Carl Kingsford

ORCID

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 67

Top Venues

Publications

Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford
Graph-Based Genome Inference from Hi-C Data. RECOMB (2024)
Guillaume Marçais, Dan F. DeBlasio, Carl Kingsford
Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets. J. Comput. Biol. 31 (7) (2024)
Minh Hoang, Carl Kingsford
Efficient Heterogeneous Meta-Learning via Channel Shuffling Modulation. ICLR (2024)
Yutong Qiu, Yihang Shen, Carl Kingsford
Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants. Algorithms Mol. Biol. 19 (1) (2024)
C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford
A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements. RECOMB (2024)
Mohsen Ferdosi, Yuejun Ge, Carl Kingsford
Reinforcement Learning for Robotic Liquid Handler Planning. WABI (2023)
Guillaume Marçais, Dan F. DeBlasio, Carl Kingsford
Sketching methods with small window guarantee using minimum decycling sets. CoRR (2023)
Yihang Shen, Carl Kingsford
Computationally Efficient High-Dimensional Bayesian Optimization via Variable Selection. AutoML (2023)
Hongyu Zheng, Guillaume Marçais, Carl Kingsford
Creating and Using Minimizer Sketches in Computational Genomics. J. Comput. Biol. 30 (12) (2023)
Yutong Qiu, Yihang Shen, Carl Kingsford
Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants. WABI (2023)
Yutong Qiu, Yihang Shen, Carl Kingsford
Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants. CoRR (2023)
Minh Hoang, Hongyu Zheng, Carl Kingsford
Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer. J. Comput. Biol. 29 (12) (2022)
Minh Hoang, Hongyu Zheng, Carl Kingsford
DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes. RECOMB (2022)
Hongyu Zheng, Cong Ma, Carl Kingsford
Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability. J. Comput. Biol. 29 (2) (2022)
Trevor S. Frisby, Shawn J. Baker, Guillaume Marçais, Quang Minh Hoang, Carl Kingsford, Christopher J. Langmead
Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data. BMC Bioinform. 22 (1) (2021)
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length. J. Comput. Biol. 28 (4) (2021)
Yutong Qiu, Carl Kingsford
Constructing small genome graphs via string compression. Bioinform. 37 (Supplement) (2021)
Cong Ma, Hongyu Zheng, Carl Kingsford
Exact transcript quantification over splice graphs. Algorithms Mol. Biol. 16 (1) (2021)
Vaibhav Rajan, Ziqi Zhang, Carl Kingsford, Xiuwei Zhang
Maximum likelihood reconstruction of ancestral networks by integer linear programming. Bioinform. 37 (8) (2021)
Maria-Florina Balcan, Dan F. DeBlasio, Travis Dick, Carl Kingsford, Tuomas Sandholm, Ellen Vitercik
How much data is sufficient to learn high-performing algorithms? generalization guarantees for data-driven algorithm design. STOC (2021)
Laura H. Tung, Carl Kingsford
Practical selection of representative sets of RNA-seq samples using a hierarchical approach. Bioinform. 37 (Supplement) (2021)
Yihang Shen, Carl Kingsford
Computationally Efficient High-Dimensional Bayesian Optimization via Variable Selection. CoRR (2021)
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
Sequence-specific minimizers via polar sets. Bioinform. 37 (Supplement) (2021)
Yutong Qiu, Cong Ma, Han Xie, Carl Kingsford
Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem. Algorithms Mol. Biol. 15 (1) (2020)
Dan F. DeBlasio, Kwanho Kim, Carl Kingsford
More Accurate Transcript Assembly via Parameter Advising. J. Comput. Biol. 27 (8) (2020)
Hongyi Xin, Mingfu Shao, Carl Kingsford
Context-aware seeds for read mapping. Algorithms Mol. Biol. 15 (1) (2020)
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
Improved design and analysis of practical minimizers. Bioinform. 36 (Supplement-1) (2020)
Cong Ma, Hongyu Zheng, Carl Kingsford
Exact Transcript Quantification Over Splice Graphs. WABI (2020)
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
Lower density selection schemes via small universal hitting sets with short remaining path length. CoRR (2020)
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length. RECOMB (2020)
Maria-Florina Balcan, Dan F. DeBlasio, Travis Dick, Carl Kingsford, Tuomas Sandholm, Ellen Vitercik
How much data is sufficient to learn high-performing algorithms? CoRR (2019)
Mingfu Shao, Carl Kingsford
Theory and A Heuristic for the Minimum Path Flow Decomposition Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Emre Sefer, Carl Kingsford
Semi-nonparametric modeling of topological domain formation from epigenetic data. Algorithms Mol. Biol. 14 (1) (2019)
Natalie Sauerwald, Yihang Shen, Carl Kingsford
Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation. WABI (2019)
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 deCaestecker, 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 A. 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
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nat. 574 (7777) (2019)
Guillaume Marçais, Dan F. DeBlasio, Prashant Pandey, Carl Kingsford
Locality-sensitive hashing for the edit distance. Bioinform. 35 (14) (2019)
Dan F. DeBlasio, Fiyinfoluwa Gbosibo, Carl Kingsford, Guillaume Marçais
Practical Universal k-mer Sets for Minimizer Schemes. BCB (2019)
Hongyi Xin, Mingfu Shao, Carl Kingsford
Context-Aware Seeds for Read Mapping. WABI (2019)
Yutong Qiu, Cong Ma, Han Xie, Carl Kingsford
Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. WABI (2019)
Quang Minh Hoang, Trong Nghia Hoang, Bryan Kian Hsiang Low, Carl Kingsford
Collective Model Fusion for Multiple Black-Box Experts. ICML (2019)
Brad Solomon, Carl Kingsford
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. J. Comput. Biol. 25 (7) (2018)
Natalie Sauerwald, Carl Kingsford
Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinform. 34 (13) (2018)
Guillaume Marçais, Dan F. DeBlasio, Carl Kingsford
Asymptotically optimal minimizers schemes. Bioinform. 34 (13) (2018)
Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford
Improving the performance of minimizers and winnowing schemes. Bioinform. 33 (14) (2017)
Hao Wang, Joel McManus, Carl Kingsford
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. J. Comput. Biol. 24 (6) (2017)
David Pellow, Darya Filippova, Carl Kingsford
-mer Bloom Filters. J. Comput. Biol. 24 (6) (2017)
Brad Solomon, Carl Kingsford
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. RECOMB (2017)
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. PLoS Comput. Biol. 13 (10) (2017)
Hao Wang, Joel McManus, Carl Kingsford
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap. Bioinform. 32 (12) (2016)
Farhad Hormozdiari, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, Fabio Vandin
The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). RECOMB (2016)
Hao Wang, Joel McManus, Carl Kingsford
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. RECOMB (2016)
Emre Sefer, Geet Duggal, Carl Kingsford
Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. J. Comput. Biol. 23 (6) (2016)
Carl Kingsford
Teaching Computation to Biologists. Comput. Sci. Eng. 18 (1) (2016)
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
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. BMC Bioinform. 17 (2016)
Emre Sefer, Carl Kingsford
Diffusion archeology for diffusion progression history reconstruction. Knowl. Inf. Syst. 49 (2) (2016)
Hongyi Xin, Sunny Nahar, Richard Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
Optimal seed solver: optimizing seed selection in read mapping. Bioinform. 32 (11) (2016)
Nitish Gupta, Komal Sanjeev, Tim Wall, Carl Kingsford, Rob Patro
Efficient Index Maintenance Under Dynamic Genome Modification. CoRR (2016)
David Pellow, Darya Filippova, Carl Kingsford
Improving Bloom Filter Performance on Sequence Data Using k -mer Bloom Filters. RECOMB (2016)
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
Compact Universal k-mer Hitting Sets. WABI (2016)
Rob Patro, Carl Kingsford
Data-dependent bucketing improves reference-free compression of sequencing reads. Bioinform. 31 (17) (2015)
Emre Sefer, Carl Kingsford
Convex Risk Minimization to Infer Networks from probabilistic diffusion data at multiple scales. ICDE (2015)
Emre Sefer, Geet Duggal, Carl Kingsford
Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. RECOMB (2015)
Emre Sefer, Carl Kingsford
Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic Data. WABI (2015)
Darya Filippova, Carl Kingsford
Rapid, separable compression enables fast analyses of sequence alignments. BCB (2015)
Carl Kingsford, Rob Patro
Reference-based compression of short-read sequences using path encoding. Bioinform. 31 (12) (2015)
Hongyi Xin, Richard Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping. CoRR (2015)
Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping. Bioinform. 31 (10) (2015)
Emre Sefer, Carl Kingsford
Diffusion Archaeology for Diffusion Progression History Reconstruction. ICDM (2014)
Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford
Identification of alternative topological domains in chromatin. Algorithms Mol. Biol. 9 (2014)
Rob Patro, Carl Kingsford
Predicting protein interactions via parsimonious network history inference. Bioinform. 29 (13) (2013)
Rob Patro, Stephen M. Mount, Carl Kingsford
Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms. CoRR (2013)
Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford
Resolving spatial inconsistencies in chromosome conformation measurements. Algorithms Mol. Biol. 8 (2013)
Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford
Multiscale Identification of Topological Domains in Chromatin. WABI (2013)
Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford
Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. BCB (2013)
Geet Duggal, Carl Kingsford
Graph rigidity reveals well-constrained regions of chromosome conformation embeddings. BMC Bioinform. 13 (2012)
Rob Patro, Carl Kingsford
Global network alignment using multiscale spectral signatures. Bioinform. 28 (23) (2012)
Rob Patro, Geet Duggal, Emre Sefer, Hao Wang, Darya Filippova, Carl Kingsford
The missing models: a data-driven approach for learning how networks grow. KDD (2012)
Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford
Resolving Spatial Inconsistencies in Chromosome Conformation Data. WABI (2012)
Darya Filippova, Aashish Gadani, Carl Kingsford
Coral: an integrated suite of visualizations for comparing clusterings. BMC Bioinform. 13 (2012)
Darya Filippova, Michael Fitzgerald, Carl Kingsford, Fernando Benadon
Dynamic Exploration of Recording Sessions between Jazz Musicians over Time. SocialCom/PASSAT (2012)
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford
Parsimonious reconstruction of network evolution. Algorithms Mol. Biol. 7 (2012)
Saket Navlakha, Carl Kingsford
Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions. PLoS Comput. Biol. 7 (4) (2011)
Joshua Wetzel, Carl Kingsford, Mihai Pop
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinform. 12 (2011)
Emre Sefer, Carl Kingsford
Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. RECOMB (2011)
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford
Parsimonious Reconstruction of Network Evolution. WABI (2011)
David R. Kelley, Carl Kingsford
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. J. Comput. Biol. 18 (3) (2011)
Guillaume Marçais, Carl Kingsford
-mers. Bioinform. 27 (6) (2011)
Carl Kingsford
Review of Complex social networks by Fernando Vega-Redondo. SIGACT News 42 (1) (2011)
Carl Kingsford, Elena Zaslavsky, Mona Singh
A cost-aggregating integer linear program for motif finding. J. Discrete Algorithms 9 (4) (2011)
Saket Navlakha, James Robert White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. J. Comput. Biol. 17 (3) (2010)
Saket Navlakha, Carl Kingsford
The power of protein interaction networks for associating genes with diseases. Bioinform. 26 (8) (2010)
Saket Navlakha, Carl Kingsford
Network Archaeology: Uncovering Ancient Networks from Present-day Interactions CoRR (2010)
James Robert White, Saket Navlakha, Niranjan Nagarajan, Mohammadreza Ghodsi, Carl Kingsford, Mihai Pop
Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. BMC Bioinform. 11 (2010)
Saket Navlakha, Carl Kingsford
Exploring Biological Network Dynamics with Ensembles of Graph Partitions. Pacific Symposium on Biocomputing (2010)
Grecia Lapizco-Encinas, Carl Kingsford, James A. Reggia
Particle Swarm Optimization for multimodal combinatorial problems and its application to protein design. IEEE Congress on Evolutionary Computation (2010)
Carl Kingsford, Michael C. Schatz, Mihai Pop
Assembly complexity of prokaryotic genomes using short reads. BMC Bioinform. 11 (2010)
David R. Kelley, Carl Kingsford
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. RECOMB (2010)
Saket Navlakha, James Robert White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. RECOMB (2009)
Grecia Lapizco-Encinas, Carl Kingsford, James A. Reggia
A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing. SIS (2009)
Saket Navlakha, Michael C. Schatz, Carl Kingsford
Revealing Biological Modules via Graph Summarization. J. Comput. Biol. 16 (2) (2009)

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Publication Activity (10 Years)

Top Topics

Top Venues

Carl Kingsford