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Author Correction: Predicting the efficiency of prime editing guide RNAs in human cells

Nature biotechnology 2024年第3期42卷 529页

作者： Hui Kwon Kim Goosang Yu Jinman Park Seonwoo Min Sungtae Lee Sungroh Yoon Hyongbum Henry Kim Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. Electrical and Computer Engineering Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Graduate School of Data Science Seoul National University Seoul Republic of Korea. Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac. Severance Biomedical Science Institute Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of NanoScience and Technology Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac.

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Publisher Correction: Serotonin signals through a gut-liver axis to regulate hepatic steatosis

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Nature communications 2019年第1期10卷 158页

作者： Wonsuk Choi Jun Namkung Inseon Hwang Hyeongseok Kim Ajin Lim Hye Jung Park Hye Won Lee Kwang-Hyub Han Seongyeol Park Ji-Seon Jeong Geul Bang Young Hwan Kim Vijay K Yadav Gerard Karsenty Young Seok Ju Chan Choi Jae Myoung Suh Jun Yong Park Sangkyu Park Hail Kim Graduate School of Medical Science and Engineering KAIST Daejeon 34141 Republic of Korea. Department of Biochemistry Yonsei University Wonju College of Medicine Wonju 26426 Republic of Korea. Biomedical Science and Engineering Interdisciplinary Program KAIST Daejeon 34141 Republic of Korea. Department of Internal Medicine Yonsei University College of Medicine Yonsei Liver Center Severance Hospital Seoul 03722 Republic of Korea. Center for Bioanalysis Division of Metrology for Quality of Life Korea Research Institute of Standards and Science Daejeon 34113 Republic of Korea. Biomedical Omics Group Korea Basic Science Institute Chungbuk 28119 Republic of Korea. Department of Genetics and Development Columbia University Medical Center New York NY 10032 USA. Department of Pathology Chonnam National University Medical School Gwangju 61469 Republic of Korea. Department of Internal Medicine Yonsei University College of Medicine Yonsei Liver Center Severance Hospital Seoul 03722 Republic of Korea. drpjy@yuhs.ac. Graduate School of Medical Science and Engineering KAIST Daejeon 34141 Republic of Korea. 49park@cku.ac.kr. Department of Biochemistry College of Medicine Catholic Kwandong University Gangneung 25601 Republic of Korea. 49park@cku.ac.kr. Graduate School of Medical Science and Engineering KAIST Daejeon 34141 Republic of Korea. hailkim@kaist.edu. Biomedical Science and Engineering Interdisciplinary Program KAIST Daejeon 34141 Republic of Korea. hailkim@kaist.edu. KAIST Institute for the BioCentury KAIST Daejeon 34141 Republic of Korea. hailkim@kaist.edu.

The originally published version of this Article contained an error in Figure 2. In panel g, the image of brown adipose tissue from SCD-fed Tph1 GKO mice (top-right) was inadvertently replaced with the equivalent image of SCD-fed WT mice (top-left) during assembly of the figure. This error has now corrected in both the PDF and HTML versions of the Article.

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Cancer Informatics: Profiling Age-Related Epigenetic Markers of Stomach Adenocarcinoma in Young and Old Subjects

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Cancer Informatics 2015年 14卷

作者： Byoung-Chul Kim Hyoung Oh Jeong Daeui Park Chul-Hong Kim Eun Kyeong Lee Dae Hyun Kim Eunok Im Nam Deuk Kim Sunghoon Lee Byung Pal Yu Jong Bhak Hae Young Chung Molecular Inflammation Research Center for Aging Intervention Pusan National University Busan Republic of Korea.Interdisciplinary Research Program of Bioinformatics and Longevity Science Pusan National University Busan Republic of Korea. Genomictree Inc. Yuseong-gu Daejeon Republic of Korea. Molecular Inflammation Research Center for Aging Intervention Pusan National University Busan Republic of Korea. Personal Genomics Institute Genome Research Foundation Suwon Republic of Korea.BioMedical Engineering UNIST Ulsan Republic of Korea. Department of Physiology University of Texas Health Science Center at San Antonio San Antonio TX USA.

The purpose of our study is to identify epigenetic markers that are differently expressed in the stomach adenocarcinoma (STAD) condition. Based on data from The Cancer Genome Atlas (TCGA), we were able to detect an age-related difference in methylation patterns and changes in gene and miRNA expression levels in young (n = 14) and old (n = 70) STAD subjects. Our analysis identified 323 upregulated and 653 downregulated genes in old STAD subjects. We also found 76 miRNAs with age-related expression patterns and 113 differentially methylated genes (DMGs), respectively. Our further analysis revealed that significant upregulated genes (n = 35) were assigned to the cell cycle, while the muscle system process (n = 27) and cell adhesion-related genes (n = 57) were downregulated. In addition, by comparing gene and miRNA expression with methylation change, we identified that three upregulated genes (ELF3, IL1β, and MMP13) known to be involved in inflammatory responses and cell growth were significantly hypomethylated in the promoter region. We further detected target candidates for age-related, downregulated miRNAs (hsa-mir-124-3, hsa-mir-204, and hsa-mir-125b-2) in old STAD subjects. This is the first report of the results from a study exploring age-related epigenetic biomarkers of STAD using high-throughput data and provides evidence for a complex clinicopathological condition expressed by the age-related STAD progression.

关键词： stomach adenocarcinoma age TCGA RNAseq miRNA DNA methylation

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Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics

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BMC Bioinformatics 2017年第9期18卷 1-9页

作者： Eric C. Rouchka Juw Won Park Julia H. Chariker David A. Tieri Shreedharkumar Rajurkar Vikas Singh Nishchal K. Verma Yan Cui Mark Farman Bradford Condon Jolanta Jaromczyk Neil Moore Jerzy Jaromczyk Daniel Harris Patrick Calie Eun Kyong Shin Robert L. Davis Arash Shaban-Nejad Joshua M. Mitchell Hunter N. B. Moseley Robert M. Flight Qing Jun Wang Richard M. Higashi Teresa W-M Fan Andrew N. Lane Liangqun Lu Bernie J Daigle Jr. Xi Chen Andrey Smelter Jerzy W. Jaromczyk Bailey K. Phan Nathaniel J. Serpico Ethan G. Toney Li Chen Caroline E. Melton Jennifer R. Mandel Bernie J. Daigle Jr. Hao Chen Kazi I. Zaman Ramin Homayouni Patrick J. Trainor Andrew P. DeFilippis Samantha M. Carlisle Shesh N. Rai Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville KY 40292 USA Kentucky Biomedical Research Infrastructure (KBRIN) Bioinformatics Core 522 East Gray Street Louisville KY 40292 USA Department of Psychological and Brain Sciences University of Louisville Louisville KY 40292 USA Department of Anatomical Sciences and Neurobiology University of Louisville Louisville KY 40292 USA Department of Electrical Engineering IIT Kanpur India Department of Microbiology Immunology and Biochemistry University of Tennessee Health Science Center Memphis TN 38103 USA Center for Integrative and Translational Genomics University of Tennessee Health Science Center Memphis TN 38103 USA Department of Plant Pathology University of Kentucky Lexington KY 40546 USA UK Healthcare Genomics University of Kentucky Lexington KY 40536 USA Department of Entomology & Plant Pathology University of Tennessee Knoxville TN 37996 USA Department of Forestry University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40508 USA Department of Biological Sciences Eastern Kentucky University Richmond KY 40475 USA University of Tennessee Health Science Center – Oak-Ridge National Lab (UTHSC-ORNL) Center for Biomedical Informatics Department of Pediatrics Memphis TN 38103 USA Department of Molecular & Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Markey Cancer Center University of Kentucky Lexington KY 40536 USA Center for Environmental and Systems Biochemistry University of Kentucky Lexington KY 40536 USA Institute for Biomedical Informatics University of Kentucky Lexington KY 40536 USA Department of Molecular and Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Department of Statistics University of Kentucky Louisville KY

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Organ-On-A-Chip: Biomechanical Strain Exacerbates Inflammation on a Progeria-on-a-Chip Model (Small 15/2017)

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Small 2017年第15期13卷

作者： João Ribas Yu Shrike Zhang Patrícia R. Pitrez Jeroen Leijten Mario Miscuglio Jeroen Rouwkema Mehmet Remzi Dokmeci Xavier Nissan Lino Ferreira Ali Khademhosseini Biomaterials Innovation Research Center Division of Engineering in Medicine Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge MA 02139 USA Doctoral Program in Experimental Biology and Biomedicine Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research University of Coimbra 3030-789 Coimbra Portugal CNC-Centre for Neuroscience and Cell Biology University of Coimbra 3030-789 Coimbra Portugal Institute for Interdisciplinary Research University of Coimbra 3030-789 Coimbra Portugal Department of Developmental BioEngineering MIRA Institute for Biomedical Technology and Technical Medicine University of Twente 7500 AE Enschede The Netherlands Department of Biomechanical Engineering MIRA Institute for Biomedical Technology and Technical Medicine University of Twente 7500 AE Enschede The Netherlands CECS INSERM U861 I-STEM AFM Institute for Stem Cell Therapy and Exploration of Monogenic Diseases 28 Rue Henri Desbrueres 91100 Corbeil-Essones France Department of Physics King Abdulaziz University Jeddah 21569 Saudi Arabia Department of Bioindustrial Technologies College of Animal Bioscience and Technology Konkuk University Hwayang-dong Gwangjin-gu Seoul 143-701 Republic of Korea

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Time synchronization between parietal–frontocentral connectivity with MRCP and gait in post-stroke bipedal tasks

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Journal of Neuroengineering and Rehabilitation 2024年第1期21卷 101页

作者： Phang, Chun-Ren Su, Kai-Hsiang Cheng, Yuan-Yang Chen, Chia-Hsin Ko, Li-Wei International Ph.D. Program in Interdisciplinary Neuroscience (UST) College of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) College of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Biological Science and Technology College of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Physical Medicine and Rehabilitation Taichung Veterans General Hospital Taichung Taiwan Department of Post-Baccalaureate Medicine College of Medicine National Chung Hsing University Taichung Taiwan School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan Department of Physical Medicine and Rehabilitation Kaohsiung Medical University Hospital Kaohsiung Taiwan School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Regenerative Medicine and Cell Therapy Research Center Kaohsiung Medical University Kaohsiung Taiwan Institute of Electrical and Control Engineering National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Biomedical Science and Environment Biology Kaohsiung Medical University Kaohsiung Taiwan Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung Taiwan

Background: In post-stroke rehabilitation, functional connectivity (FC), motor-related cortical potential (MRCP), and gait activities are common measures related to recovery outcomes. However, the interrelationship between FC, MRCP, gait activities, and bipedal distinguishability have yet to be investigated. Methods: Ten participants were equipped with EEG devices and inertial measurement units (IMUs) while performing lower limb motor preparation (MP) and motor execution (ME) tasks. MRCP, FCs, and bipedal distinguishability were extracted from the EEG signals, while the change in knee degree during the ME phase was calculated from the gait data. FCs were analyzed with pairwise Pearson’s correlation, and the brain-wide FC was fed into support vector machine (SVM) for bipedal classification. Results: Parietal–frontocentral connectivity (PFCC) dysconnection and MRCP desynchronization were related to the MP and ME phases, respectively. Hemiplegic limb movement exhibited higher PFCC strength than nonhemiplegic limb movement. Bipedal classification had a short-lived peak of 75.1% in the pre-movement phase. These results contribute to a better understanding of the neurophysiological functions during motor tasks, with respect to localized MRCP and nonlocalized FC activities. The difference in PFCCs between both limbs could be a marker to understand the motor function of the brain of post-stroke patients. Conclusions: In this study, we discovered that PFCCs are temporally dependent on lower limb gait movement and MRCP. The PFCCs are also related to the lower limb motor performance of post-stroke patients. The detection of motor intentions allows the development of bipedal brain-controlled exoskeletons for lower limb active rehabilitation. © The Author(s) 2024.

关键词： Brain–computer interface Functional connectivity Motor execution Motor preparation Post-stroke

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

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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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Cover Feature: Gas-Phase Transformation of Fluorinated Benzoporphyrins to Porphyrin-Embedded Conical Nanocarbons (Chem. Eur. J. 53/2020)

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Chemistry – A European Journal 2020年第53期26卷 12083-12083页

作者： Dr. Dominik Lungerich Dr. Jakob Felix Hitzenberger Michael Ruppel Dr. Tibor Döpper Dr. Matthias Witt Prof. Dr. Ivana Ivanović-Burmazović Prof. Dr. Andreas Görling Prof. Dr. Norbert Jux Prof. Dr. Thomas Drewello Department of Chemistry and Pharmacy & Interdisciplinary Center for Molecular Materials (ICMM) Organic Chemistry II Friedrich-Alexander-University Erlangen-Nuernberg Nikolaus-Fiebiger-Str. 10 91058 Erlangen Germany Center for Nanomedicine Institute for Basic Science (IBS) Seoul 03722 Republic of Korea Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul 03722 Republic of Korea Department of Chemistry and Pharmacy Physical Chemistry I Friedrich-Alexander-University Erlangen-Nuernberg Egerlandstrasse 3 91058 Erlangen Germany Department of Chemistry and Pharmacy Theoretical Chemistry Friedrich-Alexander-University Erlangen-Nuernberg Egerlandstrasse 3 91058 Erlangen Germany Bruker Daltonics GmbH Fahrenheitstrasse 4 28359 Bremen Germany Department of Chemistry and Pharmacy Bioinorganic Chemistry Friedrich-Alexander-University Erlangen-Nuernberg Egerlandstrasse 1 91058 Erlangen Germany

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scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs

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Cell systems 2023年第4期14卷 302-311.e4页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Yu-Te Lin Cristhian Roman-Vicharra Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Department of Nutrition and the Program in Integrative Nutrition & Complex Diseases Texas A&M University College Station TX 77843 USA. Electronic address: r-chapkin@tamu.edu. Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA. Electronic address: jcai@tamu.edu.

We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, using LR pairs as inter-data correspondences to embed ligand and receptor genes expressed in interacting cells into a unified latent space. Neural networks are employed to minimize the distance between corresponding genes while preserving the structure of gene regression networks. We apply scTenifoldXct to real datasets for testing and demonstrate that our method detects interactions with high consistency compared with other methods. More importantly, scTenifoldXct uncovers weak but biologically relevant interactions overlooked by other methods. We also demonstrate how scTenifoldXct can be used to compare different samples, such as healthy vs. diseased and wild type vs. knockout, to identify differential interactions, thereby revealing functional implications associated with changes in cellular communication status.

关键词： cell-cell interaction cellular communication gene regression network machine learning manifold alignment neural networks scRNA-seq single-cell RNA sequencing

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Correction: Liquid-capped encoded microcapsules for multiplex assays

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Lab on a chip 2017年第4期17卷 738页

作者： Younghoon Song Yunjin Jeong Taehong Kwon Daewon Lee Dong Yoon Oh Tae-Joon Park Junhoi Kim Jiyun Kim Sunghoon Kwon Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Department of Electrical and Computer Science Seoul National University Seoul 151-742 Republic of Korea. Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Interdisciplinary Program of Bioengineering Seoul National University Seoul 151-742 Republic of Korea. Nano Systems Institute Seoul National University Seoul 151-742 Republic of Korea. Department of Materials Science and Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea. Institutes of Entrepreneurial BioConvergence Seoul National University Seoul 151-742 Republic of Korea. skwon@snu.ac.kr and Department of Electrical and Computer Science Seoul National University Seoul 151-742 Republic of Korea and Interdisciplinary Program of Bioengineering Seoul National University Seoul 151-742 Republic of Korea and Nano Systems Institute Seoul National University Seoul 151-742 Republic of Korea and Seoul National University Hospital Biomedical Research Institute Seoul National University Hospital Seoul 151-742 Republic of Korea and Quantamatrix Inc. Seoul 151-742 Republic of Korea.

Correction for 'Liquid-capped encoded microcapsules for multiplex assays' by Younghoon Song et al., Lab Chip, 2017, DOI: .

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