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Articles by Roland Eils
A single-cell multi-omic atlas of the human pancreas reveals potential for cellular plasticity across development, health, and disease
ResourceVolume 38, Issue 9p1896-1915.e12Open access Affiliations & Notes 1Josep Carreras Leukemia Research Institute, Barcelona, Spain 2Centre for Genomic Regulation, the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain 3Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland 4Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM),...
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering
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Abstract Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcriptomics, delineating higher-order anatomical structures is critical for understanding how cellular organization affects function.
By Kirti Biharie, Peiying Cai, Niklas Müller-Bötticher, Paul Kiessling, Meghan Turner, Martin Emons, Samuel Gunz, Sven O. Twardziok, Amin El-Heliebi, Martin Zacharias, Roland Eils, Marcel Reinders, Raphael Gottardo, Christoph Kuppe, Brian Long, Ahmed Mahfouz, Mark Robinson, Naveed Ishaque, Jieran Sun, Søren Helweg Dam, Florian Heyl, Sarusan Kathirchelvan
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Nature
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Aberrant brain-type neuronal programs in large-cell pancreatic neuroendocrine carcinoma
Abstract High-grade pancreatic neuroendocrine carcinoma (panNEC) is a rare, aggressive cancer with limited tissue availability. Single-nucleus transcriptomics of five large-cell panNECs revealed two clinically relevant neuroendocrine cell states: one highly proliferative with an aberrant brain-specific neuronal differentiation program and another stress-responsive state enriched for heat stress, hypoxia, and glycolysis.
Large language models are powerful electronic health record encoders
Abstract Electronic health records (EHRs) offer considerable potential for clinical prediction, but their complexity and heterogeneity challenge traditional machine learning. Domain-specific electronic health record foundation models trained on unlabeled EHR data have shown improved predictive accuracy and generalization. However, their development is constrained by limited data access and site-specific vocabularies.
CLUES A Comprehensive Workflow for Integrating Geospatial Data in Biomedical Research
Abstract Environmental exposures play a critical role in shaping physical and mental health, yet integrating such data into biomedical research remains technically complex and fragmented. The EnvironMENTAL Climate, Urbanicity, Environment and Society (CLUES) framework is an open-source, end-to-end workflow for generating individual-level environmental exposure data.
Identifying 3D signal overlaps in spatial transcriptomics data with ovrlpy - Nature Biotechnology
Abstract Imaging-based spatially resolved transcriptomics can localize transcripts within tissue sections in three dimensions. However, cell segmentation, which assigns transcripts to cells, is usually performed in two dimensions and spatial doublets in the vertical dimension result in segmented cells containing transcripts originating from multiple cell types.
Multi-center benchmarking of large language models for clinical decision support in lung cancer screening
ReportOnline now102465Open access 1Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China 2Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China 3Department of Statistics, University of Illinois Urbana-Champaign, Champaign, IL, USA 4Department of Immunology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China 5School of Clinical Medicine, Shanghai Medical College, Fudan University, Shanghai, China...
AI sparking a global health revolution
Editor's note: China has attached great importance to the development of artificial intelligence in order to build itself into a major global AI innovation center. As a strategic technology leading a new round of scientific and technological revolution, AI will promote the deep integration of digital technology and the economy. Four experts share their views on the issue with China Daily.
Benchmark evaluation of DeepSeek large language models in clinical decision-making - Nature Medicine
Abstract Large language models (LLMs) are increasingly transforming medical applications. However, proprietary models such as GPT-4o face significant barriers to clinical adoption because they cannot be deployed on site within healthcare institutions, making them noncompliant with stringent privacy regulations.
Author Correction: Virus-induced senescence is a driver and therapeutic target in COVID-19 - Nature
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Correction to: Nature https://doi.org/10.1038/s41586-021-03995-1 Published online 13 September 2021 In the version of the article initially published, in the p16INK4a immunfluorescence microscopy pictures in Extended Data Fig. 1a, the “mock” images for Tig3 and WI38 were identical (visible only at enhanced brightness). The correct Tig3 mock image has been located and the corrected figure is now available in the HTML and PDF versions of the article. About this article Lee, S., Yu, Y., Trimpert, J.
By Soyoung Lee, Jakob Trimpert, Fahad Benthani, Emanuel Wyler, Dimitri Belenki, Theresa C. Firsching, Michael Schotsaert, Carles Martínez-Romero, Gagandeep Singh, Séverine Kunz, Daniela Niemeyer, Susanne Kimeswenger, Achim D. Gruber, Bernd Lamprecht, Markus Landthaler, Christian Drosten, Adolfo Garcia-Sastre, Roland Eils
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Nature
Verified
An open-source framework for end-to-end analysis of electronic health record data
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Hillary Clinton 2 days ago Hillary Clinton Left 9/11 Event During Solemn Moment Due to Pneumonia, Leading Trump to Attack Her The Inquisitr - By Tavishi • 2d During a 9/11 memorial event in 2016, Hillary Clinton had to leave abruptly due to her deteriorating health and diagnosis of pneumonia. The … Medical Conditions 2 days ago 30 Unusual Ways People Almost Died cracked.com - Ian Garner • 2d You can die doing pretty much anything.
By Lukas Heumos, Tim Treis, Eljas Roellin, Lilly May, Vladimir A. Shitov, Xinyue Zhang, Luke Zappia, Rainer Knoll, Niklas Lang, Leon Hetzel, Isaac Virshup, Lisa Sikkema, Fabiola Curion, Roland Eils, Herbert Schiller, Anne Hilgendorff, Fabian J. Theis, Philipp Ehmele, Altana Namsaraeva, Nastassya Horlava
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SpatialLeiden - Spatially-aware Leiden clustering
Abstract Clustering can identify the natural structure that is inherent to measured data. For single-cell omics, clustering finds cells with similar molecular phenotype after which cell types are annotated. Leiden clustering is the algorithm of choice in the single-cell community. However, in the field of spatial omics, Leiden has been considered a non-spatial clustering method.
Sainsc: a computational tool for segmentation-free analysis of in-situ capture
Abstract Spatially resolved transcriptomics has become the method of choice to characterise the complexity of biomedical tissue samples. Until recently, scientists have been restricted to profiling methods with high spatial resolution but for a limited set of genes or methods that can profile transcriptome-wide but at low spatial resolution. Through recent developments, there are now methods which offer subcellular spatial resolution and full transcriptome coverage.
Directed acyclic graph for epidemiological studies in childhood food allergy: Construction, user's guide, and application
DAG Directed acyclic graph EAACI European Academy of Allergy and Clinical Immunology ETS Environmental tobacco exposure FA Food allergies GERD Gastroesophageal reflux disease RCTs Randomized control trials Th cell T Helper cell 1 INTRODUCTION The natural history of food allergies (FA) usually starts in patients' early life.1 Main symptoms of FA in children include hives, swelling, vomiting, and diarrhea; fatal respiratory symptoms such as breathing difficulty may also occur.2 Eggs, cow's...
Author Correction: The landscape of viral associations in human cancers - Nature Genetics
Author notes These authors contributed equally: Marc Zapatka, Ivan Borozan, Daniel S. Brewer, Murat Iskar. These authors jointly supervised this work: Marc Zapatka, Peter Lichter. A list of authors and their affiliations appears at the end of the paper. A list of authors and their affiliations appears online.
Metabolomic profiles predict individual multidisease outcomes - Nature Medicine
Abstract Risk stratification is critical for the early identification of high-risk individuals and disease prevention. Here we explored the potential of nuclear magnetic resonance (NMR) spectroscopy-derived metabolomic profiles to inform on multidisease risk beyond conventional clinical predictors for the onset of 24 common conditions, including metabolic, vascular, respiratory, musculoskeletal and neurological diseases and cancers.
The genomic and transcriptional landscape of primary central nervous system lymphoma - Nature Communications
Abstract Primary lymphomas of the central nervous system (PCNSL) are mainly diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). Molecular drivers of PCNSL have not been fully elucidated. Here, we profile and compare the whole-genome and transcriptome landscape of 51 CNS lymphomas (CNSL) to 39 follicular lymphoma and 36 DLBCL cases outside the CNS.
SSAM-lite: a light-weight web app for rapid analysis of spatially resolved transcriptomics data
SSAM-lite: a light-weight web app for rapid analysis of spatially resolved transcriptomics data Sebastian Tiesmeyer, Shashwat Sahay, Niklas Müller-Bötticher, Roland Eils, Sebastian D. Mackowiak, Naveed Ishaque bioRxiv 2021.09.29.462194; doi: https://doi.org/10.1101/2021.09.29.462194
Virus-induced senescence is a driver and therapeutic target in COVID-19 - Nature
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Abstract Derailed cytokine and immune cell networks account for the organ damage and the clinical severity of COVID-19 (refs. 1,2,3,4). Here we show that SARS-CoV-2, like other viruses, evokes cellular senescence as a primary stress response in infected cells.
By Soyoung Lee, Jakob Trimpert, Emanuel Wyler, Dimitri Belenki, Theresa C. Firsching, Michael Schotsaert, Carles Martínez-Romero, Gagandeep Singh, Séverine Kunz, Daniela Niemeyer, Achim D. Gruber, Bernd Lamprecht, Markus Landthaler, Christian Drosten, Adolfo Garcia-Sastre, Roland Eils, Clemens A. Schmitt, Fahad Benthani, Susanne Kimeswenger
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Nature
Verified
Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson’s disease
Abstract Rare variants in the beta-glucocerebrosidase gene (GBA1) are common genetic risk factors for alpha synucleinopathy, which often manifests clinically as GBA-associated Parkinson’s disease (GBA-PD). Clinically, GBA-PD closely mimics idiopathic PD, but it may present at a younger age and often aggregates in families. Most carriers of GBA variants are, however, asymptomatic. Moreover, symptomatic PD patients without GBA variant have been reported in families with seemingly GBA-PD.
Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype
Abstract Glioblastoma frequently exhibits therapy-associated subtype transitions to mesenchymal phenotypes with adverse prognosis. Here, we perform multi-omic profiling of 60 glioblastoma primary tumours and use orthogonal analysis of chromatin and RNA-derived gene regulatory networks to identify 38 subtype master regulators, whose cell population-specific activities we further map in published single-cell RNA sequencing data.
Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19 - Nature Neuroscience
Study design Thirty-three deceased individuals with COVID-19 either confirmed by PCR for SARS-CoV-2 (n = 31 of 33) or with clinical features highly suggestive of COVID-19 (n = 2 of 33) were included (Supplementary Table 1). Individuals were not preselected with regard to their clinical symptoms.
The landscape of viral associations in human cancers - Nature Genetics
Abstract Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and—for a subset—whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets.
Impact of cancer mutational signatures on transcription factor motifs in the human genome
Impact of cancer mutational signatures on transcription factor motifs in the human genome Calvin WY Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann bioRxiv 422386; doi: https://doi.org/10.1101/422386
The landscape of genomic alterations across childhood cancers
The cohort analysed in this study is a compilation of individual sequencing datasets from various sources: the International Cancer Genome Consortium (ICGC) – Pedbrain Tumor and MMML-seq (http://www.icgc.org), the German Cancer Consortium (DKTK) (https://dktk.dkfz.de/en/home), the Pediatric Cancer Genome Project (PCGP) (http://explore.pediatriccancergenomeproject.org/), the Heidelberg Institute for Personalized Oncology (HIPO) (http://www.dkfz.de/en/hipo), the Individualized Therapy For...
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