Q. Nguyen and L. Oesper. Generalized Matching Distance: Tumor Phylogeny Comparison
Beyond the Infinite Sites Assumption. Accepted to ACB-BCB 2023.
Y. Guang, M. Smith-Erb and L. Oesper. A weighted distance-based approach for deriving
consensus tumor evolutionary trees. Bioinformatics, 2023 Jun; 39(Suppl 1): i204–i212. (Also accepted to ISMB/ECCB 2023.)
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PDF
M. El-Kebir, Q. Morris, L. Oesper and S C. Sahinalp. Emerging Topics in Cancer Evolution. Pacific Symposium on Biocomputing, 397-401, 2022.
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*K. Govek, *C. Sikes, Y. Zhou and L. Oesper. GraPhyC: A Consensus Approach to Infer Tumor Evolutionary Histories. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020.
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L. Oesper. What is the Role for Algorithmics and Computational Biology in Responding to the COVID-19 Pandemic? Interdisciplinary Science. Cell Systems, 10(5): 379-380, 2020. (Invited article.)
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L. Oesper and A. Vostinar. Expanding Undergraduate Exposure to Computer Science Subfields: Resources and Lessons from a Hands-on Computational Biology Workshop. 51st ACM Technical Symposium on Computer Science Education (SIGCSE),1214-1219, 2020.
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*Z. DiNardo, *K. Tomlinson, A. Ritz, L. Oesper. Distance Measures for Tumor Evolutionary Trees. Bioinformatics, 36(7):2090-2097, 2020. (Also accepted to the 2019 RECOMB-CCB Meeting.)
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Software Release.
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature,578, 82-93, 2020.
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Gerstung, Mortiz, PCAWG Evolution & Heterogeneity Working Group, et al. (Layla Oesper is listed as a member of the working group). The evolutionary history of 2,658 cancers. Nature, 578 (7793), 122-128, 2020.
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K. Tomlinson, L. Oesper. Parameter, Noise, and Tree Topology Effects in Tumor Phylogeny Inference. BMC Medical Genomics,12(10):1-14,2019.
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Associated Data.
K. Tomlinson, L. Oesper. Examining Tumor Phylogeny Inference in Noisy Sequencing Data. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 36-43, 2018.
Proceedings PDF.
K. Govek, C. Sikes, L. Oesper. A Consensus Approach to Infer Tumor Evolutionary Histories. Proceedings of the 9th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), 63-72, 2018. Best Paper Award
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Software Release.
L. Oesper, S. Dantas, B.J. Raphael. Identifying Simultaneous Rearrangements in Cancer Genomes. Bioinformatics (Proceedings of 4th RECOMB Satellite Workshop on Computational Cancer Biology (RECOMB-CCB)), 34(2):346-352, 2017.
Publisher Link.
Software Release.
M. El-Kebir, G. Satas, L. Oesper, B.J. Raphael. Inferring the Mutational History of a Tumor Using Multi-State Perfect Phylogeny Mixtures. Cell Systems 3(1), 43-53, 2016.
Publisher Link.
Software Release.
M. El-Kebir, G. Satas, L. Oesper, B.J. Raphael. Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. Proceedings of the 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2016.
Full Paper.
*M. El-Kebir, *L. Oesper, H. Acheson-Field, B.J. Raphael. Reconstruction of clonal trees and tumor composition from multi-sample cancer sequencing data. Bioinformatics
(Proceedings of 23rd Annual Conference on Intelligent Systems for Molecular Biology (ISMB)),
31(12):i62-i70, 2015.
Publisher Link.
Software Release.
*L. Oesper, *G. Satas, B.J. Raphael. Quantifying Tumor Heterogeneity in Whole-Genome and Whole-Exome Sequencing Data. Bioinformatics, 30(24), 2014.
Publisher Link.
Software Release.
*C. Weinreb, *L. Oesper, B.J. Raphael. Open adjacencies and k-breaks: detecting simultaneous events in cancer genomes. BMC Genomics (Special issue for the 12th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics (RECOMB-CG 2014)), 15(Suppl 6):S4, 2014.
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B.J. Raphael, J.R. Dobson, L. Oesper, F. Vandin. Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. Genome Medicine, 6:5, 2014.
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L. Oesper, A. Mahmoody, B.J. Raphael. THetA: Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. Genome Biology, 14:R80, 2013.
Publisher Link.
Software Release.
L.Oesper, A. Mahmoody, B.J. Raphael. Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. Proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB), LNCS 7821:171-172, 2013.
Publisher Link.
Software Release.
L. Oesper, A. Ritz, S.J. Aerni, R. Drebin, B.J. Raphael. Reconstructing Cancer Genomes from Paired-end Sequencing Data. BMC Bioinformatics (Proceedings of 2nd Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq)). 13(Suppl 6):S10, 2012.
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Software Release.
L. Oesper, D. Merico, R. Isserlin, G.D. Bader. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code for Biology and Medicine, 6(1):7, 2011.
Publisher Link.
Software Release.
A. Breiland, L. Oesper, L. Taalman. p-Coloring Classes of Torus Knots. Missouri Journal of Mathematical Sciences, 21(2):120-126, 2009.
Publisher Link.