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arXiv 2024年

作者： Radtke, Andrea J. Anidi, Ifeanyichukwu Arakkal, Leanne Arroyo-Mejias, Armando Beuschel, Rebecca T. Börner, Katy Chu, Colin J. Clark, Beatrice Clatworthy, Menna R. Colautti, Jake Croteau, Joshua Denha, Saven Dever, Rose Dutra, Walderez O. Fritzsche, Sonja Fullam, Spencer Gerner, Michael Y. Gola, Anita Gollob, Kenneth J. Hernandez, Jonathan M. Hor, Jyh Liang Ichise, Hiroshi Jing, Zhixin Jonigk, Danny Kandov, Evelyn Kastenmüller, Wolfgang Koenig, Joshua F.E. Kothurkar, Aanandita Kreins, Alexandra Y. Lamborn, Ian Lin, Yuri Morais, Katia Luciano Pereira Lunich, Aleksandra Luz, Jean C.S. MacDonald, Ryan B. Makranz, Chen Maltez, Vivien I. Moriaty, Ryan V. Ocampo-Godinez, Juan M. Olyntho, Vitoria M. Padhan, Kartika Remmert, Kirsten Richoz, Nathan Schrom, Edward C. Shang, Wanjing Shi, Lihong Shih, Rochelle M. Speranza, Emily Stierli, Salome Teichmann, Sarah A. Veres, Tibor Z. Vierhout, Megan Wachter, Brianna T. Wade-Vallance, Adam K. Williams, Margaret Zangger, Nathan Germain, Ronald N. Yaniv, Ziv Lymphocyte Biology Section Center for Advanced Tissue Imaging Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Critical Care Medicine and Pulmonary Branch National Heart Lung and Blood Institute National Institutes of Health BethesdaMD United States Lymphocyte Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Department of Intelligent Systems Engineering Indiana University BloomingtonIN United States UCL Institute of Ophthalmology NIHR Moorfields Biomedical Research Centre London United Kingdom Cambridge Institute for Therapeutic Immunology and Infectious Diseases University of Cambridge Department of Medicine Molecular Immunity Unit Laboratory of Molecular Biology Cambridge United Kingdom McMaster Immunology Research Centre Schroeder Allergy and Immunology Research Institute Department of Medicine Faculty of Health Sciences McMaster University HamiltonON Canada Department of Business Development BioLegend Inc. San DiegoCA United States Functional Immunogenomics Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health BethesdaMD United States Laboratory of Cell-Cell Interactions Department of Morphology Institute of Biological Sciences Universidade Federal de Minas Gerais MG Belo Horizonte Brazil Spatial Proteomics Group Berlin Germany Division of Rheumatology Rush University Medical Center ChicagoIL United States Department of Immunology University of Washington School of Medicine SeattleWA United States Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development The Rockefeller University New YorkNY United States Hospital Israelita Albert Einstein SP Sao Paulo Brazil Surgical Oncology Program National Cancer Institute National Institutes of Health BethesdaMD United St

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, p... 详细信息

关键词： Cleaning

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Mechanistic Insights into CLNS1A-Mediated Chemoresistance and Tumor Progression in Non-small Cell Lung Cancer

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Cancer letters 2025年 626卷 217783页

作者： Tong-You Wade Wei Jiun-Yi Hsia Tsung-Ying Yang Yu-Xu Huang Guo-Zhi Wang Yi-Chung Liu Yi-Wun Wang Fangzhou He Jo-Mei Maureen Chen Guo-Jun Zhao Ping-Chiang Lyu Li-Jen Su Shao-Chih Chiu Chang-Tze Ricky Yu Department of Applied Chemistry National Chi Nan University Nantou Taiwan Division of Cardiology Department of Medicine University of California San Diego La Jolla California USA. Electronic address: t1wei@health.ucsd.edu. Division of Thoracic Surgery Chung Shan Medical University Hospital Taichung Taiwan School of Medicine Chung Shan Medical University Taichung Taiwan. Department of Chest Medicine Taichung Veterans General Hospital Taichung Taiwan Doctoral Program in Translational Medicine National Chung Hsing University Taichung Taiwan. Department of Medicine JingGangShan University Ji'an China. Division of Thoracic Surgery Chung Shan Medical University Hospital Taichung Taiwan. Department of Life Sciences National Tsing Hua University Hsinchu Taiwan. Cardiovascular Research Center School of Basic Medical Sciences Xi'an Jiaotong University Health Science Center Xi'an China. Department of Applied Chemistry National Chi Nan University Nantou Taiwan. Department of Cardiology The First Affiliated Hospital of Zhengzhou University Zhengzhou China. Institute of Bioinformatics and Structural Biology Department of Life Science National Tsing Hua University Hsinchu Taiwan. Department of Biomedical Sciences and Engineering Education and Research Center for Technology Assisted Substance Abuse Prevention and Management and Core Facilities for High Throughput Experimental Analysis National Central University Taoyuan Taiwan. Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan Translational Cell Therapy Center Department of Medical Research China Medical University Hospital Taichung Taiwan. Electronic address: scchiu@mail.cmu.edu.tw. Department of Applied Chemistry National Chi Nan University Nantou Taiwan. Electronic address: ctyu@ncnu.edu.tw.

CLNS1A is a chloride channel protein and an essential component of the methylosome complex, which additionally comprises PRMT5 and MEP50. In this study, we investigated its contribution to lung cancer and its potential as a therapeutic target. Analysis of transcriptomic datasets and western blotting revealed that CLNS1A, PRMT5, and MEP50 were overexpressed in lung cancer tissues, with elevated CLNS1A expression correlating with poor patient survival. CLNS1A overexpression enhanced platinum clearance from cells, increased the IC values for chemotherapy, and improved cell survival. Conversely, the knockdown of CLNS1A increased drug accumulation, reduced survival, and increased sensitivity to chemotherapy. The 3W mutant, a chloride channel-defective variant with steric hindrance at key bottleneck residues, impaired chloride ion transport, thereby reducing drug resistance, migration, and anchorage-independent growth. Mechanistically, CLNS1A promotes drug efflux through its chloride channel activity and activates the FAK-SRC-RAC1 pathway to enhance motility and clonogenicity. It also facilitates PRMT5-mediated RUVBL1 methylation to support anti-apoptotic DNA damage response signaling. In vivo, CLNS1A overexpression accelerated tumor growth and reduced survival, whereas CLNS1A knockdown sensitized tumors to cisplatin, enhancing therapeutic efficacy. These findings suggest that CLNS1A is a potential biomarker and therapeutic target, and its inhibition offers a strategy to overcome drug resistance and limit the metastatic progression of lung cancer.

关键词： Chemoresistance Chloride channel DNA damage response Lung cancer Metastasis

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

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NATURE 2023年第7948期614卷 E42-E42页

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

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Revised JNLPBA corpus: A revised version of biomedical NER corpus for relation extraction task

arXiv

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arXiv 2019年

作者： Huang, Ming-Siang Lai, Po-Ting Tsai, Richard Tzong-Han Hsu, Wen-Lian Bioinformatics Program Taiwan International Graduate Program Institute of Information Science Academia Sinica Taipei Taiwan Institute of Biomedical Informatics National Yang Ming University Taipei Taiwan Department of Computer Science National Tsing-Hua University Hsinchu Taiwan Intelligent Agent Systems Laboratory Institute of Information Science Academia Sinica Taipei Taiwan Intelligent Information Service Research Laboratory Department of Computer Science and Information Engineering National Central University Taoyuan Taiwan

The advancement of biomedical named entity recognition (BNER) and biomedical relation extraction (BRE) researches promotes the development of text mining in biological domains. As a cornerstone of BRE, robust BNER system is required to identify the mentioned NEs in plain texts for further relation extraction stage. However, the current BNER corpora, which play important roles in these tasks, paid less attention to achieve the criteria for BRE task. In this study, we present Revised JNLPBA corpus, the revision of JNLPBA corpus, to broaden the applicability of a NER corpus from BNER to BRE task. We preserve the original entity types including protein, DNA, RNA, cell line and cell type while all the abstracts in JNLPBA corpus are manually curated by domain experts again basis on the new annotation guideline focusing on the specific NEs instead of general terms. Simultaneously, several imperfection issues in JNLPBA are pointed out and made up in the new corpus. To compare the adaptability of different NER systems in Revised JNLPBA and JNLPBA corpora, the F1-measure was measured in three open sources NER systems including BANNER, Gimli and NERSuite. In the same circumstance, all the systems perform average 10% better in Revised JNLPBA than in JNLPBA. Moreover, the cross-validation test is carried out which we train the NER systems on JNLPBA/Revised JNLPBA corpora and access the performance in both protein-protein interaction extraction (PPIE) and biomedical event extraction (BEE) corpora to confirm that the newly refined Revised JNLPBA is a competent NER corpus in biomedical relation application. The revised JNLPBA corpus is freely available at ***/BNER/Content/Revised_***. Copyright © 2019, The Authors. All rights reserved.

关键词： Proteins

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An atlas of dynamic chromatin landscapes in mouse fetal development (vol 583, pg 744, 2020)

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NATURE 2021年第7842期589卷 E4-E4页

作者： Gorkin, David U. Barozzi, Iros Zhao, Yuan Zhang, Yanxiao Huang, Hui Lee, Ah Young Li, Bin Chiou, Joshua Wildberg, Andre Ding, Bo Zhang, Bo Wang, Mengchi Strattan, J. Seth Davidson, Jean M. Qiu, Yunjiang Afzal, Veena Akiyama, Jennifer A. Plajzer-Frick, Ingrid Novak, Catherine S. Kato, Momoe Garvin, Tyler H. Pham, Quan T. Harrington, Anne N. Mannion, Brandon J. Lee, Elizabeth A. Fukuda-Yuzawa, Yoko He, Yupeng Preissl, Sebastian Chee, Sora Han, Jee Yun Williams, Brian A. Trout, Diane Amrhein, Henry Yang, Hongbo Cherry, J. Michael Wang, Wei Gaulton, Kyle Ecker, Joseph R. Shen, Yin Dickel, Diane E. Visel, Axel Pennacchio, Len A. Ren, Bing Ludwig Institute for Cancer Research La Jolla CA USA Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Biomedical Sciences Graduate Program University of California San Diego School of Medicine La Jolla CA USA Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA Institute of Genomic Medicine University of California San Diego School of Medicine La Jolla CA USA Moores Cancer Center University of California San Diego School of Medicine La Jolla CA USA Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA Department of Surgery and Cancer Imperial College London London UK US Department of Energy Joint Genome Institute Berkeley CA USA School of Natural Sciences University of California Merced Merced CA USA Comparative Biochemistry Program University of California Berkeley Berkeley CA USA Genomic Analysis Laboratory Salk Institute for Biological Studies La Jolla CA USA Department of Pediatrics University of California San Diego School of Medicine La Jolla CA USA Department of Biochemistry and Molecular Biology Penn State School of Medicine Hershey PA USA Stanford University School of Medicine Department of Genetics Stanford CA USA Howard Hughes Medical Institute Salk Institute for Biological Studies La Jolla CA USA Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA Institute for Human Genetics and University of California San Francisco San Francisco CA USA Department of Neurology University of California San Francisco San Francisco CA USA

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The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

NPJ Biodiversity

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NPJ Biodiversity 2024年第1期3卷 28页

作者： Mc Cartney, Ann M. Formenti, Giulio Mouton, Alice De Panis, Diego Marins, Luísa S. Leitão, Henrique G. Diedericks, Genevieve Kirangwa, Joseph Morselli, Marco Salces-Ortiz, Judit Escudero, Nuria Iannucci, Alessio Natali, Chiara Svardal, Hannes Fernández, Rosa De Pooter, Tim Joris, Geert Strazisar, Mojca Wood, Jonathan M. D. Herron, Katie E. Seehausen, Ole Watts, Phillip C. Shaw, Felix Davey, Robert P. Minotto, Alice Fernández, José M. Böhne, Astrid Alegria, Carla Alioto, Tyler Alves, Paulo C. Amorim, Isabel R. Aury, Jean-Marc Backstrom, Niclas Baldrian, Petr Baltrunaite, Laima Barta, Endre Bedhom, Bertrand Belser, Caroline Bergsten, Johannes Bertrand, Laurie Bilandija, Helena Binzer-Panchal, Mahesh Bista, Iliana Blaxter, Mark Borges, Paulo A. V. Dias, Guilherme Borges Bosse, Mirte Brown, Tom Bruggmann, Rémy Buena-Atienza, Elena Burgin, Josephine Buzan, Elena Cariani, Alessia Casadei, Nicolas Chiara, Matteo Chozas, Sergio Jr, Fedor Čiampor Crottini, Angelica Cruaud, Corinne Cruz, Fernando Dalen, Love Biase, Alessiode Delcampo, Javier Delic, Teo Dennis, Aliceb. Derks, Martijn F. L. Diroma, Maria Angela Djan, Mihajla Duprat, Simone Eleftheriadi, Klara Feulner, Philine G. D. Flot, Jean-François Forni, Giobbe Fosso, Bruno Fournier, Pascal Fournier-Chambrillon, Christine Gabaldon, Toni Garg, Shilpa Gissi, Carmela Giupponi, Luca Gomez-Garrido, Jessica González, Josefa Grilo, Miguel L. Grüning, Björn Guerin, Thomas Guiglielmoni, Nadege Gut, Marta Haesler, Marcel P. Hahn, Christoph Halpern, Balint Harrison, Peter W. Heintz, Julia Hindrikson, Maris Höglund, Jacob Howe, Kerstin Hughes, Graham M. Istace, Benjamin Cock, Mark J. Janžekovič, Franc Jonsson, Zophonias O. Joye-Dind, Sagane Koskimäki, Janne J. Krystufek, Boris Kubacka, Justyna Kuhl, Heiner Kusza, Szilvia Labadie, Karine Lähteenaro, Meri Lantz, Henrik Lavrinienko, Anton Leclère, Lucas Lopes, Ricardo Jorge Madsen, Ole Magdelenat, Ghislaine Magoga, Giulia Manousaki, Tereza Mappes, Tapio Marques, Joao Pedro Redondo, Gemma I. Martinez Maumus, Florian McCarthy, Shane A. M Genomics Institute University of California SantaCruz CA United States TheVertebrate Genome Laboratory The Rockefeller University NewYork NY United States Department of Biology University of Florence Sesto Fiorentino Italy InBios-Conservation Genetics Laboratory University of Liege Liege Belgium Leibniz Institut für Zoo und Wildtierforschung Berlin Germany Berlin Center for Genomics in Biodiversity Research Berlin Germany Department of Biology University of Antwerp Antwerp Belgium Institute of Zoology University of Cologne Cologne Germany Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parma Italy Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra Barcelona Spain Naturalis Biodiversity Center Leiden Netherlands Neuromics Support Facility VIB Center for Molecular Neurology VIB Antwerp Belgium Neuromics Support Facility Department of Biomedical SciencesUniversity ofAntwerp Antwerp Belgium Tree of Life WellcomeSanger Institute Cambridge Hinxton United Kingdom School of Biology and Environmental Science University College Dublin Belfield Ireland Aquatic Ecology & Evolution Institute of Ecology & Evolution University of Bern Bern Switzerland Department of Fish Ecology & Evolution Eawag Kastanienbaum Switzerland Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland The EarlhamInstitute NorwichResearchPark Norwich United Kingdom Digital Science London United Kingdom Barcelona Supercomputing Center Spanish National Bioinformatics Institute ELIXIR Spain Getafe Spain Leibniz Institute for the Analysis of Biodiversity Change Museum Koenig Bonn Bonn Germany CE3C—Centre for Ecology Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute Faculdade de Ciências Universidade de Lisboa Campo Grande Lisboa Portugal Centro Nacional de Análisis Genómico (CNAG) Barcelona Spain Universitat de Barcelona (UB) Barcelona Spain CIBIO Cen

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries;however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of highquality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP. © The Author(s) 2024, corrected publication 2024.

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Custom CRISPR-Cas9 PAM variants via scalable engineering and machine learning

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Nature 2025年 2025 Apr 22页

作者： Rachel A Silverstein Nahye Kim Ann-Sophie Kroell Russell T Walton Justin Delano Rossano M Butcher Martin Pacesa Blaire K Smith Kathleen A Christie Leillani L Ha Ronald J Meis Aaron B Clark Aviv D Spinner Cicera R Lazzarotto Yichao Li Azusa Matsubara Elizabeth O Urbina Gary A Dahl Bruno E Correia Debora S Marks Shengdar Q Tsai Luca Pinello Suk See De Ravin Qin Liu Benjamin P Kleinstiver PhD Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA. Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. Department of Pathology Massachusetts General Hospital Boston MA USA. Department of Pathology Harvard Medical School Boston MA USA. Institute of Pharmacy and Molecular Biotechnology (IPMB) Faculty of Engineering Sciences Heidelberg University Heidelberg Germany. Department of Biomedical Informatics Harvard Medical School Boston MA USA. Molecular Pathology Unit Massachusetts General Hospital Charlestown MA USA. Krantz Family Center for Cancer Research Massachusetts General Hospital Charlestown Charlestown MA USA. Broad Institute of Harvard and MIT Cambridge MA USA. Ocular Genomics Institute Massachusetts Eye and Ear Boston MA USA. Department of Ophthalmology Harvard Medical School Boston MA USA. Laboratory of Protein Design and Immunoengineering École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics Lausanne Switzerland. CELLSCRIPTTM Madison WI USA. Department of Systems Biology Harvard Medical School Boston MA USA. Department of Hematology St. Jude Children's Research Hospital Memphis TN USA. Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MD USA. Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. bkleinstiver@mgh.harvard.edu. Department of Pathology Massachusetts General Hospital Boston MA USA. bkleinstiver@mgh.harvard.edu. Department of Pathology Harvard Medical School Boston MA USA. bkleinstiver@mgh.harvard.edu.

engineering and characterizing proteins can be time-consuming and cumbersome, motivating the development of generalist CRISPR-Cas enzymes to enable diverse genome editing applications. However, such enzymes have caveats such as an increased risk of off-target editing. To enable scalable reprogramming of Cas9 enzymes, here we combined high-throughput protein engineering with machine learning (ML) to derive bespoke editors more uniquely suited to specific targets. Via structure/function-informed saturation mutagenesis and bacterial selections, we obtained nearly 1,000 engineered SpCas9 enzymes and characterized their protospacer-adjacent motif (PAM) requirements to train a neural network that relates amino acid sequence to PAM specificity. By utilizing the resulting PAM ML algorithm (PAMmla) to predict the PAMs of 64 million SpCas9 enzymes, we identified efficacious and specific enzymes that outperform evolution-based and engineered SpCas9 enzymes as nucleases and base editors in human cells while reducing off-targets. An in silico directed evolution method enables user-directed Cas9 enzyme design, including for allele-selective targeting of the RHO P23H allele in human cells and mice. Together, PAMmla integrates ML and protein engineering to curate a catalog of SpCas9 enzymes with distinct PAM requirements, and motivates the use of efficient and safe bespoke Cas9 enzymes instead of generalist enzymes for various applications.

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Computation of Microbial Ecosystems in Time and Space (COMETS): An open source collaborative platform for modeling ecosystems metabolism

arXiv

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arXiv 2020年

作者： Dukovski, Ilija Bajić, Djordje Chacón, Jeremy M. Quintin, Michael Vila, Jean C.C. Sulheim, Snorre Pacheco, Alan R. Bernstein, David B. Riehl, William J. Korolev, Kirill S. Sanchez, Alvaro Harcombe, William R. Segrè, Daniel Bioinformatics Program Boston University BostonMA United States Biological Design Center Boston University BostonMA United States Department of Ecology and Evolutionary Biology Yale University New HavenCT United States Microbial Sciences Institute Yale University West HavenCT United States Department of Ecology Evolution and Behavior University of Minnesota St. PaulMN United States BioTechnology Institute University of Minnesota St. PaulMN United States Department of Biotechnology and Food Science Norwegian University of Science and Technology Trondheim Norway Department of Biotechnology and Nanomedicine SINTEF Industry Trondheim Norway Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory BerkeleyCA United States Department of Biomedical Engineering Boston University BostonMA United States Department of Physics Boston University BostonMA United States Department of Biology Boston University BostonMA United States

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and designing microbial communities. COMETS (Computation Of Microbial Ecosystems in Time and Space) was initially developed as an extension of dynamic flux balance analysis, which incorporates cellular and molecular diffusion, enabling simulations of multiple microbial species in spatially structured environments. Here we describe how to best use and apply the most recent version of this platform, COMETS 2, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, as well as several new biological simulation modules, including evolutionary dynamics and extracellular enzyme activity. COMETS 2 provides user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, and comprehensive documentation and tutorials, facilitating the use of COMETS for researchers at all levels of expertise with metabolic simulations. This protocol provides a detailed guideline for installing, testing and applying COMETS 2 to different scenarios, with broad applicability to microbial communities across biomes and scales. Copyright © 2020, The Authors. All rights reserved.

关键词： Microorganisms

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

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

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

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Spectral characteristics of microcirculatory signals response to muscle stretching among diabetic smokers 17

Spectral characteristics of microcirculatory signals respons...

引用

4th International Conference on biomedical and bioinformatics engineering, ICBBE 2017

作者： Bau, Jian-Guo Lin, Yue-Der Huang, Bo-Wen Department of Biomedical Engineering Hungkuang University Taichung43302 Taiwan Department of Automatic Control Engineering Feng Chia University Taichung40724 Taiwan Master's Program of Bioinformatics and Biomedical Engineering Feng Chia University Taichung40724 Taiwan

ISBN: (纸本)9781450354844

Cigarette smoking is reported to be the major risk factor for endothelial dysfunction. The variations of the spectral compositions of microcirculatory perfusion signal could provide the information related to the regulatory function of microvasculature. The aim of the present study was to compare the spectral characteristics response to muscle stretching between diabetic smokers and non-smokers, and investigate the influence of cigarette smoking on microvascular function. Twenty four diabetic patients (12 smokers v.s. 12 non-smokers) and twelve normal non-smoking subjects were recruited. We observed that the diabetic smokers had a significantly reduced endothelial activity. The mechanisms for the reduction of the endothelial activity remain to be elucidated. The spectral analysis might be used to evaluate endothelial function for research, for diagnostic purposes, and maybe also to assess effects of therapy in cardiovascular diseases. © 2017 Association for Computing Machinery.

关键词： Spectrum analysis

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