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IEEE Symposium on Computational Intelligence and bioinformatics and Computational biology (CIBCB)

作者： G.B. Bezerra T.V. Barra F.J. von Zuben L.N. de Castro Laboratory of Bioinformatics and Bio-Inspired Computing (LBiC) Department of Computer Engineering and Industrial Automation State University of Campinas-UNICAMP Sao Paulo Brazil Graduate Program on Informatics Catholic University of Santos Sao Paulo Brazil

One of the main problems related to regulatory network reconstruction from expression data concerns the small size and low quality of the available dataset. When trying to infer a model from little information it is necessary to give much more precedence to generalization, rather than specificity, otherwise, any attempt will be fated to overfitting. In this paper we address this issue by focusing on data sparseness and noisy information, and propose a density estimation technique that achieves regularized curves when data is scarce. We first compare the proposed method with the EM algorithm for mixture models on density estimation problems. Next, we apply the method, together with Bayesian networks, on realistic simulations of static gene networks, and compare the obtained results with the standard discrete Bayesian network model. We intend to demonstrate that adopting a discrete approach is not justifiable when only a small amount of information is available.

关键词： Intelligent networks Bayesian methods Genetics bioinformatics Computer networks Reverse engineering Cellular networks Noise robustness Laboratories Data engineering

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Hitting two birds with one stone: The unforeseen consequences of nested gene knockouts in Caenorhabditis elegans

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Worm 2016年第2期5卷 e1156835页

作者： Richard Jovelin Asher D Cutter Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada Informatics and Bio-Computing Program Ontario Institute for Cancer Research Toronto Ontario Canada. Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada.

Nested genes represent an intriguing form of non-random genomic organization in which the boundaries of one gene are fully contained within another, longer host gene. The C. elegans genome contains over 10,000 nested genes, 92% of which are ncRNAs, which occur inside 16% of the protein coding gene complement. Host genes are longer than non-host coding genes, owing to their longer and more numerous introns. Indel alleles are available for nearly all of these host genes that simultaneously alter the nested gene, raising the possibility of nested gene disruption contributing to phenotypes that might be attributed to the host gene. Such dual-knockouts could represent a source of misinterpretation about host gene function. Dual-knockouts might also provide a novel source of synthetic phenotypes that reveal the functional effects of ncRNA genes, whereby the host gene disruption acts as a perturbed genetic background to help unmask ncRNA phenotypes.

关键词： gene knockout mutations nested genes non-coding RNAs polymorphism

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Synthetic biology in Indonesia: Potential and projection in a country with mega biodiversity

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biotechnology Notes 2023年第1期4卷 41-48页

作者： Sanka, Immanuel Kusuma, Ali Budhi Martha, Faustina Hendrawan, Andre Pramanda, Ihsan Tria Wicaksono, Adhityo Jati, Afif Pranaya Mazaya, Maulida Dwijayanti, Ari Izzati, Nurul Maulana, Muhammad Farhan Widyaningrum, Aulia Reski Synthetic Biology Indonesia (Synbio.id) Jl. Raya Lintas Sumbawa-Bima Block AA No. 1 Boak Village Subdistrict Unter Iwes Sumbawa 84316 Indonesia Department of Chemistry and Biotechnology Tallinn University of Technology Akadeemia tee 15 Tallinn 12618 Estonia Indonesian Centre for Extremophile Bioresources and Biotechnology (ICEBB) Faculty of Life Sciences and Technology Sumbawa University of Technology Jl. Raya Olat Maras Sumbawa 84371 Indonesia Science Communication Steering Committee iGEM Foundation 45 Prospect St Cambridge 02139 MA United States Department of Bio Technology Indonesia International Institute for Life Sciences (i3L) Jl. Pulomas Barat Kav. 88 Pulomas Jakarta 13210 Indonesia Division of Biotechnology Genbinesia Foundation Jalan Swadaya Barat no. 4 Gresik 61171 Indonesia Infection Program Monash Biomedicine Discovery Institute and Department of Microbiology Monash University Melbourne VIC Australia Research Center for Computing Research Organization for Electronics and Informatics National Research and Innovation Agency (BRIN) Cibinong Science Center Jl. Raya Jakarta-Bogor KM 46 West Java Cibinong 16911 Indonesia

Synthetic biology has gained many interest around the globe in the last two decades, not only due to its rapid development but also the potential to provide addressable solutions using standardized design of biological systems. Considering its huge population, biodiversity, and natural resources, Indonesia could play an important role in shaping the future of synthetic biology towards a sustainable bio-circular economy. Here, we provide an overview of synthetic biology development in Indonesia, especially on exploring the potential of our biodiversity. We also discuss some potentials of synthetic biology in solving national issues. Furthermore, we also provide the projection and future landscape of synthetic biology development in Indonesia. In addition, we briefly explain the potential challenges that may arise during the development. © 2023 The Authors

关键词： Indonesia Mega biodiversity Synbio development Synthetic biology

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25th Annual Computational Neuroscience Meeting CNS-2016, Seogwipo City, South Korea, July 2-7, 2016 Abstracts

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BMC NEUROSCIENCE 2016年第1期17卷 1-112页

作者： [Anonymous] Computational Neurobiology Laboratory The Salk Institute for Biological Studies San Diego USA UNIC CNRS Gif sur Yvette France The European Institute for Theoretical Neuroscience (EITN) Paris France ATR Computational Neuroscience Laboratories Kyoto Japan Krembil Research Institute University Health Network Toronto Canada Department of Physiology University of Toronto Toronto Canada Department of Medicine (Neurology) University of Toronto Toronto Canada Department of Physics University of New Hampshire Durham USA Department of Neurophysiology Nencki Institute of Experimental Biology Warsaw Poland Department of Theory Wigner Research Centre for Physics of the Hungarian Academy of Sciences Budapest Hungary Department of Mathematical Sciences KAIST Daejoen Republic of Korea Department of Mathematics University of Houston Houston USA Department of Biochemistry & Cell Biology and Institute of Biosciences and Bioengineering Rice University Houston USA Department of Biology and Biochemistry University of Houston Houston USA Grupo de Neurocomputación Biológica Dpto. de Ingeniería Informática Escuela Politécnica Superior Universidad Autónoma de Madrid Madrid Spain Department of Biological Sciences University of Southern California Los Angeles USA Center for Neuroscience Korea Institute of Science and Technology Seoul South Korea Department of Neurology Albert Einstein College of Medicine Bronx USA Center for Neuroscience KIST Seoul South Korea Department of Neuroscience University of Science and Technology Daejon South Korea Systems Neuroscience Group QIMR Berghofer Medical Research Institute Herston Australia Department of Psychology Yonsei University Seoul South Korea Department of Psychiatry Kyung Hee University Hospital at Gangdong Seoul South Korea Department of Psychiatry Veterans Administration Boston Healthcare System and Harvard Medical School Brockton USA Department of Electrical and Electronic Engineering The University of Melbourne Parkvil

A1 Functional advantages of cell-type heterogeneity in neural circuits Tatyana O. Sharpee A2 Mesoscopic modeling of propagating waves in visual cortex Alain Destexhe A3 Dynamics and biomarkers of mental disorders Mitsuo Kawato F1 Precise recruitment of spiking output at theta frequencies requires dendritic h-channels in multi-compartment models of oriens-lacunosum/moleculare hippocampal interneurons Vladislav Sekulić, Frances K. Skinner F2 Kernel methods in reconstruction of current sources from extracellular potentials for single cells and the whole brains Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári F3 The synchronized periods depend on intracellular transcriptional repression mechanisms in circadian clocks. Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Kresimir Josić O1 Assessing irregularity and coordination of spiking-bursting rhythms in central pattern generators Irene Elices, David Arroyo, Rafael Levi, Francisco B. Rodriguez, Pablo Varona O2 Regulation of top-down processing by cortically-projecting parvalbumin positive neurons in basal forebrain Eunjin Hwang, Bowon Kim, Hio-Been Han, Tae Kim, James T. McKenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun Choi O3 Modeling auditory stream segregation, build-up and bistability James Rankin, Pamela Osborn Popp, John Rinzel O4 Strong competition between tonotopic neural ensembles explains pitch-related dynamics of auditory cortex evoked fields Alejandro Tabas, André Rupp, Emili Balaguer-Ballester O5 A simple model of retinal response to multi-electrode stimulation Matias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, Michael R. Ibbotson, Hamish Meffin O6 Noise correlations in V4 area correlate with behavioral performance in visual discrimination task Veronika Koren, Timm Lochmann, Valentin Dragoi, Klaus Obermayer O7 Input-location dependent gain modulation in cerebellar nucleus neurons Maria Psarrou, Maria Schilstra, Neil Davey, Benjamin Torben-Ni

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Author Correction: The landscape of viral associations in human cancers

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Nature genetics 2023年第6期55卷 1077页

作者： Marc Zapatka Ivan Borozan Daniel S Brewer Murat Iskar Adam Grundhoff Malik Alawi Nikita Desai Holger Sültmann Holger Moch Colin S Cooper Roland Eils Vincent Ferretti Peter Lichter Division of Molecular Genetics German Cancer Research Center (DKFZ) Heidelberg Germany. Informatics and Bio-computing Program Ontario Institute for Cancer Research Toronto Ontario Canada. Norwich Medical School University of East Anglia Norwich UK. Earlham Institute Norwich UK. Heinrich-Pette-Institute Leibniz Institute for Experimental Virology Hamburg Germany. German Center for Infection Research (DZIF) Partner Site Hamburg-Borstel-Lübeck-Riems Hamburg Germany. Bioinformatics Core University Medical Center Hamburg-Eppendorf Hamburg Germany. Bioinformatics Group Department of Computer Science University College London London UK. Biomedical Data Science Laboratory Francis Crick Institute London UK. National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany. Division of Cancer Genome Research German Cancer Research Center (DKFZ) Heidelberg Germany. German Cancer Consortium (DKTK) Heidelberg Germany. Department of Pathology and Molecular Pathology University and University Hospital Zürich Zurich Switzerland. Institute of Cancer Research London UK. University of East Anglia Norwich UK. Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany. Department of Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology Heidelberg University and BioQuant Center Heidelberg Germany. Center for Digital Health Berlin Institute of Health and Charité Universitätsmedizin Berlin Berlin Germany. Ontario Institute for Cancer Research MaRS Centre Toronto Ontario Canada. Department of Biochemistry and Molecular Medicine University of Montreal Montreal Québec Canada. Division of Molecular Genetics German Cancer Research Center (DKFZ) Heidelberg Germany. peter.lichter@dkfz-heidelberg.de. German Cancer Consortium (DKTK) Heidelberg Germany. peter.lichter@dkfz-heidelberg.de.

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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHEMinformatics 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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