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Publications

* Indicates Corresponding and/or Senior Author

Edited Volumes

  1. Proceedings of 7th International Conference on Bioinformatics and Computational Biology (BICoB), with Hisham Al-Mubaid and Nurit Haspel, March 2015.
  2. Proceedings of 6th International Conference on Bioinformatics and Computational Biology (BICoB), with Bhaskar Dasgupta, Hisham Al-Mubaid and Nurit Haspel, March 2014.
  3. Special issue on selected papers from the 5th international conference on bioinformatics and computational biology (BICoB 2013) with Bhaskar Dasgupta and Hisham Al-Mubaid, Journal of Bioinformatics and Computational Biology (JBCB) Volume 11, Issue 05, October 2013
  4. Proceedings of 5th International Conference on Bioinformatics and Computational Biology (BICoB), with Bhaskar Dasgupta, Hisham Al-Mubaid and Reda Al-Hajj (ISBN: 978-1-880843-89-5), March 2013
  5. Proceedings of 4th International Conference on Bioinformatics and Computational Biology (BICoB), with Hisham Al-Mubaid and Ashfaq Khokhar (ISBN: 978-1-880843-85-7), March 2012

Journal Publications (peer-reviewed)

  1. Sandino Vargas-Pérez and Fahad Saeed*, "A Hybrid MPI-OpenMP Strategy to Speedup the Compression of Big Next-Generation Sequencing Datasets", IEEE Transactions on Parallel and Distributed Systems, March 2017 Tech Report | IEEE Xplore
  2. Pablo C. Sandoval, J’Neka S. Claxton, Jae Wook Lee, Fahad Saeed, Jason D. Hoffert and Mark A. Knepper, "Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin", Nature Scientific Reports, Vol. 6, article number 34863, October 2016 Nature | PubMed
  3. Muaaz Awan and Fahad Saeed*, "MS-REDUCE: An ultrafast technique for reduction of Big Mass Spectrometry Data for high-throughput processing", accepted in Oxford Bioinformatics, Jan 2016 Tech Report | PubMedOxford
  4. Sookkasem Khositseth, Panapat Uawithya, Poorichaya Somparn, Komgrid Charngkaew, Nattakan Thippamom, Jason D. Hoffert, Fahad Saeed, D. Michael Payne, Shu Hui Chen, Robert A. Fenton and Trairak Pisitkun, "Autophagic degradation of aquaporin-2 is an early event in hypokalemia-induced nephrogenic diabetes insipidus", Nature Scientific Reports, Dec 2015 Nature | PubMed
  5. Akshay Sanghi, Matthew Zaringhalam, Callan Corcoran, Fahad Saeed, Jason D. Hoffert, Pablo C Sandoval, Trairak Pisitkun, and Mark A. Knepper, "A Knowledge Base of Vasopressin Actions in Kidney", American Journal of Physiology, July 2014 AJP | PubMed
  6. Fahad Saeed*, Jason Hoffert, Trairak Pisitkun, Mark Knepper, "Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architectures"Network Modeling Analysis in Health Informatics and Bioinformatics, Vol. 3, No. 1, pp 1-19, Feb. 2014 Springer | PubMed
  7. Jason D. HoffertTrairak PisitkunFahad SaeedJustin L. Wilson and, Mark A. Knepper, "Global analysis of the effects of the V2 receptor antagonist satavaptan on protein phosphorylation in collecting duct ", American Journal of Physiology, Vol. 306, No. 410-421, Feb. 2014 AJP | PubMed 
  8. Fahad Saeed*, Jason Hoffert and Mark Knepper, "CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data using Restricted Search Space and Intelligent Random-Sampling",  IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.11, No.1, pp.128,141, Jan. 2014 Tech Report | PubMed | IEEE Xplore
  9. Fahad Saeed*, Trairak Pisitkun, Jason D. Hoffert, Sara Rashidian, Guanghui Wang, Marjan Gucek, and Mark A. Knepper, "PhosSA: Fast and Accurate Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data", Proteome Science Volume 11, Supplement 1, November 2013 Proteome Science | PubMed
  10. Pablo C. Sandoval, Dane H. Slentz, Trairak Pisitkun, Fahad Saeed, Jason D. Hoffert and Mark A. Knepper, "Proteome-wide measurement of protein half-lives and translation rates in vasopressin-sensitive collecting duct cells", Journal of the American Society of Nephrology (JASN), March 2013 JASN PubMed
  11. Steven Bolger, Patricia Gonzales Hurtado, Jason Hoffert, Fahad Saeed, Trairak Pisitkun, and Mark Knepper, "Quantitative Phosphoproteomics in Nuclei of Vasopressin-Sensitive Renal Collecting Duct Cells", American Journal of Physiology (AJP), September 2012 AJP | PubMed
  12. Boyang Zhao, Trairak Pisitkun, Jason D. Hoffert, Mark A. Knepper, and Fahad Saeed*, "CPhos: A Program to Calculate and Visualize Evolutionarily Conserved Functional Phosphorylation Sites", Wiley PROTEOMICS, August 2012 Wiley | PubMed
  13. Jacqueline Douglass, Ruwan Gunaratne, Davis Bradford, Fahad Saeed, Jason D. Hoffert, Peter J. Steinbach, Mark A. Knepper, and Trairak Pisitkun, "Identifying Protein Kinase Target Preferences Using Mass Spectrometry", American Journal of Physiology (AJP), June 2012 AJP | PubMed
  14. Fahad Saeed, Alan Perez-Rathke, Jaroslaw Gwarnicki, Tanya Berger-Wolf, Ashfaq Khokhar, "A High Performance Multiple Sequence Alignment System for Pyrosequencing Reads from Multiple Reference Genomes", Journal of Parallel and Distributed Computing (JPDC), Volume 72, Issue 1, Pages 83-93, January 2012 JPDC |PubMed
  15. Jason D. Hoffert, Trairak Pisitkun, Fahad Saeed, Jae H. Song, Chung-Lin Chou, and Mark A. Knepper, "Dynamics of the G protein-coupled vasopressin V2 receptor Signaling Network revealed by Quantitative Phosphoproteomics" Mol Cell Proteomics (MCP), Feb 2012 MCP | PubMed
  16. Trairak Pisitkun, Jason D. Hoffert, Fahad Saeed and Mark Knepper, "NHLBI-AbDesigner: An online tool for design of peptide-directed antibodies", American Journal of Physiology (AJP), Jan 2012 AJP | PubMed
  17. Fahad Saeed, Ashfaq Khokhar, "A Domain Decomposition Strategy for Alignment of Multiple Biological Sequences on Multiprocessor Platforms", Journal of Parallel and Distributed Computing (JPDC) Vol 69, Issue 7, July 2009 arXiv:0905.1744v1 | JPDC
  18. Fahad Saeed, Ashfaq Khokhar, Osvaldo Zagordi and Niko Beerenwinkel. "Multiple Sequence Alignment System for Pyrosequencing Reads" Lecture Notes in Computer Science (LNCS), Volume 5462/2009, 2009 arXiv:0901.2753 | Springer  

 Conference publications (peer-reviewed)

  1. Usman Tariq, Umer Cheema and Fahad Saeed*, "Power-Efficient and Highly Scalable Parallel Graph Sampling using FPGAs", Proceedings of International Conference on Reconfigurable Computing and FPGAs (ReConFig), Cancun, Mexico, December 4-6, 2017 Tech Report
  2. Sandino Vargas-P'erez and Fahad Saeed*, "Scalable Data Structure to Compress Next-Generation Sequencing Files and its Application to Compressive Genomics", Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Kansas City, MO, USA, Nov 13-16, 2017 Tech Report
  3. Muaaz Gul Awan and Fahad Saeed*, "An Out-of-Core GPU based dimensionality reduction algorithm for Big Mass Spectrometry Data and its application in bottom-up Proteomics", Proceedings of ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)Boston MA, August 2017 Tech Report
  4. Taban Eslami, Muaaz Gul Awan and Fahad Saeed*, "GPU-PCC: A GPU based technique to compute pairwise Pearson's Correlation Coefficients for big fMRI data", Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio), Proceedings of ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)Boston MA, August 2017 Tech Report
  5. Mohammed Aledhari, Ali Marhoon, Ali Al-Qaabi, and Fahad Saeed*, "A New Cryptography Algorithm to Protect Cloud-based Healthcare Services", Proceedings of Workshop on Safe, Energy-Aware, & Reliable Connected Health, IEEE/ACM Conference on Connected Health: Applications, Systems and Engineering Technologies (IEEE/ACM CHASE-SEARCH), Philadelphia PA, July 2017
  6. Muaaz Gul Awan and Fahad Saeed*, "GPU-ArraySort: A parallel, in-place algorithm for sorting large number of arrays", Proceedings of Workshop on High Performance Computing for Big Data, International Conference on Parallel Processing (ICPP-2016), Philadelphia PA, August 2016 Tech Report | IEEE Xplore
  7. Majdi Maabreh, Ajay Gupta and Fahad Saeed*, "A Parallel Peptide Indexer and Decoy Generator for Crux Tide using OpenMP", Proceedings of Workshop on High Performance Computing Systems for Biomedical, Bioinformatics and Life Sciences, International Conference on High Performance Computing & Simulation (HPCS 2016), Innsbruck, Austria, July 2016 IEEE Xplore
  8. Mohammed Aledhari, Mohamed S Hefeida and Fahad Saeed*, "A Variable-Length Network Encoding Protocol for Big Genomic Data", Proceedings of International Conference on Wired & Wireless Internet Communications (WWIC 2016), Thessaloniki, Greece May 2016 Springer
  9. Mohamed S Hefeida and Fahad Saeed*, "Data Aware Communication for Energy Harvesting Sensor Networks", Proceedings of International Conference on Wired & Wireless Internet Communications (WWIC 2016), Thessaloniki, Greece May 2016 Springer
  10. Fahad Saeed*,  "Big Data Proteogenomics and High Performance Computing: Challenges and Opportunities", Symposium on Signal and Information Processing for Software-Defined Ecosystems, and Green Computing, Proceedings of IEEE Global Conference on Signal and Information Processing (IEEE GlobalSIP), Orlando Florida, Dec 2015 Tech Report | IEEE Xplore
  11. Sandino N. V. Perez and Fahad Saeed*,  "A Parallel Algorithm for Compression of Big Next-Generation Sequencing (NGS) Datasets", Proceedings of Parallel and Distributed Processing with Applications (IEEE ISPA-15), Vol.3. pp. 196-201 Helsinki Finland, Aug 2015 Tech Report | IEEE Xplore
  12. Mohammed Aledhari and Fahad Saeed*, "Design and Implementation of Network Transfer Protocol for Big Genomic Data", Proceedings of IEEE International Congress on Big Data (IEEE BigData Congress), pp. 281-288, New York City, USA, June 2015 (18% acceptance rate) Tech Report | IEEE Xplore
  13. Muaaz Awan and Fahad Saeed*, "On the sampling of Big Mass Spectrometry Data", Proceedings of Bioinformatics and Computational Biology (BICoB) Conference, Honolulu Hawaii, March 2015 Tech Report
  14. Fahad Saeed*, Jason D. Hoffert, and Mark A. Knepper, "A High Performance Algorithm for Clustering of Large-Scale Protein Mass Spectrometry Data using Multi-Core Architectures", proceedings of IEEE/ACM International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics (HI-BI-BI), August 2013 (25%  acceptance rate for full papers) Tech Report | IEEE Xplore
  15. Fahad Saeed*, Trairak Pisitkun, Jason Hoffert, Guanghui Wang, Marjan Gucek, and Mark Knepper, "An Efficient Dynamic Programming Algorithm for Phosphorylation Site Assignment of Large-Scale Mass Spectrometry Data", International Workshop on Computational Proteomics, proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia USA, Oct 2012 (20% acceptance rate) IEEE XplorePubMed
  16. Fahad Saeed*, Trairak Pisitkun, Jason Hoffert, and Mark A. Knepper, "High Performance Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data using Multicore Systems", accepted in International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio), ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Orlando Florida USA, Oct 2012 (33 papers accepted out of 159 papers submitted: 21% acceptance rate) ACM | Tech Report 
  17. Fahad Saeed*, Trairak Pisitkun, Mark Knepper, and Jason Hoffert, "An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data", accepted in IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philidelphia USA, Oct 2012. (62 short paper accepted out of 299 papers submitted: 20.7 % acceptance rate) IEEE Xplore | arXiv:1301.0834 | PubMed
  18. Fahad Saeed* and Ashfaq Khokhar, "Parallel Algorithm for Center-Star Sequence Alignments with applications to Short Reads" accepted in 4th International Conference on Bioinformatics and Computational Biology (BICoB), Las Vegas, Nevada, USA, March 12 - 14, 2012 
  19. Fahad Saeed*, Trairak Pisitkun, Mark A. Knepper, and Jason D. Hoffert, "Mining Temporal Patterns from iTRAQ Mass Spectrometry(LC-MS/MS) Data" In proceedings of Bioinformatics and Computational Biology Conference (BICoB) pp 152-159, New Orleans USA, March 23-25, 2011 arXiv:1104.5510v1
  20. Fahad Saeed and Ashfaq Khokhar, "Sample-Align-D: A High Performance Multiple Sequence Alignment System using Phylogenetic Sampling and Domain Decomposition", in Proc. IEEE International Workshop on High Performance Computational Biology (HiCOMB 2008), IPDPS, Monday, April 14, 2008. arXiv:0901.2742 | IEEE Xplore

Abstracts and Technical Reports       

  1. Steven J Bolger, Patricia A Gonzales, Jason D Hoffert, Fahad Saeed, Trairak Pisitkun and Mark A Knepper, "Quantitative phosphoproteomics implicates clusters of proteins involved in cell-cell adhesion and transcriptional regulation in the vasopressin signaling network." FASEB JOURNAL. Vol. 27. 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA: FEDERATION AMER SOC EXP BIOL, 2013.
  2. Boyang Zhao, Trairak Pisitkun, Jason D. Hoffert, Mark A. Knepper, and Fahad Saeed, "An Information Theory-Based Approach to Assess the Functional Significance of Phosphorylation Sites in Proteomes of Renal Tubule Epithelia", poster at International Society of  Nephrology (ISN) Symposium, Ann Arbor Michigan, USA, June 2012
  3. Fahad Saeed, J. Hoffert, P. Pisitkun, M. Knepper, "Mapping-based temporal pattern mining algorithm identifies unique clusters of phosphopeptides regulated by vasopressin in collecting duct", meeting abstracts Experimental Biology (EB),  Washington DC, USA  April 2011
  4. J. Hoffert, T. Pisitkun, Fahad Saeed, J. Song, M. Knepper, "Large-scale iTRAQ-based quantification of phosphorylation changes during vasopressin signaling", Featured Topic and abstract Experimental Biology (EB) , Washington DC USA  April 2011
  5. Fahad Saeed and Ashfaq Khokhar, "Parallel Algorithm for Center Star Sequence and Alignments with applications to short readsInternational conference on bioinformatics and computational biology (ACM-BCB) Poster Session, in August 2010
  6. Fahad Saeed, Lukas Burger, Ashfaq Khokhar, and Mihaela Zavolan, "A graph-theoretic framework for efficient computation of HMM based motif finder", Technical Report, University of Illinois at Chicago, Jan 2010
  7. Fahad Saeed and Lukas Burger "High Performance Graph Theoretic model for finding Regulatory Elements and motifs", Technical Report, Zavolan Group, Swiss Institute of Bioinformatics (SIB), University of Basel Switzerland, August 2009
  8. Fahad Saeed"Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number", Technical Report, Beerenwinkel Group Computational Biology, Department of Biosystems Science and Engineering, Eth Zurich Switzerland, August 2008. arXiv:0901.2751
  9. Fahad Saeed and Ashfaq Khokhar, "An overview of multiple sequence alignments and their limitations", Technical Report, Multimedia System Laboratory, University of Illinois at Chicago, May 2007 arXiv:0901.2747

Talks and Presentations

  1. "Big Data Proteomics: High Performance Computing Methods & Applications", at School of Science & Engineering, Lahore University of Management Science (LUMS), Lahore Pakistan, January 2015 (Invited Seminar)
  2. "Solving Big Data Problems in Computational Biology using High Performance Architectures and Algorithms", at Department of Electrical Engineering and Computer Systems, University of Cincinnati, Cincinnati Ohio, November 2013
  3. "Big Data Problems in high-throughput Genomics and Proteomics", at Cincinnati Children’s Hospital Medical Center, Cincinnati Ohio, November 2013
  4. "Solving Big Data Problems in Computational Biology using High Performance Architectures and Algorithms", at Department of Computer Science, Western Michigan University, Kalamazoo MI , October 2013
  5. "Solving Big Data Problems in Computational Biology using High Performance Architectures and Algorithms", at Department of Electrical and Computer Engineering, Western Michigan University, Kalamazoo MI , August 2013
  6. "Solving Big Data Problems in Computational Biology using High Performance Architectures and Algorithms", at Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington DC, August 2013
  7. "Clustering and Consensus of Large-Scale Mass Spectrometry Data", Work in Progress Series, Systems Biology Interest Group, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), May 2013.
  8. "High Performance Algorithm Engineering for Large-Scale Next Generation Genomics (NGS) Data", at Computer Science Department, University of Massachusetts Boston, Boston MA, March 2013.
  9. "High Performance Algorithm Engineering for Large-Scale Next Generation Genomics (NGS) Data", at Electrical, Computer and Systems Engineering Department, Rensselaer Polytechnic Institute (RPI), Albany NY, March 2013
  10. "High Performance Algorithm Engineering for Large-Scale Next Generation Genomics (NGS) Data", at Electrical and Computer Engineering Department, George Washington University, Washington DC, Feb 2013.
  11. "High Performance Algorithm Engineering for Large-Scale Next Generation Sequencing (NGS) Data", at Center for Genome Research and Biocomputing (CGBC), Oregon State University, Corvallis Oregon, Oct 2012.
  12. "An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data", IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia Pennsylvania, Oct 2012
  13. "
  14. An Effi.cient Dynamic Programming Algorithm for Phosphorylation Site Assignment of Large-Scale Mass 
  15. Spectrometry Data", 
  16. International workshop on computational proteomics, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia Pennsylvania, Oct 2012
  17. "HPC approaches to computational problems in high-throughput genomics and proteomics", at Electrical and Computer Engineering Department, State University of New york (SUNY) at Binghamton, Feb 2012
  18. "A graph theoretic approach to spectral clustering of mass spectrometry data", Systems Biology Interest Group, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Jan 2012
  19. "Computational problems in large-scale protein phosphorylation studies using iTRAQ labeled LC MS/MS data", Bioinformatics and Computational Biology Conference (BICoB), New Orleans USA, March 24, 2011
  20. "Dynamic Programming Algorithm for Phosphorylation Site Assignment of Mass Spectrometry Data", Systems Biology Interest Group, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Feb 2011
  21. "Challenges in multiple alignment of huge number of pyrosequencing reads on multiprocessor platforms", at Institute of Genetic Medicine, Keck School of medicine, University of Southern California (USC), March 2010
  22. "Challenges in multiple alignment of huge number of pyrosequencing reads on multiprocessor platforms", at school of medicine, University of Colorado at Denver, Feb 2010
  23. "How to multiple align huge number of short reads", at CAMDA Oct 2009. (Invited)
  24. "An Efficient Multiple Alignment system for Pyrosequencing Reads", at BICoB April 09.
  25. "Online scheduling of equal length Jobs on Parallel Machines", Seminar UIC CS501, Dec 08.
  26. "A Domain Decomposition strategy for Multiple Alignment of Biological Reads", at Laboratory of Computational Population Biology UIC, Nov 08. (Invited)
  27. "A Sampling based High Performance Multiple Alignment systems", at HICOMB IPDPS, April 08.
  28. "An overview of Multiple Alignment systems, parallel approaches and their limitations", Seminar UIC CS502, May 07.

Others

  • Fahad Saeed, "High performance computational biology algorithms", (Doctoral dissertation). Retrieved from ProQuest Dissertations and Theses (Accession Order No. AAT 3431281, ISBN: 9781124308067) ProQuest
  • Fahad Saeed, "Securing Suparco's Computer Networks and Linux Operating Systems", Research Report Suparco's Computer Networks X11/04/2006-I, made official on April 2006
  • Fahad Saeed, Fahad Ali Arshad and Salman Javed "Design and Implementation of Linux based wireless ad-hoc network", Linux Focus, article 390  LinuxFocus