People
Trupti Joshi
Director of Translational Bioinformatics, School of Medicine – Medical Research Office; Assistant Research Professor, Department of Molecular Microbiology & Immunology; Core Faculty MU Informatics Institute and Department of Computer Science
Phone: 573-884-3528
JoshiTr@missouri.edu
271B Bond Life Sciences Center
Trupti Joshi is the Director of Translational Bioinformatics at the School of Medicine Medical Research Office and Assistant Research Professor in the Department of Molecular Microbiology and Immunology (MMI) 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. Her labs conducts research in many areas of computational biology and bioinformatics, including genomics and translational bioinformatics research in several biological systems, techniques involving high-throughput data analysis, multi-omics data integration, graphical visualization, in silico hypothesis generation and its application to systems biology studies. She is the lead designer and developer of Soybean Knowledge Base (SoyKB), a comprehensive multi-omics web resource for bridging translational genomics and molecular breeding. Her current research also focuses on building biomedical knowledge base for genomics and mutli-omics data integration in clinical and biomedical domains, development of computational methodologies and data analysis pipelines using HPC resources and application of translational bioinformatics techniques towards advances in precision medicine and personalized medicine.
News about Trupti Joshi
Feb 17, 2022
Pancreatic tumor composition provides insight on treatment response
Feb 12, 2021
#IAmScience Shuai Zeng
2023
Sprouty4 is epigenetically upregulated in human colorectal cancer. Stuckel, Alexei J. ; Zeng, Shuai ; Lyu, Zhen , ; Zhang, Wei ; Zhang, Xu ; Dougherty, Urszula ; Mustafi, Reba ; Khare, Tripti ; Zhang, Qiong; Joshi, Trupti b,; Bissonnette, Marc; Khare, Sharad. Epigenetics; Volume 18, Issue 1.
Date published: August 1, 2023Featured in this article: Trupti Joshi.
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The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Sinha, Ranjita ; Induri, Sai Preethi ; Peláez-Vico, María Ángeles ; Tukuli, Adama ; Shostak, Benjamin ; Zandalinas, Sara I.; Joshi, Trupti; Fritschi, Felix B.; Mittler, Ron. Plant Journal; .
Date published: August 1, 2023Featured in this article: Trupti Joshi.
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Adventitial macrophage accumulation impairs perivascular nerve function in mesenteric arteries with inflammatory bowel disease. Grunz, Elizabeth A. ; Jones, Benjamin W. ; Lateef, Olubodun Michael ; Sen, Sidharth ; Wilkinson, Katie ; Joshi, Trupti , ; Boerman, Erika M.. Frontiers in Physiology; Volume 14.
Date published: August 1, 2023Featured in this article: Trupti Joshi.
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Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis. Coulis, Gerald ; Jaime, Diego ; Guerrero-Juarez, Christian ; Kastenschmidt, Jenna M.; Farahat, Philip K. ; Nguyen, Quy ; Pervolarakis, Nicholas ; McLinden, Katherine ; Thurlow, Lauren ; Movahedi, Saba; Hughes, Brandon S.; Duarte, Jorge. Science advances; Volume 9, Issue 27, Pages eadd9984.
Date published: July 7, 2023Featured in this article: Trupti Joshi.
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Differential transpiration between pods and leaves during stress combination in soybean. Sinha, Ranjita ; Shostak, Benjamin ; Induri, Sai Preethi ; Sen, Sidharth ; Zandalinas, Sara I. ; Joshi, Trupti; Fritschi, Felix B. ; Mittler, Ron. Plant Physiology; Volume 192, Issue 2, Pages 753 - 766.
Date published: June 1, 2023Featured in this article: Trupti Joshi.
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The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis. Chan Y O, Dietz N, Zeng S, Wang J, Flint-Garcia S, Salazar-Vidal M N, Skrabisova M, Bilyeu K, Joshi T. BMC Genomics; Volume 24, Issue 1.
Date published: March 10, 2023Featured in this article: Yen On Chan, , Trupti Joshi.
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De novo transcriptome assembly from the nodal root growth zone of hydrated and water-deficit stressed maize inbred line FR697. Sen S, King S, McCubbin T, Greeley L A, Mertz R A, Becker C, Niehues N, Zeng S, Stemmle J T, Peck S, Oliver M, Fritschi F B, Braun D M, Sharp R E, Joshi T. Scientific Reports; Volume 13, Issue 1.
Date published: February 4, 2023Featured in this article: , , Scott Peck, Trupti Joshi.
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Domain-Specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities. Zhang Y, Calyam P, Joshi T, Nair S, Xu D. IEEE Transactions on Knowledge and Data Engineering; Volume 35, Issue 2, Pages 1402 - 1420.
Date published: February 1, 2023Featured in this article: Dong Xu, Trupti Joshi.
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Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting Bacterium Azoarcus olearius DQS-4T. Plucani do Amaral F, Wang J, Williams J, Tuleski T R, Joshi T, Ferreira M A R, Stacey G. Microorganisms; Volume 11, Issue 2.
Date published: February 1, 2023Featured in this article: Trupti Joshi, Gary Stacey.
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AccuCalc: A Python Package for Accuracy Calculation in GWAS. Biova J, Dietz N, Chan Y O, Joshi T, Bilyeu K, Skrabisova M. Genes; Volume 14, Issue 1.
Date published: January 1, 2023Featured in this article: Yen On Chan, Trupti Joshi.
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New Frontiers in Endocrine Disruptor Research. Cooke, Paul S. ; Rosenfeld, Cheryl S. b, ; Denslow, Nancy D. ; Martyniuk, Christopher J. ; Mesa, Ana M. ; Bowden, John A. ; Joshi, Trupti ; Wang, Juexin ; Aristizabal-Henao, Juan J. ; Martynyuk, Anatoly E. . Haschek and Rousseaux's Handbook of Toxicologic Pathology, Volume 3: Environmental Toxicologic Pathology and Major Toxicant Classes; Pages 765 - 796.
Date published: January 1, 2023Featured in this article: Trupti Joshi.
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2022
A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes. Skrabisova M, Dietz N, Zeng S, Chan Y O, Wang J, Liu Y, Biova J, Joshi T, Bilyeu K D. Journal of Advanced Research; Volume 42, Pages 117 - 133.
Date published: December 1, 2022Featured in this article: , Yen On Chan, Trupti Joshi.
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Prostanoid receptors in hyperfiltration-mediated glomerular injury: Novel agonists and antagonists reveal opposing roles for EP2 and EP4 receptors. Srivastava T, Garola R E, Zhou J, Boinpelly V C, Priya L, Ali M F, Rezaiekhaligh M H, Heruth D P, Novak J, Alon U S, Joshi T, Jiang Y, McCarthy E T, Savin V J, Johnson M L, Sharma R, Sharma Mukut. FASEB Journal; Volume 36, Issue 10.
Date published: October 1, 2022Featured in this article: Trupti Joshi, Yuexu Jiang.
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Long-Term Effects of Developmental Exposure to Oxycodone on Gut Microbiota and Relationship to Adult Behaviors and Metabolism. Lyu, Zhen, Schmidt, Robert R., Martin Rachel E., Green, Madison T, Kinkade, Jessica A, Mao, Jiude, Bivens, Nathan, Trupti, Joshi, Rosenfeld, Cheryl S.. mSystems; Volume 7, Issue 4.
Date published: August 1, 2022Featured in this article: Nathan Bivens, Jessica Kinkade, Trupti Joshi, Zhen Lyu.
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Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession. Yang, Yia,, La,Thang C, Gillman, Jason D, Lyu, Zhen, Joshi, Trupti, Usovsky, Mariola, Song, Quijian, Scaboo, Andrew. Frontiers in Plant Science; Volume 13.
Date published: July 29, 2022Featured in this article: Zhen Lyu, Trupti Joshi.
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Differential regulation of flower transpiration during abiotic stress in annual plants. Sinha, Ranjita, Zandalians, Sara I., Fichman, Yosef, Sen, Sidharth, Zeng,Shuai, Gomez-Cadenas, Aurelio, Joshi, Trupti, Fritschi, Felix B, Mittler, Ron. New Phytologist; Volume 235, Issue 2, Pages 611 - 629.
Date published: July 1, 2022Featured in this article: Ron Mittler, Trupti Joshi.
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Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations. Basnet, Pawan, Meinhardt, Clinton G., Usovsky, Mariola, Gillman, Jason, D, Joshi Trupti, Song, Quijian, Diers, Brian, Mitchum, Melissa G., Scaboo, Andrew M. Theoretical and Applied Genetics; Volume 135, Issue 6, Pages 2025 - 2039.
Date published: June 1, 2022Featured in this article: Trupti Joshi.
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Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution. Dietz, Nicholas, Chan, Yen On, Scaboo, Andrew, Graef, George, Hyten, David, Happ, Mary, Diers, Brian, Lorenz, Aaron, Wang, Dechun, Joshi, Trupti, Bilyeu, Kristin. Frontiers in Plant Science; Volume 13.
Date published: April 29, 2022Featured in this article: Trupti Joshi.
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Bioinformatics for plant and agricultural discoveries in the age of multiomics: A review and case study of maize nodal root growth under water deficit. Wang, Juexin, Sidharth, Sen, Zeng, Shuai, Jiang, Yuexu, Chan, Yen On, Lyu, Zhen, McCubbin, Tyler, Mertz, Rachel, Sharp, Robert E., Joshi, Trupti. Physiologia Plantarum; Volume 174, Issue 2 Article number e13672.
Date published: April 1, 2022Featured in this article: Trupti Joshi.
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The adeno-associated virus 2 genome and Rep 68/78 proteins interact with cellular sites of DNA damage. Majumder, Kinjal, Pintel, David J., Joshi, Trupti, Lorson, Christian L., Kaifer, Kevin A., Burger, Lisa R., Shepherd, Phoenix, Wang, Juexin, Whittle, Fawn B., Boftsi, Maria. Human Molecular Genetics; Volume 31, Issue 6, Pages 985 - 998.
Date published: March 15, 2022Featured in this article: , , Christian Lorson, Trupti Joshi.
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Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model. Su, Lingtao, Xu, Chunhui, Zeng, Shuai, Su, Li, Joshi, Trupti. Stacey, Gary, Xu, Dong. Frontiers in Plant Science; Volume 13 Article number 831204.
Date published: March 3, 2022Featured in this article: Gary Stacey, Trupti Joshi.
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Glomerular Biomechanical Stress and Lipid Mediators during Cellular Changes Leading to Chronic Kidney Disease. Sharma M. , Singh V. , Sharma R. ,Koul A. , McCarthy E.T. , Savin V.J. , Joshi T. ,Srivastava T.. Biomedicines; Volume 10, Issue 2.
Date published: February 1, 2022Featured in this article: Trupti Joshi.
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Single-cell RNA sequencing to characterize the response of pancreatic cancer to anti-PD-1 immunotherapy. Zhou J., Jiang Y., Huang Y. ,Wang Q. ,Kaifi J.T. , Kimchi E.T. ,Chabu C.Y. ,Liu Z. , Joshi T. , Li G.. Translational Oncology; Volume 15, Issue 1.
Date published: January 1, 2022Featured in this article: , Trupti Joshi.
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2021
Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Valliyodan B, Brown AV, Wang J, Patil G, Liu Y, Otyama PI, Nelson RT, Vuong T, Song Q, Musket TA, Wagner R, Marri P, Reddy S, Sessions A, Wu X, Grant D, Bayer PE, Roorkiwal M, Varshney RK, Liu X, Edwards D, Xu D, Joshi T, Cannon SB, Nguyen HT. Scientific Data; 8(1):50.
Date published: December 1, 2021Featured in this article: Dong Xu, Trupti Joshi.
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Developmental exposure to silver nanoparticles leads to long term gut dysbiosis and neurobehavioral alterations. Lyu Z, Ghoshdastidar S, Rekha KR, Suresh D, Mao J, Bivens N, Kannan R, Joshi T, Rosenfeld CS, Upendran A. Scientific Reports; 11(1):6558.
Date published: December 1, 2021Featured in this article: Trupti Joshi.
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A mouse model of prenatal exposure to Interleukin-6 to study the developmental origin of health and disease. Srivastava T, Joshi T, Heruth DP, Rezaiekhaligh MH, Garola RE, Zhou J, Boinpelly VS, Ali MF, Alon US, Sharma M, Vanden Heuvel GB, Mahajan P, Priya L, Jiang Y, McCarthy ET, Savin VJ, Sharma R, Sharma M. Scientific Reports; 11(1):13260.
Date published: December 1, 2021Featured in this article: Trupti Joshi.
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G2PDeep: A web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. Zeng S, Mao Z, Ren Y, Wang D, Xu D, Joshi T. Nucleic Acids Research; 49(W1):W228-W236.
Date published: July 2, 2021Featured in this article: Dong Xu, Trupti Joshi.
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Domain-specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities. Zhang Y, Calyam P, Joshi T, Nair S, Xu D. IEEE Transactions on Knowledge and Data Engineering; 1-19.
Date published: July 1, 2021Featured in this article: Trupti Joshi, Dong Xu.
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Transcription Factor β-Catenin Plays a Key Role in Fluid Flow Shear Stress-Mediated Glomerular Injury in Solitary Kidney. Srivastava T, Heruth DP, Duncan RS, Rezaiekhaligh MH, Garola RE, Priya L, Boinpelly VC, Novak J, Ali MF, Joshi T, Alon US, Jiang Y, McCarthy ET, Savin VJ, Sharma R, Johnson ML, Sharma M. Cells; 10(5).
Date published: May 19, 2021Featured in this article: Trupti Joshi.
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Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes. Deshmukh R, Rana N, Liu Y, Zeng S, Agarwal G, Sonah H, Varshney R, Joshi T, Patil GB, Nguyen HT. Physiologia Plantarum; 171(4):756-770.
Date published: April 1, 2021Featured in this article: Trupti Joshi.
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A medicago truncatula metabolite atlas enables the visualization of differential accumulation of metabolites in root tissues. Kranawetter C, Zeng S, Joshi T, Sumner LW. Metabolites; 11(4):238.
Date published: April 1, 2021Featured in this article: Trupti Joshi, Lloyd Sumner.
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Multi-Cloud Performance and Security Driven Federated Workflow Management. Dickinson M, Debroy S, Calyam P, Valluripally S, Zhang Y, Antequera RB, Joshi T, White T, Xu D. IEEE Transactions on Cloud Computing; 9(1):240-257.
Date published: January 1, 2021Featured in this article: Trupti Joshi, Dong Xu.
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Application of SNPViz v2.0 using next-generation sequencing data sets in the discovery of potential causative mutations in candidate genes associated with phenotypes. Zeng S, Škrabišová M, Lyu Z, Chan YO, Dietz N, Bilyeu K, Joshi T. International Journal of Data Mining and Bioinformatics; 25(1-2):65-85.
Date published: January 1, 2021Featured in this article: Trupti Joshi.
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2020
A multiomics discriminatory analysis approach to identify drought-related signatures in maize nodal roots. Sen S, McCubbin T, King SK, Greeley LA, Zeng S, Baker C, Mertz R, Niehues ND, Stemmle JT, Fristchi FB, Braun D, Peck SC, Oliver MJ, Sharp RE, Joshi T. Proceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020; 1856-1861.
Date published: December 16, 2020Featured in this article: Scott Peck, Trupti Joshi.
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SNPViz v2.0: A web-based tool for enhanced haplotype analysis using large scale resequencing datasets and discovery of phenotypes causative gene using allelic variations. Zeng S, Skrabisova M, Lyu Z, Chan YO, Bilyeu K, Joshi T. Proceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020; 1408-1415.
Date published: December 16, 2020Featured in this article: Trupti Joshi.
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A Formative Usability Study to Improve Prescriptive Systems for Bioinformatics Big Data. Singh K, Li S, Jahnke I, Pandey A, Lyu Z, Joshi T, Calyam P. Proceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020; 735-742.
Date published: December 16, 2020Featured in this article: Kamlendra Singh, Zhen Lyu, Trupti Joshi.
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Developmental exposure of California mice to endocrine disrupting chemicals and potential effects on the microbiome-gut-brain axis at adulthood. Kaur S, Sarma SJ, Marshall BL, Liu Y, Kinkade JA, Bellamy MM, Mao J, Helferich WG, Schenk AK, Bivens NJ, Lei Z, Sumner LW, Bowden JA, Koelmel JP, Joshi T, Rosenfeld CS. Scientific Reports; 10(1):10902.
Date published: December 1, 2020Featured in this article: Lloyd Sumner, Trupti Joshi.
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Author Correction: Developmental exposure of California mice to endocrine disrupting chemicals and potential effects on the microbiome-gut-brain axis at adulthood (Scientific Reports, (2020), 10, 1, (10902), 10.1038/s41598-020-67709-9). Kaur S, Sarma SJ, Marshall BL, Liu Y, Kinkade JA, Bellamy MM, Mao J, Helferich WG, Schenk AK, Bivens NJ, Lei Z, Sumner LW, Bowden JA, Koelmel JP, Joshi T, Rosenfeld CS. Scientific Reports; 10(1):12524.
Date published: December 1, 2020Featured in this article: Lloyd Sumner, Trupti Joshi.
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Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway. Vekaria K, Calyam P, Sivarathri SS, Wang S, Zhang Y, Pandey A, Chen C, Xu D, Joshi T, Nair S. Concurrency Computation; 33:e6080.
Date published: November 11, 2020Featured in this article: Dong Xu, Trupti Joshi.
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Correction: Stuckel, et al.; Enhanced CXCR4 expression associates with increased gene body 5-hydroxymethylcytosine modification but not decreased promoter methylation in colorectal cancer. (Cancers 2020, 12, 539). Stuckel AJ, Zhang W, Zhang X, Zeng S, Dougherty U, Mustafi, Zhang Q, Perreand E, Khare T, Joshi T, West-Szymanski DC, Bissonnette M, Khare S. Cancers; 12(11):1-3.
Date published: November 1, 2020Featured in this article: Trupti Joshi.
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The NS1 protein of the parvovirus MVM Aids in the localization of the viral genome to cellular sites of DNA damage. Majumder K, Boftsi M, Whittle FB, Wang J, Fuller MS, Joshi T, Pintel DJ. PLoS Pathogens; 16(10):e1009002.
Date published: October 16, 2020Featured in this article: Trupti Joshi.
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Upregulated proteoglycan-related signaling pathways in fluid flow shear stress-treated podocytes. Srivastava T, Joshi T, Jiang Y, Heruth DP, Rezaiekhaligh MH, Novak J, Staggs VS, Alon US, Garola RE, El-Meanawy A, McCarthy ET, Zhou J, Boinpelly VS, Sharma R, Savin VJ, Sharma M. American Journal of Physiology - Renal Physiology; 319(2):F312-F322.
Date published: August 1, 2020Featured in this article: Trupti Joshi.
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Correction: Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples (PLOS ONE (2019) 14:10 (e0224537) DOI: 10.1371/journal.pone.0224537). Zhao Q, Liu Y, Zhang N, Hu M, Zhang H, Joshi T, Xu D. PLoS ONE; 15(3):e0230146.
Date published: March 11, 2020Featured in this article: Trupti Joshi, Dong Xu.
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Enhanced CXCR4 expression associates with increased gene body 5-hydroxymethylcytosine modification but not decreased promoter methylation in colorectal cancer. Stuckel AJ, Zhang W, Zhang X, Zeng S, Dougherty U, Mustafi, Zhang Q, Perreand E, Khare T, Joshi T, West-Szymanski DC, Bissonnette M, Khare S. Cancers; 12(3):539.
Date published: March 1, 2020Featured in this article: Trupti Joshi.
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IMPRes-Pro: A high dimensional multiomics integration method for in silico hypothesis generation. Jiang Y, Wang D, Xu D, Joshi T. Methods; 173:16-23.
Date published: February 15, 2020Featured in this article: Dong Xu, Trupti Joshi.
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Security-aware Resource Brokering for Bioinformatics Workflows across Federated Multi-cloud Infrastructures. Nguyen M, Debroy S, Calyam P, Lyu Z, Joshi T. ACM International Conference Proceeding Series; F165625:3369791.
Date published: January 4, 2020Featured in this article: Zhen Lyu, Trupti Joshi.
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Proteomic and Metabolomic Analysis of Azospirillum brasilense ntrC Mutant under High and Low Nitrogen Conditions. Kukolj C, Pedrosa FO, De Souza GA, Sumner LW, Lei Z, Sumner B, Do Amaral FP, Juexin W, Trupti J, Huergo LF, Monteiro RA, Valdameri G, Stacey G, De Souza EM. Journal of Proteome Research; 19(1):92-105.
Date published: January 3, 2020Featured in this article: Lloyd Sumner, Trupti Joshi, Gary Stacey.
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A dynamic programing approach to integrate gene expression data and network information for pathway model generation. Jiang Y, Liang Y, Wang D, Xu D, Joshi T. Bioinformatics; 36(1):169-176.
Date published: January 1, 2020Featured in this article: Dong Xu, Trupti Joshi.
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Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. Rosenfeld CS, Hekman JP, Johnson JL, Lyu Z, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Hecht EE, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV. Genes, Brain and Behavior; 19(1):e12614.
Date published: January 1, 2020Featured in this article: Trupti Joshi.
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Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation. Mesa AM, Mao J, Nanjappa MK, Medrano TI, Tevosian S, Yu F, Kinkade J, Lyu Z, Liu Y, Joshi T, Wang D, Rosenfeld CS, Cooke PS. Physiological Genomics; 52(2):81-95.
Date published: January 1, 2020Featured in this article: Trupti Joshi.
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Inductive inference of gene regulatory network using supervised and semi-supervised graph neural networks. Wang J, Ma A, Ma Q, Xu D, Joshi T. Computational and Structural Biotechnology Journal; 18:3335-3343.
Date published: January 1, 2020Featured in this article: Dong Xu, Trupti Joshi.
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2019
Knowledge Base Commons (KBCommons) v1.1: A universal framework for multi-omics data integration and biological discoveries. Zeng S, Lyu Z, Narisetti SRK, Xu D, Joshi T. BMC Genomics; 20:947.
Date published: December 20, 2019Featured in this article: Dong Xu, Trupti Joshi.
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Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization. Hans CP, Sharma N, Sen S, Zeng S, Dev R, Jiang Y, Mahajan A, Joshi T. Scientific Reports; 9(1):7999.
Date published: December 1, 2019Featured in this article: Trupti Joshi.
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Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean. Liu Y, Wang D, He F, Wang J, Joshi T, Xu D. Frontiers in Genetics; 10:1091.
Date published: November 22, 2019Featured in this article: Trupti Joshi, Dong Xu.
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OnTimeURB: Multi-Cloud Resource Brokering for Bioinformatics Workflows. Pandey A, Lyu Z, Joshi T, Calyam P. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019; 466-473.
Date published: November 18, 2019Featured in this article: Zhen Lyu, Trupti Joshi.
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Mutational Forks: Inferring Deregulated Flow of Signal Transduction Based on Patient-Specific Mutations. Kholod O, Lyu Z, Mitchem J, Tonellato P, Joshi T, Shin D. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019; 2063-2068.
Date published: November 18, 2019Featured in this article: Zhen Lyu, Trupti Joshi.
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Genome Editing in Plants: Exploration of Technological Advancements and Challenges. Vats S, Kumawat S, Kumar V, Patil GB, Joshi T, Sonah H, Sharma TR, Deshmukh R. Cells; 8(11).
Date published: November 4, 2019Featured in this article: Trupti Joshi.
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Multi-cloud performance and security-driven brokering for bioinformatics workflows. Nguyen M, Debroy S, Calyam P, Lyu Z, Joshi T. Proceedings - International Conference on Network Protocols, ICNP; 2019-October:8888071.
Date published: October 7, 2019Featured in this article: Zhen Lyu, Trupti Joshi.
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12-Hydroxy-Jasmonoyl-l-Isoleucine Is an Active Jasmonate That Signals through CORONATINE INSENSITIVE 1 and Contributes to the Wound Response in Arabidopsis. Poudel AN, Holtsclaw RE, Kimberlin A, Sen S, Zeng S, Joshi T, Lei Z, Sumner LW, Singh K, Matsuura H, Koo AJ. Plant and Cell Physiology; 60(10):2152-2166.
Date published: October 1, 2019Featured in this article: Trupti Joshi, Lloyd Sumner, Kamlendra Singh.
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Correction: Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples (PLoS ONE (2019) 13:6 (e0187519) DOI: 10.1371/journal.pone.0187519). Zhao Q, Liu Y, Zhang N, Hu M, Zhang H, Joshi T, Xu D. PLoS ONE; 14(10):e0224537.
Date published: October 1, 2019Featured in this article: Trupti Joshi, Dong Xu.
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Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data. Akter S, Xu D, Nagel SC, Bromfield JJ, Pelch K, Wilshire GB, Joshi T. Frontiers in Genetics; 10:766.
Date published: September 4, 2019Featured in this article: Dong Xu, Trupti Joshi.
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SoyCSN: Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data. Wang J, Hossain MS, Lyu Z, Schmutz J, Stacey G, Xu D, Joshi T. Plant Direct; 3(9):e00167.
Date published: September 1, 2019Featured in this article: Gary Stacey, Dong Xu, Trupti Joshi.
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A seed germination transcriptomic study contrasting two soybean genotypes that differ in terms of their tolerance to the deleterious impacts of elevated temperatures during seed fill. Gillman JD, Biever JJ, Ye S, Spollen WG, Givan SA, Lyu Z, Joshi T, Smith JR, Fritschi FB. BMC Research Notes; 12(1):522.
Date published: August 19, 2019Featured in this article: Bill Spollen, Scott Givan, Zhen Lyu, Trupti Joshi.
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Silencing AXL by covalent siRNA-gelatin-antibody nanoconjugate inactivates mTOR/EMT pathway and stimulates p53 for TKI sensitization in NSCLC. Suresh D, Zambre A, Mukherjee S, Ghoshdastidar S, Jiang Y, Joshi T, Upendran A, Kannan R. Nanomedicine: Nanotechnology, Biology, and Medicine; 20:102007.
Date published: August 1, 2019Featured in this article: Trupti Joshi.
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Early genistein exposure of California mice and effects on the gut microbiota-brain axis. Marshall BL, Liu Y, Farrington MJ, Mao J, Helferich WG, Schenk AK, Bivens NJ, Sarma SJ, Lei Z, Sumner LW, Joshi T, Rosenfeld CS. Journal of Endocrinology; 242(2):139-157.
Date published: August 1, 2019Featured in this article: Lloyd Sumner, Trupti Joshi.
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Increasing protected data accessibility for age-related cataract research using a semi-automated honest broker. Valluripally S, Raju M, Calyam P, Lemus M, Purohit S, Mosa A, Joshi T. Modeling and Artificial Intelligence in Ophthalmology; 2(3):115-132.
Date published: July 25, 2019Featured in this article: Trupti Joshi.
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Plant-derived phosphocholine facilitates cellular uptake of anti-pulmonary fibrotic HJT-sRNA-m7. Du J, Liang Z, Xu J, Zhao Y, Li X, Zhang Y, Zhao D, Chen R, Liu Y, Joshi T, Chang J, Wang Z, Zhang Y, Zhu J, Liu Q, Xu D, Jiang C. Science China Life Sciences; 62(3):309-320.
Date published: March 1, 2019Featured in this article: Trupti Joshi, Dong Xu.
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Molecular tools for detecting Pdh1 can improve soybean breeding efficiency by reducing yield losses due to pod shatter. Miranda C, Culp C, Škrabišová M, Joshi T, Belzile F, Grant DM, Bilyeu K. Molecular Breeding; 39(2):27.
Date published: February 1, 2019Featured in this article: Trupti Joshi.
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Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities. Zhang Y, Calyam P, Joshi T, Nair S, Xu D. Proceedings - 2018 IEEE International Conference on Big Data, Big Data 2018; 4886-4895.
Date published: January 22, 2019Featured in this article: Trupti Joshi, Dong Xu.
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Knowledge Base Commons (KBCommons) v1.0: A multi OMICS’ web-based data integration framework for biological discoveries. Zeng S, Lyu Z, Narisetti SRK, Xu D, Joshi T. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018; 589-594.
Date published: January 21, 2019Featured in this article: Dong Xu, Trupti Joshi.
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Integrating Gene Expression Data and Pathway Knowledge for in Silico Hypothesis Generation with IMPRes. Jiang Y, Wang D, Xu D, Joshi T. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018; 102-107.
Date published: January 21, 2019Featured in this article: Dong Xu, Trupti Joshi.
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A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. Akter S, Xu D, Nagel SC, Joshi T. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018; 969-972.
Date published: January 21, 2019Featured in this article: Dong Xu, Trupti Joshi.
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Community cloud architecture to improve use accessibility with security compliance in health big data applications. Valluripally S, Raju M, Calyam P, Chrisholm M, Sivarathri SS, Mosa A, Joshi T. ACM International Conference Proceeding Series; 377-380.
Date published: January 4, 2019Featured in this article: Trupti Joshi.
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Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number. Prince SJ, Valliyodan B, Ye H, Yang M, Tai S, Hu W, Murphy M, Durnell LA, Song L, Joshi T, Liu Y, Van de Velde J, Vandepoele K, Grover Shannon J, Nguyen HT. Plant Cell and Environment; 42(1):212-229.
Date published: January 1, 2019Featured in this article: Trupti Joshi.
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2018
The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family. Galli M, Khakhar A, Lu Z, Chen Z, Sen S, Joshi T, Nemhauser JL, Schmitz RJ, Gallavotti A. Nature Communications; 9(1):4526.
Date published: December 1, 2018Featured in this article: Trupti Joshi.
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Phosphate deficiency negatively affects early steps of the symbiosis between common bean and Rhizobia. Isidra-Arellano MC, Reyero-Saavedra MR, Sánchez-Correa MS, Pingault L, Sen S, Joshi T, Girard L, Castro-Guerrero NA, Mendoza-Cozatl DG, Libault M, Valdés-López O. Genes; 9(10):498.
Date published: October 15, 2018Featured in this article: Trupti Joshi, David Mendoza-Cózatl.
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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. Khan MA, Castro-Guerrero NA, McInturf SA, Nguyen NT, Dame AN, Wang J, Bindbeutel RK, Joshi T, Jurisson SS, Nusinow DA, Mendoza-Cozatl DG. Plant Cell and Enviroment; 41(10):2263-2276.
Date published: October 1, 2018Featured in this article: Trupti Joshi, David Mendoza-Cózatl.
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Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection. Majumder K, Wang J, Boftsi M, Fuller MS, Rede JE, Joshi T, Pintel DJ. eLife; 7:e37750.
Date published: July 20, 2018Featured in this article: Trupti Joshi.
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Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples. Zhao Q, Liu Y, Zhang N, Hu M, Zhang H, Joshi T, Xu D. PLoS ONE; 13(6):e0187519.
Date published: June 1, 2018Featured in this article: Trupti Joshi, Dong Xu.
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Gene expression profiles of ion channels and receptors in mouse resistance arteries: Effects of cell type, vascular bed, and age. Boerman EM, Sen S, Shaw RL, Joshi T, Segal SS. Microcirculation; 25(4):e12452.
Date published: May 1, 2018Featured in this article: Trupti Joshi.
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2017
MusiteDeep: A deep-learning framework for general and kinase-specific phosphorylation site prediction. Wang D, Zeng S, Xu C, Qiu W, Liang Y, Joshi T, Xu D. Bioinformatics; 33(24):3909-3916.
Date published: December 15, 2017Featured in this article: Trupti Joshi, Dong Xu.
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Development of ‘KBCommons’ – Universal informatics framework for multi-omics translational research. Narisetti SRK, Zeng S, Lyu Z, Joshi T. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; 2017-January:2285-2286.
Date published: December 15, 2017Featured in this article: Trupti Joshi.
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A multi-omics informatics approach for identifying molecular mechanisms and biomarkers in clinical patients with endometriosis. Akter S, Wilshire G, Davis JW, Bromfield J, Crowder S, Joshi T, Pelch K, Schust DJ, Meng A, Barrier B, Nagel SC. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; 2017-January:2221-2223.
Date published: December 15, 2017Featured in this article: Trupti Joshi.
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Development of an informatics analytics workflow for DAP-seq data exploration and validation for auxin response factors in maize. Sen, S, Galli M, Gallavotti A, Joshi T. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; 2017-January:2300-2301.
Date published: December 15, 2017Featured in this article: Trupti Joshi.
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Water-deficit-induced changes in transcription factor expression in maize seedlings. Seeve CM, Cho I-J, Hearne LB, Srivastava GP, Joshi T, Smith DO, Sharp RE, Oliver MJ. Plant Cell and Environment; 40(5):686-701.
Date published: May 1, 2017Featured in this article: Trupti Joshi.
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Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. 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. New Phytologist; 214(2):808-819.
Date published: April 1, 2017Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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End-to-end security formalization and alignment for federated workflow management. Dickinson M, Debroy S, Calyam P, Valluripally S, Zhang Y, Joshi T, Xu D. IEEE International Conference on Cloud Computing, CLOUD; 59-67.
Date published: January 17, 2017Featured in this article: Trupti Joshi, Dong Xu.
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The evolution of soybean knowledge base (SoyKB). Joshi T, Wang J, Zhang H, Chen S, Zeng S, Xu B, Xu D. Methods in Molecular Biology; 1533:149-159.
Date published: January 1, 2017Featured in this article: Trupti Joshi, Dong Xu.
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2016
PGen: Large-scale genomic variations analysis workflow and browser in SoyKB. Liu Y, Khan SM, Wang J, Rynge M, Zhnag Y, Zeng S, Chen S, Maldonado dos Santos JV, Valliyodan B, Calyam PP, Merchant N, Nguyen HT, Xu D, Joshi T. BMC Bioinformatics; 17:337.
Date published: October 6, 2016Featured in this article: Dong Xu, Trupti Joshi.
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Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles. Valdés-López O, Batek J, Gomez-Hernandez N, Nguyen CT, Isidra-Arellano MC, Zhang N, Joshi T, Xu D, Hixson KK, Weitz KK, Alrich JT, Paša-Tolić L, Stacey G. Frontiers in Plant Science; 7(APR2016):517.
Date published: April 25, 2016Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Landscape of genomic diversity and trait discovery in soybean. Valliyodan B, Dan Qiu, Patil G, Zeng P, Huang J, Dai L, Chen C, Li Y, Joshi T, Song L, Vuong TD, Musket TA, Xu D, Shannon JG, Shifeng C, Liu X, Nguyen HT. Scientific Reports; 6:23598.
Date published: March 31, 2016Featured in this article: Trupti Joshi, Dong Xu.
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Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing. dos Santos JVM, Valliyodan B, Joshi T, Khan SM, Liu Y, Wang J, Vuong TD, de Oliveira MF, Marcelino-Guimarães FC, Xu D, Nguyen HT, Abdelnoor RV. BMC Genomics; 17(1):110.
Date published: February 13, 2016Featured in this article: Trupti Joshi, Dong Xu.
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Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. Song L, Prince S, Valliyodan B, Joshi T, Maldonado dos Santos JV, Wang J, Lin L, Wan J, Wang Y, Xu D, Nugyen HT. BMC Genomics; 17(1):57.
Date published: January 15, 2016Featured in this article: Trupti Joshi, Dong Xu.
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RDF Sketch Maps – Knowledge complexity reduction for precision medicine analytics. Thanintorn N, Wang J, Ersoy I, Al-Taie Z, Jiang Y, Wang D, Verma M, Joshi T, Hammer R, Xu D, Shin D. Pacific Symposium on Biocomputing; 417-428.
Date published: January 4, 2016Featured in this article: Trupti Joshi, Dong Xu.
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Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Yan Z, Hossain MS, Valdés-López O, Hoang NT, Zhai J, Wang J, Liabault M, Brechenmacher L, Findley S, Joshi T, Qiu L, Sherrier DJ, Ji T, Meyers BC, Xu D, Stacey G. Plant Biotechnology Journal; 14(1):332-341.
Date published: January 1, 2016Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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2015
Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe). Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Xu D, Nguyen HT. BMC Genomics; 16(1):148.
Date published: December 12, 2015Featured in this article: Trupti Joshi, Dong Xu.
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Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. Syed NH, Prince SJ, Mutava RN, Patil G, Li S, Chen W, Babu V, Joshi T, Khan S, Nguyen HT. Journal of Experimental Botany; 66(22):7129-7149.
Date published: December 1, 2015Featured in this article: Trupti Joshi.
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A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. Wang J, Joshi T, Valliyodan B, Shi H, Liang Y, Nguyen HT, Zhang J, Xu D. BMC Genomics; 16(1):1011.
Date published: November 25, 2015Featured in this article: Trupti Joshi, Dong Xu.
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Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Prince SJ, Joshi T, Mutava RN, Syed N, Joao Vitor MDS, Patil G, Song L, Wang J, Lin L, Chen W, Shannon JG, Valliyodan B, Xu D, Nguyen HT. Plant Science; 240:65-78.
Date published: November 1, 2015Featured in this article: Trupti Joshi, Dong Xu.
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Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings. Tanaka K, Cho S-H, Lee H, Pham AQ, Batek JM, Cui S, Qiu J, Khan SM, Joshi T, Zhang ZT, Xu D, Stacey G. Journal of Experimental Botany; 66(19):5727-5738.
Date published: September 1, 2015Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Soybean transcription factor ORFeome associated with drought resistance: A valuable resource to accelerate research on abiotic stress resistance. Chai C, Wang Y, Joshi T, Valliyodan B, Prince S, Michel L, Xu D, Nguyen HT. BMC Genomics; 16(1):596.
Date published: August 13, 2015Featured in this article: Trupti Joshi, Dong Xu.
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Soybean (Glycine max) SWEET gene family: Insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. 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, Nguyen HT. BMC Genomics; 16(1):520.
Date published: July 11, 2015Featured in this article: Trupti Joshi, Dong Xu.
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Identification of quantitative trait loci underlying resistance to southern root-knot and reniform nematodes in soybean accession PI 567516C. Jiao Y, Vuong TD, Liu Y, Li Z, Noe J, Robbins RT, Joshi T, Xu D, Shannon JG, Nguyen HT. Molecular Breeding; 35(6):131.
Date published: June 26, 2015Featured in this article: Trupti Joshi, Dong Xu.
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Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response. Quach TN, Nguyen HTM, Valliyodan B, Joshi T, Xu D, Nguyen HT. Molecular Genetics and Genomics; 290(3):1095-1115.
Date published: June 23, 2015Featured in this article: Trupti Joshi, Dong Xu.
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System approaches to study root hairs as a single cell plant model: Current status and future perspectives. Hossain MS, Joshi T, Stacey G. Frontiers in Plant Science; 6(MAY):1-7.
Date published: May 19, 2015Featured in this article: Trupti Joshi, Gary Stacey.
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An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus. Xu C, Ju X, Song D, Huang F, Tang D, Zou Z, Zhang C, Joshi T, Jia L, Xu W, Xu K-F, Wang Q, Xiong Y, Guo Z, Chen X, Huang F, Xu J, Zhong Y, Zhu Y, Peng Y, Wang L, Zhang X, Jiang R, Li D, Jiang T, Xu D, Jiang C. Molecular Psychiatry; 20(4):536-544.
Date published: April 2, 2015Featured in this article: Trupti Joshi, Dong Xu.
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Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. Prince SJ, Song L, Qiu D, Maldonado dos Santos JV, Chai C, Joshi T, Patil G, Valliyodan B, Vuong TD, Murphy M, Krampis K, Tucker DM, Biyashev R, Dorrance AE, Maroof MAS, Xu D, Shannon JG, Nguyen HT. BMC Genomics; 16(1):132.
Date published: February 25, 2015Featured in this article: Trupti Joshi, Dong Xu.
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Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655. Jiao Y, Vuong TD, Liu Y, Meinhardt C, Liu Y, Joshi T, Cregan PB, Xu D, Shannon JG, Nguyen HT. Theoretical and Applied Genetics; 128(1):15-23.
Date published: January 17, 2015Featured in this article: Trupti Joshi, Dong Xu.
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2014
Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores. Appel HM, Fescemyer H, Ehlting J, Weston D, Rehrig E, Joshi T, Xu D, Bohlmann J, Schultz J. Frontiers in Plant Science; 5(November):1-20.
Date published: November 14, 2014Featured in this article: Trupti Joshi, Dong Xu.
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Genotypic variation of gene expression during the soybean innate immunity response. Valdés-López O, Khan SM, Schmitz RJ, Cui S, Qiu J, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. Plant Genetic Resources: Characterisation and Utilisation; 12(SUPPL.1):S27-S30.
Date published: July 1, 2014Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Comparative transcriptomic analysis of symbiotic Bradyrhizobium japonicum. Franck S, Franck WL, Birke SR, Chang W-S, Sangurdekar DP, Cytryn E, Joshi T, Sadowsky M, Stacey G, Xu D, Emerich DW. Symbiosis; 63(3):123-135.
Date published: July 1, 2014Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.
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Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes. Langewisch T, Zhang H, Vincent R, Joshi T, Xu D, Bilyeu K. PLoS ONE; 9(4):e94150.
Date published: April 11, 2014Featured in this article: Trupti Joshi, Dong Xu.
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Soybean knowledge base (SoyKB): A web resource for integration of soybean translational genomics and molecular breeding. Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D. Nucleic Acids Research; 42(D1):D1245-D1252.
Date published: January 1, 2014Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.
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Virtual physical examination (VPE): A multimedia system for education in medicine. Joshi T, Williamson R, Patil K, Viyanon S, Li X, Zhang Y, Qi W, Li D, Zimmer J, Illindala U, Foley S, Campbell R, Duan Y, Xu D. International Journal of Functional Informatics and Personalised Medicine; 4(3-4):181-197.
Date published: January 1, 2014Featured in this article: Trupti Joshi, Dong Xu.
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2013
Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding. Joshi T, Fitzpatrick MR, Chen S, Liu Y, Zhang H, Endacott RZ, Gaudiello EC, Stacey G, Nguyen HT, Xu D. Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013; 42-44.
Date published: December 18, 2013Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.
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Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Genome Research; 23(10):1663-1674.
Date published: October 1, 2013Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Genomic differences between cultivated soybean, G. max and its wild relative G. soja. Joshi T, Valliyodan B, Wu J-H, Lee S-H, Xu D, Nguyen HT. BMC Genomics; 14:S5.
Date published: January 21, 2013Featured in this article: Trupti Joshi, Dong Xu.
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2012
Elongation Factor 1 alpha1 and Genes Associated with Usher Syndromes Are Downstream Targets of GBX2. Roeseler DA, Sachdev S, Buckley DM, Joshi T, Wu DK, Xu D, Hannink M, Waters ST. PLoS ONE; 7(11):e47366.
Date published: November 8, 2012Featured in this article: Trupti Joshi, Dong Xu, .
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Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. Zhu M, Deng X, Joshi T, Xu D, Stacey G, Cheng J. BMC Genomics; 13(1):437.
Date published: August 31, 2012Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Soybean knowledge base (SoyKB): A web resource for soybean translational genomics. 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. Series on Advances in Bioinformatics and Computational Biology; 13:S15.
Date published: January 17, 2012Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.
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2011
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Lee E-J, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi J-H, Robertson KD, Wang X, Colbourne JK, Zhang L, Schroth GP, Xu D, Zhang K, Shi H. Nucleic Acids Research; 39(19).
Date published: October 1, 2011Featured in this article: Trupti Joshi, Dong Xu.
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Prediction of Drought-Resistant genes in Arabidopsis thaliana using SVM-RFE. Liang Y, Zhang F, Wang J, Joshi T, Wang Y, Xu D. PLoS ONE; 6(7):e21750.
Date published: January 1, 2011Featured in this article: Trupti Joshi, Dong Xu.
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2010
SoyMetDB: The Soybean Metabolome Database. Joshi T, Yao Q, Franklin LD, Brechenmacher L, Valliyodan B, Stacey G, Nguyen H, Xu D. Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010; 203-208.
Date published: December 18, 2010Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.
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Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. Guttikonda SK, Trupti J, Bisht NC, Chen H, An Y-QC, Pandey S, Xu D, Yu O. BMC Plant Biology; 10:243.
Date published: November 9, 2010Featured in this article: Trupti Joshi, Dong Xu.
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SNP discovery by high-throughput sequencing in soybean. Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. BMC Genomics; 11(1):469.
Date published: August 11, 2010Featured in this article: Trupti Joshi, Dong Xu.
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An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G. Plant Journal; 63(1):86-99.
Date published: July 1, 2010Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Erratum: Genome sequence of the palaeopolyploid soybean (Nature (2010) 463 (178-183)). 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, Skaurai 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 X-C, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. Nature; 465(7294):120.
Date published: May 6, 2010Featured in this article: Jay Thelen, Dong Xu, Trupti Joshi, Gary Stacey.
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Systems analysis of seed filling in Arabidopsis: Using general linear modeling to assess concordance of transcript and protein expression. Hajduch M, Hearne LB, Miernyk JA, Casteel JE, Joshi T, Agrawal GK, Song Z, Zhou M, Xu D, Thelen JJ. Plant Physiology; 152(4):2078-2087.
Date published: April 1, 2010Featured in this article: Trupti Joshi, Dong Xu, Jay Thelen.
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Prediction of novel miRNAs and associated target genes in Glycine max. Joshi T, Yan Z, Libault M, Jeong D-H, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G. BMC Bioinformatics; 11(SUPPLL.1):S14.
Date published: January 18, 2010Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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SoyDB: A knowledge database of soybean transcription factors. Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J. BMC Plant Biology; 10:14.
Date published: January 18, 2010Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Genome sequence of the palaeopolyploid soybean. 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, Skaurai 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 X-C, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. Nature; 463(7278):178-183.
Date published: January 14, 2010Featured in this article: Jay Thelen, Dong Xu, Trupti Joshi, Gary Stacey.
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2009
Legume transcription factor genes: What makes legumes so special?. Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G. Plant Physiology; 151(3):991-1001.
Date published: November 1, 2009Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Large-scale analysis of putative soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Libault M, Joshi T, Takahashi K, Hurley-Sommer A, Puricelli K, Blake S, Finger RE, Taylor CS, Xu D, Nguyen HT, Stacey G. Plant Physiology; 151(3):1207-1220.
Date published: November 1, 2009Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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System analysis of an arabidopsis mutant altered in de novo fatty acid synthesis reveals diverse changes in seed composition and metabolism. Chen M, Mooney BP, Hajduch M, Joshi T, Zhou M, Xu D, Thelen JJ. Plant Physiology; 150(1):27-41.
Date published: May 1, 2009Featured in this article: Trupti Joshi, Dong Xu, Jay Thelen.
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Establishment of a protein reference map for soybean root hair cells. Brechenmacher L, Lee J, Sachdev S, Song Z, Nguyen THN, Joshi T, Oehrle N, Libault M, Mooney B, Xu D, Cooper B, Stacey G. Plant Physiology; 149(2):670-682.
Date published: February 1, 2009Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection. Thibivilliers S, Joshi T, Campbell KB, Scheffler B, Xu D, Cooper B, Nguyen HT, Stacey G. BMC Plant Biology; 9:46.
Date published: January 1, 2009Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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A linear programming framework for inferring gene regulatory networks by integrating heterogeneous data. Wang Y, Wang R-S, Joshi T, Xu D, Zhang X-S, Chen L, Xia Y. Handbook of Research on Computational Methodologies in Gene Regulatory Networks; 450-475.
Date published: January 1, 2009Featured in this article: Trupti Joshi, Dong Xu.
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2008
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. 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, Highes TR, Roth FP. Genome Biology; 9(SUPPL. 1):S2.
Date published: June 27, 2008Featured in this article: Trupti Joshi, Dong Xu.
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Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Brechenmacher L, Kim M-Y, Benitez M, Li M, Joshi T, Calla B, Mei PL, Libault M, Vodkin LO, Xu D, Lee S-H, Clough SJ, Stacey G. Molecular Plant-Microbe Interactions; 21(5):631-645.
Date published: May 1, 2008Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. Zhang C, Joshi T, Lin GN, Xu D. International Journal of Computational Biology and Drug Design; 1(3):254-274.
Date published: January 1, 2008Featured in this article: Trupti Joshi, Dong Xu.
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GeneFAS: A tool for prediction of gene function using multiple sources of data. Joshi T, Zhang C, Lin GN, Song Z, Xu D. Methods in Molecular Biology; 439:369-386.
Date published: January 1, 2008Featured in this article: Trupti Joshi, Dong Xu.
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2007
Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress (Journal of Bacteriology (2007) 189, 19, (6751-6752)). Cytryn EJ, Sangurdekar DP, Streeter JG, Frank WL, Chang W-S, Stacey G, Emerich DW, Joshi T, Xu D, Sadowsky MJ. Journal of Bacteriology; 189(24):9150.
Date published: December 1, 2007Featured in this article: Gary Stacey, Trupti Joshi, Dong Xu.
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An oligonucleotide microarray resource for transcriptional profiling of bradyrhizobium japonicum. Chang W-S, Frank WL, Cytryn E, Jeong S, Joshi T, Emerich DW, Sadowsky MJ, Xu D, Stacey G. Molecular Plant-Microbe Interactions; 20(10):1298-1307.
Date published: October 1, 2007Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. Cytryn EJ, Sangurdekar DP, Streeter JG, Frank WL, Chang W-S, Stacey G, Emerich DW, Joshi T, Xu D, Sadowsky MJ. Journal of Bacteriology; 189(19):6751-6762.
Date published: October 1, 2007Featured in this article: Gary Stacey, Trupti Joshi, Dong Xu.
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Quantitative assessment of relationship between sequence similarity and function similarity. Joshi T, Xu D. BMC Genomics; 8:222.
Date published: July 9, 2007Featured in this article: Trupti Joshi, Dong Xu.
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Bioinformatics Analyses of Arabidopsis thaliana Tiling Array Expression Data. Joshi T, Wan J, Palm CJ, Juneau K, Davis R, Southwick A, Ramonell KM, Stacey G, Xu D. Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications; 57-70.
Date published: May 23, 2007Featured in this article: Trupti Joshi, Gary Stacey, Dong Xu.
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Single feature polymorphism discovery in rice. Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT. PLoS ONE; 2(3):e284.
Date published: March 14, 2007Featured in this article: Trupti Joshi, Dong Xu.
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2006
Inferring gene regulatory networks from multiple microarray datasets. Wang Y, Joshi T, Zhang X-S, Xu D, Chen L. Bioinformatics; 22(19):2413-2420.
Date published: October 1, 2006Featured in this article: Trupti Joshi, Dong Xu.
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Supervised inference of gene regulatory networks by linear programming. Wang Y, Joshi T, Xu D, Zhang X-S, Chen L. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 4115 LNBI-III:551-561.
Date published: August 16, 2006Featured in this article: Trupti Joshi, Dong Xu.
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Survey sequencing of soybean elucidates the genome structure, composition and identifies novel repeats. Nunberg A, Bedell JA, Budiman MA, Citek RW, Clifton SW, Fulton L, Pape D, Cai Z, Joshi T, Nguyen H, Xu D, Stacey G. Functional Plant Biology; 33(8):765-773.
Date published: January 1, 2006Featured in this article: Trupti Joshi, Dong Xu, Gary Stacey.
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2005
Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. Joshi T, Chen Y, Alexandrov NN, Xu D. International Journal of Bioinformatics Research and Applications; 1(3):335-350.
Date published: January 1, 2005Featured in this article: Trupti Joshi, Dong Xu.
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2004
Cellular function prediction and biological pathway discovery in arabidopsis thaliana using microarray data. Joshi T, Chen Y, Alexandrov N, Xu D. Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings; 26(IV):2881-2884.
Date published: September 1, 2004Featured in this article: Trupti Joshi, Dong Xu.
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Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. Joshi T, Chen Y, Becker JM, Alexandrov N, Xu D. OMICS A Journal of Integrative Biology; 8(4):322-333.
Date published: January 1, 2004Featured in this article: Trupti Joshi, Dong Xu.
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2003
Towards automated derivation of biological pathways using high-throughput biological data. Chen Y, Joshi T, Xu Y, Xu D. Proceedings - 3rd IEEE Symposium on BioInformatics and BioEngineering, BIBE 2003; 18-25.
Date published: March 10, 2003Featured in this article: Trupti Joshi, Dong Xu.
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