[{"type":"conference","article_number":"9158054","abstract":[{"text":"We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients.","lang":"eng"}],"publisher":"IEEE","department":[{"_id":"HeEd"}],"status":"public","title":"The application of persistent homology in the analysis of heart rate variability","publication_status":"published","_id":"8580","year":"2020","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","date_created":"2020-09-28T08:59:27Z","date_updated":"2023-08-22T09:33:34Z","author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"full_name":"Graff, Beata","first_name":"Beata","last_name":"Graff"},{"first_name":"Grzegorz","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz"},{"full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz","first_name":"Krzysztof"}],"scopus_import":"1","publication_identifier":{"isbn":["9781728157511"]},"article_processing_charge":"No","month":"08","day":"01","isi":1,"quality_controlled":"1","citation":{"chicago":"Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE, 2020. https://doi.org/10.1109/ESGCO49734.2020.9158054.","mla":"Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , 9158054, IEEE, 2020, doi:10.1109/ESGCO49734.2020.9158054.","short":"G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , IEEE, 2020.","ista":"Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent homology in the analysis of heart rate variability. 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular Oscillations, 9158054.","ieee":"G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of persistent homology in the analysis of heart rate variability,” in 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , Pisa, Italy, 2020.","apa":"Graff, G., Graff, B., Jablonski, G., & Narkiewicz, K. (2020). The application of persistent homology in the analysis of heart rate variability. In 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . Pisa, Italy: IEEE. https://doi.org/10.1109/ESGCO49734.2020.9158054","ama":"Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent homology in the analysis of heart rate variability. In: 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . IEEE; 2020. doi:10.1109/ESGCO49734.2020.9158054"},"external_id":{"isi":["000621172600045"]},"publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","language":[{"iso":"eng"}],"date_published":"2020-08-01T00:00:00Z","doi":"10.1109/ESGCO49734.2020.9158054","conference":{"start_date":"2020-07-15","location":"Pisa, Italy","end_date":"2020-07-15","name":"ESGCO: European Study Group on Cardiovascular Oscillations"}},{"type":"journal_article","abstract":[{"text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.","lang":"eng"}],"issue":"21","_id":"8592","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","intvolume":" 7","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":7835833,"creator":"dernst","file_name":"2020_AdvScience_Tian.pdf","access_level":"open_access","date_updated":"2020-12-10T14:07:24Z","date_created":"2020-12-10T14:07:24Z","checksum":"92818c23ecc70e35acfa671f3cfb9909","success":1,"relation":"main_file","file_id":"8938"}],"keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"day":"04","article_processing_charge":"No","has_accepted_license":"1","publication":"Advanced Science","citation":{"short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020).","mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724.","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724.","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724","apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. Wiley. https://doi.org/10.1002/advs.202001724","ieee":"A. Tian et al., “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020.","ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724."},"article_type":"original","date_published":"2020-11-04T00:00:00Z","article_number":"2001724","file_date_updated":"2020-12-10T14:07:24Z","ec_funded":1,"acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","year":"2020","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Wiley","author":[{"first_name":"Anhao","last_name":"Tian","full_name":"Tian, Anhao"},{"full_name":"Kang, Bo","first_name":"Bo","last_name":"Kang"},{"full_name":"Li, Baizhou","last_name":"Li","first_name":"Baizhou"},{"last_name":"Qiu","first_name":"Biying","full_name":"Qiu, Biying"},{"full_name":"Jiang, Wenhong","last_name":"Jiang","first_name":"Wenhong"},{"first_name":"Fangjie","last_name":"Shao","full_name":"Shao, Fangjie"},{"last_name":"Gao","first_name":"Qingqing","full_name":"Gao, Qingqing"},{"full_name":"Liu, Rui","last_name":"Liu","first_name":"Rui"},{"first_name":"Chengwei","last_name":"Cai","full_name":"Cai, Chengwei"},{"full_name":"Jing, Rui","last_name":"Jing","first_name":"Rui"},{"full_name":"Wang, Wei","first_name":"Wei","last_name":"Wang"},{"full_name":"Chen, Pengxiang","last_name":"Chen","first_name":"Pengxiang"},{"first_name":"Qinghui","last_name":"Liang","full_name":"Liang, Qinghui"},{"first_name":"Lili","last_name":"Bao","full_name":"Bao, Lili"},{"full_name":"Man, Jianghong","last_name":"Man","first_name":"Jianghong"},{"full_name":"Wang, Yan","first_name":"Yan","last_name":"Wang"},{"full_name":"Shi, Yu","first_name":"Yu","last_name":"Shi"},{"first_name":"Jin","last_name":"Li","full_name":"Li, Jin"},{"full_name":"Yang, Minmin","first_name":"Minmin","last_name":"Yang"},{"first_name":"Lisha","last_name":"Wang","full_name":"Wang, Lisha"},{"full_name":"Zhang, Jianmin","first_name":"Jianmin","last_name":"Zhang"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"first_name":"Junming","last_name":"Zhu","full_name":"Zhu, Junming"},{"last_name":"Bian","first_name":"Xiuwu","full_name":"Bian, Xiuwu"},{"full_name":"Wang, Ying‐Jie","first_name":"Ying‐Jie","last_name":"Wang"},{"full_name":"Liu, Chong","first_name":"Chong","last_name":"Liu"}],"date_created":"2020-10-01T09:44:13Z","date_updated":"2023-08-22T09:53:01Z","volume":7,"month":"11","publication_identifier":{"issn":["2198-3844"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000573860700001"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"doi":"10.1002/advs.202001724","language":[{"iso":"eng"}]},{"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000573756600004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-18610-6","publication_identifier":{"issn":["2041-1723"]},"month":"09","department":[{"_id":"StFr"}],"publisher":"Springer Nature","publication_status":"published","year":"2020","volume":11,"date_updated":"2023-08-22T09:37:24Z","date_created":"2020-09-25T07:23:13Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-19720-x","relation":"erratum"}]},"author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Fitzek, Harald","last_name":"Fitzek","first_name":"Harald"},{"full_name":"Kothleitner, Gerald","first_name":"Gerald","last_name":"Kothleitner"},{"first_name":"Volker","last_name":"Presser","full_name":"Presser, Volker"},{"full_name":"Gollas, Bernhard","last_name":"Gollas","first_name":"Bernhard"},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Abbas, Qamar","last_name":"Abbas","first_name":"Qamar"}],"article_number":"4838","file_date_updated":"2020-09-28T13:16:15Z","article_type":"original","citation":{"ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 2020;11. doi:10.1038/s41467-020-18610-6","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6","ieee":"C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020.","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer Nature, 2020, doi:10.1038/s41467-020-18610-6.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6."},"publication":"Nature Communications","date_published":"2020-09-24T00:00:00Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","article_processing_charge":"No","day":"24","intvolume":" 11","ddc":["530"],"status":"public","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","_id":"8568","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2020-09-28T13:16:15Z","date_updated":"2020-09-28T13:16:15Z","checksum":"eada7bc8dd16a49390137cff882ef328","success":1,"relation":"main_file","file_id":"8585","content_type":"application/pdf","file_size":1822469,"creator":"dernst","file_name":"2020_NatureComm_Prehal.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors."}],"intvolume":" 10","title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","status":"public","ddc":["570"],"_id":"8643","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"8651","checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","success":1,"date_created":"2020-10-12T12:39:10Z","date_updated":"2020-10-12T12:39:10Z","access_level":"open_access","file_name":"2020_ScientificReport_Deichler.pdf","file_size":3906744,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","article_type":"original","citation":{"ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220.","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0","ieee":"A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020.","mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0."},"publication":"Scientific Reports","date_published":"2020-10-01T00:00:00Z","article_number":"16220","file_date_updated":"2020-10-12T12:39:10Z","department":[{"_id":"MaJö"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","year":"2020","volume":10,"date_created":"2020-10-11T22:01:14Z","date_updated":"2023-08-22T09:58:21Z","author":[{"full_name":"Deichler, Alfonso","last_name":"Deichler","first_name":"Alfonso"},{"full_name":"Carrasco, Denisse","last_name":"Carrasco","first_name":"Denisse"},{"full_name":"Lopez-Jury, Luciana","first_name":"Luciana","last_name":"Lopez-Jury"},{"full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Natalia","last_name":"Marquez","full_name":"Marquez, Natalia"},{"first_name":"Jorge","last_name":"Mpodozis","full_name":"Mpodozis, Jorge"},{"full_name":"Marin, Gonzalo","first_name":"Gonzalo","last_name":"Marin"}],"publication_identifier":{"eissn":["20452322"]},"month":"10","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000577142600032"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-020-72848-0"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"file_date_updated":"2020-10-12T12:02:09Z","publisher":"Oxford Academic","department":[{"_id":"FyKo"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","volume":36,"date_created":"2020-10-11T22:01:14Z","date_updated":"2023-08-22T09:57:29Z","author":[{"last_name":"Esteban","first_name":"Laura A","full_name":"Esteban, Laura A"},{"first_name":"Lyubov R","last_name":"Lonishin","full_name":"Lonishin, Lyubov R"},{"first_name":"Daniil M","last_name":"Bobrovskiy","full_name":"Bobrovskiy, Daniil M"},{"full_name":"Leleytner, Gregory","first_name":"Gregory","last_name":"Leleytner"},{"full_name":"Bogatyreva, Natalya S","last_name":"Bogatyreva","first_name":"Natalya S"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"last_name":"Ivankov","first_name":"Dmitry N ","full_name":"Ivankov, Dmitry N "}],"publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"month":"03","project":[{"call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000538696800054"],"pmid":["31742320"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/btz841","type":"journal_article","issue":"6","abstract":[{"text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.","lang":"eng"}],"intvolume":" 36","ddc":["000","570"],"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8645","file":[{"creator":"dernst","file_size":308341,"content_type":"application/pdf","file_name":"2020_Bioinformatics_Esteban.pdf","access_level":"open_access","date_updated":"2020-10-12T12:02:09Z","date_created":"2020-10-12T12:02:09Z","success":1,"checksum":"21d6f71839deb3b83e4a356193f72767","file_id":"8649","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"15","page":"1960-1962","article_type":"original","citation":{"short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841","ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962."},"publication":"Bioinformatics","date_published":"2020-03-15T00:00:00Z"}]