{"id":5061,"global_id":"www.ibs.re.kr\/bimag?id=5061","global_id_lineage":["www.ibs.re.kr\/bimag?id=5061"],"author":"3","status":"publish","date":"2021-10-22 04:00:00","date_utc":"2021-09-30 07:36:41","modified":"2021-10-01 15:25:13","modified_utc":"2021-10-01 06:25:13","url":"https:\/\/www.ibs.re.kr\/bimag\/event\/2021-10-22-2\/","rest_url":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/tribe\/events\/v1\/events\/5061","title":"Filtering and inference for stochastic oscillators with distributed delays","description":"

We will discuss about \u201cFiltering and inference for stochastic oscillators with distributed delays\u201d, Calderazzo et al., Bioinformatics<\/i>, 2018 at the Journal Club<\/p>\n

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Motivation<\/div>\n

The time evolution of molecular species involved in biochemical reaction networks often arises from complex stochastic processes involving many species and reaction events. Inference for such systems is profoundly challenged by the relative sparseness of experimental data, as measurements are often limited to a small subset of the participating species measured at discrete time points. The need for model reduction can be realistically achieved for oscillatory dynamics resulting from negative translational and transcriptional feedback loops by the introduction of probabilistic time-delays. Although this approach yields a simplified model, inference is challenging and subject to ongoing research. The linear noise approximation (LNA) has recently been proposed to address such systems in stochastic form and will be exploited here.<\/p>\n<\/div>\n

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Results<\/div>\n

We develop a novel filtering approach for the LNA in stochastic systems with distributed delays, which allows the parameter values and unobserved states of a stochastic negative feedback model to be inferred from univariate time-series data. The performance of the methods is tested for simulated data. Results are obtained for real data when the model is fitted to imaging data on Cry<\/em>1, a key gene involved in the mammalian central circadian clock, observed via a luciferase reporter construct in a mouse suprachiasmatic nucleus.<\/p>\n<\/div>\n

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Availability and implementation<\/div>\n

Programmes are written in MATLAB and Statistics Toolbox Release 2016\u2009b, The MathWorks, Inc., Natick, Massachusetts, USA. Sample code and Cry<\/em>1 data are available on GitHub https:\/\/github.com\/scalderazzo\/FLNADD<\/a>.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/section>","excerpt":"","slug":"2021-10-22-2","image":false,"all_day":false,"start_date":"2021-10-22 13:00:00","start_date_details":{"year":"2021","month":"10","day":"22","hour":"13","minutes":"00","seconds":"00"},"end_date":"2021-10-22 14:00:00","end_date_details":{"year":"2021","month":"10","day":"22","hour":"14","minutes":"00","seconds":"00"},"utc_start_date":"2021-10-22 04:00:00","utc_start_date_details":{"year":"2021","month":"10","day":"22","hour":"04","minutes":"00","seconds":"00"},"utc_end_date":"2021-10-22 05:00:00","utc_end_date_details":{"year":"2021","month":"10","day":"22","hour":"05","minutes":"00","seconds":"00"},"timezone":"Asia\/Seoul","timezone_abbr":"KST","cost":"","cost_details":{"currency_symbol":"","currency_code":"","currency_position":"prefix","values":[]},"website":"","show_map":false,"show_map_link":false,"hide_from_listings":false,"sticky":false,"featured":false,"categories":[{"name":"Journal Club","slug":"journal-club","term_group":0,"term_taxonomy_id":219,"taxonomy":"tribe_events_cat","description":"","parent":231,"count":209,"filter":"raw","id":219,"urls":{"self":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/tribe\/events\/v1\/categories\/219","collection":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/tribe\/events\/v1\/categories","up":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/tribe\/events\/v1\/categories\/231"}}],"tags":[],"venue":{"id":5070,"author":"3","status":"publish","date":"2021-10-01 15:24:54","date_utc":"2021-10-01 06:24:54","modified":"2021-10-01 15:24:54","modified_utc":"2021-10-01 06:24:54","url":"https:\/\/www.ibs.re.kr\/bimag\/venue\/b378-seminar-room-ibs\/","venue":"B378 Seminar room, IBS","slug":"b378-seminar-room-ibs","address":"55 Expo-ro Yuseong-gu","city":"Daejeon","country":"Korea, Republic of","zip":"34126","json_ld":{"@type":"Place","name":"B378 Seminar room, IBS","description":"","url":"","address":{"@type":"PostalAddress","streetAddress":"55 Expo-ro Yuseong-gu","addressLocality":"Daejeon","postalCode":"34126","addressCountry":"Korea, Republic of"},"telephone":"","sameAs":""},"show_map":true,"show_map_link":true,"global_id":"www.ibs.re.kr\/bimag?id=5070","global_id_lineage":["www.ibs.re.kr\/bimag?id=5070"]},"organizer":[{"id":3971,"author":"3","status":"publish","date":"2021-02-23 18:10:12","date_utc":"2021-02-23 09:10:12","modified":"2021-02-23 18:10:12","modified_utc":"2021-02-23 09:10:12","url":"https:\/\/www.ibs.re.kr\/bimag\/organizer\/jae-kyoung-kim\/","organizer":"Jae Kyoung Kim","slug":"jae-kyoung-kim","email":"jaekkim@kaist.ac.kr","json_ld":{"@type":"Person","name":"Jae Kyoung Kim","description":"","url":"","telephone":"","email":"jaekkim@kaist.ac.kr","sameAs":""},"global_id":"www.ibs.re.kr\/bimag?id=3971","global_id_lineage":["www.ibs.re.kr\/bimag?id=3971"]}],"custom_fields":[],"json_ld":{"@context":"http:\/\/schema.org","@type":"Event","name":"Filtering and inference for stochastic oscillators with distributed delays","description":"<p>We will discuss about \u201cFiltering and inference for stochastic oscillators with distributed delays\u201d, Calderazzo et al., Bioinformatics, 2018 at the Journal Club Motivation The time evolution of molecular species involved … <\/p>\\n<p class="link-more"><a href="https:\/\/www.ibs.re.kr\/bimag\/event\/2021-10-22-2\/" class="more-link">Continue reading<span class="screen-reader-text"> "Filtering and inference for stochastic oscillators with distributed delays"<\/span><\/a><\/p>\\n","url":"https:\/\/www.ibs.re.kr\/bimag\/event\/2021-10-22-2\/","eventAttendanceMode":"https:\/\/schema.org\/OfflineEventAttendanceMode","eventStatus":"https:\/\/schema.org\/EventScheduled","startDate":"2021-10-22T13:00:00+09:00","endDate":"2021-10-22T14:00:00+09:00","location":{"@type":"Place","name":"B378 Seminar room, IBS","description":"","url":"","address":{"@type":"PostalAddress","streetAddress":"55 Expo-ro Yuseong-gu","addressLocality":"Daejeon","postalCode":"34126","addressCountry":"Korea, Republic of"},"telephone":"","sameAs":""},"organizer":{"@type":"Person","name":"Jae Kyoung Kim","description":"","url":"","telephone":"","email":"jaekkim@kaist.ac.kr","sameAs":""},"performer":"Organization"}}