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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

BMC NEUROscience 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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ESALP2: Efficient Signature Aggregation with Location Privacy Preservation in Wireless Body Area Networks

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ACM Transactions on Sensor Networks 1000年

作者： Arun Sekar Rajasekaran Azees Maria Basker Palaniswamy Ashok Kumar Das Mohammed J.F. Alenazi Department of Electronics and Communication Engineering SR University Hanamakonda India School of Computer Science and Engineering VIT-AP University Amaravati India Insight Centre for Data Analytics School of Computer Science and Information Technology University College Cork Cork Ireland Center for Security Theory and Algorithmic Research International Institute of Information Technology Hyderabad Hyderabad India Department of Computer Engineering College of Computer and Information Sciences CCIS) King Saud University Riyadh Saudi Arabia

For Wireless Body Area Networks (WBANs), the security of sensitive data of patients is of the utmost importance, particularly in healthcare environments. This study presents a novel methodology for improving the efficacy of signature aggregation in a scenario involving doctors and patients while mitigating concerns about location privacy. Though there have been prior proposals for signature aggregation schemes, the proposed approach seeks to optimize the aggregation process within the considered scenario, thereby improving performance and reducing computational and communication burden. In addition, the proposed scheme integrates a resilient mechanism that safeguards the doctor’s location privacy by utilizing the Chinese Remainder Theorem (CRT). Advanced cryptographic algorithms and location-anonymization techniques are employed in the proposed method to safeguard the confidentiality of the doctors’ location. The security of the proposed scheme is formally analyzed using the Burrows-Abadi-Needham (BAN) logic and formally verified using the automated software validation tool, known as the Scyther tool, and an informal analysis of various security attributes confirms the security robustness of the proposed scheme. The efficacy is evaluated in comparison to analogous works utilizing the Cygwin software. The performance evaluation shows that the proposed scheme has lower communication costs as compared to existing competing schemes. Moreover, the serving ratio in the proposed scheme is high even if the number of patients is low for doctors.

关键词： Wireless Body Area Networks (WBAN) Authentication Aggregate signature Location privacy Security Scyther Smart healthcare.

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Chemically inspired Erdős-Rényi oriented hypergraphs

arXiv

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arXiv 2023年

作者： Garcia-Chung, Angel Bermúdez-Montaña, Marisol Stadler, Peter F. Jost, Jürgen Restrepo, Guillermo Tecnológico de Monterrey Escuela de Ingeniería y Ciencias Estado de México52926 Mexico Max Planck Institute for Mathematics in the Sciences Leipzig Germany Interdisciplinary Center for Bioinformatics Universität Leipzig Leipzig Germany Bioinformatics Group Department of Computer Science Universität Leipzig Leipzig Germany Institute for Theoretical Chemistry University of Vienna Vienna Austria The Santa Fe Institute Santa FeNM United States Facultad de Ciencias Universidad Nacional de Colombia Bogotá Colombia Center for Scalable Data Analytics and Artificial Intelligence Universität Leipzig Leipzig Germany School of Applied Sciences and Engineering EAFIT University Medellín Colombia

High-order structures have been recognised as suitable models for systems going beyond the binary relationships for which graph models are appropriate. Despite their importance and surge in research on these structures, their random cases have been only recently become subjects of interest. One of these high-order structures is the oriented hypergraph, which relates couples of subsets of an arbitrary number of vertices. Here we develop the Erdős-Rényi model for oriented hypergraphs, which corresponds to the random realisation of oriented hyperedges of the complete oriented hypergraph. A particular feature of random oriented hypergraphs is that the ratio between their expected number of oriented hyperedges and their expected degree or size is 3/2 for large number of vertices. We highlight the suitability of oriented hypergraphs for modelling large collections of chemical reactions and the importance of random oriented hypergraphs to analyse the unfolding of chemistry. © 2023, CC BY-SA.

关键词： Graph theory

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SMILE-UHURA Challenge - Small Vessel Segmentation at Mesoscopic Scale from Ultra-High Resolution 7T Magnetic Resonance Angiograms

arXiv

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arXiv 2024年

作者： Chatterjee, Soumick Mattern, Hendrik Dörner, Marc Sciarra, Alessandro Dubost, Florian Schnurre, Hannes Khatun, Rupali Yu, Chun-Chih Hsieh, Tsung-Lin Tsai, Yi-Shan Fang, Yi-Zeng Yang, Yung-Ching Huang, Juinn-Dar Xu, Marshall Liu, Siyu Ribeiro, Fernanda L. Bollmann, Saskia Chintalapati, Karthikesh Varma Radhakrishna, Chethan Mysuru Ram Kumar, Sri Chandana Hudukula Sutrave, Raviteja Qayyum, Abdul Mazher, Moona Razzak, Imran Rodero, Cristobal Niederer, Steven Lin, Fengming Xia, Yan Wang, Jiacheng Qiu, Riyu Wang, Liansheng Panah, Arya Yazdan Jurdi, Rosana El Fu, Guanghui Arslan, Janan Vaillant, Ghislain Valabregue, Romain Dormont, Didier Stankoff, Bruno Colliot, Olivier Vargas, Luisa Chacón, Isai Daniel Pitsiorlas, Ioannis Arbeláez, Pablo Zuluaga, Maria A. Schreiber, Stefanie Speck, Oliver Nürnberger, Andreas Faculty of Computer Science Otto von Guericke University Magdeburg Magdeburg Germany Data and Knowledge Engineering Group Otto von Guericke University Magdeburg Magdeburg Germany Genomics Research Centre Human Technopole Milan Italy Biomedical Magnetic Resonance Otto von Guericke University Magdeburg Magdeburg Germany Department of Neurology Medical Faculty University Hospital of Magdeburg Magdeburg Germany German Centre for Neurodegenerative Diseases Magdeburg Germany Centre for Behavioural Brain Sciences Magdeburg Germany University Hospital Zurich University of Zurich Zurich Switzerland Google Inc. United States Translational Radiobiology Department of Radiation Oncology Universitätsklinikum Erlangen Friedrich-Alexnder-Universität Erlangen-Nürnberg Erlangen Germany National Yang Ming Chiao Tung University Hsinchu Taiwan School of Electrical Engineering and Computer Science University of Queensland Brisbane Australia Australian eHealth Research Centre Chile National Heart and Lung Institute Faculty of Medicine Imperial College London London United Kingdom Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Computer Science and Engineering University of New South Wales Sydney Australia Mohamed bin Zayed University of Artificial Intelligence Abu Dhabi United Arab Emirates The Alan Turing Institute London United Kingdom School of Computing University of Leeds Leeds United Kingdom Department of Computer Science School of Informatics Xiamen University Xiamen China Manteia Technologies Co. Ltd Xiamen China Leicester International Institute Dalian University of Technology Dalian China Sorbonne Université Institut du Cerveau - Paris Brain Institute ICM CNRS Inria Inserm AP-HP Hôpital de la Pitié Salpêtrière ParisF-75013 France Centre of Formation and Research in Artificial Intelligence Universidad de Los Andes Colombia Data Science Department EURECOM Sophia Antipolis Franc

The human brain receives nutrients and oxygen through an intricate network of blood vessels. Pathology affecting small vessels, at the mesoscopic scale, represents a critical vulnerability within the cerebral blood supply and can lead to severe conditions, such as Cerebral Small Vessel Diseases. The advent of 7 Tesla MRI systems has enabled the acquisition of higher spatial resolution images, making it possible to visualise such vessels in the brain. However, the lack of publicly available annotated datasets has impeded the development of robust, machine learning-driven segmentation algorithms. To address the complexities of mesoscopic vessel segmentation and to highlight the need for advanced techniques to manage the high noise levels and poor vessel-to-background contrast inherent in"ultra-high-resolution" data, the SMILE-UHURA challenge was organised. This challenge, held in conjunction with the ISBI 2023, in Cartagena de Indias, Colombia, aimed to provide a platform for researchers working on related topics. The SMILE-UHURA challenge addresses the gap in publicly available annotated datasets by providing an annotated dataset of Time-of-Flight angiography acquired with 7T MRI. This dataset was created through a combination of automated pre-segmentation and extensive manual refinement. In this manuscript, sixteen submitted methods and two baseline methods are compared both quantitatively and qualitatively on two different datasets: held-out test MRAs from the same dataset as the training data (with labels kept secret) and a separate 7T ToF MRA dataset where both input volumes and labels are kept secret. The results demonstrate that most of the submitted deep learning methods, trained on the provided training dataset, achieved reliable segmentation performance. Dice scores reached up to 0.838 ± 0.066 and 0.716 ± 0.125 on the respective datasets, with an average performance of up to 0.804 ± 0.15. Copyright © 2024, The Authors. All rights reserved.

关键词： Deep learning

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Molecular and Serologic Diagnostic Technologies for SARS-CoV-2

arXiv

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arXiv 2022年

作者： Rando, Halie M. Brueffer, Christian Lordan, Ronan Dattoli, Anna Ada Manheim, David Meyer, Jesse G. Mundo, Ariel I. Perrin, Dimitri Mai, David Wellhausen, Nils Gitter, Anthony Greene, Casey S. Department of SystemsPharmacology and Translational Therapeutics University of Pennsylvania PhiladelphiaPA United States Department of Biochemistry and MolecularGenetics University of Colorado School of Medicine AuroraCO United States Center for Health AI University of Colorado School of Medicine AuroraCO United States Department of Clinical Sciences Lund University Lund Sweden Institute for TranslationalMedicine and Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA19104-5158 United States Department of Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA19104 United States Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA19104 United States Department of Pathology Laboratory Medicine The Children’s Hospital of Philadelphia PhiladelphiaPA United States Department of Systems Pharmacology & Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States 1DaySooner Delaware United States Communication Research Center School of Public Health University of Haifa Haifa Israel Technion Israel Institute of Technology Haifa Israel Department of Biochemistry Medical College of Wisconsin MilwaukeeWI United States Department of Biomedical Engineering University of Arkansas FayettevilleAR United States School of Computer Science Queensland University of Technology Brisbane Australia Centre for Data Science Queensland University of Technology Brisbane Australia Department of Bioengineering University of Pennsylvania PhiladelphiaPA United States Center for Cellular Immunotherapies Perelman School of Medicine Parker Institute for Cancer Immunotherapy University of Pennsylvania PhiladelphiaPA United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania PhiladelphiaPA United States Department of Biostatistics Medical

The COVID-19 pandemic has presented many challenges that have spurred biotechnological research to address specific problems. Diagnostics is one area where biotechnology has been critical. Diagnostic tests play a vital role in managing a viral threat by facilitating the detection of infected and/or recovered individuals. From the perspective of what information is provided, these tests fall into two major categories, molecular and serological. Molecular diagnostic techniques assay whether a virus is present in a biological sample, thus making it possible to identify individuals who are currently infected. Additionally, when the immune system is exposed to a virus, it responds by producing antibodies specific to the virus. Serological tests make it possible to identify individuals who have mounted an immune response to a virus of interest and therefore facilitate the identification of individuals who have previously encountered the virus. These two categories of tests provide different perspectives valuable to understanding the spread of SARS-CoV-2. Within these categories, different biotechnological approaches offer specific advantages and disadvantages. Here we review the categories of tests developed for the detection of the SARS-CoV-2 virus or antibodies against SARS-CoV-2 and discuss the role of diagnostics in the COVID-19 pandemic. © 2022, CC BY.

关键词： SARS

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The 2021 report of the Lancet Countdown on health and climate change: code red for a healthy future

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The Lancet 2021年第10311期398卷 1619-1662页

作者： Romanello, Marina McGushin, Alice Di Napoli, Claudia Drummond, Paul Hughes, Nick Jamart, Louis Kennard, Harry Lampard, Pete Solano Rodriguez, Baltazar Arnell, Nigel Ayeb-Karlsson, Sonja Belesova, Kristine Cai, Wenjia Campbell-Lendrum, Diarmid Capstick, Stuart Chambers, Jonathan Chu, Lingzhi Ciampi, Luisa Dalin, Carole Dasandi, Niheer Dasgupta, Shouro Davies, Michael Dominguez-Salas, Paula Dubrow, Robert Ebi, Kristie L Eckelman, Matthew Ekins, Paul Escobar, Luis E Georgeson, Lucien Grace, Delia Graham, Hilary Gunther, Samuel H Hartinger, Stella He, Kehan Heaviside, Clare Hess, Jeremy Hsu, Shih-Che Jankin, Slava Jimenez, Marcia P Kelman, Ilan Kiesewetter, Gregor Kinney, Patrick L Kjellstrom, Tord Kniveton, Dominic Lee, Jason K W Lemke, Bruno Liu, Yang Liu, Zhao Lott, Melissa Lowe, Rachel Martinez-Urtaza, Jaime Maslin, Mark McAllister, Lucy McMichael, Celia Mi, Zhifu Milner, James Minor, Kelton Mohajeri, Nahid Moradi-Lakeh, Maziar Morrissey, Karyn Munzert, Simon Murray, Kris A Neville, Tara Nilsson, Maria Obradovich, Nick Sewe, Maquins Odhiambo Oreszczyn, Tadj Otto, Matthias Owfi, Fereidoon Pearman, Olivia Pencheon, David Rabbaniha, Mahnaz Robinson, Elizabeth Rocklöv, Joacim Salas, Renee N Semenza, Jan C Sherman, Jodi Shi, Liuhua Springmann, Marco Tabatabaei, Meisam Taylor, Jonathon Trinanes, Joaquin Shumake-Guillemot, Joy Vu, Bryan Wagner, Fabian Wilkinson, Paul Winning, Matthew Yglesias, Marisol Zhang, Shihui Gong, Peng Montgomery, Hugh Costello, Anthony Hamilton, Ian Institute for Global Health University College London London UK United Kingdom Institute for Sustainable Resources University College London London UK United Kingdom UCL Energy Institute University College London London UK United Kingdom Institute for Environmental Design and Engineering University College London London UK United Kingdom Department of Geography University College London London UK United Kingdom The Bartlett School of Sustainable Construction University College London London UK United Kingdom Centre for Human Health and Performance University College London London UK United Kingdom School of Agriculture Policy and Development University of Reading Reading United Kingdom Department of Meteorology University of Reading Reading United Kingdom The Walker Institute University of Reading Reading United Kingdom Department of Health Sciences University of York York United Kingdom Institute for Environment and Human Security United Nations University Bonn Germany Centre on Climate Change and Planetary Health London School of Hygiene & Tropical Medicine London UK United Kingdom Centre for Mathematical Modelling of Infectious Diseases London School of Hygiene & Tropical Medicine London UK United Kingdom Department of Public Health Environments and Society London School of Hygiene & Tropical Medicine London UK United Kingdom Department of Earth System Science Tsinghua University Beijing China Department of Environment Climate Change and Health World Health Organization Geneva Switzerland Institute for Environmental Sciences World Health Organization Geneva Switzerland Centre for Climate Change and Social Transformations School of Psychology Cardiff University Cardiff United Kingdom Yale Center on Climate Change and Health Yale University New Haven CT United States School of Government University of Birmingham Birmingham United Kingdom Economic analysis of Climate Impacts and Policy Centro Euro-Mediterraneo sui Cambiamenti Climatic

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IROS 2019 lifelong robotic vision challenge lifelong object recognition report

arXiv

引用

arXiv 2020年

作者： She, Qi Feng, Fan Liu, Qi Chan, Rosa H.M. Hao, Xinyue Lan, Chuanlin Yang, Qihan Lomonaco, Vincenzo Parisi, German I. Ma, Liang Wu, Jianwen Zhong, Qiaoyong Xie, Di Pu, Shiliang Graffieti, Gabriele Pellegrini, Lorenzo Lomonaco, Vincenzo Maltoni, Davide Wang, Zhengwei Brophy, Eoin Ward, Tomás E. Zhou, Liguang Yang, Lin Goel, Vidit Sheet, Debdoot Kumar, Somesh Song, Soonyong Bae, Heechul Han, Hyonyoung Son, Youngsung Piyasena, Duvindu Kanagarajah, Sathursan Lam, Siew-Kei Wu, Meiqing Department of Electrical Engineering City University of Hong Kong Hong Kong Department of Electronic Engineering Tsinghua University Beijing University of Posts and Telecommunications Beijing China School of Electronic Information Wuhan University Wuhan China ContinualAI Research University of Bologna Italy ContinualAI Research University of Hamburg Germany Intel Labs and ContinualAI Research Hikvision Research Institute Hangzhou China University of Bologna Bologna Italy V-SENSE School of Computer Science and Statistics Trinity College Dublin Dublin Ireland Inisht Centre for Data Analytics School of Computing Dublin City University Dublin Ireland Shenzhen China Shenzhen Institute of Artificial Intelligence and Robotics for Society China Peking University Beijing China Shandong University Qingdao China Beijing Film Academy Beijing China Indian Institute of Technology Kharagpur India Korea Republic of Nanyang Technological University Singapore Singapore

This report summarizes IROS 2019-Lifelong Robotic Vision Competition (Lifelong Object Recognition Challenge) with methods and results from the top 8 finalists (out of over 150 teams). The competition dataset (L)ifel(O)ng (R)obotic V(IS)ion (OpenLORIS) - Object Recognition (OpenLORIS-object) is designed for driving lifelong/continual learning research and application in robotic vision domain, with everyday objects in home, office, campus, and mall scenarios. The dataset explicitly quantifies the variants of illumination, object occlusion, object size, camera-object distance/angles, and clutter information. Rules are designed to quantify the learning capability of the robotic vision system when faced with the objects appearing in the dynamic environments in the contest. Individual reports, dataset information, rules, and released source code can be found at the project homepage. Copyright © 2020, The Authors. All rights reserved.

关键词： Object recognition

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GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows

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Communications engineering 2023年第1期2卷 23页

作者： Pati, Sarthak Thakur, Siddhesh P. Hamamcı, İbrahim Ethem Baid, Ujjwal Baheti, Bhakti Bhalerao, Megh Güley, Orhun Mouchtaris, Sofia Lang, David Thermos, Spyridon Gotkowski, Karol González, Camila Grenko, Caleb Getka, Alexander Edwards, Brandon Sheller, Micah Wu, Junwen Karkada, Deepthi Panchumarthy, Ravi Ahluwalia, Vinayak Zou, Chunrui Bashyam, Vishnu Li, Yuemeng Haghighi, Babak Chitalia, Rhea Abousamra, Shahira Kurc, Tahsin M. Gastounioti, Aimilia Er, Sezgin Bergman, Mark Saltz, Joel H. Fan, Yong Shah, Prashant Mukhopadhyay, Anirban Tsaftaris, Sotirios A. Menze, Bjoern Davatzikos, Christos Kontos, Despina Karargyris, Alexandros Umeton, Renato Mattson, Peter Bakas, Spyridon MLCommons Medical Working Group San Francisco CA United States Center For Artificial Intelligence And Data Science For Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Department of Informatics Technical University of Munich Bavaria Munich Germany International School of Medicine Istanbul Medipol University Marmara Istanbul Turkey Department of Bioengineering School of Engineering and Applied Science University of Pennsylvania Philadelphia PA United States Department of Mathematics School of Arts and Sciences University of Pennsylvania Philadelphia PA United States Institute for Digital Communications School of Engineering The University of Edinburgh United Kingdom Department of Computer Science Technical University of Darmstadt Hesse Darmstadt Germany Intel Corporation Santa Clara CA United States Department of Computer Science Stony Brook University Stony Brook New York NY United States Department of Biomedical Informatics Stony Brook University Stony Brook New York NY United States Mallinckrodt Institute of Radiology Washington University School of Medicine St. Louis MO United States Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Institute of Image-Guided Surgery of Strasbourg Strasbourg France Department of Informatics & amp Analytics Dana-Farber Cancer Institute Boston MA United States Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY United States Department of Biostatistics Harvard T.H. Chan School of Public Health Boston MA United States Department of Biological Engineering Department of Mechanical Engineering Massachusetts In

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows. © The Author(s) 2023.

关键词： Image processing Magnetic resonance imaging Computational science Biomedical engineering Information technology

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Generation of a Compendium of Transcription Factor Cascades and Identification of Potential Therapeutic Targets using Graph Machine Learning

arXiv

引用

arXiv 2023年

作者： Sivarajkumar, Sonish Tandale, Pratyush Bhardwaj, Ankit Johnson, Kipp W. Titus, Anoop Glicksberg, Benjamin S. Khader, Shameer Yadav, Kamlesh K. Subramanian, Lakshminarayanan Molecular Robotics Kerala India School of Computing and Information University of Pittsburgh Pennsylvania PA United States Health Informatics & Data Science Georgetown University WashingtonDC United States Department of Computer Science Courant Institute of Mathematical Sciences New York University New YorkNY United States Institute for Next Generation Healthcare Mount Sinai Health System New YorkNY United States Department of Preventive Cardiology DeBakey Heart & Vascular Center Houston Methodist HoustonTX United States Hasso Plattner Institute for Digital Health Icahn School of Medicine at Mount Sinai New YorkNY United States Faculty of Medicine Imperial College London London United Kingdom School of Engineering Medicine Texas A&M University HoustonTX United States Department of Translational Medical Sciences Center for Genomic and Precision Medicine Texas A&M University HoustonTX United States

Transcription factors (TFs) play a vital role in the regulation of gene expression thereby making them critical to many cellular processes. In this study, we used graph machine learning methods to create a compendium of TF cascades using data extracted from the STRING database. A TF cascade is a sequence of TFs that regulate each other, forming a directed path in the TF network. We constructed a knowledge graph of 81,488 unique TF cascades, with the longest cascade consisting of 62 TFs. Our results highlight the complex and intricate nature of TF interactions, where multiple TFs work together to regulate gene expression. We also identified 10 TFs with the highest regulatory influence based on centrality measurements, providing valuable information for researchers interested in studying specific TFs. Furthermore, our pathway enrichment analysis revealed significant enrichment of various pathways and functional categories, including those involved in cancer and other diseases, as well as those involved in development, differentiation, and cell signaling. The enriched pathways identified in this study may have potential as targets for therapeutic intervention in diseases associated with dysregulation of transcription factors. We have released the dataset, knowledge graph, and graphML methods for the TF cascades, and created a website to display the results, which can be accessed by researchers interested in using this dataset. Our study provides a valuable resource for understanding the complex network of interactions between TFs and their regulatory roles in cellular processes. Copyright © 2023, The Authors. All rights reserved.

关键词： Transcription factors

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Correction: Content and Dynamics of Websites Shared Over Vaccine-Related Tweets in COVID-19 Conversations: Computational Analysis

引用

Journal of medical Internet research 2023年 25卷 e43279页

作者： Iain Cruickshank Tamar Ginossar Jason Sulskis Elena Zheleva Tanya Berger-Wolf Center for Computational Analysis of Social and Organizational Systems Carnegie Mellon University Pittsburgh PA United States. Department of Communication and Journalism University of New Mexico Albuquerque NM United States. Department of Computer Science The University of Illinois at Chicago Chicago IL United States. Translational Data Analytics Institute The Ohio State University Colombus OH United States.

[This corrects the article DOI: 10.2196/29127.].

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