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ORCIDTrupti Joshi
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2020 – today
- 2024
[j19]Chunhui Xu
, Trey Shaw, Sai Akhil Choppararu, Yiwei Lu, Shaik Naveed Farooq, Yongfang Qin, Matt Hudson, Brock Weekley, Michael Fisher, Fei He, Jose Roberto Da Silva Nascimento, Nicholas Wergeles, Trupti Joshi, Philip D. Bates, Abraham J. Koo, Doug K. Allen, Edgar B. Cahoon, Jay J. Thelen, Dong Xu:
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants. Database J. Biol. Databases Curation 2024 (2024)- 2023
- [j18]Yuanxun Zhang, Prasad Calyam, Trupti Joshi, Satish S. Nair, Dong Xu:
Domain-Specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities. IEEE Trans. Knowl. Data Eng. 35(2): 1402-1420 (2023) - [j17]Ashish Pandey, Prasad Calyam, Zhen Lyu, Songjie Wang, Dmitrii Chemodanov, Trupti Joshi:
Knowledge-Engineered Multi-Cloud Resource Brokering for Application Workflow Optimization. IEEE Trans. Netw. Serv. Manag. 20(3): 3072-3088 (2023) - 2021
- [j16]Komal Vekaria, Prasad Calyam, Sai Swathi Sivarathri, Songjie Wang, Yuanxun Zhang, Ashish Pandey, Cong Chen, Dong Xu, Trupti Joshi, Satish S. Nair:
Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway. Concurr. Comput. Pract. Exp. 33(19) (2021) - [j15]Shuai Zeng, Mária Skrabisová, Zhen Lyu, Yen On Chan, Nicholas Dietz, Kristin Bilyeu, Trupti Joshi:
Application of SNPViz v2.0 using next-generation sequencing data sets in the discovery of potential causative mutations in candidate genes associated with phenotypes. Int. J. Data Min. Bioinform. 25(1/2): 65-85 (2021) - [j14]Shuai Zeng, Ziting Mao, Yijie Ren, Duolin Wang, Dong Xu, Trupti Joshi:
G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. Nucleic Acids Res. 49(Webserver-Issue): 228-236 (2021) - [j13]Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Ronny Bazan Antequera, Trupti Joshi, Tommi A. White, Dong Xu:
Multi-Cloud Performance and Security Driven Federated Workflow Management. IEEE Trans. Cloud Comput. 9(1): 240-257 (2021) - [c28]Ashish Pandey, Prasad Calyam, Zhen Lyu, Trupti Joshi:
Fuzzy-Engineered Multi-Cloud Resource Brokering for Data-intensive Applications. CCGRID 2021: 257-266 - 2020
- [j12]Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi:
A dynamic programing approach to integrate gene expression data and network information for pathway model generation. Bioinform. 36(1): 169-176 (2020) - [c27]Kanupriya Singh, Shangman Li, Isa Jahnke, Ashish Pandey, Zhen Lyu, Trupti Joshi, Prasad Calyam:
A Formative Usability Study to Improve Prescriptive Systems for Bioinformatics Big Data. BIBM 2020: 735-742 - [c26]Shuai Zeng, Mária Skrabisová, Zhen Lyu, Yen On Chan, Kristin Bilyeu, Trupti Joshi:
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. BIBM 2020: 1408-1415 - [c25]Sidharth Sen, Tyler McCubbin, Shannon K. King, Laura A. Greeley, Shuai Zeng, Cheyenne Baker, Rachel Mertz, Nicole D. Niehues, Jonathon T. Stemmle, Felix B. Fristchi, David Braun, Scott C. Peck, Melvin J. Oliver, Robert E. Sharp, Trupti Joshi:
A multiomics discriminatory analysis approach to identify drought-related signatures in maize nodal roots. BIBM 2020: 1856-1861 - [c24]Minh Nguyen, Saptarshi Debroy, Prasad Calyam, Zhen Lyu, Trupti Joshi:
Security-aware Resource Brokering for Bioinformatics Workflows across Federated Multi-cloud Infrastructures. ICDCN 2020: 26:1-26:10
2010 – 2019
- 2019
- [c23]Ashish Pandey, Zhen Lyu, Trupti Joshi, Prasad Calyam:
OnTimeURB: Multi-Cloud Resource Brokering for Bioinformatics Workflows. BIBM 2019: 466-473 - [c22]Olha Kholod, Zhen Lyu, Jonathan B. Mitchem, Peter J. Tonellato, Trupti Joshi, Dmitriy Shin:
Mutational Forks: Inferring Deregulated Flow of Signal Transduction Based on Patient-Specific Mutations. BIBM 2019: 2063-2068 - [c21]Samaikya Valluripally, Murugesan Raju, Prasad Calyam, Matthew Chisholm, Sai Swathi Sivarathri, Abu Saleh Mohammad Mosa, Trupti Joshi:
Community cloud architecture to improve use accessibility with security compliance in health big data applications. ICDCN 2019: 377-380 - [c20]Minh Nguyen, Saptarshi Debroy, Prasad Calyam, Zhen Lyu, Trupti Joshi:
Multi-Cloud Performance and Security-driven Brokering for Bioinformatics Workflows. ICNP 2019: 1-2 - 2018
- [j11]Ronny Bazan Antequera, Prasad Calyam, Saptarshi Debroy, Longhai Cui, Sripriya Seetharam, Matthew Dickinson, Trupti Joshi, Dong Xu, Tsegereda Beyene:
ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science. IEEE Trans. Cloud Comput. 6(3): 640-655 (2018) - [c19]Sadia Akter, John Bromfield, Katherine Pelch, Gil Wilshire, Sarah Crowder, Danny J. Schust, Bret Barrier, J. Wade Davis, Susan C. Nagel, Trupti Joshi:
Integrative Analysis of DNA Methylation and RNA-Seq Data for Biomarker Detection of Endometriosis. AMIA 2018 - [c18]Yuexu Jiang, Duolin Wang, Dong Xu, Trupti Joshi:
Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes. BIBM 2018: 102-107 - [c17]Shuai Zeng, Zhen Lyu, Siva Ratna Kumari Narisetti, Dong Xu, Trupti Joshi:
Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries. BIBM 2018: 589-594 - [c16]Sadia Akter, Dong Xu, Susan C. Nagel, Trupti Joshi:
A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. BIBM 2018: 969-972 - [c15]Yuanxun Zhang, Prasad Calyam, Trupti Joshi, Satish S. Nair, Dong Xu:
Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities. IEEE BigData 2018: 4886-4895 - 2017
- [j10]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. Bioinform. 33(24): 3909-3916 (2017) - [c14]Sadia Akter, Gil Wilshire, J. Wade Davis, John Bromfield, Sarah Crowder, Trupti Joshi, Katherine Pelch, Danny J. Schust, Angela Meng, Bret Barrier, Susan C. Nagel:
A multi-omics informatics approach for identifying molecular mechanisms and biomarkers in clinical patients with endometriosis. BIBM 2017: 2221-2223 - [c13]Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi:
IMPRes: Integrative MultiOmics pathway resolution algorithm and tool. BIBM 2017: 2260 - [c12]Zhen Lyu, Shuai Zeng, Trupti Joshi:
Enabling precision medicine with CancerKB and KBCommons informatics framework. BIBM 2017: 2281 - [c11]Siva Ratna Kumari Narisetti, Shuai Zeng, Zhen Lyu, Trupti Joshi:
Development of "KBCommons" - universal informatics framework for multi-omics translational research. BIBM 2017: 2285-2286 - [c10]Sidharth Sen, Mary Galli, Andrea Gallavotti, Trupti Joshi:
Development of an informatics analytics workflow for DAP-seq data exploration and validation for auxin response factors in maize. BIBM 2017: 2300-2301 - [c9]Juexin Wang, Zhen Lyu, Shakhawat Hossain, Gary Stacey, Dong Xu, Trupti Joshi:
SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB. BIBM 2017: 2326 - [c8]Shuai Zeng, Siva Ratna Kumari Narisetti, Zhen Lyu, Trupti Joshi:
KBCommons: A multi 'OMICS' integrative framework for database and informatics tools. BIBM 2017: 2336 - 2016
- [j9]Yang Liu, Saad M. Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, João V. Maldonado dos Santos, Babu Valliyodan, Prasad Calyam, Nirav C. Merchant, Henry T. Nguyen, Dong Xu, Trupti Joshi:
PGen: large-scale genomic variations analysis workflow and browser in SoyKB. BMC Bioinform. 17(S-13): 337 (2016) - [c7]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. CLOUD 2016: 59-67 - [c6]Zainab Al-Taie, Nattaphon Thanintorn, Ilker Ersoy, Richard D. Hammer, Dong Xu, Trupti Joshi, Dmitriy Shin:
Complexity Reduction and Visualization of RDF Knowledge Networks for Precision medicine. AMIA 2016 - [c5]Nattaphon Thanintorn, Juexin Wang, Ilker Ersoy, Zainab Al-Taie, Yuexu Jiang, Duolin Wang, Megha Verma, Trupti Joshi, Richard D. Hammer, Dong Xu, Dmitriy Shin:
RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics. PSB 2016: 417-428 - 2014
- [j8]Trupti Joshi, Robert Williamson, Kapil Patil, Suwit Viyanon, Xiangge Li, Yufu Zhang, Wenchuan Qi, Dong Li, Jeremy Zimmer, Uday Illindala, Shawn Foley, Robert Campbell, Ye Duan, Dong Xu:
Virtual physical examination (VPE): a multimedia system for education in medicine. Int. J. Funct. Informatics Pers. Medicine 4(3/4): 181-197 (2014) - [j7]Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, Dong Xu:
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. Nucleic Acids Res. 42(Database-Issue): 1245-1252 (2014) - 2013
- [j6]Trupti Joshi, Babu Valliyodan, Jeng-Hung Wu, Suk-Ha Lee, Dong Xu, Henry T. Nguyen:
Genomic differences between cultivated soybean, G. max and its wild relative G. soja. BMC Genom. 14(S-1): S5 (2013) - [c4]Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, Dong Xu:
Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding. BIBM 2013: 42-44 - 2012
- [j5]Trupti Joshi, Kapil Patil, Michael R. Fitzpatrick, D. Franklin Levi, Qiuming Yao, Jeffrey R. Cook, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry T. Nguyen, Dong Xu:
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genom. 13(S-1): S15 (2012) - 2010
- [j4]Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J. Green, D. Janine Sherrier, Andrew Farmer, Greg May, Blake C. Meyers, Dong Xu, Gary Stacey:
Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinform. 11(S-1): 14 (2010) - [c3]Trupti Joshi, Qiuming Yao, D. Franklin Levi, Laurent Brechenmacher, Babu Valliyodan, Gary Stacey, Henry T. Nguyen, Dong Xu:
SoyMetDB: The soybean metabolome database. BIBM 2010: 203-208
2000 – 2009
- 2008
- [j3]Chao Zhang, Trupti Joshi, Guan Ning Lin, Dong Xu:
An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. Int. J. Comput. Biol. Drug Des. 1(3): 254-274 (2008) - 2006
- [j2]Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen:
Inferring gene regulatory networks from multiple microarray datasets. Bioinform. 22(19): 2413-2420 (2006) - [c2]Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen:
Supervised Inference of Gene Regulatory Networks by Linear Programming. ICIC (3) 2006: 551-561 - 2005
- [j1]Trupti Joshi, Yu Chen, Nickolai Alexandrov, Dong Xu:
Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. Int. J. Bioinform. Res. Appl. 1(3): 335-350 (2005) - 2003
- [c1]Yu Chen, Trupti Joshi, Ying Xu, Dong Xu:
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. BIBE 2003: 18-25
Coauthor Index
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