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FungalTraits:a user-friendly traits database of fungi and fungus-like stramenopiles

Fungal Diversity 2020年第6期105卷 I0001-I0016页

作者： Sergei Põlme Kessy Abarenkov RHenrik Nilsson Björn D.Lindahl Karina Engelbrecht Clemmensen Havard Kauserud Nhu Nguyen Rasmus Kjøller Scott T.Bates Petr Baldrian Tobias Guldberg Frøslev Kristjan Adojaan Alfredo Vizzini Ave Suija Donald Pfister Hans-Otto Baral Helle Järv Hugo Madrid Jenni Nordén Jian-Kui Liu Julia Pawlowska Kadri Põldmaa Kadri Pärtel Kadri Runnel Karen Hansen Karl-Henrik Larsson Kevin David Hyde Marcelo Sandoval-Denis Matthew E.Smith Merje Toome-Heller Nalin N.Wijayawardene Nelson Menolli Jr Nicole K.Reynolds Rein Drenkhan Sajeewa S.N.Maharachchikumbura Tatiana B.Gibertoni Thomas Læssøe William Davis Yuri Tokarev Adriana Corrales Adriene Mayra Soares Ahto Agan Alexandre Reis Machado Andrés Argüelles-Moyao Andrew Detheridge Angelina de Meiras-Ottoni Annemieke Verbeken Arun Kumar Dutta Bao-Kai Cui C.K.Pradeep César Marín Daniel Stanton Daniyal Gohar Dhanushka N.Wanasinghe Eveli Otsing Farzad Aslani Gareth W.Griffith Thorsten H.Lumbsch Hans-Peter Grossart Hossein Masigol Ina Timling Inga Hiiesalu Jane Oja John Y.Kupagme József Geml Julieta Alvarez-Manjarrez Kai Ilves Kaire Loit Kalev Adamson Kazuhide Nara Kati Küngas Keilor Rojas-Jimenez Krišs Bitenieks Laszlo Irinyi LászlóGNagy Liina Soonvald Li-Wei Zhou Lysett Wagner M.Catherine Aime MaarjaÖpik María Isabel Mujica Martin Metsoja Martin Ryberg Martti Vasar Masao Murata Matthew PNelsen Michelle Cleary Milan C.Samarakoon Mingkwan Doilom Mohammad Bahram Niloufar Hagh-Doust Olesya Dulya Peter Johnston Petr Kohout Qian Chen Qing Tian Rajasree Nandi Rasekh Amiri Rekhani Hansika Perera Renata dos Santos Chikowski Renato L.Mendes-Alvarenga Roberto Garibay-Orijel Robin Gielen Rungtiwa Phookamsak Ruvishika S.Jayawardena Saleh Rahimlou Samantha C.Karunarathna Saowaluck Tibpromma Shawn P.Brown Siim-Kaarel Sepp Sunil Mundra Zhu-Hua Luo Tanay Bose Tanel Vahter Tarquin Netherway Teng Yang Tom May Torda Varga Wei Li Victor Rafael Matos Coimbra Virton Rodrigo Targino de Oliveira Vitor Xavier de Lima Vladimir S.Mikryukov Yongzhong Lu Yosuke Matsuda Yumiko Miyamoto Urm Institute of Ecology and Earth Sciences University of Tartu14A Ravila50411 TartuEstonia Natural History Museum University of Tartu46 Vanemuise Str51003 TartuEstonia Gothenburg Global Biodiversity Centre Box 46140530 GothenburgSweden Department of Biological and Environmental Sciences University of GothenburgGothenburgSweden Department of Soil and Environment Swedish University of Agricultural SciencesBox 701475007 UppsalaSweden Department of Forest Mycology and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden Section for Genetics and Evolutionary Biology(EvoGene) Department of BiosciencesUniversity of OsloP.O.Box 1066BlindernNO-0316 OsloNorway University of Hawaiʻi at Mānoa 3190 Maile WaySt.John 102HonoluluHIUSA Department of Biology University of CopenhagenUniversitetsparken 152100 CopenhagenØDenmark Purdue University Northwest WestvilleIN 46391USA Institute of Microbiology Czech Academy of SciencesVidenska 108314220 Praha 4Czech Republic GLOBE Institute University of CopenhagenØster Farimagsgade 5KH7.2.321353 CopenhagenDenmark Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale Mattioli 2510125 TorinoItaly Department of Organismic and Evolutionary Biology and Farlow Library and Herbarium Harvard University22 Divinity AveCambridgeMA 02138USA Blaihofstr.42 72074 TübingenGermany SYNLAB Estonia Veerenni 53aTallinn 11313Estonia Escuela de Tecnología Médica Universidad Santo TomásLos Carreras 753OsornoChile Centro de Genómica y Bioinformática Universidad MayorCamino La Pirámide 5750HuechurabaSantiagoChile Norwegian Institute for Nature Research(NINA) Sognsveien 680855 OsloNorway School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Evolutionary Biology Faculty of BiologyBiological and Chemical Research CentreUniversity of Warsawul.Zwirki i Wigury 10102-089 WarsawPoland Department of Botany Swedish Museum of

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental *** the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and ***,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains *** order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis *** the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,*** resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental *** order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS *** the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.

关键词： Fungal traits Trophic modes Function Guild bioinformatics High-throughput sequencing Community ecology

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Stroke genetics informs drug discovery and risk prediction across ancestries (vol 611, pg 115, 2022)

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NATURE 2022年第7938期612卷 E7-E7页

作者： Mishra, Aniket Malik, Rainer Hachiya, Tsuyoshi Jurgenson, Tuuli Namba, Shinichi Posner, Daniel C. Kamanu, Frederick K. Koido, Masaru Le Grand, Quentin Shi, Mingyang He, Yunye Georgakis, Marios K. Caro, Ilana Krebs, Kristi Liaw, Yi-Ching Vaura, Felix C. Lin, Kuang Winsvold, Bendik Slagsvold Srinivasasainagendra, Vinodh Parodi, Livia Bae, Hee-Joon Chauhan, Ganesh Chong, Michael R. Tomppo, Liisa Akinyemi, Rufus Roshchupkin, Gennady V. Habib, Naomi Jee, Yon Ho Thomassen, Jesper Qvist Abedi, Vida Carcel-Marquez, Jara Nygaard, Marianne Leonard, Hampton L. Yang, Chaojie Yonova-Doing, Ekaterina Knol, Maria J. Lewis, Adam J. Judy, Renae L. Ago, Tetsuro Amouyel, Philippe Armstrong, Nicole D. Bakker, Mark K. Bartz, Traci M. Bennett, David A. Bis, Joshua C. Bordes, Constance Borte, Sigrid Cain, Anael Ridker, Paul M. Cho, Kelly Chen, Zhengming Cruchaga, Carlos Cole, John W. de Jager, Phil L. de Cid, Rafael Endres, Matthias Ferreira, Leslie E. Geerlings, Mirjam I. Gasca, Natalie C. Gudnason, Vilmundur Hata, Jun He, Jing Heath, Alicia K. Ho, Yuk-Lam Havulinna, Aki S. Hopewell, Jemma C. Hyacinth, I. Hyacinth Inouye, Michael Jacob, Mina A. Jeon, Christina E. Jern, Christina Kamouchi, Masahiro Keene, Keith L. Kitazono, Takanari Kittner, Steven J. Konuma, Takahiro Kumar, Amit Lacaze, Paul Launer, Lenore J. Lee, Keon-Joo Lepik, Kaido Li, Jiang Li, Liming Manichaikul, Ani Markus, Hugh S. Marston, Nicholas A. Meitinger, Thomas Mitchell, Braxton D. Montellano, Felipe A. Morisaki, Takayuki Mosley, Thomas H. Nalls, Mike A. Nordestgaard, Borge G. O'Donnell, Martin J. Okada, Yukinori Onland-Moret, N. Charlotte Ovbiagele, Bruce Peters, Annette Psaty, Bruce M. Rich, Stephen S. Rosand, Jonathan Sabatine, Marc S. Sacco, Ralph L. Saleheen, Danish Sandset, Else Charlotte Salomaa, Veikko Sargurupremraj, Muralidharan Sasaki, Makoto Satizabal, Claudia L. Schmidt, Carsten O. Shimizu, Atsushi Smith, Nicholas L. Sloane, Kelly L. Sutoh, Yoichi Sun, Yan V. Tanno, Kozo Tiedt, Steffen Tatlisumak, Turgut Torres-Aguila, Nuria P. Tiwari, Hemant K. Tregouet, Bordeaux Population Health Research Center University of Bordeaux Inserm UMR 1219 Bordeaux France Department of Public Health Bordeaux University Hospital Bordeaux France Department of Neurology Memory Clinic Bordeaux University Hospital Bordeaux France Department of Neurology Institute for Neurodegenerative Diseases CHU de Bordeaux Bordeaux France Institute for Stroke and Dementia Research (ISD) University Hospital LMU Munich Munich Germany Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Program in Medical and Population Genetics Broad Institute of Harvard and the Massachusetts Institute of Technology Cambridge MA USA Munich Cluster for Systems Neurology Munich Germany German Center for Neurodegenerative Diseases (DZNE) Munich Germany Iwate Tohoku Medical Megabank Organization Iwate Medical University Iwate Japan Estonian Genome Centre Institute of Genomics University of Tartu Tartu Estonia Institute of Mathematics and Statistics University of Tartu Tartu Estonia Department of Computational Biology University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland University Center for Primary Care and Public Health Lausanne Switzerland Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan Department of Genome Informatics Graduate School of Medicine The University of Tokyo Tokyo Japan Laboratory for Systems Genetics RIKEN Center for Integrative Medical Sciences Yokohama Japan Laboratory of Statistical Immunology Immunology Frontier Research Center (WPI-IFReC) Osaka University Suita Japan Integrated Frontier Research for Medical Science Division Institute for Open and Transdisciplinary Research Initiatives Osaka University Suita Japan Center for Infectious Disease Education and Research (CiDER) Osaka University Suita Japan Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) VA Boston Healthcare System Boston MA USA TIMI S

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Contributory presentations/posters

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Journal of Biosciences 1999年第1期24卷 33-198页

作者： N. Manoj V. R. Srinivas A. Surolia M. Vijayan K. Suguna R. Ravishankar R. Schwarzenbacher K. Zeth Diederichs G. M. Kostner A. Gries P. Laggner R. Prassl Madhusudan Pearl Akamine Nguyen-huu Xuong Susan S. Taylor M. Bidva Sagar K. Saikrishnan S. Roy K. Purnapatre P. Handa U. Varshney B. K. Biswal N. Sukumar J. K. Mohana Rao A. Johnson Vasantha Pattabhi S. Sri Krishna Mira Sastri H. S. Savithri M. R. N. Murthy Bindu Pillai Kannan M. V. Hosur Mukesh Kumar Swati Patwardhan K. K. Kannan B. Padmanabhaa S. Sasaki-Sugio M. Nukaga T. Matsuzaki S. Karthikevan S. Sharma A. K. Sharma M. Paramasivam P. Kumar J. A. Khan S. Yadav A. Srinivasan T. P. Singh S. Gourinath Neelima Alam A. Srintvasan Vikas Chandra Punit Kaur Ch. Betzel S. Ghosh A. K. Bera S. Bhattacharya S. Chakraborty A. K. Pal B. P. Mukhopadhyay I. Dey U. Haldar Asok Baneriee Jozef Sevcik Adriana Solovicova K. Sekar M. Sundaralingam N. Genov Dong-cai Liang Tao Jiang Ji-ping Zhang Wen-rui Chang Wolfgang Jahnke Marcel Blommers S. C. Panchal R. V. Hosur Bindu Pillay Puniti Mathur S. Srivatsun Ratan Mani Joshi N. R. Jaganathan V. S. Chauhan H. S. Atreya S. C. Sahu K. V. R. Chary Girjesh Govil Elisabeth Adjadj Éric Quinjou Nadia Izadi-Pruneyre Yves Blouquit Joël Mispelter Bernadette Heyd Guilhem Lerat Philippe Milnard Michel Desmadreil Y. Lin B. D. Nageswara Rao Vidva Raghunathan Mei H. Chau Prashant Pesais Sudha Srivastava Evans Coutinho Anil Saran Leizl F. Sapico Jayson Gesme Herbert Lijima Raymond Paxton Thamarapu Srikrishnan C. R. Grace G. Nagenagowda A. M. Lynn Sudha M. Cowsik Sarata C. Sahu S. Chauhan A. Bhattacharya G. Govil Anil Kumar Maurizio Pellecchia Erik R. P. Zuiderweg Keiichi Kawano Tomoyasu Aizawa Naoki Fujitani Yoichi Hayakawa Atsushi Ohnishi Tadayasu Ohkubo Yasuhiro Kumaki Kunio Hikichi Katsutoshi Nitta V. Rani Parvathy R. M. Kini Takumi Koshiba Yoshihiro Kobashigawa Min Yao Makoto Demura Astushi Nakagawa Isao Tanaka Kunihiro Kuwajima Jens Linge Seán O. Donoghue Michael Nilges G. Chakshusmathi Girish S. Ratnaparkhi P. K. Madhu R. Varadarajan C. Tetreau Molecular Biophysics Unit Indian Institute of Science Bangalore India Austrian Academy of Sciences Institute of Biophysics and X-ray Structure Research Graz Austria Faculty of Biology University of Konstanz Germany Institute of Medical Biochemistry University of Graz Austria Howard Huges Medical Institute Department of Chemistry & Biochemistry University of California La Jolla USA Department of Chemistry & Biochemistry University of California San Diego La Jolla USA Molecular Biophysics Unit India Department of Microbiology &Cell Biology Indian Institute of Science Bangalore India Macromolecular Structure Laboratory NCI - Frederick Cancer Research and Development Center ABL - Basic Research Program Frederick USA Department of Crystallography and Biophysics University of Madras Chennai Biochemistry Department Indian Institute of Science Bangalore India Condensed Matter Physics Division B.A.R.C. Trombay Mumbai Condensed Matter Physics Division Bhabha Atomic Research Centre Trombay Mumbai IMCB The University of Tokyo Tokyo Japan Mitsubishi Chemical Corporation Yokohama Research Center Yokohama Japan Faculty of Pharmaceutical Sciences Chiba University Chiba Japan Department of Biophysics All India Institute of Medical Sciences New Delhi India Department of Biophysics All India Institute of Medical sciences New Delhi India Institüt Physiologische Chemie Hamburg Germany Biophysics Department Bose Institute Calcutta India Slovak Academy of Sciences Institute of Molecular Biology Bratislava Slovakia Indian Institute of Science Bioinformatics Centre Bangalore Departments of Chemistry and Biochemistry Biological Macromolecular Structure Center USA Bulgarian Academy of Sciences Institute of Organic Chemistry Sofia Bulgaria Chinese Academy of Sciences Institute of Biophysics Beijing China Novartis Pharma AG Preclinical Research Basel Switzerland Department of Chemical Sciences Tata Institute of Fundamental Research Mumbai India Solid State Physics Div

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Erratum to: The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

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Genome biology 2017年第1期18卷 11页

作者： Alexie Papanicolaou Marc F Schetelig Peter Arensburger Peter W Atkinson Joshua B Benoit Kostas Bourtzis Pedro Castañera John P Cavanaugh Hsu Chao Christopher Childers Ingrid Curril Huyen Dinh HarshaVardhan Doddapaneni Amanda Dolan Shannon Dugan Markus Friedrich Giuliano Gasperi Scott Geib Georgios Georgakilas Richard A Gibbs Sarah D Giers Ludvik M Gomulski Miguel González-Guzmán Ana Guillem-Amat Yi Han Artemis G Hatzigeorgiou Pedro Hernández-Crespo Daniel S T Hughes Jeffery W Jones Dimitra Karagkouni Panagiota Koskinioti Sandra L Lee Anna R Malacrida Mosè Manni Kostas Mathiopoulos Angela Meccariello Monica Munoz-Torres Shwetha C Murali Terence D Murphy Donna M Muzny Georg Oberhofer Félix Ortego Maria D Paraskevopoulou Monica Poelchau Jiaxin Qu Martin Reczko Hugh M Robertson Andrew J Rosendale Andrew E Rosselot Giuseppe Saccone Marco Salvemini Grazia Savini Patrick Schreiner Francesca Scolari Paolo Siciliano Sheina B Sim George Tsiamis Enric Ureña Ioannis S Vlachos John H Werren Ernst A Wimmer Kim C Worley Antigone Zacharopoulou Stephen Richards Alfred M Handler Hawkesbury Institute for the Environment Western Sydney University Sydney Australia. Justus-Liebig-University Giessen Institute for Insect Biotechnology 35394 Giessen Germany. Department of Biological Sciences Cal Poly Pomona Pomona CA 91768 USA. Department of Entomology and Center for Disease Vector Research University of California Riverside Riverside CA 92521 USA. Interdepartmental Graduate Program in Genetics Genomics & Bioinformatics University of California Riverside Riverside CA 92521 USA. Department of Biological Sciences University of Cincinnati Cincinnati OH 45221 USA. Insect Pest Control Laboratory Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture Seibersdorf Vienna Austria. Department of Environmental and Natural Resources Management University of Patras Agrinio Greece. Department of Environmental Biology Centro de Investigaciones Biológicas CSIC 28040 Madrid Spain. Human Genome Sequencing Center Department of Human and Molecular Genetics Baylor College of Medicine 77030 Houston TX USA. National Agricultural Library USDA 20705 Beltsville MD USA. Georg-August-Universität Göttingen Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie 37077 Göttingen Germany. Department of Biology University of Rochester 14627 Rochester NY USA. Department of Biological Sciences Wayne State University 48202 Detroit MI USA. Department of Biology and Biotechnology University of Pavia 27100 Pavia Italy. USDA-ARS Pacific Basin Agricultural Research Center 96720 Hilo HI USA. DIANA-Lab Department of Electrical & Computer Engineering University of Thessaly 382 21 Volos Greece and Hellenic Pasteur Institute 11521 Athens Greece. Department of Entomology University of Illinois at Urbana-Champaign 61801 Urbana IL USA. Department of Biological Sciences Oakland University 48309 Rochester MI USA. Department of Biochemistry and Biotechnology University of Thessaly Larissa Greece. Department of Biology Univer

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Author Correction: Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes

Nature cancer

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Nature cancer 2023年 2023 May 19页

作者： Do Young Hyeon Dowoon Nam Youngmin Han Duk Ki Kim Gibeom Kim Daeun Kim Jingi Bae Seunghoon Back Dong-Gi Mun Inamul Hasan Madar Hangyeore Lee Su-Jin Kim Hokeun Kim Sangyeop Hyun Chang Rok Kim Seon Ah Choi Yong Ryoul Kim Juhee Jeong Suwan Jeon Yeon Woong Choo Kyung Bun Lee Wooil Kwon Seunghyuk Choi Taewan Goo Taesung Park Young-Ah Suh Hongbeom Kim Ja-Lok Ku Min-Sik Kim Eunok Paek Daechan Park Keehoon Jung Sung Hee Baek Jin-Young Jang Daehee Hwang Sang-Won Lee School of Biological Sciences Seoul National University Seoul Republic of Korea. Department of Chemistry and Center for Proteogenome Research Korea University Seoul Republic of Korea. Department of Surgery and Cancer Research Institute Seoul National University College of Medicine Seoul Republic of Korea. Department of Anatomy and Cell Biology and Department of Biomedical Sciences Seoul National University College of Medicine Seoul Republic of Korea. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) Seoul Republic of Korea. Creative Research Initiatives Center for Epigenetic Code and Diseases Seoul National University Seoul Republic of Korea. Department of Biological Sciences College of Natural Sciences and Department of Molecular Science and Technology Ajou University Suwon Republic of Korea. Department of Pathology Seoul National University College of Medicine Seoul Korea. Department of Computer Science Hanyang University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Department of Statistics Seoul National University Seoul Republic of Korea. Korean Cell Line Bank Laboratory of Cell Biology Cancer Research Institute Seoul National University College of Medicine Seoul Korea. Department of New Biology Daegu Gyeongbuk Institute of Science and Technology Daegu Republic of Korea. Department of Biological Sciences College of Natural Sciences and Department of Molecular Science and Technology Ajou University Suwon Republic of Korea. dpark@ajou.ac.kr. Department of Anatomy and Cell Biology and Department of Biomedical Sciences Seoul National University College of Medicine Seoul Republic of Korea. keehoon.jung@snu.ac.kr. Institute of Allergy and Clinical Immunology Seoul National University Medical Research Center Seoul Republic of Korea. keehoon.jung@snu.ac.kr. School of Biological Sciences Seoul National University Seoul Republic of

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Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity (vol 50, pg 765, 2017)

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NATURE GENETICS 2018年第5期50卷 765-766页

作者： Turcot, Valerie Lu, Yingchang Highland, Heather M. Schurmann, Claudia Justice, Anne E. Fine, Rebecca S. Bradfield, Jonathan P. Esko, Tonu Giri, Ayush Graff, Mariaelisa Guo, Xiuqing Hendricks, Audrey E. Karaderi, Tugce Lempradl, Adelheid Locke, Adam E. Mahajan, Anubha Marouli, Eirini Sivapalaratnam, Suthesh Young, Kristin L. Alfred, Tamuno Feitosa, Mary F. Masca, Nicholas G. D. Manning, Alisa K. Medina-Gomez, Carolina Mudgal, Poorva Ng, Maggie C. Y. Reiner, Alex P. Vedantam, Sailaja Willems, Sara M. Winkler, Thomas W. Abecasis, Goncalo Aben, Katja K. Alam, Dewan S. Alharthi, Sameer E. Allison, Matthew Amouyel, Philippe Asselbergs, Folkert W. Auer, Paul L. Balkau, Beverley Bang, Lia E. Barroso, Ines Bastarache, Lisa Benn, Marianne Bergmann, Sven Bielak, Lawrence F. Bluher, Matthias Boehnke, Michael Boeing, Heiner Boerwinkle, Eric Boger, Carsten A. Bork-Jensen, Jette Bots, Michiel L. Bottinger, Erwin P. Bowden, Donald W. Brandslund, Ivan Breen, Gerome Brilliant, Murray H. Broer, Linda Brumat, Marco Burt, Amber A. Butterworth, Adam S. Campbell, Peter T. Cappellani, Stefania Carey, David J. Catamo, Eulalia Caulfield, Mark J. Chambers, John C. Chasman, Daniel I. Chen, Yii-Der I. Chowdhury, Rajiv Christensen, Cramer Chu, Audrey Y. Cocca, Massimiliano Collins, Francis S. Cook, James P. Corley, Janie Galbany, Jordi Corominas Cox, Amanda J. Crosslin, David S. Cuellar-Partida, Gabriel D'Eustacchio, Angela Danesh, John Davies, Gail Bakker, Paul I. W. Groot, Mark C. H. Mutsert, Renee Deary, Ian J. Dedoussis, George Demerath, Ellen W. Heijer, Martin Hollander, Anneke I. Ruijter, Hester M. Dennis, Joe G. Denny, Josh C. Angelantonio, Emanuele Drenos, Fotios Du, Mengmeng Dube, Marie-Pierre Dunning, Alison M. Easton, Douglas F. Edwards, Todd L. Ellinghaus, David Ellinor, Patrick T. Elliott, Paul Evangelou, Evangelos Farmaki, Aliki-Eleni Farooqi, I. Sadaf Faul, Jessica D. Fauser, Sascha Feng, Shuang Ferrannini, Ele Ferrieres, Jean Florez, Jose C. Ford, Ian Fornage, Myriam Franco, Oscar H. Franke, Andre Franks, Paul W. Friedrich, Ne Montreal Heart Institute Université de Montréal Montreal Quebec Canada Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University School of Medicine Nashville TN USA Charles Bronfman Institute for Personalized Medicine Icahn School of Medicine at Mount Sinai New York NY USA Genetics of Obesity and Related Metabolic Traits Program Icahn School of Medicine at Mount Sinai New York NY USA Department of Epidemiology University of North Carolina Chapel Hill NC USA Human Genetics Center University of Texas School of Public Health University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences University of Texas Health Science Center at Houston Houston TX USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Genetics Harvard Medical School Boston MA USA Division of Endocrinology and Center for Basic and Translational Obesity Research Boston Children’s Hospital Boston MA USA Center for Applied Genomics Division of Human Genetics Children’s Hospital of Philadelphia Philadelphia PA USA Quantinuum Research LLC San Diego CA USA Estonian Genome Center University of Tartu Tartu Estonia Division of Epidemiology Department of Medicine Institute for Medicine and Public Health Vanderbilt Genetics Institute Vanderbilt University Nashville TN USA Institute for Translational Genomics and Population Sciences LABioMed at Harbor-UCLA Medical Center Torrance CA USA Wellcome Trust Sanger Institute Hinxton UK Department of Mathematical and Statistical Sciences University of Colorado Denver CO USA Wellcome Trust Centre for Human Genetics University of Oxford Oxford UK Department of Biological Sciences Faculty of Arts and Sciences Eastern Mediterranean University Famagusta Cyprus Max Planck Institute of Immunobiology and Epigenetics Freiburg Germany Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor

Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are ~10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (***35Ter, MAF = 0.01%), who weighed ~7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.

关键词： Genome-wide association studies Obesity

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Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

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Nature genetics 2023年第3期55卷 519-520页

作者： Ceres Fernandez-Rozadilla Maria Timofeeva Zhishan Chen Philip Law Minta Thomas Stephanie Schmit Virginia Díez-Obrero Li Hsu Juan Fernandez-Tajes Claire Palles Kitty Sherwood Sarah Briggs Victoria Svinti Kevin Donnelly Susan Farrington James Blackmur Peter Vaughan-Shaw Xiao-Ou Shu Jirong Long Qiuyin Cai Xingyi Guo Yingchang Lu Peter Broderick James Studd Jeroen Huyghe Tabitha Harrison David Conti Christopher Dampier Mathew Devall Fredrick Schumacher Marilena Melas Gad Rennert Mireia Obón-Santacana Vicente Martín-Sánchez Ferran Moratalla-Navarro Jae Hwan Oh Jeongseon Kim Sun Ha Jee Keum Ji Jung Sun-Seog Kweon Min-Ho Shin Aesun Shin Yoon-Ok Ahn Dong-Hyun Kim Isao Oze Wanqing Wen Keitaro Matsuo Koichi Matsuda Chizu Tanikawa Zefang Ren Yu-Tang Gao Wei-Hua Jia John Hopper Mark Jenkins Aung Ko Win Rish Pai Jane Figueiredo Robert Haile Steven Gallinger Michael Woods Polly Newcomb David Duggan Jeremy Cheadle Richard Kaplan Timothy Maughan Rachel Kerr David Kerr Iva Kirac Jan Böhm Lukka-Pekka Mecklin Pekka Jousilahti Paul Knekt Lauri Aaltonen Harri Rissanen Eero Pukkala Johan Eriksson Tatiana Cajuso Ulrika Hänninen Johanna Kondelin Kimmo Palin Tomas Tanskanen Laura Renkonen-Sinisalo Brent Zanke Satu Männistö Demetrius Albanes Stephanie Weinstein Edward Ruiz-Narvaez Julie Palmer Daniel Buchanan Elizabeth Platz Kala Visvanathan Cornelia Ulrich Erin Siegel Stefanie Brezina Andrea Gsur Peter Campbell Jenny Chang-Claude Michael Hoffmeister Hermann Brenner Martha Slattery John Potter Konstantinos Tsilidis Matthias Schulze Marc Gunter Neil Murphy Antoni Castells Sergi Castellví-Bel Leticia Moreira Volker Arndt Anna Shcherbina Mariana Stern Bens Pardamean Timothy Bishop Graham Giles Melissa Southey Gregory Idos Kevin McDonnell Zomoroda Abu-Ful Joel Greenson Katerina Shulman Flavio Lejbkowicz Kenneth Offit Yu-Ru Su Robert Steinfelder Temitope Keku Bethany van Guelpen Thomas Hudson Heather Hampel Rachel Pearlman Sonja Berndt Richard Hayes Marie Elena Martinez Sushma Thomas Douglas Corley Paul Pharoah Susanna Larsson Yun Yen Heinz-Jo Edinburgh Cancer Research Centre Institute of Genomics and Cancer University of Edinburgh Edinburgh UK. Genomic Medicine Group Instituto de Investigacion Sanitaria de Santiago Santiago de Compostela Spain. Colon Cancer Genetics Group Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK. Danish Institute for Advanced Study Department of Public Health University of Southern Denmark Odense Denmark. Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University Medical Center Nashville TN USA. Division of Genetics and Epidemiology Institute of Cancer Research London UK. Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle WA USA. Genomic Medicine Institute Cleveland Clinic Cleveland OH USA. Population and Cancer Prevention Program Case Comprehensive Cancer Center Cleveland OH USA. Colorectal Cancer Group ONCOBELL Program Bellvitge Biomedical Research Institute Barcelona Spain. Oncology Data Analytics Program Catalan Institute of Oncology Barcelona Spain. Consortium for Biomedical Research in Epidemiology and Public Health Madrid Madrid Spain. Department of Clinical Sciences Faculty of Medicine University of Barcelona Barcelona Spain. Department of Biostatistics School of Public Health University of Washington Seattle WA USA. Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Birmingham UK. Department of Public Health Richard Doll Building University of Oxford Oxford UK. Department of Biomedical Informatics Vanderbilt University School of Medicine Nashville TN USA. Department of Preventive Medicine USC Norris Comprehensive Cancer Center Keck School of Medicine University of Southern California Los Angeles CA USA. Center for Public Health Genomics Department of Public Health Sciences University of Virginia Charlottesville VA USA. De

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Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

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Nature genetics 2023年第6期55卷 1080页

作者： Bernardo Rodriguez-Martin Eva G Alvarez Adrian Baez-Ortega Jorge Zamora Fran Supek Jonas Demeulemeester Martin Santamarina Young Seok Ju Javier Temes Daniel Garcia-Souto Harald Detering Yilong Li Jorge Rodriguez-Castro Ana Dueso-Barroso Alicia L Bruzos Stefan C Dentro Miguel G Blanco Gianmarco Contino Daniel Ardeljan Marta Tojo Nicola D Roberts Sonia Zumalave Paul A Edwards Joachim Weischenfeldt Montserrat Puiggròs Zechen Chong Ken Chen Eunjung Alice Lee Jeremiah A Wala Keiran M Raine Adam Butler Sebastian M Waszak Fabio C P Navarro Steven E Schumacher Jean Monlong Francesco Maura Niccolo Bolli Guillaume Bourque Mark Gerstein Peter J Park David C Wedge Rameen Beroukhim David Torrents Jan O Korbel Iñigo Martincorena Rebecca C Fitzgerald Peter Van Loo Haig H Kazazian Kathleen H Burns Peter J Campbell Jose M C Tubio Department of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela Santiago de Compostela Spain. 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. Transmissible Cancer Group Department of Veterinary Medicine University of Cambridge Cambridge UK. The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain. Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK. Genome Data Science Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. The Francis Crick Institute London UK. Department of Human Genetics University of Leuven Leuven Belgium. Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea. Cancer Ageing and Somatic Mutation Programme Wellcome Sanger Institute Cambridge UK. Department of Biochemistry Genetics and Immunology University of Vigo Vigo Spain. Galicia Sur Health Research Institute Vigo Spain. Faculty of Science and Technology University of Vic-Central University of Catalonia (UVic-UCC) Vic Spain. Barcelona Supercomputing Center (BSC) Barcelona Spain. Experimental Cancer Genetics Wellcome Sanger Institute Cambridge UK. Oxford Big Data Institute University of Oxford Oxford UK. DNA Repair and Genome Integrity Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Department of Biochemistry and Molecular Biology Universidade de Santiago de Compostela Santiago de Compostela Spain. Medical R

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A structural variation reference for medical and population genetics (vol 581, pg 444, 2020)

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NATURE 2021年第7846期590卷 E55-E55页

作者： Collins, Ryan L. Brand, Harrison Karczewski, Konrad J. Zhao, Xuefang Alfoldi, Jessica Francioli, Laurent C. Khera, Amit V. Lowther, Chelsea Gauthier, Laura D. Wang, Harold Watts, Nicholas A. Solomonson, Matthew O'Donnell-Luria, Anne Baumann, Alexander Munshi, Ruchi Walker, Mark Whelan, Christopher W. Huang, Yongqing Brookings, Ted Sharpe, Ted Stone, Matthew R. Valkanas, Elise Fu, Jack Tiao, Grace Laricchia, Kristen M. Ruano-Rubio, Valentin Stevens, Christine Gupta, Namrata Cusick, Caroline Margolin, Lauren Taylor, Kent D. Lin, Henry J. Rich, Stephen S. Post, Wendy S. Chen, Yii-Der Ida Rotter, Jerome I. Nusbaum, Chad Philippakis, Anthony Lander, Eric Gabriel, Stacey Neale, Benjamin M. Kathiresan, Sekar Daly, Mark J. Banks, Eric MacArthur, Daniel G. Talkowski, Michael E. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Division of Medical Sciences Harvard Medical School Boston MA USA Department of Neurology Massachusetts General Hospital and Harvard Medical School Boston MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Department of Medicine Harvard Medical School Boston MA USA Data Science Platform Broad Institute of MIT and Harvard Cambridge MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK Cardiac Arrhythmia Service Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Diabetes Unit Massachusetts General Hospital Boston MA USA Program in Metabolism Broad Institute of MIT and Harvard Cambridge MA USA Division of Cardiology Massachusetts General Hospital Boston MA USA Cardiovascular Disease Initiative Broad Institute of MIT and Harvard Cambridge MA USA Division of General Internal Medicine Massachusetts General Hospital Boston MA USA Institute for Molecular Medicine Finland (FIMM) HiLIFE University of Helsinki Helsinki Finland Department of Public Health Faculty of Medicine University

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Gene expression imputation across multiple brain regions provides insights into schizophrenia risk (vol 51, pg 659, 2019)

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NATURE GENETICS 2019年第6期51卷 1068-1068页

作者： Huckins, Laura M. Dobbyn, Amanda Ruderfer, Douglas M. Hoffman, Gabriel Wang, Weiqing Pardinas, Antonio F. Rajagopal, Veera M. Als, Thomas D. Nguyen, Hoang T. Girdhar, Kiran Boocock, James Roussos, Panos Fromer, Menachem Kramer, Robin Domenici, Enrico Gamazon, Eric R. Purcell, Shaun Demontis, Ditte Borglum, Anders D. Walters, James T. R. O'Donovan, Michael C. Sullivan, Patrick Owen, Michael J. Devlin, Bernie Sieberts, Solveig K. Cox, Nancy J. Im, Hae Kyung Sklar, Pamela Stahl, Eli A. Pamela Sklar Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Genetics and Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Psychiatry Icahn School of Medicine at Mount Sinai New York NY USA Icahn Institute for Genomics and Multiscale Biology Icahn School of Medicine at Mount Sinai New York NY USA Vanderbilt University Medical Center Nashville TN USA MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff UK Department of Biomedicine Aarhus University Aarhus Denmark The Lundbeck Foundation Initiative for Integrative Psychiatric Research iPSYCH Denmark Center for Integrative Sequencing Aarhus University Aarhus Denmark Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA Human Brain Collection Core National Institute of Mental Health Bethesda MD USA Laboratory of Neurogenomic Biomarkers Centre for Integrative Biology (CIBIO) University of Trento Trento Italy Clare Hall University of Cambridge Cambridge UK University of North Carolina at Chapel Hill Chapel Hill NC USA Karolinska Institutet Stockholm Sweden Department of Psychiatry University of Pittsburgh Pittsburgh PA USA Systems Biology Sage Bionetworks Seattle WA USA Section of Genetic Medicine Department of Medicine University of Chicago Chicago IL USA Integrated Technology Research Laboratories Pharmaceutical Research Division Takeda Pharmaceutical Company Limited Fujisawa Japan Neuropsychiatry Section Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Neuropsychiatric Signaling Program Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Psychiatry JJ Peters Virginia Medical Center Bronx NY USA Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York NY USA Friedman Brain Institute

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.

关键词： Gene expression Genome-wide association studies Schizophrenia Transcriptomics

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