David Sankoff

2024

• Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes (Hyun-oh Lee, Jacob S Stai, Qiaoji Xu, Thulani Hewavithana, Rabnoor Batra3, Alex Liu4 , Brandon D Jordan, Rachel Walstead, Jerry Jenkins, Melissa Williams, Jenell Webber, Jane Grimwood, John T Lovell, Tomáš Brůna, Shengqiang Shu, Keykhosrow Keymanesh7, Joanne Eichenberger, Jeremy Schmutz6,7, David M Goodstein, Kerrie Barry, David Sankoff, Lingling Jin, James H Leebens-Mack, Steven B Cannon) BioRxiv, (2024). [PDF]
• Residual immunity and seasonality of an epidemic (Siyu Chen ; D. Sankoff) MedRxiv, (2024). [PDF]
• On the number of breakpoint medians of random genomes (P.H. da Silva, A. Jamshidpey ; D. Sankoff) submitted, (2024). [PDF]
• Sampling gene adjacencies and geodesic points of random genomes , In RECOMB International Workshop on Comparative Genomics 2024 (pp. 189-210). Springer Nature Switzerland (2024),(2024). [PDF]
• The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars (Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Munoz, Joao Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor Krabbenhoft, Zhen Qin Wang, Steven Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Metairon, Deborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Wai Ching Man, Nicolas Dauchot, Simon Orozco-Arias, Andrea Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stephane Plaisance, Valerie Poncet, Stephane Rombauts, David Sankoff, Victor A Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes), Nature Genetics. 2024 Apr;56(4):721-731 (2024). [PDF]

2023

• Capacity, Collision Avoidance and Shopping Rate under a Social Distancing Regime ( H.Zhong , D.Sankoff ), Entropy 25 (12), 1668(2023). [PDF]
• Gene Order Phylogeny via Ancestral Genome Reconstruction Under Dollo ( Q.Xu , D.Sankoff ), vol 13883. Springer, Cham, RECOMB International Workshop on Comparative Genomics, 100-111 (2023). [PDF]
• From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes( Q.Xu, L.Jin, C.Zheng, X.Zhang, J.Leebens-Mack, D.Sankoff ), Scientific Reports 13 (1), 6095 (2023). [PDF]
• Escape from parsimony of a double-cut-and-join genome evolution process( MM.Miardan, A.Jamshidpey, D.Sankoff ), Journal of Computational Biology 30 (2), 118-130 (2023). [PDF]

2022

• Syntenic Dimensions of Genomic Evolution ( Z.Yu, D.Sankoff ), RECOMB International Workshop on Comparative Genomics, 21-30(2022). [PDF]
• Buxus and Tetracentron genomes help resolve polyploidy events defining the major early-branching eudicot clades (A. Chanderbali, L. Jin, Q. Xu, Y. Zhang, J. Zhang, D. Sankoff, V.A. Albert, D. Howarth, D. Solti & P. Soltis ), Nature Communications 13: 643. [PDF]
• Peripheral structures in unlabelled trees and the accumulation of subgenomes in the evolution of polyploids ( F Pouryahya, D Sankoff ), Journal of Theoretical Biology 532, 110924(2022). [PDF]
• Two divergent haplotypes from a highly heterozygous lychee genome point to independent domestication events for early and later-maturing cultivars (G. Hu, J. Feng, X. Xiang, J. Wang, J. Salojärvi, C. Liu, Z. Wu, J. Zhang, X. Liang, Z. Jiang, W. Liu, L. Ou, J. Li, G. Fan, Y. Mai, C. Chen, H. Peng, L. Yao, C.M. Wai, X. Luo, J. Fu, H. Tang, T. Lan, B. Lai, J. Sun, Y. Wei, H. Li, J. Chen, X. Huang, X. Liu, L.K. McHale, W. Rolling, R. Guyot, D. Sankoff, C. Zheng, V.A. Albert, R. Ming, H. Chen, R. Xia & J. Li), Nature Genetics 54, 73-83 (2022). [PDF]

2021

• The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny (Q. Xu, X. Zhang, Y. Zhang, C. Zheng, J.H. Leeben-Mack, L. Jin & D. Sankoff), Journal of Bioinformatics and Computational Biology 19, 6 DOI: 10.1142/S0219720021400084 (2021) [PDF]
• Peripheral structures in unlabelled trees and the accumulation of subgenomes in the evolution of polyploids (F. Pouryahya & D. Sankoff), Journal of Theoretical Biology 532, 7 DOI: 10.1016/j.jtbi.2021.110924 (2021) [PDF]
• Validation of automated chromosome recovery in the reconstruction of ancestral gene order (Q. Xu, L. Jin, J.H. Leeben-Mack & D. Sankoff), Algorithms 14, 6: 160 (2021) [PDF]
• Guest Editorial for the 17th Asia Pacific Bioinformatics Conference (L Zhang, S Peng, YPP Chen, D Sankoff, G Li, HY Zhang), IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 18, Issue 06, Pages 2123-2124(2021) [PDF]
• RACCROCHE: Ancestral flowering plant chromosomes and gene orders based on generalized adjacencies and chromosomal gene co-occurrences (Q. Xu, L. Jin, C. Zheng, J.H. Leeben-Mack & D. Sankoff), Computational Advances in Bio and Medical Sciences, ICCABS 2020: Lecture Notes in Computer Science 12686 (S.K. Jha, I. Măndoiu, S. Rajasekaran, P. Skums & A. Zelikovsky, eds.), 97-115 (2021) [PDF]
• Ancestral flowering plant chromosomes and gene orders based on generalized adjacencies and chromosomal gene co-occurrences (Q. Xu, L. Jin, C. Zheng, J.H. Leeben-Mack & D. Sankoff), Journal of Computational Biology 28, 11: 1156-1179 (2021) [PDF]
• Genome sequence and evolution of Betula platyphylla (S. Chen, Y. Wang, L. Yu, T. Zheng, Z. Yue, J. Jiang, C. Gunasekara, C. Zheng, H. Tang, J. Li, S. Kumari, Y. Li, J. Chen, L. Luo, W. Zhang, J. Zohren, H. Kuang, N. Wang, J.S. Robertson, L.J. Kelly, P.X. Zhao, X. Dai, X. Ji, C. Su, H. Li, S. Shu, Y.S. Yordanov, W. Deng, J.S. Borrell, D.M. Goodstein, Y. Gai, Q. Qi, J. Min, X. Xu, C. Xu, Z. Han, S. Wang, Z. Wang, J.S.M. Sabir, Y.S. Sun, G.Z. Qu, A.H. Paterson, R.J.A. Buggs, D. Sankoff, J. Wang, H. Wei, G. Liu & C. Yang), Horticulture Research 8, 37 DOI: 10.1038/s41438-021-00481-7 (2021) [PDF]
• Integrated synteny- and similarity-based inference on the polyploidization-fractionation cycle (Y. Zhang, Z. Yu, C. Zheng & D. Sankoff), Interface Focus 11, 4 DOI: 10.1098/rsfs.2020.0059 (2021) [PDF]
• The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible (Y. Hao, M.E. Mabry, P. Edger, M. Freeling, C. Zheng, L. Jin, R. VanBuren, M. Colle, H. An, R.S. Abrahams, J.D. Washburn, X. Qi, K. Barry, C. Daum, S. Shu, J. Schmutz, D. Sankoff, M.S. Barker, E. Lyons, J.C. Pires & G.C. Conant), Genome Research 31, doi: 10.1101/gr.270033.120 (2021) [PDF]
• Branching out to speciation in a model of fractionation: the Malvaceae (Y. Zhang, C. Zheng, S. Islam, Y.M. Kim & D. Sankoff), IEEE/ACM Transactions in Computational Biology and Bioinformatics 18, 5: 1875-1884 (2021) [PDF]

2020

• Excision dominates pseudogenization in gene loss after speciation and in fractionation after whole genome duplication (Z. Yu, C. Zheng & D. Sankoff), International Conference on Algorithms for Computational Biology, AlCoB 2020: Algorithms for Computational Biology, Lecture Notes in Computer Science 12099: 49-60 (2020) [PDF]
• RACCROCHE: Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-occurrences (Q.Xu, L.Jin, C.Zheng, JH.Leebens Mack, D.Sankoff), International Conference on Computational Advances in Bio and Medical Sciences, Pages 97-115(2020) [PDF]
• Gaps and runs in syntenic alignments (Z. Yu, C. Zheng & D. Sankoff), International Conference on Algorithms for Computational Biology, AlCoB 2020: Algorithms for Computational Biology, Lecture Notes in Computer Science 12099: 49-60 (2020) [PDF]
• High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome (S. Perumal, C. Shin Koh, L. Jin, M. Buchwaldt, E. Higgins, C. Zheng, D. Sankoff, S.J. Robinson, S. Kagale, Z.K. Navabi, L. Tang, K.N. Horner, Z. He, I. Bancroft, B. Chalhoub, A.G. Sharpe & I.A.P. Parkin), Nature Plants 6, 929-941 (2020) [PDF]

2019

• Branching out to Speciation in a Model of Fractionation: the Malvaceae (Y.Zhang, C.Zheng, S.Islam, YM.Kim, D.Sankoff), IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 18, Issue 5, Pages 1875-1884(2019) [PDF]
• Ultrasound tongue contour extraction using BowNet network: a deep learning approach (H. Mozaffari, D. Sankoff & W.S. Lee), Proceedings of Meetings on Acoustics 39, 1 DOI: 10.1121/2.0001117 (2019) [PDF]
• Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment (Y. Zhang, C. Zheng & D. Sankoff), BMC Bioinformatics 19, 20 (S20):635 (2019) [PDF]
• A branching process for homology distribution-based inference of polyploidy, speciation and loss (Y. Zhang, C. Zheng & D. Sankoff), Algorithms for Molecular Biology 14, 18 DOI: 10.1186/s13015-019-0153-8 (2019) [PDF]
• The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridzation, and reveals pathogen-influenced gene space adaptation (M. Rendón-Anaya, E. Ibarra-Laclette, A. Méndez Bravo, T. Lan, C. Zheng, L. Carretero-Paulet, C. Anahí Perez-Torres, A. Chacón-López, G. Hernandez-Guzmán, T.H. Chang, K.M. Farr, W.B. Barbazuk, S. Chamala, M. Mutwil, D. Shivhare, D. Alvarez-Ponce, N. Mitter, A. Hayward, S. Fletcher, J. Rozas, A. Sánchez Gracia, D. Kuhn, A.F. Barrientos-Priego, J. Salojärvi, P. Librado, D. Sankoff, A. Herrera-Estrella, V.A. Albert & L. Herrera-Estrella), Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1822129116 (2019). [PDF]
• Models for similarity distributions of syntenic homologs and applications to phylogenomics (D. Sankoff, C. Zheng, Y. Zhang, J. Meidanis, E. Lyons & H. Tang), IEEE/ACM Transactions in Computational Biology and Bioinformatics 16, 3: 727-737 (2019). [PDF]
• Selected articles from the 17th Asia Pacific Bioinformatics Conference (APBC 2019), BMC Systems Biology 20(S3) (D. Sankoff, G. Li, L. Zhang, Y.P.P. Chen, S. Peng & H.Y. Zhang, eds.), (2019). [Site]
• Evolutionary rate change and the transformation from additive to ultrametric: modal similarity of orthologs in fish and flower phylogenomics (D. Santos Muñoz, E. Lam & D. Sankoff), Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret (T. Warnow, ed.), 175-192 (2019). [PDF]

2018

• Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. (J. Zhang, X. Zhang, H. Tang, Q. Zhang, X. Hua, X. Ma, F. Zhu, T. Jones, X. Zhu, J. Bowers, C.M. Wai, C. Zheng, Y. Shi, S. Chen, X. Xu, J. Yue, D.R. Nelson, L. Huang, Z. Li, H. Xu, D. Zhou, Y. Wang, W. Hu, J. Lin, Y. Deng, N. Pandey, M. Mancini, D. Zerpa, J.K. Nguyen, L. Wang, L. Yu, Y. Xin, L. Ge, J. Arro, J.O. Han, S. Chakrabarty, M. Pushko, W. Zhang, Y. Ma, P. Ma, M. Lv, F. Chen, G. Zheng, J. Xu, Z. Yang, F. Deng, X. Chen, Z. Liao, X. Zhang, Z. Lin, H. Lin, H. Yan, Z. Kuang, W. Zhong, P. Liang, G. Wang, Y. Yuan, J. Shi, J. Hou, J. Lin, J. Jin, P. Cao, Q. Shen, Q. Jiang, P. Zhou, Y. Ma, X. Zhang, R. Xu, J. Liu, Y. Zhou, H. Jia, Q. Ma, R. Qi, Z. Zhang, J. Fang, H. Fang, J. Song, M. Wang, G. Dong, G. Wang, Z. Chen, T. Ma, H. Liu, S.R. Dhungana, S.E. Huss, X. Yang, A. Sharma, J.H. Trujillo, M.C. Martinez, M. Hudson, J.J. Riascos, M. Schuler, L.Q. Chen, D.M. Braun, L. Li, Q. Yu, J. Wang, K. Wang, M.C. Schatz, D. Heckerman, M.A. Van Sluys, G. Mendes Souza, P.H. Moore, D. Sankoff, R. VanBuren, A.H. Paterson, C. Nagai & R. Ming), Nature Genetics 50, (11):1565-1573 (2018). [PDF]
• Accurate prediction of orthologs in the presence of divergence after duplication (M. Lafond, M. Meghdari Miardan & D. Sankoff), Bioinformatics 34, (13):i366-i375 (2018). [PDF]
• Models for similarity distributions of syntenic homologs and applications to phylogenomics (D Sankoff, C Zheng, Y Zhang, J Meidanis, E Lyons, H Tang), IEEE/ACM transactions on computational biology and bioinformatics Volume 16, Issue 3, Pages 727-737 (2018). [PDF]
• A randomized FPT approximation algorithm for maximum alternating-cycle decomposition with application (H. Jiang, L. Pu, L. Qingge, D. Sankoff & B. Zhu), Proceedings of the 24th International Conference, COCOON 2018: Computing and Combinatorics (L. Wang & D. Zhu, eds.), 26-38 (2018). [PDF]
• Speciation and rate variation in a birth-and-death account of WGD and fractionation; the case of Solanaceae (Y. Zhang, C. Zheng & D. Sankoff), Proceedings of the 16th International Conference, RECOMB-CG 2018: Comparative Genomics (M. Blanchette & A. Ouangraoua, eds.), 146-160 (2018). [PDF]
• Proceedings of the 29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018, LIPIcs 105 (G. Navarro, D. Sankoff & B. Zhu, eds.), (2018). [Site]
• Partial geodesics on symmetric groups endowed with breakpoint distance (PH da Silva, A Jamshidpey, D Sankoff), arXiv preprint arXiv:1801.04673 (2018). [PDF]
• Pinning down ploidy in paleopolyploid plants (Y. Zhang, C. Zheng & D. Sankoff), BMC Genomics 18, 19(Suppl 5): 287 (2018). [PDF]
• Resolution effects in reconstructing ancestral genomes (C. Zheng, Y. Jeong, M.G. Turcotte & D. Sankoff)BMC Genomics 18, 19(Suppl 2): 100 (2018). [PDF]
• Whole genome duplications in plants; implications for evolutionary analysis (D. Sankoff & C. Zheng) Comparative Genomics (J. Stoye, J. Setubal & P. Stadler, eds.) in Methods in Molecular Biology, Humana Press, New York, NY 1704: 291-315 (2018). [PDF]

2017

• Asymptotic medians of random permutations sampled from reversal random walks (A. Jamshidpey & D. Sankoff), Theoretical Computer Science, 698: 9-13 (2017). [PDF]
• Evolutionary model for the statistical divergence of paralogous and orthologous gene pairs generated by whole genome duplication and speciation (Y. Zhang, C. Zheng & D. Sankoff),IEEE/ACM Transactions in Computational Biology and Bioinformatics, 1545-5963 (2017). [PDF]
• Statistical analysis of fractionation resistance by functional category and expression (E.C.H. Chen, A. Morin, J.H. Chauchat & D. Sankoff), BMC Genomics 18, S4:366 (2017). [PDF]
• Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome (T. Lan, T. Renner, E. Ibarra-Laclette, K.M. Farr, T.H. Chang, S.A. Cervantes-Pérez, C. Zheng, D. Sankoff, H. Tang, R.W. Purbojati, A. Putra, D.I. Drautz-Moses, S.C. Schuster, L. Herrera-Estrella & V.A. Albert), Proc Natl Acad Sci U S A, doi: 10.1073/pnas (2017). [PDF]
• Genome of pitcher plant Cephalotus reveals genetic changes associated with carnivory (K. Fukushima, X. Fang, D. Alvarez-Ponce, H. Cai, L. Carretero-Paulet, C. Chen, T.H. Chang, K.M. Farr, T. Fujita, Y. Hiwatashi, Y. Hoshi, T. Imai, M. Kasahara, P. Librado, L. Mao, H. Mori, T. Nishiyama, M. Nozawa, G. Pálfalvi, S.T. Pollard, J. Rozas, A. Sánchez-Gracia, D. Sankoff, T.F. Shibata, S. Shigenobu, N. Sumikawa, T. Uzawa, M. Xie, C. Zheng, D.D. Pollock, V.A. Albert, S. Li & M. Hasebe), Nature Ecology and Evolution 1:0059 (2017). [PDF]

2016

• The trees in the peaks (D. Sankoff, C. Zheng, E. Lyons & H. Tang), Third International Conference on Algorithms for Computational Biology, Algorithms for Computational Biology pp 3-14 (2016). [PDF]
• A continuous analog of run length distributions reflecting accumulated fractionation events (Z. Yu & D. Sankoff), BMC Bioinformatics 17, (Suppl 14):412 (2016). [PDF]
• The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocyanaceae (J.S.M. Sabir, R.K. Jansen, D. Arasappan, V. Calderón, E. Noutahi, C. Zheng, S. Park, M.J. Sabir, M.N. Baeshen, N.H. Hajrah, M.A. Khiyami, N.A. Baeshen, A.Y. Obaid, A.L. Al-Malki, D. Sankoff, N. El-Mabrouk & T.A. Ruhlman), Scientific Reports 6, DOI:10.1038/srep33782 (2016). [PDF]

Supplementary material: [SUP]

• Compromise or optimize? The breakpoint anti-median (C. A. Larlee, A. Brandts & D. Sankoff), 8th International Conference on Bioinformatics and Computational Biology (BICOB) (T. Ioeger & N. Haspel, eds.) 129-133 (2016). [PDF]
• Locating rearrangement events in a phylogeny based on highly fragmented assemblies (C. Zheng & D. Sankoff), BMC Genomics 17, (Suppl 1):1 (2016). [PDF]
• Economic importance, taxonomic representation and scientific priority as drivers of genome sequencing projects (G.C. Vallée, D. Santos Muñoz & D. Sankoff), BMC Genomics 17, (Suppl 10):782 (2016). [PDF]

2015

• Statistical analysis of fractionation resistance by functional category and expression level (E. C.H. Chen, A. Morin, JH. Chauchat & D. Sankoff), BMC Genomics 16, 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), (2015). [PDF]
• The pineapple genome and the evolution of CAM photosynthesis (R. Ming, R. Van Buren, C.M. Wai, H. Tang, M.C. Schatz, J.E. Bowers, E. Lyons, M. Wang, J. Chen, E. Biggers, J. Zhang, L. Huang, L. Zhang, W. Miao, J. Zhang, Z. Ye, C. Miao, Z. Lin, H. Wang, H. Zhou, W.C. Yim, H.D. Priest, C. Zheng, M. Woodhouse, P.P. Edger, R. Guyot, H. Guo, H. Guo, G. Zheng, R. Singh, A. Sharma, X. Min, Y. Zheng, H. Lee, J. Gurtowski, F. Sedlazeck, A. Harkess, M.R. McKain, Z. Liao, J. Fang, J. Liu, X. Zhang, Q. Zhang, W. Hu, Y. Qin, K. Wang, L. Chen, N. Shirley, Y. Lin, L. Liu, A.G. Hernandez, C.L. Wright, V. Bulone, G.A. Tuskan, K. Heath, F. Zee, P.H. Moore, R. Sunkar, J.H. Leebens-Mack, T. Mockler, J.L. Bennetzen, M. Freeling, D. Sankoff, A.H. Paterson, X. Zhu, X. Yang, A.C. Smith, J.C. Cushman, R.E. Paul & Q. Yu), Nature Genetics, DOI: 10.1038/ng.3435 (2015). [PDF]

Supplementary material: [SUP]

• Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events (C. Zheng, D. Santos Muñoz, V.A. Albert & D. Sankoff), BMC Genomics 16, S10:S8 (2015). [PDF]
• Comparing variables in different corpora with context-based model-free variant probabilities (D. Sankoff, N. Dion, A. Brandts, M. Alvo, S. Balasch & J. Adams), In Linguistic variation: Confronting fact and theory (Rena Tores Cacoullos, Nathalie Dion & André Lapierre ed.) . Routledge, 335-345 (2015).
• Graph-theoretic modelling of the domain chaining problem (P.H. da Silva, S. Dantas, C. Zheng & D. Sankoff), Algorithms in Bioinformatics - Lecture Notes in Computer Science 9289 296-307 (2015). [PDF]
• Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling (D. Sankoff, C. Zheng, B. Wang & C. Fernando Buen Abad Najar), BMC Genomics 15, DOI: 10.1109/ICCABS.2014.6863915 (2015). [PDF]

2014

• Near-medians that avoid the corners; a combinatorial probability approach (C. A. Larlee, C. Zheng & D. Sankoff), BMC Genomics 15 S6:S1 (2014). [PDF]
• Sets of medians in the non-geodesic pseudometric space of unsigned genomes with breakpoints (A. Jamshidpey, A. Jamshidpey & D. Sankoff), BMC Genomics 15 S6:S3 (2014). [PDF]
• Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants (C. Zheng, A. Kononenko, J. Leebens-Mack, E. Lyons & D. Sankoff), BMC Genomics 15 S6:S8 (2014). [PDF]
• Gene expression and fractionation resistance (E. C.H. Chen & D. Sankoff), BMC Genomics 15 S6:S19 (2014). [PDF]
• The coffee genome provides insight into the convergent evolution of caffeine biosynthesis (F. Denoeud, L. Carretero-Paulet, A. Dereeper, G. Droc, R. Guyot, M. Pietrella, C. Zheng, A. Alberti, F. Anthony, G. Aprea, JM. Aury, P. Bento, M. Bernard, S. Bocs, C. Campa, A. Cenci, M. Combes, D. Crouzillat, C. Da Silva, L. Daddiego, F. De Bellis, S. Dussert, O. Garsmeur, T. Gayraud, V. Guignon, K. Jahn, V. Jamilloux, T. Joët, K. Labadie, T. Lan, J. Leclercq, M. Lepelley, T. Leroy, LT. Li, P. Librado, L. Lopez, A. Muñoz, B. Noel, A. Pallavicini, G. Perrotta, V. Poncet, D. Pot, Priyono, M. Rigoreau, M. Rouard, J. Rozas, C. Tranchant-Dubreuil, R. VanBuren, Q. Zhang, AC. Andrade, X. Argout, B. Bertrand, A. de Kochko, G. Graziosi, RJ. Henry, Jayarama, R. Ming, C. Nagai, S. Rounsley, D. Sankoff, G. Giuliano, VA. Albert, P. Wincker, P. Lashermes) Science 345, 1181-1184 (2014). [PDF]
[SUP]
• Exercicis en demolingüística (R. Casesnoves Ferrer & D. Sankoff), Ens queda la paraula. Estudis de lingüística aplicada en honor a M.Teresa Turell (R Casesnoves Ferrer, M. Forcadell & N. Gavaldà eds.), Barcelona: Universitat Pompeu Fabra, IEC. 139-152 (2014). [PDF]
• Practical halving; the Nelumbo nucifera evidence on early eudicot evolution (C. Zheng & D. Sankoff) Computational Biology and Chemistry 50 75-81 (2014). [PDF]

2013

• The Amborella genome and the evolution of flowering plants (Amborella genome project: V.A. Albert, W.B. Barbazuk, C.W. dePamphilis, J.P. Der, J. Leebens-Mack, H. Ma, J.D. Palmer, S. Rounsley, D. Sankoff, S.C. Schuster, D.E. Soltis, P.S. Soltis, S.R. Wessler, R.A. Wing, J.S. Ammiraju, S. Chamala, A.S. Chanderbali, R. Determann, P. Ralph, J. Talag, L. Tomsho, B. Walts, S. Wanke, T.H. Chang, T. Lan, S. Arikit, M.J. Axtell, S. Ayyampalayam, J.M 3rd. Burnette, E. De Paoli, J.C. Estill, N.P. Farrell, A. Harkess, Y. Jiao, K. Liu, W. Mei, B.C. Meyers, S. Shahid, E. Wafula, J. Zhai, X. Zhang, L. Carretero-Paulet, E. Lyons, H. Tang, C. Zheng, N.S. Altman, F. Chen, J.Q. Chen, V. Chiang, E. De Paoli, B. Fogliani, C. Guo, J. Harholt, C. Job, D. Job, S. Kim, H. Kong, G. Li, L. Li, J. Liu, J. Park, X. Qi, L. Rajjou, V. Burtet-Sarramegna, R. Sederoff, Y.H. Sun, P. Ulvskov, M. Villegente, J.Y. Xue, T.F. Yeh, X. Yu, J. Zhai, J.J. Acosta, R.A. Bruenn, A. de Kochko, L.R. Herrera-Estrella, E. Ibarra-Laclette, M. Kirst, S.P. Pissis, & V. Poncet) Science 342, 1241089 (2013). [PDF]
• Fractionation, rearrangement, consolidation, reconstruction (D. Sankoff & C. Zheng), Models and algorithms for genome evolution (C. Chauve, N El-Mabrouk & E. Tannier eds.), Springer, 247-260 (2013). [PDF]
• Phase change for the accuracy of the median value in estimating divergence time (A. Jamshidpey & D. Sankoff) BMC Bioinformatics 14, S15:S7 (2013). [PDF]
• Practical aliquoting of flowering plant genomes (C. Zheng & D. Sankoff) BMC Bioinformatics 14, S15:S8 (2013). [PDF]
• The dynamics of functional classes of plant genes in rediploidized ancient polyploids (E. CH. Chen, C. Buen Abad Najar. C. Zheng, A. Brandts, E. Lyons, H. Tang, L. Carretero-Paulet, V. A. Albert & D. Sankoff) BMC Bioinformatics 14, S15:S19 (2013). [PDF]
• Ancient eudicot hexaploidy meets ancestral eurosid gene order (C. Zheng, E. Chen, V. A. Albert, E. Lyons & D. Sankoff) BMC Genomics 14, S7:S3 (2013). [PDF]

2012

• A consolidation algorithm for genomes fractionated after higher order polyploidization (K. Jahn, C. Zheng, Jakub Kováč & D. Sankoff) BMC Bioinformatics 13, S19:S8 (2012). [PDF]
• Medians seek the corners, and other conjectures (M. Haghighi & D. Sankoff) BMC Bioinformatics 13, S19:S5 (2012). [PDF]
• Fractionation, rearrangement and subgenome dominance (C. Zheng & D. Sankoff) Bioinformatics 28, i402-i408 (2012). [PDF]
• The kernel of maximum agreement subtrees (K.M. Swenson, E. Chen, N. Pattengale & D. Sankoff) Transactions on Computational Biology and Bioinformatics 9, 1023-1031 (2012). [PDF]
• Scaffold filling under the breakpoint and related distances (H. Jiang, C. Zheng, D. Sankoff & B. Zhu) Transactions on Computational Biology and Bioinformatics 9, 1220-1229 (2012). [PDF]
• Gene order in Rosid phylogeny, inferred from pairwise syntenies among extant genomes (C. Zheng & D. Sankoff) BMC Bioinformatics 13, S10:S9 (2012). [PDF]
• Ancient angiosperm hexaploidy meets gene order reconstruction of the eudicot ancestor (C. Zheng, V. Albert, E. Lyons, & D. Sankoff) Second IEEE International Conference on Computational Advances in Bio and Medical Sciences, (2012). [PDF]
• Generalized adjacency in genetic networks and the conservation of functional gene clusters (Z. Yang & D. Sankoff) BMC Bioinformatics 13 S9:S8 (2012). [PDF]
• Gene clusters as intersections of powers of paths (V.Costa, S.Dantas, D. Sankoff & X. Xu) Journal of the Brazilian Computer Society 18, 129-136 (2012). [PDF]
• Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution ( A. Muñoz & D. Sankoff) BMC Bioinformatics 13, S3:S6 (2012). [PDF]
• A model for biased fractionation after whole genome duplication (D. Sankoff, C. Zheng, & B. Wang), BMC Genomics 13 S1:S8 (2012). [PDF]
• Analysis of gene order evolution beyond single-copy genes (N. El-Mabrouk & D. Sankoff) Evolutionary Genomics : statistical and computational methods (M. Anisimova, ed.) Springer, 397-429 (2012). [PDF]

2011

• *Changes in gene expression near evolutionary breakpoints (A. Muñoz & D. Sankoff) Second ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), 393-398 (2011) [PDF]
• *Gene clusters as intersections of powers of paths (V.Costa, S.Dantas, D. Sankoff & X. Xu) Fourth Latin American Workshop on Cliques in Graphs, Matemática Contemporânea 39, 169-178 (2011) [PDF]
• *Generalized adjacency in genetic networks and the conservation of functional gene clusters (Z. Yang & D. Sankoff) Proceedings of 2011 IEEE International Conference on Bioinformatics & Biomedicine (BIBM) 173-178 (2011) [PDF]
• Fractionation statistics (B. Wang, C. Zheng & D. Sankoff) BMC Bioinformatics 12:9, S5 (2011) [PDF]
• OMG! Orthologs in multiple genomes - competing graph-theoretical formulations (C. Zheng, K.M. Swenson, E. Lyons, & D. Sankoff),WABI'11 Proceedings of the 11th International Conference on Algorithms in Bioinformatics (T. Przytycka & MF. Sagot ed.) Lecture Notes in Computer Science 6833, 364-375 (2011). [PDF]
• *Gene order in Rosid phylogeny, inferred from pairwise syntenies among extant genomes (C. Zheng & D. Sankoff), Bioinformatics Research and Applications, 7th International Symposium (ISBRA) (J. Chen, J. Wang & A. Zelikovsky, eds.) Lecture Notes in Computer Science 6674, 123-135 (2011). [PDF]
• *The Kernel of Maximum Agreement Subtrees (K.M. Swenson, E. Chen, N. Pattengale & D. Sankoff), Bioinformatics Research and Applications, 7th International Symposium (ISBRA) (J. Chen, J. Wang & A. Zelikovsky, eds.) Lecture Notes in Computer Science 6674, 123-135 (2011). [PDF]
• Listing all parsimonious reversal sequences: New algorithms and perspectives (G. Badr, K.M. Swenson & D. Sankoff) Journal of Computational Biology 18, 1201-1210 (2011) [PDF]
• Listing all sorting reversals in quadratic time (K.M. Swenson, G. Badr & D. Sankoff) Algorithms for Molecular Biology 6, Doi: 10.1186/1748-7188-6-11 (2011) [PDF]
• Genome aliquoting revisited (R. Warren & D. Sankoff) Journal of Computational Biology 18, 1065-1075 (2011) [PDF]
• On the Pathgroups approach to rapid small phylogeny (C. Zheng & D. Sankoff) BMC Bioinformatics 12, S4 (2011) [PDF]

2010

• Scaffold filling, contig fusion and comparative gene order inference (A. Muñoz, C. Zheng, Q. Zhu, V.A. Albert, S. Rounsley, & D. Sankoff) BMC Bioinformatics 11, 304 (2010). [PDF]
• A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances (Z. Adam & D. Sankoff) Journal of Computational Biology 11, 1299-1314 (2010) [PDF]
• Natural parameter values for generalized gene adjacency (Z. Yang & D. Sankoff) Journal of Computational Biology 11, 1113-1128 (2010) [PDF]
• Rearrangement phylogeny of genomes in contig form (A. Muñoz & D. Sankoff) Transactions on Computational Biology and Bioinformatics 7, 579-587 (2010) [PDF]
• Issues in the reconstruction of gene order evolution (D. Sankoff, C. Zheng, A. Muñoz, Z. Yang, Z. Adam, R. Warren, V. Choi & Q. Zhu,) Journal of Computer Science and Technology 25, 10-25 (2010) [PDF]
• The collapse of gene complement following whole genome duplication (D. Sankoff, C. Zheng & Q. Zhu) BMC Genomics 11, 313 (2010) [PDF]
• *Listing all sorting reversals in quadratic time (K.M. Swenson G. Badr & D. Sankoff ) WABI'10 Proceedings of the 10th International Conference on Algorithms in Bioinformatics, 102-110, (2010). [PDF]
• Listing all parsimonious reversal sequences: new algorithms and perspectives (G. Badr, K.M. Swenson & D. Sankoff) Comparative Genomics, 8th International Workshop, (RECOMB-CG) (E. Tannier, ed.) Lecture Notes in Computer Science 6398, 39-49 (2010) [PDF]
• *Genome aliquoting revisited (R. Warren & D. Sankoff) Comparative Genomics, 8th International Workshop, (RECOMB-CG) (E. Tannier, ed.) Lecture Notes in Computer Science 6398, 1-12 (2010) [PDF]
• Scaffold filling under the breakpoint distance (H. Jiang, C. Zheng, D. Sankoff & B. Zhu) Comparative Genomics, 8th International Workshop, (RECOMB-CG) (E. Tannier, ed.) Lecture Notes in Computer Science 6398, 83-92 (2010) [PDF]

2009

• The where and wherefore of evolutionary breakpoints (D. Sankoff ) Journal of Biology 8, 66 (2009) [PDF]
• Towards improved reconstruction of ancestral gene order in angiosperm phylogeny (D. Sankoff, C. Zheng, P.K. Wall, C. dePamphilis, J. Leebens-Mack & V.A. Albert) Journal of Computational Biology 16, 1353-1367 (2009). [PDF]
• Reconstructing the history of yeast genomes (D. Sankoff ) Public Library of Science, Genetics 5, e1000483 (2009) [PDF]
• Genome aliquoting with double cut and join (R. Warren & D. Sankoff) BMC Bioinformatics 10, S2 (2009) [PDF]
• Multichromosomal median and halving problems under different genomic distances (E. Tannier, E., C. Zheng & D. Sankoff) BMC Bioinformatics 10, 120 (2009) [PDF]
• Gene loss under neighbourhood selection following whole genome duplication and the reconstruction of the ancestral Populus diploid (C. Zheng , P. K. Wall, J. Leebens-Mack, C. dePamphilis, V.A. Albert & D. Sankoff) Journal of Bioinformatics and Computational Biology 7, 499-520 (2009) [PDF]
• Generalized gene adjacencies, graph bandwidth and clusters in yeast evolution (Q. Zhu, Z. Adam, V. Choi & D. Sankoff), Transactions on Computational Biology and Bioinformatics 6, 213-220 (2009) [PDF]
• Genome halving with double cut and join (R. Warren & D. Sankoff) Journal of Bioinformatics and Computational Biology 7, 357-371 (2009) [PDF]
• Polyploidy and angiosperm diversification (D.E. Soltis, V.A. Albert, J. Leebens-Mack, C.D. Bell, A.H. Paterson, C. Zheng, D. Sankoff, C.W. dePamphilis, P. Kerr Wall & P.S. Soltis) American Journal of Botany 95, 336-348 (2009) [PDF]
• *Natural parameter values for generalized gene adjacency (Z. Yang & D. Sankoff) Comparative Genomics, 7th International Workshop (RECOMB-CG) (F. Ciccarelli & I. Miklós, eds.) Lecture Notes in Computer Science 5817, 13-23 (2009) [PDF]
• *Rearrangement phylogeny of genomes in contig form (A. Muñoz & D. Sankoff) Bioinformatics Research and Applications, 5th International Symposium (ISBRA) (I. I. Mandoiu, G. Narasimhan & Y. Zhang, eds.) Lecture Notes in Computer Science 5542, 160-172 (2009) [PDF]
• *A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances (Z.Adam & D. Sankoff) Comparative Genomics, 7th International Workshop (RECOMB-CG) (F. Ciccarelli & I. Miklós, eds.) 193-204 (2009) [PDf]

2008

• Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes (C. Zheng, Q. Zhu, Z. Adam & D. Sankoff) Bioinformatics 24, i96-i10 (2008) [PDF]
• Poisson adjacency distributions in genome comparison: multichromosomal , circular, signed and unsigned cases (W. Xu, B. Alain and D. Sankoff) Bioinformatics 24, i146-i152 (2008) [PDF]
• Descendants of whole genome duplication within gene order phylogeny (C. Zheng, Q. Zhu & D. Sankoff), Journal of Computational Biology 15, 947-964 (2008). [PDF]
• The ABCs of MGR with DCJ (Z. Adam & D.Sankoff), Evolutionary Bioinformatics 4, 69-74 (2008) [PDF]
• How to predict the evolution of a bilingual community. Sociolinguistics of Multilingual Communities (M. Meyerhoff & N. Nagy, eds.) John Benjamins Publishers, 179-194 (2008) [Book]
• Generalized gene adjacencies, graph bandwidth and clusters in yeast evolution, (Q. Zhu, Z. Adam, V. Choi & D. Sankoff) Transactions on Computational Biology and Bioinformatics (2008). [PDF]
• Internal validation of ancestral gene order reconstruction in angiosperm phylogeny (D. Sankoff, C. Zheng, P.K. Wall, C. dePamphilis, J. Leebens-Mack, V. Albert) Proceedings of the RECOMB 2008 Workshop on Comparative Genomics (S. Vialette & C. Nelson, eds.) Lecture Notes in Computer Science, Springer (2008) [PDF]
• Decompositions of multiple breakpoint graphs and rapid exact solutions to the median problem (W. Xu, D. Sankoff) Workshop on Algorithms in Bioinformatics WABI 2008, Lecture Notes in Bioinformatics 5251, Springer (2008) [PDF]
• Multichromosomal median and halving problems under different genomic distances (E. Tannier, C. Zheng, D. Sankoff) Workshop on Algorithms in Bioinformatics WABI 2008, Lecture Notes in Bioinformatics 5251, Springer (2008) [PDF]
• *The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral Populus diploid (C. Zheng, P.K. Wall, J. Leebens-Mack, C. dePamphilis, V.A. Albert, D. Sankoff) Annual International Conference on Computational Systems Bioinformatics CSB 2008 [PDF]
• A customized class of functions for modelling and clustering gene expression profiles in embryonic stem cells (S. Li, M. Andrade-Navarro & D. Sankoff), Brazilian Symposium on Bioinformatics BSB 2008, (A.L.C. Bazzan, Mark Craven & Natália F. Martins, eds.) Lecture Notes in Computer Science 5251, 92-103, Springer (2008) [PDF]
• Tests for gene clusters satisfying the generalized adjacency criterion (X. Xu & D. Sankoff), Proceedings of the Brazilian Symposium on Bioinformatics BSB 2008, (A.L.C. Bazzan, Mark Craven & Natália F. Martins, eds.) Lecture Notes in Computer Science 5251, 152-160, Springer (2008) [PDF]
• Hierarchical clustering using constraints (M. Kant, M. LeBon & D. Sankoff), Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA) 2008 (I. Mandoiu, R. Sunderraman, & A. Zelikovsky, eds.) Lecture Notes in Bioinformatics 4983, Springer, 2-13. (2008) [PDF]
• *Generalized gene adjacencies, graph bandwidth and clusters in yeast evolution (Q. Zhu, Z. Adam, V. Choi & D. Sankoff), Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA) 2008 (I. Mandoiu, R. Sunderraman, & A. Zelikovsky, eds.) Lecture Notes I n Bioinformatics 4983, Springer, 134-145. (2008) [PDF]
• *Genome halving with general operations (R. Warren & D. Sankoff), Proceedings of the Asia Pacific Bioinformatics Conference 2008 (A. Brazma, S. Miyano & T. Akutsu, eds.) Imperial College Press, 231-240 (2008) [PDF]

2007

• Proceedings of the 5th Asia-Pacific Bioinformatics Conference (D. Sankoff, L. Wang & F. Chin), Hongkong, 2007, 388 pp. [PDF]
• *Parts of the problem of polyploids in rearrangement phylogeny (C. Zheng, Q. Zhu & D. Sankoff), Proceedings of the RECOMB 2007 Workshop on Comparative Genomics (G. Tesler & D. Durand, eds.) Lecture Notes in Computer Science 4751, Springer, 162-176. (2007) [PDF]
• Algorithms for the extraction of synteny blocks from comparative maps (V. Choi, C. Zheng, Q. Zhu & D. Sankoff), Proceedings of the WABI 2007 Workshop on Algorithms in Bioinformatics (R. Giancarlo & S. Hannenhalli, eds.) Lecture Notes in Bioinformatics 4645, Springer, 277-288. (2007) [PDF]
• Polyploids, genome halving and phylogeny (D. Sankoff, C. Zheng & Q. Zhu), Bioinformatics 23, i433-i439 (2007) [PDF]
• Common intervals and symmetric difference in a model-free phylogenomics, with an application to streptophyte evolution. (Z. Adam, M. Turmel, C. Lemieux & D. Sankoff) Journal of Computational Biology 14, 436-445 (2007) [PDF]
• Paths and cycles in breakpoint graphs of random multichromosomal genomes. (W. Xu, C. Zheng & D. Sankoff) Journal of Computational Biology 14, 423-435 (2007) [PDF]
• Removing noise and ambiguities from comparative maps in rearrangement analysis (C. Zheng, Q. Zhu & D. Sankoff) Transactions on Computational Biology and Bioinformatics, 4, 515-522 (2007) [PDF]

2006

• Genome Halving with an Outgroup (C. Zheng, Q. Zhu & D. Sankoff) Evolutionary Bioinformatics 2, 319-326, (2006) [PDF]
• Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution (Z. Adam, M. Turmel, C. Lemieux & D. Sankoff) Proceedings of the RECOMB 2006 Workshop on Comparative Genomics (G. Bourque & N. El-Mabrouk, eds.) Lecture Notes in Bioinformatics 4205, Springer, 63-74. (2006) [PDF]
• Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes (W. Xu, C. Zheng & D. Sankoff) Proceedings of the RECOMB 2006 Workshop on Comparative Genomics (G. Bourque & N. El-Mabrouk, eds.) Lecture Notes in Bioinformatics 4205, Springer, 51-62. (2006) [PDF]
• Stability of rearrangement measures in the comparison of genome sequences (M. Mazowita, L. Haque & D. Sankoff) Journal of Computational Biology 13, 554-566. (2006) [PDF]
• El proceso de inversión de la sustitución linguistica: modelos de transmisión, escolarización y asimilación para proyecciones demolinguisticas (R. Casesnoves Ferrer & D. Sankoff) Haciendo linguistica. Homenaje a Paola (M. Sedano, A. Bolívar & M. Shiro, eds.) Caracas: Universidad Central de Venezuela, 713-731. (2006)
• The signal in the genomes (David Sankoff) Public Library of Science Computational Biology 2, e35. (2006) [PDF]
• Linguistic shift and community language: the effect of demographic factors in the Valencian Region, Balearic Islands and Catalonia (R. Casesnoves Ferrer, D. Sankoff & M.T. Turell) Globalization and Language in the Spanish-speaking World (C. Mar-Molinero & M. Stewart, eds.) Palgrave Macmillan, 197-219. (2006)
• The distribution of genomic distance between random genomes (D. Sankoff and L. Haque) Journal of Computational Biology 13, 1005-1012. (2006) [PDF]
• Genome rearrangements with partially ordered chromosomes (C. Zheng & D. Sankoff) Journal of Combinatorial Optimization 11, 133-144. (2006) [PDF]

2005

• The statistical analysis of spatially clustered genes under the maximum gap criterion (R. Hoberman, D. Sankoff & D. Durand) Journal of Computational Biology 12, 1081-1100, (2005) [PDF]
• Chromosomal breakpoint re-use in genome sequence rearrangement (D. Sankoff & P. Trinh) Journal of Computational Biology 12, 812-821, (2005) [PDF]
• Reversal distance for partially ordered genomes. (C. Zheng, A. Lenert & D. Sankoff) Bioinformatics 21, i502-i508, (2005) [PDF]
• Power boosts for cluster tests (D. Sankoff & L. Haque) Proceedings of the RECOMB 2005 Workshop on Comparative Genomics (A. McLysaght & D. Huson, eds.) Lecture Notes in Bioinformatics 3678, Springer, 121-130. (2005) [PDF]
• Reversals of fortune (D. Sankoff, C. Zheng, & A. Lenert) Proceedings of the RECOMB 2005 Workshop on Comparative Genomics (A. McLysaght & D. Huson, eds.) Lecture Notes in Bioinformatics 3678, Springer, 131-141. (2005) [PDF]
• *Genome rearrangements with partially ordered chromosomes (C. Zheng & D. Sankoff) Proceedings of the Computing and Combinatorics: 11th Annual International Conference, 52-62. (2005) [PDF]
• *Stability of rearrangement measures in the comparison of genome sequences (D. Sankoff & M. Mazowita) Proceedings of the RECOMB 2005 Workshop on Comparative Genomics (A. McLysaght & D. Huson, eds.) Lecture Notes in Bioinformatics 3678, Springer, 603-614. (2005) [PDF]
• Conserved segment statistics and rearrangement inferences in comparative genomics (D. Sankoff) Mathematics of Evolution and Phylogeny (O. Gascuel, ed.) Oxford University Press, 236-261. (2005) [PDF]

2004

• *Chromosomal breakpoint re-use in genome sequence rearrangement (D. Sankoff & P. Trinh) Proceedings of the RECOMB 2004 Workshop on Comparative Genomics, LNBI 3388, 30-35, (2005) [PDF]
• The statistical Significance of Max-Gap Clusters (R. Hoberman, D. Sankoff & D. Durand) Proceedings of the RECOMB 2004 Workshop on Comparative Genomics, LNBI 3388, 55-71, (2005) [PDF]
• The Distribution of Inversion Lengths in Bacteria (D. Sankoff, J.F. Lefebvre, E. Tillier, A. Maler & N. El-Mabrouk) Proceedings of the RECOMB 2004 Workshop on Comparative Genomics, LNBI 3388, 97-108, (2005) [PDF]
• Estimators of translocations and Inversions in Comparative Maps (D. Sankoff & M. Mazowita) Proceedings of the RECOMB 2004 Workshop on Comparative Genomics , LNBI 3388, 109-122, (2005) [PDF]
• Combinatorial Pattern Matching, Special Issue of Journal of Discrete Algorithms (R. Giancarlo & D. Sankoff), vol. 2, no. 2, Elsevier, 135-136 (2004) [PDF]
• Improving gene network inference by comparing expression time-series across species, developmental stages or tissues (G. Bourque & D. Sankoff) Journal of Bioinformatics and Computational Biology, 765-783 (2004) [PDF]
• La base démolinguistique pour évaluer l'aménagement linguistique dans un contexte bilingue (R. Casesnoves Ferrer, M.T. Turell & D. Sankoff) Linguapax conference, (2004) [PDF]
• Transmission, education and integration in projections of language shift in Valencia (R. Casesnoves Ferrer & D. Sankoff), Language Policy 3, 107-131, (2004) [PDF]
• Genomic features in the breakpoint regions between syntenic blocks (P. Trinh, A. McLysaght & D. Sankoff), Bioinformatics 20, Suppl 1:I318-I325, (2004) [PDF]
• The Valencian revival: why usage lags behind competence (R. Casesnoves Ferrer & D. Sankoff), Language in Society 33, 1-31 (2004) [PDF]

2003

• Rearrangements and chromosomal evolution (D. Sankoff), Current Opinion in Genetics and Development 13, 583-587, (2003) [PDF]
• Chromosome rearrangements in evolution: From gene order to genome sequence and back (D. Sankoff & J.H. Nadeau) Proceedings of the National Academy of Sciences USA 100, 11188-11189, (2003) [PDF]
• Structural dynamics of eukaryotic chromosome evolution (E. Eichler & D. Sankoff) Science 301, 793-797 (2003) [PDF]
• Testing for gene clusters ( D. Durand & D. Sankoff) Journal of Computational Biology 10, 453-482 (2003) [PDF]
• Detection and validation of single-gene inversions (J.-F Lefebvre, N. El-Mabrouk, E. Tillier & D. Sankoff), Bioinformatics 19, Suppl. 1, i190-i196 (2003) [PDF]
• The reconstruction of doubled genomes (N. El-Mabrouk & D. Sankoff), SIAM Journal on Computing 32, 754-792 (2003) [PDF]
• Identity as the primary determinant of language choice in Valencia (R. Casesnoves Ferrer & D. Sankoff) Journal of Sociolinguistics 7, 50-64 (2003) [PDF]

2002

• Genome rearrangement (D. Sankoff & N. El-Mabrouk), Current Topics in Computational Biology (T. Jiang, T. Smith, Y. Xu & M. Zhang eds.), MIT Press, 135-155 (2002) [PDF]
• Chromosomal distributions of breakpoints in cancer, infertility and evolution (D. Sankoff, M. Deneault, P. Turbis & C.P. Allen), Theoretical Population Biology 61, 497-501 (2002) [PDF]
• Genetic and molecular control of folate-homocysteine metabolism in mutant mice (S.R. Ernest, B. Christensen, B. Gilfix, O. Mamer, A. Hosack, M. Rodier, C. Colmenares, J. McGrath, A. Bale, R. Balling, D. Sankoff, D. Rosenblatt & J.H. Nadeau), Mammalian Genome 13, 259-267 (2002) [PDF]
• Short inversions and conserved gene clusters (D. Sankoff), Bioinformatics 18, 1305-1308 (2002) [PDF]
• *Short inversions and conserved gene clusters (D. Sankoff) Proceedings of the 2002 ACM Symposium on Applied Computing, 164-167 (2002) [PDF]

2001

• Currents in Computational Molecular Biology (N. El-Mabrouk, T. Lengauer & D. Sankoff), Centre de recherches mathématiques, Montreal, (2001). [PDF]
• Proceedings, Fifth Annual International Conference on Computational Molecular Biology (T. Lengauer, D. Sankoff, S. Istrail, P. Pevzner & M. Waterman), New York: ACM, 2001, 316 pp. [PDF]
• The variationist approach toward discourse structural effects and socio-interactional dynamics (S. Dubois & D. Sankoff), Handbook of Discourse Analysis (D. Schiffrin, D. Tannen and H. Hamilton eds.) Blackwell, 282-303 (2001) [PDF]
• William Labov (D. Sankoff), Concise Encyclopedia of Sociolinguistics, Elsevier, 885-887 (2001) [PDF]
• Statistics in sociolinguistics (D. Sankoff), Concise Encyclopedia of Sociolinguistics, Elsevier, 828-834 (2001) [PDF]
• Gene and genome duplication (D. Sankoff), Current Opinion in Genetics and Development 11, 681-684 (2001) [PDF]

2000

• Combinatorial Pattern Matching, Eleventh Annual Symposium (R. Giancarlo & D. Sankoff), Lecture Notes in Computer Science 1848, Springer Verlag, 422 pp. (2000) [PDF]
• Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and Evolution of Gene Families (D. Sankoff & J.H. Nadeau), Kluwer, 562 pp. (2000) [PDF]
• Early eukaryote evolution based on mitochondrial gene order breakpoints (D. Sankoff, D. Bryant, M. Deneault, B.F. Lang & G. Burger), Journal of Computational Biology 7, 521-535 (2000) [PDF]
• The early introduction of dynamic programming into computational biology (D. Sankoff), Bioinformatics 16, 41-47 (2000) [PDF]
• *Early eukaryote evolution based on mitochondrial gene order breakpoints (D. Sankoff, D. Bryant, M. Deneault, B.F. Lang, & G. Burger), Proceedings of the Fourth Annual International Conference on Computational Molecular Biology (RECOMB 2000) (R. Shamir, S. Miyano, S. Istrail, P. Pevzner & M.S. Waterman eds.), New York: ACM Press, 254-262 (2000) [PDF]
• Comparative genomics via phylogenetic invariants for Jukes-Cantor semigroups (D. Sankoff & M. Blanchette), Stochastic Models: A Conference in Honour of Professor Donald A. Dawson (L.G. Gorostiza & B.G. Ivanoff, eds.), American Mathematical Society, 399-418 (2000) [PDF]
• Reconstitution de l'ordre des génes dans les génomes ancestraux à partir de données sur les familles multigéniques (D. Sankoff & N. El-Mabrouk), Journées Ouvertes Biologie Informatique Mathematiques (JOBIM 2000), Recueil des Actes (G. Caraux, O. Gascuel and M.-F. Sagot eds.), Laboratoire d'Informatique de Robotique et de Microélectronique, Montpellier, p. 303-313 [PDF]
• Duplication, rearrangement and reconciliation (D. Sankoff & N. El-Mabrouk), Comparative Genomics (D. Sankoff and J.H. Nadeau eds.) Springer, 537-550 (2000) [PDF]
• Accuracy and robustness of analyses based on numbers of genes in observed segments (D. Sankoff, M.N. Parent & D. Bryant), Comparative Genomics (D. Sankoff and J.H. Nadeau eds.) Springer, 299-306 (2000) [PDF]
• Chloroplast gene order and the divergence of plants and algae, from the normalized number of induced breakpoints (D. Sankoff, M. Deneault, D. Bryant, C. Lemieux, & M. Turmel) , Comparative Genomics (D. Sankoff and J.H. Nadeau eds.) Springer, 89-98 (2000) [PDF]

1999

• Time Warps, String Edits and Macromolecules. The Theory and Practice of Sequence Comparison (D. Sankoff & J.B. Kruskal) CSLI & Cambridge,1999, 382 pp. (reprint of 1983 Addison-Wesley edition) [PDF]
• Genome rearrangement with gene families (D. Sankoff), Bioinformatics 15, p. 909-917 [PDF]
• Phylogenetic invariants for genome rearrangements (D. Sankoff & M. Blanchette), Journal of Computational Biology 6, p. 431-445 [PDF]
• Gene order breakpoint evidence in animal mitochondrial phylogeny (M. Blanchette, T. Kunisawa & D. Sankoff), Journal of Molecular Evolution 49, p. 193-203 [PDF]
• A genomics appoach to mitochondrial evolution (M.W. Gray, G. Burger, R. Cedergren, G.B. Golding, C. Lemieux, D. Sankoff, M. Turmel & B.F. Lang), The Biological Bulletin 196, p. 400-403 [PDF]
• Generating 3D virtual populations from pictures of a few individuals (W.-S. Lee, P. Beylot, D. Sankoff & N. Magnenat Thalmann), Algorithms and Data Structures, Proceedings of the Sixth International Workshop, WADS 99 (F. Dehne, A. Gupta, J.-R. Sack, N. Santoro & R. Tamassia eds.), Springer Verlag, Lecture Notes in Computer Science 1663, p. 134-144 [PDF]
• Probability models for genome rearrangement and linear invariants for phylogenetic inference (D. Sankoff & M. Blanchette), Proceeedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB 99) (S. Istrail, P. Pevzner & M. Waterman eds.), ACM Press, p. 302-309 [PDF]
• Reconstructing the pre-doubling genome (N. El-Mabrouk, D. Bryant, D. Sankoff), Proceeedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB 99) (S. Istrail, P. Pevzner and M. Waterman eds.), ACM Press, p. 154-163 [PDF]
• On the reconstruction of ancient doubled circular genomes using minimum reversals (N. El-Mabrouk & D. Sankoff), Genome Informatics 1999 (K. Asai, S. Miyano and T. Takagi eds.), Universal Academy Press, p. 83-93 [PDF]
• Hybridization and genome rearrangement (N. El-Mabrouk & D. Sankoff), Combinatorial Pattern Matching. Ninth Annual Symposium (M. Crochemore and M. Paterson eds.), Springer Verlag, Lecture Notes in Computer Science 1645, p. 78-87. [PDF]
• Comparative mapping and genome rearrangement (D. Sankoff), From Jay Lush to Genomics: Visions for Animal Breeding and Genetics (J.C.M. Dekkers, S.J. Lamont & M.F. Rothschild eds.), Iowa State University, p. 124-134 [PDF]
• In memorium: Robert Cedergreen (1939-1998) (N. Beauchemin, D. Sankoff & H. Grosjean), RNA 5, Cambridge University Press, p. 147-148 [PDF]

1998

• Proceedings, Sixth International Conference on Intelligent Systems for Molecular Biology (J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff & C. Sensen) AIII Press, 1998, 223 pp. [PDF]
• Counting on comparative maps (J.H. Nadeau & D. Sankoff), Trends in Genetics 14, p. 495-501 [PDF]
• A formal production-based explanation of the facts of code-switching (D. Sankoff), Bilingualism, Language and Cognition 1, p. 39-50 [PDF]
• The lengths of undiscovered segments in comparative maps (J.H. Nadeau & D. Sankoff), Mammalian Genome 9, p. 491-495 [PDF]
• Genome structure and gene content in protist mitochondrial DNAs (M.W. Gray, B.F. Lang, R. Cedergren, G.B. Golding, C. Lemieux, D. Sankoff, M. Turmel, N. Brossard, E. Delage, T.G. Littlejohn, I. Plante, P. Rioux, D. Saint-Louis, Y. Zhu & G. Burger), Nucleic Acid Research 26, p. 865-878 [PDF]
• Multiple genome rearrangement (D. Sankoff & M. Blanchette), Proceeedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB 98) (S. Istrail, P. Pevzner & M. Waterman, eds.), New York: ACM Press, p. 243-247 [PDF]
• Genome halving (N. El-Mabrouk, J.H. Nadeau & D. Sankoff), Combinatorial Pattern Matching. Ninth Annual Symposium (M. Farach-Colton eds.), Springer Verlag, Lecture Notes in Computer Science 1448, p. 235-250 [PDF]
• Phylogenetic invariants for metazoan mitochondrial genome evolution (D. Sankoff & M. Blanchette), Genome Informatics 1998 (S. Miyano & T. Takagi, eds.), Tokyo: Universal Academy Press, p. 22-31 [PDF]
• The production of code-mixed discourse (D. Sankoff), Proceedings of the 36th Annual Meeting of the Association for Computational Linguistics and the 17th International Conference on Computational Linguistics, New Brunswick, NJ: ACL Press, p. 8-21 [PDF]
• Multiple genome rearrangement and breakpoint phylogeny (D. Sankoff & M. Blanchette), Journal of Computational Biology 5, p. 555-570 [PDF]

1997

• *Conserved segment identification (D. Sankoff & V. Ferretti), Proceeedings of the First Annual International Conference on Computational Molecular Biology (RECOMB 97) (S. Istrail, P. Pevzner and M. Waterman eds.), ACM Press, p. 252-256 Journal of Computational Biology 4, p. 559-565. [PDF]
• Conserved segment identification (D. Sankoff & V. Ferretti), (S. Istrail, P. Pevzner and M. Waterman eds.), ACM Press, p. 252-256 Journal of Computational Biology 4, p. 559-565. [PDF]
• Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution (J.H. Nadeau & D. Sankoff), Genetics 147, p. 1259-1266 [PDF]
• Gene order comparison for phylogenetic inference of plastid genomes (T. Kunisawa, M. Blanchette, D. Sankoff), Research Communications in Biochemistry and Cell & Molecular Biology 1, p. 133-142 [PDF]
• Breakpoint phylogenies (M. Blanchette, G. Bourque & D. Sankoff), Genome Informatics 1997 (S. Miyano & T. Takagi, eds.) Tokyo: Universal Academy Press, p. 25-34 [PDF]
• The median problem for breakpoints in comparative genomics (D. Sankoff & M. Blanchette), Computing and Combinatorics, Proceeedings of COCOON 97. (T. Jiang and D.T. Lee, eds.), Lecture Notes in Computer Science 1276, Springer Verlag, p. 251-263 [PDF]
• Synteny conservation and chromosome rearrangements during mammalian evolution (J. Ehrlich, D. Sankoff & J.H. Nadeau), Genetics 147, p. 289-396 [PDF]
• Discourse enumerators and Schegloff's denominator (S. Dubois & D. Sankoff), Towards a Social Science of Language: Papers in Honor of William Labov, Vol. 2: Social Interaction and Discourse Structures (G. Guy, C. Feagin, D. Schiffrin, & J. Baugh, eds.), Amsterdam /Philadelphia: John Benjamins, p. 153-182
• On the Nadeau-Taylor theory of conserved chromosome segments (D. Sankoff, M.-N. Parent, I. Marchand & V. Ferretti), Combinatorial Pattern Matching. Eighth Annual Symposium (A. Apostolico & J. Hein, ed.), Lecture Notes in Computer Science 1264, Springer Verlag, p. 262-274 [PDF]
• The early introduction of dynamic programming into computational biology (D. Sankoff), Advances in the Mathematical Sciences - CRM's 25 years (L. Vinet, ed.) CRM Proceedings and Lecture Notes. vol. 11, Providence, RI: American Mathematical Society, p. 403-413 [PDF]
• L'absence de flexion sur les emprunts à l'anglais dans le français cadjin (S. Dubois & D. Sankoff), Explorations du lexique (J. Auger and Y. Ryan, eds.), Québec: Centre international de recherche en amenagement linguistique, p. 163-176
• An ancestral mitochondrial DNA resembling a eubacterial genome in miniature (B.F. Lang, G. Burger, C.J. O'Kelly, R. Cedergren, G.B. Golding, C. Lemieux, D. Sankoff, M. Turmel & M.W. Gray), Nature 387, p. 493 [PDF]
• Landmarks in the Rosetta stone of mammalian comparative maps (J.H. Nadeau & D. Sankoff), Nature Genetics 15, p. 6-7 [PDF]

1996

• Conserved synteny as a measure of genomic distance (D. Sankoff & J.H. Nadeau), Discrete Applied Mathematics 71, p. 247-257 [PDF]
• Steiner points in the space of genome rearrangements (D. Sankoff, G. Sundaram & J. Kececioglu), International Journal of the Foundations of Computer Science 7, p. 1-9 [PDF]
• Original synteny (V. Ferretti , J.H. Nadeau & D. Sankoff), Combinatorial Pattern Matching. Seventh Annual Symposium (D. Hirschberg & G. Myers, ed.), Lecture Notes in Computer Science 1075, Springer Verlag, p. 159-167 [PDF]
• The quantitative analysis of turntaking in multiparticipant conversations (S. Dubois, M. Boutin & D. Sankoff), (N)WAVES and MEANS: a selection of papers from NWAVE 24. University of Pennsylvania Working Papers in Linguistics 3.1, p. 257-276 [PDF]
• A remarkable nonlinear invariant for evolution with heterogeneous rates (V. Ferretti & D. Sankoff), Mathematical Biociences 134, p. 71-83 [PDF]
• Evolution of fragmented mitochondrial ribosomal RNA genes in Chlamydomonas (E.M. Denovan-Wright, D. Sankoff, D. Spencer & R.W. Lee), Journal of Molecular Evolution 42, p. 382-391 [PDF]
• Parametric analysis of genome rearrangement (M. Blanchette, T. Kunisawa & D. Sankoff), Gene-Combis (revue éléctronique) and Gene 172, GC, p.11-17 [PDF]
• Karyotype distributions in a stochastic model of reciprocal translocation (D. Sankoff & V. Ferretti), Genome Research 6, p. 1-9 [PDF]

1995

• Phylogenetic invariants for more general evolutionary models (V. Ferretti & D. Sankoff), Journal of Theoretical Biology 173, p. 147-162 [PDF]
• Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement (J. Kececioglu & D. Sankoff), Algorithmica 13, p. 180-210 [PDF]
• An efficient algorithm for supertrees (M. Constantinescu & D. Sankoff), Journal of Classification 12, p. 101-112 [PDF]

1994

• Social interest, linguistic indifference (D. Sankoff), Culture 14, p. 27-37
• Skewed base compositions, asymmetric transition matrices and phylogenetic invariants (V. Ferretti, B.F .Lang & D. Sankoff), Journal of Computational Biology 1, p. 77-92 [PDF]
• A Tree · A Window · A Hill; Generalization of nearest-neighbour interchange in phylogenetic optimisation (D. Sankoff, Y. Abel & J. Hein), Journal of Classification 11, p. 209-232 [PDF]
• Efficient bounds for oriented chromosome inversion distance (J. Kececioglu & D. Sankoff), Combinatorial Pattern Matching. Fifth Annual Symposium (M. Crochemore & D. Gusfield, eds.) Lecture Notes in Computer Science 807, Springer Verlag, p. 307-325 [PDF]

1993

• Analytical approaches to genomic evolution (D. Sankoff), Biochimie 75, p. 409-413 [PDF]
• Le vocabulaire partagé par des sous-groupes d'une communauté (D. Sankoff), Mathématiques, Informatique et Science Humaine 121, p. 41-47 [PDF]
• The empirical discovery of phylogenetic invariants (V. Ferretti & D. Sankoff), Advances in Applied Probability 25, p. 290-302 [PDF]
• Exact and approximation algorithms for the inversion distance between two chromosomes (J. Kececioglu & D. Sankoff), Combinatorial Pattern Matching. Fourth Annual Symposium. (A. Apostolico M. Crochemore, Z. Galil, & U. Manber, eds.) Lecture Notes in Computer Science 684. Springer Verlag, p. 87-105 [PDF]
• Models and analyses of genomic evolution (D. Sankoff), Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis (H.A. Lim, J.W. Fickett, C.R. Cantor & R.J. Robbins, eds.), Singapore: World Scientific (1993) p. 177-183 [PDF]

1992

• Punctors: a pragmatic variable (D. Vincent & D. Sankoff), Language Variation and Change 4, p. 205-216 [PDF]
• Efficient optimal decomposition of a sequence into disjoint regions, each matched to some template in an inventory (D. Sankoff), Mathematical Biosciences 111, p. 279-293 [PDF]
• Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome (D. Sankoff, G. Leduc, N. Antoine, B. Paquin, B.F. Lang & R. Cedergren), Proceedings of the National Academy of Sciences USA 89, p. 6575-6579 [PDF]
• Edit distance for genome comparison based on non-local operations (D. Sankoff), Combinatorial Pattern Matching. Third Annual Symposium (A. Apostolico, M. Crochemore, Z. Galil, & U. Manber, ed.), Lecture Notes in Computer Science 644. Springer Verlag, p. 121-135 [PDF]
• Analyses de l'évolution des génomes (D. Sankoff), Cahiers IMABIO, CNRS

1991

• The empirical study of code-switching (D. Sankoff, S. Poplack & S. Vanniarajan), Papers for the Symposium on Code- switching in Bilingual Studies: Theory, Significance and Perspectives. Strasbourg: European Science Foundation, p. 181-206 [PDF]
• Evaluating gene versus genome evolution (R.J. Cedergren, Y. Abel & D. Sankoff), NATO ASI Series H 57. Molecular Techniques in Taxonomy (G.M. Hewitt, A.W.B. Johnston & J.P.W. Young, ed.), p. 87-99
• A test for mixed rules (D. Sankoff & P. Rousseau), New Ways of Analyzing Sound Change (P. Eckert, ed.), Academic Press [PDF]

1990

• The case of the nonce loan in Tamil (D. Sankoff, S. Poplack & S. Vanniarajan), Language Variation & Change 2, p. 71-101 [PDF]
• Comparison of musical sequences (M. Mongeau & D. Sankoff), Computers & the Humanities 126, p. 161-175 [PDF]
• Genome divergence through gene rearrangement (D. Sankoff, R. Cedergren & Y. Abel), Methods in Enzymology 183, p. 428-438 [PDF]
• Designer invariants for large phylogenies (D. Sankoff), Molecular Biology & Evolution 7, p. 255-269 [PDF]
• Quadratic invariants for multivalued characters (S. Drolet & D. Sankoff), Journal of Theoretical Biology 144, p. 117-129 [PDF]
• Relationships from gene sequences (R.J. Cedergren, D. Sankoff & Y. Abel), Nature 345, p. 484 [PDF]

1989

• A continuous analog for RNA folding (V. Ferretti & D. Sankoff), Bulletin of Mathematical Biology 51, p. 167-171 [PDF]
• Probabilistic models for genome shuffling (D. Sankoff & M. Goldstein), Bulletin of Mathematical Biology 51, p. 117-124 [PDF]
• The development of syntactic complexity in narrative, informative and argumentative discourse (C. Dubuisson, L. Emirkanian & D. Sankoff), Language Change and Variation (R.W. Fasold & D. Schiffrin, eds.) Amsterdam: John Benjamins, p. 333-350
• New results on Montreal French /r/ (C. Tousignant, D. Sankoff & L. Santerre), Language Change and Variation (R.W. Fasold & D. Schiffrin, eds.) Amsterdam: John Benjamins, p. 85-94
• Montreal French: language, class and ideology (D. Sankoff, H.J. Cedergren, W. Kemp, P. Thibault & D. Vincent), Language Change and Variation (R.W. Fasold & D. Schiffrin, eds.), Amsterdam: John Benjamins, p. 107-118
• The emergent syntax of pre-sentential turn-openings (A. Vicher & D. Sankoff), Journal of Pragmatics 13, p. 81-97 [PDF]
• On the evolutionary origin of the plant mitochondrion and its genome (M.W. Gray, R.J. Cedergren, Y. Abel & D. Sankoff), Proceedings of the National Academy of Sciences (U.S.A.) 86, p. 2267-2271 [PDF]
• The inference of hierarchical schemes for multinomial data (P. Rousseau & D. Sankoff), Journal of Classification 6, p. 73-95 [PDF]
• Statistical evidence for rule ordering (D. Sankoff & P. Rousseau), Language Variation and Change 1, p. 1-18 [PDF]
• Mechanisms of genome evolution: models and inference (D. Sankoff), Bulletin of the International Statistical Institute 47.3, p. 461-475

1988

• Supercomputing for molecular cladistics (D. Sankoff, Y. Abel, R.J. Cedergren & M.W. Gray), Classification and Related Methods of Data Analysis (H.H. Bock, ed.) Amsterdam: North-Holland, p. 385-394
• Sociolinguistics and syntactic variation (D. Sankoff), Linguistics: the Cambridge Survey. IV Language: the socio-cultural context (F. Newmeyer, ed.), Cambridge: Cambridge University Press, p. 140-161
• The social correlates and linguistic processes of lexical borrowing and assimilation (S. Poplack, D. Sankoff & C. Miller), Linguistics 26, p. 47-104 [PDF]
• Le discours mixte arabe/français: emprunts ou alternances de langue? (M. Naït M'barek & D. Sankoff), Revue canadienne de linguistique 33, p. 143-154
• The evolutionary relationships among known life forms (R.J. Cedergren, M.W. Gray, Y. Abel & D. Sankoff), Journal of Molecular Evolution 28, p. 98-112 [PDF]
• Code-switching (S. Poplack & D. Sankoff), Sociolinguistics. An International handbook of the Science of Language and Society (U. Ammon, N. Dittmar & K.J. Mattheier, eds.), Berlin: Walter de Gruyter, p. 1173-1180
• Variable rules (D. Sankoff), Sociolinguistics. An International handbook of the Science of Language and Society (U. Ammon, N. Dittmar & K.J. Mattheier, eds.), Berlin: Walter de Gruyter, p. 984-997
• Problems of representativeness (D. Sankoff), Sociolinguistics. An International handbook of the Science of Language and Society (U. Ammon, N. Dittmar & K.J. Mattheier, eds.), Berlin: Walter de Gruyter, p. 899-903
• Activités physiques, habitus corporels et styles de vie (S. Laberge & D. Sankoff), Sport et Pouvoir (J. Harvey & H. Cantelon, eds.) Ottawa: University of Ottawa Press, p. 277-297

1987

• The computational complexity of inferring phylogenies from chromosome inversion data (W.H.E. Day & D. Sankoff), Journal of Theoretical Biology 127, p. 213-218 [PDF]
• Computational complexity and cladistics, (D. Sankoff), Biological Metaphor and Cladistic Classification (H. Hoenigswald & L. Wiener, eds.), Philadelphia: University of Pennsylvania Press, p. 269-280 [PDF]
• Delimiting the Sydney speech community (B. Horvath & D. Sankoff), Language in Society 16, p. 179-204 [PDF]
• A quantitative and qualitative analysis of speech markers in the native and second language speech of bilinguals (M. Olynyk, A. d'Anglejan & D. Sankoff), Applied Psycholinguistics 8, 121-136 [PDF]
• Archetypical features in tRNA families (K. Nicoghosian, M. Bigras, D. Sankoff & R.J. Cedergren), Journal of Molecular Evolution 26, p. 341-346 [PDF]
• The Philadelphia story in the Spanish Caribbean (S. Poplack & D. Sankoff), American Speech 62, p. 291-314 [PDF]
• El principio de consistencia universal en el español andino del Ecuador (M. Luján, D. Sankoff & I. Bordelois), Actas del I Congreso Internacional sobre el Español de América (H. López Morales & María Vaquero, eds.) San Juan: Academia Puertorriqueña de la Lengua Española, p. 825-838

1986

• Diversity and Diachrony (D. Sankoff) Amsterdam: John Benjamins, 1986, 430 pp. [PDF]
• Un modèle pour l'alternance de langue sous la contrainte d'équivalence (D. Sankoff & S. Mainville), Revue Québecoise de Linguistique 15, p. 233-246 [PDF]
• Allele and locus classification in electrophoretic population studies (D. Sankoff, V. Ferretti & D. Roby), Journal of Theoretical Biology 119, p. 397-407 [PDF]
• La variabilidad de /r/ implosiva en el español de Panamáy los modelos de ordenación de reglas (H. Cedergren, P. Rousseau & D. Sankoff), Estudios sobre la Fonología del Español del Caribe (R. Núñez Cedeño, I. Páez Urdaneta & J. Guitart, eds.) Caracas: La Casa de Bello, p. 13-20
• Ordenamiento de reglas variables: /r/ implosiva en un dialecto puertorriqueño (D. Sankoff), Estudios sobre la Fonología del Español del Caribe (R. Núñez Cedeño, I. Páez Urdaneta & J. Guitart, eds.) Caracas: La Casa de Bello, p. 109-115
• The computational complexity of inferring rooted phylogenies by parsimony (W.H.E. Day, D. Johnson & D. Sankoff), Mathematical Biosciences 81, p. 33-42 [PDF]
• Quantificateur et marqueur de discours (M. Lemieux, C. Fontaine & D. Sankoff), Diversity and Diachrony (D. Sankoff, ed.) Amsterdam: John Benjamins, p. 381-390
• The computational complexity of inferring phylogenies by compatibility (W.H.E. Day & D. Sankoff), Systematic Zoology 35, p. 224-229 [PDF]
• Enumerating trees modulo a consensus (M. Constantinescu & D. Sankoff), Journal of Classification 3, p. 349-356 [PDF]
• Code-switching of context-free grammars (D. Sankoff & S. Mainville), Theoretical Linguistics 13, p. 75-90 [PDF]

1985

• Le futur simple et le futur périphrastique (L. Emirkanian & D. Sankoff), Les Tendances Dynamiques du Français Parlé à Montréal. v. 1 (H.J. Cedergren & M. Lemieux, ed.), Montreal: Office de la langue française, p. 189-204, Also: Actes du 17e Congrès de Linguistique et Philologie Romane v. 4 (1986) 397-407
• Statistics in linguistics (D. Sankoff), Encyclopedia of the Statistical Sciences 5, New York: John Wiley & Sons, p. 74-81
• Simultaneous solution of the RNA folding, alignment and protosequence problems (D. Sankoff), SIAM Journal on Applied Mathematics 45, p. 810-825 [PDF]
• TUT en français de Montréal: un cas de neutralisation morphologique (M. Lemieux, M. St-Amour & D. Sankoff), Les Tendances Dynamiques du Français Parlé de Montréal. v. 2 (H.J. Cedergren & M. Lemieux, ed.), Montreal: Office de la langue française, p.7- 90

1984

• Binomial decompositions for multinomial data in logistic-linear models (D. Sankoff & P. Rousseau), Topics in Applied Statistics (Y.P. Chaubey & T.D. Dwivedi, eds.) Montreal: Concordia University, p. 199-208
• Le trajet linguistique et social des emprunts (S. Poplack & D. Sankoff ) Revue Québécoise de Linguistique 14, 141-186 [PDF]
• Borrowing: the synchrony of integration (S. Poplack & D. Sankoff), Linguistics 22, p. 99-135. Also: Le trajet linguistique et social des emprunts, Revue Québécoise de Linguistique 14:1, 141-186 [PDF]
• RNA secondary structures and their prediction (M. Zuker & D. Sankoff), Bulletin of Mathematical Biology 46, p. 591-621 [PDF]
• On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA (M.W. Gray, D. Sankoff & R.J. Cedergren), Nucleic Acids Research 12, p. 5837-5852 [PDF]
• The universal consistency hypothesis and the prediction of word order acquisition stages in the speech of bilingual children (M. Luján, L. Minaya & D. Sankoff), Language 60, p. 343-371 [PDF]

1983

• Fast algorithms to predict RNA secondary structures containing multiple loops (D. Sankoff, R.J. Cedergren, J.B. Kruskal & S. Mainville), Time Warps, String Edits and Macromolecules. The Theory and Practice of Sequence Comparison (D. Sankoff & J.B. Kruskal, eds.) Reading, Massachussetts: Addison-Wesley, p. 93-120
• Simultaneous comparison of three or more sequences related by a tree (D. Sankoff & R.J. Cedergren), Time Warps, String Edits and Macromolecules. The Theory and Practice of Sequence Comparison (D. Sankoff & J.B. Kruskal, eds.) Reading, Massachussetts: Addison-Wesley, 253-263
• An anthology of algorithms and concepts for sequence comparison (J.B. Kruskal & D. Sankoff), Time Warps, String Edits and Macromolecules. The Theory and Practice of Sequence Comparison (D. Sankoff & J.B. Kruskal, eds.) Reading, Massachussetts: Addison-Wesley, 265-310
• Peut-on /TUT/ désambiguer? (D. Sankoff & M. Lemieux), Revue de l'Association Québecoise de Linguistique, p. 159-164
• Common subsequences and monotone subsequences (D. Sankoff & S. Mainville), Time Warps, String Edits and Macromolecules. The Theory and Practice of Sequence Comparison (D. Sankoff & J.B. Kruskal, eds.) Reading, Massachussetts: Addison-Wesley, p. 363-365
• An upper bound technique for the lengths of common subsequence problem (V. Chvátal & D. Sankoff), Time Warps, String Edits and Macromolecules. The Theory and Practice of Sequence Comparison (D. Sankoff & J.B. Kruskal, eds.) Reading, Massachussetts: Addison-Wesley, p. 353-357
• Word order acquisition in the bilingual context (M. Luján, L. Minaya & D. Sankoff), Comparability of Language Contacts (P. Nelde, ed.), Bonn: Dümmler, p. 411-425
• Second language fluency and the subjective evaluation of officer cadets in a military college (M. Olynyk, D. Sankoff & A. D'Anglejan), Studies in Language Acquisition 5, p. 213-236 [PDF]

1982

• A strategy for sequence phylogeny research (D. Sankoff, R.J. Cedergren & W. McKay), Nucleic Acids Research 10, p. 421-431 [PDF]
• Maximum likelihood clustering of binomial data sets (P. Rousseau & D. Sankoff), Classifying Social Data (H. Hudson, ed.) San Francisco: Jossey-Bass, p. 84-92
• Sociolinguistic method and linguistic theory (D. Sankoff), Logic, Methodology and Philosophy of Science VI (L.J. Cohen, J. Los, H. Pfeiffer & K.P. Podewski, eds.) Amsterdam: North-Holland & Warsaw: Polish Scientific, p. 677-689 [PDF]
• Un diagnosticó para reglas convergentes (D. Sankoff & P. Rousseau), Español del Caribe (O. Alba, ed.) Dominican Republic: Universidad Madre y Maestra, p. 291-300
• Competing influences on gender assignment: variable process, stable outcome (S. Poplack , A. Pousada & D. Sankoff), Lingua 57, p. 1-28, Also: Un estudio comparativo de la asignación de género a préstamos nominales, Español del Caribe (O. Alba, ed.) Dominican Republic: Universidad Madre y Maestra, p. 239-269 [PDF]
• An algorithm for the display of nucleic acid secondary structure (G. Lapalme, R.J. Cedergren & D. Sankoff), Nucleic Acids Research 10, p. 8351-8356 [PDF]

1981

• Variation Omnibus (D. Sankoff & H.J. Cedergren), Edmonton: Linguistic Research Incorporated, 1981, 602 pp.
• A formal grammar for code-switching (D. Sankoff & S. Poplack), Papers in Linguistics 14, p. 3-46 [PDF]
• The evolving tRNA molecule (R.J. Cedergren, B. LaRue, D. Sankoff & H. Grosjean), Critical Reviews in Biochemistry 11, p. 35- 104 [PDF]
• The evolution of multi-isoacceptor tRNA families (B. Larue, N. Newhouse, K. Nicogkosian & R.J. Cedergren, with the assistance of D. Sankoff), Journal of Biological Chemistry 256, p. 1539-1543 [PDF]
• Weak complementarity: tense and aspect in Monteal French (D. Sankoff & P. Thibault), Syntactic change (B.B. Johns & D.R. Strong, eds.) Natural Language Studies 25, p. 205-216
• Echelles et règles (D. Sankoff & P. Rousseau), Variation Omnibus (D. Sankoff & H.J. Cedergren, eds.) Edmonton: Linguistic Research Incorporated, p. 257-269
• El principio de consistencia universal en el habla de los niños bilingües peruanos (M. Luján, L. Minaya & D. Sankoff), Lexis V, p. 95-110

1980

• Quantitative interpretation of archaeological surface assemblages (D. Sankoff & L.I. Paradis), Proceedings of the Second International Conference on Mathematical Modelling (X.J.R. Avula, R. Bellman, Y.L. Luke & A.K. Rigler, eds.), University of Missouri-Rolla, p. 745-752
• Categorical contexts and variable rules (D. Sankoff & P. Rousseau), Papers from the Scandinavian Symposium on Syntactic Variation (S. Jacobson, ed.) Stockholm: Almqvist & Wiksell, p. 7-22
• Convergence and minimal mutation criteria for evaluating early events in tRNA evolution (R.J. Cedergren, B. LaRue, D. Sankoff, G. Lapalme & H. Grosjean), Proceedings of the National Academy of Science (U.S.A.) 77, p. 2741-2795 [PDF]
• El ingles de Samaná y la hipotesis del origen criollo (S. Poplack & D. Sankoff), Boletín de la Academia Puertorriqueña de la Lengua Española VIII, p. 103-121 [PDF]

1979

• On the uses of variable rules (D. Sankoff & W. Labov), Language in Society 8, p. 189-222 [PDF]
• Coordination et effacement (L. Emirkanian & D. Sankoff), Le Français Parlé: Études Sociolinguistiques (P. Thibault, ed.) Edmonton: Linguistic Research Incorporated, p. 75-94
• Aspects de la compétence productive et réceptive: la liaison à Montréal (C. Tousignant & D. Sankoff), Le Français Parlé: Études Sociolinguistiques (P. Thibault, ed.) Edmonton: Linguistic Research Incorporated, p. 41-52
• Evolution of methionine initiator and phenylalanine transfer RNAs (B. LaRue, R.J. Cedergren, D. Sankoff & H. Grosjean), Journal of Molecular Evolution 14, p. 287-300 [PDF]

1978

• Linguistic Variation: Models and Methods (D. Sankoff), New York: Academic Press, 1978, 296 pp.
• Probability and linguistic variation (D. Sankoff), Synthese 37, p. 217-238 [PDF]
• Computational linguistics and statistics in the analysis of the Montreal French corpus (D. Sankoff, R. Lessard & B.T. Nguyen), Computers and the Humanities 11, p. 185-191 [PDF]
• Semantic field variability (D. Sankoff, P. Thibault & H. Bérubé), Linguistic Variation: Models and Methods (D. Sankoff, ed.) New York: Academic Press, p. 23-43
• Advances in variable rule methodology (P. Rousseau & D. Sankoff), Linguistic Variation: Models and Methods (D. Sankoff, ed.) New York: Academic Press, p. 57-69
• A solution to the problem of grouping speakers (P. Rousseau & D. Sankoff), Linguistic Variation: Models and Methods (D. Sankoff, ed.) New York: Academic Press, p. 97-117
• Statistical dependence among successive occurrences of a variable in discourse (D. Sankoff & S. Laberge), Linguistic Variation: Models and Methods (D. Sankoff, ed.) New York: Academic Press, p.119-126
• The linguistic market and the statistical explanation of variability (D. Sankoff & S. Laberge), Linguistic Variation: Models and Methods (D. Sankoff, ed.) New York: Academic Press, p. 239-250
• The evolution of 5S RNA secondary structures (D. Sankoff, A.-M. Morin & R.J. Cedergren), Canadian Journal of Biochemistry 56, p. 440-443 [PDF]
• Singularities in the analysis of binomial data (P. Rousseau & D. Sankoff), Biometrika 65, p. 603-609 [PDF]
• Bacteriophage MS-2 RNA: a correlation between the stability of codon-anticodon interaction and the choice of code words (H. Grosjean, D. Sankoff, W. Min Jou, W. Fiers & R.J. Cedergren), Journal of Molecular Evolution 12, p.113-119 [PDF]

1977

• Harmonie et conditionnement consonnantique dans le système vocalique du franais parlé à Montréal (M. Yaeger, D. Sankoff & H.J. Cedergren), Phonologie et Société (H. Walter, ed.), Studia Phonetica 13, p. 25-33
• The computation of branching rules for representations of semisimple Lie algebras (W. McKay, J. Patera & D. Sankoff), Computers in Nonassociative Rings and Algebras (R.E. Beck & B. Kolman, eds.) New York: Academic Press, p. 235-277
• Programmation dynamique et l'analyse d'ensembles de séquences macromoléculaires (D. Sankoff), Analyse des Données et Informatique, IRIA, France, p. 741-750
• D'une classification hiérarchique à une classification disjointe (D. Sankoff), Annales des Sciences Mathématiques du Québec 1, p. 325-336

1976

• The dimensionality of grammatical variation (D. Sankoff & H.J. Cedergren), Language 52, p. 163-178 [PDF]
• Evolutionary origin of 5.8S RNA (R.J. Cedergren & D. Sankoff), Nature 259, p.74-76 [PDF]
• Frequency of insertion/deletion, transversion and transition in the evolution of 5S ribosomal RNA (D. Sankoff, R.J. Cedergren & G. Lapalme), Journal of Molecular Evolution 7, p. 133-149 [PDF]
• Nucleic acid sequence evidence for the evolutionary origin of major phyla including plants and algae (B. LaRue, R.J. Cedergren & D. Sankoff), Acides Nucleiques et Synthése des Protéines chez les Végétaux, Colloques Internationaux du CNRS 261, p. 119-125
• Sample survey methods and computer-assisted analysis in the study of grammatical variation (D. Sankoff & G. Sankoff), Canadian Languages in their Social Context (R. Darnell, ed.), Edmonton: Linguistic Research Incorporated, p. 7-64. Also: Méthodes d'échantillonage et utilisation de l'ordinateur dans l'étude de la variation grammaticale (D. Sankoff, G. Sankoff, S. Laberge & M. Topham) Cahiers Linguistiques de l'Université du Québec 6 , p. 85-125 [PDF]

1975

• Minimal mutation trees of sequences (D. Sankoff), SIAM Journal on Applied Mathematics 28, p. 35-42 [PDF]
• Locating the vertices of a Steiner tree in an arbitrary metric space (D. Sankoff & P. Rousseau), Mathematical Programming 9, p. 240-246, Also: Advances in Discrete Mathematics and Computer Science, Vol. IV-V: Steiner Minimal Trees (F.K. Hwang & D. Richards, eds.) Nonantun, MA: Hadronic Press [PDF]
• Longest common subsequences of two random sequences (V. Chvátal & D. Sankoff), Journal of Applied Probability 12, p. 306- 315 [PDF]
• Gravity models and interaction probabilities (L.-N. Tellier & D. Sankoff), Journal of Regional Science 15, p. 317-322 [PDF]
• Vocabulary richness: a sociolinguistic analysis (D. Sankoff & R. Lessard), Science 190, p. 689-690 [PDF]
• Nasals: a sociolinguistic study of change in progress (H.J. Cedergren & D. Sankoff), Nasalfest (C. Ferguson, L. Hyman & J. Ohala, eds.), Stanford University, p. 67-80 [PDF]
• Wave versus Stammbaum explanations of lexical similarities (D. Sankoff & G. Sankoff), Cahiers de l'Institut de Linguistique de Louvain 3, p. 29-41. Also: The Social Life of Language (G. Sankoff) Philadelphia: University of Pennsylvania Press (1980) p. 143-151

1974

• A method for assessing variable rule and implicational scale analyses of linguistic variation (D. Sankoff & P. Rousseau), Computers in the Humanities (J.L. Mitchell, ed.) Edinburgh University Press, p. 3-15
• Variable rules: performance as a statistical reflection of competence (H.J. Cedergren & D. Sankoff), Language 50, p. 333-355 [PDF]
• Party strategy and the relationship between votes and seats (D. Sankoff & K. Mellos), Theory and Decision 5, p.289-294 [PDF]
• Spatial configuration of ribosomal proteins (A. Bollen, R.J. Cedergren, D. Sankoff & G. Lapalme), Biochemical and Biophysical Research Communications 59, p. 1069-1078 [PDF]
• Similarités des régions critiques de quatorze tests d'homogénéité de deux échantillons (D. Sankoff & P. Rousseau), Revue Canadienne de Statistique 2, p. 113-126

1973

• Tables of Branching Rules for Representations of Simple Lie Algebras (J. Patera & D. Sankoff) Montreal: Presses de l'Université de Montréal, 1973, 100 pp.
• Parallels between genetics and lexicostatistics (D. Sankoff), Lexicostatistics and Genetic Linguistics (I. Dyen, ed.) The Hague: Mouton, p. 64-94
• A test for nucleotide sequence homology (D. Sankoff & R.J. Cedergren), Journal of Molecular Biology 77, p. 159-164 [PDF]
• La régionalisation électorale et l'amplification des proportions (D. Sankoff & K. Mellos), Revue Canadienne de Science Politique 6, p. 380-398 [PDF]
• Evolution of 5S RNA and the non-randomness of base replacement (D. Sankoff, C. Morel & R.J. Cedergren), Nature New Biology 245, p. 232-234 [PDF]
• Mathematical developments in lexicostatistic theory (D. Sankoff), Current Trends in Linguistics XI (T. Sebeok, ed.), The Hague: Mouton, p. 93-113
• Shortcuts, diversions and maximal chains in partially ordered sets (D. Sankoff & P.H. Sellers), Discrete Mathematics 4, p. 287-293 [PDF]

1972

• Context-free grammars and non-negative matrices (D. Sankoff), Linear Algebra and Applications 5, p. 277-281 [PDF]
• The swing ratio and game theory (D. Sankoff & K. Mellos), American Political Science Review 66, p. 551-554 [PDF]
• Lexical replacement processes (D. Sankoff), Computer Studies in the Humanities and Verbal Behavior 3, p. 208-212
• Reconstructing the history and geography of an evolutionary tree (D. Sankoff), American Mathematical Monthly 79, p. 596-603 [PDF]
• The mathematics of glottochronology revisited (A.J. Dobson, J.B. Kruskal, D. Sankoff & L.J. Savage), Anthropological Linguistics 14, p. 205-212[PDF]
• Matching sequences under deletion/insertion constraints (D. Sankoff), Proceedings of the National Academy of Sciences (U.S.A.) 69, p. 4-6. [PDF]

1971

• Branching processes with terminal types: application to context-free grammars (D. Sankoff), Journal of Applied Probability 8, p. 233-240 [PDF]
• Dictionary structure and probability measures (D. Sankoff), Information and Control 19, p. 104-113 [PDF]
• Duration of detectible synchrony in a binary branching process (D. Sankoff), Biometrika 58, p. 77-81 [PDF]
• Stochastic models for glottochronology (D. Sankoff), Mathematics in Archaeology and the Historical Sciences (F.R. Hodson, D.G. Kendall & P. Tautu, eds.), Edinburgh University Press, p. 381-386

1970

• On the rate of replacement of word-meaning relationships (D. Sankoff), Language 46, p. 564-569 [PDF]

1967

• An inequality for probabilities (D.A. Dawson & D. Sankoff), Proceedings of the American Mathematical Society 18, p. 504-507 [PDF]
• A packing problem for measurable sets (D. Sankoff & D.A. Dawson), Canadian Journal of Mathematics 19, p. 749-756 [PDF]

1963

• Radiobiological studies of vaccinia virus (J.D. Friesen, D. Sankoff & L. Siminovitch ), Virology 21, p. 411-424 [PDF]