{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/104916"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/104916","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Towards characterizing the solution space of the 1-Dollo Phylogeny problem","abstract":"Cancer cells may mutate multiple times, from a normal state to a mutated state and vice versa. Given our sequenced data, we can model the mutation process with a phylogenetic tree. One representative model is the k-Dollo parsimony, where all observed mutations mutate from a single normal cell and each character of a cell is gained at most once and lost at most k times. We examine the 1-Dollo Phylogeny problem, does a 1-Dollo phylogeny, a tree that follows the 1-Dollo parsimony model, exist for the observations. Current algorithms to solve the 1-Dollo Phylogeny problem only tell us whether or not a set of observations has a 1-Dollo phylogeny by outputting a single solution. We explore the structure of 1-Dollo phylogenies and use our idea of a skeleton to develop an algorithm that enumerates all 1-Dollo phylogenies for any set of observations. This algorithm runs much faster than the naive brute force enumeration algorithm for random input. The implementation is here: https://github.com/sxie12/skeleton_solver.","abstract_html":"Cancer cells may mutate multiple times, from a normal state to a mutated state and vice versa. Given our sequenced data, we can model the mutation process with a phylogenetic tree. One representative model is the k-Dollo parsimony, where all observed mutations mutate from a single normal cell and each character of a cell is gained at most once and lost at most k times. We examine the 1-Dollo Phylogeny problem, does a 1-Dollo phylogeny, a tree that follows the 1-Dollo parsimony model, exist for the observations. Current algorithms to solve the 1-Dollo Phylogeny problem only tell us whether or not a set of observations has a 1-Dollo phylogeny by outputting a single solution. We explore the structure of 1-Dollo phylogenies and use our idea of a skeleton to develop an algorithm that enumerates all 1-Dollo phylogenies for any set of observations. This algorithm runs much faster than the naive brute force enumeration algorithm for random input. The implementation is here: https://github.com/sxie12/skeleton_solver.","abstract_has_math":false,"creators":["Xie, Shunping"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Computer Science","degree_department":null,"school":null,"contributors":["El-Kebir, Mohammed"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-08-23T20:01:16Z","date_published":"2019-08-23T20:01:16Z","updated_at":"2026-07-22T22:24:42Z","subjects":["1-Dollo phylogeny","Skeleton","Enumeration algorithm"],"languages":["en"],"rights":["Copyright 2019 Shunping Xie"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/104916","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["El-Kebir, Mohammed"]},{"key":"dc:creator","label":"Author","values":["Xie, Shunping"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2019-08-23T20:01:16Z","2019-04-25","2019-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Computer Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["1-Dollo phylogeny","Skeleton","Enumeration algorithm"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2019 Shunping Xie"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/104916"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Cancer cells may mutate multiple times, from a normal state to a mutated state and vice versa. Given our sequenced data, we can model the mutation process with a phylogenetic tree. One representative model is the k-Dollo parsimony, where all observed mutations mutate from a single normal cell and each character of a cell is gained at most once and lost at most k times. We examine the 1-Dollo Phylogeny problem, does a 1-Dollo phylogeny, a tree that follows the 1-Dollo parsimony model, exist for the observations. Current algorithms to solve the 1-Dollo Phylogeny problem only tell us whether or not a set of observations has a 1-Dollo phylogeny by outputting a single solution. We explore the structure of 1-Dollo phylogenies and use our idea of a skeleton to develop an algorithm that enumerates all 1-Dollo phylogenies for any set of observations. This algorithm runs much faster than the naive brute force enumeration algorithm for random input. The implementation is here: https://github.com/sxie12/skeleton_solver.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2019-08-22 without embargo terms","The student, Shunping Xie, accepted the attached license on 2019-04-24 at 15:15.","The student, Shunping Xie, submitted this Thesis for approval on 2019-04-24 at 15:17.","This Thesis was approved for publication on 2019-04-25 at 07:39.","DSpace SAF Submission Ingestion Package generated from Vireo submission #13858 on 2019-08-22 at 14:46:21","Made available in DSpace on 2019-08-23T20:01:16Z (GMT). No. of bitstreams: 2 XIE-THESIS-2019.pdf: 256136 bytes, checksum: d73d3f572be5eb7ed12c98e587f914c3 (MD5) LICENSE.txt: 4209 bytes, checksum: 9b3adbf48f426e8d4bb726d4c71f9722 (MD5) Previous issue date: 2019-04-25"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Towards characterizing the solution space of the 1-Dollo Phylogeny problem"]}]}],"canonical_facts":{"dc:contributor":["El-Kebir, Mohammed"],"dc:creator":["Xie, Shunping"],"dc:date":["2019-08-23T20:01:16Z","2019-04-25","2019-05"],"dc:description":["Cancer cells may mutate multiple times, from a normal state to a mutated state and vice versa. Given our sequenced data, we can model the mutation process with a phylogenetic tree. One representative model is the k-Dollo parsimony, where all observed mutations mutate from a single normal cell and each character of a cell is gained at most once and lost at most k times. We examine the 1-Dollo Phylogeny problem, does a 1-Dollo phylogeny, a tree that follows the 1-Dollo parsimony model, exist for the observations. Current algorithms to solve the 1-Dollo Phylogeny problem only tell us whether or not a set of observations has a 1-Dollo phylogeny by outputting a single solution. We explore the structure of 1-Dollo phylogenies and use our idea of a skeleton to develop an algorithm that enumerates all 1-Dollo phylogenies for any set of observations. This algorithm runs much faster than the naive brute force enumeration algorithm for random input. The implementation is here: https://github.com/sxie12/skeleton_solver.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2019-08-22 without embargo terms","The student, Shunping Xie, accepted the attached license on 2019-04-24 at 15:15.","The student, Shunping Xie, submitted this Thesis for approval on 2019-04-24 at 15:17.","This Thesis was approved for publication on 2019-04-25 at 07:39.","DSpace SAF Submission Ingestion Package generated from Vireo submission #13858 on 2019-08-22 at 14:46:21","Made available in DSpace on 2019-08-23T20:01:16Z (GMT). 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