检索结果-内蒙古大学图书馆

arXiv 2024年

作者： Yaniv, Ziv Anidi, Ifeanyichukwu U. Arakkal, Leanne Arroyo-Mejías, Armando J. Beuschel, Rebecca T. Börner, Katy Chu, Colin J. Clark, Beatrice Clatworthy, Menna R. Colautti, Jake Coscia, Fabian 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 Kortekaas, Rosa K. Kreins, Alexandra Y. Lamborn, Ian T. Lin, Yuri Morais, Katia Luciano Pereira Lunich, Aleksandra Luz, Jean C.S. MacDonald, Ryan B. Makranz, Chen Maltez, Vivien I. McDonough, John E. Moriarty, Ryan V. Ocampo-Godinez, Juan M. Olyntho, Vitoria M. Oxenius, Annette 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. Williams, Margaret Zangger, Nathan Germain, Ronald N. Radtke, Andrea J. Bioinformatics and Computational Bioscience Branch 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 NIAID NIH 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 Spatial Proteomics Group Berlin Germany 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 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 States Institute of Pathology Aachen Medical University RWTH Aachen Aachen Germany Hannover Germany Würzburg Institute

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.g., primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data. © 2024, CC BY.

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Author Correction: Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer's disease

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Nature medicine 2025年 2025 Mar 28页

作者： Lynn van Olst Brooke Simonton Alex J Edwards Anne V Forsyth Jake Boles Pouya Jamshidi Thomas Watson Nate Shepard Talia Krainc Benney Mr Argue Ziyang Zhang Joshua Kuruvilla Lily Camp Mengwei Li Hang Xu Jeanette L Norman Joshua Cahan Robert Vassar Jinmiao Chen Rudolph J Castellani James Ar Nicoll Delphine Boche David Gate Abrams Research Center on Neurogenomics Northwestern University Feinberg School of Medicine Chicago IL USA. The Ken & Ruth Davee Department of Neurology Northwestern University Feinberg School of Medicine Chicago IL USA. Department of Pathology Northwestern University Feinberg School of Medicine Chicago IL USA. Bioinformatics Institute Agency for Science Technology and Research Singapore Singapore. Clinical Neurosciences School of Clinical and Experimental Sciences Faculty of Medicine University of Southampton Southampton UK. Mesulam Center for Cognitive Neurology and Alzheimer's Disease Northwestern University Feinberg School of Medicine Chicago IL USA. Centre for Computational Biology and Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore. Immunology Translational Research Program Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore. Department of Cellular Pathology University Hospital Southampton National Health Service Trust Southampton UK. Abrams Research Center on Neurogenomics Northwestern University Feinberg School of Medicine Chicago IL USA. dgate@northwestern.edu. The Ken & Ruth Davee Department of Neurology Northwestern University Feinberg School of Medicine Chicago IL USA. dgate@northwestern.edu.

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Correction: The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes

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BMC genomics 2024年第1期25卷 537页

作者： Rick Masonbrink Tom R Maier Usha Muppirala Arun S Seetharam Etienne Lord Parijat S Juvale Jeremy Schmutz Nathan T Johnson Dmitry Korkin Melissa G Mitchum Benjamin Mimee Sebastian Eves-van den Akker Matthew Hudson Andrew J Severin Thomas J Baum Department of Plant Pathology Iowa State University Ames IA USA. Genome Informatics Facility Iowa State University Ames IA USA. Agriculture and Agri-Food Canada Saint-Jean-sur-Richelieu QC Canada. Department of Energy Joint Genome Institute Walnut Creek CA USA. HudsonAlpha Institute for Biotechnology Huntsville AL USA. Bioinformatics and Computational Biology Program Worcester Polytechnic Institute Worcester MA USA. Department of Computer Science Worcester Polytechnic Institute Worcester MA USA. Division of Plant Sciences University of Missouri Columbia MO USA. Department of Plant Sciences University of Cambridge Cambridge UK. Department of Crop Sciences University of Illinois Urbana IL USA. Genome Informatics Facility Iowa State University Ames IA USA. severin@iastate.edu.

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Contact network changes in ordered and disordered disk packings

arXiv

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arXiv 2020年

作者： Tuckman, Philip J. VanderWerf, Kyle Yuan, Ye Zhang, Shiyun Zhang, Jerry Shattuck, Mark D. O’Hern, Corey S. Department of Physics Yale University New HavenCT06520 United States Department of Mechanics and Engineering Science College of Engineering Peking University Beijing100871 China Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Benjamin Levich Institute and Physics Department City College of New York New YorkNY10031 United States Department of Physics Yale University Department of Applied New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

We investigate the mechanical response of packings of purely repulsive, frictionless disks to quasistatic deformations. The deformations include simple shear strain at constant packing fraction and at constant pressure, "polydispersity" strain (in which we change the particle size distribution) at constant packing fraction and at constant pressure, and isotropic compression. For each deformation, we show that there are two classes of changes in the interparticle contact networks: jump changes and point changes. Jump changes occur when a contact network becomes mechanically unstable, particles "rearrange", and the potential energy (when the strain is applied at constant packing fraction) or enthalpy (when the strain is applied at constant pressure) and all derivatives are discontinuous. During point changes, a single contact is either added to or removed from the contact network. For repulsive linear spring interactions, second- and higher-order derivatives of the potential energy/enthalpy are discontinuous at a point change, while for Hertzian interactions, third- and higher-order derivatives of the potential energy/enthalpy are discontinuous. We illustrate the importance of point changes by studying the transition from a hexagonal crystal to a disordered crystal induced by applying polydispersity strain. During this transition, the system only undergoes point changes, with no jump changes. We emphasize that one must understand point changes, as well as jump changes, to predict the mechanical properties of jammed packings. Copyright © 2020, The Authors. All rights reserved.

关键词： Potential energy

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Current md forcefields fail to capture key features of protein structure and fluctuations: a case study of cyclophilin a and t4 lysozyme

arXiv

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arXiv 2020年

作者： Mei, Zhe Grigas, Alex T. Treado, John D. Corres, Gabriel Melendez Vuorte, Maisa Sammalkorpi, Maria Regan, Lynne Levine, Zachary A. O’Hern, Corey S. Department of Chemistry Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Biology UPR Humacao Puerto RicoHumacao00792 Puerto Rico Department of Chemistry and Materials Science School of Chemical Engineering Aalto University Aalto Finland Department of Bioproducts and Biosystems School of Chemical Engineering Aalto University Aalto Finland Institute of Quantitative Biology Biochemistry and Biotechnology Center for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Edinburgh United Kingdom Department of Pathology Yale School of Medicine New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways when they are solved by x-ray crystallography versus solution-based NMR spectroscopy. Given these discrepancies, it is unclear whether molecular dynamics (MD) simulations can accurately recapitulate protein conformations. We therefore perform extensive MD simulations across multiple force fields and sampling techniques to investigate the degree to which computer simulations can capture the ensemble of conformations observed in experiments. By analyzing fluctuations in the atomic coordinates and core packing, we show that conformations sampled in MD simulations both move away from and sample a larger conformational space than the ensemble of structures observed in NMR experiments. However, we find that adding inter-residue distance restraints that match those obtained via Nuclear Overhauser Effect measurements enables the MD simulations to sample more NMR-like conformations, though significant differences between the core packing features in restrained MD and the NMR ensemble remain. Given that the protein structures obtained from the MD simulations possess smaller and less dense protein cores compared to those solved by NMR, we suggest that future improvements to MD forcefields should aim to increase the packing of hydrophobic residues in protein cores. © 2020, CC BY.

关键词： Molecular dynamics

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Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2

arXiv

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arXiv 2020年

作者： Law, Jeffrey N. Akers, Kyle Tasnina, Nure Della Santina, Catherine M. Deutsch, Shay Kshirsagar, Meghana Klein-Seetharaman, Judith Crovella, Mark Rajagopalan, Padmavathy Kasif, Simon Murali, T.M. Interdisciplinary Ph.D. Program in Genetics Bioinformatics and Computational Biology BlacksburgVA United States Department of Computer Science Virginia Tech BlacksburgVA United States Department of Biomedical Engineering Boston University BostonMA United States Department of Mathematics University of California Los AngelesCA United States AI for Good Lab Microsoft RedmondWA United States Department of Chemistry Colorado School of Mines GoldenCO United States Department of Computer Science Boston University BostonMA United States Department of Chemical Engineering Virginia Tech BlacksburgVA United States

Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this context, e.g., determining how much any experimental observation in the input contributes to the score of every prediction. Results: We design a network propagation framework with two novel components and apply it to predict human proteins that directly or indirectly interact with SARS-CoV-2 proteins. First, we trace the provenance of each prediction to its experimentally validated sources, which in our case are human proteins experimentally determined to interact with viral proteins. Second, we design a technique that helps to reduce the manual adjustment of parameters by users. We find that for every top-ranking prediction, the highest contribution to its score arises from a direct neighbor in a human protein-protein interaction network. We further analyze these results to develop functional insights on SARS-CoV-2 that expand on known biology such as the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents. Conclusions: We examine how our provenance tracing method can be generalized to a broad class of network-based algorithms. We provide a useful resource for the SARS-CoV-2 community that implicates many previously undocumented proteins with putative functional relationships to viral infection. This resource includes potential drugs that can be opportunistically repositioned to target these proteins. We also discuss how our overall framework can be extended to other, newly-emerging viruses. © 2020, CC BY-NC-SA.

关键词： SARS

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Publisher Correction: Atomistic mechanisms underlying the activation of the G protein-coupled sweet receptor heterodimer by sugar alcohol recognition

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Scientific reports 2019年第1期9卷 18996页

作者： Panupong Mahalapbutr Nitchakan Darai Wanwisa Panman Aunchan Opasmahakul Nawee Kungwan Supot Hannongbua Thanyada Rungrotmongkol Structural and Computational Biology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Program in Biotechnology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Multidisciplinary Program of Petrochemistry and Polymer Science Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Computational Chemistry Center of Excellent Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Department of Chemistry Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand. Center of Excellence in Materials Science and Technology Chiang Mai University Chiang Mai 50200 Thailand. Structural and Computational Biology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. t.rungrotmongkol@***. Ph.D. Program in Bioinformatics and Computational Biology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. t.rungrotmongkol@***. Molecular Sensory Science Center Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. t.rungrotmongkol@***.

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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Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

Research Square

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Research Square 2021年

作者： Wang, Guan Kitaoka, Traci Crawford, Ali Mao, Qian Hesketh, Andrew Guppy, Fergus M. Ash, Garrett I. Liu, Jason Gerstein, Mark B. Pitsiladis, Yannis P. Sport and Exercise Science and Sports Medicine Research and Enterprise Group University of Brighton Brighton United Kingdom Centre for Regenerative Medicine and Devices University of Brighton Brighton United Kingdom Illumina San DiegoCA United States BGI Shenzhen China School of Pharmacy and Biomolecular Sciences University of Brighton Brighton United Kingdom Centre for Stress and Age-related Disease University of Brighton Brighton United Kingdom Veterans Affairs Connecticut Healthcare System West HavenCT United States Center for Medical Informatics Yale University New HavenCT United States Program in Computational Biology & Bioinformatics Yale University New HavenCT United States Department of Molecular Biophysics & Biochemistry Yale University New HavenCT United States Department of Computer Science Yale University New HavenCT United States Department of Statistics and Data Science Yale University New HavenCT United States

RNA-seq has matured and become an important tool for studying RNA biology. Here we compared two RNA-seq (Illumina sequencing by synthesis and MGI DNBSEQTM) and two microarray platforms (Illumina Expression BeadChip and GeneChipTM Human Transcriptome Array 2.0) in healthy individuals administered recombinant human erythropoietin for transcriptome-wide quantification of differential gene expression. The results show that total RNA sequencing combined with DNB-seq produced a multitude of genes of biological relevance and significance in response to recombinant human erythropoietin, in contrast to other platforms. Through data triangulation linking genes to functions, genes representing the processes of erythropoiesis as well as non-erythropoietic functions of erythropoietin were unveiled. This study provides a knowledge base of genes characterising the responses to recombinant human erythropoietin through cross-platform comparison and validation. © 2021, CC BY.

关键词： RNA

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Erratum to 'Core Biopsies from Prostate Cancer Patients in Active Surveillance Protocols Harbor PTEN and MYC Alterations'[European Urology Oncology 2 (2019) 277-285]

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European urology oncology 2021年第1期4卷 129页

作者： Paolo Gandellini Nicola Casiraghi Tiziana Rancati Matteo Benelli Valentina Doldi Alessandro Romanel Maurizio Colecchia Cristina Marenghi Riccardo Valdagni Francesca Demichelis Nadia Zaffaroni Molecular Pharmacology Unit Fondazione IRCCS Istituto Nazionale dei Tumori Milan Italy. Laboratory of Computational and Functional Oncology Centre for Integrative Biology (CIBIO) University of Trento Trento Italy. Prostate Cancer Program Fondazione IRCCS Istituto Nazionale dei Tumori Milan Italy. Bioinformatics Unit Hospital of Prato Prato Italy. Laboratory of Bioinformatics and Computational Genomics Centre for Integrative Biology (CIBIO) University of Trento Trento Italy. Department of Pathology and Laboratory Medicine Fondazione IRCCS Istituto Nazionale dei Tumori Milan Italy. Department of Radiation Oncology 1 Fondazione IRCCS Istituto Nazionale dei Tumori Milan Italy. Department of Oncology and Hemato-oncology Università degli Studi di Milano Milan Italy. Laboratory of Computational and Functional Oncology Centre for Integrative Biology (CIBIO) University of Trento Trento Italy. Electronic address: f.demichelis@unitn.it. Molecular Pharmacology Unit Fondazione IRCCS Istituto Nazionale dei Tumori Milan Italy. Electronic address: nadia.zaffaroni@istitutotumori.mi.it.

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