Carl Kingsford
Orcid: 0000-0002-0118-5516Affiliations:
- Carnegie Mellon University, Pittsburgh, USA
According to our database1,
Carl Kingsford
authored at least 86 papers
between 2001 and 2023.
Collaborative distances:
Collaborative distances:
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Online presence:
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on orcid.org
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on cs.cmu.edu
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Bibliography
2023
J. Comput. Biol., December, 2023
CoRR, 2023
Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants.
Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023
Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023
Computationally Efficient High-Dimensional Bayesian Optimization via Variable Selection.
Proceedings of the International Conference on Automated Machine Learning, 2023
2022
Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.
J. Comput. Biol., 2022
J. Comput. Biol., 2022
DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes.
Proceedings of the Research in Computational Molecular Biology, 2022
2021
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length.
J. Comput. Biol., 2021
Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data.
BMC Bioinform., 2021
Practical selection of representative sets of RNA-seq samples using a hierarchical approach.
Bioinform., 2021
Maximum likelihood reconstruction of ancestral networks by integer linear programming.
Bioinform., 2021
How much data is sufficient to learn high-performing algorithms? generalization guarantees for data-driven algorithm design.
Proceedings of the STOC '21: 53rd Annual ACM SIGACT Symposium on Theory of Computing, 2021
2020
Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem.
Algorithms Mol. Biol., 2020
Proceedings of the 37th International Conference on Machine Learning, 2020
2019
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
Nat., 2019
Algorithms Mol. Biol., 2019
Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation.
Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019
Proceedings of the 36th International Conference on Machine Learning, 2019
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
2018
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.
J. Comput. Biol., 2018
Quantifying the similarity of topological domains across normal and cancer human cell types.
Bioinform., 2018
2017
Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.
PLoS Comput. Biol., 2017
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.
J. Comput. Biol., 2017
Improving Bloom Filter Performance on Sequence Data Using <i>k</i>-mer Bloom Filters.
J. Comput. Biol., 2017
2016
Knowl. Inf. Syst., 2016
Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.
J. Comput. Biol., 2016
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
BMC Bioinform., 2016
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Bioinform., 2016
Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016
The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB).
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016
2015
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.
Bioinform., 2015
Bioinform., 2015
Bioinform., 2015
Convex Risk Minimization to Infer Networks from probabilistic diffusion data at multiple scales.
Proceedings of the 31st IEEE International Conference on Data Engineering, 2015
Proceedings of the 6th ACM Conference on Bioinformatics, 2015
2014
Algorithms Mol. Biol., 2014
Proceedings of the 2014 IEEE International Conference on Data Mining, 2014
2013
Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms.
CoRR, 2013
Bioinform., 2013
Algorithms Mol. Biol., 2013
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013
Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin.
Proceedings of the ACM Conference on Bioinformatics, 2013
2012
BMC Bioinform., 2012
Graph rigidity reveals well-constrained regions of chromosome conformation embeddings.
BMC Bioinform., 2012
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012
Proceedings of the 2012 International Conference on Privacy, 2012
Proceedings of the 18th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2012
2011
PLoS Comput. Biol., 2011
J. Discrete Algorithms, 2011
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression.
J. Comput. Biol., 2011
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies.
BMC Bioinform., 2011
A fast, lock-free approach for efficient parallel counting of occurrences of <i>k</i>-mers.
Bioinform., 2011
Proceedings of the Research in Computational Molecular Biology, 2011
2010
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information.
J. Comput. Biol., 2010
Alignment and clustering of phylogenetic markers - implications for microbial diversity studies.
BMC Bioinform., 2010
Bioinform., 2010
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Particle Swarm Optimization for multimodal combinatorial problems and its application to protein design.
Proceedings of the IEEE Congress on Evolutionary Computation, 2010
2009
A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing.
Proceedings of the 2009 IEEE Swarm Intelligence Symposium, 2009
2008
Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008
2006
Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006
2005
Solving and analyzing side-chain positioning problems using linear and integer programming.
Bioinform., 2005
2004
A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies.
INFORMS J. Comput., 2004
2003
The Side-Chain Positioning Problem: A Semidefinite Programming Formulation With New Rounding Schemes.
Proceedings of the PCK50, 2003
2001
Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability.
Proceedings of the DNA Computing, 7th International Workshop on DNA-Based Computers, 2001