Tak Wah Lam

According to our database1, Tak Wah Lam authored at least 179 papers between 1989 and 2019.

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Bibliography

2019
RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature.
Proceedings of the Research in Computational Molecular Biology, 2019

2018
AC-DIAMOND v1: accelerating large-scale DNA-protein alignment.
Bioinformatics, 2018

Dictionary Matching with a Bounded Gap in Pattern or in Text.
Algorithmica, 2018

MegaPath: Low-Similarity Pathogen Detection from Metagenomic NGS Data (Extended Abstract).
Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018

2017
Accurate annotation of metagenomic data without species-level references.
IJDMB, 2017

MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs.
BMC Bioinformatics, 2017

2016
Parallel Connectivity and Minimum Spanning Trees.
Encyclopedia of Algorithms, 2016

PnpProbs: a better multiple sequence alignment tool by better handling of guide trees.
BMC Bioinformatics, 2016

AC-DIAMOND: Accelerating Protein Alignment via Better SIMD Parallelization and Space-Efficient Indexing.
Proceedings of the Bioinformatics and Biomedical Engineering, 2016

2015
GLProbs: Aligning Multiple Sequences Adaptively.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

Non-clairvoyant Weighted Flow Time Scheduling on Different Multi-processor Models.
Theory Comput. Syst., 2015

Improving multiple sequence alignment by using better guide trees.
BMC Bioinformatics, 2015

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC).
BMC Bioinformatics, 2015

database.bio: a web application for interpreting human variations.
Bioinformatics, 2015

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Bioinformatics, 2015

Compressing Dictionary Matching Index via Sparsification Technique.
Algorithmica, 2015

Guest Editors Foreword.
Algorithmica, 2015

Predicting RNA Secondary Structures: One-grammar-fits-all Solution.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

A simple and economical method for improving whole-genome alignment.
Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2015

Dictionary Matching with Uneven Gaps.
Proceedings of the Combinatorial Pattern Matching - 26th Annual Symposium, 2015

Scheduling with Gaps: New Models and Algorithms.
Proceedings of the Algorithms and Complexity - 9th International Conference, 2015

2014
GPU-Accelerated BWT Construction for Large Collection of Short Reads.
CoRR, 2014

MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC).
CoRR, 2014

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.
Bioinformatics, 2014

FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data.
Bioinformatics, 2014

2013
Scheduling for weighted flow time and energy with rejection penalty.
Theor. Comput. Sci., 2013

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.
Bioinformatics, 2013

Online Speed Scaling Based on Active Job Count to Minimize Flow Plus Energy.
Algorithmica, 2013

Nonclairvoyant sleep management and flow-time scheduling on multiple processors.
Proceedings of the 25th ACM Symposium on Parallelism in Algorithms and Architectures, 2013

A Local Structural Prediction Algorithm for RNA Triple Helix Structure.
Proceedings of the Pattern Recognition in Bioinformatics, 2013

LCR_Finder: A de Novo Low Copy Repeat Finder for Human Genome.
Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013

Competitive Online Algorithms for Multiple-Machine Power Management and Weighted Flow Time.
Proceedings of the Nineteenth Computing: The Australasian Theory Symposium, 2013

2012
Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Improved multi-processor scheduling for flow time and energy.
J. Scheduling, 2012

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.
Bioinformatics, 2012

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.
Bioinformatics, 2012

Continuous Monitoring of Distributed Data Streams over a Time-Based Sliding Window.
Algorithmica, 2012

Non-clairvoyant weighted flow time scheduling with rejection penalty.
Proceedings of the 24th ACM Symposium on Parallelism in Algorithms and Architectures, 2012

Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples.
Proceedings of the ACM International Conference on Bioinformatics, 2012

Online Flow Time Scheduling in the Presence of Preemption Overhead.
Proceedings of the Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques, 2012

2011
Cache-oblivious index for approximate string matching.
Theor. Comput. Sci., 2011

Tradeoff between energy and throughput for online deadline scheduling.
SUSCOM, 2011

A linear size index for approximate pattern matching.
J. Discrete Algorithms, 2011

Structural Alignment of RNA with Complex Pseudoknot Structure.
Journal of Computational Biology, 2011

Non-clairvoyant Scheduling for Weighted Flow Time and Energy on Speed Bounded Processors.
Chicago J. Theor. Comput. Sci., 2011

RNASAlign: RNA Structural Alignment System.
Bioinformatics, 2011

Approximating Frequent Items in Asynchronous Data Stream over a Sliding Window.
Algorithms, 2011

Nonclairvoyant Speed Scaling for Flow and Energy.
Algorithmica, 2011

Energy-Efficient Due Date Scheduling.
Proceedings of the Theory and Practice of Algorithms in (Computer) Systems, 2011

Edit Distance to Monotonicity in Sliding Windows.
Proceedings of the Algorithms and Computation - 22nd International Symposium, 2011

Sleep Management on Multiple Machines for Energy and Flow Time.
Proceedings of the Automata, Languages and Programming - 38th International Colloquium, 2011

Algorithms for pseudoknot classification.
Proceedings of the ACM International Conference on Bioinformatics, 2011

Detection of novel tandem duplication with next-generation sequencing.
Proceedings of the ACM International Conference on Bioinformatics, 2011

2010
Deadline scheduling and power management for speed bounded processors.
Theor. Comput. Sci., 2010

Improving the accuracy of signal transduction pathway construction using level-2 neighbours.
IJBRA, 2010

Compressed Indexes for Approximate String Matching.
Algorithmica, 2010

Online Tracking of the Dominance Relationship of Distributed Multi-dimensional Data.
Proceedings of the Approximation and Online Algorithms - 8th International Workshop, 2010

Local Structural Alignment of RNA with Affine Gap Model.
Proceedings of the Bioinformatics Research and Applications, 6th International Symposium, 2010

Non-clairvoyant Speed Scaling for Weighted Flow Time.
Proceedings of the Algorithms, 2010

Non-clairvoyant Scheduling for Weighted Flow Time and Energy on Speed Bounded Processors.
Proceedings of the Theory of Computing 2010, 2010

Indexing Similar DNA Sequences.
Proceedings of the Algorithmic Aspects in Information and Management, 2010

2009
Optimizing throughput and energy in online deadline scheduling.
ACM Trans. Algorithms, 2009

Correcting short reads with high error rates for improved sequencing result.
IJBRA, 2009

SOAP2: an improved ultrafast tool for short read alignment.
Bioinformatics, 2009

Structural Alignment of RNA with Complex Pseudoknot Structure.
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Succinct Text Indexing with Wildcards.
Proceedings of the String Processing and Information Retrieval, 2009

Succinct Index for Dynamic Dictionary Matching.
Proceedings of the Algorithms and Computation, 20th International Symposium, 2009

Sleep with Guilt and Work Faster to Minimize Flow Plus Energy.
Proceedings of the Automata, Languages and Programming, 36th International Colloquium, 2009

The 2-Interval Pattern Matching Problems and Its Application to ncRNA Scanning.
Proceedings of the Bioinformatics and Computational Biology, 2009

High Throughput Short Read Alignment via Bi-directional BWT.
Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009

2008
Parallel Connectivity and Minimum Spanning Trees.
Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Nonmigratory Multiprocessor Scheduling for Response Time and Energy.
IEEE Trans. Parallel Distrib. Syst., 2008

Dynamic bin packing of unit fractions items.
Theor. Comput. Sci., 2008

Extra Unit-Speed Machines Are Almost as Powerful as Speedy Machines for Flow Time Scheduling.
SIAM J. Comput., 2008

Non-overlapping Common Substrings Allowing Mutations.
Mathematics in Computer Science, 2008

Finding Alternative Splicing Patterns with Strong Support from expressed Sequences on Individual exons/introns.
J. Bioinformatics and Computational Biology, 2008

Compressed indexing and local alignment of DNA.
Bioinformatics, 2008

Improved Approximate String Matching Using Compressed Suffix Data Structures.
Algorithmica, 2008

Competitive non-migratory scheduling for flow time and energy.
Proceedings of the SPAA 2008: Proceedings of the 20th Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2008

Scheduling for Speed Bounded Processors.
Proceedings of the Automata, Languages and Programming, 35th International Colloquium, 2008

Speed Scaling Functions for Flow Time Scheduling Based on Active Job Count.
Proceedings of the Algorithms, 2008

Compressed Index for Dictionary Matching.
Proceedings of the 2008 Data Compression Conference (DCC 2008), 2008

A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2007
Compressed indexes for dynamic text collections.
ACM Trans. Algorithms, 2007

A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays.
Algorithmica, 2007

Online Deadline Scheduling with Bounded Energy Efficiency.
Proceedings of the Theory and Applications of Models of Computation, 2007

Energy efficient online deadline scheduling.
Proceedings of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2007

Space Efficient Indexes for String Matching with Don't Cares.
Proceedings of the Algorithms and Computation, 18th International Symposium, 2007

Energy Efficient Deadline Scheduling in Two Processor Systems.
Proceedings of the Algorithms and Computation, 18th International Symposium, 2007

An Experimental Study of Compressed Indexing and Local Alignments of DNA.
Proceedings of the Combinatorial Optimization and Applications, 2007

Finding Alternative Splicing Patterns with Strong Support From Expressed Sequences.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

Efficiency of Data Distribution in BitTorrent-Like Systems.
Proceedings of the Algorithmic Aspects in Information and Management, 2007

2006
Approximate string matching using compressed suffix arrays.
Theor. Comput. Sci., 2006

New resource augmentation analysis of the total stretch of SRPT and SJF in multiprocessor scheduling.
Theor. Comput. Sci., 2006

Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix.
J. Bioinformatics and Computational Biology, 2006

Extra unit-speed machines are almost as powerful as speedy machines for competitive flow time scheduling.
Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2006

A More Accurate and Efficient Whole Genome Phylogeny.
Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

2005
Nonmigratory Online Deadline Scheduling on Multiprocessors.
SIAM J. Comput., 2005

On-line Stream Merging with Max Span and Min Coverage.
Theory Comput. Syst., 2005

A Tighter Extra-Resource Analysis of Online Deadline Scheduling.
J. Comb. Optim., 2005

Efficient Constrained Multiple Sequence Alignment with Performance Guarantee.
J. Bioinformatics and Computational Biology, 2005

Filtering of Ineffective siRNAs and Improved siRNA Design Tool.
Bioinformatics, 2005

The mutated subsequence problem and locating conserved genes.
Bioinformatics, 2005

Dynamic dictionary matching and compressed suffix trees.
Proceedings of the Sixteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2005

Allowing mismatches in anchors for wholw genome alignment: Generation and effectiveness.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

2004
Extra Processors versus Future Information in Optimal Deadline Scheduling.
Theory Comput. Syst., 2004

Performance guarantee for EDF under overload.
J. Algorithms, 2004

Non-shared edges and nearest neighbor interchanges revisited.
Inf. Process. Lett., 2004

Subtree Transfer Distance For Degree-D Phylogenies.
Int. J. Found. Comput. Sci., 2004

Aggressive Online Deadline Scheduling.
Electron. Notes Theor. Comput. Sci., 2004

An efficient algorithm for optimizing whole genome alignment with noise.
Bioinformatics, 2004

Non-migratory online deadline scheduling on multiprocessors.
Proceedings of the Fifteenth Annual ACM-SIAM Symposium on Discrete Algorithms, 2004

Finding motifs for insufficient number of sequences with strong binding to transcription facto.
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Compressed Index for Dynamic Text.
Proceedings of the 2004 Data Compression Conference (DCC 2004), 2004

Compressed Index for a Dynamic Collection of Texts.
Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 2004

New Results on On-Demand Broadcasting with Deadline via Job Scheduling with Cancellation.
Proceedings of the Computing and Combinatorics, 10th Annual International Conference, 2004

A Mutation-Sensitive Approach for Locating Conserved Gene Pairs between Related Species.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004

Practical aspects of Compressed Suffix Arrays and FM-Index in Searching DNA Sequences.
Proceedings of the Sixth Workshop on Algorithm Engineering and Experiments and the First Workshop on Analytic Algorithmics and Combinatorics, 2004

2003
On-line scheduling with tight deadlines.
Theor. Comput. Sci., 2003

On-line stream merging in a general setting.
Theor. Comput. Sci., 2003

Competitive Deadline Scheduling via Additional or Faster Processors.
J. Scheduling, 2003

Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs.
Journal of Computational Biology, 2003

Improving the efficiency of parallel minimum spanning tree algorithms.
Discret. Appl. Math., 2003

Efficient Algorithms for Optimizing Whole Genome Alignment with Noise.
Proceedings of the Algorithms and Computation, 14th International Symposium, 2003

Constructing Compressed Suffix Arrays with Large Alphabets.
Proceedings of the Algorithms and Computation, 14th International Symposium, 2003

Efficient Constrained Multiple Sequence Alignment with Performance Guarantee.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
Automatic construction of online catalog topologies.
IEEE Trans. Systems, Man, and Cybernetics, Part C, 2002

On-line load balancing of temporary tasks revisited.
Theor. Comput. Sci., 2002

Improved Phylogeny Comparisons: Non-Shared Edges Nearest Neighbor Interchanges, and Subtree Transfers
CoRR, 2002

A unified analysis of hot video schedulers.
Proceedings of the Proceedings on 34th Annual ACM Symposium on Theory of Computing, 2002

Competitive Analysis of On-line Stream Merging Algorithms.
Proceedings of the Mathematical Foundations of Computer Science 2002, 2002

A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays.
Proceedings of the Computing and Combinatorics, 8th Annual International Conference, 2002

2001
A Decomposition Theorem for Maximum Weight Bipartite Matchings.
SIAM J. Comput., 2001

An Even Faster and More Unifying Algorithm for Comparing Trees via Unbalanced Bipartite Matchings.
J. Algorithms, 2001

Concurrent threads and optimal parallel minimum spanning trees algorithm.
J. ACM, 2001

Approximating the Nearest Neighbor Intercharge Distance for Non-Uniform-Degree Evolutionary Trees.
Int. J. Found. Comput. Sci., 2001

Optimal Edge Ranking of Trees in Linear Time.
Algorithmica, 2001

Performance guarentee for online deadline scheduling in the presence of overload.
Proceedings of the Twelfth Annual Symposium on Discrete Algorithms, 2001

On-Line Scheduling with Tight Deadlines.
Proceedings of the Mathematical Foundations of Computer Science 2001, 2001

On the speed requirement for optimal deadline scheduling in overloaded systems.
Proceedings of the 15th International Parallel & Distributed Processing Symposium (IPDPS-01), 2001

An 5-competitive on-line scheduler for merging video streams.
Proceedings of the 15th International Parallel & Distributed Processing Symposium (IPDPS-01), 2001

Improved On-Line Stream Merging: From a Restricted to a General Setting.
Proceedings of the Computing and Combinatorics, 7th Annual International Conference, 2001

2000
Cavity Matchings, Label Compressions, and Unrooted Evolutionary Trees.
SIAM J. Comput., 2000

Selecting the k largest elements with parity tests.
Discret. Appl. Math., 2000

Construction of Online Catalog Topologies Using Decision Trees.
Proceedings of the Second International Workshop on Advance Issues of E-Commerce and Web-Based Information Systems (WECWIS 2000), 2000

Unbalanced and Hierarchical Bipartite Matchings with Applications to Labeled Tree Comparison.
Proceedings of the Algorithms and Computation, 11th International Conference, 2000

Improved Phylogeny Comparisons: Non-shared Edges, Nearest Neighbor Interchanges, and Subtree Transfers.
Proceedings of the Algorithms and Computation, 11th International Conference, 2000

A Faster and Unifying Algorithm for Comparing Trees.
Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000

1999
Trade-offs Between Speed and Processor in Hard-Deadline Scheduling.
Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 1999

On the Parallel Time Complexity of Undirected Connectivity and Minimum Spanning Trees.
Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 1999

A Decomposition Theorem for Maximum Weight Bipartite Matchings with Applications to Evolutionary Trees.
Proceedings of the Algorithms, 1999

Approximating the Nearest Neighbor Interchange Distance for Evolutionary Trees with Non-uniform Degrees.
Proceedings of the Computing and Combinatorics, 5th Annual International Conference, 1999

Improving Parallel Computation with Fast Integer Sorting.
Proceedings of the Computing and Combinatorics, 5th Annual International Conference, 1999

Requirement-Based Data Cube Schema Design.
Proceedings of the 1999 ACM CIKM International Conference on Information and Knowledge Management, 1999

1998
An Improved Scheme for Set Equality Testing and Updating.
Theor. Comput. Sci., 1998

Edge Ranking of Graphs Is Hard.
Discret. Appl. Math., 1998

Approximating Biconnectivity in Parallel.
Algorithmica, 1998

Default-Sensitive PreProcessings for Finding Maxima.
Proceedings of Computing: The Fourth Australasian Theory Symposium (CATS'98), 1998

1997
Dynamic Suffix Tree and Two-Dimensional Texts Management.
Inf. Process. Lett., 1997

General Techniques for Comparing Unrooted Evolutionary Trees.
Proceedings of the Twenty-Ninth Annual ACM Symposium on the Theory of Computing, 1997

All-Cavity Maximum Matchings.
Proceedings of the Algorithms and Computation, 8th International Symposium, 1997

1996
Computing the Unrooted Maximum Agreement Subtree in Sub-quadratic Time.
Nord. J. Comput., 1996

Improving Biconnectivity Approximation via Local Optimization.
Proceedings of the Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, 1996

Towards More Precise Parallel Biconnectivity Approximation.
Proceedings of the Algorithms and Computation, 7th International Symposium, 1996

Two-Dimensional Dynamic Dictionary Matching.
Proceedings of the Algorithms and Computation, 7th International Symposium, 1996

1995
Finding Connected Components in O(log n log log n) Time on the EREW PRAM.
J. Algorithms, 1995

Two-Dimensional Pattern Matching on a Dynamic Library of Texts.
Proceedings of the Computing and Combinatorics, First Annual International Conference, 1995

Efficient Equality-Testing and Updating of Sets.
Proceedings of the Algorithms, 1995

1994
On Set Equality-Testing.
Proceedings of the Algorithms and Complexity, Second Italian Conference, 1994

1993
An on-line algorithm for navigating in unknown environment.
Int. J. Comput. Geometry Appl., 1993

Finding Least-Weight Subsequences with Fewer Processors.
Algorithmica, 1993

1992
Trade-Offs between Communication and Space.
J. Comput. Syst. Sci., 1992

Results on Communication Complexity Classes.
J. Comput. Syst. Sci., 1992

The Implicit Dictionary Problem Revisited.
Proceedings of the Algorithms and Computation, Third International Symposium, 1992

1991
An On-Line Algorithm for Navigating in Unknown Terrain.
Proceedings of the ISA '91 Algorithms, 1991

1989
Tradeoffs Between Communication and Space
Proceedings of the 21st Annual ACM Symposium on Theory of Computing, 1989

The Power of Parallel Pointer Manipulation.
Proceedings of the ACM Symposium on Parallel Algorithms and Architectures, 1989

An Optimal EREW Parallel Algorithm for Parenthesis Matching.
Proceedings of the International Conference on Parallel Processing, 1989


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