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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Yingzi Li Hammad Naveed Sema Kachalo Lisa X. Xu Jie Liang Department of Biomedical Engineering Shanghai Jiao Tong University Shanghai China Bioinformatics Program Department of Bioengineering University of Illinois Chicago Chicago IL USA Department of Biomedical Engineering and Med-X Research Institute Shanghai Jiao Tong University Shanghai China Shanghai Center of Systems Biomedicine Shanghai Jiao Tong University Shanghai China

Regulation of cell growth and proliferation has a fundamental role in tissue development, organogenesis, and disease progression. Conserved distribution of the number of sides of cells with a mean value of six was found in a variety of proliferating epithelia. Previous studies have shown that clones of proliferating cells bounded by quiescent cells have fewer sides than normal epithelia. However, the mechanisms for mediating such localized topological change remain poorly understood. In this study, we use a two-dimensional vertex model with consideration of mechanical forces to investigate how differential proliferation and forces can influence cell shape and tissue morphogenesis, and how they may lead to distorted topological change. We find that differential proliferation alone is insufficient to affect the topology of boundary proliferating cells. Rather, increased surface tension on the boundary, in addition to differential proliferation, can significantly decrease the average number of cell sides. Our results are consistent with experimental observations. We conclude that mechanical forces in addition to localized differential proliferation are required to produce the distorted topological change which significantly impacts the overall cell shape and tissue morphogenesis.

关键词： Biological system modeling Shape Topology Educational institutions Force Surface tension Stress

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Microfluidic assembly blocks

Microfluidic assembly blocks

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作者： Rhee, Minsoung Burns, Mark A. Department of Chemical Engineering University of Michigan 3074 H.H. Dow Building 2300 Hayward St. Ann Arbor MI 48109-2136 United States Bioinformatics Program Medical School University of Michigan 100 Washtenaw Avenue Ann Arbor MI 48109-2218 United States Department of Biomedical Engineering University of Michigan 2200 Bonisteel Blvd. Ann Arbor MI 48109-2099 United States

ISBN: (纸本)9780816910502

We propose a method for microdevice construction where non-expert users can assemble the blocks on glass slides to build their custom devices in minutes without any complicated fabrication steps. This approach involves prefabrication of individual microfluidic assembly blocks (MABs) in PDMS are pre-fabricated and readily assembled to form microfluidic systems. We describe the construction process, the assembly of the devices, and various bonding techniques to accomplish hermetic assembly. Finally, we demonstrate common microfluidic applications including laminar flow development, valve control, and cell culture.

关键词： Microfluidics

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Data analysis guidelines for single‑cell RNA‑seq in biomedical studies and clinical applications

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Military Medical Research 2023年第4期10卷 529-553页

作者： Min Su Tao Pan Qiu‑Zhen Chen Wei‑Wei Zhou Yi Gong Gang Xu Huan‑Yu Yan Si Li Qiao‑Zhen Shi Ya Zhang Xiao He Chun‑Jie Jiang Shi‑Cai Fan Xia Li Murray J.Cairns Xi Wang Yong‑Sheng Li State Key Laboratory of Reproductive Medicine Nanjing Medical UniversityNanjing 211166China College of Biomedical Information and Engineering the First Affiliated Hospital of Hainan Medical UniversityHainan Medical UniversityHaikou 571199HainanChina College of Bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081HeilongjiangChina Department of Immunology Nanjing Medical UniversityNanjing 211166China Department of Laboratory Medicine Women and Children’s Hospital of Chongqing Medical UniversityChongqing 401174China Baylor College of Medicine HoustonTX 77030USA Shenzhen Institute for Advanced Study University of Electronic Science and Technology of ChinaShenzhen 518110GuangdongChina School of Biomedical Sciences and Pharmacy Faculty of Health and Medicinethe University of NewcastleUniversity DriveCallaghanNSW 2308Australia Precision Medicine Research Program Hunter Medical Research InstituteNew Lambton HeightsNSW 2305Australia

The application of single-cell RNA sequencing(scRNA-seq)in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic *** the expansion of capacity for high-throughput scRNA-seq,including clinical samples,the analysis of these huge volumes of data has become a daunting prospect for researchers entering this ***,we review the workflow for typical scRNA-seq data analysis,covering raw data processing and quality control,basic data analysis applicable for almost all scRNA-seq data sets,and advanced data analysis that should be tailored to specific scientific *** summarizing the current methods for each analysis step,we also provide an online repository of software and wrapped-up scripts to support the *** and caveats are pointed out for some specific analysis tasks and *** hope this resource will be helpful to researchers engaging with scRNA-seq,in particular for emerging clinical applications.

关键词： Single-cell RNA-sequencing(scRNA-seq) Data analysis biomedical research Clinical applications

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SeqMapPDB: A Standalone Pipeline to Identify Representative Structures of Protein Sequences and Mapping Residue Indices in Real-Time at Proteome Scale

arXiv

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arXiv 2022年

作者： Wang, Boshen Lei, Xue Tian, Wei Perez-Rathke, Alan Liang, Jie Tseng, Yan-Yuan Boinformatics Program Center for Bioinformatics and Quntitative Biology Richard and Loan Hill Department of Biomedical Engineering University of Illinois at Chicago Chicago60612 United States DMolecular Medicine and Genetics Wayne State University Detroit48201 United States

Motivation: 3D structures of proteins provide rich information for understanding their biochemical roles. Identifying the representative protein structures for protein sequences is essential for analysis of proteins at proteome scale. However, there are technical difficulties in identifying the representative structure of a given protein sequence and providing accurate mapping of residue indices. Existing databases of mapping between structures and sequences are usually static that are not suitable for studying proteomes with frequent gene model revisions. They often do not provide reliable and consistent representative structures that maximizes sequence coverage. Furthermore, proteins isomers are usually not properly resolved. Results: To overcome these difficulties, we have developed a computational pipeline called SeqMapPDB to provide high-quality representative PDB structures of given sequences. It provides mapping to structures that fully cover the sequences when available, or to the set of partial non-overlapping structural domains that maximally cover the query sequence. The residue indices are accurate mapped and isomeric proteins are resolved. SeqMapPDB is efficient and can rapidly carry out proteome-wide mapping to the selected version of reference genomes in real-time. Furthermore, SeqMapPDB provides the flexibility of a stand-alone pipeline for large scale mapping of in-house sequence and structure data. Availability: Our method is available at https://***/lianglabuic/seqmappdb with GNU GPL license. © 2022, CC BY.

关键词： Proteins

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Author Correction: A comprehensive human embryo reference tool using single-cell RNA-sequencing data

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Nature methods 2025年第3期22卷 636页

作者： Cheng Zhao Alvaro Plaza Reyes John Paul Schell Jere Weltner Nicolás M Ortega Yi Zheng Åsa K Björklund Laura Baqué-Vidal Joonas Sokka Ras Trokovic Brian Cox Janet Rossant Jianping Fu Sophie Petropoulos Fredrik Lanner Department of Clinical Science Intervention and Technology Karolinska Institutet and Division of Obstetrics and Gynecology Karolinska Universitetssjukhuset Stockholm Sweden. Department of Integrative Pathophysiology and Therapy Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER) Seville Spain. Stem Cells and Metabolism Research Program University of Helsinki Helsinki Finland. Folkhälsan Research Center Helsinki Finland. Department of Mechanical Engineering University of Michigan Ann Arbor MI USA. Department of Biomedical and Chemical Engineering Syracuse University Syracuse NY USA. Department of Cell and Molecular Biology National Bioinformatics Infrastructure Sweden Science for Life Laboratory Uppsala University Uppsala Sweden. Department of Physiology Faculty of Medicine University of Toronto Toronto Ontario Canada. Program in Developmental and Stem Cell Biology Hospital for Sick Children Toronto Ontario Canada. Department of Cell and Developmental Biology University of Michigan Medical School Ann Arbor MI USA. Department of Biomedical Engineering University of Michigan Ann Arbor MI USA. Department of Clinical Science Intervention and Technology Karolinska Institutet and Division of Obstetrics and Gynecology Karolinska Universitetssjukhuset Stockholm Sweden. sophie.petropoulos@ki.se. Département de Médecine Université de Montréal Montreal Quebec Canada. sophie.petropoulos@ki.se. Centre de Recherche du Centre Hospitalier de l'Université de Montréal Axe Immunopathologie Montreal Quebec Canada. sophie.petropoulos@ki.se. Department of Clinical Science Intervention and Technology Karolinska Institutet and Division of Obstetrics and Gynecology Karolinska Universitetssjukhuset Stockholm Sweden. fredrik.lanner@ki.se. Ming Wai Lau Center for Reparative Medicine Stockholm Node Karolinska Institutet Stockholm Sweden. fredrik.lanner@ki.se.

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PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions

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Protein & Cell 2019年第10期10卷 709-725页

作者： Xiaona Huang Chao Wei Fenjie Li Lumeng Jia Pengguihang Zeng Jiahe Li Jin Tan Tuanfeng Sun Shaoshuai Jiang Jia Wang Xiuxiao Tang Bin Liu Limin Rong Cheng Li Junjun Ding RNA Biomedical Institute Sun Yat-Sen Memorial HospitalZhongshan School of MedicineSun Yat-Sen UniversityGuangzhou 510080China Center for Stem Cell Biology and Tissue Engineering Key Laboratory for Stem Cells and Tissue EngineeringMinistry of EducationSun Yat-Sen UniversityGuangzhou 510080China Department of Cell Biology Zhongshan School of MedicineSun Yat-sen UniversityGuangzhou 510080China Program in Stem Cell and Regenerative Medicine The Third Affiliated Hospital of Sun Yat-sen UniversityZhongshan School of MedicineSun Yat-Sen UniversityGuangzhouChina Center for Bioinformatics School of Life SciencesPeking UniversityBeijing 100871China Department of Spine Surgery The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630China Department of Histology and Embryology School of Basic Medical SciencesGuangzhou Medical UniversityGuangzhou 511436China

Polycomb group(PcG)ring finger protein 6(PCGF6),though known as a member of the transcription-re-pressing complexes,PcG,also has activation function in regulating pluripotency gene ***,the mechanism underlying the activation function of PCGF6 is poorly ***,we found that PCGF6 co-localizes to gene activation regions along with pluripotency factors such as *** addition,PCGF6 was recruited to a subset of the super-enhancer(SE)regions upstream of cell cycle-associated genes by OCT4,and increased their *** combining with promoter capture Hi-C data,we found that PCGF6 activates cell cycle genes by regulating SE-promoter interactions via 3D *** fin dings highlight a novel mechanism of PcG protein in regulating pluripotency,and provide a research basis for the therapeutic application of pluripotent stem cells.

关键词： PCGF6 Polycomb group super-enhancer 3D chromatin pluripotency

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Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application

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Journal of Pharmaceutical Analysis 2023年第7期13卷 691-693页

作者： Dan Li Zhou Fang Qiang Shi Nicholas Zhang Binsheng Gong Weida Tong Ahmet F.Coskun Joshua Xu Division of Bioinformatics and Biostatistics National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Wallace H.Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory UniversityAtlantaGA30332USA Machine Learning Graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Division of Systems Biology National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Interdisciplinary Bioengineering Graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Parker H.Petit Institute for Bioengineering and Bioscience Georgia Institute of TechnologyAtlantaGA30332USA

Reducing the use of animal models in drug development and safety assessment has long been supported by the *** and Drug Administration(FDA).The report by Royal Society for the Prevention of Cruelty to Animals indicates that in 2020,experiments involved the use of over 100 million animals,with the United States leading the list by utilizing 20 million *** ethical considerations associated with animal testing and the costs in terms of time and money,animal models are not always effective in predicting human reactions to drug *** animal testing has been the traditional method for assessing the safety and efficacy of drugs.

关键词： money utilizing testing

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Diversity and Suitability of the State-of-the-Art Wearable and Wireless EEG Systems Review

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IEEE Journal of biomedical and Health Informatics 2023年第8期27卷 3830-3843页

作者： He, Congying Chen, Yu-Yi Phang, Chun-Ren Stevenson, Cory Chen, I-Ping Jung, Tzyy-Ping Ko, Li-Wei Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu30010 Taiwan Institute of Applied Arts National Yang Ming Chiao Tung University Hsinchu30010 Taiwan International Ph.D. Program in Interdisciplinary Neuroscience National Yang Ming Chiao Tung University Hsinchu30010 Taiwan Institute for Neural Computation and Institute of Engineering in Medicine University of California San DiegoCA90093 United States National Yang Ming Chiao Tung University Hsinchu30010 Taiwan Institute of Electrical and Control Engineering Department of Electronics and Electrical Engineering Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu30010 Taiwan Department of Biomedical Science and Environment Biology Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung80708 Taiwan

Wireless electroencephalography (EEG) systems have been attracting increasing attention in recent times. Both the number of articles discussing wireless EEG and their proportion relative to general EEG publications have increased over years. These trends indicate that wireless EEG systems could be more accessible to researchers and the research community has recognized the potential of wireless EEG systems. To explore the development and diverse applications of wireless EEG systems, this review highlights the trends in wearable and wireless EEG systems over the past decade and compares the specifications and research applications of the major wireless systems marketed by 16 companies. For each product, five parameters (number of channels, sampling rate, cost, battery life, and resolution) were assessed for comparison. Currently, these wearable and portable wireless EEG systems have three main application areas: consumer, clinical, and research. To address this multitude of options, the article also discussed the thought process to find a suitable device that meets personalization and use cases specificities. These investigations suggest that low-price and convenience are key factors for consumer applications, wireless EEG systems with FDA or CE-certification may be more suitable for clinical settings, and devices that provide raw EEG data with high-density channels are important for laboratory research. This article presents an overview of the current state of the wireless EEG systems specifications and possible applications and serves as a guide point as it is expected that more influential and novel research will cyclically promote the development of such EEG systems. © 2023 IEEE.

关键词： Electroencephalography

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The cell surface marker CD36 selectively identifies matured,mitochondria-rich hPSC-cardiomyocytes

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细胞研究（英文版） 2020年第7期30卷 626-629页

作者： Ellen Ngar-Yun Poon Xiao-ling Luo Sarah E.Webb Bin Yan Rui Zhao Stanley Chun Ming Wu Yong Yang Peng Zhang Huajun Bai Jiaofang Shao Ching Man Chan Godfrey Chi-Fung Chan Suk Ying Tsang Rebekah L.Gundry Huang-Tian Yang Kenneth R.Boheler Department of Medicine and Therapeutics and Centre for Cardiovascular Genomics and Medicine The Chinese University of Hong Kong (CUHK) HKSAR China CAS Key Laboratory of Tissue Microenvironment and Tumor Laboratory of Molecular CardiologyShanghai Institute of Nutrition and Health University of Chinese Academy of Sciences (CAS) CAS Shanghai China Division of Life Science and State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology HKSAR China Department of Computer Science The University of Hong Kong (HKU) HKSAR China Intervention and Cell Therapy Center Peking University Shenzhen Hospital Shenzhen China School of Life Sciences CUHK HKSAR China Department of Paediatrics and Adolescent Medicine HKU HKSAR China School of Biomedical Sciences HKU HKSAR China SUSTech Academy for Advanced Interdisciplinary Studies Southern University of Science and Technology (SUSTech) Shenzhen China Department of Bioinformatics School of Biomedical Engineering and InformaticsNanjing Medical University Nanjing Jiangsu China State Key Laboratory of Agrobiotechnology CUHK HKSAR China Department of Biochemistry and Center for Biomedical Mass Spectrometry Research Medical College of Wisconsin Milwaukee WIUSA CardiOmics Program Center for Heart and Vascular Research Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology University of Nebraska Medical Center Omaha NE USA Institute for Stem Cell and Regeneration Medicine CASBeijing China Division of Cardiology Department of Medicineand Department of Biomedical Engineering The Johns Hopkins University Baltimore MD USA

Dear Editor,Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) are of significant translational value to in vitro studies of human cardiac development, drug and cardiotoxicity testing and cardiac disease *** of hPSCs to CMs,however, yields mixed cultures of atrial-, ventricular-, and pacemaker-like cells as well as non-CMs in variable proportions.1

关键词： Stem-cell differentiation Stem cells

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PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

arXiv

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arXiv 2024年

作者： Tang, Sophia Zhang, Yinuo Chatterjee, Pranam Department of Biomedical Engineering Duke University United States Management and Technology Program University of Pennsylvania United States Center of Computational Biology Duke-NUS Medical School Singapore Department of Computer Science Duke University United States Department of Biostatistics and Bioinformatics Duke University United States

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and target structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with bond-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity. Using PepTune, we generate diverse, chemically modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling for various disease-relevant targets. In total, our results demonstrate that MCTS-guided masked discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces. © 2024, CC BY-NC-ND.

关键词： Trees (mathematics)

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