Papers

Publications

Preprints

Predicting peptide properties from mass spectrometry data using deep attention-based multitask network and uncertainty quantification

Tariq, Usman; Saeed, Fahad; , bioRxiv :1-22 (2024).

MLSPred-Bench: ML-Ready Benchmark Leveraging Seizure Detection EEG data for Predictive Models

Mohammad, Umair; Saeed, Fahad; , bioRxiv :1-8 (2024).

In Press

Utilizing Pretrained Vision Transfomers and Large Language Models for Epileptic Seizure Prediction

Parani, Paras; Mohammad, Umair; Saeed, Fahad; , Proceedings of the 8th International Conference on Data Science and Machine Learning (CDMA 2024) :1-8 (2024).

2024

PVTAD: Alzheimer’s Disease Diagnosis Using Pyramid Vision Transformer Applied to White Matter of T1-Weighted Structural MRI Data Aghdam, Maryam Akhavan; Bozdag, Serdar; Saeed, Fahad; Alzheimer’s Disease Neuroimaging Initiative; , Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI) :1-4 (2024).	Making MS Omics Data ML-Ready: SpeCollate Protocols Tariq,Muhammad Usman; Ebert, Samuel; Saeed, Fahad;, Springer Protein Bioinformatics :142-162 (2024).
Heterogeneity Aware Distributed Machine Learning at the Wireless Edge for Health IoT Applications: An EEG Data Case Study Mohammad, Umair; Saeed, Fahad; , Springer Distributed Machine Learning and Computing: Theory and Applications :33-70 (2024).	Communication Evaluation of a Wireless 4-Channel Wearable EEG for Brain-Computer Interface (BCI) and Healthcare Applications Bhattarai, Abhishek; Mohammad, Umair; Saeed, Fahad; , IEEE SoutheastCon 2024 :902-903 (2024).

2023

Systems and methods for matching mass spectrometry data with a peptide database Kumar, Sumesh; Saeed, Fahad; , US Patent 11,842,799 (2023).	Statistical and Machine Learning Analysis of the Human Brain Functional Network in a Multi-Site Resting-State Functional MRI Database Framework Artiles, Oswaldo; Saeed, Fahad; , (2023).
Q-CASA Invited Speakers Quantum-Centric Supercomputing Strategies for Neuroscience problems: Challenges and Progress Loredo, Robert; Saeed, Fahad; , IEEE 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) :499-499 (2023).	PPAD: a deep learning architecture to predict progression of Alzheimer’s disease Al Olaimat, Mohammad; Martinez, Jared; Saeed, Fahad; Bozdag, Serdar; Alzheimer’s Disease Neuroimaging Initiative; , Oxford University Press Bioinformatics 39 :i149-i157 (2023).
High Performance Computing Algorithms for Accelerating Peptide Identification from Mass-Spectrometry Data Using Heterogeneous Supercomputers Haseeb, Muhammad; Saeed, Fahad; , (2023).	GPU-acceleration of the distributed-memory database peptide search of mass spectrometry data Haseeb, Muhammad; Saeed, Fahad; , Nature Publishing Group UK London Scientific Reports 13 :18713 (2023).
Energy Efficient AI/ML based Continuous Monitoring at the Edge: ECG and EEG Case Study Mohammad, Umair; Saeed, Fahad; , IEEE 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) :3313-3320 (2023).	Description of Dissolved Organic Matter Transformational Networks at the Molecular Level Leyva, Dennys; Usman Tariq, Muhammad; Jaffé, Rudolf; Saeed, Fahad; Fernandez-Lima, Francisco; , American Chemical Society Environmental Science & Technology 57 :2672-2681 (2023).
Confounding Effects on the Performance of Machine Learning Analysis of Static Functional Connectivity Computed from rs-fMRI Multi-site Data Artiles, Oswaldo; Al Masry, Zeina; Saeed, Fahad; , Springer US New York Neuroinformatics 21 :651-668 (2023).	ASD-GResTM: Deep Learning Framework for ASD classification using Gramian Angular Field Almuqhim, Fahad; Saeed, Fahad; , IEEE 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) :2837-2843 (2023).
22nd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2023) de Melo, Alba Cristina MA; Kalyanaraman, Ananth; Saeed, Fahad; Bozdag, Serdar; Ahmed, Zeeshan; Alser, Mohammed; Awan, Muaaz Gul; Baur, Brittany; Bhowmick, Sanjukta; Bose, Banabithi; , (2023).

2022

Unsupervised structural classification of dissolved organic matter based on fragmentation pathways Leyva, Dennys; Tariq, Muhammad Usman; Jaffé, Rudolf; Saeed, Fahad; Lima, Francisco Fernandez; , American Chemical Society Environmental Science & Technology 56 :1458-1468 (2022).	Systems and methods for peptide identification Saeed, Fahad; Haseeb, Muhammad; , US Patent 11,309,061 (2022).
Systems and methods for measuring similarity between mass spectra and peptides Saeed, Fahad; Tariq, Muhammad Usman; , US Patent 11,251,031 (2022).	Systems And Methods For Diagnosing Autism Spectrum Disorder Using fMRI Data Saeed, Fahad; Almuqhim, Fahad; , US Patent 11,379,981 (2022).
SPERTL: Epileptic Seizure Prediction using EEG with ResNets and Transfer Learning Mohammad, Umair; Saeed, Fahad; , IEEE 2022 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) :1-5 (2022).	Re-configurable Hardware for Computational Proteomics Saeed, Fahad; Haseeb, Muhammad; Kumar, Sumesh; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :111-124 (2022).
Need for High-Performance Computing for MS-Based Omics Data Analysis Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :1-5 (2022).	Molecular level characterization of DOM along a freshwater-to-estuarine coastal gradient in the Florida Everglades Leyva, Dennys; Jaffé, Rudolf; Courson, Jessica; Kominoski, John S; Tariq, Muhammad Usman; Saeed, Fahad; Fernandez-Lima, Francisco; , Springer International Publishing Cham Aquatic Sciences 84 :63 (2022).
Machine-Learning and the Future of HPC for MS-Based Omics Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :125-129 (2022).	Introduction to Mass Spectrometry Data Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :7-19 (2022).
High-Performance Computing Strategy Using Distributed-Memory Supercomputers Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :37-56 (2022).	High-Performance Algorithms for Mass Spectrometry-Based Omics Saeed, Fahad; Haseeb, Muhammad; , Springer (2022).
G-MSR: A GPU-Based Dimensionality Reduction Algorithm Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :99-110 (2022).	Fast Spectral Pre-processing for Big MS Data Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :57-75 (2022).
Existing HPC Methods and the Communication Lower Bounds for Distributed-Memory Computations for Mass Spectrometry-Based Omics Data Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :21-35 (2022).	Computational CPU-GPU Template for Pre-processing of Floating-Point MS Data Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :89-97 (2022).
Communication lower-bounds for distributed-memory computations for mass spectrometry based omics data Saeed, Fahad; Haseeb, Muhammad; Iyengar, SS; , Academic Press Journal of Parallel and Distributed Computing 161 :37-47 (2022).	Classification of Autism Spectrum Disorder Using rs-fMRI data and Graph Convolutional Networks Yang, Tianren; Al-Duailij, Mai A; Bozdag, Serdar; Saeed, Fahad; , IEEE 2022 IEEE International Conference on Big Data (Big Data) :3131-3138 (2022).
Biomedical IoT: Enabling Technologies, Architectural Elements, Challenges, and Future Directions Aledhari, Mohammed; Razzak, Rehma; Qolomany, Basheer; Al-Fuqaha, Ala; Saeed, Fahad; , IEEE IEEE Access 10 :31306-31339 (2022).	A Easy to Use Generalized Template to Support Development of GPU Algorithms Saeed, Fahad; Haseeb, Muhammad; , Springer High-Performance Algorithms for Mass Spectrometry-Based Omics :77-87 (2022).

2021

TurboBFS: GPU Based Breadth-First Search (BFS) Algorithms in the Language of Linear Algebra Artiles, Oswaldo; Saeed, Fahad; , IEEE 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) :520-528 (2021).	TurboBC: A Memory Efficient and Scalable GPU Based Betweenness Centrality Algorithm in the Language of Linear Algebra Artiles, Oswaldo; Saeed, Fahad; , :1-10 (2021).
SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions Tariq, Muhammad Usman; Saeed, Fahad; , Public Library of Science San Francisco, CA USA PloS one 16 :e0259349 (2021).	Source data: high performance computing framework for tera-scale database search of mass spectrometry data Haseeb, Muhammad; Saeed, Fahad; , (2021).
Simulation Testbed for Evaluating Distributed Querying and Searching of Mass Spectrometry Big Data in a Network-based Infrastructure Mohammad, Umair; Saeed, Fahad; , IEEE 2021 IEEE Seventh International Conference on Big Data Computing Service and Applications (BigDataService) :137-142 (2021).	Search feasibility in distributed MS-proteomics big data Mohammad, Umair; Saeed, Fahad; , :1-1 (2021).
Real-time peptide identification from high-throughput mass-spectrometry data Kumar, Sumesh; Saeed, Fahad; , (2021).	Neural Engineering Techniques for Autism Spectrum Disorder: Volume 1: Imaging and Signal Analysis El-Baz, Ayman S; Suri, Jasjit S; , Academic Press (2021).
Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey Tariq, Muhammad Usman; Haseeb, Muhammad; Aledhari, Mohammed; Razzak, Rehma; Parizi, Reza M; Saeed, Fahad; , IEEE IEEE Access (2021).	Machine Learning methods for diagnosing Autism Spectrum Disorder and Attention-deficit/Hyperactivity Disorder using functional and structural MRI: A Survey Eslami, Taban; Almuqhim, Fahad; Raiker, Joseph S; Saeed, Fahad; , Frontiers Frontiers in Neuroinformatics 14 :62 (2021).
High performance computing framework for tera-scale database search of mass spectrometry data Haseeb, Muhammad; Saeed, Fahad; , Nature Publishing Group Nature computational science 1 :550-561 (2021).	HiCOPS: High Performance Computing Framework for Tera-Scale Database Search of Mass Spectrometry based Omics Data Haseeb, Muhammad; Saeed, Fahad; , (2021).
Graph Theoretic Approach for the Analysis of Comprehensive Mass-Spectrometry (MS/MS) Data of Dissolved Organic Matter Tariq, Muhammad Usman; Leyvay, Dennys; Limaz, Francisco Alberto Fernandez; Saeed, Fahad; , IEEE 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) :3742-3746 (2021).	Explainable and scalable machine learning algorithms for detection of autism spectrum disorder using fMRI data Eslami, Taban; Raiker, Joseph S; Saeed, Fahad; , Academic Press Neural Engineering Techniques for Autism Spectrum Disorder :39-54 (2021).
DeepCOVIDNet: Deep Convolutional Neural Network for COVID-19 Detection from Chest Radiographic Images Ahmed, Khandaker Mamun; Eslami, Taban; Saeed, Fahad; Amini, M Hadi; , IEEE 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) :1703-1710 (2021).	Communication-avoiding micro-architecture to compute Xcorr scores for peptide identification Kumar, Sumesh; Saeed, Fahad; , IEEE 2021 31st International Conference on Field-Programmable Logic and Applications (FPL) :99-103 (2021).
Benchmarking mass spectrometry based proteomics algorithms using a simulated database Awan, Muaaz Gul; Awan, Abdullah Gul; Saeed, Fahad; , Springer Vienna Vienna Network Modeling Analysis in Health Informatics and Bioinformatics 10 :23 (2021).	ASD-SAENet: a sparse autoencoder, and deep-neural network model for detecting autism spectrum disorder (ASD) using fMRI data Almuqhim, Fahad; Saeed, Fahad; , Frontiers Media SA Frontiers in Computational Neuroscience 15 :654315 (2021).
A Multi-Factorial Assessment of Functional Human Autistic Spectrum Brain Network Analysis Artiles, Oswaldo; Saeed, Fahad; , IEEE 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) :3526-3531 (2021).

2020

ASD-DiagNet: A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data Eslami T, Mirjalili V, Fong A, Laird AR, Saeed F, Front Neuroinform 13 :70 (2020).	NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes’ factors Wen, Bronte; Jung, Hyun Jun; Chen, Lihe; Saeed, Fahad; Knepper, Mark A; , BioMed Central BMC genomics 21 :1-7 (2020).
Methods and systems for compressing data Saeed, Fahad; Haseeb, Muhammad; , US Patent 10,810,180 (2020).	High Performance and Machine Learning Algorithms for Brain fMRI Data Eslami, Taban; , Western Michigan University (2020).
Federated learning: A survey on enabling technologies, protocols, and applications Aledhari, Mohammed; Razzak, Rehma; Parizi, Reza M; Saeed, Fahad; , IEEE IEEE Access 8 :140699-140725 (2020).

2019

Slm-transform: A method for memory-efficient indexing of spectra for database search in lc-ms/ms proteomics Haseeb, Muhammad; Awan, Muaaz G; Cadigan, Alexander S; Saeed, Fahad; , Cold Spring Harbor Laboratory bioRxiv :531681 (2019).	Optimized CNN-based diagnosis system to detect the pneumonia from chest radiographs Aledhari, Mohammed; Joji, Shelby; Hefeida, Mohamed; Saeed, Fahad; , IEEE 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) :2405-2412 (2019).
NGS‐Integrator: A Tool for Combining Information from Multiple Genome‐Wide NGS Data Tracks Using Minimum Bayes Factors Jung, Hyun Jun; Wen, Bronte; Chen, Lihe; Saeed, Fahad; Knepper, Mark A; , The Federation of American Societies for Experimental Biology The FASEB Journal 33 :637.2-637.2 (2019).	LBE: A Computational Load Balancing Algorithm for Speeding up Parallel Peptide Search in Mass-Spectrometry based Proteomics Haseeb, Muhammad; Afzali, Fatima; Saeed, Fahad; , (2019).
High-Performance Reductive Strategies for Big Data from LC-MS/MS Proteomics Awan, Muaaz Gul; , Western Michigan University (2019).	GPU-SFFT: A GPU based parallel algorithm for computing the Sparse Fast Fourier Transform (SFFT) of k-sparse signals Artiles, Oswaldo; Saeed, Fahad; , IEEE 2019 IEEE International Conference on Big Data (Big Data) :3303-3311 (2019).
GPU-DFC: A GPU-based parallel algorithm for computing dynamic-functional connectivity of big fMRI data Eslami, Taban; Saeed, Fahad; , (2019).	Efficient shared peak counting in database peptide search using compact data structure for fragment-ion index Haseeb, Muhammad; Saeed, Fahad; , IEEE 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) :275-278 (2019).
Auto-ASD-Network: A technique based on Deep Learning and Support Vector Machines for diagnosing Autism Spectrum Disorder using fMRI data Eslami, Taban; Saeed, Fahad; , (2019).	ASD-DiagNet: A hybrid learning approach for detection of Autism Spectrum Disorder using fMRI data Eslami, Taban; Mirjalili, Vahid; Fong, Alvis; Laird, Angela; Saeed, Fahad; , Frontiers Frontiers in Neuroinformatics 13 :70 (2019).
2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Haseeb, Muhammad; Saeed, Fahad; , (2019).

2018

Towards quantifying psychiatric diagnosis using machine learning algorithms and big fMRI data Saeed, Fahad; , BMC BMC Big Data Analytics 3 :7 (2018).	Similarity based classification of ADHD using Singular Value Decomposition Eslami, Taban; Saeed, Fahad; , (2018).
Parallel sampling-pipeline for indefinite stream of heterogeneous graphs using OpenCL for FPGAs Tariq, Muhammad Usman; Saeed, Fahad; , IEEE 2018 IEEE International Conference on Big Data (Big Data) :4752-4761 (2018).	MaSS‐Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms Awan, Muaaz Gul; Saeed, Fahad; , Wiley PROTEOMICS (2018).
GPU-DAEMON: GPU algorithm design, data management & optimization template for array based big omics data Awan, Muaaz Gul; Eslami, Taban; Saeed, Fahad; , Pergamon Computers in biology and medicine 101 :163-173 (2018).	Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson’s Correlation Coefficients for Time Series Data - An fMRI Study Eslami, Taban; Saeed, Fahad; , MDPI High-Throughput Journal (2018).
A Fourier-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic Datasets Aledhari, Mohammed; Pierro, Marianne Di; Saeed, Fahad; , (2018).	A deep learning-based data minimization algorithm for fast and secure transfer of big genomic datasets Aledhari, Mohammed; Di Pierro, Marianne; Hefeida, Mohamed; Saeed, Fahad; , IEEE IEEE Transactions on Big Data 7 :271-284 (2018).

2017

Scalable data structure to compress next-generation sequencing files and its application to compressive genomics Pérez, Sandino Vargas; Saeed, Fahad; , IEEE 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) :1923-1928 (2017).	Power-Efficient and Highly Scalable Parallel Graph Sampling using FPGAs Tariq, Usman; Cheema, Umer; Saeed, Fahad; , (2017).
GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Big fMRI Data Eslami, Taban; Awan, Muaaz Gul; Saeed, Fahad; , :723-728 (2017).	An out-of-core gpu based dimensionality reduction algorithm for big mass spectrometry data and its application in bottom-up proteomics Awan, Muaaz Gul; Saeed, Fahad; , :550-555 (2017).
A new cryptography algorithm to protect cloud-based healthcare services Aledhari, Mohammed; Marhoon, Ali; Hamad, Ali; Saeed, Fahad; , IEEE 2017 IEEE/ACM International Conference on Connected Health: Applications, Systems and Engineering Technologies (CHASE) :37-43 (2017).	A Hybrid MPI-OpenMP Strategy to Speedup the Compression of Big Next-Generation Sequencing Datasets Vargas-Perez, Sandino; Saeed, Fahad; , (2017).

2016

Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin Sandoval, Pablo C; Claxton, J’Neka S; Lee, Jae Wook; Saeed, Fahad; Hoffert, Jason D; Knepper, Mark A; , Nature Publishing Group UK London Scientific reports 6 :34863 (2016).	Selected Papers from BICoB2015 BICoB; , World Scientific (2016).
Reductive Analytics on Big MS Data leads to tremendous reduction in time for peptide deduction Awan, Muaaz Gul; Saeed, Fahad; , Cold Spring Harbor Laboratory bioRxiv :73064 (2016).	MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing Awan, Muaaz Gul; Saeed, Fahad; , Oxford University Press Bioinformatics 32 :1518-1526 (2016).
Introduction to the selected papers from the 7th International Conference on Bioinformatics and Computational Biology (BICoB 2015) Saeed, Fahad; Haspel, Nurit; Al-Mubaid, Hisham; , World Scientific Publishing Company Journal of Bioinformatics and Computational Biology 14 :1602002 (2016).	GPU-ArraySort: A parallel, in-place algorithm for sorting large number of arrays Awan, Muaaz; Saeed, Fahad; , (2016).
Data Aware Communication for Energy Harvesting Sensor Networks Hefeida, Mohamed S; Saeed, Fahad; , Springer International Publishing Wired/Wireless Internet Communications: 14th IFIP WG 6.2 International Conference, WWIC 2016, Thessaloniki, Greece, May 25-27, 2016, Proceedings 14 :121-132 (2016).	A variable-length network encoding protocol for big genomic data Aledhari, Mohammed; Hefeida, Mohamed S; Saeed, Fahad; , Springer International Publishing Wired/Wireless Internet Communications: 14th IFIP WG 6.2 International Conference, WWIC 2016, Thessaloniki, Greece, May 25-27, 2016, Proceedings 14 :212-224 (2016).
A Parallel Peptide Indexer and Decoy Generator for Crux Tide using OpenMP Maabreh, Majdi; Gupta, Ajay; Saeed, Fahad; , IEEE 2016 International Conference on High Performance Computing Simulation (HPCS) :411-418 (2016).

2015

On the sampling of big mass spectrometry data Awan, Muaaz Gul; Saeed, Fahad; , :143-148 (2015).	Design and implementation of network transfer protocol for big genomic data Aledhari, Mohammed; Saeed, Fahad; , IEEE 2015 IEEE International Congress on Big Data :281-288 (2015).
Big data proteogenomics and high performance computing: Challenges and opportunities Saeed, Fahad; , IEEE 2015 IEEE Global Conference on Signal and Information Processing (GlobalSIP) :141-145 (2015).	Autophagic degradation of aquaporin-2 is an early event in hypokalemia-induced nephrogenic diabetes insipidus Khositseth, Sookkasem; Uawithya, Panapat; Somparn, Poorichaya; Charngkaew, Komgrid; Thippamom, Nattakan; Hoffert, Jason D; Saeed, Fahad; Michael Payne, D; Chen, Shu-Hui; Fenton, Robert A; , Nature Publishing Group UK London Scientific reports 5 :18311 (2015).
A parallel algorithm for compression of big next-generation sequencing datasets Pérez, Sandino Vargas; Saeed, Fahad; , IEEE 2015 IEEE Trustcom/BigDataSE/ISPA 3 :196-201 (2015).	A High Performance Architecture for an Exact Match Short-Read Aligner Using Burrows-Wheeler Aligner on FPGAs Qader, Dana Abdul; , (2015).

2014

Global analysis of the effects of the V2 receptor antagonist satavaptan on protein phosphorylation in collecting duct Hoffert, Jason D; Pisitkun, Trairak; Saeed, Fahad; Wilson, Justin L; Knepper, Mark A; , American Physiological Society Bethesda, MD American Journal of Physiology-Renal Physiology 306 :410-421 (2014).	Foreword to the special issue on selected papers from the 6th International Conference on Bioinformatics and Computational Biology (BICoB 2014). Saeed, Fahad; Al-Mubaid, Hisham; Dasgupta, Bhaskar; , 12 :1402001-1402001 (2014).
Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architectures Saeed, Fahad; Hoffert, Jason D; Pisitkun, Trairak; Knepper, Mark A; , Springer Vienna Network Modeling Analysis in Health Informatics and Bioinformatics 3 :1-19 (2014).	Cams-rs: clustering algorithm for large-scale mass spectrometry data using restricted search space and intelligent random sampling Saeed, Fahad; Hoffert, Jason D; Knepper, Mark A; , IEEE Computer Society Press IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 11 :128-141 (2014).
A knowledge base of vasopressin actions in the kidney Sanghi, Akshay; Zaringhalam, Matthew; Corcoran, Callan C; Saeed, Fahad; Hoffert, Jason D; Sandoval, Pablo; Pisitkun, Trairak; Knepper, Mark A; , American Physiological Society Bethesda, MD American Journal of Physiology-Renal Physiology 307 :F747-F755 (2014).	6th International Conference on Bioinformatics and Computational Biology (BICoB 2014) Saeed, Fahad; DasGupta, B; , (2014).

2013

Quantitative phosphoproteomics implicates clusters of proteins involved in cell‐cell adhesion and transcriptional regulation in the vasopressin signaling network Bolger, Steven J; Hurtado, Patricia A Gonzales; Hoffert, Jason D; Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; , The Federation of American Societies for Experimental Biology (2013).	Proteome-wide measurement of protein half-lives and translation rates in vasopressin-sensitive collecting duct cells Sandoval, Pablo C; Slentz, Dane H; Pisitkun, Trairak; Saeed, Fahad; Hoffert, Jason D; Knepper, Mark A; , LWW Journal of the American Society of Nephrology 24 :1793-1805 (2013).
PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data Saeed, Fahad; Pisitkun, Trairak; Hoffert, Jason D; Rashidian, Sara; Wang, Guanghui; Gucek, Marjan; Knepper, Mark A; , BioMed Central Proteome science 11 :1-15 (2013).	Foreword to the special issue on selected papers from the 5th International Conference on Bioinformatics and Computational Biology (BICoB 2013) Dasgupta, Bhaskar; Al-Mubaid, Hisham; Saeed, Fahad; , Imperial College Press Journal of Bioinformatics and Computational Biology 11 :1302002 (2013).
A high performance algorithm for clustering of large-scale protein mass spectrometry data using multi-core architectures Saeed, Fahad; Hoffert, Jason D; Knepper, Mark A; , :923-930 (2013).	A Graphical User Interface (GUI) for Phosphorylation Site Assignment of Protein Mass Spectrometry Data Saeed, Fahad; , (2013).

2012

Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells Bolger, Steven J; Hurtado, Patricia A Gonzales; Hoffert, Jason D; Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; , American Physiological Society Bethesda, MD American Journal of Physiology-Cell Physiology 303 :C1006-C1020 (2012).	Proteomic and Metabolomic Approaches to Cell Physiology and Pathophysiology: Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells Bolger, Steven J; Hurtado, Patricia A Gonzales; Hoffert, Jason D; Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; , American Physiological Society American Journal of Physiology-Cell Physiology 303 :C1006 (2012).
NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies Pisitkun, Trairak; Hoffert, Jason D; Saeed, Fahad; Knepper, Mark A; , American Physiological Society Bethesda, MD American Journal of Physiology-Cell Physiology 302 :C154-C164 (2012).	Identifying protein kinase target preferences using mass spectrometry Douglass, Jacqueline; Gunaratne, Ruwan; Bradford, Davis; Saeed, Fahad; Hoffert, Jason D; Steinbach, Peter J; Knepper, Mark A; Pisitkun, Trairak; , American Physiological Society Bethesda, MD American Journal of Physiology-Cell Physiology 303 :C715-C727 (2012).
High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems Saeed, Fahad; Hoffert, Jason; Pisitkun, Trairak; Knepper, Mark; , :667-672 (2012).	Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics Hoffert, Jason D; Pisitkun, Trairak; Saeed, Fahad; Song, Jae H; Chou, Chung-Lin; Knepper, Mark A; , Elsevier Molecular & cellular proteomics 11 (2012).
CP hos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites Zhao, Boyang; Pisitkun, Trairak; Hoffert, Jason D; Knepper, Mark A; Saeed, Fahad; , 12 :3299-3303 (2012).	An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data Saeed, Fahad; Pisitkun, Trairak; Hoffert, Jason D; Wang, Guanghui; Gucek, Marjan; Knepper, Mark A; , IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops :618-625 (2012).
An efficient algorithm for clustering of large-scale mass spectrometry data Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; Hoffert, Jason D; , IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine :1-4 (2012).	A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq; , Academic Press Journal of parallel and distributed computing 72 :83-93 (2012).

2011

Mining temporal patterns from iTRAQ mass spectrometry (LC-MS/MS) data Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; Hoffert, Jason D; , (2011).	Mapping‐based temporal pattern mining algorithm (MTPMA) identifies unique clusters of phosphopeptides regulated by vasopressin in collecting duct Saeed, Fahad; Hoffert, Jason; Pisitkun, Trairak; Knepper, Mark; , Federation of American Societies for Experimental Biology (2011).
Large‐scale iTRAQ‐based quantification of phosphorylation changes during vasopressin signaling Hoffert, Jason; Pisitkun, T; Saeed, F; Song, J; Knepper, M; , Federation of American Societies for Experimental Biology (2011).

2010

Parallel Algorithm for Center Star Sequence and Alignments with Applications to Short Reads Saeed, Fahad; Khokhar, Ashfaq; , (2010).	High performance computational biology algorithms Saeed, Fahad; , University of Illinois at Chicago (2010).
A graph-theoretic framework for efficient computation of HMM based motif finder Saeed, Fahad; Burger, Lukas; Khokhar, Ashfaq; Zavolan, Mihaela; , (2010).

2009

Pyro-align: Sample-align based multiple alignment system for pyrosequencing reads of large number Saeed, Fahad; , (2009).	Multiple sequence alignment system for pyrosequencing reads Saeed, Fahad; Khokhar, Ashfaq; Zagordi, Osvaldo; Beerenwinkel, Niko; , Springer Berlin Heidelberg Bioinformatics and Computational Biology: First International Conference, BICoB 2009, New Orleans, LA, USA, April 8-10, 2009. Proceedings :362-375 (2009).
An Overview of Multiple Sequence Alignment Systems Saeed, Fahad; Khokhar, Ashfaq; , (2009).	A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platforms Saeed, Fahad; Khokhar, Ashfaq; , Academic Press Journal of Parallel and Distributed Computing 69 :666-677 (2009).

2008

Sample-align-d: A high performance multiple sequence alignment system using phylogenetic sampling and domain decomposition

Saeed, Fahad; Khokhar, Ashfaq; , IEEE 2008 IEEE International Symposium on Parallel and Distributed Processing :1-9 (2008).