Saeed, Fahad
- Associate Professor, School of Computing and Information Sciences , College of Engineering and Computing

Overview
overview
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Fahad Saeed is a tenured Associate Professor in the Knight Foundation School of Computing and Information Sciences at Florida International University (FIU), Miami FL and is the director of Saeed Lab which is a parallel computing and data science group (https://saeedlab.cis.fiu.edu/). His research interests include parallel and distributed algorithms and architectures, computational proteomics, genomics, connectomics and big data problems in computational biology and bioinformatics.
Prior to joining FIU, Prof. Saeed was an Assistant Professor (2014-2018) in the Department of Electrical & Computer Engineering and Department of Computer Science at Western Michigan University (WMU), Kalamazoo Michigan. He was tenured and promoted to the rank of Associate Professor at WMU in July 2018. Dr. Saeed was a Post-Doctoral Fellow and then a Research Fellow in the Systems Biology Center at National Institutes of Health (NIH), Bethesda MD from Aug 2010 to January 2014. He received his PhD in the Department of Electrical and Computer Engineering, University of Illinois at Chicago (UIC) in 2010.
Dr. Saeed has served as the program co-chair of the Bioinformatics and Computational Biology (BICoB) Conference and IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM). He is the founding chair of IEEE Workshop on HPC solutions to Big Data Computational Biology (IEEE HPC-BCB). He also serves on the editorial board of Springer Journal of Network Modeling Analysis in Health Informatics and Bioinformatics since 2014. He has served on numerous IEEE/ACM program committees and is peer-reviewer for more than a dozen journals.
Dr. Saeed is a Senior Member of ACM and also a Senior Member of IEEE. His honors include ThinkSwiss Fellowship (2007, 2008), NIH Postdoctoral Fellowship Award (2010), Fellows Award for Research Excellence (FARE) at NIH (2012), NSF CRII Award (2015), WMU Outstanding New Researcher Award (2016), WMU Distinguished Research and Creative Scholarship Award (2018), and NSF CAREER Award (2017).
research interests
- High performance computing, big data, machine-leanrning, bioinformatics (Proteomics/neuroinformatics)
Scholarly & Creative Works
selected publications
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Article
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2022Unsupervised Structural Classification of Dissolved Organic Matter Based on Fragmentation PathwaysFull Text via DOI: 10.1021/acs.est.1c04726 Web of Science: 000741110700001
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2022Biomedical IoT: Enabling Technologies, Architectural Elements, Challenges, and Future DirectionsFull Text via DOI: 10.1109/ACCESS.2022.3159235 Web of Science: 000773233700001
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2021Communication lower-bounds for distributed-memory computations for mass spectrometry based omics dataFull Text via DOI: 10.1016/j.jpdc.2021.11.001 Web of Science: 000744258500003
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2021SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductionsFull Text via DOI: 10.1371/journal.pone.0259349 Web of Science: 000755042500051
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2021A Deep Learning-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic DatasetsFull Text via DOI: 10.1109/TBDATA.2018.2805687 Web of Science: 000655792600003
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2021ASD-SAENet: A Sparse Autoencoder, and Deep-Neural Network Model for Detecting Autism Spectrum Disorder (ASD) Using fMRI DataFull Text via DOI: 10.3389/fncom.2021.654315 Web of Science: 000642086700001
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2021Benchmarking mass spectrometry based proteomics algorithms using a simulated databaseFull Text via DOI: 10.1007/s13721-021-00298-3 Web of Science: 000633385700001
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2021Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A SurveyFull Text via DOI: 10.1109/ACCESS.2020.3047588 Web of Science: 000608198100001
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2020NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes' factorsFull Text via DOI: 10.1186/s12864-020-07220-7 Web of Science: 000594951400003
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2020Federated Learning: A Survey on Enabling Technologies, Protocols, and ApplicationsFull Text via DOI: 10.1109/ACCESS.2020.3013541 Web of Science: 000556701400001
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2019ASD-DiagNet: A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI DataFull Text via DOI: 10.3389/fninf.2019.00070 Web of Science: 000502132500001
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2018GPU-DAEMON: GPU algorithm design, data management & optimization template for array based big omics dataFull Text via DOI: 10.1016/j.compbiomed.2018.08.015 Web of Science: 000446282300018
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2018MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics AlgorithmsFull Text via DOI: 10.1002/pmic.201800206 Web of Science: 000448086000007
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2017A Hybrid MPI-OpenMP Strategy to Speedup the Compression of Big Next-Generation Sequencing DatasetsFull Text via DOI: 10.1109/TPDS.2017.2692782 Web of Science: 000410653500004
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2016Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressinFull Text via DOI: 10.1038/srep34863 Web of Science: 000385243800001
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2016MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processingFull Text via DOI: 10.1093/bioinformatics/btw023 Web of Science: 000376656900011
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2015Autophagic degradation of aquaporin-2 is an early event in hypokalemia-induced nephrogenic diabetes insipidusFull Text via DOI: 10.1038/srep18311 Web of Science: 000366570500002
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2014Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architecturesFull Text via DOI: 10.1007/s13721-014-0054-1 Web of Science: 000447428800007
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2014A knowledge base of vasopressin actions in the kidneyFull Text via DOI: 10.1152/ajprenal.00012.2014 Web of Science: 000341704300014
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2014Global analysis of the effects of the V2 receptor antagonist satavaptan on protein phosphorylation in collecting ductFull Text via DOI: 10.1152/ajprenal.00497.2013 Web of Science: 000332410700005
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2013PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry dataFull Text via DOI: 10.1186/1477-5956-11-S1-S14 Web of Science: 000328327300014
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2013Proteome-Wide Measurement of Protein Half-Lives and Translation Rates in Vasopressin-Sensitive Collecting Duct CellsFull Text via DOI: 10.1681/ASN.2013030279 Web of Science: 000329911300012
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2012CPhos: A program to calculate and visualize evolutionarily conserved functional phosphorylation sitesFull Text via DOI: 10.1002/pmic.201200189 Web of Science: 000311616000004
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2012Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cellsFull Text via DOI: 10.1152/ajpcell.00260.2012 Web of Science: 000311208900003
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2012Identifying protein kinase target preferences using mass spectrometryFull Text via DOI: 10.1152/ajpcell.00166.2012 Web of Science: 000309527100004
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2012Dynamics of the G Protein-coupled Vasopressin V2 Receptor Signaling Network Revealed by Quantitative PhosphoproteomicsFull Text via DOI: 10.1074/mcp.M111.014613 Web of Science: 000300056200027
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2012A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomesFull Text via DOI: 10.1016/j.jpdc.2011.08.001 Web of Science: 000296997700008
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2012NHLBI-AbDesigner: an online tool for design of peptide-directed antibodiesFull Text via DOI: 10.1152/ajpcell.00325.2011 Web of Science: 000298374100018
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2009A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platformsFull Text via DOI: 10.1016/j.jpdc.2009.03.006 Web of Science: 000266945000007
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Book Chapter
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Conference
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2021Communication-avoiding micro-architecture to compute Xcorr scores for peptide identification. 99-103.Full Text via DOI: 10.1109/FPL53798.2021.00024 Web of Science: 000728589800016
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2021TurboBC: A Memory Efficient and Scalable GPU Based Betweenness Centrality Algorithm in the Language of Linear AlgebraFull Text via DOI: 10.1145/3458744.3474047 Web of Science: 000747651900032
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2021Real-time peptide identification from high-throughput mass-spectrometry data. 1-1.Full Text via DOI: 10.1145/3459930.3470856
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2021Search feasibility in distributed MS-proteomics big data. 1-1.Full Text via DOI: 10.1145/3459930.3470855
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2021TurboBFS: GPU Based Breadth-First Search (BFS) Algorithms in the Language of Linear Algebra. 520-528.Full Text via DOI: 10.1109/IPDPSW52791.2021.00084 Web of Science: 000689576200066
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2021A Multi-Factorial Assessment of Functional Human Autistic Spectrum Brain Network Analysis. 3526-3531.Full Text via DOI: 10.1109/BIBM52615.2021.9669679
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2021DeepCOVIDNet: Deep Convolutional Neural Network for COVID-19 Detection from Chest Radiographic Images. 1703-1710.Full Text via DOI: 10.1109/BIBM52615.2021.9669767
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2021Graph Theoretic Approach for the Analysis of Comprehensive Mass-Spectrometry (MS/MS) Data of Dissolved Organic Matter. 3742-3746.Full Text via DOI: 10.1109/BIBM52615.2021.9669289
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2019
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2019
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2019Optimized CNN-based Diagnosis System to Detect the Pneumonia from Chest Radiographs. 2405-2412.Web of Science: 000555804900417
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2019Auto-ASD-Network: A Technique Based on Deep Learning and Support Vector Machines for Diagnosing Autism Spectrum Disorder using fMRI Data. 646-651.Full Text via DOI: 10.1145/3307339.3343482 Web of Science: 000722622700113
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2019LBE: A Computational Load Balancing Algorithm for Speeding up Parallel Peptide Search in Mass-Spectrometry based Proteomics. 191-198.Full Text via DOI: 10.1109/IPDPSW.2019.00040 Web of Science: 000543704600027
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2019GPU-DFC: A GPU-based parallel algorithm for computing dynamic-functional connectivity of big fMRI data. 114-121.Full Text via DOI: 10.1109/BigDataService.2019.00022 Web of Science: 000593976100015
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2018Parallel Sampling-Pipeline for Indefinite Stream of Heterogeneous Graphs using OpenCL for FPGAs. 4752-4761.Web of Science: 000468499304121
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2018A Fourier-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic Datasets. 128-134.Full Text via DOI: 10.1109/BigDataCongress.2018.00024 Web of Science: 000450160400016
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2018Similarity based classification of ADHD using Singular Value Decomposition. 19-25.Full Text via DOI: 10.1145/3203217.3203239 Web of Science: 000455156500005
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2017
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2017
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2017An Out-of-Core GPU based Dimensionality Reduction Algorithm for Big Mass Spectrometry Data and Its Application in Bottom-up Proteomics. 550-555.Full Text via DOI: 10.1145/3107411.3107466 Web of Science: 000426494700067
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2017GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Big fMRI Data. 723-728.Full Text via DOI: 10.1145/3107411.3108173 Web of Science: 000426494700151
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2017A New Cryptography Algorithm to Protect Cloud-based Healthcare Services. 37-43.Full Text via DOI: 10.1109/CHASE.2017.57 Web of Science: 000426965000007
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2016GPU-ArraySort: A parallel, in-place algorithm for sorting large number of arrays. 78-87.Full Text via DOI: 10.1109/ICPPW.2016.27 Web of Science: 000392498600011
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2016A Parallel Peptide Indexer and Decoy Generator for Crux Tide using OpenMP. 411-418.Web of Science: 000389590600056
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2016A Variable-Length Network Encoding Protocol for Big Genomic Data. 212-224.Full Text via DOI: 10.1007/978-3-319-33936-8_17 Web of Science: 000389727600017
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2016Data Aware Communication for Energy Harvesting Sensor Networks. 121-132.Full Text via DOI: 10.1007/978-3-319-33936-8_10 Web of Science: 000389727600010
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2015Big Data Proteogenomics and High Performance Computing: Challenges and Opportunities. 141-145.Web of Science: 000380477600030
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2015A Parallel Algorithm for Compression of Big Next-Generation Sequencing Datasets. 196-201.Full Text via DOI: 10.1109/Trustcom.2015.632 Web of Science: 000380431400027
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2015Design and Implementation of Network Transfer Protocol for Big Genomic Data. 281-288.Full Text via DOI: 10.1109/BigDataCongress.2015.47 Web of Science: 000380443700037
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2015
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2015
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2014CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling. 128-141.Full Text via DOI: 10.1109/TCBB.2013.152 Web of Science: 000336659800014
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2012An efficient algorithm for clustering of large-scale mass spectrometry data. 516-519.Full Text via DOI: 10.1109/BIBM.2012.6392738
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2012High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems. 667-672.Full Text via DOI: 10.1145/2382936.2383056
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2009Multiple Sequence Alignment System for Pyrosequencing Reads. 362-+.Web of Science: 000265785800034
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Other Scholarly Work
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Preprint
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Review
Research
principal investigator on
- Multimodal Machine-Learning and High Performance Computing Strategies for Big MS Proteomics Data awarded by General Medical Sciences 2020 - 2023
- CAREER: Towards Fast and Scalable Algorithms for Big Proteogenomics Data Analytics awarded by National Science Foundation 2018 - 2023
- I-Corps: Utilizing Machine learning and Artificial Intelligence (AI) for Early Detection and Identification of Mental Disorders awarded by National Science Foundation 2021 - 2022
- CRII: SHF: HPC Solutions to Big NGS Data Compression awarded by National Science Foundation 2018 - 2020
Contact
full name
- Fahad Saeed
Identifiers
ORCID iD
- https://orcid.org/0000-0002-3410-9552 (confirmed)
visualizations
publication subject areas
Citation index-derived subject areas the researcher has published in