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Relevant bibliographies by topics / Spatial proteomcis

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Academic literature on the topic 'Spatial proteomcis'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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Journal articles on the topic "Spatial proteomcis"

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Gatto, Laurent. "Data Management Plan for a Biotechnology and Biological Sciences Research Council (BBSRC) Tools and Resources Development Fund (TRDF) Grant." Research Ideas and Outcomes 3 (January 5, 2017): e11624. https://doi.org/10.3897/rio.3.e11624.

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This Data Management Plan (DMP) was created for Laurent Gatto's BBSRC Tools and Resources Development Fund award (BB/N023129/1). The DMP describes the management and sharing of all data and code associated with the grant, including software dissemination and release schedule, source code development and open source licensing, software documentation, reproducible framework and data annotation and dissemination.

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Hulahan, Taylor S., Laura Spruill, Elizabeth N. Wallace, et al. "Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics." International Journal of Molecular Sciences 25, no. 12 (2024): 6748. http://dx.doi.org/10.3390/ijms25126748.

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Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) alterations with breast cancer progression. However, the spatial regulation of the ECM proteome in DCIS has yet to be investigated in relation to IBC. We hypothesized that DCIS and IBC present distinct ECM proteomes that could discriminate between these pathologies. Tissue sections of pure DCIS, mixed DCIS-IBC, or pure IBC (n = 22) with detai

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Ozorun, Gulsev, Alexander Eckersley, Eleanor Bradley, Rachel Watson, Michael Sherrat, and Joe Swift. "P28 Data-independent acquisition mass spectrometry improves spatially resolved analysis of the human skin proteome." British Journal of Dermatology 190, no. 6 (2024): e92-e92. http://dx.doi.org/10.1093/bjd/ljae105.050.

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Abstract Introduction and aims Proteomic analysis of the extracellular matrix (ECM) presents challenges because of the highly crosslinked and low-solubility nature of ECM proteins. Traditional homogenization and protein digestion approaches result in the loss of crucial information regarding protein localization and spatial relationships. To address this, spatially resolved proteomics emerges as a powerful tool for exploring heterogeneity within bulk tissues. This study aims to determine the minimum tissue volume required for comprehensive proteome coverage using data-independent acquisition m

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Dereli, Zeynep, Behnaz Bozorgui, Huamin Wang, John Weinstein, Michael Overman, and Anil Korkut. "Abstract 3646: A spatially resolved single cell proteomic atlas of small bowel adenocarcinoma." Cancer Research 84, no. 6_Supplement (2024): 3646. http://dx.doi.org/10.1158/1538-7445.am2024-3646.

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Abstract Small bowel adenocarcinoma (SBA) is a rare malignancy associated with poor prognosis. The cellular and proteomic heterogeneity within the tumor immune microenvironment (TIME) of SBA is a likely driver of prognosis, disease progression and response to therapy. There is, however, a major gap in our knowledge of tumor and immune interactions in SBA. Cyclic Immunofluorescence (CycIF), an antibody-based, highly multiplexed imaging technology for spatially resolved single cell level proteomic profiling, is well suited to map the proteomic heterogeneity and organization of TIME in SBA. Here,

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Smythers, Amanda L., and Leslie M. Hicks. "Mapping the plant proteome: tools for surveying coordinating pathways." Emerging Topics in Life Sciences 5, no. 2 (2021): 203–20. http://dx.doi.org/10.1042/etls20200270.

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Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein–protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass sp

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Rosenbloom, Alyssa, Shilah Bonnett, Mark Conner, et al. "Abstract 3649: A novel spatial multi-omic approach for biological discoveries in colonic diseased tissues using a comprehensive Immuno-Oncology Proteome Atlas and Whole Transcriptome Atlas." Cancer Research 84, no. 6_Supplement (2024): 3649. http://dx.doi.org/10.1158/1538-7445.am2024-3649.

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Abstract The advancement of spatially resolved, multiplex proteomic and transcriptomic technologies has revolutionized and redefined the approaches to complex biological questions pertaining to tissue heterogeneity, tumor microenvironments, cellular interactions, cellular diversity, and therapeutic response. While spatial transcriptomics has traditionally led the way in plex, multiple studies have demonstrated a poor correlation between RNA expression and protein abundance, owing to transcriptional and translational regulation, target turnover, and most critically, post-translational protein m

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Min, Jimin, Lisa Schweizer, Gijs Zonderland, et al. "Abstract 753: AI-powered deep visual proteomics (DVP) for early pancreatic cancer insights." Cancer Research 85, no. 8_Supplement_1 (2025): 753. https://doi.org/10.1158/1538-7445.am2025-753.

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Abstract Pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, presents a formidable clinical challenge. Patients experience 70-80% post-resection mortality due to recurrence. Identifying aberrant molecular pathways and drivers of pre-cancer progression is an unmet area of importance for developing effective biomarkers and enabling early detection. Pancreatic intraepithelial neoplasia (PanINs) represent the key precursor to PDAC. While genomic and transcriptomic profiling of these lesions has been performed at depth, the deep proteomic profiles of these precursors

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Jackson, Charles E., Matthew H. Ingalls, Kayla E. Cashion, et al. "Abstract 6483: Powerful end-to-end spatial analyses using precise spatial proteomics." Cancer Research 85, no. 8_Supplement_1 (2025): 6483. https://doi.org/10.1158/1538-7445.am2025-6483.

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Abstract Spatial biology supports our understanding of the progression and treatment of cancer by distilling complex cellular interactions into actionable spatial signatures. The most actionable targets to study with spatial methods are protein biomarkers, but non-destructive, high-plex spatial proteomics has been challenging to achieve due to technical limitations posted by available technologies. With the recent advent of enhanced photobleaching in cyclic immunofluorescence (EpicIF™) technology, multiplex immunofluorescence (mIF) can now be achieved more easily and inexpensively. EpicIF tech

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Heywood, Wendy E., Jon Searle, Richard Collis, et al. "A Proof of Principle 2D Spatial Proteome Mapping Analysis Reveals Distinct Regional Differences in the Cardiac Proteome." Life 14, no. 8 (2024): 970. http://dx.doi.org/10.3390/life14080970.

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Proteomics studies often explore phenotypic differences between whole organs and systems. Within the heart, more subtle variation exists. To date, differences in the underlying proteome are only described between whole cardiac chambers. This study, using the bovine heart as a model, investigates inter-regional differences and assesses the feasibility of measuring detailed, cross-tissue variance in the cardiac proteome. Using a bovine heart, we created a two-dimensional section through a plane going through two chambers. This plane was further sectioned into 4 × 4 mm cubes and analysed using la

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Bouamrani, Ali, Jessica Ternier, David Ratel, et al. "Direct-Tissue SELDI-TOF Mass Spectrometry Analysis: A New Application for Clinical Proteomics." Clinical Chemistry 52, no. 11 (2006): 2103–6. http://dx.doi.org/10.1373/clinchem.2006.070979.

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Abstract Background: New molecular profiling technologies can aid in analysis of small pathologic samples obtained by minimally invasive biopsy and may enable the discovery of key biomarkers synergistic with anatomopathologic analysis related to prognosis, therapeutic response, and innovative target validation. Thus proteomic analysis at the histologic level in healthy and pathologic settings is a major issue in the field of clinical proteomics. Methods: We used surface-enhanced laser desorption ionization-time-of-flight mass spectrometry (SELDI-TOF MS) technology with surface chromatographic

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Dissertations / Theses on the topic "Spatial proteomcis"

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Buczak, Katarzyzna [Verfasser], and Martin [Akademischer Betreuer] Beck. "Spatial proteomics: from tissue organization to protein function / Katarzyzna Buczak ; Betreuer: Martin Beck." Heidelberg : Universitätsbibliothek Heidelberg, 2019. http://d-nb.info/1177045656/34.

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Huang, Peiwu. "Method development and application for spatial proteome and glycoproteome profiling." HKBU Institutional Repository, 2020. https://repository.hkbu.edu.hk/etd_oa/788.

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Tissues are heterogeneous ecosystems comprised of various cell types. For example, in tumor tissues, malignant cancer cells are surround by various non-malignant stromal cells. Proteins, especially N-linked glycoproteins, are key players in tumor microenvironment and respond to many extracellular stimuli for involving and regulating intercellular signaling. Understanding the human proteome and glycoproteome in heterogeneous tissues with spatial resolution are meaningful for exploring intercellular signaling networks and discovering protein biomarkers for various diseases, such as cancer. In th

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Cox, Kurt J. (Kurt James). "Spatially restricted proteomic mapping of excitatory and inhibitory post-synaptic termini through enzymatic labeling." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/107565.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2016.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>The neuronal synapse is the seat of cognitive computation in the brain, where the minor adjustments in electrical activity between various neuronal circuits results from the sophisticated orchestration of molecules at the synapse. The molecular interplay between the diverse range of synapses and circuits in the brain makes comprehending the full scope of cognition a major challenge for modem neuroscience, one that is limited b

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Basu, Amrita. "Spatial Learning and Memory, Transcriptional and Proteomic Analysis of Growth Hormone Action in the Brain of bGH and GHA Mice." Ohio University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1440073471.

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Fant, Bruno. "Importance du contexte cellulaire et de la régulation spatio-temporelle de l'expression du facteur de transcription Otx2 dans la modulation de ses fonctions." Electronic Thesis or Diss., Nice, 2014. http://www.theses.fr/2014NICE4100.

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Cette thèse s’intéresse aux mécanismes permettant d’expliquer plusieurs des fonctions de l’homéogène Otx2 au cours du développement. Une première partie étudie l’importance de la régulation de son expression dans la régionalisation du système nerveux central. A la fin de la gastrulation la frontière d’expression postérieure d’Otx2 déterminera la position de l’organiseur isthmique responsable de l’induction du mésencéphale et du métencéphale. Un modèle murin a été mis au point dans lequel cette frontière est abolie au profit d’une présence uniforme du gène. A l’encontre du modèle actuel, l’isth

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Karaca, Samir [Verfasser], Henning [Akademischer Betreuer] Urlaub, and Dirk [Akademischer Betreuer] Görlich. "MS-based quantitative analysis of the CRM1 export pathway and spatial proteomics of the Xenopus laevis oocyte / Samir Karaca. Gutachter: Henning Urlaub ; Dirk Görlich. Betreuer: Henning Urlaub." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2015. http://d-nb.info/1076911471/34.

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Fant, Bruno. "Importance du contexte cellulaire et de la régulation spatio-temporelle de l'expression du facteur de transcription Otx2 dans la modulation de ses fonctions." Thesis, Nice, 2014. http://www.theses.fr/2014NICE4100/document.

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Cette thèse s’intéresse aux mécanismes permettant d’expliquer plusieurs des fonctions de l’homéogène Otx2 au cours du développement. Une première partie étudie l’importance de la régulation de son expression dans la régionalisation du système nerveux central. A la fin de la gastrulation la frontière d’expression postérieure d’Otx2 déterminera la position de l’organiseur isthmique responsable de l’induction du mésencéphale et du métencéphale. Un modèle murin a été mis au point dans lequel cette frontière est abolie au profit d’une présence uniforme du gène. A l’encontre du modèle actuel, l’isth

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"Multiplexed Single-cell Spatial Proteomics and Transcriptomics." Doctoral diss., 2018. http://hdl.handle.net/2286/R.I.51771.

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abstract: Single-cell proteomics and transcriptomics analysis are crucial to gain insights of healthy physiology and disease pathogenesis. The comprehensive profiling of biomolecules in individual cells of a heterogeneous system can provide deep insights into many important biological questions, such as the distinct cellular compositions or regulation of inter- and intracellular signaling pathways of healthy and diseased tissues. With multidimensional molecular imaging of many different biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal tr

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Karaca, Samir. "MS-based quantitative analysis of the CRM1 export pathway and spatial proteomics of the Xenopus laevis oocyte." Doctoral thesis, 2014. http://hdl.handle.net/11858/00-1735-0000-0023-9622-6.

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Goyette, Guillaume. "Caractérisation moléculaire de la modulation spatio-temporelle des fonctions du phagosome." Thèse, 2009. http://hdl.handle.net/1866/3585.

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La phagocytose est un processus par lequel des cellules spécialisées du système immunitaire comme les macrophages ingèrent des microorganismes envahisseurs afin de les détruire. Les microbes phagocytés se retrouvent dans un compartiment intracellulaire nommé le phagosome, qui acquiert graduellement de nombreuses molécules lui permettant de se transformer en phagolysosome possédant la capacité de tuer et dégrader son contenu. L’utilisation de la protéomique a permis de mettre en évidence la présence de microdomaines (aussi nommés radeaux lipidiques ou radeaux membranaires) sur les phagosomes de

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Books on the topic "Spatial proteomcis"

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Madan, Esha. Cutting Edge Artificial Intelligence, Spatial Transcriptomics and Proteomics Approaches to Analyze Cancer. Elsevier Science & Technology Books, 2024.

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Book chapters on the topic "Spatial proteomcis"

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Thielert, Marvin, Caroline A. M. Weiss, Matthias Mann, and Florian A. Rosenberger. "Spatial Proteomics of Single Hepatocytes with Multiplexed Data-Independent Acquisition (mDIA)." In Mass Spectrometry Based Single Cell Proteomics. Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-3934-4_9.

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AbstractSpatially resolved mass spectrometry-based proteomics at single-cell resolution promises to provide insights into biological heterogeneity. We describe a protocol based on multiplexed data-independent acquisition (mDIA) with dimethyl labeling to enhance proteome depth, accuracy, and throughput while minimizing costs. It enables high-quality proteome analysis of single isolated hepatocytes and utilizes liver zonation for single-cell proteomics benchmarking. This adaptable, modular protocol will promote the use of single-cell proteomics in spatial biology.

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Doherty, Mary. "Advancing Technologies for Spatial and Temporal Proteomics." In Methods in Animal Proteomics. Wiley-Blackwell, 2011. http://dx.doi.org/10.1002/9780470960660.ch7.

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Das, Hirak, Alexandros Zografakis, Silke Oeljeklaus, and Bettina Warscheid. "Analysis of Yeast Peroxisomes via Spatial Proteomics." In Methods in Molecular Biology. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3048-8_2.

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Yan, Wei, Daehee Hwang, and Ruedi Aebersold. "Quantitative Proteomic Analysis to Profile Dynamic Changes in the Spatial Distribution of Cellular Proteins." In Organelle Proteomics. Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-028-7_26.

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Hondius, David C., Jeroen J. M. Hoozemans, Annemieke J. M. Rozemuller, and August B. Smit. "Laser Microdissection for Spatial Proteomics of Postmortem Brain Tissue." In Neuromethods. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9662-9_4.

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Moradian, Annie, Tanya R. Porras-Yakushi, Michael J. Sweredoski, and Sonja Hess. "A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-3341-9_6.

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Christoforou, Andy, Claire Mulvey, Lisa M. Breckels, Laurent Gatto, and Kathryn S. Lilley. "CHAPTER 9. Spatial Proteomics: Practical Considerations for Data Acquisition and Analysis in Protein Subcellular Localisation Studies." In Quantitative Proteomics. Royal Society of Chemistry, 2014. http://dx.doi.org/10.1039/9781782626985-00185.

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Squires, Steven, Rob Ewing, Adam Prügel-Bennett, and Mahesan Niranjan. "A Method of Integrating Spatial Proteomics and Protein-Protein Interaction Network Data." In Neural Information Processing. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-70139-4_79.

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Chicano-Galvez, Eduardo, Michel Salzet, and Isabelle Fournier. "Chapter 11. MALDI Mass Spectrometry Imaging and Spatially-resolved Proteomics." In MALDI Mass Spectrometry Imaging. Royal Society of Chemistry, 2021. http://dx.doi.org/10.1039/9781839165191-00234.

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Piga, Isabella, Fabio Pagni, Fulvio Magni, and Andrew Smith. "Cytological Cytospin Preparation for the Spatial Proteomics Analysis of Thyroid Nodules Using MALDI-MSI." In Methods in Molecular Biology. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3319-9_9.

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Conference papers on the topic "Spatial proteomcis"

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Martens, William L., Philip Poronnik, and Darren Saunders. "Hypothesis-Driven Sonification of Proteomic Data Distributions Indicating Neurodegredation in Amyotrophic Lateral Sclerosis." In The 22nd International Conference on Auditory Display. The International Community for Auditory Display, 2016. http://dx.doi.org/10.21785/icad2016.024.

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Three alternative sonifications of proteomic data distributions were compared as a means to indicate the neuropathology associated with Amyotrophic Lateral Sclerosis (ALS) via auditory display (through exploration of the differentiation of induced pluripotent stem cell derived neurons). Pure visual displays of proteomic data often result in ”visual overload” such that detailed or subtle data important to describe ALS neurodegradation may be glossed over, and so three competing approaches to the sonification of proteomic data were designed to capitalize upon human auditory capacities that compl

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Wu, Eric, Zhenqin Wu, Aaron T. Mayer, Alexandro E. Trevino, and James Zou. "PEPSI: Polarity measurements from spatial proteomics imaging suggest immune cell engagement." In Pacific Symposium on Biocomputing 2024. WORLD SCIENTIFIC, 2023. http://dx.doi.org/10.1142/9789811286421_0038.

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Chen, Y., J. Schniering, P. Albanese, et al. "Spatial ECM proteomics resolves instructive tissue niches in the distal human lung." In ERS International Congress 2022 abstracts. European Respiratory Society, 2022. http://dx.doi.org/10.1183/13993003.congress-2022.1287.

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Chen, Yuexin, Janine Schniering, Pascal Albanese, et al. "Spatial ECM proteomics resolves instructive tissue niches in the distal human lung." In ERS Lung Science Conference 2022 abstracts. European Respiratory Society, 2022. http://dx.doi.org/10.1183/23120541.lsc-2022.256.

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Samorodnitsky, Sarah N., and Michael C. Wu. "1239 Persistent homology detects clinically-relevant topological structures in multiplexed spatial proteomics." In SITC 39th Annual Meeting (SITC 2024) Abstracts. BMJ Publishing Group Ltd, 2024. http://dx.doi.org/10.1136/jitc-2024-sitc2024.1239.

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Fuchsberger, Christian, Heidi Hübl, Georg Schäfer, et al. "Analysis and Visualization of Spatial Proteomic Data for Tissue Characterization." In 2008 21st International Symposium on Computer-Based Medical Systems (CBMS). IEEE, 2008. http://dx.doi.org/10.1109/cbms.2008.119.

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Fava, A., C. Y. Lee, M. C. Marlin, et al. "OP0176 SINGLE-CELL SPATIAL PROTEOMICS IDENTIFIES INTRAGLOMERULAR MYELOID CELLS IN MEMBRANOUS LUPUS NEPHRITIS." In EULAR 2024 European Congress of Rheumatology, 12-15 June. Vienna, Austria. BMJ Publishing Group Ltd and European League Against Rheumatism, 2024. http://dx.doi.org/10.1136/annrheumdis-2024-eular.5685.

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Rahal, Zahraa, Sujuan Yang, Tieling Zhou, et al. "565 Multimodal spatial transcriptomics and proteomics analysis of the resectable NSCLC ecosystem following neoadjuvant chemoimmunotherapy." In SITC 39th Annual Meeting (SITC 2024) Abstracts. BMJ Publishing Group Ltd, 2024. http://dx.doi.org/10.1136/jitc-2024-sitc2024.0565.

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Ali, Hira, Aaron E. Chiou, Feng Feng, et al. "70 Spatial proteomic profiling of VISTA and PSGL-1 interactions across cancer indications." In SITC 39th Annual Meeting (SITC 2024) Abstracts. BMJ Publishing Group Ltd, 2024. http://dx.doi.org/10.1136/jitc-2024-sitc2024.0070.

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Saurav, Jillur Rahman, Mohammad Sadegh Nasr, Helen H. Shang, et al. "A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels." In 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2023. http://dx.doi.org/10.1109/cibcb56990.2023.10264899.

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