Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. - Yu Chen; Trupti Joshi; Ying Xu 001; Dong Xu 002 (BIBE, 2003)

Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. - Trupti Joshi; Yu Chen; Nickolai Alexandrov; Dong Xu 002 (Int. J. Bioinform. Res. Appl., 2005)

Supervised Inference of Gene Regulatory Networks by Linear Programming. - Yong Wang 001; Trupti Joshi; Dong Xu 002; Xiang-Sun Zhang; Luonan Chen (ICIC (3), 2006)

Inferring gene regulatory networks from multiple microarray datasets. - Yong Wang 001; Trupti Joshi; Xiang-Sun Zhang; Dong Xu 002; Luonan Chen (Bioinform., 2006)

An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. - Chao Zhang 032; Trupti Joshi; Guan Ning Lin; Dong Xu 002 (Int. J. Comput. Biol. Drug Des., 2008)

SoyMetDB: The soybean metabolome database. - Trupti Joshi; Qiuming Yao; D. Franklin Levi; Laurent Brechenmacher; Babu Valliyodan; Gary Stacey; Henry T. Nguyen; Dong Xu 002 (BIBM, 2010)

Prediction of novel miRNAs and associated target genes in Glycine max. - 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 002; Gary Stacey (BMC Bioinform., 2010)

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. - Trupti Joshi; Kapil Patil; Michael R. Fitzpatrick; D. Franklin Levi; Qiuming Yao; Jeffrey R. Cook; Zheng Wang 019; Marc Libault; Laurent Brechenmacher; Babu Valliyodan; Xiaolei Wu; Jianlin Cheng; et al. (BMC Genom., 2012)

Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding. - Trupti Joshi; Michael R. Fitzpatrick; Shiyuan Chen; Yang Liu; Hongxin Zhang; Ryan Z. Endacott; Eric C. Gaudiello; Gary Stacey; Henry T. Nguyen; Dong Xu 002 (BIBM, 2013)

Genomic differences between cultivated soybean, G. max and its wild relative G. soja. - Trupti Joshi; Babu Valliyodan; Jeng-Hung Wu; Suk-Ha Lee; Dong Xu 002; Henry T. Nguyen (BMC Genom., 2013)

Virtual physical examination (VPE): a multimedia system for education in 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; et al. (Int. J. Funct. Informatics Pers. Medicine, 2014)

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. - Trupti Joshi; Michael R. Fitzpatrick; Shiyuan Chen; Yang Liu; Hongxin Zhang; Ryan Z. Endacott; Eric C. Gaudiello; Gary Stacey; Henry T. Nguyen; Dong Xu 002 (Nucleic Acids Res., 2014)

End-to-End Security Formalization and Alignment for Federated Workflow Management. - Matthew Dickinson; Saptarshi Debroy; Prasad Calyam; Samaikya Valluripally; Yuanxun Zhang; Trupti Joshi; Dong Xu 002 (CLOUD, 2016)

Complexity Reduction and Visualization of RDF Knowledge Networks for Precision medicine. - Zainab Al-Taie; Nattaphon Thanintorn; Ilker Ersoy; Richard D. Hammer; Dong Xu 002; Trupti Joshi; Dmitriy Shin (AMIA, 2016)

RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics. - Nattaphon Thanintorn; Juexin Wang; Ilker Ersoy; Zainab Al-Taie; Yuexu Jiang; Duolin Wang; Megha Verma; Trupti Joshi; Richard D. Hammer; Dong Xu 002; Dmitriy Shin (PSB, 2016)

PGen: large-scale genomic variations analysis workflow and browser in SoyKB. - 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; et al. (BMC Bioinform., 2016)

A multi-omics informatics approach for identifying molecular mechanisms and biomarkers in clinical patients with endometriosis. - 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 (BIBM, 2017)

IMPRes: Integrative MultiOmics pathway resolution algorithm and tool. - Yuexu Jiang; Yanchun Liang 001; Duolin Wang; Dong Xu 002; Trupti Joshi (BIBM, 2017)

Enabling precision medicine with CancerKB and KBCommons informatics framework. - Zhen Lyu; Shuai Zeng; Trupti Joshi (BIBM, 2017)

Development of "KBCommons" - universal informatics framework for multi-omics translational research. - Siva Ratna Kumari Narisetti; Shuai Zeng; Zhen Lyu; Trupti Joshi (BIBM, 2017)

Development of an informatics analytics workflow for DAP-seq data exploration and validation for auxin response factors in maize. - Sidharth Sen; Mary Galli; Andrea Gallavotti; Trupti Joshi (BIBM, 2017)

SoyTSN: A web-based prediction tool for soybean tissue specific network within SoyKB. - Juexin Wang; Zhen Lyu; Shakhawat Hossain; Gary Stacey; Dong Xu 002; Trupti Joshi (BIBM, 2017)

KBCommons: A multi 'OMICS' integrative framework for database and informatics tools. - Shuai Zeng; Siva Ratna Kumari Narisetti; Zhen Lyu; Trupti Joshi (BIBM, 2017)

MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction. - Duolin Wang; Shuai Zeng; Chunhui Xu; Wangren Qiu; Yanchun Liang 001; Trupti Joshi; Dong Xu 002 (Bioinform., 2017)

Integrative Analysis of DNA Methylation and RNA-Seq Data for Biomarker Detection of Endometriosis. - Sadia Akter; John Bromfield; Katherine Pelch; Gil Wilshire; Sarah Crowder; Danny J. Schust; Bret Barrier; J. Wade Davis; Susan C. Nagel; Trupti Joshi (AMIA, 2018)

A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. - Sadia Akter; Dong Xu 002; Susan C. Nagel; Trupti Joshi (BIBM, 2018)

Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes. - Yuexu Jiang; Duolin Wang; Dong Xu 002; Trupti Joshi (BIBM, 2018)

Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries. - Shuai Zeng; Zhen Lyu; Siva Ratna Kumari Narisetti; Dong Xu 002; Trupti Joshi (BIBM, 2018)

Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities. - Yuanxun Zhang; Prasad Calyam; Trupti Joshi; Satish S. Nair; Dong Xu 002 (IEEE BigData, 2018)

ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science. - Ronny Bazan Antequera; Prasad Calyam; Saptarshi Debroy; Longhai Cui; Sripriya Seetharam; Matthew Dickinson; Trupti Joshi; Dong Xu 002; Tsegereda Beyene (IEEE Trans. Cloud Comput., 2018)

Mutational Forks: Inferring Deregulated Flow of Signal Transduction Based on Patient-Specific Mutations. - Olha Kholod; Zhen Lyu; Jonathan B. Mitchem; Peter J. Tonellato; Trupti Joshi; Dmitriy Shin (BIBM, 2019)

OnTimeURB: Multi-Cloud Resource Brokering for Bioinformatics Workflows. - Ashish Pandey; Zhen Lyu; Trupti Joshi; Prasad Calyam (BIBM, 2019)

Community cloud architecture to improve use accessibility with security compliance in health big data applications. - Samaikya Valluripally; Murugesan Raju; Prasad Calyam; Matthew Chisholm; Sai Swathi Sivarathri; Abu Saleh Mohammad Mosa; Trupti Joshi (ICDCN, 2019)

Multi-Cloud Performance and Security-driven Brokering for Bioinformatics Workflows. - Minh Nguyen; Saptarshi Debroy; Prasad Calyam; Zhen Lyu; Trupti Joshi (ICNP, 2019)

A multiomics discriminatory analysis approach to identify drought-related signatures in maize nodal roots. - 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; et al. (BIBM, 2020)

A Formative Usability Study to Improve Prescriptive Systems for Bioinformatics Big Data. - Kanupriya Singh; Shangman Li; Isa Jahnke; Ashish Pandey; Zhen Lyu; Trupti Joshi; Prasad Calyam (BIBM, 2020)

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. - Shuai Zeng; Mária Skrabisová; Zhen Lyu; Yen On Chan; Kristin Bilyeu; Trupti Joshi (BIBM, 2020)

Security-aware Resource Brokering for Bioinformatics Workflows across Federated Multi-cloud Infrastructures. - Minh Nguyen; Saptarshi Debroy; Prasad Calyam; Zhen Lyu; Trupti Joshi (ICDCN, 2020)

A dynamic programing approach to integrate gene expression data and network information for pathway model generation. - Yuexu Jiang; Yanchun Liang 001; Duolin Wang; Dong Xu 002; Trupti Joshi (Bioinform., 2020)

Fuzzy-Engineered Multi-Cloud Resource Brokering for Data-intensive Applications. - Ashish Pandey; Prasad Calyam; Zhen Lyu; Trupti Joshi (CCGRID, 2021)

Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway. - Komal Vekaria; Prasad Calyam; Sai Swathi Sivarathri; Songjie Wang; Yuanxun Zhang; Ashish Pandey; Cong Chen; Dong Xu 002; Trupti Joshi; Satish S. Nair (Concurr. Comput. Pract. Exp., 2021)

Application of SNPViz v2.0 using next-generation sequencing data sets in the discovery of potential causative mutations in candidate genes associated with phenotypes. - Shuai Zeng; Mária Skrabisová; Zhen Lyu; Yen On Chan; Nicholas Dietz; Kristin Bilyeu; Trupti Joshi (Int. J. Data Min. Bioinform., 2021)

G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. - Shuai Zeng; Ziting Mao; Yijie Ren; Duolin Wang; Dong Xu 002; Trupti Joshi (Nucleic Acids Res., 2021)

Multi-Cloud Performance and Security Driven Federated Workflow Management. - Matthew Dickinson; Saptarshi Debroy; Prasad Calyam; Samaikya Valluripally; Yuanxun Zhang; Ronny Bazan Antequera; Trupti Joshi; Tommi A. White; Dong Xu 002 (IEEE Trans. Cloud Comput., 2021)

Domain-Specific Topic Model for Knowledge Discovery in Computational and Data-Intensive Scientific Communities. - Yuanxun Zhang; Prasad Calyam; Trupti Joshi; Satish S. Nair; Dong Xu 002 (IEEE Trans. Knowl. Data Eng., 2023)

Knowledge-Engineered Multi-Cloud Resource Brokering for Application Workflow Optimization. - Ashish Pandey; Prasad Calyam; Zhen Lyu; Songjie Wang; Dmitrii Chemodanov; Trupti Joshi (IEEE Trans. Netw. Serv. Manag., 2023)

Impact of Extracellular Vesicles Derived from Human Placenta Cells on Neural Progenitor Cell Transcriptome Dynamics. - Pallav Singh; Jessica A. Kinkade; Mohit Verma; Teka Khan; Toshihiko Ezashi; Nathan J. Bivens; R. Michael Roberts; Cheryl S. Rosenfeld; Trupti Joshi (BIBM, 2024)

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants. - Chunhui Xu; Trey Shaw; Sai Akhil Choppararu; Yiwei Lu; Shaik Naveed Farooq; Yongfang Qin; Matt Hudson; Brock Weekley; Michael Fisher 008; Fei He; Jose Roberto Da Silva Nascimento; Nicholas Wergeles; et al. (Database J. Biol. Databases Curation, 2024)