{"610675":{"#nid":"610675","#data":{"type":"event","title":" Annotating the \u0027Dark Matter\u0027 of Bacterial Genomes Using Hybrid Experimental\/Computational Approaches","body":[{"value":"\u003Cp\u003E\u003Cstrong\u003EPeter Freddolino, \u003C\/strong\u003E\u003Cstrong\u003EPh.D\u003C\/strong\u003E\u003Cstrong\u003E.\u003Cbr \/\u003E\r\nDepartment of Biological Chemistry\u003Cbr \/\u003E\r\nDepartment of Computational Medicine and Bioinformatics\u003Cbr \/\u003E\r\nUniversity of Michigan\u003C\/strong\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003EAbstract\u003C\/strong\u003E\u003Cbr \/\u003E\r\nRecent advances in high-throughput sequencing technology have yielded a huge increase in our knowledge of genomic sequences, but DNA sequence\u0026nbsp;information remains meaningless without corresponding functional insight. It is only through a synthesis of computational approaches and high-throughput experiments that any meaningful headway can be made in the task of moving from genome sequence information to functional information at\u0026nbsp;the scales of modern biology.We have recently launched two such initiatives, aimed at completely mapping the transcriptional regulatory logic and\u0026nbsp;functional proteome of\u0026nbsp;Escherichia coli. Using a broadly applicable non-specific method for mapping genome-wide protein occupancy, we have begun to\u0026nbsp;identify the binding motifs, functions, and condition-dependent behavior of many cryptic\u0026nbsp;E. coli\u0026nbsp;transcription factors. In the process, we have also\u0026nbsp;identified the presence of heterochromatin-like silenced regions on bacterial chromosomes, which we have found play a key role in regulating stress-response and virulence genes across several bacterial species. To address the problem of assigning functions to poorly annotated proteins without\u0026nbsp;suitably close homologs for sequence-based annotation methods to be effective, we have recently developed a hybrid pipeline combining structural\u0026nbsp;prediction\/alignment, sequence alignment, and protein-protein interaction information to obtain combined structure predictions and functional annotations\u0026nbsp;for entire proteomes. We find that our inclusion of structural information makes our workflow unusually strong in performance on difficult targets with\u0026nbsp;limited sequence identity to annotated proteins. Application of our methods at the scale of entire proteomes yields a rich\u0026nbsp;new source of information to seed\u0026nbsp;detailed investigation of the functions of many previously mysterious protein-coding genes.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Ca href=\u0022http:\/\/freddolino-lab.med.umich.edu\/\u0022\u003EMore about the Freddolino Lab\u003C\/a\u003E\u003C\/p\u003E\r\n","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":"","field_summary_sentence":[{"value":"A Biological Sciences Seminar by Peter Freddolino, Ph.D."}],"uid":"27964","created_gmt":"2018-08-30 20:44:32","changed_gmt":"2018-08-30 20:44:32","author":"Jasmine Martin","boilerplate_text":"","field_publication":"","field_article_url":"","field_event_time":{"event_time_start":"2018-10-18T11:55:00-04:00","event_time_end":"2018-10-18T11:55:00-04:00","event_time_end_last":"2018-10-18T11:55:00-04:00","gmt_time_start":"2018-10-18 15:55:00","gmt_time_end":"2018-10-18 15:55:00","gmt_time_end_last":"2018-10-18 15:55:00","rrule":null,"timezone":"America\/New_York"},"extras":[],"groups":[{"id":"1275","name":"School of Biological Sciences"}],"categories":[],"keywords":[{"id":"178908","name":"Peter Freddolino"},{"id":"178909","name":"James Gumbart"},{"id":"166882","name":"School of Biological Sciences"},{"id":"166892","name":"School of Biological Sciences Seminar"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[{"id":"1795","name":"Seminar\/Lecture\/Colloquium"}],"invited_audience":[{"id":"78761","name":"Faculty\/Staff"},{"id":"177814","name":"Postdoc"},{"id":"78771","name":"Public"},{"id":"174045","name":"Graduate students"},{"id":"78751","name":"Undergraduate students"}],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003E\u003Ca href=\u0022mailto:jasmine.martin@biosci.gatech.edu\u0022\u003EJasmine Martin\u003C\/a\u003E\u003C\/p\u003E\r\n","format":"limited_html"}],"email":[],"slides":[],"orientation":[],"userdata":""}}}