# Desh Ranjan

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^{1}, Desh Ranjan## Timeline

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## Bibliography

2017

An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images.

IEEE/ACM Trans. Comput. Biology Bioinform., 2017

GPU-accelerated high-fidelity simulation of beam-beam effects in particle colliders.

Proceedings of the Summer Simulation Multi-Conference, 2017

A Machine Learning Approach for Efficient Parallel Simulation of Beam Dynamics on GPUs.

Proceedings of the 46th International Conference on Parallel Processing, 2017

2016

Optimizing a Multiple Right-Hand Side Dslash Kernel for Intel Knights Corner.

Proceedings of the High Performance Computing, 2016

Memory-Efficient Parallel Simulation of Electron Beam Dynamics Using GPUs.

Proceedings of the 23rd IEEE International Conference on High Performance Computing, 2016

Challenges in matching secondary structures in cryo-EM: An exploration.

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data.

Journal of Computational Biology, 2015

ISQuest: finding insertion sequences in prokaryotic sequence fragment data.

Bioinformatics, 2015

High-fidelity simulation of collective effects in electron beams using an innovative parallel method.

Proceedings of the Conference on Summer Computer Simulation, 2015

A Novel Computational Method for Deriving Protein Secondary Structure Topologies Using Cryo-EM Density Maps and Multiple Secondary Structure Predictions.

Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

2014

Solving the Secondary Structure MatchingProblem in Cryo-EM De Novo ModelingUsing a Constrained $K$-Shortest Path Graph Algorithm.

IEEE/ACM Trans. Comput. Biology Bioinform., 2014

Maximal clique enumeration for large graphs on hadoop framework.

Proceedings of the first workshop on Parallel programming for analytics applications, 2014

pbitMCE: A bit-based approach for maximal clique enumeration on multicore processors.

Proceedings of the 20th IEEE International Conference on Parallel and Distributed Systems, 2014

ParK: An efficient algorithm for k-core decomposition on multicore processors.

Proceedings of the 2014 IEEE International Conference on Big Data, 2014

Big data challenges for estimating genome assembler quality.

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013

High-performance implementation of planted motif problem on multicore and GPU.

Concurrency and Computation: Practice and Experience, 2013

Genome Assembly on a Multicore System.

Proceedings of the 12th IEEE International Conference on Trust, 2013

An Efficient Deterministic Parallel Algorithm for Adaptive Multidimensional Numerical Integration on GPUs.

Proceedings of the 42nd International Conference on Parallel Processing, 2013

A memory efficient algorithm for adaptive multidimensional integration with multiple GPUs.

Proceedings of the 20th Annual International Conference on High Performance Computing, 2013

A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps.

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

Upper and lower I/O bounds for pebbling r-pyramids.

J. Discrete Algorithms, 2012

Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data.

J. Bioinformatics and Computational Biology, 2012

Vertex isoperimetric parameter of a Computation Graph.

Int. J. Found. Comput. Sci., 2012

Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions.

Proceedings of the ACM International Conference on Bioinformatics, 2012

2011

Ranking Valid Topologies of the Secondary Structure Elements Using a Constraint Graph.

J. Bioinformatics and Computational Biology, 2011

High performance implementation of planted motif problem using suffix trees.

Proceedings of the 2011 International Conference on High Performance Computing & Simulation, 2011

Strong I/O Lower Bounds for Binomial and FFT Computation Graphs.

Proceedings of the Computing and Combinatorics - 17th Annual International Conference, 2011

A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors.

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2010

Upper and Lower I/O Bounds for Pebbling

*r*-Pyramids.
Proceedings of the Combinatorial Algorithms - 21st International Workshop, 2010

An efficient multicore implementation of planted motif problem.

Proceedings of the 2010 International Conference on High Performance Computing & Simulation, 2010

Computational and Biological Approach to Understand the 3' UTR-Mediated Posttranscriptional Regulation of Alfalfa Cytosolic Glutamine Synthetase Genes.

Proceedings of the ISCA 2nd International Conference on Bioinformatics and Computational Biology, 2010

2009

Historical sources as a teaching tool.

Proceedings of the 40th SIGCSE Technical Symposium on Computer Science Education, 2009

Lower Bounds for Accessing Information on Pure Pointer Machines.

Proceedings of the 2009 International Conference on Foundations of Computer Science, 2009

2007

Positive Influence and Negative Dependence.

Combinatorics, Probability & Computing, 2007

Tools for Cis-element Recognition and Phylogenetic Tree Construction Based on Conserved Patterns.

Proceedings of the 22nd International Conference on Computers and Their Applications, 2007

Computational Identification of Cis-regulatory Elements Associated with Pungency of Chili Peppers.

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006

Sequential and parallel algorithms for the NCA problem on pure pointer machines.

Theor. Comput. Sci., 2006

A project in algorithms based on a primary historical source about catalan numbers.

Proceedings of the 39th SIGCSE Technical Symposium on Computer Science Education, 2006

Some Separation Results Between Classes of Pointer Algorithms.

Proceedings of the 8th International Workshop on Descriptional Complexity of Formal Systems - DCFS 2006, Las Cruces, New Mexico, USA, June 21, 2006

2005

A Simple Optimal Solution for the Temporal Precedence Problem on Pure Pointer Machines.

Theory Comput. Syst., 2005

Identity orientation of complete bipartite graphs.

Discrete Mathematics, 2005

Computational Issues in Exploiting Dependent And-Parallelism in Logic Programming: Leftness Detection in Dynamic Search Trees.

Proceedings of the Logic for Programming, 2005

2004

Detecting Local Symmetry Axis in 3-dimensional Virus Structures.

Proceedings of the Second Asia-Pacific Bioinformatics Conference (APBC 2004), 2004

2003

The Level-Ancestor problem on Pure Pointer Machines.

Inf. Process. Lett., 2003

On the Complexity of Dependent And-Parallelism in Logic Programming.

Proceedings of the Logic Programming, 19th International Conference, 2003

An Agent-based Domain Specific Framework for Rapid Prototyping of Applications in Evolutionary Biology.

Proceedings of the Declarative Agent Languages and Technologies, 2003

2002

Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins.

IEEE Trans. Parallel Distrib. Syst., 2002

An optimal data structure to handle dynamic environments in non-deterministic computations.

Comput. Lang., 2002

An Optimal Algorithm for Finding NCA on Pure Pointer Machines.

Proceedings of the Algorithm Theory, 2002

Semantics-Based Filtering: Logic Programming's Killer App?

Proceedings of the Practical Aspects of Declarative Languages, 4th International Symposium, 2002

Ancestor Problems on Pure Pointer Machines.

Proceedings of the LATIN 2002: Theoretical Informatics, 2002

An Efficient Parallel Pointer Machine Algorithm for the NCA Problem.

Proceedings of the Foundations of Information Technology in the Era of Networking and Mobile Computing, 2002

F-LOG: A Domain Specific Language for Solving Phylogenetic Inference Problems.

Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002

2001

Interoperability between Bioinformatics Tools: A Logic Programming Approach.

Proceedings of the Practical Aspects of Declarative Languages, 2001

2000

The Temporal Precedence Problem.

Algorithmica, 2000

Data structures for order-sensitive predicates in parallel nondeterministic systems.

Acta Inf., 2000

1999

On the Complexity of Or-Parallelism.

New Generation Comput., 1999

Complexity Analysis of Late Binding in Dynamic Object-Oriented Languages

Journal of Functional and Logic Programming, 1999

A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation.

Proceedings of the High Performance Computing, 1999

1998

Balls and bins: A study in negative dependence.

Random Struct. Algorithms, 1998

On the Computational Complexity of Some Classical Equivalence Relations on Boolean Functions.

Theory Comput. Syst., 1998

Efficient Algorithms for the Temporal Precedence Problem.

Inf. Process. Lett., 1998

Breaking Symmetry in Complete Graphs by Orienting Edges: Asymptotic Bounds.

Inf. Process. Lett., 1998

The Complexity of Late-Binding in Dynamic Object-Oriented Languages.

Proceedings of the Principles of Declarative Programming, 10th International Symposium, 1998

1997

Space-Filling Curves and Their Use in the Design of Geometric Data Structures.

Theor. Comput. Sci., 1997

On the Complexity of Parallel Implementation of Logic Programs.

Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 1997

1996

On the Computational Complexity of some Classical Equivalence Relations on Boolean Functions

Electronic Colloquium on Computational Complexity (ECCC), 1996

1995

A Simple Proof on the Decidability of Equivalence Between Recursive and Nonrecursive Datalog Programs.

Inf. Process. Lett., 1995

Space Filling Curves and Their Use in the Design of Geometric Data Structures.

Proceedings of the LATIN '95: Theoretical Informatics, 1995

1994

The Random Oracle Hypothesis Is False.

J. Comput. Syst. Sci., 1994

1993

On IP = PSPACE and Theorems with Narrow Proofs.

Proceedings of the Current Trends in Theoretical Computer Science - Essays and Tutorials, 1993

Relativization: a Revisionistic Retrospective.

Proceedings of the Current Trends in Theoretical Computer Science - Essays and Tutorials, 1993

Quantifiers and Approximation.

Theor. Comput. Sci., 1993

A Tool for the Analysis of Manipulation.

Inf. Process. Lett., 1993

Improving Known Solutions is Hard.

Computational Complexity, 1993

Searching, Sorting and Randomised Algorithms for Central Elements and Ideal Counting in Posets.

Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 1993

1992

Relativization: a revisionistic retrospective.

Bulletin of the EATCS, 1992

On the Complexity of Incremental Computation.

Proceedings of the Mathematical Foundations of Computer Science 1992, 1992

On Randomized Reductions to Sparse Sets.

Proceedings of the Seventh Annual Structure in Complexity Theory Conference, 1992

1991

Space Bounded Computations: Review and New Separation Results.

Theor. Comput. Sci., 1991

Improving Known Solutions is Hard.

Proceedings of the Automata, Languages and Programming, 18th International Colloquium, 1991

1990

On Unique Staisfiability and Randomized Reductions.

Bulletin of the EATCS, 1990

Structural Complexity Theory: recent Surprises.

Proceedings of the SWAT 90, 1990

Quantifiers and Approximation (Extended Abstract)

Proceedings of the 22nd Annual ACM Symposium on Theory of Computing, 1990

Quantifiers and Approximation (Abstract).

Proceedings of the Proceedings: Fifth Annual Structure in Complexity Theory Conference, 1990

1989

Space Bounded Computations: Review And New Separation Results.

Proceedings of the Mathematical Foundations of Computer Science 1989, 1989