Sample-Align-D: A high performance Multiple Sequence Alignment system using phylogenetic sampling and domain decomposition. - Fahad Saeed; Ashfaq A. Khokhar (IPDPS, 2008)

Multiple Sequence Alignment System for Pyrosequencing Reads. - Fahad Saeed; Ashfaq A. Khokhar; Osvaldo Zagordi; Niko Beerenwinkel (BICoB, 2009)

An Overview of Multiple Sequence Alignment Systems - Fahad Saeed; Ashfaq A. Khokhar (CoRR, 2009)

Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number - Fahad Saeed (CoRR, 2009)

A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platforms. - Fahad Saeed; Ashfaq A. Khokhar (J. Parallel Distributed Comput., 2009)

Mining Temporal Patterns from iTRAQ Mass Spectrometry(LC-MS/MS) Data. - Fahad Saeed; Trairak Pisitkun; Mark A. Knepper; Jason D. Hoffert (BICoB, 2011)

High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems. - Fahad Saeed; Jason D. Hoffert; Trairak Pisitkun; Mark A. Knepper (BCB, 2012)

An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data. - Fahad Saeed; Trairak Pisitkun; Jason D. Hoffert; Guanghui Wang 015; Marjan Gucek; Mark A. Knepper (BIBM Workshops, 2012)

An efficient algorithm for clustering of large-scale mass spectrometry data. - Fahad Saeed; Trairak Pisitkun; Mark A. Knepper; Jason D. Hoffert (BIBM, 2012)

A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes. - Fahad Saeed; Alan Perez-Rathke; Jaroslaw Gwarnicki; Tanya Y. Berger-Wolf; Ashfaq A. Khokhar (J. Parallel Distributed Comput., 2012)

A high performance algorithm for clustering of large-scale protein mass spectrometry data using multi-core architectures. - Fahad Saeed; Jason D. Hoffert; Mark A. Knepper (ASONAM, 2013)

Foreword to the Special Issue on Selected Papers from the 5th International Conference on Bioinformatics and Computational Biology (Bicob 2013). - Bhaskar DasGupta; Hisham Al-Mubaid; Fahad Saeed (J. Bioinform. Comput. Biol., 2013)

Foreword. - Fahad Saeed; Hisham Al-Mubaid; Bhaskar DasGupta (J. Bioinform. Comput. Biol., 2014)

Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architectures. - Fahad Saeed; Jason D. Hoffert; Trairak Pisitkun; Mark A. Knepper (Netw. Model. Anal. Health Informatics Bioinform., 2014)

CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling. - Fahad Saeed; Jason D. Hoffert; Mark A. Knepper (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Design and Implementation of Network Transfer Protocol for Big Genomic Data. - Mohammed Aledhari; Fahad Saeed (BigData Congress, 2015)

Big data proteogenomics and high performance computing: Challenges and opportunities. - Fahad Saeed (GlobalSIP, 2015)

A Parallel Algorithm for Compression of Big Next-Generation Sequencing Datasets. - Sandino Vargas Perez; Fahad Saeed (TrustCom/BigDataSE/ISPA (3), 2015)

GPU-ArraySort: A Parallel, In-Place Algorithm for Sorting Large Number of Arrays. - Muaaz Gul Awan; Fahad Saeed (ICPP Workshops, 2016)

A parallel peptide indexer and decoy generator for crux tide using OpenMP. - Majdi Maabreh; Ajay Gupta 001; Fahad Saeed (HPCS, 2016)

A Variable-Length Network Encoding Protocol for Big Genomic Data. - Mohammed Aledhari; Mohamed S. Hefeida; Fahad Saeed (WWIC, 2016)

Data Aware Communication for Energy Harvesting Sensor Networks. - Mohamed S. Hefeida; Fahad Saeed (WWIC, 2016)

MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing. - Muaaz Gul Awan; Fahad Saeed (Bioinform., 2016)

Introduction to the selected papers from the 7th International Conference on Bioinformatics and Computational Biology (BICoB 2015). - Fahad Saeed; Nurit Haspel; Hisham Al-Mubaid (J. Bioinform. Comput. Biol., 2016)

An Out-of-Core GPU based Dimensionality Reduction Algorithm for Big Mass Spectrometry Data and Its Application in Bottom-up Proteomics. - Muaaz Gul Awan; Fahad Saeed (BCB, 2017)

GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Big fMRI Data. - Taban Eslami; Muaaz Gul Awan; Fahad Saeed (BCB, 2017)

Scalable data structure to compress next-generation sequencing files and its application to compressive genomics. - Sandino Vargas Perez; Fahad Saeed (BIBM, 2017)

A New Cryptography Algorithm to Protect Cloud-Based Healthcare Services. - Mohammed Aledhari; Ali F. Marhoon; Ali Hamad; Fahad Saeed (CHASE, 2017)

Power-efficient and highly scalable parallel graph sampling using FPGAs. - Muhammad Usman Tariq; Umer I. Cheema; Fahad Saeed (ReConFig, 2017)

A Hybrid MPI-OpenMP Strategy to Speedup the Compression of Big Next-Generation Sequencing Datasets. - Sandino Vargas Perez; Fahad Saeed (IEEE Trans. Parallel Distributed Syst., 2017)

A Fourier-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic Datasets. - Mohammed Aledhari; Marianne Di Pierro; Fahad Saeed (BigData Congress, 2018)

Parallel Sampling-Pipeline for Indefinite Stream of Heterogeneous Graphs using OpenCL for FPGAs. - Muhammad Usman Tariq; Fahad Saeed (IEEE BigData, 2018)

Similarity based classification of ADHD using singular value decomposition. - Taban Eslami; Fahad Saeed (CF, 2018)

Efficient Resource Distribution in Cloud and Fog Computing. - Mubashar Mehmood; Nadeem Javaid; Junaid Akram; Sadam Hussain Abbasi; Abdul Rahman; Fahad Saeed (NBiS, 2018)

GPU-DAEMON: GPU algorithm design, data management & optimization template for array based big omics data. - Muaaz Gul Awan; Taban Eslami; Fahad Saeed (Comput. Biol. Medicine, 2018)

Auto-ASD-Network: A Technique Based on Deep Learning and Support Vector Machines for Diagnosing Autism Spectrum Disorder using fMRI Data. - Taban Eslami; Fahad Saeed (BCB, 2019)

Optimized CNN-based Diagnosis System to Detect the Pneumonia from Chest Radiographs. - Mohammed Aledhari; Shelby Joji; Mohamed Hefeida; Fahad Saeed (BIBM, 2019)

Efficient Shared Peak Counting in Database Peptide Search Using Compact Data Structure for Fragment-Ion Index. - Muhammad Haseeb; Fahad Saeed (BIBM, 2019)

GPU-SFFT: A GPU based parallel algorithm for computing the Sparse Fast Fourier Transform (SFFT) of k-sparse signals. - Oswaldo Artiles; Fahad Saeed (IEEE BigData, 2019)

GPU-DFC: A GPU-Based Parallel Algorithm for Computing Dynamic-Functional Connectivity of Big fMRI Data. - Taban Eslami; Fahad Saeed (BigDataService, 2019)

LBE: A Computational Load Balancing Algorithm for Speeding up Parallel Peptide Search in Mass-Spectrometry Based Proteomics. - Muhammad Haseeb; Fatima Afzali; Fahad Saeed (IPDPS Workshops, 2019)

ASD-DiagNet: A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data. - Taban Eslami; Vahid Mirjalili; Alvis Cheuk M. Fong; Angela R. Laird; Fahad Saeed (Frontiers Neuroinformatics, 2019)

Federated Learning: A Survey on Enabling Technologies, Protocols, and Applications. - Mohammed Aledhari; Rehma Razzak; Reza M. Parizi; Fahad Saeed (IEEE Access, 2020)

Explainable and Scalable Machine-Learning Algorithms for Detection of Autism Spectrum Disorder using fMRI Data. - Taban Eslami; Joseph S. Raiker; Fahad Saeed (CoRR, 2020)

Communication Lower-Bounds for Distributed-Memory Computations for Mass Spectrometry based Omics Data. - Fahad Saeed (CoRR, 2020)

Machine Learning Methods for Diagnosing Autism Spectrum Disorder and Attention- Deficit/Hyperactivity Disorder Using Functional and Structural MRI: A Survey. - Taban Eslami; Fahad Almuqhim; Joseph S. Raiker; Fahad Saeed (Frontiers Neuroinformatics, 2020)

Real-time peptide identification from high-throughput mass-spectrometry data. - Sumesh Kumar; Fahad Saeed (BCB, 2021)

Search feasibility in distributed MS-proteomics big data. - Umair Mohammad; Fahad Saeed (BCB, 2021)

DeepCOVIDNet: Deep Convolutional Neural Network for COVID-19 Detection from Chest Radiographic Images. - Khandaker Mamun Ahmed; Taban Eslami; Fahad Saeed; M. Hadi Amini (BIBM, 2021)

A Multi-Factorial Assessment of Functional Human Autistic Spectrum Brain Network Analysis. - Oswaldo Artiles; Fahad Saeed (BIBM, 2021)

Graph Theoretic Approach for the Analysis of Comprehensive Mass-Spectrometry (MS/MS) Data of Dissolved Organic Matter. - Muhammad Usman Tariq; Dennys Leyvay; Francisco Alberto Fernandez Limaz; Fahad Saeed (BIBM, 2021)

Simulation Testbed for Evaluating Distributed Querying and Searching of Mass Spectrometry Big Data in a Network-based Infrastructure. - Umair Mohammad; Fahad Saeed (BigDataService, 2021)

Communication-avoiding micro-architecture to compute Xcorr scores for peptide identification. - Sumesh Kumar; Fahad Saeed (FPL, 2021)

TurboBC: A Memory Efficient and Scalable GPU Based Betweenness Centrality Algorithm in the Language of Linear Algebra. - Oswaldo Artiles; Fahad Saeed (ICPP Workshops, 2021)

TurboBFS: GPU Based Breadth-First Search (BFS) Algorithms in the Language of Linear Algebra. - Oswaldo Artiles; Fahad Saeed (IPDPS Workshops, 2021)

Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey. - Muhammad Usman Tariq; Muhammad Haseeb; Mohammed Aledhari; Rehma Razzak; Reza M. Parizi; Fahad Saeed (IEEE Access, 2021)

HiCOPS: High Performance Computing Framework for Tera-Scale Database Search of Mass Spectrometry based Omics Data. - Muhammad Haseeb; Fahad Saeed (CoRR, 2021)

ASD-SAENet: A Sparse Autoencoder, and Deep-Neural Network Model for Detecting Autism Spectrum Disorder (ASD) Using fMRI Data. - Fahad Almuqhim; Fahad Saeed (Frontiers Comput. Neurosci., 2021)

High performance computing framework for tera-scale database search of mass spectrometry data. - Muhammad Haseeb; Fahad Saeed (Nat. Comput. Sci., 2021)

Benchmarking mass spectrometry based proteomics algorithms using a simulated database. - Muaaz Gul Awan; Abdullah Gul Awan; Fahad Saeed (Netw. Model. Anal. Health Informatics Bioinform., 2021)

Smart delivery and retrieval of swab collection kit for COVID-19 test using autonomous Unmanned Aerial Vehicles. - Fahad Saeed; Amjad Mehmood; Muhammad Faran Majeed; Carsten Maple; Khalid Saeed 004; Muhammad Kashif Khattak; Huihui Wang 001; Gregory Epiphaniou (Phys. Commun., 2021)

A Deep Learning-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic Datasets. - Mohammed Aledhari; Marianne Di Pierro; Mohamed Hefeida; Fahad Saeed (IEEE Trans. Big Data, 2021)

SPERTL: Epileptic Seizure Prediction using EEG with ResNets and Transfer Learning. - Umair Mohammad; Fahad Saeed (BHI, 2022)

Classification of Autism Spectrum Disorder Using rs-fMRI data and Graph Convolutional Networks. - Tianren Yang; Mai A. Al-Duailij; Serdar Bozdag; Fahad Saeed (IEEE Big Data, 2022)

Biomedical IoT: Enabling Technologies, Architectural Elements, Challenges, and Future Directions. - Mohammed Aledhari; Rehma Razzak; Basheer Qolomany; Ala I. Al-Fuqaha; Fahad Saeed (IEEE Access, 2022)

Communication lower-bounds for distributed-memory computations for mass spectrometry based omics data. - Fahad Saeed; Muhammad Haseeb; S. S. Iyengar 001 (J. Parallel Distributed Comput., 2022)

High-Performance Algorithms for Mass Spectrometry-Based Omics - Fahad Saeed; Muhammad Haseeb; Sumesh Kumar (Springer, 2022)

ASD-GResTM: Deep Learning Framework for ASD classification using Gramian Angular Field. - Fahad Almuqhim; Fahad Saeed (BIBM, 2023)

Energy Efficient AI/ML based Continuous Monitoring at the Edge: ECG and EEG Case Study. - Umair Mohammad; Fahad Saeed (BIBM, 2023)

Q-CASA Invited Speakers Quantum-Centric Supercomputing Strategies for Neuroscience problems: Challenges and Progress. - Robert Loredo; Fahad Saeed (IPDPS Workshops, 2023)

PPAD: a deep learning architecture to predict progression of Alzheimer's disease. - Mohammad Al Olaimat; Jared Martinez; Fahad Saeed; Serdar Bozdag (Bioinform., 2023)

Confounding Effects on the Performance of Machine Learning Analysis of Static Functional Connectivity Computed from rs-fMRI Multi-site Data. - Oswaldo Artiles; Zeina Al Masry; Fahad Saeed (Neuroinformatics, 2023)

Lightweight Transformer exhibits comparable performance to LLMs for Seizure Prediction: A case for light-weight models for EEG data. - Paras Parani; Umair Mohammad; Fahad Saeed (IEEE Big Data, 2024)

Robustness of ML-Based Seizure Prediction Using Noisy EEG Data From Limited Channels. - Umair Mohammad; Fahad Saeed (DCOSS-IoT, 2024)

Pvtad: Alzheimer's Disease Diagnosis Using Pyramid Vision Transformer Applied to White Matter of T1-Weighted Structural Mri Data. - Maryam Akhavan Aghdam; Serdar Bozdag; Fahad Saeed (ISBI, 2024)

Machine-learning models for Alzheimer's disease diagnosis using neuroimaging data: survey, reproducibility, and generalizability evaluation. - Maryam Akhavan Aghdam; Serdar Bozdag; Fahad Saeed (Brain Informatics, 2025)