- Nitish Gupta, Komal Sanjeev, Tim Wall, Carl Kingsford, Rob Patro. Efficient Index Maintenance Under Dynamic Genome Modification. Presented at RECOMB-seq 2016 satellite conference.
- Mingfu Shao and Carl Kingsford. Scallop Enables Accurate Assembly Of Transcripts Through Phasing-Preserving Graph Decomposition.
- Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford. Improving the performance of minimizers and winnowing schemes. To appear in ISMB 2017 / Bioinformatics.
- Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference. Nature Methods (2017). doi:10.1038/nmeth.4197 (pre-print at http://dx.doi.org/10.1101/021592)
- Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar. Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nuc. Acids Res., in press. (2017) doi: http://dx.doi.org/10.1101/08118
- Mingfu Shao and Carl Kingsford. Efficient Heuristic for Decomposing a Flow with Minimum Number of Paths. To appear in RECOMB-seq (2017). doi: http://dx.doi.org/10.1101/087759.
- Brad Solomon and Carl Kingsford. Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. (To appear RECOMB.)
- Y. Orenstein, D. Pellow, G. Marçais, R. Shamir and C. Kingsford. Compact universal k-mer hitting sets. Proceedings of the 15th Annual Workshop on Algorithms in Bioinformatics (WABI) (2016)
- Hiren Karathia, Carl Kingsford, Michelle Girvan, Sridhar Hannenhalli. A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. Scientific Reports 39279 (2016). doi:10.1038/srep39279 [preprint]
- Hao Wang, Joel McManus, Carl Kingsford. Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap. Bioinformatics (2016). [Preprint]
- Brad Solomon and Carl Kingsford. Fast search of thousands of short-read sequencing experiments, Nature Biotechnology (2016). [Preprint]
- Hao Wang, Joel McManus and Carl Kingsford. Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. In RECOMB 2016 (Journal version to appear in Journal of Comp. Biol.)
- David Pellow, Darya Filippova and Carl Kingsford. Improving Bloom filter performance on sequence data using k-mer Bloom filters. In RECOMB 2016 (Journal version to appear in Journal of Comp. Biol.)
- Darya Filippova and Carl Kingsford. Rapid Separable Compression Enables Fast Analyses of Sequence Alignments. In ACM-BCB 2015.
- E. Sefer and C. Kingsford. Semi-nonparametric Modeling of Topological Domain Formation From Epigenetic Data. In WABI 2015.
- R. Patro and C. Kingsford. Data-dependent bucketing improves reference-free compression of sequencing reads Bioinformatics 2015.
- C. Kingsford and R. Patro. Reference-based compression of short-read sequences using path encoding. Bioinformatics 2015; doi:10.1093/bioinformatics/btv071
- E. Sefer, G. Duggal, and C. Kingsford. Deconvolution Of Ensemble Chromatin Interaction Data Reveals The Latent Mixing Structures In Cell Subpopulations. In RECOMB 2015.
- H Xin, J Greth, J Emmons, G Pekhimenko, C Kingsford, Can Alkan, Onur Mutlu. Shifted Hamming Distance: A Fast and Accurate SIMD-Friendly Filter to Accelerate Alignment Verification in Read Mapping. Bioinformatics 2015; doi:10.1093/bioinformatics/btu856
- R. Patro, S. M. Mount, and Carl Kingsford. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology (2014). doi:10.1038/nbt.2862.
- G Duggal, H Wang, and Carl Kingsford. Higher-order chromatin domains link eQTLs with the expression of far-away genes. Nucleic Acids Research 2013; doi: 10.1093/nar/gkt857
- H. Wang, G. Duggal, R. Patro, M. Girvan, S. Hannenhalli, and C. Kingsford. Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. In ACM BCB 2013.
- D. Filippova†, R. Patro†, G. Duggal†, and C. Kingsford. Identification of alternative topological domains in chromatin. Algorithms for Molecular Biology.2014, 9:14 DOI: 10.1186/1748-7188-9-14 (conference version in WABI 2013).
- G. Duggal and C. Kingsford. Graph rigidity reveals well-constrained regions of chromosome conformation embeddings. BMC Bioinformatics 13:241, 2012. [PSB 2012 presentation]
- G. Duggal, R. Patro, E. Sefer, H. Wang, D. Filippova, S. Khuller, and C. Kingsford. Resolving Spatial Inconsistencies in Chromosome Conformation Data. In WABI 2012. Lecture Notes in Computer Science, 2012, Volume 7534/2012, 288-300.
- G. Marçais and C. Kingsford. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 2011. [Software]
- J. Wetzel, C. Kingsford, and M. Pop. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read assemblies. BMC Bioinformatics 12:95, 2011.
- J. R. White, S. Navlakha, N. Nagarajan, M. Ghodsi, C. Kingsford, and M. Pop. Alignment and clustering of phylogenetic markers – implications for microbial diversity studies. BMC Bioinformatics 2010, 11:152.
- C. Kingsford, M. C. Schatz, and M. Pop. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11:21, 2010. (Top 10 most-viewed articles Jan/Feb 2010. Top-10 cited article in BMC Bioinformatics for 2010)
- C. Kingsford†, N. Nagarajan†, and S. L. Salzberg. 2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates. PLoS ONE 4(7):e6402, 2009.
- N. Nagarajan and C. Kingsford. Uncovering Genomic Reassortments Among Influenza Strains by Enumerating Maximal Bicliques. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, pages 223-230, 2008. [Preprint]
- S. Salzberg, C. Kingsford, G. Cattoli, D.J. Spiro, D.A. Janies, M.M. Aly et al. Genome analysis linking recent European and African influenza (H5N1) viruses. Emerging Infectious Diseases 13(5), 2007.
- C. Kingsford, A. Delcher, and S. Salzberg. A Unified Model Explaining the Offsets of Overlapping and Near-Overlapping Prokaryotic Genes. Molecular Biology and Evolution, 24(9):2091–2098 (2007). (Journal Page)
- C. Kingsford, K. Ayanbule, and S. Salzberg. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biology 8:R22 (2007). [Preprint] [Software Download]
- C. Kingsford, E. Zaslavsky, and M. Singh. A compact mathematical programming formulation for DNA motif finding. In the proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching (2006). [PDF of Talk Slides] [Preprint] Journal version J. Discrete Algorithms 9(4):326-334 (2011).
Biological Network Analysis
- R Patro, R Norel, et al. A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. BMC Bioinformatics 2016. (This reports on the winning system in the DREAM5 Challenge 1 competition, and was originally presented at the RECOMB Systems Biology satellite conference.)
- E. Sefer and Carl Kingsford. Convex Risk Minimization to Infer Networks From Probabilistic Diffusion Data At Multiple Scales. In ICDE 2015.
- E. Sefer and Carl Kingsford. Diffusion Archaeology for Diffusion Progression History Reconstruction. In ICDM 2014.
- R. Patro and C. Kingsford. Predicting protein interactions via parsimonious network history inference. In ISMB/ECCB 2013.
- D. Filippova, A. Gadani, and C. Kingsford. Coral: an integrated suite of visualizations for comparing clusterings. BMC Bioinformatics 13:276, 2012. [Software]
- R. Patro and C. Kingsford. Global network alignment using multiscale spectral signatures. Bioinformatics 28(23):3105-3114 (2012).
- D. Filippova, M. Fitzgerald, C. Kingsford and F. Benadon. Dynamic exploration of recording sessions between jazz musicians over time. In SocialCom 2012 [software]
- R. Patro†, G. Duggal†, E. Sefer, H. Wang, D. Filippova, and C. Kingsford. The Missing Models: A Data-Driven Approach for Learning How Networks Grow. In KDD pp. 42-50, 2012. [Teaser Video] Won best video at KDD.
- R. Patro, E. Sefer, J. Malin, G. Marçais, S. Navlakha, and C. Kingsford. Parsimonious Reconstruction of Network Evolution. In WABI 2011, LNCS 6833, pages 237-249. Journal version
in Algorithms for Molecular Biology 2012, 7:25. [software]
- E. Sefer and C. Kingsford. Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. In RECOMB 2011, pages 392-407.
- N. Nagarajan and C. Kingsford. GiRaF: Robust, Computational Identification of Influenza Reassortments via Graph Mining. Nuc. Acids Res., 39(6):e34, 2011.
- S. Navlakha and C. Kingsford. Network Archaeology: Uncovering Ancient Networks from Present-day Interactions. PLoS Computational Biology 7(4): e1001119. doi:10.1371/journal.pcbi.1001119. [Website]
- G. Duggal, S. Navlakha, M. Girvan, and C. Kingsford. Uncovering Many Views of Biological Networks Using Ensembles of Near-Optimal Partitions. In MultiClust: 1st International Workshop on Discovering, Summarizing and Using Multiple Clusterings at KDD 2010. [Website]
- S. Navlakha and C. Kingsford. The Power of Protein Interaction Networks for Associating Genes with Diseases. Bioinformatics, 2010; doi: 10.1093/bioinformatics/btq076. Recommended by the Faculty of 1000 [Website]
- D. E. Kelley and C. Kingsford. Extracting between-pathway models from E-MAP interactions using expected graph
compression. In RECOMB 2010, Lecture Notes in Computer Science, Volume 6044/2010, pp. 248-262. Journal version in J. Comp. Biol. 18(3):379-390, 2011.
- S. Navlakha and C. Kingsford. Exploring Biological Network Dynamics with Ensembles of Graph Partitions. In Proceedings of Pac. Symp. Biocomp. 2010, pages 166-177.
- S. Navlakha, J. White, N. Nagarajan, M. Pop, and C. Kingsford. Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. In Proceedings of RECOMB 2009, Lectures Notes in
Computer Science 5541, pages 400-417. [Preprint] Journal version in J. Comp. Biol. 17(3):503-516, 2010 [Website]
- S. Navlakha, M. Schatz, and C. Kingsford. Revealing Biological Modules via Graph Summarization. Presented at RECOMB-SB/RG/DREAM3 satellite conference, 2008. Journal version J. Comp. Biol. 16(2):253-264, 2009. [Preprint] [Video of RECOMB-SB Talk]
- G. Lapizco Encinas, C. Kingsford, and J. Reggia. Particle Swarm Optimization for Multimodal Combinatorial Problems and its application to Protein Design. In IEEE Congress on Evolutionary Computation, 2010.
- G. Lapizco-Encinas, C. Kingsford, and J. Reggia. A Cooperative Combinatorial Particle Swarm Optimization for Side-chain Packing. Proceedings of IEEE Swarm Intelligence Symposium 2009, pages 22-29. [Preprint]
- C. Kingsford, B. Chazelle, and M. Singh. Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics 21(7):1028-1039 (2005). (Advanced access publication on 11/16/2004.) [Preprint] [Software Download]
- B. Chazelle*, C. Kingsford*, and M. Singh*. A semidefinite programming approach to side-chain positioning with new rounding strategies. INFORMS Journal on Computing, Special Issue on Computational Molecular Biology/Bioinformatics, 16:380-392 (2004). [Preprint]
- C. Kingsford* and G. Marçais.* A synthesis for exactly 3-edge-connected graphs. [Preprint]
- C. Kingsford* and G. Marçais.* Vertices of degree k in edge-minimal, k-edge-connected graphs. [Preprint]
- C. Kingsford and S. L. Salzberg. What are decision trees? Nature Biotechnology 26:1011-1013 (2008).
* indicates alphabetized authors. † indicates equal contribution.