Papers matching “transcriptomic data analysis” 54
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Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequencing data analysis2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tamim Abdelaal, Jeroen Eggermont, Thomas Höllt, Ahmed Essam Mahfouz, Marcel J. T. Reinders, Boudewijn P. F. Lelieveldt
2citations -
Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
Chengyu Zhang, Feiran Li, Cheng Wei Quan Eiden, William Taussig Scott, Ulf W. Liebal, Lars M. Blank, +8 more
8citations -
Collaborative network analysis for the interpretation of transcriptomics data in rare diseases, an application to Huntington’s disease2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Ozan Özışık, Tooba Abbassi‐Daloii, Morgane Térézol, Núria Queralt-Rosiñach, Annika Jacobsen, Osman Uğur Sezerman, +5 more
0citations -
A comprehensive and centralized database for exploring omics data in Autoimmune Diseases2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Jordi Martorell‐Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro Dominguez, Juan Antonio Villatoro-García, Guillermo Barturen, +10 more
1citations -
A Network-based Transcriptomic Landscape of HepG2 cells to Uncover Causal Gene Cytotoxicity Interactions Underlying Drug-Induced Liver Injury2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Lukas S. Wijaya, Attila Gábor, Iris Pot, Luca van de Have, Julio Sáez-Rodríguez, James L. Stevens, +3 more
1citations -
Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access
Óscar Lapuente-Santana, Gregor Sturm, Markus Außerhofer, Constantin Zackl, Maria Zopoglou, Nicholas McGranahan, +5 more
0citations -
Fast model-free standardization and integration of single-cell transcriptomics data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Rafael Kramann, Rachel Patton McCord, Sikander Hayat
0citations -
SpaceWalker: Interactive Gradient Exploration for Spatial Transcriptomics Data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Tamim Abdelaal, Thomas Höllt, Boudewijn P. F. Lelieveldt
2citations -
Multimodal Data Integration Advances Longitudinal Prediction of the Naturalistic Course of Depression and Reveals a Multimodal Signature of Disease Chronicity2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Treatment of Major Depression Open access
Philippe C. Habets, Rajat Mani Thomas, Yuri Milaneschi, Rick Jansen, René Pool, Wouter J. Peyrot, +4 more
0citations -
Correcting differential gene expression analysis for cyto-architectural alterations in substantia nigra of Parkinson’s disease patients reveals known and potential novel disease-associated genes and pathways2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Parkinson's Disease Mechanisms and Treatments Open access
Federico Ferraro, Fevga Christina, Bonifati Vincenzo, Mandemakers Wim, Mahfouz Ahmed, Reinders Marcel
0citations -
Transcriptomic mapping of the inter-individual variability of cellular stress response activation in primary human hepatocytes2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access
Marije Niemeijer, Witold Więcek, Suzanna Huppelschoten, Peter Bouwman, Audrey Baze, Celine Parmentier, +4 more
3citations -
Spatial Transcriptomic Characterization of Novel Pathologic Niches in IPF2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis Open access
Christoph H. Mayr, Diana Santacruz, Sebastian Jarosch, Charlotte Lempp, Lavinia Neubert, Berenice Rath, +7 more
1citations -
Reference-based cell type matching of spatial transcriptomics data2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. F. Lelieveldt, Brian Long, Tamim Abdelaal, +12 more
5citations -
Transcriptomic signatures associated with regional cortical thickness changes in Parkinson’s disease2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Parkinson's Disease Mechanisms and Treatments Open access
Arlin Keo, Oleh Dzyubachyk, Jeroen van der Grond, Jacobus Johannes van Hilten, Marcel J. T. Reinders, Ahmed Essam Mahfouz
0citations -
Systems-wide analysis of the GATC-binding nucleoid-associated protein Gbn and its impact on Streptomyces development2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bacterial Genetics and Biotechnology Open access
Chao Du, Joost J. Willemse, Amanda M. Erkelens, Víctor J. Carrión, Remus Thei Dame, Gilles P. van Wezel
0citations -
GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
Explainable multi-view framework for dissecting intercellular signaling from highly multiplexed spatial data2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jovan Tanevski, Ricardo O. Ramirez Flores, Attila Gábor, Denis Schapiro, Julio Sáez-Rodríguez
28citations -
WALDO: community-Wide Annotation of γδ Lymphocytes in single-cell Data, Openly benchmarked2026 Zenodo (CERN European Organization for Nuclear Research) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Farid Keramati, Moosa Rezwani, Likai Tan, David Hamilton, Zheng Song, Tao Yang, +10 more
0citations -
mcBERT: Patient-Level Single-cell Transcriptomics Data Representation2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Benedikt von Querfurth, Johannes Lohmöller, Jan Pennekamp, Tore Bleckwehl, Rafael Kramann, Klaus Wehrle, +1 more
3citations -
A patient-centric knowledge graph approach to prioritize mutants for selective anti-cancer targeting2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Marina Gorostiola González, Adriaan P. IJzerman, Gerard J. P. van Westen
0citations -
The genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi has been driven by two major evolutionary lineages2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Yeasts and Rust Fungi Studies Open access
Vinícius Delgado da Rocha, Everton Geraldo Capote Ferreira, Fernanda Machado Castanho, Marcia Kamogae Kuwahara, Claudia Vieira Godoy, M. C. Meyer, +10 more
2citations -
Plant PhysioSpace: a robust tool to compare stress response across plant species2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Ali Hadizadeh Esfahani, Janina Maß, Asis Hallab, Bernhard Schuldt, David Nevarez, Björn Usadel, +3 more
1citations -
AtlasOT - The Fused Unbalanced Gromov-Wasserstein for Multimodal Integration of Disease Atlases2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kai Peng, Mayra L. Ruiz Tejada Segura, Barthélémy Caron, Christoph Kuppe, James Shiniti Nagai, Ivan G. Costa
0citations