Publications

A word cloud of publication titles

2025

Towards Robust Federated Learning: Investigating Poisoning Attacks Under Clients Data Heterogeneity
Towards Robust Federated Learning: Investigating Poisoning Attacks Under Clients Data Heterogeneity
Abdenour Soubih, Seyyid Ahmed Lahmer, Mohammed Abuhamad, Tamer Abuhmed
2025 19th International Conference on Ubiquitous Information Management and Communication (IMCOM)  ·  03 Jan 2025  ·  doi:10.1109/imcom64595.2025.10857574
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Stealthy Query-Efficient Opaque Attack Against Interpretable Deep Learning
Stealthy Query-Efficient Opaque Attack Against Interpretable Deep Learning
Eldor Abdukhamidov, Mohammed Abuhamad, Simon S. Woo, Eric Chan-Tin, Tamer Abuhmed
IEEE Transactions on Reliability  ·  01 Jan 2025  ·  doi:10.1109/TR.2025.3551717
Responsible Artificial Intelligence for Mental Health Disorders: Current Applications and Future Challenges
Responsible Artificial Intelligence for Mental Health Disorders: Current Applications and Future Challenges
Shaker El-Sappagh, Waleed Nazih, Meshal Alharbi, Tamer Abuhmed
Journal of Disability Research  ·  01 Jan 2025  ·  doi:10.57197/JDR-2024-0101
FiSC: A Novel Approach for Fitzpatrick Scale-Based Skin Analyzer’s Image Classification
FiSC: A Novel Approach for Fitzpatrick Scale-Based Skin Analyzer’s Image Classification
Guillermo Crocker Garcia, Muhammad Numan Khan, Aftab Alam, Josue Obregon, Tamer Abuhmed, Eui-Nam Huh
IEEE Access  ·  01 Jan 2025  ·  doi:10.1109/ACCESS.2025.3547573

2024

Explainable Multi-Layer Dynamic Ensemble Framework Optimized for Depression Detection and Severity Assessment
Explainable Multi-Layer Dynamic Ensemble Framework Optimized for Depression Detection and Severity Assessment
Dillan Imans, Tamer Abuhmed, Meshal Alharbi, Shaker El-Sappagh
Diagnostics  ·  25 Oct 2024  ·  doi:10.3390/diagnostics14212385  ·  PMID: 39518353  ·  PMCID: PMC11545061
Alzheimer's disease diagnosis in the metaverse
Alzheimer's disease diagnosis in the metaverse
Jalal Safari Bazargani, Nasir Rahim, Abolghasem Sadeghi-Niaraki, Tamer Abuhmed, Houbing Song, Soo-Mi Choi
Computer Methods and Programs in Biomedicine  ·  01 Oct 2024  ·  doi:10.1016/j.cmpb.2024.108348  ·  PMID: 39067138
Smart Collaborative Intrusion Detection System for Securing Vehicular Networks Using Ensemble Machine Learning Model
Smart Collaborative Intrusion Detection System for Securing Vehicular Networks Using Ensemble Machine Learning Model
Mostafa Mahmoud El-Gayar, Faheed A. F. Alrslani, Shaker El-Sappagh
Information  ·  24 Sep 2024  ·  doi:10.3390/info15100583
Hardening Interpretable Deep Learning Systems: Investigating Adversarial Threats and Defenses
Hardening Interpretable Deep Learning Systems: Investigating Adversarial Threats and Defenses
Eldor Abdukhamidov, Mohammed Abuhamad, Simon S. Woo, Eric Chan-Tin, Tamer Abuhmed
IEEE Transactions on Dependable and Secure Computing  ·  01 Jul 2024  ·  doi:10.1109/TDSC.2023.3341090
A Survey on Deep Packet Inspection for Intrusion Detection Systems
A Survey on Deep Packet Inspection for Intrusion Detection Systems
Tamer AbuHmed, Abedelaziz Mohaisen, DaeHun Nyang
arXiv  ·  19 Feb 2024  ·  arxiv:0803.0037
An Exploration of Geo-temporal Characteristics of Users' Reactions on Social Media During the Pandemic
An Exploration of Geo-temporal Characteristics of Users' Reactions on Social Media During the Pandemic
Eldor Abdukhamidov, Firuz Juraev, Mohammed Abuhamad, Tamer AbuHmed
arXiv  ·  19 Feb 2024  ·  arxiv:2103.13032
Interpretations Cannot Be Trusted: Stealthy and Effective Adversarial Perturbations against Interpretable Deep Learning
Interpretations Cannot Be Trusted: Stealthy and Effective Adversarial Perturbations against Interpretable Deep Learning
Eldor Abdukhamidov, Mohammed Abuhamad, Simon S. Woo, Eric Chan-Tin, Tamer Abuhmed
arXiv  ·  19 Feb 2024  ·  arxiv:2211.15926
Unveiling Vulnerabilities in Interpretable Deep Learning Systems with Query-Efficient Black-box Attacks
Unveiling Vulnerabilities in Interpretable Deep Learning Systems with Query-Efficient Black-box Attacks
Eldor Abdukhamidov, Mohammed Abuhamad, Simon S. Woo, Eric Chan-Tin, Tamer Abuhmed
arXiv  ·  19 Feb 2024  ·  arxiv:2307.11906
Single-Class Target-Specific Attack against Interpretable Deep Learning Systems
Single-Class Target-Specific Attack against Interpretable Deep Learning Systems
Eldor Abdukhamidov, Mohammed Abuhamad, George K. Thiruvathukal, Hyoungshick Kim, Tamer Abuhmed
arXiv  ·  19 Feb 2024  ·  arxiv:2307.06484
Microbial Genetic Algorithm-based Black-box Attack against Interpretable Deep Learning Systems
Microbial Genetic Algorithm-based Black-box Attack against Interpretable Deep Learning Systems
Eldor Abdukhamidov, Mohammed Abuhamad, Simon S. Woo, Eric Chan-Tin, Tamer Abuhmed
arXiv  ·  19 Feb 2024  ·  arxiv:2307.06496
SingleADV: Single-Class Target-Specific Attack Against Interpretable Deep Learning Systems
SingleADV: Single-Class Target-Specific Attack Against Interpretable Deep Learning Systems
Eldor Abdukhamidov, Mohammed Abuhamad, George K. Thiruvathukal, Hyoungshick Kim, Tamer Abuhmed
IEEE Transactions on Information Forensics and Security  ·  01 Jan 2024  ·  doi:10.1109/TIFS.2024.3407652

2023

Time-series visual explainability for Alzheimer’s disease progression detection for smart healthcare
Time-series visual explainability for Alzheimer’s disease progression detection for smart healthcare
Nasir Rahim, Tamer Abuhmed, Seyedali Mirjalili, Shaker El-Sappagh, Khan Muhammad
Alexandria Engineering Journal  ·  01 Nov 2023  ·  doi:10.1016/j.aej.2023.09.050
Explainable Artificial Intelligence (XAI): What we know and what is left to attain Trustworthy Artificial Intelligence
Explainable Artificial Intelligence (XAI): What we know and what is left to attain Trustworthy Artificial Intelligence
Sajid Ali, Tamer Abuhmed, Shaker El-Sappagh, Khan Muhammad, Jose M. Alonso-Moral, Roberto Confalonieri, Riccardo Guidotti, Javier Del Ser, Natalia Díaz-Rodríguez, Francisco Herrera
Information Fusion  ·  01 Nov 2023  ·  doi:10.1016/j.inffus.2023.101805
Computer aided progression detection model based on optimized deep LSTM ensemble model and the fusion of multivariate time series data
Computer aided progression detection model based on optimized deep LSTM ensemble model and the fusion of multivariate time series data
Hager Saleh, Eslam Amer, Tamer Abuhmed, Amjad Ali, Ala Al-Fuqaha, Shaker El-Sappagh
Scientific Reports  ·  28 Sep 2023  ·  doi:10.1038/s41598-023-42796-6  ·  PMID: 37770490  ·  PMCID: PMC10539296
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DrugMechDB: A Curated Database of Drug Mechanisms
DrugMechDB: A Curated Database of Drug Mechanisms
Adriana Carolina Gonzalez-Cavazos, Anna Tanska, Michael Mayers, Denise Carvalho-Silva, Brindha Sridharan, Patrick A. Rewers, Umasri Sankarlal, Lakshmanan Jagannathan, Andrew I. Su
Scientific Data  ·  16 Sep 2023  ·  doi:10.1038/s41597-023-02534-z  ·  PMID: 37717042  ·  PMCID: PMC10505144
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TruMuzic: A Deep Learning and Data Provenance-Based Approach to Evaluating the Authenticity of Music
TruMuzic: A Deep Learning and Data Provenance-Based Approach to Evaluating the Authenticity of Music
Kuldeep Gurjar, Yang-Sae Moon, Tamer Abuhmed
Applied Sciences  ·  19 Aug 2023  ·  doi:10.3390/app13169425
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Underwater Image Restoration and Enhancement: A Comprehensive Review of Recent Trends, Challenges, and Applications
Underwater Image Restoration and Enhancement: A Comprehensive Review of Recent Trends, Challenges, and Applications
Yasmin M. Alsakar, Nehal A Sakr, Shaker El-Sappagh, Tamer Abuhmed, Mohammed Elmogy
MDPI AG  ·  10 Jul 2023  ·  doi:10.20944/preprints202307.0585.v1
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Wildfire Susceptibility Mapping Using Deep Learning Algorithms in Two Satellite Imagery Dataset
Wildfire Susceptibility Mapping Using Deep Learning Algorithms in Two Satellite Imagery Dataset
Nazanin Bahadori, Seyed Vahid Razavi-Termeh, Abolghasem Sadeghi-Niaraki, Khalifa M. Al-Kindi, Tamer Abuhmed, Behrokh Nazeri, Soo-Mi Choi
Forests  ·  28 Jun 2023  ·  doi:10.3390/f14071325
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Association study between drug prescriptions and Alzheimer’s disease claims in a commercial insurance database
Association study between drug prescriptions and Alzheimer’s disease claims in a commercial insurance database
Eric Hu, Tong Shu Li, Nathan E. Wineinger, Andrew I. Su
Alzheimer's Research & Therapy  ·  24 Jun 2023  ·  doi:10.1186/s13195-023-01255-0  ·  PMID: 37355615  ·  PMCID: PMC10290352
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Explainable machine learning models based on multimodal time-series data for the early detection of Parkinson’s disease
Explainable machine learning models based on multimodal time-series data for the early detection of Parkinson’s disease
Muhammad Junaid, Sajid Ali, Fatma Eid, Shaker El-Sappagh, Tamer Abuhmed
Computer Methods and Programs in Biomedicine  ·  01 Jun 2023  ·  doi:10.1016/j.cmpb.2023.107495  ·  PMID: 37003039
Effective Multitask Deep Learning for IoT Malware Detection and Identification Using Behavioral Traffic Analysis
Effective Multitask Deep Learning for IoT Malware Detection and Identification Using Behavioral Traffic Analysis
Sajid Ali, Omar Abusabha, Farman Ali, Muhammad Imran, Tamer Abuhmed
IEEE Transactions on Network and Service Management  ·  01 Jun 2023  ·  doi:10.1109/TNSM.2022.3200741
Henry gas solubility optimization double machine learning classifier for neurosurgical patients
Henry gas solubility optimization double machine learning classifier for neurosurgical patients
Diana T. Mosa, Amena Mahmoud, John Zaki, Shaymaa E. Sorour, Shaker El-Sappagh, Tamer Abuhmed
PLOS ONE  ·  11 May 2023  ·  doi:10.1371/journal.pone.0285455  ·  PMID: 37167226  ·  PMCID: PMC10174516
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DrugMechDB: A Curated Database of Drug Mechanisms
DrugMechDB: A Curated Database of Drug Mechanisms
Adriana Carolina Gonzalez-Cavazos, Anna Tanska, Michael D. Mayers, Denise Carvalho-Silva, Brindha Sridharan, Patrik A. Rewers, Umasri Sankarlal, Lakshmanan Jagannathan, Andrew I. Su
Cold Spring Harbor Laboratory  ·  02 May 2023  ·  doi:10.1101/2023.05.01.538993  ·  PMID: 37205439  ·  PMCID: PMC10187194
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Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
Marco A. Cano, Ginger Tsueng, Xinghua Zhou, Jiwen Xin, Laura D. Hughes, Julia L. Mullen, Andrew I. Su, Chunlei Wu
BMC Bioinformatics  ·  20 Apr 2023  ·  doi:10.1186/s12859-023-05258-4  ·  PMID: 37081398  ·  PMCID: PMC10116472
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Enabling profile updates through the Data Discovery Engine (DDE)
Enabling profile updates through the Data Discovery Engine (DDE)
Ginger Tsueng, Sahar Frika, Alasdair J. G. Gray, Marcos Casado Barbero, Alban Gaignard, Ivan Mičetić, Leyla Jael Castro, Nick Juty
Center for Open Science  ·  03 Apr 2023  ·  doi:10.37044/osf.io/3b9gp
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Prediction of Alzheimer's progression based on multimodal Deep-Learning-based fusion and visual Explainability of time-series data
Prediction of Alzheimer's progression based on multimodal Deep-Learning-based fusion and visual Explainability of time-series data
Nasir Rahim, Shaker El-Sappagh, Sajid Ali, Khan Muhammad, Javier Del Ser, Tamer Abuhmed
Information Fusion  ·  01 Apr 2023  ·  doi:10.1016/j.inffus.2022.11.028
Toward Comprehensive Chronic Kidney Disease Prediction Based on Ensemble Deep Learning Models
Toward Comprehensive Chronic Kidney Disease Prediction Based on Ensemble Deep Learning Models
Deema Mohammed Alsekait, Hager Saleh, Lubna Abdelkareim Gabralla, Khaled Alnowaiser, Shaker El-Sappagh, Radhya Sahal, Nora El-Rashidy
Applied Sciences  ·  20 Mar 2023  ·  doi:10.3390/app13063937
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Trustworthy artificial intelligence in Alzheimer’s disease: state of the art, opportunities, and challenges
Trustworthy artificial intelligence in Alzheimer’s disease: state of the art, opportunities, and challenges
Shaker El-Sappagh, Jose M. Alonso-Moral, Tamer Abuhmed, Farman Ali, Alberto Bugarín-Diz
Artificial Intelligence Review  ·  12 Mar 2023  ·  doi:10.1007/s10462-023-10415-5
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Emory Hufbauer, …, Marc A. Suchard, Chunlei Wu, Andrew I. Su, Kristian G. Andersen, Laura D. Hughes
Nature Methods  ·  23 Feb 2023  ·  doi:10.1038/s41592-023-01769-3  ·  PMID: 36823332  ·  PMCID: PMC10399614
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Developing a standardized but extendable framework to increase the findability of infectious disease datasets
Developing a standardized but extendable framework to increase the findability of infectious disease datasets
Ginger Tsueng, Marco A. Alvarado Cano, José Bento, Candice Czech, Mengjia Kang, …, Chunlei Wu, Liliana Brown, Reed S. Shabman, Laura D. Hughes, Serdar Turkarslan
Scientific Data  ·  23 Feb 2023  ·  doi:10.1038/s41597-023-01968-9  ·  PMID: 36823157  ·  PMCID: PMC9950378
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Addressing barriers in FAIR data practices for biomedical data
Addressing barriers in FAIR data practices for biomedical data
Laura D. Hughes, Ginger Tsueng, Jack DiGiovanna, Thomas D. Horvath, Luke V. Rasmussen, …, Serdar Turkarslan, Qinglong Wu, Chunlei Wu, Andrew I. Su, Lars Pache
Scientific Data  ·  23 Feb 2023  ·  doi:10.1038/s41597-023-01969-8  ·  PMID: 36823198  ·  PMCID: PMC9950056
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Predicting CTS Diagnosis and Prognosis Based on Machine Learning Techniques
Predicting CTS Diagnosis and Prognosis Based on Machine Learning Techniques
Marwa Elseddik, Reham R. Mostafa, Ahmed Elashry, Nora El-Rashidy, Shaker El-Sappagh, Shimaa Elgamal, Ahmed Aboelfetouh, Hazem El-Bakry
Diagnostics  ·  29 Jan 2023  ·  doi:10.3390/diagnostics13030492  ·  PMID: 36766597  ·  PMCID: PMC9914125
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A deep learning based dual encoder–decoder framework for anatomical structure segmentation in chest X-ray images
A deep learning based dual encoder–decoder framework for anatomical structure segmentation in chest X-ray images
Ihsan Ullah, Farman Ali, Babar Shah, Shaker El-Sappagh, Tamer Abuhmed, Sang Hyun Park
Scientific Reports  ·  16 Jan 2023  ·  doi:10.1038/s41598-023-27815-w  ·  PMID: 36646735  ·  PMCID: PMC9842654
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A Holistic Approach to Identify and Classify COVID-19 from Chest Radiographs, ECG, and CT-Scan Images Using ShuffleNet Convolutional Neural Network
A Holistic Approach to Identify and Classify COVID-19 from Chest Radiographs, ECG, and CT-Scan Images Using ShuffleNet Convolutional Neural Network
Naeem Ullah, Javed Khan, Shaker El-Sappagh, Nora El-Rashidy, Mohammad Khan
Diagnostics  ·  03 Jan 2023  ·  doi:10.3390/diagnostics13010162  ·  PMID: 36611454  ·  PMCID: PMC9818310
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An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E. Thessen, …, Casey Ta, Paul B. Watkins, Mark D. Williams, Chunlei Wu, Colleen H. Xu
Journal of Clinical and Translational Science  ·  01 Jan 2023  ·  doi:10.1017/cts.2023.619  ·  PMID: 37900350  ·  PMCID: PMC10603356
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Early Detection of Alzheimer’s Disease Based on Laplacian Re-Decomposition and XGBoosting
Early Detection of Alzheimer’s Disease Based on Laplacian Re-Decomposition and XGBoosting
Hala Ahmed, Hassan Soliman, Shaker El-Sappagh, Tamer Abuhmed, Mohammed Elmogy
Computer Systems Science and Engineering  ·  01 Jan 2023  ·  doi:10.32604/csse.2023.036371

2022

Multitask Deep Learning for Cost-Effective Prediction of Patient's Length of Stay and Readmission State Using Multimodal Physical Activity Sensory Data
Multitask Deep Learning for Cost-Effective Prediction of Patient's Length of Stay and Readmission State Using Multimodal Physical Activity Sensory Data
Sajid Ali, Shaker El-Sappagh, Farman Ali, Muhammad Imran, Tamer Abuhmed
IEEE Journal of Biomedical and Health Informatics  ·  01 Dec 2022  ·  doi:10.1109/JBHI.2022.3202178  ·  PMID: 36037451
Colon Cancer Diagnosis Based on Machine Learning and Deep Learning: Modalities and Analysis Techniques
Colon Cancer Diagnosis Based on Machine Learning and Deep Learning: Modalities and Analysis Techniques
Mai Tharwat, Nehal A. Sakr, Shaker El-Sappagh, Hassan Soliman, Kyung-Sup Kwak, Mohammed Elmogy
Sensors  ·  28 Nov 2022  ·  doi:10.3390/s22239250  ·  PMID: 36501951  ·  PMCID: PMC9739266
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AR Search Engine: Semantic Information Retrieval for Augmented Reality Domain
AR Search Engine: Semantic Information Retrieval for Augmented Reality Domain
Maryam Shakeri, Abolghasem Sadeghi-Niaraki, Soo-Mi Choi, Tamer AbuHmed
Sustainability  ·  25 Nov 2022  ·  doi:10.3390/su142315681
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Multilayer dynamic ensemble model for intensive care unit mortality prediction of neonate patients
Multilayer dynamic ensemble model for intensive care unit mortality prediction of neonate patients
Firuz Juraev, Shaker El-Sappagh, Eldor Abdukhamidov, Farman Ali, Tamer Abuhmed
Journal of Biomedical Informatics  ·  01 Nov 2022  ·  doi:10.1016/j.jbi.2022.104216  ·  PMID: 36208833
Automatic detection of Alzheimer’s disease progression: An efficient information fusion approach with heterogeneous ensemble classifiers
Automatic detection of Alzheimer’s disease progression: An efficient information fusion approach with heterogeneous ensemble classifiers
Shaker El-Sappagh, Farman Ali, Tamer Abuhmed, Jaiteg Singh, Jose M. Alonso
Neurocomputing  ·  01 Nov 2022  ·  doi:10.1016/j.neucom.2022.09.009
Developing a standardized but extendable framework to increase the findability of infectious disease datasets
Developing a standardized but extendable framework to increase the findability of infectious disease datasets
Ginger Tsueng, Marco A. Alvarado Cano, José Bento, Candice Czech, Mengjia Kang, …, Andrew I. Su, Chunlei Wu, Liliana Brown, Reed S. Shabman, Laura D. Hughes
Cold Spring Harbor Laboratory  ·  13 Oct 2022  ·  doi:10.1101/2022.10.10.511492
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AHA-AO: Artificial Hummingbird Algorithm with Aquila Optimization for Efficient Feature Selection in Medical Image Classification
AHA-AO: Artificial Hummingbird Algorithm with Aquila Optimization for Efficient Feature Selection in Medical Image Classification
Mohamed Abd Elaziz, Abdelghani Dahou, Shaker El-Sappagh, Alhassan Mabrouk, Mohamed Medhat Gaber
Applied Sciences  ·  27 Sep 2022  ·  doi:10.3390/app12199710
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An approach for measuring spatial similarity among COVID-19 epicenters
An approach for measuring spatial similarity among COVID-19 epicenters
Neda Kaffash Charandabi, Abolghasem Sadeghi-Niaraki, Soo-Mi Choi, Tamer Abuhmed
Geo-spatial Information Science  ·  05 Jul 2022  ·  doi:10.1080/10095020.2022.2088303
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Laura Hughes, Karthik Gangavarapu, Alaa Abdel Latif, Julia Mullen, Manar Alkuzweny, …, Sebastian Maurer-Stroh, Marc Suchard, Chunlei Wu, Andrew Su, Kristian Andersen
Research Square Platform LLC  ·  28 Jun 2022  ·  doi:10.21203/rs.3.rs-1723829/v1  ·  PMID: 35794893  ·  PMCID: PMC9258294
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Outbreak.info Research Library: A standardized, searchable platform to discover and explore COVID-19 resources
Outbreak.info Research Library: A standardized, searchable platform to discover and explore COVID-19 resources
Laura Hughes, Ginger Tsueng, Julia Mullen, Manar Alkuzweny, Marco Cano, …, Mark Zeller, Kristian Andersen, Chunlei Wu, Andrew Su, Karthik Gangavarapu
Research Square Platform LLC  ·  28 Jun 2022  ·  doi:10.21203/rs.3.rs-1723808/v1
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Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, …, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall
Clinical and Translational Science  ·  06 Jun 2022  ·  doi:10.1111/cts.13302  ·  PMID: 36125173  ·  PMCID: PMC9372416
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Sentiment Analysis of Users’ Reactions on Social Media during the Pandemic
Sentiment Analysis of Users’ Reactions on Social Media during the Pandemic
Eldor Abdukhamidov, Firuz Juraev, Mohammed Abuhamad, Shaker El-Sappagh, Tamer AbuHmed
Electronics  ·  22 May 2022  ·  doi:10.3390/electronics11101648
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Two-stage deep learning model for Alzheimer’s disease detection and prediction of the mild cognitive impairment time
Two-stage deep learning model for Alzheimer’s disease detection and prediction of the mild cognitive impairment time
Shaker El-Sappagh, Hager Saleh, Farman Ali, Eslam Amer, Tamer Abuhmed
Neural Computing and Applications  ·  08 May 2022  ·  doi:10.1007/s00521-022-07263-9
Crystal structure guided machine learning for the discovery and design of intrinsically hard materials
Crystal structure guided machine learning for the discovery and design of intrinsically hard materials
Russlan Jaafreh, Tamer Abuhmed, Jung-Gu Kim, Kotiba Hamad
Journal of Materiomics  ·  01 May 2022  ·  doi:10.1016/j.jmat.2021.11.004
A Comparative Study of Strain Rate Constitutive and Machine Learning Models for Flow Behavior of AZ31-0.5 Ca Mg Alloy during Hot Deformation
A Comparative Study of Strain Rate Constitutive and Machine Learning Models for Flow Behavior of AZ31-0.5 Ca Mg Alloy during Hot Deformation
Umer Masood Chaudry, Russlan Jaafreh, Abdul Malik, Tea-Sung Jun, Kotiba Hamad, Tamer Abuhmed
Mathematics  ·  27 Feb 2022  ·  doi:10.3390/math10050766
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Age-hardening behavior guided by the multi-objective evolutionary algorithm and machine learning
Age-hardening behavior guided by the multi-objective evolutionary algorithm and machine learning
Russlan Jaafreh, Umer Masood Chaudry, Kotiba Hamad, Tamer Abuhmed
Journal of Alloys and Compounds  ·  01 Feb 2022  ·  doi:10.1016/j.jallcom.2021.162104
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Emory Hufbauer, …, Marc A. Suchard, Chunlei Wu, Andrew I. Su, Kristian G. Andersen, Laura D. Hughes
Cold Spring Harbor Laboratory  ·  29 Jan 2022  ·  doi:10.1101/2022.01.27.22269965
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An Enhanced Grey Wolf Optimizer with a Velocity-Aided Global Search Mechanism
An Enhanced Grey Wolf Optimizer with a Velocity-Aided Global Search Mechanism
Farshad Rezaei, Hamid Reza Safavi, Mohamed Abd Elaziz, Shaker H. Ali El-Sappagh, Mohammed Azmi Al-Betar, Tamer Abuhmed
Mathematics  ·  24 Jan 2022  ·  doi:10.3390/math10030351
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An IoT-Based Approach for Learning Geometric Shapes in Early Childhood
An IoT-Based Approach for Learning Geometric Shapes in Early Childhood
Jalal Safari Bazargani, Abolghasem Sadeghi-Niaraki, Fatema Rahimi, Tamer Abuhmed, Soo-Mi Choi
IEEE Access  ·  01 Jan 2022  ·  doi:10.1109/ACCESS.2022.3229440

2021

Sepsis prediction in intensive care unit based on genetic feature optimization and stacked deep ensemble learning
Sepsis prediction in intensive care unit based on genetic feature optimization and stacked deep ensemble learning
Nora El-Rashidy, Tamer Abuhmed, Louai Alarabi, Hazem M. El-Bakry, Samir Abdelrazek, Farman Ali, Shaker El-Sappagh
Neural Computing and Applications  ·  03 Nov 2021  ·  doi:10.1007/s00521-021-06631-1
A Short Review on the Machine Learning-Guided Oxygen Uptake Prediction for Sport Science Applications
A Short Review on the Machine Learning-Guided Oxygen Uptake Prediction for Sport Science Applications
Haneen Alzamer, Tamer Abuhmed, Kotiba Hamad
Electronics  ·  13 Aug 2021  ·  doi:10.3390/electronics10161956
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Large-scale and Robust Code Authorship Identification with Deep Feature Learning
Large-scale and Robust Code Authorship Identification with Deep Feature Learning
Mohammed Abuhamad, Tamer Abuhmed, David Mohaisen, Daehun Nyang
ACM Transactions on Privacy and Security  ·  19 Jul 2021  ·  doi:10.1145/3461666
An Extended Semantic Interoperability Model for Distributed Electronic Health Record Based on Fuzzy Ontology Semantics
An Extended Semantic Interoperability Model for Distributed Electronic Health Record Based on Fuzzy Ontology Semantics
Ebtsam Adel, Shaker El-Sappagh, Sherif Barakat, Jong-Wan Hu, Mohammed Elmogy
Electronics  ·  19 Jul 2021  ·  doi:10.3390/electronics10141733
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Comprehensive Survey of Using Machine Learning in the COVID-19 Pandemic
Comprehensive Survey of Using Machine Learning in the COVID-19 Pandemic
Nora El-Rashidy, Samir Abdelrazik, Tamer Abuhmed, Eslam Amer, Farman Ali, Jong-Wan Hu, Shaker El-Sappagh
Diagnostics  ·  24 Jun 2021  ·  doi:10.3390/diagnostics11071155  ·  PMID: 34202587  ·  PMCID: PMC8303306
Machine learning-aided design of aluminum alloys with high performance
Machine learning-aided design of aluminum alloys with high performance
Umer Masood Chaudry, Kotiba Hamad, Tamer Abuhmed
Materials Today Communications  ·  01 Mar 2021  ·  doi:10.1016/j.mtcomm.2020.101897
Robust hybrid deep learning models for Alzheimer’s progression detection
Robust hybrid deep learning models for Alzheimer’s progression detection
Tamer Abuhmed, Shaker El-Sappagh, Jose M. Alonso
Knowledge-Based Systems  ·  01 Feb 2021  ·  doi:10.1016/j.knosys.2020.106688
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Alzheimer’s disease progression detection model based on an early fusion of cost-effective multimodal data
Alzheimer’s disease progression detection model based on an early fusion of cost-effective multimodal data
Shaker El-Sappagh, Hager Saleh, Radhya Sahal, Tamer Abuhmed, S.M. Riazul Islam, Farman Ali, Eslam Amer
Future Generation Computer Systems  ·  01 Feb 2021  ·  doi:10.1016/j.future.2020.10.005
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses
Andra Waagmeester, Egon L. Willighagen, Andrew I. Su, Martina Kutmon, Jose Emilio Labra Gayo, Daniel Fernández-Álvarez, Quentin Groom, Peter J. Schaap, Lisa M. Verhagen, Jasper J. Koehorst
BMC Biology  ·  22 Jan 2021  ·  doi:10.1186/s12915-020-00940-y  ·  PMID: 33482803  ·  PMCID: PMC7820539
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Classification and Analysis of Android Malware Images Using Feature Fusion Technique
Classification and Analysis of Android Malware Images Using Feature Fusion Technique
Jaiteg Singh, Deepak Thakur, Tanya Gera, Babar Shah, Tamer Abuhmed, Farman Ali
IEEE Access  ·  01 Jan 2021  ·  doi:10.1109/ACCESS.2021.3090998
Automatic Diabetic Retinopathy Grading System Based on Detecting Multiple Retinal Lesions
Automatic Diabetic Retinopathy Grading System Based on Detecting Multiple Retinal Lesions
Eman Abdelmaksoud, Shaker El-Sappagh, Sherif Barakat, Tamer Abuhmed, Mohammed Elmogy
IEEE Access  ·  01 Jan 2021  ·  doi:10.1109/ACCESS.2021.3052870
Alzheimer’s Disease Diagnosis Based on a Semantic Rule-Based Modeling and Reasoning Approach
Alzheimer’s Disease Diagnosis Based on a Semantic Rule-Based Modeling and Reasoning Approach
Nora Shoaip, Amira Rezk, Shaker EL-Sappagh, Tamer Abuhmed, Sherif Barakat, Mohammed Elmogy
Computers, Materials & Continua  ·  01 Jan 2021  ·  doi:10.32604/cmc.2021.019069
The Role of Medication Data to Enhance the Prediction of Alzheimer’s Progression Using Machine Learning
The Role of Medication Data to Enhance the Prediction of Alzheimer’s Progression Using Machine Learning
Shaker El-Sappagh, Tamer Abuhmed, Bader Alouffi, Radhya Sahal, Naglaa Abdelhade, Hager Saleh
Computational Intelligence and Neuroscience  ·  01 Jan 2021  ·  doi:10.1155/2021/8439655  ·  PMID: 34603436  ·  PMCID: PMC8481044
Timing and Classification of Patellofemoral Osteoarthritis Patients Using Fast Large Margin Classifier
Timing and Classification of Patellofemoral Osteoarthritis Patients Using Fast Large Margin Classifier
Mai Ramadan Ibraheem, Jilan adel, Alaa Eldin Balbaa, Shaker El-Sappagh, Tamer Abuhmed, Mohammed Elmogy
Computers, Materials & Continua  ·  01 Jan 2021  ·  doi:10.32604/cmc.2021.014446
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A Comprehensive Fuzzy Ontology-Based Decision Support System for Alzheimer’s Disease Diagnosis
A Comprehensive Fuzzy Ontology-Based Decision Support System for Alzheimer’s Disease Diagnosis
Nora Shoaip, Amira Rezk, Shaker El-Sappagh, Louai Alarabi, Sherif Barakat, Mohammed M. Elmogy
IEEE Access  ·  01 Jan 2021  ·  doi:10.1109/access.2020.3048435
An intelligent healthcare monitoring framework using wearable sensors and social networking data
An intelligent healthcare monitoring framework using wearable sensors and social networking data
Farman Ali, Shaker El-Sappagh, S.M. Riazul Islam, Amjad Ali, Muhammad Attique, Muhammad Imran, Kyung-Sup Kwak
Future Generation Computer Systems  ·  01 Jan 2021  ·  doi:10.1016/j.future.2020.07.047

2020

Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer
Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer
Justin Wang, Ingrid Vallee, Aditi Dutta, Yu Wang, Zhongying Mo, Ze Liu, Haissi Cui, Andrew I. Su, Xiang-Lei Yang
Genes  ·  22 Nov 2020  ·  doi:10.3390/genes11111384  ·  PMID: 33266490  ·  PMCID: PMC7700366
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A smart healthcare monitoring system for heart disease prediction based on ensemble deep learning and feature fusion
A smart healthcare monitoring system for heart disease prediction based on ensemble deep learning and feature fusion
Farman Ali, Shaker El-Sappagh, S.M. Riazul Islam, Daehan Kwak, Amjad Ali, Muhammad Imran, Kyung-Sup Kwak
Information Fusion  ·  01 Nov 2020  ·  doi:10.1016/j.inffus.2020.06.008
Contextual Identification of Windows Malware through Semantic Interpretation of API Call Sequence
Contextual Identification of Windows Malware through Semantic Interpretation of API Call Sequence
Eslam Amer, Shaker El-Sappagh, Jong Wan Hu
Applied Sciences  ·  30 Oct 2020  ·  doi:10.3390/app10217673
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Objective Diagnosis for Histopathological Images Based on Machine Learning Techniques: Classical Approaches and New Trends
Objective Diagnosis for Histopathological Images Based on Machine Learning Techniques: Classical Approaches and New Trends
Naira Elazab, Hassan Soliman, Shaker El-Sappagh, S. M. Riazul Islam, Mohammed Elmogy
Mathematics  ·  24 Oct 2020  ·  doi:10.3390/math8111863
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Multimodal multitask deep learning model for Alzheimer’s disease progression detection based on time series data
Multimodal multitask deep learning model for Alzheimer’s disease progression detection based on time series data
Shaker El-Sappagh, Tamer Abuhmed, S.M. Riazul Islam, Kyung Sup Kwak
Neurocomputing  ·  01 Oct 2020  ·  doi:10.1016/j.neucom.2020.05.087
Staging Melanocytic Skin Neoplasms Using High-Level Pixel-Based Features
Staging Melanocytic Skin Neoplasms Using High-Level Pixel-Based Features
Mai Ramadan Ibraheem, Shaker El-Sappagh, Tamer Abuhmed, Mohammed Elmogy
Electronics  ·  04 Sep 2020  ·  doi:10.3390/electronics9091443
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End-To-End Deep Learning Framework for Coronavirus (COVID-19) Detection and Monitoring
End-To-End Deep Learning Framework for Coronavirus (COVID-19) Detection and Monitoring
Nora El-Rashidy, Shaker El-Sappagh, S. M. Riazul Islam, Hazem M. El-Bakry, Samir Abdelrazek
Electronics  ·  03 Sep 2020  ·  doi:10.3390/electronics9091439
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Alzheimer Disease Prediction Model Based on Decision Fusion of CNN-BiLSTM Deep Neural Networks
Alzheimer Disease Prediction Model Based on Decision Fusion of CNN-BiLSTM Deep Neural Networks
Shaker El-Sappagh, Tamer Abuhmed, Kyung Sup Kwak
Advances in Intelligent Systems and Computing  ·  25 Aug 2020  ·  doi:10.1007/978-3-030-55190-2_36
Performance Analysis and Constellation Design for the Parallel Quadrature Spatial Modulation
Performance Analysis and Constellation Design for the Parallel Quadrature Spatial Modulation
Manar Mohaisen, Tasnim Holoubi, Tamer Abuhmed
Entropy  ·  30 Jul 2020  ·  doi:10.3390/e22080841  ·  PMID: 33286611  ·  PMCID: PMC7517441
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Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing
Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing
Laura Riva, Shuofeng Yuan, Xin Yin, Laura Martin-Sancho, Naoko Matsunaga, …, Andrew I. Su, Adolfo García-Sastre, Arnab K. Chatterjee, Kwok-Yung Yuen, Sumit K. Chanda
Nature  ·  24 Jul 2020  ·  doi:10.1038/s41586-020-2577-1  ·  PMID: 32707573  ·  PMCID: PMC7603405
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Multi-χ: Identifying Multiple Authors from Source Code Files
Multi-χ: Identifying Multiple Authors from Source Code Files
Mohammed Abuhamad, Tamer Abuhmed, DaeHun Nyang, David Mohaisen
Proceedings on Privacy Enhancing Technologies  ·  01 Jul 2020  ·  doi:10.2478/popets-2020-0044
A Semantic Approach for Extracting Medical Association Rules
A Semantic Approach for Extracting Medical Association Rules
Mohammed Thamer, Shaker El-Sappagh, Tarek El-Shishtawy
International Journal of Intelligent Engineering and Systems  ·  30 Jun 2020  ·  doi:10.22266/ijies2020.0630.26
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A Real-time Framework for Patient Monitoring Systems based on a Wireless Body Area Network
A Real-time Framework for Patient Monitoring Systems based on a Wireless Body Area Network
Nora Mahmoud, Shaker El-Sappagh, Samir M., Hazem M.
International Journal of Computer Applications  ·  18 Jun 2020  ·  doi:10.5120/ijca2020920274
AUTo<i>Sen</i>: Deep-Learning-Based Implicit Continuous Authentication Using Smartphone Sensors
AUToSen: Deep-Learning-Based Implicit Continuous Authentication Using Smartphone Sensors
Mohammed Abuhamad, Tamer Abuhmed, David Mohaisen, DaeHun Nyang
IEEE Internet of Things Journal  ·  01 Jun 2020  ·  doi:10.1109/JIOT.2020.2975779
Data validation and schema interoperability
Data validation and schema interoperability
Leyla Jael Castro, Jerven Bolleman, michel dumontier, Simon Jupp, Jose Emilio Labra-Gayo, Thomas Liener, Tazro Ohta, Núria Queralt-Rosinach, Chunlei Wu
Center for Open Science  ·  07 Apr 2020  ·  doi:10.37044/osf.io/8qdse
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Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas
Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas
Kim M. Summers, Stephen J. Bush, Chunlei Wu, Andrew I. Su, Charity Muriuki, …, Lel Eory, Lindsey A. Waddell, Richard Talbot, Alan L. Archibald, David A. Hume
Frontiers in Genetics  ·  14 Feb 2020  ·  doi:10.3389/fgene.2019.01355  ·  PMID: 32117413  ·  PMCID: PMC7034361
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Intensive Care Unit Mortality Prediction: An Improved Patient-Specific Stacking Ensemble Model
Intensive Care Unit Mortality Prediction: An Improved Patient-Specific Stacking Ensemble Model
Nora El-Rashidy, Shaker El-Sappagh, Tamer Abuhmed, Samir Abdelrazek, Hazem M. El-Bakry
IEEE Access  ·  01 Jan 2020  ·  doi:10.1109/ACCESS.2020.3010556
Medical Diagnostic Systems Using Artificial Intelligence (AI) Algorithms: Principles and Perspectives
Medical Diagnostic Systems Using Artificial Intelligence (AI) Algorithms: Principles and Perspectives
Simarjeet Kaur, Jimmy Singla, Lewis Nkenyereye, Sudan Jha, Deepak Prashar, Gyanendra Prasad Joshi, Shaker El-Sappagh, Md. Saiful Islam, S. M. Riazul Islam
IEEE Access  ·  01 Jan 2020  ·  doi:10.1109/access.2020.3042273
Intensive Care Unit Mortality Prediction: An Improved Patient-Specific Stacking Ensemble Model
Intensive Care Unit Mortality Prediction: An Improved Patient-Specific Stacking Ensemble Model
Nora El-Rashidy, Shaker El-Sappagh, Tamer Abuhmed, Samir Abdelrazek, Hazem M. El-Bakry
IEEE Access  ·  01 Jan 2020  ·  doi:10.1109/access.2020.3010556
Advancing Modern Healthcare With Nanotechnology, Nanobiosensors, and Internet of Nano Things: Taxonomies, Applications, Architecture, and Challenges
Advancing Modern Healthcare With Nanotechnology, Nanobiosensors, and Internet of Nano Things: Taxonomies, Applications, Architecture, and Challenges
Pijush Kanti Dutta Pramanik, Arun Solanki, Abhinaba Debnath, Anand Nayyar, Shaker El-Sappagh, Kyung-Sup Kwak
IEEE Access  ·  01 Jan 2020  ·  doi:10.1109/access.2020.2984269
A semantic interoperability framework for distributed electronic health record based on fuzzy ontology
A semantic interoperability framework for distributed electronic health record based on fuzzy ontology
Ebtsam Adel, Shaker El Sappagh, Sherif Barakat, Mohammed Elmogy
International Journal of Medical Engineering and Informatics  ·  01 Jan 2020  ·  doi:10.1504/ijmei.2020.107081
A framework for disease diagnosis based on fuzzy semantic ontology approach
A framework for disease diagnosis based on fuzzy semantic ontology approach
Nora Shoaip, Shaker El Sappagh, Sherif Barakat, Mohammed Elmogy
International Journal of Medical Engineering and Informatics  ·  01 Jan 2020  ·  doi:10.1504/ijmei.2020.109942
A Three-Step Authentication Model for Mobile Phone User Using Keystroke Dynamics
A Three-Step Authentication Model for Mobile Phone User Using Keystroke Dynamics
Baljit Singh Saini, Parminder Singh, Anand Nayyar, Navdeep Kaur, Kamaljit Singh Bhatia, Shaker El-Sappagh, Jong-Wan Hu
IEEE Access  ·  01 Jan 2020  ·  doi:10.1109/access.2020.3008019
A Proposed Frequent Itemset Discovery Algorithm Based on Item Weights and Uncertainty
A Proposed Frequent Itemset Discovery Algorithm Based on Item Weights and Uncertainty
Hanaa Ibrahim Abu Zahra, Shaker El-Sappagh, Tarek Ahmef El Shishtawy
International Journal of Sociotechnology and Knowledge Development  ·  01 Jan 2020  ·  doi:10.4018/ijskd.2020010106
Quality of Service Provisioning for Heterogeneous Services in Cognitive Radio-Enabled Internet of Things
Quality of Service Provisioning for Heterogeneous Services in Cognitive Radio-Enabled Internet of Things
Amjad Ali, Li Feng, Ali Kashif Bashir, Shaker El-Sappagh, Syed Hassan Ahmed, Muddesar Iqbal, Gunasekaran Raja
IEEE Transactions on Network Science and Engineering  ·  01 Jan 2020  ·  doi:10.1109/tnse.2018.2877646
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2019

Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network
Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network
Michael Mayers, Tong Shu Li, Núria Queralt-Rosinach, Andrew I. Su
BMC Bioinformatics  ·  01 Dec 2019  ·  doi:10.1186/s12859-019-3297-0  ·  PMID: 31829175  ·  PMCID: PMC6907279
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Advancing computational biology and bioinformatics research through open innovation competitions
Advancing computational biology and bioinformatics research through open innovation competitions
Andrea Blasco, Michael G. Endres, Rinat A. Sergeev, Anup Jonchhe, N. J. Maximilian Macaluso, …, Bryan Briney, Chunlei Wu, Andrew I. Su, Aravind Subramanian, Karim R. Lakhani
PLOS ONE  ·  27 Sep 2019  ·  doi:10.1371/journal.pone.0222165  ·  PMID: 31560691  ·  PMCID: PMC6764653
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Benchmarking large-scale data management for Internet of Things
Benchmarking large-scale data management for Internet of Things
Abdeltawab Hendawi, Jayant Gupta, Jiayi Liu, Ankur Teredesai, Naveen Ramakrishnan, Mohak Shah, Shaker El-Sappagh, Kyung-Sup Kwak, Mohamed Ali
The Journal of Supercomputing  ·  10 Sep 2019  ·  doi:10.1007/s11227-019-02984-6
Position β57 of I-A <sup>g7</sup> controls early anti-insulin responses in NOD mice, linking an MHC susceptibility allele to type 1 diabetes onset
Position β57 of I-A g7 controls early anti-insulin responses in NOD mice, linking an MHC susceptibility allele to type 1 diabetes onset
Louis Gioia, Marie Holt, Anne Costanzo, Siddhartha Sharma, Brian Abe, …, Andrew Su, Clayton Mathews, Yi-Guang Chen, Emil Unanue, Luc Teyton
Science Immunology  ·  02 Aug 2019  ·  doi:10.1126/sciimmunol.aaw6329  ·  PMID: 31471352  ·  PMCID: PMC6816460
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A Comprehensive Medical Decision–Support Framework Based on a Heterogeneous Ensemble Classifier for Diabetes Prediction
A Comprehensive Medical Decision–Support Framework Based on a Heterogeneous Ensemble Classifier for Diabetes Prediction
Shaker El-Sappagh, Mohammed Elmogy, Farman Ali, Tamer ABUHMED, S. M. Riazul Islam, Kyung-Sup Kwak
Electronics  ·  05 Jun 2019  ·  doi:10.3390/electronics8060635
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Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements.
Aligning Needs: Integrating Citizen Science Efforts into Schools Through Service Requirements.
Ginger Tsueng, Arun Kumar, Steven Max Nanis, Andrew I Su
Human Computation  ·  02 Jun 2019  ·  doi:10.15346/hc.v6i1.4
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Code authorship identification using convolutional neural networks
Code authorship identification using convolutional neural networks
Mohammed Abuhamad, Ji-su Rhim, Tamer AbuHmed, Sana Ullah, Sanggil Kang, DaeHun Nyang
Future Generation Computer Systems  ·  01 Jun 2019  ·  doi:10.1016/j.future.2018.12.038
Transportation sentiment analysis using word embedding and ontology-based topic modeling
Transportation sentiment analysis using word embedding and ontology-based topic modeling
Farman Ali, Daehan Kwak, Pervez Khan, Shaker El-Sappagh, Amjad Ali, Sana Ullah, Kye Hyun Kim, Kyung-Sup Kwak
Knowledge-Based Systems  ·  01 Jun 2019  ·  doi:10.1016/j.knosys.2019.02.033
A mobile health monitoring-and-treatment system based on integration of the SSN sensor ontology and the HL7 FHIR standard
A mobile health monitoring-and-treatment system based on integration of the SSN sensor ontology and the HL7 FHIR standard
Shaker El-Sappagh, Farman Ali, Abdeltawab Hendawi, Jun-Hyeog Jang, Kyung-Sup Kwak
BMC Medical Informatics and Decision Making  ·  10 May 2019  ·  doi:10.1186/s12911-019-0806-z  ·  PMID: 31077222  ·  PMCID: PMC6511155
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Applying Citizen Science to Gene, Drug, Disease Relationship Extraction from Biomedical Abstracts
Applying Citizen Science to Gene, Drug, Disease Relationship Extraction from Biomedical Abstracts
Ginger Tsueng, Max Nanis, Jennifer T. Fouquier, Michael Mayers, Benjamin M. Good, Andrew I Su
Cold Spring Harbor Laboratory  ·  28 Feb 2019  ·  doi:10.1101/564187
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Fuzzy Ontology and LSTM-Based Text Mining: A Transportation Network Monitoring System for Assisting Travel
Fuzzy Ontology and LSTM-Based Text Mining: A Transportation Network Monitoring System for Assisting Travel
Farman Ali, Shaker El-Sappagh, Daehan Kwak
Sensors  ·  09 Jan 2019  ·  doi:10.3390/s19020234  ·  PMID: 30634527  ·  PMCID: PMC6358771
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Reasoning methodologies in clinical decision support systems: A literature review
Reasoning methodologies in clinical decision support systems: A literature review
Nora Shoaip, Shaker El-Sappagh, Sherif Barakat, Mohammed Elmogy
U-Healthcare Monitoring Systems  ·  01 Jan 2019  ·  doi:10.1016/b978-0-12-815370-3.00004-9
Ontology-based electronic health record semantic interoperability: A survey
Ontology-based electronic health record semantic interoperability: A survey
Ebtsam Adel, Shaker El-Sappagh, Sherif Barakat, Mohammed Elmogy
U-Healthcare Monitoring Systems  ·  01 Jan 2019  ·  doi:10.1016/b978-0-12-815370-3.00013-x
Ontology enhanced fuzzy clinical decision support system
Ontology enhanced fuzzy clinical decision support system
Nora Shoaip, Shaker El-Sappagh, Sherif Barakat, Mohammed Elmogy
U-Healthcare Monitoring Systems  ·  01 Jan 2019  ·  doi:10.1016/b978-0-12-815370-3.00007-4
Mobile Health Technologies for Diabetes Mellitus: Current State and Future Challenges
Mobile Health Technologies for Diabetes Mellitus: Current State and Future Challenges
Shaker El-Sappagh, Farman Ali, Samir El-Masri, Kyehyun Kim, Amjad Ali, Kyung-Sup Kwak
IEEE Access  ·  01 Jan 2019  ·  doi:10.1109/access.2018.2881001
A unified fuzzy ontology for distributed electronic health record semantic interoperability
A unified fuzzy ontology for distributed electronic health record semantic interoperability
Ebtsam Adel, Shaker El-Sappagh, Sherif Barakat, Mohammed Elmogy
U-Healthcare Monitoring Systems  ·  01 Jan 2019  ·  doi:10.1016/b978-0-12-815370-3.00014-1
A Fuzzy Ontological Infrastructure for Semantic Interoperability in Distributed Electronic Health Record
A Fuzzy Ontological Infrastructure for Semantic Interoperability in Distributed Electronic Health Record
Ebtsam Adel, Shaker El-sappagh, Mohammed Elmogy, Sherif Barakat, Kyung-Sup Kwak
Intelligent Automation and Soft Computing  ·  01 Jan 2019  ·  doi:10.31209/2019.100000151

2018

A Fibrosis Diagnosis Clinical Decision Support System Using Fuzzy Knowledge
A Fibrosis Diagnosis Clinical Decision Support System Using Fuzzy Knowledge
Sara Sweidan, Shaker El-Sappagh, Hazem El-Bakry, Sahar Sabbeh, Farid A. Badria, Kyung-Sup Kwak
Arabian Journal for Science and Engineering  ·  13 Dec 2018  ·  doi:10.1007/s13369-018-3670-8
Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges
Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges
Siddhartha Sharma, Louis Gioia, Brian Abe, Marie Holt, Anne Costanzo, Lisa Kain, Andrew Su, Luc Teyton
Molecular Immunology  ·  01 Nov 2018  ·  doi:10.1016/j.molimm.2018.09.020  ·  PMID: 30300798  ·  PMCID: PMC6258053
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Association study of long-term kidney transplant rejection using whole-exome sequencing
Association study of long-term kidney transplant rejection using whole-exome sequencing
Louis Gioia, Sunil Kurian, Tony S. Mondala, Laia Bassaganyas, Pui-Yan Kwok, Daniel R. Salomon, Andrew I. Su
Cold Spring Harbor Laboratory  ·  16 Oct 2018  ·  doi:10.1101/444497
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Large-Scale and Language-Oblivious Code Authorship Identification
Large-Scale and Language-Oblivious Code Authorship Identification
Mohammed Abuhamad, Tamer AbuHmed, Aziz Mohaisen, DaeHun Nyang
Proceedings of the 2018 ACM SIGSAC Conference on Computer and Communications Security  ·  15 Oct 2018  ·  doi:10.1145/3243734.3243738
Feature-based Transportation Sentiment Analysis Using Fuzzy Ontology and SentiWordNet
Feature-based Transportation Sentiment Analysis Using Fuzzy Ontology and SentiWordNet
Farman Ali, Shaker EI-Sappagh, Pervez Khan, Kyung-Sup Kwak
2018 International Conference on Information and Communication Technology Convergence (ICTC)  ·  01 Oct 2018  ·  doi:10.1109/ictc.2018.8539607
Priority-Based Cloud Computing Architecture for Multimedia-Enabled Heterogeneous Vehicular Users
Priority-Based Cloud Computing Architecture for Multimedia-Enabled Heterogeneous Vehicular Users
Amjad Ali, Hongwu Liu, Ali Kashif Bashir, Shaker El-Sappagh, Farman Ali, Adeel Baig, Daeyoung Park, Kyung Sup Kwak
Journal of Advanced Transportation  ·  27 Sep 2018  ·  doi:10.1155/2018/6235379
The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app
The Healthy Pregnancy Research Program: transforming pregnancy research through a ResearchKit app
Jennifer M. Radin, Steven R. Steinhubl, Andrew I. Su, Hansa Bhargava, Benjamin Greenberg, Brian M. Bot, Megan Doerr, Eric J. Topol
npj Digital Medicine  ·  05 Sep 2018  ·  doi:10.1038/s41746-018-0052-2  ·  PMID: 31304325  ·  PMCID: PMC6550256
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SNOMED CT standard ontology based on the ontology for general medical science
SNOMED CT standard ontology based on the ontology for general medical science
Shaker El-Sappagh, Francesco Franda, Farman Ali, Kyung-Sup Kwak
BMC Medical Informatics and Decision Making  ·  31 Aug 2018  ·  doi:10.1186/s12911-018-0651-5  ·  PMID: 30170591  ·  PMCID: PMC6119323
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Triflic acid treatment enables LC-MS/MS analysis of insoluble bacterial biomass
Triflic acid treatment enables LC-MS/MS analysis of insoluble bacterial biomass
Ana Y. Wang, Peter S. Thuy-Boun, Gregory S. Stupp, Andrew I. Su, Dennis W. Wolan
Cold Spring Harbor Laboratory  ·  11 Jul 2018  ·  doi:10.1101/367599
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A case-base fuzzification process: diabetes diagnosis case study
A case-base fuzzification process: diabetes diagnosis case study
Shaker El-Sappagh, Mohammed Elmogy, Farman Ali, Kyung-Sup Kwak
Soft Computing  ·  30 May 2018  ·  doi:10.1007/s00500-018-3245-3
A genome-wide survey of mutations in the Jurkat cell line
A genome-wide survey of mutations in the Jurkat cell line
Louis Gioia, Azeem Siddique, Steven R. Head, Daniel R. Salomon, Andrew I. Su
BMC Genomics  ·  08 May 2018  ·  doi:10.1186/s12864-018-4718-6  ·  PMID: 29739316  ·  PMCID: PMC5941560
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Biocuration: Distilling data into knowledge
Biocuration: Distilling data into knowledge
PLOS Biology  ·  16 Apr 2018  ·  doi:10.1371/journal.pbio.2002846  ·  PMID: 29659566  ·  PMCID: PMC5919672
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A framework for chronic kidney disease diagnosis based on case based reasoning
A framework for chronic kidney disease diagnosis based on case based reasoning
Seham Abd Elkader, Mohammed Elmogy, Shaker El-Sappagh, Abde Nasser H. Zaied
International Journal of Advanced Computer Research  ·  26 Mar 2018  ·  doi:10.19101/ijacr.2018.834003
DMTO: a realistic ontology for standard diabetes mellitus treatment
DMTO: a realistic ontology for standard diabetes mellitus treatment
Shaker El-Sappagh, Daehan Kwak, Farman Ali, Kyung-Sup Kwak
Journal of Biomedical Semantics  ·  06 Feb 2018  ·  doi:10.1186/s13326-018-0176-y  ·  PMID: 29409535  ·  PMCID: PMC5800094
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Metaproteomics of Colonic Microbiota Unveils Discrete Protein Functions among Colitic Mice and Control Groups
Metaproteomics of Colonic Microbiota Unveils Discrete Protein Functions among Colitic Mice and Control Groups
Clara Moon, Gregory S. Stupp, Andrew I. Su, Dennis W. Wolan
PROTEOMICS  ·  01 Feb 2018  ·  doi:10.1002/pmic.201700391  ·  PMID: 29319931  ·  PMCID: PMC5921860
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Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration
Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara, Ginger Tsueng, Andrew I. Su, Chunlei Wu
BMC Bioinformatics  ·  01 Feb 2018  ·  doi:10.1186/s12859-018-2041-5  ·  PMID: 29390967  ·  PMCID: PMC5796402
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Clinical Decision Support System for Liver Fibrosis Prediction in Hepatitis Patients: A Case Comparison of Two Soft Computing Techniques
Clinical Decision Support System for Liver Fibrosis Prediction in Hepatitis Patients: A Case Comparison of Two Soft Computing Techniques
Shaker El-Sappagh, Farman Ali, Amjad Ali, Abdeltawab Hendawi, Farid A. Badria, Doug Young Suh
IEEE Access  ·  01 Jan 2018  ·  doi:10.1109/access.2018.2868802
An Ontology-Based Interpretable Fuzzy Decision Support System for Diabetes Diagnosis
An Ontology-Based Interpretable Fuzzy Decision Support System for Diabetes Diagnosis
Shaker El-Sappagh, Jose M. Alonso, Farman Ali, Amjad Ali, Jun-Hyeog Jang, Kyung-Sup Kwak
IEEE Access  ·  01 Jan 2018  ·  doi:10.1109/access.2018.2852004

2017

Distributed electronic health record based on semantic interoperability using fuzzy ontology: a survey
Distributed electronic health record based on semantic interoperability using fuzzy ontology: a survey
Ebtsam Adel, Shaker El-Sappagh, Sherif Barakat, Mohammed Elmogy
International Journal of Computers and Applications  ·  28 Dec 2017  ·  doi:10.1080/1206212x.2017.1418237
A high resolution atlas of gene expression in the domestic sheep (Ovis aries)
A high resolution atlas of gene expression in the domestic sheep (Ovis aries)
Emily L. Clark, Stephen J. Bush, Mary E. B. McCulloch, Iseabail L. Farquhar, Rachel Young, …, C. Bruce Whitelaw, Tom C. Freeman, Kim M. Summers, Alan L. Archibald, David A. Hume
PLOS Genetics  ·  15 Sep 2017  ·  doi:10.1371/journal.pgen.1006997  ·  PMID: 28915238  ·  PMCID: PMC5626511
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Academics can help shape Wikipedia
Academics can help shape Wikipedia
Thomas Shafee, Daniel Mietchen, Andrew I. Su
Science  ·  11 Aug 2017  ·  doi:10.1126/science.aao0462  ·  PMID: 28798122
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Science Game Lab: tool for the unification of biomedical games with a purpose
Science Game Lab: tool for the unification of biomedical games with a purpose
Benjamin M. Good, Sarah Santini, Margaret Wallace, Nicholas Fortugno, John Szeder, Patrick Mooney, Jerome Waldispuhl, Ginger Tsueng, Andrew I Su
Cold Spring Harbor Laboratory  ·  10 Jul 2017  ·  doi:10.1101/156141
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Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes
Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes
R. Akagi, Y. Akatsu, K.M. Fisch, O. Alvarez-Garcia, T. Teramura, Y. Muramatsu, M. Saito, T. Sasho, A.I. Su, M.K. Lotz
Osteoarthritis and Cartilage  ·  01 Jun 2017  ·  doi:10.1016/j.joca.2016.11.007  ·  PMID: 27884645  ·  PMCID: PMC5438901
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A fuzzy ontology modeling for case base knowledge in diabetes mellitus domain
A fuzzy ontology modeling for case base knowledge in diabetes mellitus domain
Shaker El-Sappagh, Mohammed Elmogy
Engineering Science and Technology, an International Journal  ·  01 Jun 2017  ·  doi:10.1016/j.jestch.2017.03.009
EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices
EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices
Nikhil Gopal, Andrew Su, Chunlei Wu, Sean D. Mooney
Cold Spring Harbor Laboratory  ·  29 Mar 2017  ·  doi:10.1101/121178
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Effects of diluents on cell culture viability measured by automated cell counter
Effects of diluents on cell culture viability measured by automated cell counter
Aaron Chen, Matthew Leith, Roger Tu, Gurpreet Tahim, Anish Sudra, Swapnil Bhargava
PLOS ONE  ·  06 Mar 2017  ·  doi:10.1371/journal.pone.0173375  ·  PMID: 28264018  ·  PMCID: PMC5338812
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Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease
Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease
Michael D. Mayers, Clara Moon, Gregory S. Stupp, Andrew I. Su, Dennis W. Wolan
Journal of Proteome Research  ·  23 Jan 2017  ·  doi:10.1021/acs.jproteome.6b00938  ·  PMID: 28052195  ·  PMCID: PMC5441882
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A Fuzzy Ontology and SVM–Based Web Content Classification System
A Fuzzy Ontology and SVM–Based Web Content Classification System
Farman Ali, Pervez Khan, Kashif Riaz, Daehan Kwak, Tamer Abuhmed, Daeyoung Park, Kyung Sup Kwak
IEEE Access  ·  01 Jan 2017  ·  doi:10.1109/access.2017.2768564
Merged Ontology and SVM-Based Information Extraction and Recommendation System for Social Robots
Merged Ontology and SVM-Based Information Extraction and Recommendation System for Social Robots
Farman Ali, Daehan Kwak, Pervez Khan, Shaker Hassan A. Ei-Sappagh, S. M. Riazul Islam, Daeyoung Park, Kyung-Sup Kwak
IEEE Access  ·  01 Jan 2017  ·  doi:10.1109/access.2017.2718038

2016

Citizen Science for Mining the Biomedical Literature
Citizen Science for Mining the Biomedical Literature
Ginger Tsueng, Steven M. Nanis, Jennifer Fouquier, Benjamin M. Good, Andrew I. Su
Citizen Science: Theory and Practice  ·  31 Dec 2016  ·  doi:10.5334/cstp.56  ·  PMID: 30416754  ·  PMCID: PMC6226017
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Gene Wiki Reviews—Raising the quality and accessibility of information about the human genome
Gene Wiki Reviews—Raising the quality and accessibility of information about the human genome
Ginger Tsueng, Benjamin M. Good, Peipei Ping, Erica Golemis, Israel Hanukoglu, Andre J. van Wijnen, Andrew I. Su
Gene  ·  01 Nov 2016  ·  doi:10.1016/j.gene.2016.04.053  ·  PMID: 27150585  ·  PMCID: PMC5944608
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Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy
Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy
O. Alvarez-Garcia, M. Olmer, R. Akagi, Y. Akasaki, K.M. Fisch, T. Shen, A.I. Su, M.K. Lotz
Osteoarthritis and Cartilage  ·  01 Sep 2016  ·  doi:10.1016/j.joca.2016.04.015  ·  PMID: 27118398  ·  PMCID: PMC4992644
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A comprehensive and scalable database search system for metaproteomics
A comprehensive and scalable database search system for metaproteomics
Sandip Chatterjee, Gregory S. Stupp, Sung Kyu Robin Park, Jean-Christophe Ducom, John R. Yates, Andrew I. Su, Dennis W. Wolan
BMC Genomics  ·  16 Aug 2016  ·  doi:10.1186/s12864-016-2855-3  ·  PMID: 27528457  ·  PMCID: PMC4986259
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Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems
Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems
Maggie P. Y. Lam, Vidya Venkatraman, Yi Xing, Edward Lau, Quan Cao, Dominic C. M. Ng, Andrew I. Su, Junbo Ge, Jennifer E. Van Eyk, Peipei Ping
Journal of Proteome Research  ·  19 Jul 2016  ·  doi:10.1021/acs.jproteome.6b00095  ·  PMID: 27356587  ·  PMCID: PMC5120959
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Medical Case Based Reasoning Frameworks
Medical Case Based Reasoning Frameworks
Shaker El-Sappagh, Mohammed Mahfouz Elmogy
International Journal of Decision Support System Technology  ·  01 Jul 2016  ·  doi:10.4018/ijdsst.2016070103
An encoding methodology for medical knowledge using SNOMED CT ontology
An encoding methodology for medical knowledge using SNOMED CT ontology
Shaker El-Sappagh, Mohammed Elmogy
Journal of King Saud University - Computer and Information Sciences  ·  01 Jul 2016  ·  doi:10.1016/j.jksuci.2015.10.002
High-performance web services for querying gene and variant annotation
High-performance web services for querying gene and variant annotation
Jiwen Xin, Adam Mark, Cyrus Afrasiabi, Ginger Tsueng, Moritz Juchler, …, Patricia L. Whetzel, Christopher J. Mungall, Sean D. Mooney, Andrew I. Su, Chunlei Wu
Genome Biology  ·  06 May 2016  ·  doi:10.1186/s13059-016-0953-9  ·  PMID: 27154141  ·  PMCID: PMC4858870
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Extending gene ontology in the context of extracellular RNA and vesicle communication
Extending gene ontology in the context of extracellular RNA and vesicle communication
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, …, Kasey Vickers, Marca H.M. Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C. Laurent
Journal of Biomedical Semantics  ·  12 Apr 2016  ·  doi:10.1186/s13326-016-0061-5  ·  PMID: 27076901  ·  PMCID: PMC4830068
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Nanotextured Shrink Wrap Superhydrophobic Surfaces by Argon Plasma Etching
Nanotextured Shrink Wrap Superhydrophobic Surfaces by Argon Plasma Etching
Jolie Nokes, Himanshu Sharma, Roger Tu, Monica Kim, Michael Chu, Ali Siddiqui, Michelle Khine
Materials  ·  14 Mar 2016  ·  doi:10.3390/ma9030196  ·  PMID: 28773318  ·  PMCID: PMC5456652
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The Implicitome: A Resource for Rationalizing Gene-Disease Associations
The Implicitome: A Resource for Rationalizing Gene-Disease Associations
Kristina M. Hettne, Mark Thompson, Herman H. H. B. M. van Haagen, Eelke van der Horst, Rajaram Kaliyaperumal, …, Gert-Jan B. van Ommen, Marco Roos, Peter A.C. ‘t Hoen, Barend Mons, Erik A. Schultes
PLOS ONE  ·  26 Feb 2016  ·  doi:10.1371/journal.pone.0149621  ·  PMID: 26919047  ·  PMCID: PMC4769089
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Citizen Science for Mining the Biomedical Literature
Citizen Science for Mining the Biomedical Literature
Ginger Tsueng, Steven M. Nanis, Jennifer Fouquier, Benjamin M Good, Andrew I Su
Cold Spring Harbor Laboratory  ·  27 Jan 2016  ·  doi:10.1101/038083
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2015

MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services
MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services
Jiwen Xin, Adam Mark, Cyrus Afrasiabi, Ginger Tsueng, Moritz Juchler, …, Patricia L. Whetzel, Christopher J. Mungall, Sean D. Mooney, Andrew I. Su, Chunlei Wu
Cold Spring Harbor Laboratory  ·  30 Dec 2015  ·  doi:10.1101/035667
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UOIT Keyboard: A Constructive Keyboard for Small Touchscreen Devices
UOIT Keyboard: A Constructive Keyboard for Small Touchscreen Devices
Tamer AbuHmed, Kyunghee Lee, DaeHun Nyang
IEEE Transactions on Human-Machine Systems  ·  01 Dec 2015  ·  doi:10.1109/thms.2015.2449309
A fuzzy-ontology-oriented case-based reasoning framework for semantic diabetes diagnosis
A fuzzy-ontology-oriented case-based reasoning framework for semantic diabetes diagnosis
Shaker El-Sappagh, Mohammed Elmogy, A.M. Riad
Artificial Intelligence in Medicine  ·  01 Nov 2015  ·  doi:10.1016/j.artmed.2015.08.003  ·  PMID: 26303105
OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
Tobias Meißner, Kathleen M Fisch, Louis Gioia, Andrew I Su
BMC Medical Genomics  ·  21 May 2015  ·  doi:10.1186/s12920-015-0095-z  ·  PMID: 25989980  ·  PMCID: PMC4494802
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The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors
The nicotinic α6 subunit gene determines variability in chronic pain sensitivity via cross-inhibition of P2X2/3 receptors
Jeffrey S. Wieskopf, Jayanti Mathur, Walrati Limapichat, Michael R. Post, Mona Al-Qazzaz, …, Sarah C. R. Lummis, M. Imad Damaj, Henry A. Lester, Ardem Patapoutian, Jeffrey S. Mogil
Science Translational Medicine  ·  13 May 2015  ·  doi:10.1126/scitranslmed.3009986  ·  PMID: 25972004  ·  PMCID: PMC5018401
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A CBR system for diabetes mellitus diagnosis: case-base standard data model
A CBR system for diabetes mellitus diagnosis: case-base standard data model
Shaker El Sappagh, Mohammed Elmogy, Alaa Eldin M. Riad
International Journal of Medical Engineering and Informatics  ·  01 Jan 2015  ·  doi:10.1504/ijmei.2015.070116

2014

A standard fragment of EHR relational data model for diabetes mellitus diagnosis
A standard fragment of EHR relational data model for diabetes mellitus diagnosis
Shaker El-Sappagh, Mohammed El Mogy, Alaa M. Riad
2014 9th International Conference on Informatics and Systems  ·  01 Dec 2014  ·  doi:10.1109/infos.2014.7036701
A proposed SNOMED CT ontology-based encoding methodology for diabetes diagnosis case-base
A proposed SNOMED CT ontology-based encoding methodology for diabetes diagnosis case-base
Shaker El-Sappagh, Mohammed Elmogy, A. M. Riad, Hosam Zaghloul, Farid Badria
2014 9th International Conference on Computer Engineering & Systems (ICCES)  ·  01 Dec 2014  ·  doi:10.1109/icces.2014.7030954
MICROTASK CROWDSOURCING FOR DISEASE MENTION ANNOTATION IN PUBMED ABSTRACTS
MICROTASK CROWDSOURCING FOR DISEASE MENTION ANNOTATION IN PUBMED ABSTRACTS
BENJAMIN M GOOD, MAX NANIS, CHUNLEI WU, ANDREW I SU
Biocomputing 2015  ·  01 Nov 2014  ·  doi:10.1142/9789814644730_0028
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MyGene.info: gene annotation query as a service
MyGene.info: gene annotation query as a service
Chunlei Wu, Adam Mark, Andrew I. Su
Cold Spring Harbor Laboratory  ·  18 Sep 2014  ·  doi:10.1101/009332
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Organizing knowledge to enable personalization of medicine in cancer
Organizing knowledge to enable personalization of medicine in cancer
Benjamin M Good, Benjamin J Ainscough, Josh F McMichael, Andrew I Su, Obi L Griffith
Genome Biology  ·  27 Aug 2014  ·  doi:10.1186/s13059-014-0438-7  ·  PMID: 25222080  ·  PMCID: PMC4281950
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Functional expression of dental plaque microbiota
Functional expression of dental plaque microbiota
Scott N. Peterson, Tobias Meissner, Andrew I. Su, Erik Snesrud, Ana C. Ong, Nicholas J. Schork, Walter A. Bretz
Frontiers in Cellular and Infection Microbiology  ·  14 Aug 2014  ·  doi:10.3389/fcimb.2014.00108  ·  PMID: 25177549  ·  PMCID: PMC4132376
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The Cure: Design and Evaluation of a Crowdsourcing Game for Gene Selection for Breast Cancer Survival Prediction
The Cure: Design and Evaluation of a Crowdsourcing Game for Gene Selection for Breast Cancer Survival Prediction
Benjamin M Good, Salvatore Loguercio, Obi L Griffith, Max Nanis, Chunlei Wu, Andrew I Su
JMIR Serious Games  ·  29 Jul 2014  ·  doi:10.2196/games.3350  ·  PMID: 25654473  ·  PMCID: PMC4307816
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An Ontological Case Base Engineering Methodology for Diabetes Management
An Ontological Case Base Engineering Methodology for Diabetes Management
Shaker H. El-Sappagh, Samir El-Masri, Mohammed Elmogy, A. M. Riad, Basema Saddik
Journal of Medical Systems  ·  24 Jun 2014  ·  doi:10.1007/s10916-014-0067-4  ·  PMID: 24957391
Coxsackievirus B Exits the Host Cell in Shed Microvesicles Displaying Autophagosomal Markers
Coxsackievirus B Exits the Host Cell in Shed Microvesicles Displaying Autophagosomal Markers
Scott M. Robinson, Ginger Tsueng, Jon Sin, Vrushali Mangale, Shahad Rahawi, …, Roland Wolkowicz, Christopher T. Cornell, J. Lindsay Whitton, Roberta A. Gottlieb, Ralph Feuer
PLoS Pathogens  ·  10 Apr 2014  ·  doi:10.1371/journal.ppat.1004045  ·  PMID: 24722773  ·  PMCID: PMC3983045
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Integrated platform for functional monitoring of biomimetic heart sheets derived from human pluripotent stem cells
Integrated platform for functional monitoring of biomimetic heart sheets derived from human pluripotent stem cells
Aaron Chen, Eugene Lee, Roger Tu, Kevin Santiago, Anna Grosberg, Charless Fowlkes, Michelle Khine
Biomaterials  ·  01 Jan 2014  ·  doi:10.1016/j.biomaterials.2013.10.007  ·  PMID: 24144905  ·  PMCID: PMC9300448
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EHR Data Preparation for Case Based Reasoning Construction
EHR Data Preparation for Case Based Reasoning Construction
Shaker El-Sappagh, Mohammed Elmogy, A. M. Riad, Hosam Zaghlol, Farid A. Badria
Communications in Computer and Information Science  ·  01 Jan 2014  ·  doi:10.1007/978-3-319-13461-1_45
A distributed clinical decision support system architecture
A distributed clinical decision support system architecture
Shaker H. El-Sappagh, Samir El-Masri
Journal of King Saud University - Computer and Information Sciences  ·  01 Jan 2014  ·  doi:10.1016/j.jksuci.2013.03.005

2013

Ten Simple Rules for Cultivating Open Science and Collaborative R&D
Ten Simple Rules for Cultivating Open Science and Collaborative R&D
Hassan Masum, Aarthi Rao, Benjamin M. Good, Matthew H. Todd, Aled M. Edwards, Leslie Chan, Barry A. Bunin, Andrew I. Su, Zakir Thomas, Philip E. Bourne
PLoS Computational Biology  ·  26 Sep 2013  ·  doi:10.1371/journal.pcbi.1003244  ·  PMID: 24086123  ·  PMCID: PMC3784487
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Deep Sequencing of the Murine <i>Igh</i> Repertoire Reveals Complex Regulation of Nonrandom V Gene Rearrangement Frequencies
Deep Sequencing of the Murine Igh Repertoire Reveals Complex Regulation of Nonrandom V Gene Rearrangement Frequencies
Nancy M Choi, Salvatore Loguercio, Jiyoti Verma-Gaur, Stephanie C Degner, Ali Torkamani, Andrew I Su, Eugene M Oltz, Maxim Artyomov, Ann J Feeney
The Journal of Immunology  ·  01 Sep 2013  ·  doi:10.4049/jimmunol.1301279  ·  PMID: 23898036  ·  PMCID: PMC3778908
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Identification of Regulatory Elements That Control PPARγ Expression in Adipocyte Progenitors
Identification of Regulatory Elements That Control PPARγ Expression in Adipocyte Progenitors
Wen-Ling Chou, Andrea Galmozzi, David Partida, Kevin Kwan, Hui Yeung, Andrew I. Su, Enrique Saez
PLoS ONE  ·  29 Aug 2013  ·  doi:10.1371/journal.pone.0072511  ·  PMID: 24009687  ·  PMCID: PMC3757023
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Dizeez: An Online Game for Human Gene-Disease Annotation
Dizeez: An Online Game for Human Gene-Disease Annotation
Salvatore Loguercio, Benjamin M. Good, Andrew I. Su
PLoS ONE  ·  07 Aug 2013  ·  doi:10.1371/journal.pone.0071171  ·  PMID: 23951102  ·  PMCID: PMC3737187
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Stress-Independent Activation of XBP1s and/or ATF6 Reveals Three Functionally Diverse ER Proteostasis Environments
Stress-Independent Activation of XBP1s and/or ATF6 Reveals Three Functionally Diverse ER Proteostasis Environments
Matthew D. Shoulders, Lisa M. Ryno, Joseph C. Genereux, James J. Moresco, Patricia G. Tu, Chunlei Wu, John R. Yates, Andrew I. Su, Jeffery W. Kelly, R. Luke Wiseman
Cell Reports  ·  01 Apr 2013  ·  doi:10.1016/j.celrep.2013.03.024  ·  PMID: 23583182  ·  PMCID: PMC3754422
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A task-based approach for Gene Ontology evaluation
A task-based approach for Gene Ontology evaluation
Erik L Clarke, Salvatore Loguercio, Benjamin M Good, Andrew I Su
Journal of Biomedical Semantics  ·  01 Apr 2013  ·  doi:10.1186/2041-1480-4-S1-S4  ·  PMID: 23734599  ·  PMCID: PMC3633003
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Zone‐specific gene expression patterns in articular cartilage
Zone‐specific gene expression patterns in articular cartilage
Shawn P. Grogan, Stuart F. Duffy, Chantal Pauli, James A. Koziol, Andrew I. Su, Darryl D. D’Lima, Martin K. Lotz
Arthritis & Rheumatism  ·  28 Jan 2013  ·  doi:10.1002/art.37760  ·  PMID: 23124445  ·  PMCID: PMC3558601
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2012

A gene expression atlas of the domestic pig
A gene expression atlas of the domestic pig
Tom C Freeman, Alasdair Ivens, J Kenneth Baillie, Dario Beraldi, Mark W Barnett, …, Andrew I Su, Kim M Summers, Christopher K Tuggle, Alan L Archibald, David A Hume
BMC Biology  ·  15 Nov 2012  ·  doi:10.1186/1741-7007-10-90  ·  PMID: 23153189  ·  PMCID: PMC3814290
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BioGPS and GXD: mouse gene expression data—the benefits and challenges of data integration
BioGPS and GXD: mouse gene expression data—the benefits and challenges of data integration
Martin Ringwald, Chunlei Wu, Andrew I. Su
Mammalian Genome  ·  31 Jul 2012  ·  doi:10.1007/s00335-012-9408-0  ·  PMID: 22847375  ·  PMCID: PMC3469763
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Linking genes to diseases with a SNPedia-Gene Wiki mashup
Linking genes to diseases with a SNPedia-Gene Wiki mashup
Benjamin M Good, Erik L Clarke, Salvatore Loguercio, Andrew I Su
Journal of Biomedical Semantics  ·  24 Apr 2012  ·  doi:10.1186/2041-1480-3-S1-S6  ·  PMID: 22541597  ·  PMCID: PMC3337266
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2011

Mining the Gene Wiki for functional genomic knowledge
Mining the Gene Wiki for functional genomic knowledge
Benjamin M Good, Douglas G Howe, Simon M Lin, Warren A Kibbe, Andrew I Su
BMC Genomics  ·  01 Dec 2011  ·  doi:10.1186/1471-2164-12-603  ·  PMID: 22165947  ·  PMCID: PMC3271090
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CAFET Algorithm Reveals Wnt/PCP Signature in Lung Squamous Cell Carcinoma
CAFET Algorithm Reveals Wnt/PCP Signature in Lung Squamous Cell Carcinoma
Yue Hu, Anna V. Galkin, Chunlei Wu, Venkateshwar Reddy, Andrew I. Su
PLoS ONE  ·  10 Oct 2011  ·  doi:10.1371/journal.pone.0025807  ·  PMID: 22016777  ·  PMCID: PMC3189939
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Games with a scientific purpose
Games with a scientific purpose
Benjamin M Good, Andrew I Su
Genome Biology  ·  01 Jan 2011  ·  doi:10.1186/gb-2011-12-12-135  ·  PMID: 22204700  ·  PMCID: PMC3334605
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2010

Phenotypic Characterization of a Genetically Diverse Panel of Mice for Behavioral Despair and Anxiety
Phenotypic Characterization of a Genetically Diverse Panel of Mice for Behavioral Despair and Anxiety
Brooke H. Miller, Laura E. Schultz, Anisha Gulati, Andrew I. Su, Mathew T. Pletcher
PLoS ONE  ·  29 Dec 2010  ·  doi:10.1371/journal.pone.0014458  ·  PMID: 21206921  ·  PMCID: PMC3012073
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Integrative Analysis of Low- and High-Resolution eQTL
Integrative Analysis of Low- and High-Resolution eQTL
Salvatore Loguercio, Rupert W. Overall, Jacob J. Michaelson, Tim Wiltshire, Mathew T. Pletcher, Brooke H. Miller, John R. Walker, Gerd Kempermann, Andrew I. Su, Andreas Beyer
PLoS ONE  ·  10 Nov 2010  ·  doi:10.1371/journal.pone.0013920  ·  PMID: 21085707  ·  PMCID: PMC2978079
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A novel approach to investigate tissue-specific trinucleotide repeat instability
A novel approach to investigate tissue-specific trinucleotide repeat instability
Jong-Min Lee, Jie Zhang, Andrew I Su, John R Walker, Tim Wiltshire, …, Michel Cyr, Isaac Kohane, James F Gusella, Marcy E MacDonald, Vanessa C Wheeler
BMC Systems Biology  ·  19 Mar 2010  ·  doi:10.1186/1752-0509-4-29  ·  PMID: 20302627  ·  PMCID: PMC2856555
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Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency
Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency
Rodolfo Gonzalez, Lori L. Jennings, Mark Knuth, Anthony P. Orth, Heath E. Klock, …, Deborah G. Nguyen, Evan Y. Snyder, Peter G. Schultz, Jennifer L. Harris, Scott A. Lesley
Proceedings of the National Academy of Sciences  ·  23 Feb 2010  ·  doi:10.1073/pnas.0914019107  ·  PMID: 20133595  ·  PMCID: PMC2840467
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2009

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources
Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, …, Christopher L Hodge, James Haase, Jeff Janes, Jon W Huss, Andrew I Su
Genome Biology  ·  17 Nov 2009  ·  doi:10.1186/gb-2009-10-11-r130  ·  PMID: 19919682  ·  PMCID: PMC3091323
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Software-Based Remote Code Attestation in Wireless Sensor Network
Software-Based Remote Code Attestation in Wireless Sensor Network
Tamer AbuHmed, Nandinbold Nyamaa, DaeHun Nyang
GLOBECOM 2009 - 2009 IEEE Global Telecommunications Conference  ·  01 Nov 2009  ·  doi:10.1109/GLOCOM.2009.5425280
A Common and Unstable Copy Number Variant Is Associated with Differences in Glo1 Expression and Anxiety-Like Behavior
A Common and Unstable Copy Number Variant Is Associated with Differences in Glo1 Expression and Anxiety-Like Behavior
Richard Williams, Jackie E. Lim, Bettina Harr, Claudia Wing, Ryan Walters, …, Andrew I. Su, Greta Sokoloff, Lisa M. Tarantino, Justin O. Borevitz, Abraham A. Palmer
PLoS ONE  ·  06 Mar 2009  ·  doi:10.1371/journal.pone.0004649  ·  PMID: 19266052  ·  PMCID: PMC2650792
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Effect of cobalt and vitamin B12 on the production of salinosporamides by Salinispora tropica
Effect of cobalt and vitamin B12 on the production of salinosporamides by Salinispora tropica
Ginger Tsueng, Kin Sing Lam
The Journal of Antibiotics  ·  06 Feb 2009  ·  doi:10.1038/ja.2009.7  ·  PMID: 19198638
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Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus
Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus
John Paul Pezacki, Selena M Sagan, Angela M Tonary, Yanouchka Rouleau, Sylvie Bélanger, Lubica Supekova, Andrew I Su
BMC Chemical Biology  ·  16 Jan 2009  ·  doi:10.1186/1472-6769-9-2  ·  PMID: 19149867  ·  PMCID: PMC2651120
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2008

Genetical Genomics: Spotlight on QTL Hotspots
Genetical Genomics: Spotlight on QTL Hotspots
Rainer Breitling, Yang Li, Bruno M. Tesson, Jingyuan Fu, Chunlei Wu, …, Alice Gerrits, Leonid V. Bystrykh, Gerald de Haan, Andrew I. Su, Ritsert C. Jansen
PLoS Genetics  ·  24 Oct 2008  ·  doi:10.1371/journal.pgen.1000232  ·  PMID: 18949031  ·  PMCID: PMC2563687
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A Gene Wiki for Community Annotation of Gene Function
A Gene Wiki for Community Annotation of Gene Function
Jon W Huss, Camilo Orozco, James Goodale, Chunlei Wu, Serge Batalov, Tim J Vickers, Faramarz Valafar, Andrew I Su
PLoS Biology  ·  08 Jul 2008  ·  doi:10.1371/journal.pbio.0060175  ·  PMID: 18613750  ·  PMCID: PMC2443188
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Gene Set Enrichment in eQTL Data Identifies Novel Annotations and Pathway Regulators
Gene Set Enrichment in eQTL Data Identifies Novel Annotations and Pathway Regulators
Chunlei Wu, David L. Delano, Nico Mitro, Stephen V. Su, Jeff Janes, …, Akira Kohsaka, Joseph Bass, Enrique Saez, Tim Wiltshire, Andrew I. Su
PLoS Genetics  ·  09 May 2008  ·  doi:10.1371/journal.pgen.1000070  ·  PMID: 18464898  ·  PMCID: PMC2346558
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2007

Power-law-like distributions in biomedical publications and research funding
Power-law-like distributions in biomedical publications and research funding
Andrew I Su, John B Hogenesch
Genome Biology  ·  01 Jan 2007  ·  doi:10.1186/gb-2007-8-4-404  ·  PMID: 17472739  ·  PMCID: PMC1895997
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Effects of Halogens on the Production of Salinosporamides by the Obligate Marine Actinomycete Salinispora tropica
Effects of Halogens on the Production of Salinosporamides by the Obligate Marine Actinomycete Salinispora tropica
Kin S Lam, Ginger Tsueng, Katherine A Mcarthur, Scott S Mitchell, Barbara C M Potts, Jianlin Xu
The Journal of Antibiotics  ·  01 Jan 2007  ·  doi:10.1038/ja.2007.2  ·  PMID: 17390584
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2006

An efficient rapid system for profiling the cellular activities of molecular libraries
An efficient rapid system for profiling the cellular activities of molecular libraries
Jonathan S. Melnick, Jeff Janes, Sungjoon Kim, Jim Y. Chang, Daniel G. Sipes, …, Robert Downs, Nathanael S. Gray, Peter G. Schultz, Markus Warmuth, Jeremy S. Caldwell
Proceedings of the National Academy of Sciences  ·  21 Feb 2006  ·  doi:10.1073/pnas.0511292103  ·  PMID: 16492761  ·  PMCID: PMC1413928
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Comparative analysis of haplotype association mapping algorithms
Comparative analysis of haplotype association mapping algorithms
Phillip McClurg, Mathew T Pletcher, Tim Wiltshire, Andrew I Su
BMC Bioinformatics  ·  09 Feb 2006  ·  doi:10.1186/1471-2105-7-61  ·  PMID: 16466585  ·  PMCID: PMC1409800
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2005

Large-Scale Profiling of Rab GTPase Trafficking Networks: The Membrome
Large-Scale Profiling of Rab GTPase Trafficking Networks: The Membrome
Cemal Gurkan, Hilmar Lapp, Christelle Alory, Andrew I. Su, John B. Hogenesch, William E. Balch
Molecular Biology of the Cell  ·  01 Aug 2005  ·  doi:10.1091/mbc.E05-01-0062  ·  PMID: 15944222  ·  PMCID: PMC1182321
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Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells
Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells
Jiang F. Zhong, Yi Zhao, Susan Sutton, Andrew Su, Yuxia Zhan, …, Chunli Yan, Tim Gallaher, Patrick B. Johnston, W. French Anderson, Michael P. Cooke
Proceedings of the National Academy of Sciences  ·  04 Feb 2005  ·  doi:10.1073/pnas.0409459102  ·  PMID: 15695585  ·  PMCID: PMC548308
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2004

Use of a Dense Single Nucleotide Polymorphism Map for In Silico Mapping in the Mouse
Use of a Dense Single Nucleotide Polymorphism Map for In Silico Mapping in the Mouse
Mathew T Pletcher, Philip McClurg, Serge Batalov, Andrew I Su, S. Whitney Barnes, …, Deborah Nusskern, Molly A Bogue, Richard J Mural, Beverly Paigen, Tim Wiltshire
PLoS Biology  ·  09 Nov 2004  ·  doi:10.1371/journal.pbio.0020393  ·  PMID: 15534693  ·  PMCID: PMC526179
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A gene atlas of the mouse and human protein-encoding transcriptomes
A gene atlas of the mouse and human protein-encoding transcriptomes
Andrew I. Su, Tim Wiltshire, Serge Batalov, Hilmar Lapp, Keith A. Ching, …, Mimi Hayakawa, Gabriel Kreiman, Michael P. Cooke, John R. Walker, John B. Hogenesch
Proceedings of the National Academy of Sciences  ·  09 Apr 2004  ·  doi:10.1073/pnas.0400782101  ·  PMID: 15075390  ·  PMCID: PMC395923
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Applications of a Rat Multiple Tissue Gene Expression Data Set
Applications of a Rat Multiple Tissue Gene Expression Data Set
John R. Walker, Andrew I. Su, David W. Self, John B. Hogenesch, Hilmar Lapp, Rainer Maier, Daniel Hoyer, Graeme Bilbe
Genome Research  ·  01 Apr 2004  ·  doi:10.1101/gr.2161804  ·  PMID: 15060018  ·  PMCID: PMC383321
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2002

Genomic analysis of the host response to hepatitis C virus infection
Genomic analysis of the host response to hepatitis C virus infection
Andrew I. Su, John P. Pezacki, Lisa Wodicka, Amy D. Brideau, Lubica Supekova, …, Stefan Wieland, Jens Bukh, Robert H. Purcell, Peter G. Schultz, Francis V. Chisari
Proceedings of the National Academy of Sciences  ·  19 Nov 2002  ·  doi:10.1073/pnas.202608199  ·  PMID: 12441396  ·  PMCID: PMC137774
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Large Scale Molecular Analysis Identifies Genes with Altered Expression in Salivary Adenoid Cystic Carcinoma
Large Scale Molecular Analysis Identifies Genes with Altered Expression in Salivary Adenoid Cystic Carcinoma
Henry F. Frierson, Adel K. El-Naggar, John B. Welsh, Lisa M. Sapinoso, Andrew I. Su, Jun Cheng, Takashi Saku, Christopher A. Moskaluk, Garret M. Hampton
The American Journal of Pathology  ·  01 Oct 2002  ·  doi:10.1016/S0002-9440(10)64408-2  ·  PMID: 12368205  ·  PMCID: PMC1867312
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Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice
Gene expression during the priming phase of liver regeneration after partial hepatectomy in mice
Andrew I. Su, Luca G. Guidotti, John Paul Pezacki, Francis V. Chisari, Peter G. Schultz
Proceedings of the National Academy of Sciences  ·  12 Aug 2002  ·  doi:10.1073/pnas.122359899  ·  PMID: 12177410  ·  PMCID: PMC123230
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Large-scale analysis of the human and mouse transcriptomes
Large-scale analysis of the human and mouse transcriptomes
Andrew I. Su, Michael P. Cooke, Keith A. Ching, Yaron Hakak, John R. Walker, …, Aziz Moqrich, Ardem Patapoutian, Garret M. Hampton, Peter G. Schultz, John B. Hogenesch
Proceedings of the National Academy of Sciences  ·  19 Mar 2002  ·  doi:10.1073/pnas.012025199  ·  PMID: 11904358  ·  PMCID: PMC123671
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2001

Destabilization of Ca<sup>2+</sup>-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type
Destabilization of Ca2+-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type
Gayathri Ratnaswamy, Mary E. Huff, Andrew I. Su, Severine Rion, Jeffery W. Kelly
Proceedings of the National Academy of Sciences  ·  20 Feb 2001  ·  doi:10.1073/pnas.041452598  ·  PMID: 11226240  ·  PMCID: PMC30139
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