| 2026 | WABI | Turnpike with Uncertain Measurements: Triangle-Equality Integer Programming with a Deterministic Recovery Guarantee. | C. S. Elder, Guillaume Marais, Carl Kingsford |
| 2026 | WABI | Quantum Closest-Pair Search for Biological Sequences via k-Mer Distribution Statistics. | Zhezheng Xander Song, Carl Kingsford |
| 2024 | ICLR | Efficient Heterogeneous Meta-Learning via Channel Shuffling Modulation. | Minh Hoang, Carl Kingsford |
| 2024 | RECOMB | A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements. | C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford |
| 2024 | RECOMB | Graph-Based Genome Inference from Hi-C Data. | Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford |
| 2023 | WABI | Reinforcement Learning for Robotic Liquid Handler Planning. | Mohsen Ferdosi, Yuejun Ge, Carl Kingsford |
| 2023 | WABI | Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants. | Yutong Qiu, Yihang Shen, Carl Kingsford |
| 2022 | RECOMB | DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes. | Minh Hoang, Hongyu Zheng, Carl Kingsford |
| 2021 | STOC | How much data is sufficient to learn high-performing algorithms? generalization guarantees for data-driven algorithm design. | Maria-Florina Balcan, Dan F. DeBlasio, Travis Dick, Carl Kingsford, Tuomas Sandholm, Ellen Vitercik |
| 2020 | RECOMB | Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length. | Hongyu Zheng, Carl Kingsford, Guillaume Marais |
| 2020 | WABI | Exact Transcript Quantification Over Splice Graphs. | Cong Ma, Hongyu Zheng, Carl Kingsford |
| 2019 | ICML | Collective Model Fusion for Multiple Black-Box Experts. | Quang Minh Hoang, Trong Nghia Hoang, Bryan Kian Hsiang Low, Carl Kingsford |
| 2019 | WABI | Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. | Yutong Qiu, Cong Ma, Han Xie, Carl Kingsford |
| 2019 | WABI | Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation. | Natalie Sauerwald, Yihang Shen, Carl Kingsford |
| 2019 | WABI | Context-Aware Seeds for Read Mapping. | Hongyi Xin, Mingfu Shao, Carl Kingsford |
| 2017 | RECOMB | Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. | Brad Solomon, Carl Kingsford |
| 2016 | RECOMB | The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). | Farhad Hormozdiari, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, Fabio Vandin |
| 2016 | RECOMB | Improving Bloom Filter Performance on Sequence Data Using k -mer Bloom Filters. | David Pellow, Darya Filippova, Carl Kingsford |
| 2016 | RECOMB | Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. | Hao Wang, Joel McManus, Carl Kingsford |
| 2016 | WABI | Compact Universal k-mer Hitting Sets. | Yaron Orenstein, David Pellow, Guillaume Marais, Ron Shamir, Carl Kingsford |
| 2015 | ICDE | Convex Risk Minimization to Infer Networks from probabilistic diffusion data at multiple scales. | Emre Sefer, Carl Kingsford |
| 2015 | RECOMB | Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. | Emre Sefer, Geet Duggal, Carl Kingsford |
| 2015 | WABI | Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic Data. | Emre Sefer, Carl Kingsford |
| 2014 | ICDM | Diffusion Archaeology for Diffusion Progression History Reconstruction. | Emre Sefer, Carl Kingsford |
| 2013 | WABI | Multiscale Identification of Topological Domains in Chromatin. | Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford |
| 2012 | KDD | The missing models: a data-driven approach for learning how networks grow. | Rob Patro, Geet Duggal, Emre Sefer, Hao Wang, Darya Filippova, Carl Kingsford |
| 2012 | WABI | Resolving Spatial Inconsistencies in Chromosome Conformation Data. | Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford |
| 2011 | RECOMB | Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. | Emre Sefer, Carl Kingsford |
| 2011 | WABI | Parsimonious Reconstruction of Network Evolution. | Rob Patro, Emre Sefer, Justin Malin, Guillaume Marais, Saket Navlakha, Carl Kingsford |
| 2010 | CEC | Particle Swarm Optimization for multimodal combinatorial problems and its application to protein design. | Grecia C. Lapizco-Encinas, Carl Kingsford, James A. Reggia |
| 2010 | PSB | Exploring Biological Network Dynamics with Ensembles of Graph Partitions. | Saket Navlakha, Carl Kingsford |
| 2010 | RECOMB | Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. | David R. Kelley, Carl Kingsford |
| 2009 | RECOMB | Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. | Saket Navlakha, James Robert White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford |
| 2006 | CPM | A Compact Mathematical Programming Formulation for DNA Motif Finding. | Carl Kingsford, Elena Zaslavsky, Mona Singh |
| 2001 | DNA | Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability. | John H. Reif, Thomas H. LaBean, Michael Pirrung, Vipul S. Rana, Bo Guo, Carl Kingsford, Gene S. Wickham |