CK
Carl Kingsford
bioinformaticsAlgorithmsSoftwaregenomicsq-bio.GNRNA-seqcs.LGComputational Biologycs.DSGenomics
On Valency
published · living versionsW_92jh5vez·v1 · currentpublished
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping
with Hongyi Xin, Richard Zhu, Sunny Nahar, John Emmons +3
1 version
Preprints & journals
163 papers in the corpus · 2007–2026Sketching methods with small window guarantee using minimum decycling sets.37986724 · Marçais, Guillaume, DeBlasio, Dan, Kingsford, Carl2026 · 4 citationsArXiv. 2023
Central T cell tolerance from sparse peptide sampling.42616902 · Meyer, Hannah V, Dasgupta, Sanjoy, Banerjee, Amitava et al.2026 · 0 citationsScience advances. 2026;12(34):eaeg8240
CodonMoE: DNA language models for codon-dependent mRNA prediction.42108565 · Du, Shiyi, Liang, Litian, Li, Jiayi et al.2026 · 0 citationsBioinformatics (Oxford, England). 2026;42(6)
seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.42412804 · Kaynar, Gün, Kingsford, Carl2026 · 0 citationsBioinformatics (Oxford, England). 2026;42(1)
Data-driven AI system for learning how to run transcript assemblers.42116171 · Shen, Yihang, Yan, Zhiwen, Kingsford, Carl2026 · 0 citationsGenome biology. 2026;27(1)
Models Know Their Shortcuts: Deployment-Time Shortcut Mitigation2604.12277v2 · Jiayi Li, Shijie Tang, Gun Kaynar et al.2026 · 0 citationsarXiv
CodonMoE: DNA Language Models for mRNA Analyses.40799804 · Du, Shiyi, Liang, Litian, Li, Jiayi et al.2026 · 0 citationsArXiv. 2025
The Memory Curse: How Expanded Recall Erodes Cooperative Intent in LLM Agents2605.08060v1 · Jiayuan Liu, Tianqin Li, Shiyi Du et al.2026 · 0 citationsarXiv
Why Search When You Can Transfer? Amortized Agentic Workflow Design from Structural Priors2604.25012v1 · Shiyi Du, Jiayuan Liu, Weihua Du et al.2026 · 0 citationsarXiv
seq2ribo: Structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences10.64898/2026.02.08.700508v2 · Kaynar, G., Kingsford, C.2026 · 0 citationsbioRxiv
Turnpike with Uncertain Measurements: Triangle-Equality ILP with a Deterministic Recovery Guarantee2603.18283v1 · C. S. Elder, Guillaume Marcais, Carl Kingsford2026 · 0 citationsarXiv
Semi-nonparametric modeling of topological domain formation from epigenetic data.30867673 · Sefer, Emre, Kingsford, Carl2026 · 21 citationsAlgorithms for molecular biology : AMB. 2019;14:4
CodonRL: Multi-Objective Codon Sequence Optimization Using Demonstration-Guided Reinforcement Learning10.64898/2026.02.12.705465v1 · Du, S., Kaynar, G., Li, J. et al.2026 · 1 citationbioRxiv
Augmenting Electronic Health Records for Adverse Event Detection10.64898/2026.02.10.26345962v1 · Kaynar, G., You, Z., Boyce, R. D. et al.2026 · 0 citationsmedRxiv
Sparse, random sampling is sufficient for central tolerance10.64898/2025.12.09.693230v1 · Meyer, H. V., Dasgupta, S., Banerjee, A. et al.2025 · 0 citationsbioRxiv
A multicenter phase II study of eribulin for BRAF V600E mutant metastatic colorectal cancer: the BRAVERY study (EPOC1701).41072075 · Masuishi, T, Taniguchi, H, Kotani, D et al.2025 · 0 citationsESMO open. 2025;10(11):105839
ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering10.1101/2025.08.19.668819v2 · Li, J., Lai, H.-s., Liang, L. et al.2025 · 0 citationsbioRxiv
Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem.32467720 · Qiu, Yutong, Ma, Cong, Xie, Han et al.2025 · 3 citationsAlgorithms for molecular biology : AMB. 2020;15:9
CodonMoE: DNA Language Models for mRNA Analyses2508.04739v1 · Shiyi Du, Litian Liang, Jiayi Li et al.2025 · 0 citationsarXiv
Biological databases in the age of generative artificial intelligence.40177265 · Pop, Mihai, Attwood, Teresa K, Blake, Judith A et al.2025 · 10 citationsBioinformatics advances. 2025;5(1):vbaf044
A cost-aggregating integer linear program for motif finding.22081765 · Kingsford, Carl, Zaslavsky, Elena, Singh, Mona2025 · 3 citationsJournal of discrete algorithms (Amsterdam, Netherlands). 2011;9(4):326-334
DTMol: Pocket-based Molecular Docking using Diffusion Transformers10.1101/2025.04.13.648103v1 · Teng, H., Wang, R., Shen, Y. et al.2025 · 2 citationsbioRxiv
Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework.39406497 · Teng, Haotian, Stoiber, Marcus, Bar-Joseph, Ziv et al.2024 · 19 citationsGenome research. 2024;34(11):1987-1999
k-nonical space: sketching with reverse complements.39432565 · Marçais, Guillaume, Elder, C S, Kingsford, Carl2024 · 7 citationsBioinformatics (Oxford, England). 2024;40(11)
Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements.39387260 · Elder, C S, Hoang, Minh, Ferdosi, Mohsen et al.2024 · 0 citationsJournal of computational biology : a journal of computational molecular cell biology. 2024;31(10):908-926
Data-driven AI system for learning how to run transcript assemblers10.1101/2024.01.25.577290v2 · Shen, Y., Yan, Z., Kingsford, C.2024 · 0 citationsbioRxiv
Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets.38980804 · Marçais, Guillaume, DeBlasio, Dan, Kingsford, Carl2024 · 4 citationsJournal of computational biology : a journal of computational molecular cell biology. 2024;31(7):597-615
How has the AI boom impacted algorithmic biology?38901402 · Singh, Mona, Sahinalp, Cenk, Zeng, Jianyang et al.2024 · 0 citationsCell systems. 2024;15(6):483-487
Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants.37292475 · Qiu, Yutong, Shen, Yihang, Kingsford, Carl2024 · 0 citationsArXiv. 2023
Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants.38679703 · Qiu, Yutong, Shen, Yihang, Kingsford, Carl2024 · 1 citationAlgorithms for molecular biology : AMB. 2024;19(1):17
Context-aware seeds for read mapping.32489399 · Xin, Hongyi, Shao, Mingfu, Kingsford, Carl2024 · 5 citationsAlgorithms for molecular biology : AMB. 2020;15:10
Diffusion archeology for diffusion progression history reconstruction.27821901 · Sefer, Emre, Kingsford, Carl2024 · 17 citationsKnowledge and information systems. 2016;49(2):403-427
A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements10.1101/2024.02.15.580520v1 · Elder, C. S., Hoang, M., Ferdosi, M. et al.2024 · 1 citationbioRxiv
Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme.37975802 · Hoang, Minh, Marçais, Guillaume, Kingsford, Carl2024 · 4 citationsJournal of computational biology : a journal of computational molecular cell biology. 2024;31(1):2-20
Computationally Efficient High-Dimensional Bayesian Optimization via Variable Selection2109.09264v2 · Yihang Shen, Carl Kingsford2021 · 4 citationsarXiv
k-nonical space: sketching with reverse complements10.1101/2024.01.25.577301v1 · Marcais, G., Elder, S., Kingsford, C.2024 · 7 citationsbioRxiv
Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework10.1101/2024.01.06.574484v1 · Teng, H., Stoiber, M., Bar-Joseph, Z. et al.2024 · 5 citationsbioRxiv
Creating and Using Minimizer Sketches in Computational Genomics.37646787 · Zheng, Hongyu, Marçais, Guillaume, Kingsford, Carl2023 · 33 citationsJournal of computational biology : a journal of computational molecular cell biology. 2023;30(12):1251-1276
Improving Hi-C contact matrices using genome graphs10.1101/2023.11.08.566275v1 · Shen, Y., Yu, L., Qiu, Y. et al.2023 · 2 citationsbioRxiv
Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants2305.10577v2 · Yutong Qiu, Yihang Shen, Carl Kingsford2023 · 1 citationarXiv
Sketching methods with small window guarantee using minimum decycling sets2311.03592v1 · Guillaume Marcais, Dan DeBlasio, Carl Kingsford2023 · 4 citationsarXiv
Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer.36095142 · Hoang, Minh, Zheng, Hongyu, Kingsford, Carl2022 · 17 citationsJournal of computational biology : a journal of computational molecular cell biology. 2022;29(12):1288-1304
Masked Minimizers: Unifying sequence sketching methods10.1101/2022.10.18.512430v1 · Hoang, M., Marcais, G., Kingsford, C.2022 · 3 citationsbioRxiv
Exact transcript quantification over splice graphs.33971903 · Ma, Cong, Zheng, Hongyu, Kingsford, Carl2022 · 5 citationsAlgorithms for molecular biology : AMB. 2021;16(1):5
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance.35758819 · Qiu, Yutong, Kingsford, Carl2022 · 4 citationsBioinformatics (Oxford, England). 2022;38(Suppl 1):i404-i412
Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.35041494 · Zheng, Hongyu, Ma, Cong, Kingsford, Carl2022 · 12 citationsJournal of computational biology : a journal of computational molecular cell biology. 2022;29(2):121-139
The Effect of Genome Graph Expressiveness on the Discrepancy Between Genome Graph Distance and String Set Distance10.1101/2022.02.18.481102v1 · Qiu, Y., Kingsford, C.2022 · 4 citationsbioRxiv
DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes10.1101/2022.02.17.480870v1 · Hoang, M., Zheng, H., Kingsford, C.2022 · 6 citationsbioRxiv
VariantStore: an index for large-scale genomic variant search.34412679 · Pandey, Prashant, Gao, Yinjie, Kingsford, Carl2022 · 6 citationsGenome biology. 2021;22(1):231
Metric Labeling and Semimetric Embedding for Protein Annotation Prediction.33370163 · Sefer, Emre, Kingsford, Carl2022 · 15 citationsJournal of computational biology : a journal of computational molecular cell biology. 2021;28(5):514-525
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