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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.
A preliminary version appeared in Recomb 2005, LNBI 3500, Springer Verlag, 250-264.
Notung 2.0
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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.
A preliminary version appeared in Recomb 2005, LNBI 3500, Springer Verlag, 311-325.
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.
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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
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