{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/45869"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/45869","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"A novel computational method for inferring dynamic genetic regulatory trajectories","abstract":"We present a novel method called Time Series Affinity Propagation (TSAP) for inferring regulatory states and trajectories from time series genomic data. This method builds on the Affinity Propagation method of Frey and Dueck [10]. TSAP incorporates temporal constraints to more accurately model the dynamic nature of underlying biological mechanisms. We first apply TSAP to synthetic data and demonstrate its ability to recover underlying structure that is obscured by noise. We then apply TSAP to real data and demonstrate that it provides insight into the relationship between gene expression and histone posttranslational modifications during motor neuron development. In particular, the trajectories taken by the Hox genes through the space of regulatory states are characterized. Understanding the dynamics of Hox regulation is important because the Hox genes play a fundamental role in the establishment of motor neuron sub-type identity during development [6].","abstract_html":"We present a novel method called Time Series Affinity Propagation (TSAP) for inferring regulatory states and trajectories from time series genomic data. This method builds on the Affinity Propagation method of Frey and Dueck [10]. TSAP incorporates temporal constraints to more accurately model the dynamic nature of underlying biological mechanisms. We first apply TSAP to synthetic data and demonstrate its ability to recover underlying structure that is obscured by noise. We then apply TSAP to real data and demonstrate that it provides insight into the relationship between gene expression and histone posttranslational modifications during motor neuron development. In particular, the trajectories taken by the Hox genes through the space of regulatory states are characterized. Understanding the dynamics of Hox regulation is important because the Hox genes play a fundamental role in the establishment of motor neuron sub-type identity during development [6].","abstract_has_math":false,"creators":["Reeder, Christopher Campbell"],"institution":"Massachusetts Institute of Technology","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.","school":null,"contributors":[],"advisors":["David K. Gifford."],"committee_chairs":[],"committee_members":[],"year":2008,"date_issued":"2008","date_published":"2008","updated_at":"2026-07-22T22:21:50Z","subjects":["Electrical Engineering and Computer Science."],"languages":["eng"],"rights":["M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."],"rights_urls":["http://dspace.mit.edu/handle/1721.1/7582"],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/1721.1/45869","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["David K. Gifford."]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. 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They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://dspace.mit.edu/handle/1721.1/7582"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/1721.1/45869"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.","Includes bibliographical references (p. 75-77)."]},{"key":"dc:description.abstract","label":"Abstract","values":["We present a novel method called Time Series Affinity Propagation (TSAP) for inferring regulatory states and trajectories from time series genomic data. This method builds on the Affinity Propagation method of Frey and Dueck [10]. TSAP incorporates temporal constraints to more accurately model the dynamic nature of underlying biological mechanisms. We first apply TSAP to synthetic data and demonstrate its ability to recover underlying structure that is obscured by noise. We then apply TSAP to real data and demonstrate that it provides insight into the relationship between gene expression and histone posttranslational modifications during motor neuron development. In particular, the trajectories taken by the Hox genes through the space of regulatory states are characterized. Understanding the dynamics of Hox regulation is important because the Hox genes play a fundamental role in the establishment of motor neuron sub-type identity during development [6]."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["S.M."]},{"key":"dc:title","label":"Title","values":["A novel computational method for inferring dynamic genetic regulatory trajectories"]}]}],"canonical_facts":{"dc:contributor.advisor":["David K. Gifford."],"dc:contributor.department":["Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science."],"dc:contributor.other":["Massachusetts Institute of Technology. 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We then apply TSAP to real data and demonstrate that it provides insight into the relationship between gene expression and histone posttranslational modifications during motor neuron development. In particular, the trajectories taken by the Hox genes through the space of regulatory states are characterized. Understanding the dynamics of Hox regulation is important because the Hox genes play a fundamental role in the establishment of motor neuron sub-type identity during development [6]."],"dc:description.degree":["S.M."],"dc:identifier.uri":["http://hdl.handle.net/1721.1/45869"],"dc:language.iso":["eng"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."],"dc:rights.uri":["http://dspace.mit.edu/handle/1721.1/7582"],"dc:subject":["Electrical Engineering and Computer Science."],"dc:title":["A novel computational method for inferring dynamic genetic regulatory trajectories"],"dc:type":["Thesis"]},"updated_at":"2026-07-22T22:21:50Z"}