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Carlton Kingsford - Publications

Affiliations: 
2005-2007 Computer Science University of Maryland, College Park, College Park, MD 
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Sauerwald N, Kingsford C. Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinformatics (Oxford, England). 34: i475-i483. PMID 29949963 DOI: 10.1093/bioinformatics/bty265  0.732
2017 Sauerwald N, Zhang S, Kingsford C, Bahar I. Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Research. PMID 28334818 DOI: 10.1093/Nar/Gkx172  0.744
2017 Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods. PMID 28263959 DOI: 10.1038/Nmeth.4197  0.554
2016 Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A, Bellazzi R, Thiesen HJ, Stolovitzky G, Kingsford C. A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. Bmc Bioinformatics. 17: 155. PMID 27059896 DOI: 10.1186/S12859-016-1008-7  0.529
2015 Patro R, Kingsford C. Data-dependent bucketing improves reference-free compression of sequencing reads. Bioinformatics (Oxford, England). 31: 2770-7. PMID 25910696 DOI: 10.1093/Bioinformatics/Btv248  0.556
2015 Kingsford C, Patro R. Reference-based compression of short-read sequences using path encoding. Bioinformatics (Oxford, England). 31: 1920-8. PMID 25649622 DOI: 10.1093/Bioinformatics/Btv071  0.567
2014 Filippova D, Patro R, Duggal G, Kingsford C. Identification of alternative topological domains in chromatin. Algorithms For Molecular Biology : Amb. 9: 14. PMID 24868242 DOI: 10.1186/1748-7188-9-14  0.562
2014 Patro R, Mount SM, Kingsford C. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology. 32: 462-4. PMID 24752080 DOI: 10.1038/Nbt.2862  0.565
2013 Patro R, Kingsford C. Predicting protein interactions via parsimonious network history inference. Bioinformatics (Oxford, England). 29: i237-46. PMID 23812989 DOI: 10.1093/Bioinformatics/Btt224  0.587
2013 Duggal G, Patro R, Sefer E, Wang H, Filippova D, Khuller S, Kingsford C. Resolving spatial inconsistencies in chromosome conformation measurements. Algorithms For Molecular Biology : Amb. 8: 8. PMID 23497444 DOI: 10.1186/1748-7188-8-8  0.559
2013 Wang H, Duggal G, Patro R, Girvan M, Hannenhalli S, Kingsford C. Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 306-315. DOI: 10.1145/2506583.2506633  0.556
2013 Filippova D, Patro R, Duggal G, Kingsford C. Multiscale identification of topological domains in chromatin Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8126: 300-312. DOI: 10.1007/978-3-642-40453-5_23  0.566
2012 Patro R, Kingsford C. Global network alignment using multiscale spectral signatures. Bioinformatics (Oxford, England). 28: 3105-14. PMID 23047556 DOI: 10.1093/Bioinformatics/Bts592  0.596
2012 Patro R, Sefer E, Malin J, Marçais G, Navlakha S, Kingsford C. Parsimonious reconstruction of network evolution. Algorithms For Molecular Biology : Amb. 7: 25. PMID 22992218 DOI: 10.1186/1748-7188-7-25  0.725
2012 Patro R, Duggal G, Sefer E, Wang H, Filippova D, Kingsford C. The missing models: A data-driven approach for learning how networks grow Proceedings of the Acm Sigkdd International Conference On Knowledge Discovery and Data Mining. 42-50. DOI: 10.1145/2339530.2339541  0.583
2012 Duggal G, Patro R, Sefer E, Wang H, Filippova D, Khuller S, Kingsford C. Resolving spatial inconsistencies in chromosome conformation data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7534: 288-300. DOI: 10.1007/978-3-642-33122-0_23  0.574
2011 Kingsford C, Zaslavsky E, Singh M. A cost-aggregating integer linear program for motif finding. Journal of Discrete Algorithms (Amsterdam, Netherlands). 9: 326-334. PMID 22081765 DOI: 10.1016/J.Jda.2011.04.001  0.698
2011 Navlakha S, Kingsford C. Network archaeology: uncovering ancient networks from present-day interactions. Plos Computational Biology. 7: e1001119. PMID 21533211 DOI: 10.1371/Journal.Pcbi.1001119  0.661
2011 Wetzel J, Kingsford C, Pop M. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. Bmc Bioinformatics. 12: 95. PMID 21486487 DOI: 10.1186/1471-2105-12-95  0.726
2011 Kelley DR, Kingsford C. Extracting between-pathway models from E-MAP interactions using expected graph compression. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 379-90. PMID 21385041 DOI: 10.1089/cmb.2010.0268  0.495
2010 Navlakha S, White J, Nagarajan N, Pop M, Kingsford C. Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 503-16. PMID 20377460 DOI: 10.1089/Cmb.2009.0173  0.633
2010 White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M. Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. Bmc Bioinformatics. 11: 152. PMID 20334679 DOI: 10.1186/1471-2105-11-152  0.639
2010 Navlakha S, Kingsford C. The power of protein interaction networks for associating genes with diseases. Bioinformatics (Oxford, England). 26: 1057-63. PMID 20185403 DOI: 10.1093/Bioinformatics/Btq076  0.639
2010 Kingsford C, Schatz MC, Pop M. Assembly complexity of prokaryotic genomes using short reads. Bmc Bioinformatics. 11: 21. PMID 20064276 DOI: 10.1186/1471-2105-11-21  0.456
2010 Navlakha S, Kingsford C. Exploring biological network dynamics with ensembles of graph partitions. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 166-77. PMID 19908369  0.659
2009 Kingsford C, Nagarajan N, Salzberg SL. 2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates. Plos One. 4: e6402. PMID 19636415 DOI: 10.1371/journal.pone.0006402  0.382
2009 Navlakha S, Schatz MC, Kingsford C. Revealing biological modules via graph summarization. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 253-64. PMID 19183002 DOI: 10.1089/Cmb.2008.11Tt  0.682
2008 Kingsford C, Salzberg SL. What are decision trees? Nature Biotechnology. 26: 1011-1012. PMID 18779814 DOI: 10.1038/nbt0908-1011  0.372
2007 Kingsford C, Delcher AL, Salzberg SL. A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes Molecular Biology and Evolution. 24: 2091-2098. PMID 17642473 DOI: 10.1093/molbev/msm145  0.456
2007 Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MM, Brown IH, Couacy-Hymann E, De Mia GM, Dung do H, Guercio A, Joannis T, Maken Ali AS, Osmani A, Padalino I, et al. Genome analysis linking recent European and African influenza (H5N1) viruses. Emerging Infectious Diseases. 13: 713-8. PMID 17553249 DOI: 10.3201/eid1305.070013  0.433
2007 Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biology. 8: R22. PMID 17313685 DOI: 10.1186/gb-2007-8-2-r22  0.738
2006 Kingsford C, Zaslavsky E, Singh M. A compact mathematical programming formulation for DNA motif finding Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4009: 233-245. DOI: 10.1007/11780441_22  0.694
2005 Kingsford CL, Chazelle B, Singh M. Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics (Oxford, England). 21: 1028-36. PMID 15546935 DOI: 10.1093/Bioinformatics/Bti144  0.736
2004 Chazelle B, Kingsford C, Singh M. A semidefinite programming approach to side chain positioning with new rounding strategies Informs Journal On Computing. 16: 380-392. DOI: 10.1287/Ijoc.1040.0096  0.499
2003 Chazelle B, Kingsford C, Singh M. The Side-Chain Positioning Problem: A Semidefinite Programming Formulation with New Rounding Schemes Principles of Computing and Knowledge: Paris C. Kanellakis Memorial Workshop. 86-94.  0.486
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