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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
Lightweight Transformer exhibits comparable performance to LLMs for Seizure Prediction: A case for light-weight models for EEG data
Parani, Paras; Mohammad, Umair; Saeed, Fahad; ,
Proceedings of the 2024 IEEE International Conference on Big Data workshop HPC-BOD 2024
:1-5 (2024).
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).
Knight Foundation School of Computing and Information Sciences (KFSCIS)
Florida International University (FIU)
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