{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T01:51:34Z","timestamp":1776045094762,"version":"3.50.1"},"publisher-location":"Berlin, Heidelberg","reference-count":31,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"value":"9783540735441","type":"print"},{"value":"9783540735458","type":"electronic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-73545-8_8","type":"book-chapter","created":{"date-parts":[[2007,8,17]],"date-time":"2007-08-17T09:44:11Z","timestamp":1187343851000},"page":"51-64","source":"Crossref","is-referenced-by-count":25,"title":["Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data"],"prefix":"10.1007","author":[{"given":"Dan","family":"Gusfield","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yelena","family":"Frid","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dan","family":"Brown","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"8_CR1","series-title":"Lecture Notes in Bioinformatics","volume-title":"Comparative Genomics","author":"V. Bafna","year":"2005","unstructured":"Bafna, V., Bansal, V.: Improved recombination lower bounds for haplotype data. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol.\u00a03678, Springer, Heidelberg (2005)"},{"issue":"5","key":"8_CR2","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1089\/cmb.2004.11.858","volume":"11","author":"V. Bafna","year":"2004","unstructured":"Bafna, V., Gusfield, D., Hannenhalli, S., Yooseph, S.: A note on efficient computation of haplotypes via perfect phylogeny. Journal of Computational Biology\u00a011(5), 858\u2013866 (2004)","journal-title":"Journal of Computational Biology"},{"key":"8_CR3","doi-asserted-by":"crossref","unstructured":"Brown, D., Harrower, I.: A new formulation for haplotype inference by pure parsimony. report cs-2005-03. Technical report, University of Waterloo, School of Computer Science (2005)","DOI":"10.1142\/9781860947575_0027"},{"issue":"2","key":"8_CR4","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1109\/TCBB.2006.24","volume":"3","author":"D.G. Brown","year":"2006","unstructured":"Brown, D.G., Harrower, I.M.: Integer Programming Approaches to Haplotype Inference by Pure Parsimony. IEEE\/ACM Transactions on Computational Biology and Bioinformatics\u00a03(2), 141\u2013154 (2006)","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"8_CR5","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1038\/nature04226","volume":"437","author":"International HapMap Consortium.","year":"2005","unstructured":"International HapMap Consortium.: A haplotype map of the human genome. Nature 437 1299\u20131320 (2005)","journal-title":"Nature"},{"key":"8_CR6","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1007\/11415770_44","volume-title":"Research in Computational Molecular Biology","author":"Z. Ding","year":"2005","unstructured":"Ding, Z., Filkov, V., Gusfield, D.: A linear-time algorithm for the perfect phylogeny haplotyping problem. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol.\u00a03500, pp. 585\u2013600. Springer, Heidelberg (2005)"},{"key":"8_CR7","volume-title":"Inferring Phylogenies","author":"J. Felsenstein","year":"2004","unstructured":"Felsenstein, J.: Inferring Phylogenies. Sinauer, Sunderland, MA (2004)"},{"key":"8_CR8","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1002\/net.3230210104","volume":"21","author":"D. Gusfield","year":"1991","unstructured":"Gusfield, D.: Efficient algorithms for inferring evolutionary history. Networks\u00a021, 19\u201328 (1991)","journal-title":"Networks"},{"key":"8_CR9","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511574931","volume-title":"Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology","author":"D. Gusfield","year":"1997","unstructured":"Gusfield, D.: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge (1997)"},{"key":"8_CR10","doi-asserted-by":"crossref","unstructured":"Gusfield, D.: Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions (Extended Abstract). In: Proceedings of RECOMB 2002: The Sixth Annual International Conference on Computational Biology, pp. 166\u2013175 (2002)","DOI":"10.1145\/565196.565218"},{"key":"8_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1007\/3-540-44888-8_11","volume-title":"Combinatorial Pattern Matching","author":"D. Gusfield","year":"2003","unstructured":"Gusfield, D.: Haplotype inference by pure parsimony. In: Baeza-Yates, R.A., Ch\u00e1vez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol.\u00a02676, pp. 144\u2013155. Springer, Heidelberg (2003)"},{"key":"8_CR12","first-page":"1","volume-title":"Handbook of Computational Molecular Biology","author":"D. Gusfield","year":"2005","unstructured":"Gusfield, D., Orzack, S.: Haplotype inference. In: Aluru, S. (ed.) Handbook of Computational Molecular Biology, vol.\u00a018, pp. 1\u201325. Chapman and Hall\/CRC, Boca Raton (2005)"},{"key":"8_CR13","doi-asserted-by":"publisher","first-page":"1842","DOI":"10.1093\/bioinformatics\/bth149","volume":"20","author":"E. Halperin","year":"2004","unstructured":"Halperin, E., Eskin, E.: Haplotype reconstruction from genotype data using Imperfect Phylogeny. Bioinformatics\u00a020, 1842\u20131849 (2004)","journal-title":"Bioinformatics"},{"key":"8_CR14","volume-title":"Gene Genealogies, Variation and Evolution: A primer in coalescent theory","author":"J. Hein","year":"2005","unstructured":"Hein, J., Schierup, M., Wiuf, C.: Gene Genealogies, Variation and Evolution: A primer in coalescent theory. Oxford University Press, Oxford (2005)"},{"issue":"2","key":"8_CR15","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1093\/bioinformatics\/18.2.337","volume":"18","author":"R. Hudson","year":"2002","unstructured":"Hudson, R.: Generating samples under the Wright-Fisher neutral model of genetic variation. Bioinformatics\u00a018(2), 337\u2013338 (2002)","journal-title":"Bioinformatics"},{"key":"8_CR16","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1093\/genetics\/111.1.147","volume":"111","author":"R. Hudson","year":"1985","unstructured":"Hudson, R., Kaplan, N.: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics\u00a0111, 147\u2013164 (1985)","journal-title":"Genetics"},{"key":"8_CR17","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1073\/pnas.0404730102","volume":"102","author":"G. Kimmel","year":"2005","unstructured":"Kimmel, G., Shamir, R.: GERBIL: Genotype resolution and block identification using likelihood. PNAS\u00a0102, 158\u2013162 (2005)","journal-title":"PNAS"},{"key":"8_CR18","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1287\/ijoc.1040.0085","volume":"16","author":"G. Lancia","year":"2004","unstructured":"Lancia, G., Pinotti, C., Rizzi, R.: Haplotyping populations by pure parsimony: Complexity, exact and approximation algorithms. INFORMS J. on Computing, special issue on Computational Biology\u00a016, 348\u2013359 (2004)","journal-title":"INFORMS J. on Computing, special issue on Computational Biology"},{"key":"8_CR19","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1086\/344347","volume":"71","author":"S. Lin","year":"2002","unstructured":"Lin, S., Cutler, D., Zwick, M., Chakravarti, A.: Haplotype inference in random population samples. Am. J. of Hum. Genet.\u00a071, 1129\u20131137 (2002)","journal-title":"Am. J. of Hum. Genet."},{"key":"8_CR20","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1086\/500808","volume":"78","author":"J. Marchini","year":"2006","unstructured":"Marchini, J., Donnelly, P., et al.: A comparison of phasing algorithms for trios and unrelated individuals. Am. J. of Human Genetics\u00a078, 437\u2013450 (2006)","journal-title":"Am. J. of Human Genetics"},{"key":"8_CR21","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1137\/S0097539702406510","volume":"33","author":"I. Pe\u2019er","year":"2004","unstructured":"Pe\u2019er, I., Pupko, T., Shamir, R., Sharan, R.: Incomplete directed perfect phylogeny. SIAM J. on Computing\u00a033, 590\u2013607 (2004)","journal-title":"SIAM J. on Computing"},{"key":"8_CR22","volume-title":"Proceedings of 4th CSB Bioinformatics Conference","author":"R.V. Satya","year":"2005","unstructured":"Satya, R.V., Mukherjee, A.: An optimal algorithm for perfect phylogeny haplotyping. In: Proceedings of 4th CSB Bioinformatics Conference, IEEE Computer Society Press, Los Alamitos (2005)"},{"key":"8_CR23","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1093\/bioinformatics\/btl262","volume":"22","author":"R.V. Satya","year":"2006","unstructured":"Satya, R.V., Mukherjee, A., Alexe, G., Parida, L., Bhanot, G.: Constructing near-perfect phylogenies with multiple homoplasy events. Bioinformatics\u00a022, 514\u2013522 (2006) Bioinformatics Suppl., Proceedings of ISMB 2006","journal-title":"Bioinformatics"},{"key":"8_CR24","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1086\/502802","volume":"78","author":"P. Scheet","year":"2006","unstructured":"Scheet, P., Stephens, M.: A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Human Genetics\u00a078, 629\u2013644 (2006)","journal-title":"Am. J. Human Genetics"},{"key":"8_CR25","volume-title":"Phylogenetics","author":"C. Semple","year":"2003","unstructured":"Semple, C., Steel, M.: Phylogenetics. Oxford University Press, Oxford (2003)"},{"key":"8_CR26","series-title":"Lecture Notes in Bioinformatics","volume-title":"Algorithms in Bioinformatics","author":"Y.S. Song","year":"2005","unstructured":"Song, Y.S., Wu, Y., Gusfield, D.: Haplotyping with one homoplasy or recombination event. In: Casadio, R., Myers, G. (eds.) WABI 2005. LNCS (LNBI), vol.\u00a03692, Springer, Heidelberg (2005)"},{"key":"8_CR27","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1007\/BF02618470","volume":"9","author":"M. Steel","year":"1992","unstructured":"Steel, M.: The complexity of reconstructing trees from qualitative characters and subtrees. J. of Classification\u00a09, 91\u2013116 (1992)","journal-title":"J. of Classification"},{"key":"8_CR28","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1086\/319501","volume":"68","author":"M. Stephens","year":"2001","unstructured":"Stephens, M., Smith, N., Donnelly, P.: A new statistical method for haplotype reconstruction from population data. Am. J. Human Genetics\u00a068, 978\u2013989 (2001)","journal-title":"Am. J. Human Genetics"},{"key":"8_CR29","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1534\/genetics.166.1.537","volume":"166","author":"C. Wiuf","year":"2004","unstructured":"Wiuf, C.: Inference of recombination and block structure using unphased data. Genetics\u00a0166, 537\u2013545 (2004)","journal-title":"Genetics"},{"key":"8_CR30","unstructured":"Wu, Y.: Personal Communication"},{"key":"8_CR31","doi-asserted-by":"crossref","unstructured":"Wu, Y., Gusfield, D.: Efficient computation of minimum recombination over genotypes (not haplotypes). In: Proceedings of Life Science Society Computational Systems Bioinformatics (CSB) 2006, pp. 145\u2013156 (2006)","DOI":"10.1142\/9781860947575_0021"}],"container-title":["Lecture Notes in Computer Science","Computing and Combinatorics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-73545-8_8.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,21]],"date-time":"2021-08-21T19:49:38Z","timestamp":1629575378000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-73545-8_8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540735441","9783540735458"],"references-count":31,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-73545-8_8","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[]}}