 2010, 11:469.
  • Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G. An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 2010 Jul 1;63(1):86-99.
  • Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G. Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics, 11(Suppl 1):S14, 2010.
  • Guttikonda SK, Joshi T, Bisht NC, Chen H, An YQ, Pandey S, Xu D, Yu O. Whole Genome Co-expression Analysis of Soybean Cytochrome P450 Genes Identifies Nodulation-Specific P450 Monooxygenases. BMC Plant Biology. 10:243. 2010.
  • Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J. SoyDB: A Knowledge Database of Soybean Transcription Factors, BMC: Plant Biology 2010, 10:14.
  • Hajduch M, Hearne LB, Miernyk JA, Casteel JE, Joshi T, Agrawal GK, Song Z, Zhou M, Xu D, Thelen JJ.Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression. Plant Physiology, April 2010, Vol. 152, pp. 1-10.
  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T,Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC,Jackson SA. Genome Sequence of the Palaeopolyploid Soybean. Nature. 463:178-83, 2010.
  • Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G. Legume transcription factor genes; what makes legumes so special? Plant Physiology 151:991-1001 (2009).
  • Libault M, Joshi T, Takahashi K, Hurley-Sommer A, Puricelli K, Blake S, Finger RE, Taylor CG, Xu D, Nguyen HT, Stacey G. Large scale analysis of soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Plant Physiology 151:1207-1220 (2009)
  • Thibivilliers S, Joshi T, Campbell KB, Scheffler B, Xu D, Cooper B, Nguyen HT, Stacey G. Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection. BMC Plant Biology 2009, 9:46 (27 Apr 2009).
  • Chen M, Mooney BP, Hajduch M, Joshi T, Zhou M, Xu D, Thelen JJ. System Analysis of An Arabidopsis Mutant Altered in de novo Fatty Acid Synthesis Reveals Diverse Changes in Seed Composition and Metabolic Regulation. Plant Physiology. 150:27-41, 2009.
  • Brechenmacher L, Lee J, Sachdev S, Song Z, Nguyen TH, Joshi T, Oehrle N, Libault M, Mooney B, Xu D, Cooper B, Stacey G. Establishment of a Protein Reference Map for Soybean Root Hair Cells. Plant Physiology, February 2009, Vol. 149, pp. 670-682.
  • Zhang C, Joshi T, Lin GN, Xu D. An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. International Journal of Computational Biology and Drug Design, Volume 1, Number 3, 26 November 2008 , pp. 254-274(21).
  • Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S,Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS,Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biology, 9(Suppl 1):S2 (27 June 2008).
  • Brechenmacher L, Kim MY, Benitez M, Li M, Joshi T, Calla B, Lee MP, Libault M, Vodkin LO, Xu D, Lee SH, Clough SJ, Stacey G. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions. Vol.21, No. 5, 631-645, 2008.
  • Joshi T, Zhang C, Lin GN, Song Z, Xu D. GeneFAS : A tool for prediction of protein function using multiple sources of data. Methods Mol Biol. 2008;439:369-86. doi: 10.1007/978-1-59745-188-8_25.
  • Cytryn EJ, Sangurdekar DP, Streeter JG, Franck WL, Chang WS, Stacey G, Emerich DW, Joshi T, Xu D, Sadowsky MJ. Transcriptional and Physiological Responses of Bradyrhizobium japonicum to Desiccation-Induced Stress. Journal of Bacteriology, October 2007, p. 6751-6762, Vol. 189, No. 19.
  • Joshi T, Xu D. Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics, Vol. 8(1):222, 2007.
  • Chang WS, Franck WL, Cytryn E, Jeong S, Joshi T, Emerich DW, Sadowsky MJ, Xu D, Stacey G. An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions Vol. 20, No. 10, 1298-1307. 2007.
  • Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT. Nguyen. Single Feature Polymorphism Discovery in Rice. PLoS ONE 2(3): e284. doi:10.1371/journal.pone.0000284, 2007.
  • Wang Y, Joshi T, Zhang XS, Xu D, Chen L. Inferring Gene Regulatory Networks from Multiple Microarray Datasets. Bioinformatics. 22:2413-2420, 2006.
  • Nunberg A, Bedell JA, Budiman MA, Citek RW, Clifton SW, Fulton L, Pape D, Cai Z, Joshi T, Nguyen HT, Xu D, Stacey G. Survey sequencing of soybean elucidates the genome structure and composition. Functional Plant Biology, 33, 765-773, 2006.
  • Joshi T, Chen Y, Alexandrov NN, Xu D. Cellular Function Prediction and Biological Pathway Discovery in Arabidopsis thaliana Using Microarray Data. International Journal of Bioinformatics Research and Applications. Vol. 1, No. 3, 2005.
  • Joshi T, Chen Y, Becker JM, Alexandrov N, Xu D. Genome-Scale Gene Function Prediction Using Multiple Sources of High-Throughput Data in Yeast Saccharomyces cerevisiae. OMICS: A Journal of Integrative Biology Dec 2004, Vol. 8, No. 4: 322-333.