Muhammad Haseeb

PhD Student

B.Sc. - University of Engineering & Technology (UET), Lahore

PhD Dissertation: High Performance Computing Algorithms for Accelerating Peptide Identification from Mass-Spectrometry Data Using Heterogeneous Supercomputers

First position: Post-Doctoral Scholar at Lawrence Berkeley National Laboratory (Berkeley Lab)

Research

[method-development] HPC Engine for Mass Spectrometry based Omics Data

Papers

  1. High Performance Computing Algorithms for Accelerating Peptide Identification from Mass-Spectrometry Data Using Heterogeneous Supercomputers

  2. GPU-acceleration of the distributed-memory database peptide search of mass spectrometry data

  3. Systems and methods for peptide identification

  4. Re-configurable Hardware for Computational Proteomics

  5. Need for High-Performance Computing for MS-Based Omics Data Analysis

  6. Machine-Learning and the Future of HPC for MS-Based Omics

  7. Introduction to Mass Spectrometry Data

  8. High-Performance Computing Strategy Using Distributed-Memory Supercomputers

  9. High-Performance Algorithms for Mass Spectrometry-Based Omics

  10. G-MSR: A GPU-Based Dimensionality Reduction Algorithm

  11. Fast Spectral Pre-processing for Big MS Data

  12. Existing HPC Methods and the Communication Lower Bounds for Distributed-Memory Computations for Mass Spectrometry-Based Omics Data

  13. Computational CPU-GPU Template for Pre-processing of Floating-Point MS Data

  14. Communication lower-bounds for distributed-memory computations for mass spectrometry based omics data

  15. A Easy to Use Generalized Template to Support Development of GPU Algorithms

  16. Source data: high performance computing framework for tera-scale database search of mass spectrometry data

  17. Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey

  18. High performance computing framework for tera-scale database search of mass spectrometry data

  19. HiCOPS: High Performance Computing Framework for Tera-Scale Database Search of Mass Spectrometry based Omics Data

  20. Methods and systems for compressing data

  21. Slm-transform: A method for memory-efficient indexing of spectra for database search in lc-ms/ms proteomics

  22. LBE: A Computational Load Balancing Algorithm for Speeding up Parallel Peptide Search in Mass-Spectrometry based Proteomics

  23. Efficient shared peak counting in database peptide search using compact data structure for fragment-ion index

  24. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)