Selected Publications

Articles In Academic Journals

Year Title
2017 An effective computational method incorporating multiple secondary structure predictions in topology determination for cryo-EM images.  IEEE/ACM transactions on computational biology and bioinformatics. 578-586.
2017 GPU-accelerated high-fidelity simulation of beam-beam effects in particle colliders.  Simulation Series.
2017 Long-Term Simulations of Beam-Beam Dynamics on GPUs
2017 Near Real-Time Probabilistic Damage Diagnosis Using Surrogate Modeling and High Performance Computing
2016 A Memory-Efficient Parallel Simulation of Electron Beam Dynamics Using GPUs.  23th Annual IEEE International Conference on High Performance Computing.
2015 A dynamic programming algorithm for finding the optimal placement of a secondary structure topology in Cryo-EM data.  Journal of Computational Biology. 837-843.
2015 ISQuest: Finding insertion sequences in prokaryotic sequence fragment data.  Bioinformatics. btv388.
2014 Solving the Secondary Structure Matching Problem in CryoEM De Novo Modeling using a Constrained K-shortest Path Graph Algorithm.  IEEE/ACM transactions on computational biology and bioinformatics. 1.
2013 High-performance implementation of planted motif problem on multicore and GPU.  Concurrency and Computation: Practice and Experience. 1340-1355.
2012 Improved efficiency in cryo-EM secondary structure topology determination from inaccurate data.  Journal of bioinformatics and computational biology. 1242006.
2012 Upper and lower I/O bounds for pebbling r-pyramids.  Journal of Discrete Algorithms. 2-12.
2012 Vertex isoperimetric parameter of a computation graph.  International Journal of Foundations of Computer Science. 941-964.
2011 Ranking valid topologies of the secondary structure elements using a constraint graph.  Journal of bioinformatics and computational biology. 415-430.
2011 Using an Automated Web Harvesting System to Track Obesity-Related Policies
2010 Analysis of energy efficiency in clouds.  International Journal on Advances in Networks and Services.
2005 Ontologies and Content Management in Digital Libraries-A Standards-Based Approach for Supporting Dynamic Access Policies for a Federated Digital Library.  Lecture Notes in Computer Science. 242-252.
1988 On the conjecture of Plaisted and Hong.  Journal on Algorithms. 597-598.
Performance evaluation of Freelib, a P2P-based digital library architecture.  World Digital Libraries: An International Journal.

Chapters

Year Title
2006 A comparative study of specification models for autonomic access control of digital rights.  Digital Rights Management. Technologies, Issues, Challenges and Systems. Springer.

Conference Papers

Year Title
2017 A Machine Learning Approach for Efficient Parallel Simulation of Beam Dynamics on GPUs.  462-471.
2017 Learning word embeddings in parallel by alignment
2017 Simulations of Coherent Synchrotron Radiation on Parallel Hybrid GPU/CPU Platform.  3915-3917.
2016 Challenges in matching secondary structures in cryo-EM: An exploration.  1714-1719.
2016 High-Fidelity Simulations of Long-Term Beam-Beam Dynamics on GPUs.  40-43.
2016 Memory-Efficient Parallel Simulation of Electron Beam Dynamics Using GPUs.  212-221.
2016 Optimizing a multiple right-hand side Dslash kernel for intel knights corner.  390-401.
2015 A novel computational method for deriving protein secondary structure topologies using Cryo-EM density maps and multiple secondary structure predictions.  60-71.
2015 High-Performance Simulations of Coherent Synchrotron Radiation on Multicore GPU and CPU Platforms
2015 High-fidelity simulation of collective effects in electron beams using an innovative parallel method.  1-10.
2014 Big data challenges for estimating genome assembler quality.  653-660.
2014 ParK: An efficient algorithm for k-core decomposition on multicore processors.  9-16.
2014 pbitMCE: A bit-based approach for maximal clique enumeration on multicore processors.  478-485.
2013 A constrained k-shortest path algorithm to rank the topologies of the protein secondary structure elements detected in cryoem volume maps.  749.
2013 A memory efficient algorithm for adaptive multidimensional integration with multiple GPUs.  169-175.
2013 An efficient deterministic parallel algorithm for adaptive multidimensional numerical integration on GPUs.  486-491.
2013 Genome Assembly on a Multicore System.  1233-1240.
2012 Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions.  490-497.
2012 Social Curation of large multimedia collections on the cloud
2011 A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors.  160-163.
2011 High performance implementation of planted motif problem using suffix trees.  200-206.
2011 Parallelization of mira whole genome and est sequence assembler
2011 User Experiments of a Social, Faceted Multimedia Classification System
2009 Automated support for a collaborative system to organize a collection using facets.  187-203.
2009 Supporting multi-criteria decision making through collaborative faceted classification
2009 Towards Energy Efficient Change Management in a Cloud Computing Environment.  161-167.
2008 A unified model for multicore architectures.  1-12.
2008 Automated approach to cross linking references for a large technical collection
2008 Binomial option pricing on multicore system
2008 Efficient parallel implementations of binomial tree option price valuation.  74-81.
2008 Exploring Historical Image Collections with Collaborative Faceted
2008 Exploring historical image collections with collaborative faceted classification.  44-47.
2008 High performance implementation of binomial option pricing.  852-866.
2008 Maintaining and evolving a taxonomy with social tagging
2008 Metadata extraction
2008 Scheduling-capable autonomic manager for policy based IT change management system.  386-392.
2007 A machine learning approach for automatic text categorization: A case study for DTIC collection.  128-132.
2007 A scriptable, statistical oracle for a metadata extraction system.  396-404.
2007 A scriptable, statistical oracle for metadata extraction system
2007 Automated metadata extraction for person publishing in Kepler.  4500-4505.
2007 Automated template-based metadata extraction architecture.  327-336.
2007 Automatic approach to IT infrastructure management in a virtual computing lab environment.  128-132.
2007 Autonomic approach to IT infrastructure management in a virtual computing lab environment
2007 Collaborative faceted classification system.  223.
2007 Exploiting dynamic validation for document layout classification during metadata extraction
2007 Framework for information sharing across multiple government agencies under dynamic access policies.  934-940.
2007 Infrastructure aware autonomic manager for change management.  66-69.
2006 A prototype of the HumanVirus Interactome Resource (HVIR).  172-180.
2006 Automated building of OAI complaint repository from legacy collection
2006 Freelib: Peer-to-peer-based digital libraries.  9-14.
2006 Synchronization and multiple group server support for Kepler.  111-117.
2005 A comparitive study of access control specification models for self-protecting autonomic systems
2005 A flexible framework for content-based access management for federated digital libraries.  489-490.
2005 A high performance implementation of an OAI-based federation service.  617-625.
2005 A standards-based approach for supporting dynamic access policies for a federated digital library.  242-253.
2005 Approaches to make CDS/ISIS databases interoperable with OAI-compliant digital libraries
2005 Approaches to make CDS/ISIS databases interoperable with other digital libraries
2005 Efficient discovery service for a digital library of 3D models
2005 GRID based federated digital library.  97-105.
2005 Integrating legacy collections into an interoperable digital library framework
2005 Lessons learned with Arc, an OAI-PMH service provider.  590-603.
2005 Similarity and duplicate detection system for an OAI compliant federated digital library.  531-532.
2005 Static and dynamic approaches to make legacy databases OAI-compliant
2004 Access management in federated digital libraries
2004 Freelib: A self-sustainable digital library for education community.  15-20.
2004 Improving federated service for non-cooperating digital libraries
2004 Light-weight communal digital libraries.  237-238.
1993 Parallel Communications: An Experimental Study
1992 Multiprocessor Architectures for High Speed Networks: A Performance Study.  645-651.
1992 Parallelism for high speed networks.  1-6.
1992 Scalable parallel communications
Scheduling-Capable Autonomic Manager for Policy Based IT Change Management System

Research Overview

  • High performance computing, digital libraries, autonomic computing, and peer-to-peer networks

    • Grants

  • An Innovative GPU-Optimized Multiscale Code for High-Fidelity Simulation of Collective Effects in Electron Beams  awarded by National Science Foundation 2016 - 2019
  • Design AMD Impl Scalable Opt Kernels for Lrg Sc Simu USN Fund3d On Emer  awarded by Engility 2017 - 2018
  • ABI Innovation: Advanced Informatics And Effective Algorithms To Enable Cryoem Protein Structure Prediction And Density Analysis  awarded by National Science Foundation 2016 - 2018
  • Graduate Research Award Program On Public Sector Aviation Issues And Airport Research Competition For Universities (Cycle 3)  awarded by The National Academies 2016 - 2018
  • Development of Crabbing System For The LHC Upgrade- FY16  awarded by Fermi National Accelerator Laboratory 2015 - 2017
  • NASA Infared Spectro Molecules  awarded by NASA-Headquarters 2014 - 2017
  • Real-Time Pobabilistic Structural Health Monitoring Via High Performance Computing  awarded by National Institute of Aerospace Associates 2016
  • Jefferson Lab GRA Support: Computer Science Department  awarded by Jefferson Science Associates, LLC. (Jefferson Lab) 2015 - 2016
  • High-Performance Particle Collider Simulations on Parallel Computing Platforms  awarded by Office of Research (Research Seed Funding Program (RSFP)) 2015
  • Advanced phylogenomics of the human and animal pathogen Mycobacterium marinum  awarded by Jeffress Trust 2014 - 2015
  • III-COR: Collaborative Classification of Large, Growing Collections with Evolving Facets  awarded by NSF 2007 - 2011
  • Collaborative classification of large, growing collections with evolving facets  awarded by NSF 2009
  • Processess and tools for extracting metadata  awarded by DTIC 2009
  • REU-collaborative classification of large, growing collections with evolving facets  awarded by NSF 2009
  • Automated extraction of metadata for GPO  awarded by DTIC 1990 - 2009
  • Automated extraction of metadata for GPO  awarded by DTIC - 2009
  • Information management for Chesapeake Bay program  awarded by CBP - 2009
  • Automated extracting of metadata for GPO  awarded by DTIC 2008
  • Autonomic approach to change management and reservation of IT resources in a virtual computing lab environment  awarded by IBM 2008
  • Collaborative classification of large, growing collections with evolving facets  awarded by NSF 2008
  • Information management for Chesapeake Bay program  awarded by CBP 2008
  • Marc21 representation of metadata  awarded by DTIC 2008
  • Processess and tools for extracting metadata  awarded by DTIC 2008
  • Automated extracting of metadata for GPO  awarded by DTIC 2007
  • Automating IT infrastructure management processes in a typical university environment  awarded by IBM 2007
  • Autonomic approach to change management and reservation of IT resources in a virtual computing lab environment  awarded by IBM 2007
  • Collaborative classification of large, growing collections with evolving facets  awarded by NSF 2007
  • Information management for Chesapeake Bay program  awarded by CBP 2007
  • Kepler - A communal digital library  awarded by NSF 2007
  • Processess and tools for extracting metadata  awarded by DTIC 2007
  • Tools for extracting metadata and structure from Dtic technical documents collections using Xml technology  awarded by DTIC 2007
  • Tools for extracting metadata and structure from NASA technical documents collections  awarded by NASA 2007
  • A prototype of the Human Virus Interactome Resource (HVIR)  awarded by ODU 2006
  • A self-sustainable digital library for evolving communities  awarded by NSF 2006
  • Automating IT infrastructure management processes in a typical university environment  awarded by IBM 2006
  • Enhancing Infrastructure for OAI  awarded by Andrew Mellon Foundation 2006
  • Extracting metadata and structure from NASA technical documents collections  awarded by NASA 2006
  • Kepler - A communal digital library  awarded by NSF 2006
  • Metadata and OAI  awarded by DTIC 2006
  • Tools for extracting metadata and structure from Dtic technical documents collections using Xml technology  awarded by DTIC 2006
  • A self-sustainable digital library for evolving communities  awarded by NSF 2005
  • Dynamic distributed access control management system for a federated digital library based on IBM autonomic policy framework  awarded by IBM 2005
  • Enhancing Infrastructure for OAI  awarded by Andrew Mellon Foundation 2005
  • Kepler - A communal digital library  awarded by NSF 2005
  • Tools for extracting metadata and structure from Dtic technical documents collections using Xml technology  awarded by DTIC 2005
  • Aggregating, integrating, preserving and enhancing the NASA digital information framework  awarded by NASA 2004
  • Dynamic distributed access control management system for a federated digital library based on IBM autonomic policy framework  awarded by IBM 2004
  • Enhancing Infrastructure for OAI  awarded by Andrew Mellon Foundation 2004
  • Kepler - A communal digital library  awarded by NSF 2004
  • Tools for extracting metadata and structure from Dtic technical documents collectings using Xml technology  awarded by DTIC 2004

    • Keywords

  • Computer Science : High Performance Computing for Scientific Applications and Large Scale Data Analytics

    • Education And Training

  • Ph.D. in Computer Science, Indian Institute of Technology Delhi 1987
  • B.S. in Electrical & Electronics Engineering, University of Delhi 1981

    • Full Name

  • Mohammad Zubair