Durand Lab Publications

Durand Lab

Selected Publications

	Durand Lab Software ............................................................................................................................................................
	Human atlastin-3 is a constitutive ER membrane fusion catalyst. Bryce S, Stolzer M, Crosby D, Yang R, Durand D, Lee TH. J Cell Biol. 2023 Jul 3;222(7). doi: 10.1083/jcb.202211021. Simulating domain architecture evolution Cui X, Xue Y, McCormack C, Garces A, Rachman TW, Yi Y, Stolzer M, Durand D. Bioinformatics. 2022 Jun 24;38(Suppl 1):i134-i142. doi: 10.1093/bioinformatics/btac242. Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes Davidson P, Eutsey R, Redler B, Hiller NL, Laub MT, Durand D, 2018. PLoS Genetics, 13 September 2018, https://doi.org/10.1371/journal.pgen.1007470 Selection, periodicity and potential function for Highly Iterative Palindrome-1 (HIP1) in cyanobacterial genomes. Xu M, Lawrence JG, Durand D, 2018. Nucleic Acids Research, 46(5), 16 March 2018, pp. 2265-2278. https://doi.org/10.1093/nar/gky075 Data used in this study. Book Review: Microbes from Hell by Patrick Forterre, translated by Teresa Lavender Fagan, Reviewed by D. Durand, June, 2018. The Quarterly Review of Biology, 93(2): 165-166. *Gene Acquisition by a Distinct Phyletic Group within Streptococcus pneumoniae* Promotes Adhesion to the Ocular Epithelium I. Antic, K, M. Brothers, M. Stolzer, H. Lai, E. Powell, R. Eutsey, R. A. Cuevas, X. Miao, R. P. Kowalski, R. M. Q. Shanks, D. Durand, N. L. Hiller, 2017. mSphere, 2(5). 10.1128/mSphere.00213-17 Fast heuristics for resolving weakly supported branches using Duplication, Transfers, and Losses** H. Lai, M. Stolzer, D. Durand, 2017. Proceedings of the 15th International Workshop RECOMB CG, Barcelona, Spain, October 4-6, 2017, J. Meidanis and L. Nakhleh, eds. Lecture Notes in Bioinformatics 10562, Springer Verlag. pp. 298--320. Xenolog Classification C. Darby, M. Stolzer, Patrick J. Ropp, Daniel Barker, and D. Durand, 2017. Bioinformatics, 33 (5): 640-649. doi:10.1093/bioinformatics/btw686. Implemented in Notung 2.9 Phylogenetic data used in this study. Event inference in multidomain families with phylogenetic reconciliation. M. Stolzer, K. Siewert, H. Lai, M. Xu, and D. Durand, 2015. BMC Bioinformatics, 16(Suppl 14):S8. Notung DM Robustness of birth-death and gain models for inferring evolutionary events M. Stolzer, L. Wasserman and D. Durand, 2014. BMC Genomics, 15(Suppl 6):S9. Supplementary information How old is my gene? J.A. Capra, M. Stolzer, D. Durand and K.S. Pollard, 2013. Trends Genet. Nov;29(11):659-68. doi: 10.1016/j.tig.2013.07.001. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. M. Stolzer, H. Lai, M. Xu, D. Sathay, B. Vernot, and D. Durand, 2012. Bioinformatics 28(18):i409-i415; doi:10.1093/bioinformatics/bts386. Supplementary information Notung 2.8 Family classification without domain chaining J. M. Joseph and D. Durand, 2009. Bioinformatics 25(12):i45-i53; doi:10.1093/bioinformatics/btp207 Gene cluster statistics with gene families N. Raghupathy and D. Durand, 2009. Molecular Biology and Evolution 26: 957-968. Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins N. Song, J. M. Joseph, G. D. Davis, and D. Durand, 2008. PLoS Comput Biol 4(5): e1000063. Links to commentaries: Bioinform, Nature Reviews Genetics. Reconciliation with Non-Binary Species Trees B. Vernot, M. Stolzer, A. Goldman, D. Durand. 2008. Journal of Computational Biology, 15(8):981-1006. Two plus two does not equal three: Statistical Tests for Multiple Genome Comparison N. Raghupathy, R. Hoberman and D. Durand, 2008. Journal of Bioinformatics and Computational Biology, 6(1): 1-22. Domain Architecture Comparison for Multidomain Homology Identification N. Song, R.D. Sedgewick and D. Durand, 2007. Journal of Computational Biology, 14(4): 496-516. Diagnosing duplications: can it be done? D. Durand and R. Hoberman, 2006. Trends in Genetics, Mar;22(3):156-64. A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. D. Durand, B. V. Halldorsson, B. Vernot, 2006. Journal of Computational Biology, 13 (2): 320-335. Notung 2.0
	Graph Theoretical Insights into Evolution of Multidomain Proteins T. Przytycka, G. B. Davis, N. Song and D. Durand, 2006. Journal of Computational Biology, 13 (2): 351-363. The Incompatible Desiderata of Gene Cluster Properties R. Hoberman and D. Durand, 2005. RECOMB Workshop on Comparative Genomics, McLysaght and Huson, Eds., Lecture Notes in Bioinformatics vol. 3678, Springer-Verlag, pp. 73-87. Individual Gene Cluster Statistics in Noisy Maps. N. Raghupathy and D. Durand, 2005. RECOMB Workshop on Comparative Genomics, McLysaght and Huson, Eds., Lecture Notes in Bioinformatics vol. 3678, Springer-Verlag, pp. 106-120. The Statistical Analysis of Spatially Clustered Genes under the Maximum Gap Criterion R. Hoberman, D. Sankoff and D. Durand, 2005. Journal of Computational Biology, 12(8): 1081-1100. Link to Mathematica code.
	The Statistical Significance of Max-Gap Clusters. R. Hoberman, D. Sankoff and D. Durand, 2004. RECOMB Workshop on Comparative Genomics, J. Lagergren, ed., Lecture Notes in Bioinformatics, Vol. 3388, Springer Verlag, pp. 55 - 71 Tests for Gene Clustering. D. Durand and D. Sankoff, 2003. Journal of Computational Biology, 10 (3/4): 453-482. Vertebrate evolution: doubling and shuffling with a full deck. D. Durand, 2003. Trends in Genetics, Jan;19(1):2-5. On the Design of Optimization Criteria for Multiple Sequence Alignment. D. Durand and M. Farach-Colton, 2002. In "Biological Evolution and Statistical Physics," M. Lassig and A. Valleriani, eds. Springer Verlag, 22-36. Notung: A Program for Dating Gene Duplications and Optimizing Gene Family Trees. K. Chen, D. Durand and M. Farach-Colton, 2000. Journal of Computational Biology, 7 (3/4), 429-447. Impact of Migration and Fitness on the Stability of a Lethal t-haplotype Polymorphism in House Mice: A Computer Study. D. Durand, K. Ardlie, L.Buttel, S.A. Levin and L. M. Silver, 1997. Genetics 145, 1093-1108