Trupti Joshi

48 papers B 3C 1Misc 5Journal 19Unranked 20
YearRankTypeTitle / Venue / Authors
2024 J jnl
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.
Database J. Biol. Databases Curation
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
2024 — conf
Impact of Extracellular Vesicles Derived from Human Placenta Cells on Neural Progenitor Cell Transcriptome Dynamics.
BIBM
Pallav Singh, Jessica A. Kinkade, Mohit Verma, Teka Khan, Toshihiko Ezashi, Nathan J. Bivens, R. Michael Roberts, Cheryl S. Rosenfeld, Trupti Joshi
2023 J jnl
Domain-Specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities.
IEEE Trans. Knowl. Data Eng.
Yuanxun Zhang, Prasad Calyam, Trupti Joshi, Satish S. Nair, Dong Xu
2023 J jnl
Knowledge-Engineered Multi-Cloud Resource Brokering for Application Workflow Optimization.
IEEE Trans. Netw. Serv. Manag.
Ashish Pandey, Prasad Calyam, Zhen Lyu, Songjie Wang, Dmitrii Chemodanov, Trupti Joshi
2021 J jnl
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.
Shuai Zeng, Mária Skrabisová, Zhen Lyu, Yen On Chan, Nicholas Dietz, Kristin Bilyeu, Trupti Joshi
2021 B conf
Fuzzy-Engineered Multi-Cloud Resource Brokering for Data-intensive Applications.
CCGRID
Ashish Pandey, Prasad Calyam, Zhen Lyu, Trupti Joshi
2021 J jnl
G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers.
Nucleic Acids Res.
Shuai Zeng, Ziting Mao, Yijie Ren, Duolin Wang, Dong Xu, Trupti Joshi
2021 J jnl
Multi-Cloud Performance and Security Driven Federated Workflow Management.
IEEE Trans. Cloud Comput.
Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Ronny Bazan Antequera, Trupti Joshi, Tommi A. White, Dong Xu
2021 J jnl
Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway.
Concurr. Comput. Pract. Exp.
Komal Vekaria, Prasad Calyam, Sai Swathi Sivarathri, Songjie Wang, Yuanxun Zhang, Ashish Pandey, Cong Chen, Dong Xu, Trupti Joshi, Satish S. Nair
2020 — conf
A Formative Usability Study to Improve Prescriptive Systems for Bioinformatics Big Data.
BIBM
Kanupriya Singh, Shangman Li, Isa Jahnke, Ashish Pandey, Zhen Lyu, Trupti Joshi, Prasad Calyam
2020 J jnl
A dynamic programing approach to integrate gene expression data and network information for pathway model generation.
Bioinform.
Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi
2020 — conf
A multiomics discriminatory analysis approach to identify drought-related signatures in maize nodal roots.
BIBM
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
2020 — conf
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
Shuai Zeng, Mária Skrabisová, Zhen Lyu, Yen On Chan, Kristin Bilyeu, Trupti Joshi
2020 Misc conf
Security-aware Resource Brokering for Bioinformatics Workflows across Federated Multi-cloud Infrastructures.
ICDCN
Minh Nguyen, Saptarshi Debroy, Prasad Calyam, Zhen Lyu, Trupti Joshi
2019 Misc conf
Community cloud architecture to improve use accessibility with security compliance in health big data applications.
ICDCN
Samaikya Valluripally, Murugesan Raju, Prasad Calyam, Matthew Chisholm, Sai Swathi Sivarathri, Abu Saleh Mohammad Mosa, Trupti Joshi
2019 B conf
Multi-Cloud Performance and Security-driven Brokering for Bioinformatics Workflows.
ICNP
Minh Nguyen, Saptarshi Debroy, Prasad Calyam, Zhen Lyu, Trupti Joshi
2019 — conf
Mutational Forks: Inferring Deregulated Flow of Signal Transduction Based on Patient-Specific Mutations.
BIBM
Olha Kholod, Zhen Lyu, Jonathan B. Mitchem, Peter J. Tonellato, Trupti Joshi, Dmitriy Shin
2019 — conf
OnTimeURB: Multi-Cloud Resource Brokering for Bioinformatics Workflows.
BIBM
Ashish Pandey, Zhen Lyu, Trupti Joshi, Prasad Calyam
2018 — conf
A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis.
BIBM
Sadia Akter, Dong Xu, Susan C. Nagel, Trupti Joshi
2018 J jnl
ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science.
IEEE Trans. Cloud Comput.
Ronny Bazan Antequera, Prasad Calyam, Saptarshi Debroy, Longhai Cui, Sripriya Seetharam, Matthew Dickinson, Trupti Joshi, Dong Xu, Tsegereda Beyene
2018 — conf
Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities.
IEEE BigData
Yuanxun Zhang, Prasad Calyam, Trupti Joshi, Satish S. Nair, Dong Xu
2018 — conf
Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes.
BIBM
Yuexu Jiang, Duolin Wang, Dong Xu, Trupti Joshi
2018 Misc conf
Integrative Analysis of DNA Methylation and RNA-Seq Data for Biomarker Detection of Endometriosis.
AMIA
Sadia Akter, John Bromfield, Katherine Pelch, Gil Wilshire, Sarah Crowder, Danny J. Schust, Bret Barrier, J. Wade Davis, Susan C. Nagel, Trupti Joshi
2018 — conf
Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries.
BIBM
Shuai Zeng, Zhen Lyu, Siva Ratna Kumari Narisetti, Dong Xu, Trupti Joshi
2017 — conf
A multi-omics informatics approach for identifying molecular mechanisms and biomarkers in clinical patients with endometriosis.
BIBM
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
2017 — conf
Development of "KBCommons" - universal informatics framework for multi-omics translational research.
BIBM
Siva Ratna Kumari Narisetti, Shuai Zeng, Zhen Lyu, Trupti Joshi
2017 — conf
Development of an informatics analytics workflow for DAP-seq data exploration and validation for auxin response factors in maize.
BIBM
Sidharth Sen, Mary Galli, Andrea Gallavotti, Trupti Joshi
2017 — conf
Enabling precision medicine with CancerKB and KBCommons informatics framework.
BIBM
Zhen Lyu, Shuai Zeng, Trupti Joshi
2017 — conf
IMPRes: Integrative MultiOmics pathway resolution algorithm and tool.
BIBM
Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi
2017 — conf
KBCommons: A multi 'OMICS' integrative framework for database and informatics tools.
BIBM
Shuai Zeng, Siva Ratna Kumari Narisetti, Zhen Lyu, Trupti Joshi
2017 J jnl
MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction.
Bioinform.
Duolin Wang, Shuai Zeng, Chunhui Xu, Wangren Qiu, Yanchun Liang, Trupti Joshi, Dong Xu
2017 — conf
SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB.
BIBM
Juexin Wang, Zhen Lyu, Shakhawat Hossain, Gary Stacey, Dong Xu, Trupti Joshi
2016 Misc conf
Complexity Reduction and Visualization of RDF Knowledge Networks for Precision medicine.
AMIA
Zainab Al-Taie, Nattaphon Thanintorn, Ilker Ersoy, Richard D. Hammer, Dong Xu, Trupti Joshi, Dmitriy Shin
2016 B conf
End-to-End Security Formalization and Alignment for Federated Workflow Management.
CLOUD
Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Trupti Joshi, Dong Xu
2016 J jnl
PGen: large-scale genomic variations analysis workflow and browser in SoyKB.
BMC Bioinform.
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
2016 Misc conf
RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics.
PSB
Nattaphon Thanintorn, Juexin Wang, Ilker Ersoy, Zainab Al-Taie, Yuexu Jiang, Duolin Wang, Megha Verma, Trupti Joshi, Richard D. Hammer, Dong Xu, Dmitriy Shin
2014 J jnl
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding.
Nucleic Acids Res.
Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, Dong Xu
2014 J jnl
Virtual physical examination (VPE): a multimedia system for education in medicine.
Int. J. Funct. Informatics Pers. Medicine
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
2013 J jnl
Genomic differences between cultivated soybean, G. max and its wild relative G. soja.
BMC Genom.
Trupti Joshi, Babu Valliyodan, Jeng-Hung Wu, Suk-Ha Lee, Dong Xu, Henry T. Nguyen
2013 — conf
Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding.
BIBM
Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary Stacey, Henry T. Nguyen, Dong Xu
2012 J jnl
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics.
BMC Genom.
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
2010 J jnl
Prediction of novel miRNAs and associated target genes in
BMC Bioinform.
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
2010 — conf
SoyMetDB: The soybean metabolome database.
BIBM
Trupti Joshi, Qiuming Yao, D. Franklin Levi, Laurent Brechenmacher, Babu Valliyodan, Gary Stacey, Henry T. Nguyen, Dong Xu
2008 J jnl
An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data.
Int. J. Comput. Biol. Drug Des.
Chao Zhang, Trupti Joshi, Guan Ning Lin, Dong Xu
2006 J jnl
Inferring gene regulatory networks from multiple microarray datasets.
Bioinform.
Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen
2006 — conf
Supervised Inference of Gene Regulatory Networks by Linear Programming.
ICIC (3)
Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen
2005 J jnl
Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data.
Int. J. Bioinform. Res. Appl.
Trupti Joshi, Yu Chen, Nickolai Alexandrov, Dong Xu
2003 C conf
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data.
BIBE
Yu Chen, Trupti Joshi, Ying Xu, Dong Xu