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arXiv 2020年

作者： Caro, Josue Ortega Ju, Yilong Pyle, Ryan Dey, Sourav Brendel, Wieland Anselmi, Fabio Patel, Ankit B. Department of Neuroscience Baylor College of Medicine HoustonTX77030 United States Quantitative and Computational Bioscience Program Baylor College of Medicine HoustonTX70030 United States Department of Computer Science Rice University HoustonTX77005 United States Manifold AI United States University of Tübingen Germany Department of Electrical and Computer Engineering Rice University HoustonTX70005 United States

Adversarial Attacks are still a significant challenge for neural networks. Recent efforts has shown that adversarial perturbations typically contain high-frequency features, but the root cause of this phenomenon remains unknown. Inspired by theoretical work on linear full-width convolutional models, we hypothesize that convolutional operations with localized kernels are implicitly biased to learn high frequency features, and that this is one of the root causes of high frequency adversarial examples. To test this hypothesis, we analyzed the impact of different choices of linear and nonlinear architectures on the implicit bias of the learned features and the adversarial perturbations, in spatial and frequency domains. We find that, independently of the training dataset, convolutional operations have higher frequency adversarial attacks compared to other architectural parametrizations, and this phenomenon is exacerbated with stronger locality of the convolutional kernels. The explanation for the kernel size dependence involves the Fourier Uncertainty Principle: a spatially-limited (local in the space domain) filter cannot also be frequency-limited (local in the frequency domain). Using larger convolution kernel sizes or avoiding convolutions (e.g. by using Vision Transformers or MLP-style architectures) significantly reduces this high frequency bias. Looking forward, our work strongly suggests that understanding and controlling the implicit bias of architectures will be essential for achieving adversarial robustness. © 2020, CC BY.

关键词： Convolution

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An Open-Source Knowledge Graph Ecosystem for the Life Sciences

arXiv

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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College 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 Ne

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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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 repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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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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Heterogeneity analysis provides evidence for a genetically homogeneous subtype of bipolar-disorder

arXiv

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arXiv 2024年

作者： McGrouther, Caroline C. Rangan, Aaditya V. Florio, Arianna Di Elman, Jeremy A. Schork, Nicholas J. Kelsoe, John Stahl, Eli A. Breen, Gerome Forstner, Andreas J. McQuillin, Andrew Ripke, Stephan Trubetskoy, Vassily Mattheisen, Manuel Wang, Yunpeng Coleman, Jonathan R.I. Gaspar, Héléna A. de Leeuw, Christiaan A. Steinberg, Stacy Whitehead Pavlides, Jennifer M. Trzaskowski, Maciej Byrne, Enda M. Pers, Tune H. Holmans, Peter A. Richards, Alexander L. Abbott, Liam Agerbo, Esben Akil, Huda Albani, Diego Alliey-Rodriguez, Ney Als, Thomas D. Anjorin, Adebayo Antilla, Verneri Awasthi, Swapnil Badner, Judith A. Bækvad-Hansen, Marie Barchas, Jack D. Bass, Nicholas Bauer, Michael Belliveau, Richard Bergen, Sarah E. Pedersen, Carsten Bøcker Bøen, Erlend Boks, Marco P. Boocock, James Budde, Monika Bunney, William Burmeister, Margit Bybjerg-Grauholm, Jonas Byerley, William Casas, Miquel Cerrato, Felecia Cervantes, Pablo Chambert, Kimberly Charney, Alexander W. Chen, Danfeng Churchhouse, Claire Clarke, Toni-Kim Coryell, William Craig, David W. Cruceanu, Cristiana Curtis, David Czerski, Piotr M. Dale, Anders M. de Jong, Simone Degenhardt, Franziska Del-Favero, Jurgen DePaulo, J. Raymond Djurovic, Srdjan Dobbyn, Amanda L. Dumont, Ashley Elvsåshagen, Torbjørn Escott-Price, Valentina Fan, Chun Chieh Fischer, Sascha B. Flickinger, Matthew Foroud, Tatiana M. Forty, Liz Frank, Josef Fraser, Christine Freimer, Nelson B. Frisén, Louise Gade, Katrin Gage, Diane Garnham, Julie Giambartolomei, Claudia Pedersen, Marianne Giørtz Goldstein, Jaqueline Gordon, Scott D. Gordon-Smith, Katherine Green, Elaine K. Green, Melissa J. Greenwood, Tiffany A. Grove, Jakob Guan, Weihua Guzman-Parra, José Hamshere, Marian L. Hautzinger, Martin Heilbronner, Urs Herms, Stefan Hipolito, Maria Hoffmann, Per Holland, Dominic Huckins, Laura Jamain, Stéphane Johnson, Jessica S. Kandaswamy, Radhika Karlsson, Robert Kennedy, James L. Kittel-Schneider, Sarah Knowles, James A. Kogevinas, Manolis Koller, Anna C. Kupka, Ralph Lavebratt, Catharina Lawrence, Jacob Lawson, Courant Institute of Mathematical Sciences New York University New YorkNY United States School of Medicine Division of Psychological Medicine and Clinical Neurosciences Cardiff University Cardiff United Kingdom Department of Psychiatry University of California San Diego San DiegoCA United States The Translational Genomics Research Institute Quantitative Medicine and Systems Biology PhoenixAZ United States Department of Psychiatry University of California San Diego La Jolla CA United States Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New YorkNY United States Department of Psychiatry Icahn School of Medicine at Mount Sinai New YorkNY United States Medical and Population Genetics Broad Institute CambridgeMA United States MRC Social Genetic and Developmental Psychiatry Centre King’s College London London United Kingdom NIHR BRC for Mental Health King’s College London London United Kingdom University of Basel Basel Switzerland Institute of Human Genetics University of Bonn School of Medicine University Hospital Bonn DE Bonn Germany Centre for Human Genetics University of Marburg DE Marburg Germany Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland Division of Psychiatry University College London London United Kingdom Stanley Center for Psychiatric Research Broad Institute CambridgeMA United States Department of Psychiatry and Psychotherapy Charité - Universitätsmedizin Berlin Germany Analytic and Translational Genetics Unit Massachusetts General Hospital BostonMA United States iSEQ Center for Integrative Sequencing Aarhus University DK Aarhus Denmark Department of Biomedicine - Human Genetics Aarhus University DK Aarhus Denmark Department of Clinical Neuroscience Centre for Psychiatry Research Karolinska Institutet Stockholm Sweden Department of Psychiatry Psychosomatics and Psychotherapy Center of Mental Health University Hospital Würzburg DE Würzburg Ge

Background: Bipolar Disorder (BD) is a complex disease. It is heterogeneous, both at the phenotypic and genetic level, although the extent and impact of this heterogeneity is not fully understood. One way to assess this heterogeneity is to look for patterns in the subphenotype data. Because of the variability in how phenotypic data was collected by the various BD studies over the years, homogenizing this subphenotypic data is a challenging task, and so is replication. An alternative methodology, taken here, is to set aside the intricacies of subphenotype and allow the genetic data itself to determine which subjects define a homogeneous genetic subgroup (termed ‘bicluster’ below). Results: In this paper, we leverage recent advances in heterogeneity analysis to look for genetically-driven subgroups (i.e., biclusters) within the broad phenotype of Bipolar Disorder. We first apply this covariate-corrected biclustering algorithm to a cohort of 2524 BD cases and 4106 controls from the Bipolar Disease Research Network (BDRN) within the Psychiatric Genomics Consortium (PGC). We find evidence of genetic heterogeneity delineating a statistically significant bicluster comprising a subset of BD cases which exhibits a disease-specific pattern of differential-expression across a subset of SNPs. This disease-specific genetic pattern (i.e., ‘genetic subgroup’) replicates across the remaining data-sets collected by the PGC containing 5781/8289, 3581/7591, and 6825/9752 cases/controls, respectively. This genetic subgroup (discovered without using any BD subtype information) was more prevalent in Bipolar type-I than in Bipolar type-II. Conclusions: Our methodology has successfully identified a replicable homogeneous genetic subgroup of bipolar disorder. This subgroup may represent a collection of correlated genetic risk-factors for BDI. By investigating the subgroup’s bicluster-informed polygenic-risk-scoring (PRS), we find that the disease-specific pattern highlighted by the bicluste

关键词： Economic and social effects

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Native diversity buffers against severity of non-native tree invasions ( vol 621,pg 773 , 2023 )

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NATURE 2023年第7982期622卷 E2-E2页

作者： Delavaux, Camille S. Crowther, Thomas W. Zohner, Constantin M. Robmann, Niamh M. Lauber, Thomas van den Hoogen, Johan Kuebbing, Sara Liang, Jingjing de-Miguel, Sergio Nabuurs, Gert-Jan Reich, Peter B. Abegg, Meinrad Yao, Yves C. Adou Alberti, Giorgio Zambrano, Angelica M. Almeyda Alvarado, Braulio Vilchez Alvarez-Davila, Esteban Alvarez-Loayza, Patricia Alves, Luciana F. Ammer, Christian Anton-Fernandez, Clara Araujo-Murakami, Alejandro Arroyo, Luzmila Avitabile, Valerio Aymard, Gerardo A. Baker, Timothy R. Balazy, Radomir Banki, Olaf Barroso, Jorcely G. Bastian, Meredith L. Bastin, Jean-Francois Birigazzi, Luca Birnbaum, Philippe Bitariho, Robert Boeckx, Pascal Bongers, Frans Bouriaud, Olivier Brancalion, Pedro H. S. Brandl, Susanne Brienen, Roel Broadbent, Eben N. Bruelheide, Helge Bussotti, Filippo Gatti, Roberto Cazzolla Cesar, Ricardo G. Cesljar, Goran Chazdon, Robin Chen, Han Y. H. Chisholm, Chelsea Cho, Hyunkook Cienciala, Emil Clark, Connie Clark, David Colletta, Gabriel D. Coomes, David A. Valverde, Fernando Cornejo Corral-Rivas, Jose J. Crim, Philip M. Cumming, Jonathan R. Dayanandan, Selvadurai de Gasper, Andre L. Decuyper, Mathieu Derroire, Geraldine DeVries, Ben Djordjevic, Ilija Dolezal, Jiri Dourdain, Aurelie Obiang, Nestor Laurier Engone Enquist, Brian J. Eyre, Teresa J. Fandohan, Adande Belarmain Fayle, Tom M. Feldpausch, Ted R. Ferreira, Leandro V. Fischer, Markus Fletcher, Christine Frizzera, Lorenzo Gamarra, Javier G. P. Gianelle, Damiano Glick, Henry B. Harris, David J. Hector, Andrew Hemp, Andreas Hengeveld, Geerten Herault, Bruno Herbohn, John L. Herold, Martin Hillers, Annika Coronado, Euridice N. Honorio Hui, Cang Ibanez, Thomas T. Amaral, Ieda Imai, Nobuo Jagodzinski, Andrzej M. Jaroszewicz, Bogdan Johannsen, Vivian Kvist Joly, Carlos A. Jucker, Tommaso Jung, Ilbin Karminov, Viktor Kartawinata, Kuswata Kearsley, Elizabeth Kenfack, David Kennard, Deborah K. Kepfer-Rojas, Sebastian Keppel, Gunnar Khan, Mohammed Latif Killeen, Timothy J. Kim, Hyun Seok Kitayama, Kanehiro Kohl, Michael Korju Institute of Integrative Biology ETH Zurich (Swiss Federal Institute of Technology) Zurich Switzerland Department of Genetics Evolution and Environment University College London London UK The Forest School at The Yale School of the Environment Yale University New Haven CT USA Department of Forestry and Natural Resources Purdue University West Lafayette IN USA Department of Agriculture Forestry and Bioresources Seoul National University Seoul South Korea Department of Crop and Forest Sciences University of Lleida Lleida Spain Joint Research Unit CTFC–AGROTECNIO–CERCA Solsona Spain Wageningen University and Research Wageningen The Netherlands World Agroforestry (ICRAF) Nairobi Kenya Department of Forest Resources University of Minnesota St Paul MN USA Hawkesbury Institute for the Environment Western Sydney University Penrith New South Wales Australia Institute for Global Change Biology and School for Environment and Sustainability University of Michigan Ann Arbor MI USA Swiss Federal Institute for Forest Snow and Landscape Research WSL Birmensdorf Switzerland UFR Biosciences University Félix Houphouët-Boigny Abidjan Côte d’Ivoire Department of Agricultural Food Environmental and Animal Sciences University of Udine Udine Italy Faculty of Science and Technology Free University of Bolzano Bolzano Italy Spatial Ecology and Conservation Laboratory Department of Tourism Recreation and Sport Management University of Florida Gainesville FL USA Forestry School Tecnológico de Costa Rica TEC Cartago Costa Rica Fundacion ConVida Universidad Nacional Abierta y a Distancia UNAD Medellin Colombia Field Museum of Natural Histiory Chicago IL USA Center for Tropical Research Institute of the Environment and Sustainability UCLA Los Angeles CA USA Silviculture and Forest Ecology of the Temperate Zones University of Göttingen Göttingen Germany Division of Forest and Forest Resources Norwegian Institute of Bioeconomy Research (NIBIO) Ås Norway Museo de Hi

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Effect of climate on traits of dominant and rare tree species in the world’s forests

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Nature Communications 2025年第1期16卷 1-15页

作者： Hordijk, Iris Poorter, Lourens Liang, Jingjing Reich, Peter B. de-Miguel, Sergio Nabuurs, Gert-Jan Gamarra, Javier G. P. Chen, Han Y. H. Zhou, Mo Wiser, Susan K. Pretzsch, Hans Paquette, Alain Picard, Nicolas Hérault, Bruno Bastin, Jean-Francois Alberti, Giorgio Abegg, Meinrad Adou Yao, Yves C. Almeyda Zambrano, Angelica M. Alvarado, Braulio V. Alvarez-Davila, Esteban Alvarez-Loayza, Patricia Alves, Luciana F. Amaral, Iêda Ammer, Christian Antón-Fernández, Clara Araujo-Murakami, Alejandro Arroyo, Luzmila Avitabile, Valerio Aymard C, Gerardo A. Baker, Timothy Banki, Olaf Barroso, Jorcely Bastian, Meredith L. Birigazzi, Luca Birnbaum, Philippe Bitariho, Robert Boeckx, Pascal Bongers, Frans Bouriaud, Olivier Brancalion, Pedro H. S. Brandl, Susanne Brearley, Francis Q. Brienen, Roel Broadbent, Eben N. Bruelheide, Helge Cazzolla Gatti, Roberto Cesar, Ricardo G. Cesljar, Goran Chazdon, Robin L. Chisholm, Chelsea Cienciala, Emil Clark, Connie J. Clark, David B. Colletta, Gabriel Coomes, David Cornejo Valverde, Fernando Corral-Rivas, Jose J. Crim, Philip Cumming, Jonathan Dayanandan, Selvadurai de Gasper, André L. Decuyper, Mathieu Derroire, Géraldine DeVries, Ben Djordjevic, Ilija Dourdain, Aurélie Dolezal, Jiri Engone Obiang, Nestor Laurier Enquist, Brian Eyre, Teresa Fandohan, Adandé Belarmain Fayle, Tom M. Ferreira, Leandro V. Feldpausch, Ted R. Finér, Leena Fischer, Markus Fletcher, Christine Frizzera, Lorenzo Gianelle, Damiano Glick, Henry B. Harris, David Hector, Andrew Hemp, Andreas Herbohn, John Hillers, Annika Honorio Coronado, Eurídice N. Hui, Cang Cho, Hyunkook Ibanez, Thomas Jung, Ilbin Imai, Nobuo Jagodzinski, Andrzej M. Jaroszewicz, Bogdan Johannsen, Vivian Joly, Carlos A. Jucker, Tommaso Karminov, Viktor Kartawinata, Kuswata Kearsley, Elizabeth Kenfack, David Kennard, Deborah Kepfer-Rojas, Sebastian Keppel, Gunnar Khan, Mohammed Latif Killeen, Timothy Kim, Hyun Seok Kitayama, Kanehiro Köhl, Michael Korjus, Henn Kraxner, Florian Laarmann, Diana Lang, Mait Lewis, Simon Lu, Huicui Lukina, Natalia Maitner, Br Institute of Integrative Biology ETH Zurich (Swiss Federal Institute of Technology) Zurich Switzerland Wageningen University and Research Wageningen Netherlands Department of Forestry and Natural Resources Purdue University West Lafayette IN United States Department of Forest Resources University of Minnesota St Paul MN United States Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia Department of Agricultural and Forest Sciences and Engineering University of Lleida Lleida Spain Forest Science and Technology Centre of Catalonia (CTFC) Solsona Spain Forestry Division Food and Agriculture Organization of the United Nations Rome Italy Faculty of Natural Resources Management Lakehead University Thunder Bay ON Canada Manaaki Whenua–Landcare Research Lincoln New Zealand Chair for Forest Growth and Yield Science TUM School for Life Sciences Technical University of Munich Munich Germany Centre for Forest Research Université du Québec à Montréal Montréal QC Canada GIP ECOFOR Paris France CIRAD Forêts et Sociétés Montpellier France Forêts et Sociétés Univ Montpellier CIRAD Montpellier France Gembloux Agro Bio-Tech University of Liege Liege Belgium Faculty of Science and Technology Free University of Bolzano Bolzano Italy Department of Agricultural Food Environmental and Animal Sciences University of Udine Udine Italy Swiss Federal Institute for Forest Snow and Landscape Research WSL Birmensdorf Switzerland UFR Biosciences University Félix Houphouët-Boigny Abidjan Cote d'Ivoire Spatial Ecology and Conservation Laboratory Center for Latin American Studies University of Florida Gainesville FL United States Forestry School Tecnológico de Costa Rica TEC Cartago Costa Rica Fundacion ConVida Universidad Nacional Abierta y a Distancia UNAD Medellin Colombia Field Museum of Natural History Chicago IL United States Center for Tropical Research Institute of the Environment and Sustainability UCLA Los Angeles CA

Species’ traits and environmental conditions determine the abundance of tree species across the globe. The extent to which traits of dominant and rare tree species differ remains untested across a broad environmental range, limiting our understanding of how species traits and the environment shape forest functional composition. We use a global dataset of tree composition of >22,000 forest plots and 11 traits of 1663 tree species to ask how locally dominant and rare species differ in their trait values, and how these differences are driven by climatic gradients in temperature and water availability in forest biomes across the globe. We find three consistent trait differences between locally dominant and rare species across all biomes;dominant species are taller, have softer wood and higher loading on the multivariate stem strategy axis (related to narrow tracheids and thick bark). The difference between traits of dominant and rare species is more strongly driven by temperature compared to water availability, as temperature might affect a larger number of traits. Therefore, climate change driven global temperature rise may have a strong effect on trait differences between dominant and rare tree species and may lead to changes in species abundances and therefore strong community reassembly. © The Author(s) 2025.

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