Publications

Levy D and Pachter L (2007). The neighbor-net algorithm.  Submitted for review. Available on the arxiv.

Levy D, Reeder C, Loucas B, Hlatky L, Chen A, Cornforth M, Sachs R (2007). Interpreting chromosome aberration spectra.  Journal of Computational Biology. In press.

Mihaescu R, Levy D, and Pachter L (2006).  Why neighbor joining works.  Submitted for review. Available on the arxiv.

Levy D, Yoshida Y, and Pachter L (2006). Beyond pairwise distances: neighbor joining with phylogenetic diversity estimates. Molecular Biology and Evolution. 23(3):491-498.  pdf.

Contois M and Levy D (2005). Small trees and generalized neighbor joining.  In L. Pachter and B. Sturmfels (Eds.), Algebraic Statistics for Computational Biology (pp. 333-344).  Cambridge University Press.  amazon, webpage.

Levy D, Vazquez M, Cornforth M, Loucas B, Sachs RK, Arsuaga J (2004). Comparing DNA damage-processing pathways by computer analysis of chromosome painting data. Journal of Computational Biology, 11(4):626-41.  pdf, pubmed.

Levy D, Su F, Yoshida R (2004). Reconstructing trees from dissimilarity maps. RECOMB 2004 meeting abstracts, p. 19.  poster.

Vazquez M, Levy D, Sachs RK (2004). Genome comparison allowing complex rearrangments.  RECOMB 2004 meeting abstracts, p. 290.

Sachs RK, Levy D, Hahnfeldt P, and Hlatky L (2004). Quantitative analysis of radiation-induced chromosome aberrations. Cytogenetic and Genome Research, 104(1-4):142-8.  pubmed.

Sachs RK, Levy D, Chen AM, Simpson PJ, Cornforth MN, Ingerman EA, Hahnfeldt P, Hlatky LR (2000). Random breakage and reunion chromosome aberration formation model; an interaction-distance version based on chromatin geometry. International Journal of Radiation Biology. Dec 2000;76(12):1579-88.  pubmed.