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Corrigendum to "Identification of Differential Tumor Subtypes of T1 Bladder Cancer" [Eur. Urol. 78 (2020) 533-537]

European urology 2022年第2期81卷 e53页

作者： A Gordon Robertson Clarice S Groeneveld Brian Jordan Xiaoqi Lin Kimberly A McLaughlin Arighno Das Leigh Ann Fall Damiano Fantini Timothy J Taxter Lauren S Mogil Sia Viborg Lindskrog Lars Dyrskjøt David J McConkey Robert S Svatek Aurélien de Reyniès Mauro A A Castro Joshua J Meeks Dxige Research Inc. Courtenay BC Canada. Cartes d'Identité des Tumeurs Program Ligue Nationale Contre le Cancer Paris France Oncologie Moleculaire Institut Curie Equipe Labellisée Ligue Contre le Cancer Paris France. Department of Urology University of Washington Seattle WA USA. Department of Pathology Northwestern University Feinberg School of Medicine Chicago IL USA. Departments of Urology Biochemistry and Molecular Genetics Feinberg School of Medicine Northwestern University Chicago IL USA. Tempus Labs Inc. Chicago IL USA. Center for Translational Data Science University of Chicago Chicago IL USA. Department of Molecular Medicine Aarhus University Hospital Aarhus Denmark. Johns Hopkins Greenberg Bladder Cancer Institute Brady Urological Institute Johns Hopkins University Baltimore MD USA. Experimental Developmental Therapeutics Program UT Health MD Anderson San Antonio TX USA Department of Urology UT Health San Antonio San Antonio TX USA. Cartes d'Identité des Tumeurs Program Ligue Nationale Contre le Cancer Paris France. Bioinformatics and Systems Biology Laboratory Federal University of Paraná Curitiba Brazil. Departments of Urology Biochemistry and Molecular Genetics Feinberg School of Medicine Northwestern University Chicago IL USA Jesse Brown VA Medical Center Chicago IL USA. Electronic address: joshua.meeks@northwestern.edu.

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Erratum for Wang et al., "Clinically Applicable System for Rapidly Predicting Enterococcus faecium Susceptibility to Vancomycin"

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Microbiology spectrum 2022年第1期10卷 e0261021页

作者： Hsin-Yao Wang Chia-Ru Chung Chao-Jung Chen Ko-Pei Lu Yi-Ju Tseng Tzu-Hao Chang Min-Hsien Wu Wan-Ting Huang Ting-Wei Lin Tsui-Ping Liu Tzong-Yi Lee Jorng-Tzong Horng Jang-Jih Lu Department of Laboratory Medicine Chang Gung Memorial Hospitalgrid.413801.f at Linkou Taoyuan City Taiwan. Ph.D. Program in Biomedical Engineering Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Computer Science and Information Engineering National Central Universitygrid.37589.30 Taoyuan City Taiwan. Graduate Institute of Integrated Medicine China Medical Universitygrid.254145.3 Taichung Taiwan. Proteomics Core Laboratory China Medical Universitygrid.254145.3 Hospital Taichung Taiwan. Graduate Program in Biomedical Information Yuan-Ze University Taoyuan City Taiwan. Department of Information Management Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Graduate Institute of Biomedical Informatics Taipei Medical University Taipei City Taiwan. Clinical Big Data Research Center Taipei Medical University Hospital Taipei City Taiwan. Graduate Institute of Biomedical Engineering Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Division of Haematology/Oncology Department of Internal Medicine Chang Gung Memorial Hospitalgrid.413801.f at Linkou Taoyuan City Taiwan. Biosensor Group Biomedical Engineering Research Center Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Pathology Kaohsiung Chang Gung Memorial Hospitalgrid.413801.f and Chang Gung University College of Medicine Kaohsiung Taiwan. School of Life and Health Sciences The Chinese University of Hong Kong Shenzhen China. Warshel Institute for Computational Biology The Chinese University of Hong Kong Shenzhen China. Department of Bioinformatics and Medical Engineering Asia University Taichung City Taiwan. School of Medicine Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Medical Biotechnology and Laboratory Science Chang Gung Universitygrid.145695.a Taoyuan City Taiwan.

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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries (vol 55, pg 89, 2023)

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NATURE GENETICS 2023年第3期55卷 519-520页

作者： Fernandez-Rozadilla, Ceres Timofeeva, Maria Chen, Zhishan Law, Philip Thomas, Minta Schmit, Stephanie Diez-Obrero, Virginia Hsu, Li Fernandez-Tajes, Juan Palles, Claire Sherwood, Kitty Briggs, Sarah Svinti, Victoria Donnelly, Kevin Farrington, Susan Blackmur, James Vaughan-Shaw, Peter Shu, Xiao-ou Long, Jirong Cai, Qiuyin Guo, Xingyi Lu, Yingchang Broderick, Peter Studd, James Huyghe, Jeroen Harrison, Tabitha Conti, David Dampier, Christopher Devall, Mathew Schumacher, Fredrick Melas, Marilena Rennert, Gad Obon-Santacana, Mireia Martin-Sanchez, Vicente Moratalla-Navarro, Ferran Oh, Jae Hwan Kim, Jeongseon Jee, Sun Ha Jung, Keum Ji Kweon, Sun-Seog Shin, Min-Ho Shin, Aesun Ahn, Yoon-Ok Kim, Dong-Hyun Oze, Isao Wen, Wanqing Matsuo, Keitaro Matsuda, Koichi Tanikawa, Chizu Ren, Zefang Gao, Yu-Tang Jia, Wei-Hua Hopper, John Jenkins, Mark Win, Aung Ko Pai, Rish Figueiredo, Jane Haile, Robert Gallinger, Steven Woods, Michael Newcomb, Polly Duggan, David Cheadle, Jeremy Kaplan, Richard Maughan, Timothy Kerr, Rachel Kerr, David Kirac, Iva Bohm, Jan Mecklin, Lukka-Pekka Jousilahti, Pekka Knekt, Paul Aaltonen, Lauri Rissanen, Harri Pukkala, Eero Eriksson, Johan Cajuso, Tatiana Hanninen, Ulrika Kondelin, Johanna Palin, Kimmo Tanskanen, Tomas Renkonen-Sinisalo, Laura Zanke, Brent Mannisto, Satu Albanes, Demetrius Weinstein, Stephanie Ruiz-Narvaez, Edward Palmer, Julie Buchanan, Daniel Platz, Elizabeth Visvanathan, Kala Ulrich, Cornelia Siegel, Erin Brezina, Stefanie Gsur, Andrea Campbell, Peter Chang-Claude, Jenny Hoffmeister, Michael Brenner, Hermann Slattery, Martha Potter, John Tsilidis, Konstantinos Schulze, Matthias Gunter, Marc Murphy, Neil Castells, Antoni Castellvi-Bel, Sergi Moreira, Leticia Arndt, Volker Shcherbina, Anna Stern, Mariana Pardamean, Bens Bishop, Timothy Giles, Graham Southey, Melissa Idos, Gregory McDonnell, Kevin Abu-Ful, Zomoroda Greenson, Joel Shulman, Katerina Lejbkowicz, Flavio Offit, Kenneth Su, Yu-Ru Steinfelder, Robert Keku, Temitope van Guelpen, Bethany Hudson, Thomas Hampel, Heather Pearlman, 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 Department of Populat

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.

关键词： Colorectal cancer Epigenomics Genome-wide association studies Transcriptomics

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Author Correction: PNPO-PLP axis senses prolonged hypoxia in macrophages by regulating lysosomal activity

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Nature metabolism 2024年第12期6卷 2391页

作者： Hiroki Sekine Haruna Takeda Norihiko Takeda Akihiro Kishino Hayato Anzawa Takayuki Isagawa Nao Ohta Shohei Murakami Hideya Iwaki Nobufumi Kato Shu Kimura Zun Liu Koichiro Kato Fumiki Katsuoka Masayuki Yamamoto Fumihito Miura Takashi Ito Masatomo Takahashi Yoshihiro Izumi Hiroyuki Fujita Hitoshi Yamagata Takeshi Bamba Takaaki Akaike Norio Suzuki Kengo Kinoshita Hozumi Motohashi Department of Medical Biochemistry Tohoku University Graduate School of Medicine Sendai Japan. hiroki.sekine.c2@tohoku.ac.jp. Department of Medical Biochemistry Tohoku University Graduate School of Medicine Sendai Japan. Division of Cardiology and Metabolism Center for Molecular Medicine Jichi Medical University Shimotsuke Japan. Department of Cardiovascular Medicine Graduate School of Medicine The University of Tokyo Tokyo Japan. Department of Gene Expression Regulation IDAC Tohoku University Sendai Japan. Department of System Bioinformatics Graduate School of Information Sciences Tohoku University Sendai Japan. Department of Integrative Genomics Tohoku Medical Megabank Organization Tohoku University Sendai Japan. Data Science Center Jichi Medical University Shimotsuke Japan. Division of Oxygen Biology United Centers for Advanced Research and Translational Medicine Tohoku University Graduate School of Medicine Sendai Japan. Department of Biochemistry and Molecular Biology Tohoku Medical Megabank Organization Tohoku University Sendai Japan. Department of Biochemistry Kyushu University Graduate School of Medical Sciences Fukuoka Japan. Division of Metabolomics Medical Institute of Bioregulation Kyushu University Fukuoka Japan. Advanced Research Laboratory Canon Medical Systems Corporation Otawara Japan. Department of Environmental Medicine and Molecular Toxicology Tohoku University Graduate School of Medicine Sendai Japan. Department of Medical Biochemistry Tohoku University Graduate School of Medicine Sendai Japan. hozumi.motohashi.a7@tohoku.ac.jp. Department of Gene Expression Regulation IDAC Tohoku University Sendai Japan. hozumi.motohashi.a7@tohoku.ac.jp.

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66O Association of a blood T cell fitness gene signature with clinical benefit from ImmTAC bispecific T cell engagers

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Annals of Oncology 2024年 35卷 S239-S240页

作者： J.J. Sacco R.D. Carvajal O. Hamid P.B. Kirk L. Collins M.O. Butler A.N. Shoushtari J.C. Hassel A.P. Ikeguchi L. Hernandez-Aya P. Nathan J.M. Piulats Rodriguez H. Shaw D. Davar C. Han M.R. Middleton F. Thistlethwaite F. Peck K. Ranade T. Sato Medical Oncology Department The Clatterbridge Cancer Centre and University of Liverpool Wirral UK Medical Oncology Northwell Health Cancer Institute New York NY USA Melanoma Center and Phase I Immuno-Oncology Program The Angeles Clinic and Research Institute a Cedars-Sinai Affiliate Los Angeles CA USA Translational Medicine Immunocore Limited Abingdon-on-Thames UK Bioinformatics and Data Science Immunocore Limited Abingdon-on-Thames UK Department of Medical Oncology and Hematology Princess Margaret Cancer Center Toronto ON Canada Medical Oncology Memorial Sloan Kettering Cancer Center New York NY USA Department of Dermatology and National Center for Tumor Diseases University Hospital Heidelberg Heidelberg Germany Department of Medicine Stephenson Cancer Center/University of Oklahoma Oklahoma City OK USA Cutaneous Oncology University of Miami Sylvester Comprehensive Cancer Center Miami Beach FL USA Medical Oncology Department Mount Vernon Cancer Centre Northwood UK Medical Oncology Department ICO - Institut Català d'Oncologia l'Hospitalet (Hospital Duran i Reynals) Barcelona Spain Medical Oncology UCLH - University College London Hospitals NHS Foundation Trust London UK Medical Oncology University of Pittsburgh Cancer Institute Pittsburgh PA USA Faculty of Medical & Health Sciences University of Auckland Auckland New Zealand Department of Oncology University of Oxford Oxford UK Medical Oncology Department The Christie NHS Foundation Trust Manchester UK Clinical Development Immunocore Limited Abingdon-on-Thames UK Translational Medicine Department Immunocore LLC Rockville MD USA Sidney Kimmel Cancer Center Jefferson University Philadelphia PA USA

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Genome-wide association analysis in dilated cardiomyopathy reveals two new players in systolic heart failure on chromosomes 3p25.1 and 22q11.23 (vol 42, pg 2000, 2021)

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EUROPEAN HEART JOURNAL 2021年第20期42卷 2011-2011页

作者： Garnier, S. Sorbonne Université INSERM UMR-S1166 Research Unit on Cardiovascular Disorders Metabolism and Nutrition Team Genomics & Pathophysiology of Cardiovascular Diseases Paris 75013 France ICAN Institute for Cardiometabolism and Nutrition Paris 75013 France Department of Cardiology Division Heart & Lungs University Medical Center Utrecht Utrecht University Utrecht the Netherlands Regenerative Medicine Center University Medical Center Utrecht Utrecht the Netherlands Interfaculty Institute for Genetics and Functional Genomics Department of Functional Genomics University Medicine Greifswald Greifswald Germany DZHK (German Centre for Cardiovascular Research) partner site Greifswald Greifswald Germany Laboratory of Clinical Chemistry and Haematology University Medical Center Heidelberglaan 100 Utrecht the Netherlands Laboratory of Experimental Cardiology University Medical Center Utrecht Heidelberglaan 100 Utrecht the Netherlands Institute of Gender in Medicine and Center for Cardiovascular Research Charite University Hospital Berlin Germany DZHK (German Center for Cardiovascular Research) Berlin Germany Department of Internal Medicine Division of Cardiology Medical University of Vienna Austria Department of Internal Medicine Medical University of Regensburg Germany Penn Cardiovascular Institute and Department of Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Cardiology Department APHP Pitié-Salpêtrière Hospital Paris France IRCCS Fondazione Policlinico San Matteo Pavia Italy National Heart and Lung Institute Imperial College London London UK National Heart Centre Singapore Singapore Duke-NUS Singapore Center for Applied Genomics Children’s Hospital of Philadelphia Philadelphia PA USA Department of Genetic Epidemiology University of Regensburg Regensburg Germany Royal Brompton Hospital London UK Medical Research Council Clinical Sciences Centre Faculty of Medicine Imperial College London South Kensington Campus London

Aims Our objective was to better understand the genetic bases of dilated cardiomyopathy (DCM), a leading cause of systolic heart *** and results We conducted the largest genome-wide association study performed so far in DCM, with 2719 cases and 4440 controls in the discovery population. We identified and replicated two new DCM-associated loci on chromosome 3p25.1 [lead single-nucleotide polymorphism (SNP) rs62232870, P = 8.7 × 10−11 and 7.7 × 10−4 in the discovery and replication steps, respectively] and chromosome 22q11.23 (lead SNP rs7284877, P = 3.3 × 10−8 and 1.4 × 10−3 in the discovery and replication steps, respectively), while confirming two previously identified DCM loci on chromosomes 10 and 1, BAG3 and HSPB7. A genetic risk score constructed from the number of risk alleles at these four DCM loci revealed a 3-fold increased risk of DCM for individuals with 8 risk alleles compared to individuals with 5 risk alleles (median of the referral population). In silico annotation and functional 4C-sequencing analyses on iPSC-derived cardiomyocytes identify SLC6A6 as the most likely DCM gene at the 3p25.1 locus. This gene encodes a taurine transporter whose involvement in myocardial dysfunction and DCM is supported by numerous observations in humans and animals. At the 22q11.23 locus, in silico and data mining annotations, and to a lesser extent functional analysis, strongly suggest SMARCB1 as the candidate culprit *** This study provides a better understanding of the genetic architecture of DCM and sheds light on novel biological pathways underlying heart failure.

关键词： Dilated cardiomyopathy Heart failure GWAS Imputation 4C-sequencing Genetic risk score

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Correction to: An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids

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Genetics in medicine : official journal of the American College of Medical Genetics 2021年第12期23卷 2467页

作者： Sacha Ferdinandusse Kirsty McWalter Heleen Te Brinke Lodewijk IJlst Petra M Mooijer Jos P N Ruiter Alida E M van Lint Mia Pras-Raves Eric Wever Francisca Millan Maria J Guillen Sacoto Amber Begtrup Mark Tarnopolsky Lauren Brady Roger L Ladda Susan L Sell Catherine B Nowak Jessica Douglas Cuixia Tian Elizabeth Ulm Seth Perlman Arlene V Drack Karen Chong Nicole Martin Jennifer Brault Elly Brokamp Camilo Toro William A Gahl Ellen F Macnamara Lynne Wolfe Quinten Waisfisz Petra J G Zwijnenburg Alban Ziegler Magalie Barth Rosemarie Smith Sara Ellingwood Deborah Gaebler-Spira Somayeh Bakhtiari Michael C Kruer Antoine H C van Kampen Ronald J A Wanders Hans R Waterham David Cassiman Frédéric M Vaz Laboratory Genetic Metabolic Diseases Amsterdam UMC University of Amsterdam Department of Clinical Chemistry Amsterdam Gastroenterology Endocrinology Metabolism Amsterdam The Netherlands. s.ferdinandusse@amsterdamumc.nl. GeneDx Gaithersburg MD USA. Laboratory Genetic Metabolic Diseases Amsterdam UMC University of Amsterdam Department of Clinical Chemistry Amsterdam Gastroenterology Endocrinology Metabolism Amsterdam The Netherlands. Core Facility Metabolomics Amsterdam UMC Amsterdam The Netherlands. Bioinformatics Laboratory Department of Epidemiology and Data Science Amsterdam Public Health Research Institute Amsterdam UMC University of Amsterdam Amsterdam The Netherlands. Department of Pediatrics McMaster University Children's Hospital Hamilton ON Canada. Department of Pediatrics Penn State Children's Hospital Hershey PA USA. The Feingold Center for Children Division of Genetics and Genomics Boston Children's Hospital Boston MA USA. Division of Neurology Cincinnati Children's Hospital Medical Center Department of Pediatrics University of Cincinnati College of Medicine Cincinnati OH USA. Division of Human Genetics Cincinnati Children's Hospital Medical Center Cincinnati OH USA. Department of Neurology University of Iowa Hospitals and Clinics Iowa City IA USA. Department of Ophthalmology and Visual Sciences University of Iowa Iowa City IA USA. Mount Sinai Hospital Department of Obstetrics and Gynecology Prenatal Diagnosis and Medical Genetics Program Toronto ON Canada. Vanderbilt University Medical Center Department of Pediatrics Nashville TN USA. NIH Undiagnosed Diseases Program Office of the Clinical Director National Human Genome Research Institute NIH Bethesda MD USA. Department of Clinical Genetics Amsterdam UMC Vrije Universiteit Amsterdam Amsterdam The Netherlands. Genetic department University Hospital Angers Angers France. Division of Genetics Department of Pediatrics Maine Medical Center Portland ME USA. Feinberg Northwest

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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STAGER checklist: Standardized testing and assessment guidelines for evaluating generative artificial intelligence reliability

iMetaOmics

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iMetaOmics 2024年第1期1卷

作者： Jinghong Chen Lingxuan Zhu Weiming Mou Anqi Lin Dongqiang Zeng Chang Qi Zaoqu Liu Aimin Jiang Bufu Tang Wenjie Shi Ulf D. Kahlert Jianguo Zhou Shipeng Guo Xiaofan Lu Xu Sun Trunghieu Ngo Zhongji Pu Baolei Jia Che Ok Jeon Yongbin He Haiyang Wu Shuqin Gu Wisit Cheungpasitporn Haojie Huang Weipu Mao Shixiang Wang Xin Chen Loïc Cabannes Gerald Sng Gui Ren Iain S. Whitaker Stephen Ali Quan Cheng Kai Miao Shuofeng Yuan Peng Luo Department of Oncology Zhujiang Hospital Southern Medical University Guangzhou China The Second School of Clinical Medicine Southern Medical University Guangzhou China Department of Urology Shanghai General Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Department of Oncology Nanfang Hospital Southern Medical University Guangzhou China Institute of Logic and Computation TU Wien Wien Austria Institute of Basic Medical Sciences Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China Department of Urology Changhai Hospital Naval Medical University (Second Military Medical University) Shanghai China Department of Radiation Oncology Zhongshan Hospital Fudan University Shanghai China Molecular and Experimental Surgery University Clinic for General- Visceral- Vascular- and Trans-Plantation Surgery Medical Faculty University Hospital Magdeburg Otto-von Guericke University Magdeburg Germany Department of Oncology The Second Affiliated Hospital of Zunyi Medical University Zunyi China Translational Radiobiology Department of Radiation Oncology Universitätsklinikum Erlangen Erlangen Germany Comprehensive Cancer Center Erlangen-EMN Erlangen Germany GZDLab Chongqing China Department of Cancer and Functional Genomics Institute of Genetics and Molecular and Cellular Biology CNRS/INSERM/UNISTRA Illkirch France Linguistique Informatique UFR-Linguistique Université Paris Cité Paris France Xianghu Laboratory Hangzhou China Department of Life Science Chung-Ang University Seoul Korea School of Sport Medicine and Rehabilitation Beijing Sport University Beijing China Department of Microbiology and Immunology School of Medicine Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill Chapel Hill North Carolina USA Department of Graduate School Tianjin Medical University Tianjin China Department of Clinical College of Neurology Neurosurgery and Neurorehabilitation Tianjin Medical Universi

Generative artificial intelligence (AI) holds immense potential for medical applications, but the lack of a comprehensive evaluation framework and methodological deficiencies in existing studies hinder its effective implementation. Standardized assessment guidelines are crucial for ensuring reliable and consistent evaluation of generative AI in healthcare. Our objective is to develop robust, standardized guidelines tailored for evaluating generative AI performance in medical contexts. Through a rigorous literature review utilizing the Web of sciences, Cochrane Library, PubMed, and Google Scholar, we focused on research testing generative AI capabilities in medicine. Our multidisciplinary team of experts conducted discussion sessions to develop a comprehensive 32-item checklist. This checklist encompasses critical evaluation aspects of generative AI in medical applications, addressing key dimensions such as question collection, querying methodologies, and assessment techniques. The checklist and its broader assessment framework provide a holistic evaluation of AI systems, delineating a clear pathway from question gathering to result assessment. It guides researchers through potential challenges and pitfalls, enhancing research quality and reporting and aiding the evolution of generative AI in medicine and life sciences. Our framework furnishes a standardized, systematic approach for testing generative AI's applicability in medicine. For a concise checklist, please refer to Table S or visit *** . This work formulates the standardized testing and assessment guidelines for evaluating generative artificial intelligence (AI) reliability (STAGER) checklist, a 32-item framework offering standardized assessment guidelines tailored for evaluating generative AI systems in medical and life science contexts. It consists of key aspects, including question collection, querying approaches, and assessment techniques. It enhances research quality and facilitates advances in

关键词： generative AI medical and life science contexts reliability standardized assessment guidelines

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TREM2 Burden associates solely with Alzheimer’s Disease, and decreases the Chance to become a Centenarian

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Alzheimer's & Dementia 2023年第S12期19卷

作者： Janna I.R. Dijkstra Lisa Vermunt Geert Jan Biessels den Anouk Braber Jurgen A.H.R. Claassen Peter Paul De Deyn Mohsen Ghanbari Martijn Huisman Marc Hulsman Inez H.G.B. Ramakers Marcel J. T. Reinders Harro Seelaar Niccoló Tesi Pieter Jelle Visser Wiesje M. van der Flier Charlotte E. Teunissen Henne Holstege Sven J Van Der Lee Amsterdam Neuroscience Amsterdam Netherlands Genomics of Neurodegenerative Diseases and Aging Human Genetics Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Amsterdam Netherlands Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Neurochemistry Laboratory Amsterdam UMC Amsterdam Netherlands Amsterdam Neuroscience Neurodegeneration Amsterdam Netherlands Department of Neurology UMC Utrecht Brain Center University Medical Center Utrecht Utrecht Netherlands Department of Biological Psychology Vrije Universiteit Amsterdam Amsterdam Netherlands Department of Cardiovascular Sciences University of Leicester Leicester United Kingdom Department of Geriatrics & Radboudumc Alzheimer Center Radboud University Medical Center Nijmegen Netherlands Laboratory of Neurochemistry and Behaviour University of Antwerp Antwerp Belgium University Medical Center Groningen Neurology and Alzheimer Center Groningen Netherlands Department of Neurology and Memory Clinic Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken Antwerp Antwerp Belgium Department of Epidemiology Erasmus Medical Centre Rotterdam Netherlands Aging & Later Life Amsterdam Public Health Amsterdam Amsterdam Netherlands Department of Epidemiology & Data Science Amsterdam UMC location Vrije Universiteit Amsterdam Amsterdam Netherlands Department of Sociology Amsterdam UMC location Vrije Universiteit Amsterdam Amsterdam Netherlands Genomics of Neurodegenerative Diseases and Aging Human Genetics Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Alzheimer Center Limburg School for Mental Health and Neuroscience (MHeNs) Maastricht University Maastricht Netherlands Delft Bioinformatics Lab Delft University of Technology Delft Delft Netherlands Department of Neurology Erasmus Medical Center Rotterdam Rotterdam Netherlands Department of Neurobiology Care Sciences and Society Division of Neurog

Background Rare TREM2 variants are major risk factors for Alzheimer’s disease (AD), but TREM2 variants may also confer a higher risk for other neurodegenerative diseases and a lower probability for cognitively healthy aging. We studied the TREM2 burden associated with different types of dementia and cognitively healthy centenarians (CHCs). Method We included participants of the 100-Plus Study, Amsterdam Dementia Cohort, Longitudinal Aging Study Amsterdam and various Dutch memory clinics. TREM2 variants (R47H, R62H, Q33X, R62C, T96K) were genotyped with a high density array or imputed using standard methods (TOPMED reference panel). To avoid family bias and ethnic differences, related individuals and those of non-European ancestry were excluded. Frequencies of individual variants and the burden of TREM2 variants were compared in AD dementia, dementia with Lewy Bodies (DLB), frontotemporal dementia (FTD), cognitively normal controls and CHCs (correcting for 5 principal components). Result We identified 242 carriers of TREM2 mutations and 6,683 controls without a TREM2 mutation with a mean age of 69 years (SD ±14 years), 50% female (Table 1). TREM2 variants were significantly associated with AD dementia (OR 1.4, 95%CI 1.1-1.8, p = 0.01) (Table 2). R47H conferred the highest risk for AD (OR 2.8, 95%CI 1.4-5.6, p = 0.004), compared to 1.3-fold increased risk of R62H (95%CI 0.9-1.7, p = 0.11). The carrier frequency was not increased in DLB (OR 1.4, 95%CI 0.7-2.6, p = 0.34) and was not increased in FTD compared to controls (OR 0.59, 95%CI 0.3-1.3, p = 0.18). Of interest, the allele frequency of TREM2 variants in centenarians is half of the expected frequency (OR = 0.46, 95%CI 0.1-1.1, p = 0.10), and only concerns R62H. Conclusion We replicate the association of TREM2 with increased risk of AD. In contrast to previous reports no association was observed with DLB or FTD. Cognitively healthy centenarians show a negative trend for TREM2 allele frequency suggesting that carryin

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