Dr. Tamer ABUHMED is a Tenure-track Associate Professor in the College of Computing and Informatics at Sungkyunkwan University (SKKU), where he has served since September 2019. He is the founder and director of the SKKU Information Research Laboratory (InfoLab). Before joining SKKU, he was an Assistant Professor at Inha University, where he also founded the Software Security Research Laboratory (SecLab). He held visiting scholar positions at Loyola University Chicago (Jan 2023 – Jan 2026), the University of Notre Dame (Jun–Aug 2024), and the University of Chicago (Jun–Aug 2023), and serves as a Technology Consultant for the Gyeonggi-Do Province Government, South Korea.

Research Impact

With over 6,200+ citations, an h-index of 35+, and an i10-index of 65+ (Google Scholar), Dr. Abuhmed’s research has demonstrated significant impact in Systems Security and responsible AI. His publication record includes more than 76+ peer-reviewed journal articles and 25+ conference/chapter papers, with citation growth increasing substantially year-over-year.

Research Interests

Education

Professional Experience

Associate Professor, College of Computing and Informatics
Sungkyunkwan University (SKKU) [Global Rank #87] — Sep 2019 – Present

Visiting Scholar, Department of Computer Science
Loyola University Chicago — Jan 2023 – Jan 2026

Visiting Scholar, Department of Computer Science and Engineering
University of Notre Dame — Jun 2024 – Aug 2024

Visiting Scholar, Physical Sciences Division
The University of Chicago — Jun 2023 – Aug 2023

Assistant Professor, Computer Engineering Department
Inha University — Mar 2014 – Sep 2019

Postdoctoral Researcher / Lecturer, Inha University (Aug 2012 – Feb 2014)
Research Assistant, Information Security Research Laboratory (ISRL), Inha University (Mar 2007 – Aug 2012)

Selected Publications

Security, Trustworthy AI, and Privacy

  1. A Deep Dive into Function Inlining and its Security Implications for ML-based Binary Analysis. Network and Distributed System Security Symposium (NDSS), 2026.
  2. Infodeslib: Python Library for Dynamic Ensemble Learning using Late Fusion of Multimodal Data. ACM KDD Workshop on Knowledge-infused Learning (KiL’24), 2024.
  3. AdvChar: Attacking Interpretable NLP Systems. IEEE Transactions on Information Forensics and Security, 2025.
  4. SingleADV: Single-Class Target-Specific Attack against Interpretable Deep Learning Systems. IEEE Transactions on Information Forensics and Security, 2024.
  5. Hardening Interpretable Deep Learning Systems: Investigating Adversarial Threats and Defenses. IEEE Transactions on Dependable and Secure Computing, 2023.
  6. Stealthy Query-Efficient Opaque Attack Against Interpretable Deep Learning. IEEE Transactions on Reliability, 2025.
  7. Explainable Artificial Intelligence (XAI): What we know and what is left to attain Trustworthy Artificial Intelligence. Information Fusion, 2023.
  8. Large-scale and robust code authorship identification with deep feature learning. ACM Transactions on Privacy and Security (TOPS), 2021.
  9. Multi-χ: Identifying Multiple Authors from Source Code Files. Proceedings on Privacy Enhancing Technologies (PETS), 2020.
  10. Large-scale and Language-Oblivious Code Authorship Identification. ACM SIGSAC Conference on Computer and Communications Security (CCS), 2018.

AI for Healthcare and Biomedical Applications

  1. MM-DES: Enhancing Multimodal Clinical Prediction with Joint Contrastive Embeddings and Dynamic Ensembles. International Conference on Pattern Recognition (ICPR), 2026.
  2. Trustworthy Alzheimer’s diagnosis: Integrating robustness, fairness, and explainability in neuroimaging-based deep ensemble framework. Engineering Applications of Artificial Intelligence, 2026.
  3. Multi-plane multi-slice longitudinal MRI for deep ensemble progression detection based on enhanced residual multi-head self-attention. Knowledge-Based Systems, 2026.
  4. 4DfCF: 4D fMRI CrossFormer Vision Transformer. IEEE Journal of Biomedical and Health Informatics, 2025.
  5. Information fusion-based Bayesian optimized heterogeneous deep ensemble model based on longitudinal neuroimaging data. Applied Soft Computing, 2024.
  6. Alzheimer’s disease diagnosis in the metaverse. Computer Methods and Programs in Biomedicine, 2024.
  7. Prediction of Alzheimer’s progression based on multimodal deep-learning-based fusion and visual explainability of time-series data. Information Fusion, 2023.
  8. Explainable machine learning models based on multimodal time-series data for the early detection of Parkinson’s disease. Computer Methods and Programs in Biomedicine, 2023.
  9. Multitask Deep Learning for Cost-Effective Prediction of Patient’s Length of Stay and Readmission State Using Multimodal Physical Activity Sensory Data. IEEE Journal of Biomedical and Health Informatics, 2022.
  10. Automatic detection of Alzheimer’s disease progression: An efficient information fusion approach with heterogeneous ensemble classifiers. Neurocomputing, 2022.

Academic Services

Department and College Service

Journal Reviewer & Guest Editor

Conference Program Committee / Reviewer

Professional Memberships

Teaching

10+ Years of Teaching Experience (Mar 2014 – Present)

Graduate Courses

Undergraduate Courses

Publications

2026

Toward Trustworthy Digital Healthcare: A System-Level Convergence of IoMT, Large Language Models, and Explainable AI
Maria Bashir, Shaker El-Sappagh, Simon S. Woo, Dong In Kim, Tamer Abuhmed
Information Fusion  ·  01 May 2026  ·  doi:10.1016/j.inffus.2026.104507
Trustworthy Alzheimer’s diagnosis: Integrating robustness, fairness, and explainability in neuroimaging based deep ensemble framework
Maria Bashir, Nasir Rahim, Shaker El-Sappagh, Omar Amin El-Serafy, Tamer Abuhmed
Engineering Applications of Artificia...  ·  01 May 2026  ·  doi:10.1016/j.engappai.2026.114291
GraphShield: Advanced dynamic graph-based malware detection using graph neural networks
Eslam Amer, Shaker El-Sappagh, Tamer Abuhamad, Bander Ali Saleh Al-Rimy, Alaa Mohasseb
Expert Systems with Applications  ·  01 Mar 2026  ·  doi:10.1016/j.eswa.2025.129812
Multi-plane multi-slice longitudinal MRI for deep ensemble progression detection based on enhanced residual multi-head self-attention
Nasir Rahim, Shaker El-Sappagh, Mustaqeem Khan, Maria Bashir, Younhyun Jung, Tamer Abuhmed
Knowledge-Based Systems  ·  01 Feb 2026  ·  doi:10.1016/j.knosys.2025.115104
Robust Multi-Scale 3D Crossformer Model for Multimodal Medical Image Analysis using Volumetric MRI and Structured Data
Chensheng Zheng, Shaker El-Sappagh, Tamer Abuhmed
2026 20th International Conference on...  ·  04 Jan 2026  ·  doi:10.1109/imcom69009.2026.11360976
Explainable Ensemble Deep Learning Architecture for Fruit Disease Detection for Sustainable Agriculture and Food System Resilience
Nabila Ahmed Ali Mohammed Hafez, Mohammed Haitham Mohammed, Farah Mohamed, Mohamed Ghetas, Shaker El-Sappagh, Tamer Abuhmed
2026 20th International Conference on...  ·  04 Jan 2026  ·  doi:10.1109/imcom69009.2026.11360803
Towards Reliable and Interpretable Wheat Disease Diagnosis: Unified Framework Incorporating Vision Transformer and Advanced Object Detection
Mohamed Rady, Mohamed Elsayed, Aser Mohamed, Shaker El-Sappagh, Tamer Abuhmed
2026 20th International Conference on...  ·  04 Jan 2026  ·  doi:10.1109/imcom69009.2026.11360837
A Deep Dive into Function Inlining and its Security Implications for ML-based Binary Analysis
Omar Abusabha, Jiyong Uhm, Tamer Abuhmed, Hyungjoon Koo
Proceedings 2026 Network and Distribu...  ·  01 Jan 2026  ·  doi:10.14722/ndss.2026.241872
Smart healthcare: fusion of multimodal medical signals
Nasir Rahim, Shaker El-Sappagh, Tamer Abuhmed
Cybersecurity for Healthcare Systems ...  ·  01 Jan 2026  ·  doi:10.1016/b978-0-443-27448-0.00007-x

2025

2025 Index IEEE Transactions on Reliability Vol. 74
IEEE Transactions on Reliability  ·  01 Dec 2025  ·  doi:10.1109/tr.2025.3646839
Mortality prediction for ICU patients with mental disorders using large language models ensemble and unstructured medical notes
Waleed Nazih, Tamer Abuhmed, Meshal Alharbi, Shaker El-Sappagh
PLOS One  ·  19 Sep 2025  ·  doi:10.1371/journal.pone.0332134  ·  PMID: 40971951  ·  PMCID: PMC12448993
Stealthy Query-Efficient OpaqueAttack Against Interpretable Deep Learning
Stealthy Query-Efficient OpaqueAttack Against Interpretable Deep Learning
Eldor Abdukhamidov, Mohammed Abuhamad, Simon S. Woo, Eric Chan-Tin, Tamer Abuhmed
IEEE Transactions on Reliability  ·  01 Sep 2025  ·  doi:10.1109/TR.2025.3551717
Sustainable energy management in the AI era: a comprehensive analysis of ML and DL approaches
Haseeb Javed, Fatma Eid, Shaker El-Sappagh, Tamer Abuhmed
Computing  ·  22 May 2025  ·  doi:10.1007/s00607-025-01485-0
Chronic Kidney Disease Detection Augmented with Hybrid Explainable AI
Mohamed Desoky, Nada Gamal ElAdl, Tamer Abuhmed, Shaker El-Sappagh
2025 15th International Conference on...  ·  12 May 2025  ·  doi:10.1109/ICEENG64546.2025.11031335
Bone Densitometry Dataset for Computer Aided Osteoporosis Disease Detection
Negin Masnabadi, Abolghasem Sadeghi-Niaraki, Mohammad Karimi, Tamer AbuHmed, Nasrin Azarbani, Soo-Mi Choi
openRxiv  ·  28 Jan 2025  ·  doi:10.1101/2025.01.25.24319689
End-to-End Optimized Ensemble Model for Alzheimer's Disease Detection
Abdelrahman Hassan, Tamer Abuhmed, Shaker El-Sappagh
2025 19th International Conference on...  ·  03 Jan 2025  ·  doi:10.1109/imcom64595.2025.10857489
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...  ·  03 Jan 2025  ·  doi:10.1109/imcom64595.2025.10857574
Leveraging Large Language Models for Smart Pharmacy Systems: Enhancing Drug Safety and Operational Efficiency
Abdelrahman Osheba, Ahmed Abou-El-Ela, Osama Adel, Youssef Maaod, Tamer Abuhmed, Shaker El-Sappagh
2025 19th International Conference on...  ·  03 Jan 2025  ·  doi:10.1109/imcom64595.2025.10857582
Knowledge Augmented Significant Language Model-Based Chatbot for Explainable Diabetes Mellitus Prediction
Mazen Elfayoumi, Mohamed AbouElazm, Omar Mohamed, Tamer Abuhmed, Shaker El-Sappagh
2025 19th International Conference on...  ·  03 Jan 2025  ·  doi:10.1109/imcom64595.2025.10857525
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
Digital twin and sensor networks for healthcare monitoring frameworks
Amirhossein Danesh, Shaker El-Sappagh, Tamer Abuhmed
Sensor Networks for Smart Hospitals  ·  01 Jan 2025  ·  doi:10.1016/b978-0-443-36370-2.00011-6
AdvChar: Attacking Interpretable NLP Systems
Eldor Abdukhamidov, Tamer Abuhmed, Joanna C. S. Santos, Mohammed Abuhamad
IEEE Transactions on Information Fore...  ·  01 Jan 2025  ·  doi:10.1109/TIFS.2025.3622073
4DfCF: 4D fMRI CrossFormer Vision Transformer
Chensheng Zheng, Shaker El-Sappagh, Tamer Abuhmed
IEEE Journal of Biomedical and Health...  ·  01 Jan 2025  ·  doi:10.1109/jbhi.2025.3631655  ·  PMID: 41231696
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

2024

Robustness in deep learning models for medical diagnostics: security and adversarial challenges towards robust AI applications
Haseeb Javed, Shaker El-Sappagh, Tamer Abuhmed
Artificial Intelligence Review  ·  08 Nov 2024  ·  doi:10.1007/S10462-024-11005-9
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 Biom...  ·  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
Information fusion-based Bayesian optimized heterogeneous deep ensemble model based on longitudinal neuroimaging data
Nasir Rahim, Shaker El-Sappagh, Haytham Rizk, Omar Amin El-serafy, Tamer Abuhmed
Applied Soft Computing  ·  01 Sep 2024  ·  doi:10.1016/J.ASOC.2024.111749
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 S...  ·  01 Jul 2024  ·  doi:10.1109/TDSC.2023.3341090
MotionID: Towards practical behavioral biometrics-based implicit user authentication on smartphones
Mohsen Ali Alawami, Tamer Abuhmed, Mohammed Abuhamad, Hyoungshick Kim
Pervasive and Mobile Computing  ·  01 Jul 2024  ·  doi:10.1016/j.pmcj.2024.101922
Integrating Digital Twin Technology with Dynamic Ensemble Learning for Sepsis Prediction in Intensive Care Units
Amirhossein Danesh, Firuz Juraev, Shaker El-Sappagh, Tamer Abuhmed
Journal of Intelligence and Informati...  ·  30 Jun 2024  ·  doi:10.13088/jiis.2024.30.2.025
The Impact of Model Variations on the Robustness of Deep Learning Models in Adversarial Settings
Firuz Juraev, Mohammed Abuhamad, Simon S. Woo, George K Thiruvathukal, Tamer Abuhmed
2024 Silicon Valley Cybersecurity Con...  ·  17 Jun 2024  ·  doi:10.1109/SVCC61185.2024.10637362
Unmasking the Vulnerabilities of Deep Learning Models: A Multi-Dimensional Analysis of Adversarial Attacks and Defenses
Firuz Juraev, Mohammed Abuhamad, Eric Chan-Tin, George K. Thiruvathukal, Tamer Abuhmed
2024 Silicon Valley Cybersecurity Con...  ·  17 Jun 2024  ·  doi:10.1109/SVCC61185.2024.10637364
Integrating Digital Twin Technology with Dynamic Ensemble Learning for Sepsis Prediction in Intensive Care Units
Amirhossein Danesh, Firuz Juraev, Shaker El-Sappagh, Tamer Abuhmed
지능정보연구  ·  01 Jun 2024  ·  doi:http://dx.doi.org/10.13088/jiis.2024.30.2.025
Spatial mapping of land susceptibility to dust emissions using optimization of attentive Interpretable Tabular Learning (TabNet) model
Seyed Vahid Razavi-Termeh, Abolghasem Sadeghi-Niaraki, Armin Sorooshian, Tamer Abuhmed, Soo-Mi Choi
Journal of Environmental Management  ·  01 May 2024  ·  doi:10.1016/J.JENVMAN.2024.120682  ·  PMID: 38670008
Temporal dynamics of urban gas pipeline risks
Fatema Rahimi, Abolghasem Sadeghi-Niaraki, Mostafa Ghodousi, Tamer Abuhmed, Soo-Mi Choi
Scientific Reports  ·  06 Mar 2024  ·  doi:10.1038/S41598-024-56136-9  ·  PMID: 38448517  ·  PMCID: PMC10918077
A dynamic fuzzy rule-based inference system using fuzzy inference with semantic reasoning
Nora Shoaip, Shaker El-Sappagh, Tamer Abuhmed, Mohammed Elmogy
Scientific Reports  ·  21 Feb 2024  ·  doi:10.1038/s41598-024-54065-1  ·  PMID: 38383597  ·  PMCID: PMC10881567
Explainable Dynamic Ensemble Framework for Classification Based on the Late Fusion of Heterogeneous Multimodal Data
Firuz Juraev, Shaker El-Sappagh, Tamer Abuhmed
Intelligent Systems and Applications  ·  01 Jan 2024  ·  doi:https://doi.org/10.1007/978-3-031-47715-7_38
From Attack to Defense: Insights into Deep Learning Security Measures in Black-Box Settings
arXiv preprint arXiv:2405.01963  ·  01 Jan 2024  ·  arxiv:https://arxiv.org/abs/2405.01963
Impact of architectural modifications on deep learning adversarial robustness
arXiv preprint arXiv:2405.01934  ·  01 Jan 2024  ·  arxiv:https://arxiv.org/abs/2405.01934
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 Fore...  ·  01 Jan 2024  ·  doi:10.1109/TIFS.2024.3407652

2023

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
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
LSTM deep learning model for Alzheimer’s disease prediction based on cost-effective time series cognitive scores
Hager Saleh, Nora El-Rashidy, Tamer Abuhmed, Shaker El-Sappagh
2023 5th Novel Intelligent and Leadin...  ·  21 Oct 2023  ·  doi:10.1109/niles59815.2023.10296640
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
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
Author Correction: 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  ·  04 Sep 2023  ·  doi:10.1038/S41598-023-41661-W  ·  PMID: 37666913  ·  PMCID: PMC10477192
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
Explainable probabilistic deep learning framework for seismic assessment of structures using distribution‐free prediction intervals
Mohamed Noureldin, Tamer Abuhmed, Melike Saygi, Jinkoo Kim
Computer-Aided Civil and Infrastructu...  ·  01 Aug 2023  ·  doi:10.1111/MICE.13015
A Dynamic Fuzzy Rule-Based Inference System: Fuzzy Inference with Semantic Reasoning
Nora Shoaip, Shaker El-Sappagh, Tamer Abuhmed, Mohammed Elmogy
Research Square Platform LLC  ·  17 Jul 2023  ·  doi:10.21203/rs.3.rs-3128427/v1
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
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
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
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 Serv...  ·  01 Jun 2023  ·  doi:10.1109/TNSM.2022.3200741
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 Biom...  ·  01 Jun 2023  ·  doi:10.1016/j.cmpb.2023.107495  ·  PMID: 37003039
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
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
openRxiv  ·  02 May 2023  ·  doi:10.1101/2023.05.01.538993  ·  PMID: 37205439  ·  PMCID: PMC10187194
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
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
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
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, Ginger Tsueng, Emily Haag, Mark Zeller, Christine M. Aceves, Karina Zaiets, Marco Cano, Xinghua Zhou, Zhongchao Qian, Rachel Sattler, Nathaniel L. Matteson, Joshua I. Levy, Raphael T. C. Lee, Lucas Freitas, Sebastian Maurer-Stroh, 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
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, Lars Pache, Luke V. Rasmussen, Tor C. Savidge, Justin Starren, Qinglong Wu, Jiwen Xin, Michael R. Yeaman, Xinghua Zhou, Andrew I. Su, 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
Addressing barriers in FAIR data practices for biomedical data
Laura D. Hughes, Ginger Tsueng, Jack DiGiovanna, Thomas D. Horvath, Luke V. Rasmussen, Tor C. Savidge, Thomas Stoeger, 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
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
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
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
Real-time human detection and behavior recognition using low-cost hardware
Bojun Wang, Sajid Ali, Xinyi Fan, Tamer Abuhmed
2023 17th International Conference on...  ·  03 Jan 2023  ·  doi:10.1109/imcom56909.2023.10035603
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, Shervin Abdollahi, Sergio E. Baranzini, Basazin Belhu, William E. Byrd, Lawrence Chung, Andrew Crouse, Marc P. Duby, Stephen Ferguson, Aleksandra Foksinska, Laura Forero, Jennifer Friedman, Vicki Gardner, Gwênlyn Glusman, Jennifer Hadlock, Kristina Hanspers, Eugene Hinderer, Charlotte Hobbs, Gregory Hyde, Sui Huang, David Koslicki, Philip Mease, Sandrine Muller, Christopher J. Mungall, Stephen A. Ramsey, Jared Roach, Irit Rubin, Shepherd H. Schurman, Anath Shalev, Brett Smith, Karthik Soman, Sarah Stemann, Andrew I. Su, Casey Ta, Paul B. Watkins, Mark D. Williams, Chunlei Wu, Colleen H. Xu
Journal of Clinical and Translational...  ·  01 Jan 2023  ·  doi:10.1017/cts.2023.619  ·  PMID: 37900350  ·  PMCID: PMC10603356
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
Sajid Ali, Shaker El-Sappagh, Farman Ali, Muhammad Imran, Tamer Abuhmed
IEEE Journal of Biomedical and Health...  ·  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
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
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
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
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
Ginger Tsueng, Marco A. Alvarado Cano, José Bento, Candice Czech, Mengjia Kang, Lars Pache, Luke V. Rasmussen, Tor C. Savidge, Justin Starren, Qinglong Wu, Jiwen Xin, Michael R. Yeaman, Xinghua Zhou, Andrew I. Su, Chunlei Wu, Liliana Brown, Reed S. Shabman, Laura D. Hughes
openRxiv  ·  13 Oct 2022  ·  doi:10.1101/2022.10.10.511492
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
Integration of machine learning algorithms and GIS-based approaches to cutaneous leishmaniasis prevalence risk mapping
Negar Shabanpour, Seyed Vahid Razavi-Termeh, Abolghasem Sadeghi-Niaraki, Soo-Mi Choi, Tamer Abuhmed
International Journal of Applied Eart...  ·  01 Aug 2022  ·  doi:10.1016/J.JAG.2022.102854
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
Laura Hughes, Karthik Gangavarapu, Alaa Abdel Latif, Julia Mullen, Manar Alkuzweny, Emory Hufbauer, Ginger Tsueng, Emily Haag, Mark Zeller, Christine Aceves, Karina Zaiets, Marco Cano, Jerry Zhou, Zhongchao Qian, Rachel Sattler, Nathaniel Matteson, Joshua Levy, Raphael Lee, Lucas Freitas, Sebastian Maurer-Stroh, Marc Suchard, Chunlei Wu, Andrew Su, Kristian Andersen
Springer Science and Business Media LLC  ·  28 Jun 2022  ·  doi:10.21203/rs.3.rs-1723829/v1  ·  PMID: 35794893  ·  PMCID: PMC9258294
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, Benjamin Rush, Emily Haag, Alaa Abdel Latif, Xinghua Zhou, Zhongchao Qian, Emory Hufbauer, Mark Zeller, Kristian Andersen, Chunlei Wu, Andrew Su, Karthik Gangavarapu
Springer Science and Business Media LLC  ·  28 Jun 2022  ·  doi:10.21203/rs.3.rs-1723808/v1
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, J. Harry Caufield, Paul A. Clemons, Vlado Dancik, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, 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
MLxPack: Investigating the Effects of Packers on ML-based Malware Detection Systems Using Static and Dynamic Traits
Qirui Sun, Mohammed Abuhamad, Eldor Abdukhamidov, Eric Chan-Tin, Tamer Abuhmed
Proceedings of the 1st Workshop on Cy...  ·  30 May 2022  ·  doi:10.1145/3494108.3522768
Depth, Breadth, and Complexity: Ways to Attack and Defend Deep Learning Models
Firuz Juraev, Eldor Abdukhamidov, Mohammed Abuhamad, Tamer Abuhmed
Proceedings of the 2022 ACM on Asia C...  ·  30 May 2022  ·  doi:10.1145/3488932.3527278
Black-box and Target-specific Attack Against Interpretable Deep Learning Systems
Eldor Abdukhamidov, Firuz Juraev, Mohammed Abuhamad, Tamer Abuhmed
Proceedings of the 2022 ACM on Asia C...  ·  30 May 2022  ·  doi:10.1145/3488932.3527283
Leveraging Spectral Representations of Control Flow Graphs for Efficient Analysis of Windows Malware
Qirui Sun, Eldor Abdukhamidov, Tamer Abuhmed, Mohammed Abuhamad
Proceedings of the 2022 ACM on Asia C...  ·  30 May 2022  ·  doi:10.1145/3488932.3527294
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
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
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
Umer Masood Chaudry, Russlan Jaafreh, Abdul Malik, Tea-Sung Jun, Kotiba Hamad, Tamer Abuhmed
Mathematics  ·  27 Feb 2022  ·  doi:10.3390/math10050766
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
Karthik Gangavarapu, Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Emory Hufbauer, Ginger Tsueng, Emily Haag, Mark Zeller, Christine M. Aceves, Karina Zaiets, Marco Cano, Jerry Zhou, Zhongchao Qian, Rachel Sattler, Nathaniel L Matteson, Joshua I. Levy, Raphael TC Lee, Lucas Freitas, Sebastian Maurer-Stroh, Marc A. Suchard, Chunlei Wu, Andrew I. Su, Kristian G. Andersen, Laura D. Hughes
openRxiv  ·  29 Jan 2022  ·  doi:10.1101/2022.01.27.22269965
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
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
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
Haneen Alzamer, Tamer Abuhmed, Kotiba Hamad
Electronics  ·  13 Aug 2021  ·  doi:10.3390/electronics10161956
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
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
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
Umer Masood Chaudry, Kotiba Hamad, Tamer Abuhmed
Materials Today Communications  ·  01 Mar 2021  ·  doi:10.1016/j.mtcomm.2020.101897
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
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
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
Alzheimer Disease Prediction Model Based on Decision Fusion of CNN-BiLSTM Deep Neural Networks
Shaker El-Sappagh, Tamer Abuhmed, Kyung Sup Kwak
Intelligent Systems and Applications  ·  01 Jan 2021  ·  doi:https://doi.org/10.1007/978-3-030-55190-2_36
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
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
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
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 Neuros...  ·  01 Jan 2021  ·  doi:10.1155/2021/8439655  ·  PMID: 34603436  ·  PMCID: PMC8481044
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
AdvEdge: Optimizing Adversarial Perturbations Against Interpretable Deep Learning
Eldor Abdukhamidov, Mohammed Abuhamad, Firuz Juraev, Eric Chan-Tin, Tamer AbuHmed
Lecture Notes in Computer Science  ·  01 Jan 2021  ·  doi:10.1007/978-3-030-91434-9_9
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
Eman Abdelmaksoud, Shaker El-Sappagh, Sherif Barakat, Tamer Abuhmed, Mohammed Elmogy
IEEE Access  ·  01 Jan 2021  ·  doi:10.1109/ACCESS.2021.3052870

2020

2020 Index IEEE Internet of Things Journal Vol. 7
IEEE Internet of Things Journal  ·  01 Dec 2020  ·  doi:10.1109/jiot.2020.3046055
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
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
Eslam Amer, Shaker El-Sappagh, Jong Wan Hu
Applied Sciences  ·  30 Oct 2020  ·  doi:10.3390/app10217673
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
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
Mai Ramadan Ibraheem, Shaker El-Sappagh, Tamer Abuhmed, Mohammed Elmogy
Electronics  ·  04 Sep 2020  ·  doi:10.3390/electronics9091443
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
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 C...  ·  25 Aug 2020  ·  doi:10.1007/978-3-030-55190-2_36
An Approach for Measuring Spatial Similarity Among COVID-19 Epicenters
Neda Kaffash Charandabi, Abolghasem Sadeghi-Niaraki, Soo-Mi Choi
Springer Science and Business Media LLC  ·  04 Aug 2020  ·  doi:10.21203/rs.3.rs-49216/v1
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
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, Lars Pache, Sebastian Burgstaller-Muehlbacher, Paul D. De Jesus, Peter Teriete, Mitchell V. Hull, Max W. Chang, Jasper Fuk-Woo Chan, Jianli Cao, Vincent Kwok-Man Poon, Kristina M. Herbert, Kuoyuan Cheng, Tu-Trinh H. Nguyen, Andrey Rubanov, Yuan Pu, Courtney Nguyen, Angela Choi, Raveen Rathnasinghe, Michael Schotsaert, Lisa Miorin, Marion Dejosez, Thomas P. Zwaka, Ko-Yung Sit, Luis Martinez-Sobrido, Wen-Chun Liu, Kris M. White, Mackenzie E. Chapman, Emma K. Lendy, Richard J. Glynne, Randy Albrecht, Eytan Ruppin, Andrew D. Mesecar, Jeffrey R. Johnson, Christopher Benner, Ren Sun, Peter G. Schultz, 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
Multi-χ: Identifying Multiple Authors from Source Code Files
Mohammed Abuhamad, Tamer Abuhmed, DaeHun Nyang, David Mohaisen
Proceedings on Privacy Enhancing Tech...  ·  01 Jul 2020  ·  doi:10.2478/popets-2020-0044
A Semantic Approach for Extracting Medical Association Rules
Mohammed Thamer, Shaker El-Sappagh, Tarek El-Shishtawy
International Journal of Intelligent ...  ·  30 Jun 2020  ·  doi:10.22266/ijies2020.0630.26
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 App...  ·  18 Jun 2020  ·  doi:10.5120/ijca2020920274
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
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
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, Emily L. Clark, Heather A. Finlayson, 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
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
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
Ebtsam Adel, Shaker El Sappagh, Sherif Barakat, Mohammed Elmogy
International Journal of Medical Engi...  ·  01 Jan 2020  ·  doi:10.1504/ijmei.2020.107081
A framework for disease diagnosis based on fuzzy semantic ontology approach
Nora Shoaip, Shaker El Sappagh, Sherif Barakat, Mohammed Elmogy
International Journal of Medical Engi...  ·  01 Jan 2020  ·  doi:10.1504/ijmei.2020.109942
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
Hanaa Ibrahim Abu Zahra, Shaker El-Sappagh, Tarek Ahmef El Shishtawy
International Journal of Sociotechnol...  ·  01 Jan 2020  ·  doi:10.4018/ijskd.2020010106
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 ...  ·  01 Jan 2020  ·  doi:10.1109/tnse.2018.2877646
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

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
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, Rajiv Narayan, Ted Natoli, Jin H. Paik, 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
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 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, Lisa Kain, Maki Nakayama, Xiaoxiao Wan, 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
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
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
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
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
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 ...  ·  10 May 2019  ·  doi:10.1186/s12911-019-0806-z  ·  PMID: 31077222  ·  PMCID: PMC6511155
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
openRxiv  ·  28 Feb 2019  ·  doi:10.1101/564187
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
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
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
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
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
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
Ebtsam Adel, Shaker El-sappagh, Mohammed Elmogy, Sherif Barakat, Kyung-Sup Kwak
Intelligent Automation and Soft Compu...  ·  01 Jan 2019  ·  doi:10.31209/2019.100000151

2018

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 Engin...  ·  13 Dec 2018  ·  doi:10.1007/s13369-018-3670-8
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
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
openRxiv  ·  16 Oct 2018  ·  doi:10.1101/444497
Large-Scale and Language-Oblivious Code Authorship Identification
Mohammed Abuhamad, Tamer AbuHmed, Aziz Mohaisen, DaeHun Nyang
Proceedings of the 2018 ACM SIGSAC Co...  ·  15 Oct 2018  ·  doi:10.1145/3243734.3243738
Feature-based Transportation Sentiment Analysis Using Fuzzy Ontology and SentiWordNet
Farman Ali, Shaker EI-Sappagh, Pervez Khan, Kyung-Sup Kwak
2018 International Conference on Info...  ·  01 Oct 2018  ·  doi:10.1109/ictc.2018.8539607
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
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 ...  ·  31 Aug 2018  ·  doi:10.1186/s12911-018-0651-5  ·  PMID: 30170591  ·  PMCID: PMC6119323
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
openRxiv  ·  11 Jul 2018  ·  doi:10.1101/367599
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
Biocuration: Distilling data into knowledge
PLOS Biology  ·  16 Apr 2018  ·  doi:10.1371/journal.pbio.2002846  ·  PMID: 29659566  ·  PMCID: PMC5919672
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 Com...  ·  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
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
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
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
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
Ebtsam Adel, Shaker El-Sappagh, Sherif Barakat, Mohammed Elmogy
International Journal of Computers an...  ·  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, Lucas Lefevre, Clare Pridans, Hiu G. Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, 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
Academics can help shape Wikipedia
Thomas Shafee, Daniel Mietchen, Andrew I. Su
Science  ·  11 Aug 2017  ·  doi:10.1126/science.aao0462  ·  PMID: 28798122
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
openRxiv  ·  10 Jul 2017  ·  doi:10.1101/156141
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
A fuzzy ontology modeling for case base knowledge in diabetes mellitus domain
Shaker El-Sappagh, Mohammed Elmogy
Engineering Science and Technology, a...  ·  01 Jun 2017  ·  doi:10.1016/j.jestch.2017.03.009
EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices
Nikhil Gopal, Andrew Su, Chunlei Wu, Sean D. Mooney
openRxiv  ·  29 Mar 2017  ·  doi:10.1101/121178
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
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
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
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

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
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
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
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
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
Medical Case Based Reasoning Frameworks
Shaker El-Sappagh, Mohammed Mahfouz Elmogy
International Journal of Decision Sup...  ·  01 Jul 2016  ·  doi:10.4018/ijdsst.2016070103
An encoding methodology for medical knowledge using SNOMED CT ontology
Shaker El-Sappagh, Mohammed Elmogy
Journal of King Saud University - Com...  ·  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, Nikhil Gopal, Gregory S. Stupp, Timothy E. Putman, Benjamin J. Ainscough, Obi L. Griffith, Ali Torkamani, 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
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, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B. Gerstein, Andrew F. Hill, Robert R. Kitchen, Jan Lötvall, Tushar Patel, Dena C. Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L. Raffai, Aleksandra Shypitsyna, Andrew I. Su, Clotilde Théry, 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
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
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, Eleni Mina, Zuotian Tatum, Jeroen F. J. Laros, Erik M. van Mulligen, Martijn Schuemie, Emmelien Aten, Tong Shu Li, Richard Bruskiewich, Benjamin M. Good, Andrew I. Su, Jan A. Kors, Johan den Dunnen, 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
Citizen Science for Mining the Biomedical Literature
Ginger Tsueng, Steven M. Nanis, Jennifer Fouquier, Benjamin M Good, Andrew I Su
openRxiv  ·  27 Jan 2016  ·  doi:10.1101/038083

2015

MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services
Jiwen Xin, Adam Mark, Cyrus Afrasiabi, Ginger Tsueng, Moritz Juchler, Nikhil Gopal, Gregory S. Stupp, Timothy E. Putman, Benjamin J. Ainscough, Obi L. Griffith, Ali Torkamani, Patricia L. Whetzel, Christopher J. Mungall, Sean D. Mooney, Andrew I. Su, Chunlei Wu
openRxiv  ·  30 Dec 2015  ·  doi:10.1101/035667
Reviewer Summary for Transactions on Image Processing
IEEE Transactions on Image Processing  ·  01 Dec 2015  ·  doi:10.1109/tip.2015.2488780
UOIT Keyboard: A Constructive Keyboard for Small Touchscreen Devices
Tamer AbuHmed, Kyunghee Lee, DaeHun Nyang
IEEE Transactions on Human-Machine Sy...  ·  01 Dec 2015  ·  doi:10.1109/thms.2015.2449309
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
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, Robert E. Sorge, Loren J. Martin, Dmitri V. Zaykin, Shad B. Smith, Kelen Freitas, Jean-Sebastien Austin, Feng Dai, Jie Zhang, Jaclyn Marcovitz, Alexander H. Tuttle, Peter M. Slepian, Sarah Clarke, Ryan M. Drenan, Jeff Janes, Shakir Al Sharari, Samantha K. Segall, Eske K. Aasvang, Weike Lai, Reinhard Bittner, Christopher I. Richards, Gary D. Slade, Henrik Kehlet, John Walker, Uwe Maskos, Jean-Pierre Changeux, Marshall Devor, William Maixner, Luda Diatchenko, Inna Belfer, Dennis A. Dougherty, Andrew I. Su, 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
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 Engi...  ·  01 Jan 2015  ·  doi:10.1504/ijmei.2015.070116

2014

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 ...  ·  01 Dec 2014  ·  doi:10.1109/infos.2014.7036701
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 ...  ·  01 Dec 2014  ·  doi:10.1109/icces.2014.7030954
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
MyGene.info: gene annotation query as a service
Chunlei Wu, Adam Mark, Andrew I. Su
openRxiv  ·  18 Sep 2014  ·  doi:10.1101/009332
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
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 M...  ·  14 Aug 2014  ·  doi:10.3389/fcimb.2014.00108  ·  PMID: 25177549  ·  PMCID: PMC4132376
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
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, Laura L. McIntyre, Wesley Williams, Nelson Kha, Casey Cruz, Bryan M. Hancock, David P. Nguyen, M. Richard Sayen, Brett J. Hilton, Kelly S. Doran, Anca M. Segall, 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
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
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 Inform...  ·  01 Jan 2014  ·  doi:10.1007/978-3-319-13461-1_45
A distributed clinical decision support system architecture
Shaker H. El-Sappagh, Samir El-Masri
Journal of King Saud University - Com...  ·  01 Jan 2014  ·  doi:10.1016/j.jksuci.2013.03.005

2013

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
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
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
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
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
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
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

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, David Dorward, Alison Downing, Lynsey Fairbairn, Ronan Kapetanovic, Sobia Raza, Andru Tomoiu, Ramiro Alberio, Chunlei Wu, 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
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
Collaboration in social network-based information dissemination
Aziz Mohaisen, Tamer AbuHmed, Ting Zhu, Manar Mohaisen
2012 IEEE International Conference on...  ·  01 Jun 2012  ·  doi:10.1109/ICC.2012.6364127
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

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
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
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

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
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
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, Kihwa Kang, Ella Dragileva, Tammy Gillis, Edith T Lopez, Marie-Josee Boily, 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
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, Weija Ou, Julie Feuerhelm, Mitchell V. Hull, Eric Koesema, Yuping Wang, Jia Zhang, Chunlei Wu, Charles Y. Cho, Andrew I. Su, Serge Batalov, Hong Chen, Kristen Johnson, Bryan Laffitte, Deborah G. Nguyen, Evan Y. Snyder, Peter G. Schultz, Jennifer L. Harris, Scott A. Lesley
Proceedings of the National Academy o...  ·  23 Feb 2010  ·  doi:10.1073/pnas.0914019107  ·  PMID: 20133595  ·  PMCID: PMC2840467

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, Serge Batalov, 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
Software-Based Remote Code Attestation in Wireless Sensor Network
Tamer AbuHmed, Nandinbold Nyamaa, DaeHun Nyang
GLOBECOM 2009 - 2009 IEEE Global Tele...  ·  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, Margaret G. Distler, Meike Teschke, Chunlei Wu, Tim Wiltshire, 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
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
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

2008

Two-level Key Pool Design-based Random Key Pre-distribution in Wireless Sensor Networks
Abedelaziz Mohaisen
KSII Transactions on Internet and Inf...  ·  25 Oct 2008  ·  doi:10.3837/TIIS.2008.05.001
Genetical Genomics: Spotlight on QTL Hotspots
Genetical Genomics: Spotlight on QTL Hotspots
Rainer Breitling, Yang Li, Bruno M. Tesson, Jingyuan Fu, Chunlei Wu, Tim Wiltshire, 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
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
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, Phillip McClurg, Serge Batalov, Genevieve L. Welch, Jie Zhang, Anthony P. Orth, John R. Walker, Richard J. Glynne, Michael P. Cooke, Joseph S. Takahashi, Kazuhiro Shimomura, 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
A survey on deep packet inspection for intrusion detection systems
Magazine of Korea Telecommunication S...  ·  01 Jan 2008  ·  arxiv:arXiv:0803.0037v1

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
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

2006

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, Drew Gunderson, Laura Jarnes, Jason T. Matzen, Michael E. Garcia, Tami L. Hood, Ronak Beigi, Gang Xia, Richard A. Harig, Hayk Asatryan, S. Frank Yan, Yingyao Zhou, Xiang-Ju Gu, Alham Saadat, Vicki Zhou, Frederick J. King, Christopher M. Shaw, Andrew I. Su, Robert Downs, Nathanael S. Gray, Peter G. Schultz, Markus Warmuth, Jeremy S. Caldwell
Proceedings of the National Academy o...  ·  21 Feb 2006  ·  doi:10.1073/pnas.0511292103  ·  PMID: 16492761  ·  PMCID: PMC1413928
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

2005

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
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, Lunjian Zhu, Chunli Yan, Tim Gallaher, Patrick B. Johnston, W. French Anderson, Michael P. Cooke
Proceedings of the National Academy o...  ·  04 Feb 2005  ·  doi:10.1073/pnas.0409459102  ·  PMID: 15695585  ·  PMCID: PMC548308

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, Erica Lagler, Ron Korstanje, Xiaosong Wang, 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
A gene atlas of the mouse and human protein-encoding transcriptomes
Andrew I. Su, Tim Wiltshire, Serge Batalov, Hilmar Lapp, Keith A. Ching, David Block, Jie Zhang, Richard Soden, Mimi Hayakawa, Gabriel Kreiman, Michael P. Cooke, John R. Walker, John B. Hogenesch
Proceedings of the National Academy o...  ·  09 Apr 2004  ·  doi:10.1073/pnas.0400782101  ·  PMID: 15075390  ·  PMCID: PMC395923
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

2002

Genomic analysis of the host response to hepatitis C virus infection
Andrew I. Su, John P. Pezacki, Lisa Wodicka, Amy D. Brideau, Lubica Supekova, Robert Thimme, Stefan Wieland, Jens Bukh, Robert H. Purcell, Peter G. Schultz, Francis V. Chisari
Proceedings of the National Academy o...  ·  19 Nov 2002  ·  doi:10.1073/pnas.202608199  ·  PMID: 12441396  ·  PMCID: PMC137774
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
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 o...  ·  12 Aug 2002  ·  doi:10.1073/pnas.122359899  ·  PMID: 12177410  ·  PMCID: PMC123230
Large-scale analysis of the human and mouse transcriptomes
Andrew I. Su, Michael P. Cooke, Keith A. Ching, Yaron Hakak, John R. Walker, Tim Wiltshire, Anthony P. Orth, Raquel G. Vega, Lisa M. Sapinoso, Aziz Moqrich, Ardem Patapoutian, Garret M. Hampton, Peter G. Schultz, John B. Hogenesch
Proceedings of the National Academy o...  ·  19 Mar 2002  ·  doi:10.1073/pnas.012025199  ·  PMID: 11904358  ·  PMCID: PMC123671

2001

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 o...  ·  20 Feb 2001  ·  doi:10.1073/pnas.041452598  ·  PMID: 11226240  ·  PMCID: PMC30139

Computationally Efficient Cooperative Public Key Authentication Protocols in Ubiquitous Sensor Network
Abedelaziz Mohaisen, Tamer AbuHmed, DaeHun Nyang
Advancements in Distributed Computing...  ·  [no date info]  ·  doi:10.4018/978-1-61350-110-8.ch010

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