[{"date_published":"2020-10-19T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["15461718"],"issn":["10614036"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Nature Genetics","oa_version":"None","month":"10","language":[{"iso":"eng"}],"date_updated":"2023-08-22T10:37:10Z","citation":{"chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” <i>Nature Genetics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41588-020-00712-y\">https://doi.org/10.1038/s41588-020-00712-y</a>.","ieee":"S.  Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” <i>Nature Genetics</i>, vol. 52. Springer Nature, pp. 1247–1255, 2020.","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., &#38; Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-020-00712-y\">https://doi.org/10.1038/s41588-020-00712-y</a>","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. <i>Nature Genetics</i>. 2020;52:1247-1255. doi:<a href=\"https://doi.org/10.1038/s41588-020-00712-y\">10.1038/s41588-020-00712-y</a>","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","short":"S.  Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” <i>Nature Genetics</i>, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:<a href=\"https://doi.org/10.1038/s41588-020-00712-y\">10.1038/s41588-020-00712-y</a>."},"year":"2020","isi":1,"external_id":{"isi":["000579693500004"],"pmid":["33077914"]},"doi":"10.1038/s41588-020-00712-y","day":"19","abstract":[{"lang":"eng","text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data."}],"volume":52,"acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","_id":"8707","pmid":1,"scopus_import":"1","author":[{"full_name":" Galan, Silvia","last_name":" Galan","first_name":"Silvia"},{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","last_name":"Machnik","first_name":"Nick N","full_name":"Machnik, Nick N","orcid":"0000-0001-6617-9742"},{"full_name":"Kruse, Kai","first_name":"Kai","last_name":"Kruse"},{"last_name":"Díaz","first_name":"Noelia","full_name":"Díaz, Noelia"},{"full_name":"Marti-Renom, Marc A","last_name":"Marti-Renom","first_name":"Marc A"},{"full_name":"Vaquerizas, Juan M","first_name":"Juan M","last_name":"Vaquerizas"}],"publication_status":"published","department":[{"_id":"FyKo"}],"date_created":"2020-10-25T23:01:20Z","article_processing_charge":"No","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","intvolume":"        52","page":"1247-1255","quality_controlled":"1","publisher":"Springer Nature","article_type":"original"},{"quality_controlled":"1","ec_funded":1,"page":"358 - 366","file_date_updated":"2020-07-14T12:47:33Z","publisher":"Nature Publishing Group","article_type":"original","scopus_import":"1","pmid":1,"_id":"653","issue":"3","author":[{"full_name":"Makohon Moore, Alvin","first_name":"Alvin","last_name":"Makohon Moore"},{"full_name":"Zhang, Ming","last_name":"Zhang","first_name":"Ming"},{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"first_name":"Benjamin","last_name":"Allen","full_name":"Allen, Benjamin"},{"last_name":"Kundu","first_name":"Deepanjan","full_name":"Kundu, Deepanjan","id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wong","first_name":"Fay","full_name":"Wong, Fay"},{"last_name":"Jiao","first_name":"Yuchen","full_name":"Jiao, Yuchen"},{"full_name":"Kohutek, Zachary","last_name":"Kohutek","first_name":"Zachary"},{"full_name":"Hong, Jungeui","first_name":"Jungeui","last_name":"Hong"},{"full_name":"Attiyeh, Marc","last_name":"Attiyeh","first_name":"Marc"},{"last_name":"Javier","first_name":"Breanna","full_name":"Javier, Breanna"},{"last_name":"Wood","first_name":"Laura","full_name":"Wood, Laura"},{"first_name":"Ralph","last_name":"Hruban","full_name":"Hruban, Ralph"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"full_name":"Papadopoulos, Nickolas","last_name":"Papadopoulos","first_name":"Nickolas"},{"full_name":"Kinzler, Kenneth","first_name":"Kenneth","last_name":"Kinzler"},{"last_name":"Vogelstein","first_name":"Bert","full_name":"Vogelstein, Bert"},{"full_name":"Iacobuzio Donahue, Christine","first_name":"Christine","last_name":"Iacobuzio Donahue"}],"article_processing_charge":"No","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:47:43Z","publication_status":"published","intvolume":"        49","title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","acknowledgement":"We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).","volume":49,"ddc":["000"],"citation":{"short":"A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366.","mla":"Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” <i>Nature Genetics</i>, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:<a href=\"https://doi.org/10.1038/ng.3764\">10.1038/ng.3764</a>.","ista":"Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366.","apa":"Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng.3764\">https://doi.org/10.1038/ng.3764</a>","ama":"Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. <i>Nature Genetics</i>. 2017;49(3):358-366. doi:<a href=\"https://doi.org/10.1038/ng.3764\">10.1038/ng.3764</a>","chicago":"Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” <i>Nature Genetics</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ng.3764\">https://doi.org/10.1038/ng.3764</a>.","ieee":"A. Makohon Moore <i>et al.</i>, “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” <i>Nature Genetics</i>, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017."},"year":"2017","date_updated":"2022-06-10T09:55:08Z","external_id":{"pmid":["28092682"]},"day":"01","doi":"10.1038/ng.3764","abstract":[{"lang":"eng","text":"The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease."}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Nature Genetics","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"}],"oa_version":"Submitted Version","month":"03","file":[{"creator":"dernst","file_id":"7050","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2017_NatureGenetics_Makohon.pdf","date_updated":"2020-07-14T12:47:33Z","checksum":"e442dc3b7420a36ec805e9bb45cc1a2e","file_size":908099,"date_created":"2019-11-19T08:13:50Z"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_published":"2017-03-01T00:00:00Z","publication_identifier":{"issn":["10614036"]},"publist_id":"7092","oa":1}]