{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,7]],"date-time":"2024-06-07T00:09:04Z","timestamp":1717718944155},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation : Cell fate decisions have a strong stochastic component. The identification of the underlying mechanisms therefore requires a rigorous statistical analysis of large ensembles of single cells that were tracked and phenotyped over time.<\/jats:p><jats:p>Results : We introduce a probabilistic framework for testing elementary hypotheses on dynamic cell behavior using time-lapse cell-imaging data. Factor graphs, probabilistic graphical models, are used to properly account for cell lineage and cell phenotype information. Our model is applied to time-lapse movies of murine granulocyte-macrophage progenitor (GMP) cells. It decides between competing hypotheses on the mechanisms of their differentiation. Our results theoretically substantiate previous experimental observations that lineage instruction, not selection is the cause for the differentiation of GMP cells into mature monocytes or neutrophil granulocytes.<\/jats:p><jats:p>Availability and implementation : The Matlab source code is available at http:\/\/treschgroup.de\/Genealogies.html<\/jats:p><jats:p>Contact : failmezger@mpipz.mpg.de<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv040","type":"journal-article","created":{"date-parts":[[2015,2,1]],"date-time":"2015-02-01T01:28:41Z","timestamp":1422754121000},"page":"1816-1823","source":"Crossref","is-referenced-by-count":12,"title":["Factor graph analysis of live cell\u2013imaging data reveals mechanisms of cell fate decisions"],"prefix":"10.1093","volume":"31","author":[{"given":"Theresa","family":"Niederberger","sequence":"first","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henrik","family":"Failmezger","sequence":"additional","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diana","family":"Uskat","sequence":"additional","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Don","family":"Poron","sequence":"additional","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ingmar","family":"Glauche","sequence":"additional","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nico","family":"Scherf","sequence":"additional","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ingo","family":"Roeder","sequence":"additional","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timm","family":"Schroeder","sequence":"additional","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Achim","family":"Tresch","sequence":"additional","affiliation":[{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"},{"name":"1 Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University M\u00fcnchen, Germany, 2 Max-Planck-Institute for Plant Breeding Research, Cologne, Germany 3 Department of Biology, Albertus-Magnus University, Cologne, Germany, 4 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Germany, 5 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and 6 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,1,31]]},"reference":[{"key":"2023051505240545000_btv040-B1","volume-title":"Pattern Recognition and Machine Learning. Information Science and Statistics","author":"Bishop","year":"2006"},{"key":"2023051505240545000_btv040-B2","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1186\/1471-2105-14-297","article-title":"An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy","volume":"14","author":"Buggenthin","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023051505240545000_btv040-B3","doi-asserted-by":"crossref","first-page":"R100","DOI":"10.1186\/gb-2006-7-10-r100","article-title":"Cellprofiler: image analysis software for identifying and quantifying cell phenotypes","volume":"7","author":"Carpenter","year":"2006","journal-title":"Genome Biol."},{"key":"2023051505240545000_btv040-B4","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1109\/4234.905935","article-title":"On the design of low-density parity-check codes within 0.0045 db of the shannon limit","volume":"5","author":"Chung","year":"2001","journal-title":"Commun. Lett. IEEE"},{"key":"2023051505240545000_btv040-B5","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1083\/jcb.200910105","article-title":"Automated microscopy for high-content rnai screening","volume":"188","author":"Conrad","year":"2010","journal-title":"J. Cell Biol."},{"key":"2023051505240545000_btv040-B6","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/nmeth.1558","article-title":"Micropilot: automation of fluorescence microscopy-based imaging for systems biology","volume":"8","author":"Conrad","year":"2011","journal-title":"Nat. Methods"},{"key":"2023051505240545000_btv040-B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","article-title":"Maximum Likelihood from Incomplete Data via the EM Algorithm","volume":"39","author":"Dempster","year":"1977","journal-title":"J. R. Stat. Soc. B."},{"key":"2023051505240545000_btv040-B8","article-title":"Statistical Inference for Hidden Markov Tree Models and Application to Wavelet Trees","author":"Durand","year":"2001","journal-title":"[Research Report] RR-4248, 2001. &lt;inria-00072339&gt;"},{"key":"2023051505240545000_btv040-B9","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1111\/j.1469-8137.2005.01405.x","article-title":"Analysis of the plant architecture via tree-structured statistical models: the hidden markov tree models","volume":"166","author":"Durand","year":"2005","journal-title":"New Phytologist"},{"key":"2023051505240545000_btv040-B10","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.yexcr.2014.07.011","article-title":"Instruction of hematopoietic lineage choice by cytokine signaling","volume":"329","author":"Endele","year":"2014","journal-title":"Exp. Cell Res."},{"key":"2023051505240545000_btv040-B11","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1093\/bioinformatics\/btt179","article-title":"Learning gene network structure from time laps cell imaging in rnai knock downs","volume":"29","author":"Failmezger","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051505240545000_btv040-B12","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1186\/1471-2105-14-292","article-title":"Unsupervised automated high throughput phenotyping of rnai time-lapse movies","volume":"14","author":"Failmezger","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023051505240545000_btv040-B13","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/msb.2010.25","article-title":"Clustering phenotype populations by genome-wide rnai and multiparametric imaging","volume":"6","author":"Fuchs","year":"2010","journal-title":"Mol. Syst. Biol."},{"key":"2023051505240545000_btv040-B14","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1634\/stemcells.2007-0025","article-title":"Lineage specification of hematopoietic stem cells: mathematical modeling and biological implications","volume":"25","author":"Glauche","year":"2007","journal-title":"Stem Cells"},{"key":"2023051505240545000_btv040-B15","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1111\/j.1365-2184.2009.00586.x","article-title":"A novel view on stem cell development: analysing the shape of cellular genealogies","volume":"42","author":"Glauche","year":"2009","journal-title":"Cell Prolif."},{"key":"2023051505240545000_btv040-B16","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/nmeth.1486","article-title":"Cellcognition: time-resolved phenotype annotation in high-throughput live cell imaging","volume":"7","author":"Held","year":"2010","journal-title":"Nat. Methods"},{"key":"2023051505240545000_btv040-B17","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1126\/science.1213100","article-title":"Elastic domains regulate growth and organogenesis in the plant shoot apical meristem","volume":"335","author":"Kierzkowski","year":"2012","journal-title":"Science"},{"key":"2023051505240545000_btv040-B18","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1109\/18.910572","article-title":"Factor graphs and the sum-product algorithm","volume":"47","author":"Kschischang","year":"2001","journal-title":"Inform. Theory , IEEE Trans."},{"key":"2023051505240545000_btv040-B19","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1159\/000057688","article-title":"Tissue stem cells: definition, plasticity, heterogeneity, self-organization and models\u2013a conceptual approach","volume":"171","author":"Loeffler","year":"2002","journal-title":"Cells Tissues Organs"},{"key":"2023051505240545000_btv040-B20","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1128\/jb.142.3.808-818.1980","article-title":"Asymmetrical division of saccharomyces cerevisiae","volume":"142","author":"Lord","year":"1980","journal-title":"J. Bacteriol."},{"key":"2023051505240545000_btv040-B21","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/S0092-8674(00)81867-X","article-title":"Regulatory mechanisms in stem cell biology","volume":"88","author":"Morrison","year":"1997","journal-title":"Cell"},{"key":"2023051505240545000_btv040-B22","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/nmeth876","article-title":"High-throughput rnai screening by time-lapse imaging of live human cells","volume":"3","author":"Neumann","year":"2006","journal-title":"Nat. Methods"},{"key":"2023051505240545000_btv040-B23","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1038\/nature08869","article-title":"Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes","volume":"464","author":"Neumann","year":"2010","journal-title":"Nature"},{"key":"2023051505240545000_btv040-B24","doi-asserted-by":"crossref","first-page":"e1002568","DOI":"10.1371\/journal.pcbi.1002568","article-title":"Mc eminem maps the interaction landscape of the mediator","volume":"8","author":"Niederberger","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"2023051505240545000_btv040-B25","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1093\/bioinformatics\/btq046","article-title":"Ebimage-an r package for image processing with applications to cellular phenotypes","volume":"26","author":"Pau","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051505240545000_btv040-B26","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/nmeth.2097","article-title":"Phenoripper: software for rapidly profiling microscopy images","volume":"9","author":"Rajaram","year":"2012","journal-title":"Nat. Methods"},{"key":"2023051505240545000_btv040-B27","doi-asserted-by":"crossref","first-page":"4019","DOI":"10.4161\/cc.8.24.10261","article-title":"Instruction of lineage choice by hematopoietic cytokines","volume":"8","author":"Rieger","year":"2009","journal-title":"Cell Cycle"},{"key":"2023051505240545000_btv040-B28","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1126\/science.1171461","article-title":"Hematopoietic cytokines can instruct lineage choice","volume":"325","author":"Rieger","year":"2009","journal-title":"Science"},{"key":"2023051505240545000_btv040-B29","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/S0301-472X(02)00832-9","article-title":"A novel dynamic model of hematopoietic stem cell organization based on the concept of within-tissue plasticity","volume":"30","author":"Roeder","year":"2002","journal-title":"Exp. Hematol."},{"key":"2023051505240545000_btv040-B30","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1016\/j.smim.2011.08.011","article-title":"Integration of cytokine and transcription factor signals in hematopoietic stem cell commitment","volume":"23","author":"Sarrazin","year":"2011","journal-title":"Semin. Immunol ."},{"key":"2023051505240545000_btv040-B31","doi-asserted-by":"crossref","first-page":"i556","DOI":"10.1093\/bioinformatics\/bts404","article-title":"Imaging, quantification and visualization of spatio-temporal patterning in mesc colonies under different culture conditions","volume":"28","author":"Scherf","year":"2012","journal-title":"Bioinformatics"},{"key":"2023051505240545000_btv040-B32","doi-asserted-by":"crossref","first-page":"2207","DOI":"10.1038\/ncomms3207","article-title":"High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics","volume":"4","author":"Schmid","year":"2013","journal-title":"Nat. Commun."},{"key":"2023051505240545000_btv040-B33","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/nature08282","article-title":"Population context determines cell-to-cell variability in endocytosis and virus infection","volume":"461","author":"Snijder","year":"2009","journal-title":"Nature"},{"key":"2023051505240545000_btv040-B34","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1038\/sj.bjp.0707346","article-title":"The potential of high-content high-throughput microscopy in drug discovery","volume":"152","author":"Starkuviene","year":"2007","journal-title":"Br. J. Pharmacol."},{"key":"2023051505240545000_btv040-B35","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1109\/TIT.1981.1056404","article-title":"A recursive approach to low complexity codes","volume":"27","author":"Tanner","year":"2006","journal-title":"IEEE Trans. Inf. Theor."},{"key":"2023051505240545000_btv040-B36","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/nmeth.2046","article-title":"Unsupervised modeling of cell morphology dynamics for time-lapse microscopy","volume":"9","author":"Zhong","year":"2012","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/11\/1816\/50314331\/bioinformatics_31_11_1816.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/11\/1816\/50314331\/bioinformatics_31_11_1816.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T23:12:00Z","timestamp":1717715520000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/11\/1816\/2365018"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,31]]},"references-count":36,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2015,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv040","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,6,1]]},"published":{"date-parts":[[2015,1,31]]}}}