Single-cell analyses implicate ascites in remodeling the ecosystems of primary and metastatic tumors in ovarian cancer

Authors: Xiaodong Zheng, Xinjing Wang, Xueqing Cheng, Zhaoyuan Liu, Yujia Yin, Xiaoduan Li, Zhihao Huang, Ziliang Wang, Wei Guo, Florent Ginhoux, Ziyi Li, Zemin Zhang, Xipeng Wang

Source: Nat Cancer

Subject Terms: Immunology, Cancer research, CD8-Positive T-Lymphocytes, Article, Single-Cell, Monocytes, Metastasis, Primary tumor, Ovarian cancer, Biochemistry, Genetics and Molecular Biology, Pathology, Humans, Immunological Mechanisms in Pregnancy and Fetal-Maternal Interface, Molecular Biology, Biology, Internal medicine, Ecosystem, Cancer, Ovarian Neoplasms, Immunology and Microbiology, Macrophage Activation and Polarization, FOS: Clinical medicine, Life Sciences, Ascites, CD8, Comprehensive Integration of Single-Cell Transcriptomic Data, Tumor progression, 3. Good health, Immune system, Medicine, Female, Single-Cell Analysis

Access URL: https://pubmed.ncbi.nlm.nih.gov/37488416

Camtrap DP: An open standard for the FAIR exchange and archiving of camera trap data: an open standard for the FAIR exchange and archiving of camera trap data

Authors: Jakub W. Bubnicki, Ben Norton, Steven J. Baskauf, Tom Bruce, Francesca Cagnacci, Jim Casaer, Marcin Churski, Joris P. G. M. Cromsigt, Simone Dal Farra, Christian Fiderer, Tavis D. Forrester, Heidi Hendry, Marco Heurich, Tim R. Hofmeester, Patrick A. Jansen, Roland Kays, Dries P. J. Kuijper, Yorick Liefting, John D. C. Linnell, Matthew S. Luskin, Christopher Mann, Tanja Milotic, Peggy Newman, Jürgen Niedballa, Damiano Oldoni, Federico Ossi, Tim Robertson, Francesco Rovero, Marcus Rowcliffe, Lorenzo Seidenari, Izabela Stachowicz, Dan Stowell, Mathias W. Tobler, John Wieczorek, Fridolin Zimmermann, Peter Desmet

Contributors: Bubnicki, J.W., Norton, B., Baskauf, S.J., Bruce, T., Cagnacci, F., Casaer, J., Churski, M., Cromsigt, J.P.G.M., Dal Farra, S., Fiderer, C., Forrester, T.D., Hendry, H., Heurich, M., Hofmeester, T.R., Jansen, P.A., Kays, R., Kuijper, D.P.J., Liefting, Y., Linnell, J.D.C., Luskin, M.S., Mann, C., Milotic, T., Newman, P., Niedballa, J., Oldoni, D., Ossi, F., Robertson, T., Rovero, F., Rowcliffe, M., Seidenari, L., Stachowicz, I., Stowell, D., Tobler, M.W., Wieczorek, J., Zimmermann, F., Desmet, P.

Source: Remote Sensing in Ecology and Conservation, Vol 10, Iss 3, Pp 283-295 (2024)
Remote Sensing in Ecology and Conservation

Subject Terms: Data Integration, Technology, data sharing, SOFTWARE, Wildlife, VDP::Matematikk og Naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420, Data science, Remote Sensing, 0502 Environmental Science and Management, Camera trap, QH540-549.5, Nature and Landscape Conservation, Computers in Earth Sciences, Ecology, Ecology, Evolution, Behavior and Systematics, Species Distribution Modeling and Climate Change Impacts, CHALLENGES, camera trap, Ecological Modeling, Camera traps, 3103 Ecology, BIG-DATA, Life Sciences, Comprehensive Integration of Single-Cell Transcriptomic Data, Interoperability, Programming language, World Wide Web, Physical Sciences, Life Sciences & Biomedicine, biodiversity data, Environmental Sciences & Ecology, Citizen science, ECOLOGY, Data management, ROE DEER, Database, 4104 Environmental management, camera traps, Settore BIO/07 - ECOLOGIA, Biochemistry, Genetics and Molecular Biology, MANAGEMENT, Molecular Biology, Biology, Metadata, Science & Technology, 0602 Ecology, Botany, information standards, Data exchange, NEED, data exchange, VDP::Matematikk og Naturvitenskap: 400, 15. Life on land, Biodiversity data, Computer science, Information standard, FOS: Biological sciences, Environmental Science, remote sensing, Data sharing, BIODIVERSITY, Environmental DNA in Biodiversity Monitoring, Software

File Description: application/pdf; pdf

Access URL: https://doaj.org/article/6c197198f4a745c6846b1fd4684f5199
https://hdl.handle.net/11250/3107083
https://serval.unil.ch/notice/serval:BIB_4F1A622D0524
http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_4F1A622D05244
https://serval.unil.ch/resource/serval:BIB_4F1A622D0524.P001/REF.pdf
https://repository.publisso.de/resource/frl:6482774
https://hdl.handle.net/11250/3107077
https://discovery-pp.ucl.ac.uk/id/eprint/10186308/

A range’s core should not only be important in research

Authors: Luca Luiselli

Source: African Journal of Ecology. 61:257-261

Subject Terms: 2. Zero hunger, 0106 biological sciences, Sociology and Political Science, Geography, Social Sciences, Life Sciences, Core (optical fiber), Comprehensive Integration of Single-Cell Transcriptomic Data, 15. Life on land, Motivation and Behavior of Convention Attendees, Computer science, 01 natural sciences, 12. Responsible consumption, The Delphi Method in Research and Consensus Building, Range (aeronautics), Engineering, Aerospace engineering, 13. Climate action, Biochemistry, Genetics and Molecular Biology, 11. Sustainability, Telecommunications, 14. Life underwater, Ecological Niche, Molecular Biology

A patient-specific lung cancer assembloid model with heterogeneous tumor microenvironments

Authors: Yanmei Zhang, Qifan Hu, Yuquan Pei, Hao Luo, Zixuan Wang, Xinxin Xu, Qing Zhang, Jixun Dai, Wei Wang, Zhixing Fan, Yajun Fang, Min Ye, Binhan Li, Mailin Chen, Qi Xue, Qingfeng Zheng, Shulin Zhang, Miao Huang, Ting Zhang, Jin Gu, Zhuo Xiong

Source: Nat Commun
Nature Communications, Vol 15, Iss 1, Pp 1-17 (2024)

Subject Terms: 0301 basic medicine, Organoid, FOS: Computer and information sciences, Lung Neoplasms, Bioinformatics, Science, Biomedical Engineering, Cancer cell, Cancer research, FOS: Medical engineering, Gene, Article, Computational biology, 03 medical and health sciences, Engineering, Biochemistry, Genetics and Molecular Biology, Health Sciences, In vivo, Tumor Microenvironment, Pathology, Genetics, Humans, Cell Heterogeneity, Precision Medicine, Molecular Biology, Biology, Internal medicine, Cancer, 0303 health sciences, 3D Bioprinting Technology, Precision medicine, Life Sciences, Comprehensive Integration of Single-Cell Transcriptomic Data, Personalized medicine, 3. Good health, Organoids, Oncology, Tumor microenvironment, Cancer Stem Cells and Tumor Metastasis, FOS: Biological sciences, Physical Sciences, Medicine, Gene expression, Lung cancer, Transcriptome, Cancer Medicine, Neuroscience, Biotechnology

Access URL: https://pubmed.ncbi.nlm.nih.gov/38643164
https://doaj.org/article/fa3d1c3a662e467eb7331e0cf56a412e

Transcriptome landscape of high and low responders to an inactivated COVID-19 vaccine after 4 months using single-cell sequencing

Authors: Zhongyi Zhu, Yaling Huang, Jun Sun, Meirong Li, Yong Chen, Lei Zhang, Fubaoqian Huang, Chuanyu Liu, Weijun Chen, Jinmin Ma

Subject Terms: Regulatory T Cell Development and Function, Immunobiology of Dendritic Cells, Immunology, Population, Gene, Single-Cell, Computational biology, In vitro, Biochemistry, Genetics and Molecular Biology, Virology, Genetics, Transcriptomics, Molecular Biology, Biology, Antibody, Immunology and Microbiology, FOS: Clinical medicine, Innate immune system, Vaccination, Immunity, Life Sciences, Comprehensive Integration of Single-Cell Transcriptomic Data, Peripheral blood mononuclear cell, 3. Good health, Immune system, Environmental health, FOS: Biological sciences, Medicine, Cell, Gene expression, Transcriptome

Unique molecular and functional features of extramedullary hematopoietic stem and progenitor cell reservoirs in humans

Authors: Nicole Mende, Hugo Bastos, Antonella Santoro, Krishnaa T. Mahbubani, Valerio Ciaurro, Emily F. Calderbank, Mariana Quiroga Londoño, Kendig Sham, Giovanna Mantica, Tatsuya Morishima, Emily Mitchell, Maria Rosa Lidonnici, Fabienne Meier‐Abt, Daniel Hayler, Laura Jardine, Abbie Curd, Muzlifah Haniffa, G. Ferrari, Hajime Takizawa, Nicola K. Wilson, Berthold Göttgens, Kourosh Saeb‐Parsy, Mattia Frontini, Elisa Laurenti

Contributors: DSpace at Cambridge pro (8.1), University of Zurich

Source: Blood

Subject Terms: Adult, Acute Myeloid Leukemia, Myeloid, Cell biology, Hematopoietic Progenitor Cells, 10039 Institute of Medical Genetics, Immunology, 610 Medicine & health, Bone Marrow Cells, Extramedullary hematopoiesis, Article, Bone Marrow, Biochemistry, Genetics and Molecular Biology, Health Sciences, Humans, Erythropoiesis, Bone marrow, Hematopoietic Cell Transplantation, Molecular Biology, Biology, Internal medicine, Stem cell, Cambridge Stem Cell Institute, Blood cell, Stem Cells, FOS: Clinical medicine, Life Sciences, Anemia, Hematology, Comprehensive Integration of Single-Cell Transcriptomic Data, Hematopoietic Stem Cells, Hematopoiesis, Haematopoiesis, 10032 Clinic for Oncology and Hematology, Progenitor cell, 570 Life sciences, biology, Medicine, Hematopoietic Stem Cell Biology, Megakaryocytes, Spleen

File Description: application/pdf; blood.2021013450.pdf - application/pdf; Print

Access URL: https://ashpublications.org/blood/article-pdf/doi/10.1182/blood.2021013450/1864566/blood.2021013450.pdf
https://pubmed.ncbi.nlm.nih.gov/35073399

Comparison of neutrophil respiratory oxidative burst activity between flow cytometry using dihydrorhodamine (DHR) 123 and conventional nitroblue tetrazolium test (NBT)

Authors: Norliana Yusof, Norafiza Mohd Yasin, Rabeya Yousuf, Asrul Abdul Wahab, Siti Asma Che Aziz

Source: Bangladesh Journal of Medical Science. 21:626-633

Subject Terms: Immunology and Microbiology, Advanced Techniques in Bioimage Analysis and Microscopy, Respiratory burst, 0301 basic medicine, Molecular biology, FOS: Clinical medicine, Immunology, Biophysics, Life Sciences, Comprehensive Integration of Single-Cell Transcriptomic Data, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Role of Neutrophil Extracellular Traps in Immunity, Biochemistry, Genetics and Molecular Biology, Medicine, Cell Heterogeneity, Flow cytometry, Molecular Biology, Biology, Cytometry

scGIST: gene panel design for spatial transcriptomics with prioritized gene sets

Authors: Mashrur Ahmed Yafi, Md. Hasibul Husain Hisham, Francisco Grisanti, James F. Martin, Atif Rahman, Md. Abul Hassan Samee

Source: Genome Biol
Genome Biology, Vol 25, Iss 1, Pp 1-17 (2024)

Subject Terms: 0301 basic medicine, Artificial intelligence, Medical Sciences, QH301-705.5, Biophysics, Biomedical Engineering, Method, QH426-470, DNA Nanotechnology and Bioanalytical Applications, FOS: Medical engineering, Biochemistry, Gene, Fluorescence, Spatial Profiling, Computational biology, 03 medical and health sciences, Engineering, Selection (genetic algorithm), Biochemistry, Genetics and Molecular Biology, Medical Specialties, Medicine and Health Sciences, Genetics, Biology (General), Molecular Biology, Biology, In Situ Hybridization, In Situ Hybridization, Fluorescence, 0303 health sciences, Gene Expression Profiling, Life Sciences, Comprehensive Integration of Single-Cell Transcriptomic Data, Computer science, Programming language, FOS: Biological sciences, Physical Sciences, and Structural Biology, Paper-Based Diagnostic Devices, Gene expression, Toolbox, Transcriptome

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38408997
https://doaj.org/article/5a6db1aa711c4b0fa1cb3075008b7125

Spatially organized tumor-stroma boundary determines the efficacy of immunotherapy in colorectal cancer patients

Authors: Rongxin Zhang, Yu Feng, Wenjuan Ma, Yupeng Zang, Yanying Guo, Young Li, Yixuan Zhang, Dong Xuan, Yi Liu, Xiaojuan Zhan, Zhi-Zhong Pan, Longyong Mei, Miaoqing Wu, Ao Chen, Gong� Chen, Longqi Liu, Jingying Zhou

Subject Terms: Immunology, Cancer immunotherapy, Stroma, Cancer research, Tumor cells, Cancer Immunotherapy, Pathology and Forensic Medicine, Computational biology, Molecular Characterization of Colorectal Cancer, Biochemistry, Genetics and Molecular Biology, Health Sciences, Tumor Microenvironment, Genetics, Molecular Biology, Biology, Cancer, FOS: Clinical medicine, Life Sciences, Reprogramming, Comprehensive Integration of Single-Cell Transcriptomic Data, Colorectal cancer, Immunohistochemistry, Immune Checkpoint Blockade, 3. Good health, Oncology, Tumor microenvironment, FOS: Biological sciences, Medicine, Immunotherapy, Immune checkpoint, Cell

scX: a user-friendly tool for scRNAseq exploration

Authors: Tomás Vega Waichman, M Luz Vercesi, Ariel A. Berardino, Maximiliano S. Beckel, Damiana Giacomini, Natalí B. Rasetto, Magalí Herrero, Daniela J. Di Bella, Paola Arlotta, Alejandro F. Schinder, Ariel Chernomoretz

Source: Bioinform Adv

Subject Terms: Advanced Techniques in Bioimage Analysis and Microscopy, Interface (matter), transcriptomica, Biophysics, Computational biology, Identification (biology), Biochemistry, Genetics and Molecular Biology, Application Note, Quantitative Biology - Genomics, RNA-Seq, Molecular Biology, Source code, Data mining, Biology, Visualization, Genomics (q-bio.GN), Bubble, Data visualization, User Friendly, Botany, Life Sciences, scRNAseq, Comprehensive Integration of Single-Cell Transcriptomic Data, Computer science, Profiling (computer programming), Programming language, Stochasticity in Gene Regulatory Networks, Operating system, FOS: Biological sciences, Single-Cell Analysis, Maximum bubble pressure method

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38779177
https://pubmed.ncbi.nlm.nih.gov/37961742
http://arxiv.org/abs/2311.00012
http://hdl.handle.net/11336/261857

Consensus Nature Inspired Clustering of Single-Cell RNA-Sequencing Data

Authors: Amany H. Abou El-Naga, Akram Salah, Sabah Sayed, Heba Mohsen

Source: IEEE Access, Vol 10, Pp 98079-98094 (2022)

Subject Terms: 0301 basic medicine, Artificial intelligence, 0206 medical engineering, 02 engineering and technology, unsupervised learning, Clustering, Single-Cell, Computational biology, 03 medical and health sciences, Cluster analysis, Biochemistry, Genetics and Molecular Biology, Microarray Data Analysis and Gene Expression Profiling, Droplet-based Sequencing, Cell Heterogeneity, RNA-Seq, Molecular Biology, Data mining, Biology, Single-cell RNA-seq, automatic clustering, swarm intelligence, consensus clustering, Life Sciences, Comprehensive Integration of Single-Cell Transcriptomic Data, Computer science, metaheuristic algorithms, TK1-9971, Analysis of Gene Interaction Networks, 3. Good health, Electrical engineering. Electronics. Nuclear engineering

Access URL: https://doaj.org/article/485c5ea17339418490afa6072d69bc87

Genomic landscape of diffuse glioma revealed by whole genome sequencing

Authors: Ben Kinnersley, Josephine Jung, Alex Cornish, Daniel Chubb, Ross C. Laxton, Anna Frangou, Andreas J Gruber, Amit Sud, Giulio Caravagna, Andrea Sottoriva, David C. Wedge, Thomas C. Booth, Safa Al‐Sarraj, Stephanie Lawrence, Erminia Albanese, Guilio Anichini, David Baxter, Alexandros Boukas, Yasir Chowdhury, Pietro Ivo D'Urso, Robert Corns, Andrew Dapaah, Ellie Edlmann, Fay Greenway, Paul Grundy, Ciaran Scott Hill, Michael D. Jenkinson, Sanjay Krishna, Stuart Smith, Susruta Manivannan, Andrew Martin, Samir A Matloob, Soumya Mukherjee, Kevin O'Neill, Puneet Plaha, Jonathan Pollock, Stephen J. Price, Ola Rominiyi, Bhavesh Sachdev, Fozia Saeed, Saurabh Sinha, Lewis Thorne, Ismail Ughratdar, Peter Whitfield, Amir Saam Youshani, Helen Bulbeck, Prabhu Arumugam, Richard S. Houlston, Keyoumars Ashkan

Source: Nat Commun
Nature Communications, Vol 16, Iss 1, Pp 1-18 (2025)
Kinnersley, B, Jung, J, Cornish, A J, Chubb, D, Laxton, R, Frangou, A, Gruber, A J, Sud, A, Caravagna, G, Sottoriva, A, Wedge, D C, Booth, T, Al-Sarraj, S, Lawrence, S E D, Albanese, E, Anichini, G, Baxter, D, Boukas, A, Chowdhury, Y A, D'Urso, P, Corns, R, Dapaah, A, Edlmann, E, Greenway, F, Grundy, P, Hill, C S, Jenkinson, M D, Trichinopoly Krishna, S, Smith, S, Manivannan, S, Martin, A J, Matloob, S, Mukherjee, S, O'Neill, K, Plaha, P, Pollock, J, Price, S, Rominiyi, O, Sachdev, B, Saeed, F, Sinha, S, Thorne, L, Ughratdar, I, Whitfield, P, Youshani, A S, Bulbeck, H, Arumugam, P, Houlston, R & Ashkan, K 2025, 'Genomic landscape of diffuse glioma revealed by whole genome sequencing', Nature Communications, vol. 16, no. 1, 4233. https://doi.org/10.1038/s41467-025-59156-9
Kinnersley, B, Jung, J, Cornish, A J, Chubb, D, Laxton, R, Frangou, A, Gruber, A J, Sud, A, Caravagna, G, Sottoriva, A, Wedge, D C, Booth, T, Al-Sarraj, S, Lawrence, S E D, Albanese, E, Anichini, G, Baxter, D, Boukas, A, Chowdhury, Y A, D'Urso, P, Corns, R, Dapaah, A, Edlmann, E, Greenway, F, Grundy, P, Hill, C S, Jenkinson, M D, Trichinopoly Krishna, S, Smith, S, Manivannan, S, Martin, A J, Matloob, S, Mukherjee, S, O'Neill, K, Plaha, P, Pollock, J, Price, S, Rominiyi, O, Sachdev, B, Saeed, F, Sinha, S, Thorne, L, Ughratdar, I, Whitfield, P, Youshani, A S, Bulbeck, H, Arumugam, P, Houlston, R & Ashkan, K 2025, 'Genomic landscape of diffuse glioma revealed by whole genome sequencing', Nature Communications, vol. 16, no. 1, pp. 4233. https://doi.org/10.1038/s41467-025-59156-9

Subject Terms: Male, Cancer Research, Oligodendroglioma/genetics, Gene, Computational biology, Gliomas, DNA sequencing, Genome, Brain Neoplasms, Brain Tumor Epidemiology, Intratumor Heterogeneity, Life Sciences, Genomics, Glioma, Middle Aged, Telomere, Comprehensive Integration of Single-Cell Transcriptomic Data, Glioma/genetics, 3. Good health, Coding region, Medicine, Female, Human, Adult, DNA Copy Number Variations, Tumor Evolution, Science, Oligodendroglioma, Astrocytoma, Article, Cancer Genomics, Biochemistry, Genetics and Molecular Biology, Health Sciences, Genetics, Humans, Molecular Biology, Biology, Telomere/genetics, Aged, Brain Neoplasms/genetics, Whole Genome Sequencing, Genome, Human, DNA, Glioblastoma/genetics, Genomic Landscape of Cancer and Mutational Signatures, Astrocytoma/genetics, FOS: Biological sciences, Whole genome sequencing, Mutation, Glioblastoma

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40335506
https://doaj.org/article/329eab68944a488ebb7f0bc5928e4421
https://research.manchester.ac.uk/en/publications/be015820-6f9e-490e-ace5-62195f3569e4
https://doi.org/10.1038/s41467-025-59156-9
https://kclpure.kcl.ac.uk/portal/en/publications/b903b0e1-bcf5-4443-a18b-a7b7982e045c

AI‐based intra‐tumor heterogeneity score of Ki67 expression as a prognostic marker for early‐stage ER+/HER2− breast cancer

Authors: Wenqi Lu, Ayat Lashen, Noorul Wahab, Islam M. Miligy, Mostafa Jahanifar, Michael S. Toss, Simon Graham, Mohsin Bilal, Abhir Bhalerao, Nehal M. Atallah, Shorouk Makhlouf, Asmaa Ibrahim, David Snead, Fayyaz Minhas, Shan E Ahmed Raza, Emad A. Rakha, Nasir Rajpoot

Source: J Pathol Clin Res
The Journal of Pathology: Clinical Research, Vol 10, Iss 1, Pp n/a-n/a (2024)

Subject Terms: Cancer Research, Cell biology, Receptor, ErbB-2, Breast Neoplasms, Spatial Profiling, luminal breast cancer, Breast cancer, Artificial Intelligence, Biochemistry, Genetics and Molecular Biology, Health Sciences, Pathology, RB1-214, Humans, Estrogen receptor, Cell Heterogeneity, Molecular Biology, Internal medicine, Biology, Cancer, Life Sciences, Paleontology, Colocalization, Original Articles, Comprehensive Integration of Single-Cell Transcriptomic Data, Prognosis, 3. Good health, Ki-67 Antigen, Oncology, Cancer Stem Cells and Tumor Metastasis, Medicine, Female, AI based prognostic biomarkers, Stage (stratigraphy), computational pathology, Ki67 expression, Molecular Research on Breast Cancer

Access URL: https://pubmed.ncbi.nlm.nih.gov/37873865
https://doaj.org/article/6a155cf9d05147a98b8a08c72dc26ccc
https://e-space.mmu.ac.uk/633097/

Temporal single-cell tracing reveals clonal revival and expansion of precursor exhausted T cells during anti-PD-1 therapy in lung cancer

Authors: Baolin Liu, Xueda Hu, Kang Feng, Ranran Gao, Zhiqiang Xue, Sujie Zhang, Yuanyuan Zhang, Emily Corse, Yi Hu, Weidong Han, Zemin Zhang

Source: Nature Cancer. 3:108-121

Subject Terms: 0301 basic medicine, Lung Neoplasms, T-Lymphocytes, Programmed Cell Death 1 Receptor, Receptors, Antigen, T-Cell, Chimeric Antigen Receptor T Cell Therapy, Cancer research, PD-1 and PD-L1, Gene, Cancer Immunotherapy, Single-Cell, 03 medical and health sciences, Carcinoma, Non-Small-Cell Lung, Biochemistry, Genetics and Molecular Biology, Health Sciences, Pathology, Genetics, Humans, T-cell Exhaustion, Molecular Biology, Biology, Cancer, 0303 health sciences, Life Sciences, Comprehensive Integration of Single-Cell Transcriptomic Data, Tumor Regression, 3. Good health, Oncology, FOS: Biological sciences, Medicine, RNA, T Cell Therapy, Cell, Lung cancer

Access URL: https://www.nature.com/articles/s43018-021-00292-8.pdf
https://pubmed.ncbi.nlm.nih.gov/35121991

High‐resolution single‐cell transcriptomic survey of cardiomyocytes from patients with hypertrophic cardiomyopathy

Authors: Jiansen Lu, Jie Ren, Jie Liu, Ming‐De Lu, Yueli Cui, Yuhan Liao, Yuan Zhou, Yun Gao, Fuchou Tang, Jizheng Wang, Shuiyun Wang, Lu Wen, Lingyun Song

Source: Cell Prolif

Subject Terms: Cell biology, Cardiomyopathy, Cardiomyocyte Renewal, Immunology, Heart failure, Pathogenesis, Gene, Biochemistry, Computational biology, Biochemistry, Genetics and Molecular Biology, Heart Regeneration, Health Sciences, Genetics, Humans, Myocytes, Cardiac, Cell Heterogeneity, RNA-Seq, Cardiac Imaging, Molecular Mechanisms of Cardiac Development and Regeneration, Transcriptomics, Molecular Biology, Biology, Internal medicine, Gene Expression Profiling, FOS: Clinical medicine, Diagnosis and Management of Hypertrophic Cardiomyopathy, Life Sciences, Original Articles, Extracellular matrix, Cardiomyopathy, Hypertrophic, Comprehensive Integration of Single-Cell Transcriptomic Data, 3. Good health, Hypertrophic cardiomyopathy, FOS: Biological sciences, Myocyte, Medicine, Cell, Gene expression, Cardiology and Cardiovascular Medicine, Transcriptome

Access URL: https://pubmed.ncbi.nlm.nih.gov/37766635

ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data

Authors: Mohammad Nuwaisir Rahman, Abdullah Al Noman, Abir Mohammad Turza, Mohammed Abid Abrar, Md Abul Hassan Samee, M Saifur Rahman

Source: Bioinformatics

Subject Terms: Advanced Techniques in Bioimage Analysis and Microscopy, Artificial neural network, Artificial intelligence, Medical Sciences, Phenotypic Profiling, Biophysics, Convolutional neural network, Pattern recognition (psychology), Biochemistry, Mathematical analysis, Spatial Profiling, Identification (biology), Convolution (computer science), Biochemistry, Genetics and Molecular Biology, Field (mathematics), Microarray Data Analysis and Gene Expression Profiling, Machine learning, Medical Specialties, Medicine and Health Sciences, Image (mathematics), FOS: Mathematics, Droplet-based Sequencing, Similarity (geometry), Transcriptomics, Molecular Biology, Data mining, Biology, Original Paper, Domain (mathematical analysis), Geography, Physics, Pure mathematics, Botany, Life Sciences, Deep learning, Optics, Comprehensive Integration of Single-Cell Transcriptomic Data, Focus (optics), Computer science, and Structural Biology, Benchmark (surveying), Mathematics, Geodesy

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/37756699

Single‐cell transcriptomics identify TNFRSF1B as a novel T‐cell exhaustion marker for ovarian cancer

Authors: Yan Gao, Hui Shi, Hongyu Zhao, Mengcheng Yao, Yong He, Mei Jiang, Jie Li, Zhefeng Li, Shaofei Su, Tao Liu, Chenghong Yin, Xuebin Liao, Wentao Yue

Source: Clin Transl Med
Clinical and Translational Medicine, Vol 13, Iss 9, Pp n/a-n/a (2023)

Subject Terms: Medicine (General), CD3 Complex, TNFRSF1B, Immunology, Cancer research, CD8-Positive T-Lymphocytes, Mice, R5-920, Ovarian cancer, Biochemistry, Genetics and Molecular Biology, Tumor Microenvironment, Animals, Humans, Receptors, Tumor Necrosis Factor, Type II, Flow cytometry, single‐cell RNA‐seq, Molecular Biology, Biology, Internal medicine, Research Articles, Ecosystem, Cancer, Ovarian Neoplasms, Immunology and Microbiology, FOS: Clinical medicine, Macrophage Activation and Polarization, NK Cell Recognition, Life Sciences, CD8, Comprehensive Integration of Single-Cell Transcriptomic Data, T-Cell Exhaustion, 3. Good health, Immune system, Tumor microenvironment, Medicine, Female, tumour microenvironment, Transcriptome, Natural Killer Cells in Immunity

Access URL: https://pubmed.ncbi.nlm.nih.gov/37712139
https://doaj.org/article/55e83b2aec234c0d8fcd541fb5a411b1

Cut&tag: a powerful epigenetic tool for chromatin profiling

Authors: Peipei Li, Zhongheng Fu, Sanjie Jiang, Yiwen Sun, Shichun Zheng, Liang Zong

Source: Epigenetics
Epigenetics, Vol 19, Iss 1 (2024)

Subject Terms: single-cell CUT&Tag, Epigenomics, Bivalent chromatin, Epigenetic Modifications and Their Functional Implications, Review, Tn5 tagmentation, QH426-470, DNA Nanotechnology and Bioanalytical Applications, Gene, Epigenesis, Genetic, Computational biology, Chromatin remodeling, Epigenome, Biochemistry, Genetics and Molecular Biology, Genetics, CUT&Tag, Molecular Biology, Biology, Chromatin Structure, chromatin profiling, DNA methylation, epigenetics, High-Throughput Nucleotide Sequencing, Life Sciences, Promoter, ChIP-sequencing, DNA Methylation, Comprehensive Integration of Single-Cell Transcriptomic Data, Chromatin immunoprecipitation, Chromatin, Epigenetic Reprogramming, Histone, FOS: Biological sciences, Epigenetics, Gene expression

Access URL: https://pubmed.ncbi.nlm.nih.gov/38105608
https://doaj.org/article/02b2c60adaab4d7bac17659c1069b253

Frequency-dependent selection of neoantigens fosters tumor immune escape and predicts immunotherapy response

Authors: Zheng Hu, Shaoqing Chen, Duo Xie, Jiguang Wang, Da Zhou

Subject Terms: Regulatory T Cell Development and Function, Immunology, Population, NK Cell Development, Neutral theory of molecular evolution, Evolutionary biology, Tumor Immunity, Gene, Somatic evolution in cancer, Biochemistry, Genetics and Molecular Biology, Genetics, Molecular Biology, Biology, Cancer, Immunology and Microbiology, FOS: Clinical medicine, Life Sciences, Comprehensive Integration of Single-Cell Transcriptomic Data, 3. Good health, Immune system, Environmental health, FOS: Biological sciences, Medicine, Evolutionary dynamics, Immunotherapy, Natural Killer Cells in Immunity

Multifunctional cytokine production marks influenza A virus‐specific CD4 T cells with high expression of survival molecules

Authors: Lotus M Westerhof, Jonathan Noonan, Kerrie E Hargrave, Elizabeth Chimbayo, Zhiling Cheng, Thomas Purnell, Mark R. Jackson, Nicholas Borcherding, Megan K. L. MacLeod

Source: Eur J Immunol

Subject Terms: CD4-Positive T-Lymphocytes, Regulatory T Cell Development and Function, Cell biology, Immunology, Population, Immunity to infection, Interferon-gamma, Memory T Cells, Biochemistry, Genetics and Molecular Biology, Interleukin-7 receptor, Flow cytometry, Molecular Biology, Biology, Cytokine, Immunology and Microbiology, FOS: Clinical medicine, Life Sciences, T cell, Comprehensive Integration of Single-Cell Transcriptomic Data, IL-2 receptor, 3. Good health, Ki-67 Antigen, Interleukin 21, Immune system, Environmental health, Influenza A virus, Cytokines, Medicine, Immunologic Memory, Natural Killer Cells in Immunity

File Description: text

Access URL: https://pubmed.ncbi.nlm.nih.gov/37490492