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Author Correction: Perspectives on ENCODE

Nature 2022年第7909期605卷 E4页

作者： Michael P Snyder Thomas R Gingeras Jill E Moore Zhiping Weng Mark B Gerstein Bing Ren Ross C Hardison John A Stamatoyannopoulos Brenton R Graveley Elise A Feingold Michael J Pazin Michael Pagan Daniel A Gilchrist Benjamin C Hitz J Michael Cherry Bradley E Bernstein Eric M Mendenhall Daniel R Zerbino Adam Frankish Paul Flicek Richard M Myers Department of Genetics School of Medicine Stanford University Palo Alto CA USA. mpsnyder@stanford.edu. Cardiovascular Institute Stanford School of Medicine Stanford CA USA. mpsnyder@stanford.edu. Functional Genomics Cold Spring Harbor Laboratory Cold Spring Harbor NY USA. University of Massachusetts Medical School Program in Bioinformatics and Integrative Biology Worcester MA USA. Department of Thoracic Surgery Clinical Translational Research Center Shanghai Pulmonary Hospital The School of Life Sciences and Technology Tongji University Shanghai China. Bioinformatics Program Boston University Boston MA USA. Yale University New Haven CT USA. Ludwig Institute for Cancer Research University of California San Diego La Jolla CA USA. Center for Epigenomics University of California San Diego La Jolla CA USA. Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA USA. Altius Institute for Biomedical Sciences Seattle WA USA. Department of Genome Sciences University of Washington Seattle WA USA. Department of Medicine University of Washington Seattle WA USA. Department of Genetics and Genome Sciences Institute for Systems Genomics UConn Health Farmington CT USA. National Human Genome Research Institute National Institutes of Health Bethesda MD USA. Department of Genetics School of Medicine Stanford University Palo Alto CA USA. Broad Institute and Department of Pathology Massachusetts General Hospital and Harvard Medical School Boston MA USA. Biological Sciences University of Alabama in Huntsville Huntsville AL USA. HudsonAlpha Institute for Biotechnology Huntsville AL USA. European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Cambridge UK.

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Cheminformatics Tools for Analyzing and Designing Optimized Small Molecule Collections and Libraries

SSRN

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SSRN 2019年

作者： Moret, Nienke Clark, Nicholas A. Hafner, Marc Wang, Yuan Lounkine, Eugen Medvedovic, Mario Wang, Jinhua Gray, Nathanael Jenkins, Jeremy Sorger, Peter K. HMS LINCS and Druggable Genome Centers Laboratory of Systems Pharmacology Harvard Program in Therapeutic Science Harvard Medical School BostonMA02115 United States Department of Systems Biology Harvard Medical School BostonMA02115 United States Division of Biostatistics and Bioinformatics Department of Environmental Health University of Cincinnati CincinnatiOH45221 United States Novartis Institutes for BioMedical Research Inc. 181 Massachusetts Avenue CambridgeMA02139 United States Department of Cancer Biology Dana-Farber Cancer Institute BostonMA02115 United States Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 360 Longwood Avenue Longwood Center 2209 BostonMA02115 United States Department of Bioinformatics and Computational Biology Genentech Inc. 1 DNA Way South San FranciscoCA94080 United States Warren Alpert 444 200 Longwood Avenue BostonMA02115 United States

Libraries of well-annotated small molecules have many uses in chemical genetics, drug discovery and drug repurposing. Many such libraries have become available, but few data-driven approaches exist to compare these libraries and design new ones. In this paper, we describe an approach to scoring and creating libraries based on available data, which is often incomplete, on binding selectivity, target coverage and induced cellular phenotypes as well as chemical structure, stage of clinical development and user preference. The approach, implemented as R software and a Web-accessible tool also assembles small sets of compounds (typically 2-8) that target a protein of interest while having the lowest possible off target overlap. Analysis of six kinase inhibitor libraries using our approach reveals dramatic differences among them, leading us to design a new LSP-OptimalKinase library that outperforms all previous collections in terms of target coverage and compact size. We also assemble a mechanism of action library that optimally covers 1852 targets of the liganded genome. Using our tools, individual research groups and companies can quickly analyze private compound collections, public libraries can be updated based on the latest data and the confounding effects of off-target activities minimized in chemical genetic studies. © 2019, The Authors. All rights reserved.

关键词： Libraries

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Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex

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Nature 2024年第7996期625卷 E26页

作者： Nathan R Zemke Ethan J Armand Wenliang Wang Seoyeon Lee Jingtian Zhou Yang Eric Li Hanqing Liu Wei Tian Joseph R Nery Rosa G Castanon Anna Bartlett Julia K Osteen Daofeng Li Xiaoyu Zhuo Vincent Xu Lei Chang Keyi Dong Hannah S Indralingam Jonathan A Rink Yang Xie Michael Miller Fenna M Krienen Qiangge Zhang Naz Taskin Jonathan Ting Guoping Feng Steven A McCarroll Edward M Callaway Ting Wang Ed S Lein M Margarita Behrens Joseph R Ecker Bing Ren Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA. Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA. Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. Genomic Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA. Division of Biological Sciences University of California San Diego La Jolla CA USA. Computational Neurobiology Laboratory The Salk Institute for Biological Studies La Jolla CA USA. Department of Genetics The Edison Family Center for Genome Sciences & Systems Biology Washington University School of Medicine St Louis MO USA. Princeton Neuroscience Institute Princeton University Princeton NJ USA. Department of Genetics Harvard Medical School Boston USA. Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA. McGovern Institute for Brain Research Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA USA. Allen Institute for Brain Science Seattle WA USA. Systems Neurobiology Laboratories The Salk Institute for Biological Studies La Jolla CA USA. Department of Neurosciences University of California San Diego La Jolla CA USA. McDonnell Genome Institute Washington University School of Medicine St. Louis MO USA. Department of Neurological Surgery University of Washington Seattle WA USA. Genomic Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA. ecker@salk.edu. Howard Hughes Medical Institute The Salk Institute for Biological Studies La Jolla CA USA. ecker@salk.edu. Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA. biren@ucsd.edu. Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA. biren@ucsd.edu. Institute of Genomic Medicine Moores Cancer C

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Publisher Correction: Lineage plasticity in cancer: a shared pathway of therapeutic resistance

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Nature reviews. Clinical oncology 2020年第6期17卷 382页

作者： Álvaro Quintanal-Villalonga Joseph M Chan Helena A Yu Dana Pe'er Charles L Sawyers Triparna Sen Charles M Rudin Department of Medicine Thoracic Oncology Service Memorial Sloan Kettering Cancer Center New York NY USA. Program for Computational and Systems Biology Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. Parker Institute for Cancer Immunotherapy Memorial Sloan Kettering Cancer Center New York NY USA. Human Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer Center New York NY USA. Howard Hughes Medical Institute Chevy Chase MD USA. Department of Medicine Thoracic Oncology Service Memorial Sloan Kettering Cancer Center New York NY USA. sent@***. Department of Medicine Thoracic Oncology Service Memorial Sloan Kettering Cancer Center New York NY USA. rudinc@***.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification

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Nature communications 2024年第1期15卷 2364页

作者： Celina Tretter Niklas de Andrade Krätzig Matteo Pecoraro Sebastian Lange Philipp Seifert Clara von Frankenberg Johannes Untch Gabriela Zuleger Mathias Wilhelm Daniel P Zolg Florian S Dreyer Eva Bräunlein Thomas Engleitner Sebastian Uhrig Melanie Boxberg Katja Steiger Julia Slotta-Huspenina Sebastian Ochsenreither Nikolas von Bubnoff Sebastian Bauer Melanie Boerries Philipp J Jost Kristina Schenck Iska Dresing Florian Bassermann Helmut Friess Daniel Reim Konrad Grützmann Katrin Pfütze Barbara Klink Evelin Schröck Bernhard Haller Bernhard Kuster Matthias Mann Wilko Weichert Stefan Fröhling Roland Rad Michael Hiltensperger Angela M Krackhardt German Cancer Consortium (DKTK) partner site Munich and German Cancer Research Center (DKFZ) Heidelberg Germany. Technical University of Munich TUM School of Medicine Klinikum rechts der Isar IIIrd Medical Department Munich Germany. Technical University of Munich TUM School of Medicine Klinikum rechts der Isar IInd Medical Department Munich Germany. Technical University of Munich TUM School of Medicine Center for Translational Cancer Research (TranslaTUM) Munich Germany. Technical University of Munich TUM School of Medicine Institute of Molecular Oncology and Functional Genomics Munich Germany. Department of Proteomics and Signal Transduction Max Plank Institute of Biochemistry Munich Germany. Institute for Research in Biomedicine Università della Svizzera italiana Bellinzona Switzerland. Technical University of Munich TUM School of Life Sciences Chair of Proteomics and Bioanalytics Freising Germany. Technical University of Munich TUM School of Life Sciences Computational Mass Spectrometry Freising Germany. German Cancer Consortium (DKTK) partner site Heidelberg and German Cancer Research Center (DKFZ) Heidelberg Germany. Molecular Precision Oncology Program NCT Heidelberg Heidelberg Germany. Technical University of Munich TUM School of Medicine Klinikum rechts der Isar Institute of Pathology Munich Germany. German Cancer Consortium (DKTK) partner site Berlin and German Cancer Research Center (DKFZ) Heidelberg Germany. Charité Comprehensive Cancer Center Charité - Universitätsmedizin Berlin Berlin Germany. Department of Hematology Oncology and Tumor Immunology Charité - Universitätsmedizin Berlin Berlin Germany. German Cancer Consortium (DKTK) partner site Freiburg and German Cancer Research Center (DKFZ) Heidelberg Germany. Institute of Medical Bioinformatics and Systems Medicine (IBSM) Medical Center - University of Freiburg Faculty of Medicine University of Freiburg Freiburg Germany. Department of Hematology and Oncology Medical Center Universit

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Quantum processor-inspired machine learning in the biomedical sciences

arXiv

引用

arXiv 2019年

作者： Li, Richard Y. Gujja, Sharvari Bajaj, Sweta R. Gamel, Omar E. Cilfone, Nicholas Gulcher, Jeffrey R. Lidar, Daniel A. Chittenden, Thomas W. Department of Chemistry University of Southern California Los AngelesCA United States Computational Biology and Bioinformatics Program Department of Biological Sciences University of Southern California Los AngelesCA United States Center for Quantum Information Science & Technology University of Southern California Los AngelesCA United States Computational Statistics and Bioinformatics Group Advanced Artificial Intelligence Research Laboratory Genuity Science BostonMA United States Complex Biological Systems Alliance MedfordMA United States Cancer Genetics Group Genuity Science BostonMA United States Department of Electrical Engineering University of Southern California Los AngelesCA United States Department of Physics and Astronomy University of Southern California Los AngelesCA United States Division of Genetics and Genomics Boston Children's Hospital Harvard Medical School BostonMA United States

Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide perspective. While the deluge of genomic information is expected to increase, a bottleneck in conventional high-performance computing is rapidly approaching. Inspired in part by recent advances in physical quantum processors, we evaluated several unconventional machine learning (ML) strategies on actual human tumor data;namely "Ising-type" methods whose objective function is formulated identically to simulated annealing and quantum annealing, as well as a restricted Boltzmann machine. Here we show for the first time the efficacy of multiple Ising-type ML algorithms for classification of high-dimensional, multi-omics human cancer data from the cancer Genome Atlas. To assess algorithm performance, we compared these classifiers to a variety of standard ML methods. Our results indicate the feasibility of using Ising-type ML to provide competitive classification of human cancer types and associated molecular subtypes and superior performance with smaller training datasets, thus providing compelling empirical evidence for the potential future application of unconventional computing approaches in the biomedical sciences. © 2019, CC BY.

关键词： Machine learning

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Correction to: A multi-step genomic approach prioritized TBKBP1 gene as relevant for multiple sclerosis susceptibility

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Journal of neurology 2022年第8期269卷 4523-4524页

作者： Melissa Sorosina Nadia Barizzone Ferdinando Clarelli Santosh Anand Sara Lupoli Erika Salvi Eleonora Mangano Roberta Bordoni Tina Roostaei Elisabetta Mascia Miriam Zuccalà Domizia Vecchio Paola Cavalla Silvia Santoro Laura Ferrè Alen Zollo Cristina Barlassina Daniele Cusi Vittorio Martinelli Giancarlo Comi Maurizio Leone Massimo Filippi Nikolaos A Patsopoulos Philip L De Jager Gianluca De Bellis Federica Esposito Sandra D'Alfonso Filippo Martinelli Boneschi Laboratory of Human Genetics of Neurological Disorders Division of Neuroscience IRCCS San Raffaele Scientific Institute 20132 Milan Italy. Department of Health Sciences Interdisciplinary Research Center of Autoimmune Diseases (IRCAD) University of Eastern Piedmont Avogadro University 28100 Novara Italy. Department of Informatics Systems and Communications (DISCo) University of Milano-Bicocca Milan Italy. Department of Health Sciences University of Milan 20139 Milan Italy. Neuroalgology Unit Fondazione IRCCS Istituto Neurologico "Carlo Besta" 20133 Milan Italy. National Research Council of Italy Institute for Biomedical Technologies Segrate 20090 Milan Italy. Center for Translational and Computational Neuroimmunology Department of Neurology and the Taub Institute for Research On Alzheimer's Disease and the Aging Brain Columbia University Irving Medical Center New York NY 10032 USA. MS Centre SCDU Neurology AOU Maggiore Della Carità Department of Translational Medicine Interdisciplinary Research Center of Autoimmune Diseases (IRCAD) University of Eastern Piedmont Avogadro 28100 Novara Italy. MS Center Department of Neuroscience and Mental Health City of Health and Science University Hospital of Torino 10126 Turin Italy. Neurology Unit IRCCS San Raffaele Scientific Institute 20132 Milan Italy. Department of Pathophysiology and Transplantation (DEPT) Dino Ferrari Centre Neuroscience Section University of Milan 20122 Milan Italy. Bio4Dreams Business Nursery for Life Sciences Piazzale Principessa Clotilde 4/A 20121 Milan Italy. SC Neurologia Dipartimento Di Scienze Mediche IRCCS Casa Sollievo Della Sofferenza San Giovanni Rotondo Italy. Vita-Salute San Raffaele University 20132 Milan Italy. Neuroimaging Research Unit Division of Neuroscience IRCCS San Raffaele Scientific Institute 20132 Milan Italy. Neurophysiology Unit IRCCS San Raffaele Scientific Institute IRCCS San Raffaele Scientific Institute 20132 Milan Italy. Systems Biology and Comp

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Correction: Evaluation of copy-number variants as modifiers of breast and ovarian cancer risk for BRCA1 pathogenic variant carriers

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European journal of human genetics : EJHG 2019年第1期27卷 167-168页

作者： Logan C Walker Louise Marquart John F Pearson George A R Wiggins Tracy A O'Mara Michael T Parsons Daniel Barrowdale Lesley McGuffog Joe Dennis Javier Benitez Thomas P Slavin Paolo Radice Debra Frost Andrew K Godwin Alfons Meindl Rita Katharina Schmutzler Claudine Isaacs Beth N Peshkin Trinidad Caldes Frans B L Hogervorst Conxi Lazaro Anna Jakubowska Marco Montagna Xiaoqing Chen Kenneth Offit Peter J Hulick Irene L Andrulis Annika Lindblom Robert L Nussbaum Katherine L Nathanson Georgia Chenevix-Trench Antonis C Antoniou Fergus J Couch Amanda B Spurdle Department of Pathology University of Otago Christchurch New Zealand. logan.walker@otago.ac.nz. Statistics Unit QIMR Berghofer Medical Research Institute Brisbane Queensland Australia. Biostatistics and Computational Biology Unit Department of the Dean University of Otago Christchurch New Zealand. Department of Pathology University of Otago Christchurch New Zealand. Genetics and Computational Biology Division QIMR Berghofer Medical Research Institute Brisbane Queensland Australia. Department of Public Health and Primary Care Centre for Cancer Genetic Epidemiology University of Cambridge Strangeways Research Laboratory Worts Causeway Cambridge UK. Human Genetics Group Spanish National Cancer Centre (CNIO) Madrid Spain. Department of Population Sciences Division of Clinical Cancer Genomics City of Hope Clinical Cancer Genomics Community Research Network Duarte CA USA. Department of Preventive and Predictive Medicine Unit of Molecular Bases of Genetic Risk and Genetic Testing Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT) Milan Italy. Department of Pathology and Laboratory Medicine University of Kansas Medical Center Kansas City KS USA. Department of Gynaecology and Obstetrics Division of Tumor Genetics Klinikum rechts der Isar Technical University Munich Munich Germany. Center for Hereditary Breast and Ovarian Cancer Medical Faculty University Hospital Cologne Cologne Germany. Lombardi Comprehensive Cancer Center Georgetown University Washington USA. Molecular Oncology Laboratory CIBERONC Hospital Clinico San Carlos IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos) Madrid Spain. Family Cancer Clinic Netherlands Cancer Institute Amsterdam The Netherlands. Molecular Diagnostic Unit Hereditary Cancer Program IDIBELL (Bellvitge Biomedical Research Institute) Catalan Institute of Oncology Gran Via de l'Hospitalet Barcelona Spain. Department of Genetics and Pathology Pome

This Article was originally published under a CC BY-NC-SA 4.0 license, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the Article have been modified accordingly.

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A clonal expression biomarker associates with lung cancer mortality (vol 25, pg 1540, 2019)

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NATURE MEDICINE 2020年第7期26卷 1148-1148页

作者： Biswas, Dhruva Birkbak, Nicolai J. Rosenthal, Rachel Hiley, Crispin T. Lim, Emilia L. Papp, Krisztian Boeing, Stefan Krzystanek, Marcin Djureinovic, Dijana La Fleur, Linnea Greco, Maria Doeme, Balazs Fillinger, Janos Brunnstrom, Hans Wu, Yin Moore, David A. Skrzypski, Marcin Abbosh, Christopher Litchfield, Kevin Al Bakir, Maise Watkins, Thomas B. K. Veeriah, Selvaraju Wilson, Gareth A. Jamal-Hanjani, Mariam Moldvay, Judit Botling, Johan Chinnaiyan, Arul M. Micke, Patrick Hackshaw, Allan Bartek, Jiri Csabai, Istvan Szallasi, Zoltan Herrero, Javier McGranahan, Nicholas Swanton, Charles Cancer Research UK Lung Cancer Centre of Excellence University College London Cancer Institute Paul O’Gorman Building London UK Bill Lyons Informatics Centre University College London Cancer Institute Paul O’Gorman Building London UK Cancer Evolution and Genome Instability Laboratory The Francis Crick Institute London UK Department of Molecular Medicine Aarhus University Aarhus Denmark Bioinformatics Research Centre Aarhus University Aarhus Denmark Department of Physics of Complex Systems ELTE Eötvös Loránd University Budapest Hungary Bioinformatics and Biostatistics The Francis Crick Institute London UK Danish Cancer Society Research Center Copenhagen Denmark Department of Immunology Genetics and Pathology Uppsala University Uppsala Sweden Genomics Equipment Park The Francis Crick Institute London UK Department of Tumor Biology National Korányi Institute of Pulmonology Semmelweis University Budapest Hungary Division of Thoracic Surgery Comprehensive Cancer Center Medical University of Vienna Vienna Austria Department of Thoracic Surgery National Institute of Oncology Semmelweis University Budapest Hungary Department of Pathology National Korányi Institute of Pulmonology Semmelweis University Budapest Hungary Department of Pathology National Institute of Oncology Budapest Hungary Lund University Laboratory Medicine Region Skåne Department of Clinical Sciences Lund Pathology Lund Sweden Department of Pathology UCL Cancer Institute London UK Department of Oncology and Radiotherapy Medical University of Gdansk Gdansk Poland SE-NAP Brain Metastasis Research Group 2nd Department of Pathology Semmelweis University Budapest Hungary Michigan Center for Translational Pathology University of Michigan Ann Arbor USA Department of Pathology University of Michigan Ann Arbor USA Rogel Cancer Center University of Michigan Ann Arbor USA Department of Urology University of Michigan Ann Arbor USA Howard Hughes Medical Institute University of Michigan An

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy

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Nature communications 2022年第1期13卷 3048页

作者： Jennifer Karin Ocasio Benjamin Babcock Daniel Malawsky Seth J Weir Lipin Loo Jeremy M Simon Mark J Zylka Duhyeong Hwang Taylor Dismuke Marina Sokolsky Elias P Rosen Rajeev Vibhakar Jiao Zhang Olivier Saulnier Maria Vladoiu Ibrahim El-Hamamy Lincoln D Stein Michael D Taylor Kyle S Smith Paul A Northcott Alejandro Colaneri Kirk Wilhelmsen Timothy R Gershon Department of Neurology University of North Carolina School of Medicine Chapel Hill NC 27599 USA. UNC Neuroscience Center University of North Carolina School of Medicine Chapel Hill NC 27599 USA. Department of Genetics University of North Carolina School of Medicine Chapel Hill NC 27599 USA. Department of Cell Biology and Physiology University of North Carolina School of Medicine Chapel Hill NC 27599 USA. Carolina Institute for Developmental Disabilities University of North Carolina School of Medicine Chapel Hill NC 27599 USA. UNC Eshelman School of Pharmacy University of North Carolina School of Medicine Chapel Hill NC 27599 USA. Department of Pediatrics University of Colorado Anschutz Medical Campus Aurora CO USA. Morgan Adams Foundation Pediatric Brain Tumor Research Program Children's Hospital Colorado Aurora CO USA. Developmental & Stem Cell Biology Program The Hospital for Sick Children Toronto ON M5G 0A4 Canada. The Arthur and Sonia Labatt Brain Tumour Research Centre The Hospital for Sick Children Toronto Ontario M5G 0A4 Canada. Department of Molecular Genetics University of Toronto Toronto ON M5G 0A4 Canada. Program in Computational Biology Ontario Institute for Cancer Research Toronto ON M5G 0A3 Canada. Division of Neurosurgery The Hospital for Sick Children Toronto ON M5S 3E1 Canada. Department of Developmental Neurobiology St. Jude Children's Research Hospital Memphis TN USA. Department of Neurology University of North Carolina School of Medicine Chapel Hill NC 27599 USA. kirk@med.unc.edu. Department of Genetics University of North Carolina School of Medicine Chapel Hill NC 27599 USA. kirk@med.unc.edu. Renaissance Computing Institute at UNC (RENCI) Chapel Hill NC 27517 USA. kirk@med.unc.edu. Department of Neurology University of North Carolina School of Medicine Chapel Hill NC 27599 USA. gershont@neurology.unc.edu. UNC Neuroscience Center University of North Carolina School of Medicine Chapel Hill NC 27599 USA.

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