Search

Your search keyword '"Clatworthy, P"' showing total 425 results
Start Over Author "Clatworthy, P"
425 results on '"Clatworthy, P"'

1. The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

Author

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., and Radtke, Andrea J.

Subjects
Quantitative Biology - Tissues and Organs, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

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.

Published
2024

2. Automatic Prediction of Stroke Treatment Outcomes: Latest Advances and Perspectives

Author

Samak, Zeynel A., Clatworthy, Philip, and Mirmehdi, Majid

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Stroke is a major global health problem that causes mortality and morbidity. Predicting the outcomes of stroke intervention can facilitate clinical decision-making and improve patient care. Engaging and developing deep learning techniques can help to analyse large and diverse medical data, including brain scans, medical reports and other sensor information, such as EEG, ECG, EMG and so on. Despite the common data standardisation challenge within medical image analysis domain, the future of deep learning in stroke outcome prediction lie in using multimodal information, including final infarct data, to achieve better prediction of long-term functional outcomes. This article provides a broad review of recent advances and applications of deep learning in the prediction of stroke outcomes, including (i) the data and models used, (ii) the prediction tasks and measures of success, (iii) the current challenges and limitations, and (iv) future directions and potential benefits. This comprehensive review aims to provide researchers, clinicians, and policy makers with an up-to-date understanding of this rapidly evolving and promising field., Comment: The paper is under consideration at Biomedical Engineering Letters (Springer)

Published
2024

3. The IBEX Knowledge-Base: Achieving more together with open science

Author

Radtke, Andrea J., Anidi, Ifeanyichukwu, Arakkal, Leanne, Arroyo-Mejias, Armando, Beuschel, Rebecca T., Borner, Katy, Chu, Colin J., Clark, Beatrice, Clatworthy, Menna R., Colautti, Jake, 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, Kastenmueller, Wolfgang, Koenig, Joshua F. E., Kothurkar, Aanandita, Kreins, Alexandra Y., Lamborn, Ian, Lin, Yuri, Morais, Katia Luciano Pereira, Lunich, Aleksandra, Luz, Jean C. S., MacDonald, Ryan B., Makranz, Chen, Maltez, Vivien I., Moriaty, Ryan V., Ocampo-Godinez, Juan M., Olyntho, Vitoria M., 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., Wade-Vallance, Adam K., Williams, Margaret, Zangger, Nathan, Germain, Ronald N., and Yaniv, Ziv

Subjects
Quantitative Biology - Tissues and Organs
Abstract

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, protocols and more, to empower innovation., Comment: 8 pages, 1 figure, 9 references

Published
2024

6. Automated Radiology Report Generation: A Review of Recent Advances

Author

Sloan, Phillip, Clatworthy, Philip, Simpson, Edwin, and Mirmehdi, Majid

Subjects
Computer Science - Computer Vision and Pattern Recognition, 68T99, I.2, I.4, J.3
Abstract

Increasing demands on medical imaging departments are taking a toll on the radiologist's ability to deliver timely and accurate reports. Recent technological advances in artificial intelligence have demonstrated great potential for automatic radiology report generation (ARRG), sparking an explosion of research. This survey paper conducts a methodological review of contemporary ARRG approaches by way of (i) assessing datasets based on characteristics, such as availability, size, and adoption rate, (ii) examining deep learning training methods, such as contrastive learning and reinforcement learning, (iii) exploring state-of-the-art model architectures, including variations of CNN and transformer models, (iv) outlining techniques integrating clinical knowledge through multimodal inputs and knowledge graphs, and (v) scrutinising current model evaluation techniques, including commonly applied NLP metrics and qualitative clinical reviews. Furthermore, the quantitative results of the reviewed models are analysed, where the top performing models are examined to seek further insights. Finally, potential new directions are highlighted, with the adoption of additional datasets from other radiological modalities and improved evaluation methods predicted as important areas of future development., Comment: 24 pages, 8 figures, 6 tables. Accepted by IEEE Reviews in Biomedical Engineering

Published
2024
Full Text
View/download PDF

7. Macrophages and nociceptor neurons form a sentinel unit around fenestrated capillaries to defend the synovium from circulating immune challenge

Author

Hasegawa, Tetsuo, Lee, Colin Y. C., Hotchen, Andrew J., Fleming, Aaron, Singh, Rahul, Suzuki, Kunimichi, Yuzaki, Michisuke, Watanabe, Masahiko, Birch, Mark A., McCaskie, Andrew W., Lénárt, Nikolett, Tóth, Krisztina, Dénes, Ádám, Liu, Zhaoyuan, Ginhoux, Florent, Richoz, Nathan, and Clatworthy, Menna R.

Published
2024
Full Text
View/download PDF

11. Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunity

Author

Dean, Isaac, Lee, Colin Y. C., Tuong, Zewen K., Li, Zhi, Tibbitt, Christopher A., Willis, Claire, Gaspal, Fabrina, Kennedy, Bethany C., Matei-Rascu, Veronika, Fiancette, Rémi, Nordenvall, Caroline, Lindforss, Ulrik, Baker, Syed Murtuza, Stockmann, Christian, Sexl, Veronika, Hammond, Scott A., Dovedi, Simon J., Mjösberg, Jenny, Hepworth, Matthew R., Carlesso, Gianluca, Clatworthy, Menna R., and Withers, David R.

Published
2024
Full Text
View/download PDF

12. Early human lung immune cell development and its role in epithelial cell fate.

Author

Barnes, Josephine, Yoshida, Masahiro, He, Peng, Worlock, Kaylee, Lindeboom, Rik, Suo, Chenqu, Pett, J, Wilbrey-Clark, Anna, Dann, Emma, Mamanova, Lira, Richardson, Laura, Polanski, Krzysztof, Pennycuick, Adam, Allen-Hyttinen, Jessica, Herczeg, Iván, Arzili, Romina, Hynds, Robert, Teixeira, Vitor, Haniffa, Muzlifah, Lim, Kyungtae, Sun, Dawei, Rawlins, Emma, Oliver, Amanda, Lyons, Paul, Marioni, John, Ruhrberg, Christiana, Tuong, Zewen, Clatworthy, Menna, Reading, James, Janes, Sam, Teichmann, Sarah, Meyer, Kerstin, and Nikolić, Marko

Subjects
Humans, Immunity, Innate, Cell Differentiation, Lung, Killer Cells, Natural, Epithelial Cells
Abstract

Studies of human lung development have focused on epithelial and mesenchymal cell types and function, but much less is known about the developing lung immune cells, even though the airways are a major site of mucosal immunity after birth. An unanswered question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. Here, we profiled human embryonic and fetal lung immune cells using scRNA-seq, smFISH, and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including innate lymphoid cells, natural killer cells, myeloid cells, and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes expressing high levels of cytotoxicity genes and the presence of mature B lymphocytes, including B-1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the presence and diversity of immune cells during development, we also investigated their possible effect on epithelial maturation. We found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1β-producing myeloid cells were found throughout the lung and adjacent to epithelial tips, suggesting that immune cells may direct human lung epithelial development.

Published
2023

13. TranSOP: Transformer-based Multimodal Classification for Stroke Treatment Outcome Prediction

Author

Samak, Zeynel A., Clatworthy, Philip, and Mirmehdi, Majid

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Acute ischaemic stroke, caused by an interruption in blood flow to brain tissue, is a leading cause of disability and mortality worldwide. The selection of patients for the most optimal ischaemic stroke treatment is a crucial step for a successful outcome, as the effect of treatment highly depends on the time to treatment. We propose a transformer-based multimodal network (TranSOP) for a classification approach that employs clinical metadata and imaging information, acquired on hospital admission, to predict the functional outcome of stroke treatment based on the modified Rankin Scale (mRS). This includes a fusion module to efficiently combine 3D non-contrast computed tomography (NCCT) features and clinical information. In comparative experiments using unimodal and multimodal data on the MRCLEAN dataset, we achieve a state-of-the-art AUC score of 0.85., Comment: Accepted at IEEE ISBI 2023, 5 pages

Published
2023
Full Text
View/download PDF

14. Venous-plexus-associated lymphoid hubs support meningeal humoral immunity

Author

Fitzpatrick, Zachary, Ghabdan Zanluqui, Nagela, Rosenblum, Jared S., Tuong, Zewen Kelvin, Lee, Colin Y. C., Chandrashekhar, Vikram, Negro-Demontel, Maria Luciana, Stewart, Andrew P., Posner, David A., Buckley, Monica, Allinson, Kieren S. J., Mastorakos, Panagiotis, Chittiboina, Prashant, Maric, Dragan, Donahue, Danielle, Helmy, Adel, Tajsic, Tamara, Ferdinand, John R., Portet, Anais, Peñalver, Ana, Gillman, Eleanor, Zhuang, Zhengping, Clatworthy, Menna R., and McGavern, Dorian B.

Published
2024
Full Text
View/download PDF

15. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.

Author

Madissoon, Elo, Oliver, Amanda, Kleshchevnikov, Vitalii, Wilbrey-Clark, Anna, Polanski, Krzysztof, Richoz, Nathan, Ribeiro Orsi, Ana, Mamanova, Lira, Bolt, Liam, Elmentaite, Rasa, Pett, J, Huang, Ni, Xu, Chuan, He, Peng, Dabrowska, Monika, Pritchard, Sophie, Tuck, Liz, Prigmore, Elena, Perera, Shani, Knights, Andrew, Oszlanczi, Agnes, Hunter, Adam, Vieira, Sara, Patel, Minal, Lindeboom, Rik, Campos, Lia, Matsuo, Kazuhiko, Nakayama, Takashi, Yoshida, Masahiro, Worlock, Kaylee, Nikolić, Marko, Georgakopoulos, Nikitas, Mahbubani, Krishnaa, Saeb-Parsy, Kourosh, Bayraktar, Omer, Clatworthy, Menna, Stegle, Oliver, Kumasaka, Natsuhiko, Teichmann, Sarah, and Meyer, Kerstin

Subjects
Humans, Respiratory Mucosa, Lung, Epithelial Cells, B-Lymphocytes, Immunoglobulin A
Abstract

Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new gland-associated immune niche has implications for respiratory health.

Published
2023

17. Genetic variants associated with psychiatric disorders are enriched at epigenetically active sites in lymphoid cells.

Author

Lynall, Mary-Ellen, Soskic, Blagoje, Hayhurst, James, Schwartzentruber, Jeremy, Levey, Daniel, Pathak, Gita, Polimanti, Renato, Gelernter, Joel, Stein, Murray, Trynka, Gosia, Clatworthy, Menna, and Bullmore, Ed

Subjects
Catalytic Domain, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Lymphocytes, Mental Disorders, Polymorphism, Single Nucleotide, Schizophrenia
Abstract

Multiple psychiatric disorders have been associated with abnormalities in both the innate and adaptive immune systems. The role of these abnormalities in pathogenesis, and whether they are driven by psychiatric risk variants, remains unclear. We test for enrichment of GWAS variants associated with multiple psychiatric disorders (cross-disorder or trans-diagnostic risk), or 5 specific disorders (cis-diagnostic risk), in regulatory elements in immune cells. We use three independent epigenetic datasets representing multiple organ systems and immune cell subsets. Trans-diagnostic and cis-diagnostic risk variants (for schizophrenia and depression) are enriched at epigenetically active sites in brain tissues and in lymphoid cells, especially stimulated CD4+ T cells. There is no evidence for enrichment of either trans-risk or cis-risk variants for schizophrenia or depression in myeloid cells. This suggests a possible model where environmental stimuli activate T cells to unmask the effects of psychiatric risk variants, contributing to the pathogenesis of mental health disorders.

Published
2022

19. Mapping the developing human immune system across organs.

Author

Suo, Chenqu, Dann, Emma, Goh, Issac, Jardine, Laura, Kleshchevnikov, Vitalii, Park, Jong-Eun, Botting, Rachel, Stephenson, Emily, Engelbert, Justin, Tuong, Zewen, Polanski, Krzysztof, Yayon, Nadav, Xu, Chuan, Suchanek, Ondrej, Elmentaite, Rasa, Domínguez Conde, Cecilia, He, Peng, Pritchard, Sophie, Miah, Mohi, Moldovan, Corina, Steemers, Alexander, Mazin, Pavel, Prete, Martin, Horsfall, Dave, Marioni, John, Clatworthy, Menna, Haniffa, Muzlifah, and Teichmann, Sarah

Subjects
Genomics, Humans, Immune System, Lymphocytes, Monocytes, Organ Specificity, RNA-Seq, Single-Cell Analysis
Abstract

Single-cell genomics studies have decoded the immune cell composition of several human prenatal organs but were limited in describing the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics to reconstruct the developing human immune system. This revealed the late acquisition of immune-effector functions by myeloid and lymphoid cell subsets and the maturation of monocytes and T cells before peripheral tissue seeding. Moreover, we uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine, and disease understanding.

Published
2022

20. International stroke genetics consortium recommendations for studies of genetics of stroke outcome and recovery

Author

Lindgren, Arne G, Braun, Robynne G, Majersik, Jennifer Juhl, Clatworthy, Philip, Mainali, Shraddha, Derdeyn, Colin P, Maguire, Jane, Jern, Christina, Rosand, Jonathan, Cole, John W, Lee, Jin-Moo, Khatri, Pooja, Nyquist, Paul, Debette, Stéphanie, Wei, Loo Keat, Rundek, Tatjana, Leifer, Dana, Thijs, Vincent, Lemmens, Robin, Heitsch, Laura, Prasad, Kameshwar, Conde, Jordi Jimenez, Dichgans, Martin, Rost, Natalia S, Cramer, Steven C, Bernhardt, Julie, Worrall, Bradford B, Fernandez-Cadenas, Israel, and Consortium, International Stroke Genetics

Subjects
Health Services and Systems, Health Sciences, Rehabilitation, Brain Disorders, Stroke, Genetics, Aging, Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Neurological, Brain Injuries, Data Collection, Humans, Phenotype, Recovery of Function, Stroke Rehabilitation, Data collection, genetics, ischemic stroke, outcome, phenotype, recovery, standardization, International Stroke Genetics Consortium, Clinical Sciences, Neurology & Neurosurgery, Clinical sciences, Allied health and rehabilitation science
Abstract

Numerous biological mechanisms contribute to outcome after stroke, including brain injury, inflammation, and repair mechanisms. Clinical genetic studies have the potential to discover biological mechanisms affecting stroke recovery in humans and identify intervention targets. Large sample sizes are needed to detect commonly occurring genetic variations related to stroke brain injury and recovery. However, this usually requires combining data from multiple studies where consistent terminology, methodology, and data collection timelines are essential. Our group of expert stroke and rehabilitation clinicians and researchers with knowledge in genetics of stroke recovery here present recommendations for harmonizing phenotype data with focus on measures suitable for multicenter genetic studies of ischemic stroke brain injury and recovery. Our recommendations have been endorsed by the International Stroke Genetics Consortium.

Published
2022

21. Spatially resolved multiomics of human cardiac niches

Author

Kanemaru, Kazumasa, Cranley, James, Muraro, Daniele, Miranda, Antonio M. A., Ho, Siew Yen, Wilbrey-Clark, Anna, Patrick Pett, Jan, Polanski, Krzysztof, Richardson, Laura, Litvinukova, Monika, Kumasaka, Natsuhiko, Qin, Yue, Jablonska, Zuzanna, Semprich, Claudia I., Mach, Lukas, Dabrowska, Monika, Richoz, Nathan, Bolt, Liam, Mamanova, Lira, Kapuge, Rakeshlal, Barnett, Sam N., Perera, Shani, Talavera-López, Carlos, Mulas, Ilaria, Mahbubani, Krishnaa T., Tuck, Liz, Wang, Lu, Huang, Margaret M., Prete, Martin, Pritchard, Sophie, Dark, John, Saeb-Parsy, Kourosh, Patel, Minal, Clatworthy, Menna R., Hübner, Norbert, Chowdhury, Rasheda A., Noseda, Michela, and Teichmann, Sarah A.

Published
2023
Full Text
View/download PDF

22. Prediction of Thrombectomy Functional Outcomes using Multimodal Data

Author

Samak, Zeynel A., Clatworthy, Philip, and Mirmehdi, Majid

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Recent randomised clinical trials have shown that patients with ischaemic stroke {due to occlusion of a large intracranial blood vessel} benefit from endovascular thrombectomy. However, predicting outcome of treatment in an individual patient remains a challenge. We propose a novel deep learning approach to directly exploit multimodal data (clinical metadata information, imaging data, and imaging biomarkers extracted from images) to estimate the success of endovascular treatment. We incorporate an attention mechanism in our architecture to model global feature inter-dependencies, both channel-wise and spatially. We perform comparative experiments using unimodal and multimodal data, to predict functional outcome (modified Rankin Scale score, mRS) and achieve 0.75 AUC for dichotomised mRS scores and 0.35 classification accuracy for individual mRS scores., Comment: Accepted at Medical Image Understanding and Analysis (MIUA) 2020

Published
2020
Full Text
View/download PDF

29. Prophylaxis for preventing venous thromboembolism in knee arthroscopy and soft tissue reconstruction: consensus statements from an international panel of experts

Author

Easwaran, Raju, Khan, Moin, Sancheti, Parag, Shyam, Ashok, Bhandari, Mohit, Ranawat, Anil S., Thakkar, Savyasachi, Parikh, Shital, Musahl, Volker, Joglekar, Siddharth, J.Deshmukh, Ajit, Plancher, Kevin, Verma, Nikhil, McAllister, David, Verdonk, Peter, Lustig, Sebastien, Chandrateya, Amit, Smigleiski, Robert, Solayar, Gandhi, Chernchujit, Bancha, Yung, Patrick, Budhiparama, Nicolaas, Hoshino, Yuichi, White, Nathan, Parker, David, Clatworthy, Mark, Brown, Charlie, Manzary, Mojieb, Rajan, David, Narvekar, Abhay, Tapasvi, Sachin, Pardiwala, Dinshaw, Panigrahi, Ranjit, Arumugam, S., Kapoor, Vikash, Mody, Bharat, Maheshwari, Jitender, Dahiya, Vivek, Joseph, Clement, Laddha, Mukesh, and Rajgopal, Ashok

Published
2022
Full Text
View/download PDF

30. The Human Cell Atlas White Paper

Author

Regev, Aviv, Teichmann, Sarah, Rozenblatt-Rosen, Orit, Stubbington, Michael, Ardlie, Kristin, Amit, Ido, Arlotta, Paola, Bader, Gary, Benoist, Christophe, Biton, Moshe, Bodenmiller, Bernd, Bruneau, Benoit, Campbell, Peter, Carmichael, Mary, Carninci, Piero, Castelo-Soccio, Leslie, Clatworthy, Menna, Clevers, Hans, Conrad, Christian, Eils, Roland, Freeman, Jeremy, Fugger, Lars, Goettgens, Berthold, Graham, Daniel, Greka, Anna, Hacohen, Nir, Haniffa, Muzlifah, Helbig, Ingo, Heuckeroth, Robert, Kathiresan, Sekar, Kim, Seung, Klein, Allon, Knoppers, Bartha, Kriegstein, Arnold, Lander, Eric, Lee, Jane, Lein, Ed, Linnarsson, Sten, Macosko, Evan, MacParland, Sonya, Majovski, Robert, Majumder, Partha, Marioni, John, McGilvray, Ian, Merad, Miriam, Mhlanga, Musa, Naik, Shalin, Nawijn, Martijn, Nolan, Garry, Paten, Benedict, Pe'er, Dana, Philippakis, Anthony, Ponting, Chris, Quake, Steve, Rajagopal, Jayaraj, Rajewsky, Nikolaus, Reik, Wolf, Rood, Jennifer, Saeb-Parsy, Kourosh, Schiller, Herbert, Scott, Steve, Shalek, Alex, Shapiro, Ehud, Shin, Jay, Skeldon, Kenneth, Stratton, Michael, Streicher, Jenna, Stunnenberg, Henk, Tan, Kai, Taylor, Deanne, Thorogood, Adrian, Vallier, Ludovic, van Oudenaarden, Alexander, Watt, Fiona, Weicher, Wilko, Weissman, Jonathan, Wells, Andrew, Wold, Barbara, Xavier, Ramnik, Zhuang, Xiaowei, and Committee, Human Cell Atlas Organizing

Subjects
Quantitative Biology - Tissues and Organs
Abstract

The Human Cell Atlas (HCA) will be made up of comprehensive reference maps of all human cells - the fundamental units of life - as a basis for understanding fundamental human biological processes and diagnosing, monitoring, and treating disease. It will help scientists understand how genetic variants impact disease risk, define drug toxicities, discover better therapies, and advance regenerative medicine. A resource of such ambition and scale should be built in stages, increasing in size, breadth, and resolution as technologies develop and understanding deepens. We will therefore pursue Phase 1 as a suite of flagship projects in key tissues, systems, and organs. We will bring together experts in biology, medicine, genomics, technology development and computation (including data analysis, software engineering, and visualization). We will also need standardized experimental and computational methods that will allow us to compare diverse cell and tissue types - and samples across human communities - in consistent ways, ensuring that the resulting resource is truly global. This document, the first version of the HCA White Paper, was written by experts in the field with feedback and suggestions from the HCA community, gathered during recent international meetings. The White Paper, released at the close of this yearlong planning process, will be a living document that evolves as the HCA community provides additional feedback, as technological and computational advances are made, and as lessons are learned during the construction of the atlas.

Published
2018

32. Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity

Author

Uzzan, Mathieu, Martin, Jerome C., Mesin, Luka, Livanos, Alexandra E., Castro-Dopico, Tomas, Huang, Ruiqi, Petralia, Francesca, Magri, Giuliana, Kumar, Shashi, Zhao, Qing, Rosenstein, Adam K., Tokuyama, Minami, Sharma, Keshav, Ungaro, Ryan, Kosoy, Roman, Jha, Divya, Fischer, Jeremy, Singh, Harpriya, Keir, Mary E., Ramamoorthi, Nandhini, Gorman, William E. O’, Cohen, Benjamin L., Rahman, Adeeb, Cossarini, Francesca, Seki, Akihiro, Leyre, Louise, Vaquero, Sonia Tejedor, Gurunathan, Sakteesh, Grasset, Emilie K., Losic, Bojan, Dubinsky, Marla, Greenstein, Alexander J., Gottlieb, Zoe, Legnani, Peter, George, James, Irizar, Haritz, Stojmirovic, Aleksandar, Brodmerkel, Carrie, Kasarkis, Andrew, Sands, Bruce E., Furtado, Glaucia, Lira, Sergio A., Tuong, Zewen K., Ko, Huaibin M., Cerutti, Andrea, Elson, Charles O., Clatworthy, Menna R., Merad, Miriam, Suárez-Fariñas, Mayte, Argmann, Carmen, Hackney, Jason A., Victora, Gabriel D., Randolph, Gwendalyn J., Kenigsberg, Ephraim, Colombel, Jean Frederic, and Mehandru, Saurabh

Published
2022
Full Text
View/download PDF

33. Local and systemic responses to SARS-CoV-2 infection in children and adults

Author

Yoshida, Masahiro, Worlock, Kaylee B., Huang, Ni, Lindeboom, Rik G. H., Butler, Colin R., Kumasaka, Natsuhiko, Dominguez Conde, Cecilia, Mamanova, Lira, Bolt, Liam, Richardson, Laura, Polanski, Krzysztof, Madissoon, Elo, Barnes, Josephine L., Allen-Hyttinen, Jessica, Kilich, Eliz, Jones, Brendan C., de Wilton, Angus, Wilbrey-Clark, Anna, Sungnak, Waradon, Pett, J. Patrick, Weller, Juliane, Prigmore, Elena, Yung, Henry, Mehta, Puja, Saleh, Aarash, Saigal, Anita, Chu, Vivian, Cohen, Jonathan M., Cane, Clare, Iordanidou, Aikaterini, Shibuya, Soichi, Reuschl, Ann-Kathrin, Herczeg, Iván T., Argento, A. Christine, Wunderink, Richard G., Smith, Sean B., Poor, Taylor A., Gao, Catherine A., Dematte, Jane E., Reynolds, Gary, Haniffa, Muzlifah, Bowyer, Georgina S., Coates, Matthew, Clatworthy, Menna R., Calero-Nieto, Fernando J., Göttgens, Berthold, O’Callaghan, Christopher, Sebire, Neil J., Jolly, Clare, De Coppi, Paolo, Smith, Claire M., Misharin, Alexander V., Janes, Sam M., Teichmann, Sarah A., Nikolić, Marko Z., and Meyer, Kerstin B.

Published
2022
Full Text
View/download PDF

35. Recycling of memory B cells between germinal center and lymph node subcapsular sinus supports affinity maturation to antigenic drift

Author

Zhang, Yang, Garcia-Ibanez, Laura, Ulbricht, Carolin, Lok, Laurence S. C., Pike, Jeremy A., Mueller-Winkler, Jennifer, Dennison, Thomas W., Ferdinand, John R., Burnett, Cameron J. M., Yam-Puc, Juan C., Zhang, Lingling, Alfaro, Raul Maqueda, Takahama, Yousuke, Ohigashi, Izumi, Brown, Geoffrey, Kurosaki, Tomohiro, Tybulewicz, Victor L. J., Rot, Antal, Hauser, Anja E., Clatworthy, Menna R., and Toellner, Kai-Michael

Published
2022
Full Text
View/download PDF

38. The Human Cell Atlas.

Author

Regev, Aviv, Teichmann, Sarah A, Lander, Eric S, Amit, Ido, Benoist, Christophe, Birney, Ewan, Bodenmiller, Bernd, Campbell, Peter, Carninci, Piero, Clatworthy, Menna, Clevers, Hans, Deplancke, Bart, Dunham, Ian, Eberwine, James, Eils, Roland, Enard, Wolfgang, Farmer, Andrew, Fugger, Lars, Göttgens, Berthold, Hacohen, Nir, Haniffa, Muzlifah, Hemberg, Martin, Kim, Seung, Klenerman, Paul, Kriegstein, Arnold, Lein, Ed, Linnarsson, Sten, Lundberg, Emma, Lundeberg, Joakim, Majumder, Partha, Marioni, John C, Merad, Miriam, Mhlanga, Musa, Nawijn, Martijn, Netea, Mihai, Nolan, Garry, Pe'er, Dana, Phillipakis, Anthony, Ponting, Chris P, Quake, Stephen, Reik, Wolf, Rozenblatt-Rosen, Orit, Sanes, Joshua, Satija, Rahul, Schumacher, Ton N, Shalek, Alex, Shapiro, Ehud, Sharma, Padmanee, Shin, Jay W, Stegle, Oliver, Stratton, Michael, Stubbington, Michael JT, Theis, Fabian J, Uhlen, Matthias, van Oudenaarden, Alexander, Wagner, Allon, Watt, Fiona, Weissman, Jonathan, Wold, Barbara, Xavier, Ramnik, Yosef, Nir, and Human Cell Atlas Meeting Participants

Subjects
Human Cell Atlas Meeting Participants, Eukaryotic Cells, Humans, Human Body, International Cooperation, Atlases as Topic, cell atlas, cell biology, computational biology, human, lineage, mouse, science forum, single-cell genomics, systems biology, Biochemistry and Cell Biology
Abstract

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

Published
2017

41. Cells of the human intestinal tract mapped across space and time

Author

Elmentaite, Rasa, Kumasaka, Natsuhiko, Roberts, Kenny, Fleming, Aaron, Dann, Emma, King, Hamish W., Kleshchevnikov, Vitalii, Dabrowska, Monika, Pritchard, Sophie, Bolt, Liam, Vieira, Sara F., Mamanova, Lira, Huang, Ni, Perrone, Francesca, Goh Kai’En, Issac, Lisgo, Steven N., Katan, Matilda, Leonard, Steven, Oliver, Thomas R. W., Hook, C. Elizabeth, Nayak, Komal, Campos, Lia S., Domínguez Conde, Cecilia, Stephenson, Emily, Engelbert, Justin, Botting, Rachel A., Polanski, Krzysztof, van Dongen, Stijn, Patel, Minal, Morgan, Michael D., Marioni, John C., Bayraktar, Omer Ali, Meyer, Kerstin B., He, Xiaoling, Barker, Roger A., Uhlig, Holm H., Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Zilbauer, Matthias, Clatworthy, Menna R., Haniffa, Muzlifah, James, Kylie R., and Teichmann, Sarah A.

Published
2021
Full Text
View/download PDF

44. Gut-educated IgA plasma cells defend the meningeal venous sinuses

Author

Fitzpatrick, Zachary, Frazer, Gordon, Ferro, Ashley, Clare, Simon, Bouladoux, Nicolas, Ferdinand, John, Tuong, Zewen Kelvin, Negro-Demontel, Maria Luciana, Kumar, Nitin, Suchanek, Ondrej, Tajsic, Tamara, Harcourt, Katherine, Scott, Kirsten, Bashford-Rogers, Rachel, Helmy, Adel, Reich, Daniel S., Belkaid, Yasmine, Lawley, Trevor D., McGavern, Dorian B., and Clatworthy, Menna R.

Published
2020
Full Text
View/download PDF

48. Multifocal, multiphenotypic tumours arising from an MTORmutation acquired in early embryogenesis

Author

Pacyna, Clarissa N., Anandapadamanaban, Madhanagopal, Loudon, Kevin W., Hay, Iain M., Perisic, Olga, Li, Ruoyan, Byrne, Matthew, Allen, Laura, Roberts, Kirsty, Hooks, Yvette, Warren, Anne Y., Stewart, Grant D., Clatworthy, Menna R., Teichmann, Sarah A., Behjati, Sam, Campbell, Peter J., Williams, Roger L., and Mitchell, Thomas J.

Abstract

Embryogenesis is a vulnerable time. Mutations in developmental cells can result in the wide dissemination of cells predisposed to disease within mature organs. We characterised the evolutionary history of four synchronous renal tumours from a 14-year-old girl using whole genome sequencing alongside single cell and bulk transcriptomic sequencing. Phylogenetic reconstruction timed the origin of all tumours to a multipotent embryonic cell committed to the right kidney, around 4 weeks post-conception. Biochemical and structural analysis of their shared MTORmutation, absent from normal tissues, demonstrates enhanced protein flexibility, enabling a FAT domain hinge to dramatically increase activity of mTORC1 and mTORC2. Developmental mutations, not usually detected in traditional genetic screening, have vital clinical importance in guiding prognosis, targeted treatment, and family screening decisions for paediatric tumours.

Published
2024
Full Text
View/download PDF

49. Alan Race and Jonathan Clatworthy, eds., What Christ? Whose Christ? New Options for Old Theories

Author

Tsai, Patricia Guernelli Palazzo, Parry, John, Adams, Graham, Dixit, Shruti, Amos, Clare, Rimerman, Hayyim, Clatworthy, Jonathan, Belloli, Jack, Ross, Cathy, Webster, Alison, Brierley, Michael, Baker, Christopher, Cross, Katie, Woodward, James, Grant, Iain, Turner, Victoria, Hellier, Graham, Dorsett, Mark R., Chapman, Mark, Chandler, Andrew, Morgan, Robert, Cresswell, Rachel, Jones, Siân E., Aldous, Benjamin, and McLaughlin, Eleanor

Published
2024
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results