Trupti Joshi

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 35

Top Topics

Gene Expression

Conversational Agents

Knowledge Discovery

Top Venues

Nucleic Acids Res.

Publications

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)
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) (2023)
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) (2023)
Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Ronny Bazan Antequera, Trupti Joshi, Tommi White, Dong Xu
Multi-Cloud Performance and Security Driven Federated Workflow Management. IEEE Trans. Cloud Comput. 9 (1) (2021)
Komal Vekaria, Prasad Calyam, Sai Swathi Sivarathri, Songjie Wang, Yuanxun Zhang, Ashish Pandey, Cong Chen, Dong Xu, Trupti Joshi, Satish Nair
Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway. Concurr. Comput. Pract. Exp. 33 (19) (2021)
Ashish Pandey, Prasad Calyam, Zhen Lyu, Trupti Joshi
Fuzzy-Engineered Multi-Cloud Resource Brokering for Data-intensive Applications. CCGRID (2021)
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) (2021)
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) (2021)
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)
Minh Nguyen, Saptarshi Debroy, Prasad Calyam, Zhen Lyu, Trupti Joshi
Security-aware Resource Brokering for Bioinformatics Workflows across Federated Multi-cloud Infrastructures. ICDCN (2020)
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)
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) (2020)
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)
Minh Nguyen, Saptarshi Debroy, Prasad Calyam, Zhen Lyu, Trupti Joshi
Multi-Cloud Performance and Security-driven Brokering for Bioinformatics Workflows. ICNP (2019)
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)
Samaikya Valluripally, Murugesan Raju, Prasad Calyam, Matthew Chisholm, Sai Swathi Sivarathri, Abu Mosa, Trupti Joshi
Community cloud architecture to improve use accessibility with security compliance in health big data applications. ICDCN (2019)
Ashish Pandey, Zhen Lyu, Trupti Joshi, Prasad Calyam
OnTimeURB: Multi-Cloud Resource Brokering for Bioinformatics Workflows. BIBM (2019)
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)
Yuanxun Zhang, Prasad Calyam, Trupti Joshi, Satish Nair, Dong Xu
Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities. IEEE BigData (2018)
Sadia Akter, Dong Xu, Susan C. Nagel, Trupti Joshi
A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. BIBM (2018)
Yuexu Jiang, Duolin Wang, Dong Xu, Trupti Joshi
Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes. BIBM (2018)
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)
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) (2018)
Zhen Lyu, Shuai Zeng, Trupti Joshi
Enabling precision medicine with CancerKB and KBCommons informatics framework. BIBM (2017)
Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi
IMPRes: Integrative MultiOmics pathway resolution algorithm and tool. BIBM (2017)
Shuai Zeng, Siva Ratna Kumari Narisetti, Zhen Lyu, Trupti Joshi
KBCommons: A multi 'OMICS' integrative framework for database and informatics tools. BIBM (2017)
Siva Ratna Kumari Narisetti, Shuai Zeng, Zhen Lyu, Trupti Joshi
Development of "KBCommons" - universal informatics framework for multi-omics translational research. BIBM (2017)
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)
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)
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)
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) (2017)
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)
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)
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)
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) (2016)
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) (2014)
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) (2014)
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) (2013)
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)
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) (2012)
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
. BMC Bioinform. 11 (S-1) (2010)
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)
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) (2008)
Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen
Supervised Inference of Gene Regulatory Networks by Linear Programming. ICIC (3) (2006)
Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen
Inferring gene regulatory networks from multiple microarray datasets. Bioinform. 22 (19) (2006)
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) (2005)
Yu Chen, Trupti Joshi, Ying Xu, Dong Xu
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. BIBE (2003)