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Author Details

Carl Kingsford
Carnegie Mellon University
2005
78
23
PMIDPaper TitleJournal TitlePublished Year
37292475Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants.ArXiv2023
37986943Improving Hi-C contact matrices using genome graphs.bioRxiv2023
37646787Creating and Using Minimizer Sketches in Computational Genomics.J Comput Biol2023
35041494Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.J Comput Biol2022
35758819The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance.Bioinformatics2022
36095142Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer.J Comput Biol2022
33325773Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length.J Comput Biol2021
33794760HARVESTMAN: a framework for hierarchical feature learning and selection from whole genome sequencing data.BMC Bioinformatics2021
34412679VariantStore: an index for large-scale genomic variant search.Genome Biol2021
34252955Constructing small genome graphs via string compression.Bioinformatics2021
34252928Sequence-specific minimizers via polar sets.Bioinformatics2021
34252927Practical selection of representative sets of RNA-seq samples using a hierarchical approach.Bioinformatics2021
33971903Exact transcript quantification over splice graphs.Algorithms Mol Biol2021
33370163Metric Labeling and Semimetric Embedding for Protein Annotation Prediction.J Comput Biol2021
33135733Maximum likelihood reconstruction of ancestral networks by integer linear programming.Bioinformatics2021
32315544More Accurate Transcript Assembly via Parameter Advising.J Comput Biol2020
31687663Analysis of the structural variability of topologically associated domains as revealed by Hi-C.NAR Genom Bioinform2020
32657376Improved design and analysis of practical minimizers.Bioinformatics2020
32894187Alignment and mapping methodology influence transcript abundance estimation.Genome Biol2020
32467720Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem.Algorithms Mol Biol2020
32489399Context-aware seeds for read mapping.Algorithms Mol Biol2020
30867673Semi-nonparametric modeling of topological domain formation from epigenetic data.Algorithms Mol Biol2019
31786209Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification.Cell Syst2019
31849338Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads.Genome Biol2019
29990201Theory and A Heuristic for the Minimum Path Flow Decomposition Problem.IEEE/ACM Trans Comput Biol Bioinform2019
31510667Locality-sensitive hashing for the edit distance.Bioinformatics2019
29330118Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data.Methods2018
29858814Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami.Methods Mol Biol2018
29949995Asymptotically optimal minimizers schemes.Bioinformatics2018
29949963Quantifying the similarity of topological domains across normal and cancer human cell types.Bioinformatics2018
29641248Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.J Comput Biol2018
29415772Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery.Genome Biol2018
29650026SQUID: transcriptomic structural variation detection from RNA-seq.Genome Biol2018
27828710Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters.J Comput Biol2017
28334818Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings.Nucleic Acids Res2017
28263959Salmon provides fast and bias-aware quantification of transcript expression.Nat Methods2017
28968408Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.PLoS Comput Biol2017
29131147Accurate assembly of transcripts through phase-preserving graph decomposition.Nat Biotechnol2017
28881970Improving the performance of minimizers and winnowing schemes.Bioinformatics2017
27726445Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.J Comput Biol2017
27059896A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.BMC Bioinformatics2016
26463378Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling.Methods Mol Biol2016
26568624Optimal seed solver: optimizing seed selection in read mapping.Bioinformatics2016
27821901Diffusion archeology for diffusion progression history reconstruction.Knowl Inf Syst2016
27976707A pathway-centric view of spatial proximity in the 3D nucleome across cell lines.Sci Rep2016
27267775Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.J Comput Biol2016
27153676Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.Bioinformatics2016
26854477Fast search of thousands of short-read sequencing experiments.Nat Biotechnol2016
25577434Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.Bioinformatics2015
25910696Data-dependent bucketing improves reference-free compression of sequencing reads.Bioinformatics2015
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Collaborators

Steven L Salzberg
Center for Computational Biology, Johns Hopkins University
Co-authored papers 5
Niranjan Nagarajan
Co-authored papers 4
Mihai Pop
Co-authored papers 4
Natalie Sauerwald
Center for Computational Biology, Flatiron Institute
Co-authored papers 3
Ron Shamir
Tel Aviv University
Co-authored papers 2
Heewook Lee
Arizona State University
Co-authored papers 2
Can Alkan
Bilkent University
Co-authored papers 2
Michael I Love
University of North Carolina at Chapel Hill
Co-authored papers 2
Michael C Schatz
Johns Hopkins University
Co-authored papers 2
Gustavo Stolovitzky
IBM T.J. Watson Research Center
Co-authored papers 1
Elena Zaslavsky
Icahn School of Medicine at Mount Sinai
Co-authored papers 1
David R Kelley
Co-authored papers 1
Daniel Janies
University of North Carolina at Charlotte
Co-authored papers 1
Ivet Bahar
Laufer Center for Physical and Quantitative Biology, Stony Brook University
Co-authored papers 1
Akshat Singhal
Motilal Nehru National Institute of Technology, Stony Brook University, University of California San Diego
Co-authored papers 1
Stephen M Mount
University of Maryland, College Park
Co-authored papers 1
Raquel Norel
IBM T.J. Watson Research Center
Co-authored papers 1
Julio Saez-Rodriguez
Institute of Computational Biomedicine, Heidelberg University
Co-authored papers 1
Rafael A Irizarry
Dana-Farber Cancer Institute
Co-authored papers 1
She Zhang
University of Pittsburgh School of Medicine
Co-authored papers 1
Christopher J Langmead
Monash University
Co-authored papers 1
Arthur L Delcher
Center for Computational Biology, Johns Hopkins School of Medicine
Co-authored papers 1
Elodie Ghedin
National Institute of Allergy and Infectious Diseases, National Institutes of Health
Co-authored papers 1
Riccardo Bellazzi
University of Pavia
Co-authored papers 1
Release 1.2