Carl Kingsford

Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University , Pittsburgh, PA 15213,

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 36 papers. Top paper: “Biological databases in the age of generative artificial intelligence”.

Biological databases in the age of generative artificial intelligence

Bioinformatics Advances(2024)10.1093/bioadv/vbaf044

N/A

0.165DataRank · unranked

2 citations

Teresa K. Attwood, Judith A. Blake, Philip E. Bourne, Ana Conesa, Terry Gaasterland +17 more

Improved design and analysis of practical minimizers

Bioinformatics(2020)10.1093/bioinformatics/btaa472

N/A

0DataRank · unranked

70 citations

Carl Kingsford, Guillaume Marçais, Hongyu Zheng

Exact Transcript Quantification Over Splice Graphs

Workshop on Algorithms in Bioinformatics(2020)10.4230/lipics.wabi.2020.12

N/A

0DataRank · unranked

5 citations

Hongyu Zheng, Carl Kingsford, Ma, Cong

Context-aware seeds for read mapping

Algorithms for Molecular Biology(2020)10.1186/s13015-020-00172-3

N/A

0DataRank · unranked

5 citations

Mingfu Shao, Carl Kingsford, Hongyi Xin

Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem

Algorithms for Molecular Biology(2020)10.1186/s13015-020-00170-5

N/A

0DataRank · unranked

3 citations

Cong Ma, Han Xie, Carl Kingsford, Yutong Qiu

Maximum likelihood reconstruction of ancestral networks by integer linear programming

Bioinformatics(2020)10.1093/bioinformatics/btaa931

N/A

0DataRank · unranked

2 citations

Ziqi Zhang, Carl Kingsford, Xiuwei Zhang, Vaibhav Rajan

Improved design and analysis of practical minimizers

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.07.939025

N/A

0DataRank · unranked

7 citations

Carl Kingsford, Guillaume Marçais, Hongyu Zheng

Probabilistic method corrects previously uncharacterized Hi-C artifact

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.07.325332

N/A

0DataRank · unranked

1 citations

Carl Kingsford, Yihang Shen

Harvestman: A framework for hierarchical feature learning and selection from whole genome sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.24.005603

N/A

0DataRank · unranked

0 citations

Shawn James Baker, Guillaume Marçais, Quang Minh Hoang, Carl Kingsford, Christopher J. Langmead +1 more

Constructing small genome graphs via string compression

Bioinformatics(2021)10.1093/bioinformatics/btab281

N/A

0DataRank · unranked

21 citations

Carl Kingsford, Yutong Qiu

Sequence-specific minimizers via polar sets

Bioinformatics(2021)10.1093/bioinformatics/btab313

N/A

0DataRank · unranked

28 citations

Carl Kingsford, Guillaume Marçais, Hongyu Zheng

Practical selection of representative sets of RNA-seq samples using a hierarchical approach

Bioinformatics(2021)10.1093/bioinformatics/btab315

N/A

0DataRank · unranked

4 citations

Carl Kingsford, Laura H. Tung

VariantStore: an index for large-scale genomic variant search

Genome biology(2021)10.1186/s13059-021-02442-8

N/A

0DataRank · unranked

6 citations

Yinjie Gao, Carl Kingsford, Prashant Pandey

Exact transcript quantification over splice graphs

Algorithms for Molecular Biology(2021)10.1186/s13015-021-00184-7

N/A

0DataRank · unranked

5 citations

Hongyu Zheng, Carl Kingsford, Cong Ma

Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data

BMC Bioinformatics(2021)10.1186/s12859-021-04096-6

N/A

0DataRank · unranked

2 citations

Shawn James Baker, Guillaume Marçais, Quang Minh Hoang, Carl Kingsford, Christopher J. Langmead +1 more

Sequence-specific minimizers via polar sets

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.01.429246

N/A

0DataRank · unranked

4 citations

Carl Kingsford, Guillaume Marçais, Hongyu Zheng

How much data is sufficient to learn high-performing algorithms? generalization guarantees for data-driven algorithm design

arXiv (Cornell University)(2021)10.1145/3406325.3451036

N/A

0DataRank · unranked

3 citations

Dan DeBlasio, Travis Dick, Carl Kingsford, Tüomas Sandholm, Ellen Vitercik +1 more

Capturing the complexity of topologically associating domains through multi-feature optimization

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.04.425264

N/A

0DataRank · unranked

2 citations

Carl Kingsford, Natalie Sauerwald

Practical selection of representative sets of RNA-seq samples using a hierarchical approach

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.04.429817

N/A

0DataRank · unranked

0 citations

Carl Kingsford, Laura H. Tung

Constructing smaller genome graphs via string compression

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.08.430279

N/A

0DataRank · unranked

0 citations

Carl Kingsford, Yutong Qiu

The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance

Bioinformatics(2022)10.1093/bioinformatics/btac264

N/A

0DataRank · unranked

3 citations

Carl Kingsford, Yutong Qiu

Masked Minimizers: Unifying sequence sketching methods

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.18.512430

N/A

0DataRank · unranked

3 citations

Guillaume Marçais, Carl Kingsford, Minh Hoang

The Effect of Genome Graph Expressiveness on the Discrepancy Between Genome Graph Distance and String Set Distance

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.18.481102

N/A

0DataRank · unranked

2 citations

Carl Kingsford, Yutong Qiu

DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.17.480870

N/A

0DataRank · unranked

1 citations

Hongyu Zheng, Carl Kingsford, Minh Hoang

Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme

Journal of Computational Biology(2023)10.1089/cmb.2023.0212

N/A

0DataRank · unranked

4 citations

Guillaume Marçais, Carl Kingsford, Minh Hoang

Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants

PubMed(2023)10.4230/lipics.wabi.2023.11

N/A

0DataRank · unranked

0 citations

Yihang Shen, Carl Kingsford, Yutong Qiu

Sketching methods with small window guarantee using minimum decycling sets

arXiv (Cornell University)(2023)10.48550/arxiv.2311.03592

N/A

0DataRank · unranked

0 citations

Dan DeBlasio, Carl Kingsford, Guillaume Marçais

How Much Data Is Sufficient to Learn High-Performing Algorithms?

Journal of the ACM(2024)10.1145/3676278

N/A

0DataRank · unranked

14 citations

Dan DeBlasio, Travis Dick, Carl Kingsford, Tüomas Sandholm, Ellen Vitercik +1 more

k -nonical space: sketching with reverse complements

Bioinformatics(2024)10.1093/bioinformatics/btae629

N/A

0DataRank · unranked

7 citations

C.S. Elder, Carl Kingsford, Guillaume Marçais

Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants

Algorithms for Molecular Biology(2024)10.1186/s13015-024-00262-6

N/A

0DataRank · unranked

1 citations

Yihang Shen, Carl Kingsford, Yutong Qiu

Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets

Journal of Computational Biology(2024)10.1089/cmb.2024.0544

N/A

0DataRank · unranked

4 citations

Dan DeBlasio, Carl Kingsford, Guillaume Marçais

Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.06.574484

N/A

0DataRank · unranked

5 citations

Marcus H. Stoiber, Ziv Bar‐Joseph, Carl Kingsford, Haotian Teng

k -nonical space: sketching with reverse complements

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.25.577301

N/A

0DataRank · unranked

1 citations

C.S. Elder, Carl Kingsford, Guillaume Marçais

A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.15.580520

N/A

0DataRank · unranked

1 citations

Minh Hoang, Mohsen Ferdosi, Carl Kingsford, C.S. Elder

Data-driven AI system for learning how to run transcript assemblers

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.25.577290

N/A

0DataRank · unranked

0 citations

Zhiwen Yan, Carl Kingsford, Yihang Shen

Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements

Journal of Computational Biology(2024)10.1089/cmb.2024.0661

N/A

0DataRank · unranked

0 citations

Minh Hoang, Mohsen Ferdosi, Carl Kingsford, C.S. Elder