Carl Kingsford

113 papers A* 6B 15C 12Misc 1Journal 71Unranked 8
YearRankTypeTitle / Venue / Authors
2026 J jnl
Turnpike with Uncertain Measurements: Triangle-Equality ILP with a Deterministic Recovery Guarantee.
CoRR
C. S. Elder, Guillaume Marçais, Carl Kingsford
2025 J jnl
A synthesis for uniformly 3-edge-connected graphs.
Discret. Appl. Math.
Carl Kingsford, Guillaume Marçais
2025 J jnl
CodonMoE: DNA Language Models for mRNA Analyses.
CoRR
Shiyi Du, Litian Liang, Jiayi Li, Carl Kingsford
2024 B conf
A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements.
RECOMB
C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford
2024 J jnl
Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements.
J. Comput. Biol.
C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford
2024 J jnl
Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme.
J. Comput. Biol.
Minh Hoang, Guillaume Marçais, Carl Kingsford
2024 A* conf
Efficient Heterogeneous Meta-Learning via Channel Shuffling Modulation.
ICLR
Minh Hoang, Carl Kingsford
2024 B conf
Graph-Based Genome Inference from Hi-C Data.
RECOMB
Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford
2024 J jnl
How Much Data Is Sufficient to Learn High-Performing Algorithms?
J. ACM
Maria-Florina Balcan, Dan F. DeBlasio, Travis Dick, Carl Kingsford, Tuomas Sandholm, Ellen Vitercik
2024 J jnl
Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants.
Algorithms Mol. Biol.
Yutong Qiu, Yihang Shen, Carl Kingsford
2024 J jnl
Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets.
J. Comput. Biol.
Guillaume Marçais, Dan F. DeBlasio, Carl Kingsford
2023 — conf
Computationally Efficient High-Dimensional Bayesian Optimization via Variable Selection.
AutoML
Yihang Shen, Carl Kingsford
2023 J jnl
Creating and Using Minimizer Sketches in Computational Genomics.
J. Comput. Biol.
Hongyu Zheng, Guillaume Marçais, Carl Kingsford
2023 C conf
Reinforcement Learning for Robotic Liquid Handler Planning.
WABI
Mohsen Ferdosi, Yuejun Ge, Carl Kingsford
2023 C conf
Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants.
WABI
Yutong Qiu, Yihang Shen, Carl Kingsford
2023 J jnl
Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants.
CoRR
Yutong Qiu, Yihang Shen, Carl Kingsford
2023 J jnl
Sketching methods with small window guarantee using minimum decycling sets.
CoRR
Guillaume Marçais, Dan F. DeBlasio, Carl Kingsford
2022 B conf
DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes.
RECOMB
Minh Hoang, Hongyu Zheng, Carl Kingsford
2022 J jnl
Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.
J. Comput. Biol.
Hongyu Zheng, Cong Ma, Carl Kingsford
2022 J jnl
Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer.
J. Comput. Biol.
Minh Hoang, Hongyu Zheng, Carl Kingsford
2022 J jnl
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance.
Bioinform.
Yutong Qiu, Carl Kingsford
2021 J jnl
Computationally Efficient High-Dimensional Bayesian Optimization via Variable Selection.
CoRR
Yihang Shen, Carl Kingsford
2021 J jnl
Constructing small genome graphs via string compression.
Bioinform.
Yutong Qiu, Carl Kingsford
2021 J jnl
Exact transcript quantification over splice graphs.
Algorithms Mol. Biol.
Cong Ma, Hongyu Zheng, Carl Kingsford
2021 J jnl
Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data.
BMC Bioinform.
Trevor S. Frisby, Shawn J. Baker, Guillaume Marçais, Quang Minh Hoang, Carl Kingsford, Christopher J. Langmead
2021 A* conf
How much data is sufficient to learn high-performing algorithms? generalization guarantees for data-driven algorithm design.
STOC
Maria-Florina Balcan, Dan F. DeBlasio, Travis Dick, Carl Kingsford, Tuomas Sandholm, Ellen Vitercik
2021 J jnl
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length.
J. Comput. Biol.
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
2021 J jnl
Maximum likelihood reconstruction of ancestral networks by integer linear programming.
Bioinform.
Vaibhav Rajan, Ziqi Zhang, Carl Kingsford, Xiuwei Zhang
2021 J jnl
Practical selection of representative sets of RNA-seq samples using a hierarchical approach.
Bioinform.
Laura H. Tung, Carl Kingsford
2021 J jnl
Sequence-specific minimizers via polar sets.
Bioinform.
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
2020 C ed.
20th International Workshop on Algorithms in Bioinformatics, WABI 2020, Pisa, Italy (Virtual Conference), September 7-9, 2020
WABI
Carl Kingsford, Nadia Pisanti
2020 J jnl
Context-aware seeds for read mapping.
Algorithms Mol. Biol.
Hongyi Xin, Mingfu Shao, Carl Kingsford
2020 J jnl
Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem.
Algorithms Mol. Biol.
Yutong Qiu, Cong Ma, Han Xie, Carl Kingsford
2020 C conf
Exact Transcript Quantification Over Splice Graphs.
WABI
Cong Ma, Hongyu Zheng, Carl Kingsford
2020 J jnl
Improved design and analysis of practical minimizers.
Bioinform.
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
2020 B conf
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length.
RECOMB
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
2020 J jnl
Lower density selection schemes via small universal hitting sets with short remaining path length.
CoRR
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
2020 J jnl
More Accurate Transcript Assembly via Parameter Advising.
J. Comput. Biol.
Dan F. DeBlasio, Kwanho Kim, Carl Kingsford
2019 A* conf
Collective Model Fusion for Multiple Black-Box Experts.
ICML
Quang Minh Hoang, Trong Nghia Hoang, Bryan Kian Hsiang Low, Carl Kingsford
2019 C conf
Context-Aware Seeds for Read Mapping.
WABI
Hongyi Xin, Mingfu Shao, Carl Kingsford
2019 C conf
Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem.
WABI
Yutong Qiu, Cong Ma, Han Xie, Carl Kingsford
2019 J jnl
How much data is sufficient to learn high-performing algorithms?
CoRR
Maria-Florina Balcan, Dan F. DeBlasio, Travis Dick, Carl Kingsford, Tuomas Sandholm, Ellen Vitercik
2019 J jnl
Locality-sensitive hashing for the edit distance.
Bioinform.
Guillaume Marçais, Dan F. DeBlasio, Prashant Pandey, Carl Kingsford
2019 — conf
Practical Universal k-mer Sets for Minimizer Schemes.
BCB
Dan F. DeBlasio, Fiyinfoluwa Gbosibo, Carl Kingsford, Guillaume Marçais
2019 J jnl
Semi-nonparametric modeling of topological domain formation from epigenetic data.
Algorithms Mol. Biol.
Emre Sefer, Carl Kingsford
2019 J jnl
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
Nat.
Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark P. de Caestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma Anand Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson
2019 J jnl
Theory and A Heuristic for the Minimum Path Flow Decomposition Problem.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mingfu Shao, Carl Kingsford
2019 C conf
Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation.
WABI
Natalie Sauerwald, Yihang Shen, Carl Kingsford
2018 J jnl
Asymptotically optimal minimizers schemes.
Bioinform.
Guillaume Marçais, Dan F. DeBlasio, Carl Kingsford
2018 J jnl
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.
J. Comput. Biol.
Brad Solomon, Carl Kingsford
2018 J jnl
Quantifying the similarity of topological domains across normal and cancer human cell types.
Bioinform.
Natalie Sauerwald, Carl Kingsford
2017 J jnl
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.
J. Comput. Biol.
Hao Wang, Joel McManus, Carl Kingsford
2017 J jnl
Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.
PLoS Comput. Biol.
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
2017 B conf
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.
RECOMB
Brad Solomon, Carl Kingsford
2017 J jnl
Improving Bloom Filter Performance on Sequence Data Using
J. Comput. Biol.
David Pellow, Darya Filippova, Carl Kingsford
2017 J jnl
Improving the performance of minimizers and winnowing schemes.
Bioinform.
Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford
2016 J jnl
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
BMC Bioinform.
Rob Patro, Raquel Norel, Robert J. Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Lustrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky, Carl Kingsford
2016 B conf
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.
RECOMB
Hao Wang, Joel McManus, Carl Kingsford
2016 C conf
Compact Universal k-mer Hitting Sets.
WABI
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
2016 J jnl
Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.
J. Comput. Biol.
Emre Sefer, Geet Duggal, Carl Kingsford
2016 J jnl
Diffusion archeology for diffusion progression history reconstruction.
Knowl. Inf. Syst.
Emre Sefer, Carl Kingsford
2016 J jnl
Efficient Index Maintenance Under Dynamic Genome Modification.
CoRR
Nitish Gupta, Komal Sanjeev, Tim Wall, Carl Kingsford, Rob Patro
2016 B conf
Improving Bloom Filter Performance on Sequence Data Using k -mer Bloom Filters.
RECOMB
David Pellow, Darya Filippova, Carl Kingsford
2016 J jnl
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Bioinform.
Hao Wang, Joel McManus, Carl Kingsford
2016 J jnl
Optimal seed solver: optimizing seed selection in read mapping.
Bioinform.
Hongyi Xin, Sunny Nahar, Richard L. Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2016 J jnl
Teaching Computation to Biologists.
Comput. Sci. Eng.
Carl Kingsford
2016 B conf
The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB).
RECOMB
Farhad Hormozdiari, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, Fabio Vandin
2015 A* conf
Convex Risk Minimization to Infer Networks from probabilistic diffusion data at multiple scales.
ICDE
Emre Sefer, Carl Kingsford
2015 J jnl
Data-dependent bucketing improves reference-free compression of sequencing reads.
Bioinform.
Rob Patro, Carl Kingsford
2015 B conf
Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.
RECOMB
Emre Sefer, Geet Duggal, Carl Kingsford
2015 J jnl
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping.
CoRR
Hongyi Xin, Richard L. Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2015 — conf
Rapid, separable compression enables fast analyses of sequence alignments.
BCB
Darya Filippova, Carl Kingsford
2015 J jnl
Reference-based compression of short-read sequences using path encoding.
Bioinform.
Carl Kingsford, Rob Patro
2015 C conf
Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic Data.
WABI
Emre Sefer, Carl Kingsford
2015 J jnl
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.
Bioinform.
Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2014 A* conf
Diffusion Archaeology for Diffusion Progression History Reconstruction.
ICDM
Emre Sefer, Carl Kingsford
2014 J jnl
Identification of alternative topological domains in chromatin.
Algorithms Mol. Biol.
Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford
2013 C conf
Multiscale Identification of Topological Domains in Chromatin.
WABI
Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford
2013 J jnl
Predicting protein interactions via parsimonious network history inference.
Bioinform.
Rob Patro, Carl Kingsford
2013 J jnl
Resolving spatial inconsistencies in chromosome conformation measurements.
Algorithms Mol. Biol.
Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford
2013 J jnl
Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms.
CoRR
Rob Patro, Stephen M. Mount, Carl Kingsford
2013 — conf
Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin.
BCB
Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford
2012 J jnl
Coral: an integrated suite of visualizations for comparing clusterings.
BMC Bioinform.
Darya Filippova, Aashish Gadani, Carl Kingsford
2012 — conf
Dynamic Exploration of Recording Sessions between Jazz Musicians over Time.
SocialCom/PASSAT
Darya Filippova, Michael Fitzgerald, Carl Kingsford, Fernando Benadon
2012 J jnl
Global network alignment using multiscale spectral signatures.
Bioinform.
Rob Patro, Carl Kingsford
2012 J jnl
Graph rigidity reveals well-constrained regions of chromosome conformation embeddings.
BMC Bioinform.
Geet Duggal, Carl Kingsford
2012 J jnl
Parsimonious reconstruction of network evolution.
Algorithms Mol. Biol.
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford
2012 C conf
Resolving Spatial Inconsistencies in Chromosome Conformation Data.
WABI
Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford
2012 A* conf
The missing models: a data-driven approach for learning how networks grow.
KDD
Rob Patro, Geet Duggal, Emre Sefer, Hao Wang, Darya Filippova, Carl Kingsford
2011 J jnl
A cost-aggregating integer linear program for motif finding.
J. Discrete Algorithms
Carl Kingsford, Elena Zaslavsky, Mona Singh
2011 J jnl
A fast, lock-free approach for efficient parallel counting of occurrences of
Bioinform.
Guillaume Marçais, Carl Kingsford
2011 J jnl
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies.
BMC Bioinform.
Joshua L. Wetzel, Carl Kingsford, Mihai Pop
2011 J jnl
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression.
J. Comput. Biol.
David R. Kelley, Carl Kingsford
2011 B conf
Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction.
RECOMB
Emre Sefer, Carl Kingsford
2011 J jnl
Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions.
PLoS Comput. Biol.
Saket Navlakha, Carl Kingsford
2011 C conf
Parsimonious Reconstruction of Network Evolution.
WABI
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford
2011 J jnl
Review of Complex social networks by Fernando Vega-Redondo.
SIGACT News
Carl Kingsford
2010 J jnl
Alignment and clustering of phylogenetic markers - implications for microbial diversity studies.
BMC Bioinform.
James Robert White, Saket Navlakha, Niranjan Nagarajan, Mohammadreza Ghodsi, Carl Kingsford, Mihai Pop
2010 J jnl
Assembly complexity of prokaryotic genomes using short reads.
BMC Bioinform.
Carl Kingsford, Michael C. Schatz, Mihai Pop
2010 Misc conf
Exploring Biological Network Dynamics with Ensembles of Graph Partitions.
Pacific Symposium on Biocomputing
Saket Navlakha, Carl Kingsford
2010 B conf
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression.
RECOMB
David R. Kelley, Carl Kingsford
2010 J jnl
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information.
J. Comput. Biol.
Saket Navlakha, James Robert White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford
2010 J jnl
Network Archaeology: Uncovering Ancient Networks from Present-day Interactions
CoRR
Saket Navlakha, Carl Kingsford
2010 B conf
Particle Swarm Optimization for multimodal combinatorial problems and its application to protein design.
IEEE Congress on Evolutionary Computation
Grecia C. Lapizco-Encinas, Carl Kingsford, James A. Reggia
2010 J jnl
The power of protein interaction networks for associating genes with diseases.
Bioinform.
Saket Navlakha, Carl Kingsford
2009 — conf
A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing.
SIS
Grecia C. Lapizco-Encinas, Carl Kingsford, James A. Reggia
2009 B conf
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information.
RECOMB
Saket Navlakha, James Robert White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford
2009 J jnl
Revealing Biological Modules via Graph Summarization.
J. Comput. Biol.
Saket Navlakha, Michael C. Schatz, Carl Kingsford
2008 — conf
Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques.
BIBM
Niranjan Nagarajan, Carl Kingsford
2006 B conf
A Compact Mathematical Programming Formulation for DNA Motif Finding.
CPM
Carl Kingsford, Elena Zaslavsky, Mona Singh
2004 J jnl
A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies.
INFORMS J. Comput.
Bernard Chazelle, Carl Kingsford, Mona Singh
2003 — conf
The Side-Chain Positioning Problem: A Semidefinite Programming Formulation With New Rounding Schemes.
PCK50
Bernard Chazelle, Carl Kingsford, Mona Singh
2001 B conf
Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability.
DNA
John H. Reif, Thomas H. LaBean, Michael Pirrung, Vipul S. Rana, Bo Guo, Carl Kingsford, Gene S. Wickham