Trupti Joshi, PhD

Trupti Joshi, PhD

Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

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

573-884-5963

Profile

Trupti Joshi, PhD, is an associate professor in the Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME) in the School of Medicine (SOM), with a joint appointment with Department of Plant Sciences and Technology (DPST) at University of Missouri. She also has core faculty appointments with MU Data Science and Informatics Institute (MUIDSI), Interdisciplinary Plant Group (IPG), Christopher S. Bond Life Science Center (LSC) and Department of Electrical Engineering and Computer Science (EECS).

Dr. Joshi served as the director of translation bioinformatics with School of Medicine from 2015-2020 and currently serves as a faculty lead for translational bioinformatics for NextGen Biomedical Informatics (NextGen BMI). She has more than 20 years of experience working in academia, collaborations with multi-disciplinary researchers and several industry partners.

Her expertise is in the areas of bioinformatics and its application to biomedical sciences, plant sciences, animal sciences and health informatics fields. Dr. Joshi has published more than 150 scientific papers and co-developed several bioinformatics software systems, methods and tools. Her current research focuses primarily on:

  • Building knowledge base frameworks such as KBCommons and SoyKB, for genomics and multiomics data integration in biomedical and agricultural domains
  • Development of computational methodologies and multiomics data analysis pipelines using HPC and cloud-based resources
  • Multiomics data integration methods
  • Deep learning and machine learning methods for biomarker identification
  • IMPRes algorithm for in silico hypothesis generation
  • Application of translational bioinformatics techniques towards advances in precision medicine, precision agriculture and genomic epidemiology including novel coronavirus

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Academic Information

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

Office

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

P. 573-884-5963

Research Interests

  • Translational Bioinformatics
  • Computational Biology
  • Precision Medicine
  • Genomics and Multi‐Omics Data Integration
  • Database Frameworks and Bioinformatics Software Development

Areas of Expertise

  • Application of translational bioinformatics techniques towards advances in Precision Medicine, Precision Agriculture and One Health
  • Development of knowledge bases for genomics and multi‐omics data integration platforms
  • Development of computational methodologies and data analysis pipelines using HPC resources and hybrid cloud
  • Development of IMPRes algorithm and tool for in silico hypothesis generation using multiomics data
  • Biomarker identification
  • Genotype to phenotype inferences

Education & Training

Graduate

MS, University of Tennessee
PhD, University of Missouri

Publications

Peer-Reviewed Journal Publications

  • Y. Jiang, D. Wang, D. Xu and T. Joshi. Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 102-107. doi:10.1109/BIBM.2018.8621465.
  • S. Zeng, Z. Lyu, S. R. Narisetti, D. Xu and T. Joshi. Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 589-594. doi:10.1109/BIBM.2018.8621369.
  • S. Akter, D. Xu, S. C. Nagel, and T. Joshi. A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 969-972. doi:10.1109/BIBM.2018.8621150
  • Yuanxun Zhang, Calyam Prasad, Trupti Joshi, Satish Nair, Dong Xu. Domain-specific Topic Model for Knowledge Discovery in Computational and Data Intensive Scientific Communities. 2018. BigData’18. 4886-4895. 10.1109/BigData.2018.8622309.
  • Hans Chetan, Sharma Neekun, Sen Sidharth, Zeng Shuai, Dev Rishabh, Jiang Yuexu, Mahajan Advitiya, Joshi Trupti. Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization. Scientific Reports. 2019. In Press.
  • Miranda Carrie, Culp Carolyn, Skrabisova Maria, Joshi Trupti, Belzile François, Grant David, Bilyeu Kristin. Molecular Tools for Detecting Pdh1 Can Improve Soybean Breeding Efficiency by Reducing Yield Losses Due to Pod Shatter. Mol Breeding (2019) 39: 27. https://doi.org/10.1007/s11032-019-0935-1
  • Silvas J Prince, Babu Valliyodan, Heng Ye, Ming Yang, Shuaishuai Tai, Wushu Hu, Mackensie Murphy, Lorellin A Durnell, Li Song, Trupti Joshi, Yan Liu, Jan Van de Velde, Klaas Vandepoele, J. Grover Shannon, Henry T Nguyen. Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number. 2019. Plant Cell and Environment 42 (1): 212–229.
  • Majumder K, Wang J, Boftsi M, Fuller MS, Rede JE, Joshi T, Pintel DJ. Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection. eLife. 2018;7:e37750.
  • Mary Galli, Arjun Khakhar, Zefu Lu, Zongliang Chen, Sidharth Sen, Trupti Joshi, Jennifer L. Nemhauser, Robert J. Schmitz, and Andrea Gallavotti. The DNA binding landscape of the maize auxin response factor family. Nature Communications. Nature Communications. 2018. Volume 9, Article number: 4526 (2018).
  • Mariel C. Isidra-Arellano, María del Rocio Reyero-Saavedra, Maria del Socorro Sánchez-Correa, Lise Pingault, Sidharth Sen, Trupti Joshi, Lourdes Girard, Norma A. Castro-Guerrero, David G. Mendoza-Cozatl, Marc Libault, Oswaldo Valdés-López. Phosphate deficiency negatively affects early steps of the symbiosis between common bean and rhizobia. Genes (Basel). 2018 Oct 15;9(10). pii: E498. doi: 10.3390/genes9100498.
  • Dickinson Matthew, Debroy Saptarshi, Calyam Prasad, Valluripally Samaikya, Zhang Yuanxun, Antequera Ronny Bazan, Joshi Trupti, White Tommi, Xu Dong. Multi-cloud Performance and Security Driven Federated Workflow Management in IEEE Transactions on Cloud Computing. 2018. doi: 10.1109/TCC.2018.2849699
  • Boerman Erika, Sen Sidharth, Shaw Rebecca, Joshi Trupti, Segal Steven. Expression and Bioinformatics Analysis of Ion Channel and Receptor Genes in Mouse Resistance Arteries: Effects of Cell Type, Vessel Type and Biological Age. Microcirculation. 2018 May;25(4):e12452. doi: 10.1111/micc.12452.
  • Khan Mather A, Castro-Guerrero Norma A, McInturf Samuel A, Nguyen Nga T, Dame Ashley N, Wang Jiaojiao, Rebecca K, Joshi Trupti, Jurisson Silvia S, Nusinow, Dmitri A, Mendoza-Cozatl David G. Changes in iron availability in Arabidopsis are rapidly sensed in the leaf vasculature and impaired sensing leads to opposite transcriptional programs in leaves and roots. Plant, Cell and Environment. 2018. Oct;41(10):2263-2276. doi: 10.1111/pce.13192. Epub 2018 Jun 19.
  • Qi Zhao, Yuanning Liu, Ning Zhang, Menghan Hu, Hao Zhang, Trupti Joshi, Dong Xu. Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples. PLOS ONE 2017. 13(6): e0187519. https://doi.org/10.1371/journal.pone.0187519
  • Duolin Wang, Shuai Zeng, Chunhui Xu, Wangren Qiu, Yanchun Liang, Trupti Joshi, Dong Xu. MusiteDeep: a Deep-learning Framework for General and Kinase-specific Phosphorylation Site Prediction. Bioinformatics. 2017 Dec 15;33(24):3909-3916. doi: 10.1093/bioinformatics/btx496.
  • 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. http://dx.doi.org/10.1109/CLOUD.2016.0018
  • 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.
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