Papers matching “transcriptomic data analysis” 303
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Integrative multiomics analysis of human atherosclerosis reveals a serum response factor‐driven network associated with intraplaque hemorrhage2021 Clinical and Translational Medicine article Medicine Cerebrovascular and Carotid Artery Diseases Open access
Han Young Jin, Pieter Goossens, Peter J. Juhasz, Wouter J. Eijgelaar, Marco Manca, Joël Karel, +14 more
100citations -
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production2020 iScience article Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
Snorre Sulheim, Tjaša Kumelj, Dino van Dissel, Ali Salehzadeh‐Yazdi, Chao Du, Kay Nieselt, +3 more
46citations -
Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis2021 Journal of Proteome Research article Chemistry Advanced Proteomics Techniques and Applications Open access
Sara Kassem, Kyra van der Pan, Anniek L. de Jager, Brigitta A. E. Naber, Inge F. de Laat, Alesha Louis, +3 more
37citations -
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 -
PathwayFinder enables linked exploration of cell types and gene modules in spatially resolved transcriptomics data2026 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Lisa Koorneef, Thomas Höllt, Louise van der Weerd, +1 more
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 -
Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Sidrah Maryam, Martin Manolov, Rafael Kramann, Sikander Hayat
0citations -
Cytosplore EvoViewer: Visual Analytics of Conserved Evolutionary Patterns in multi-species single-cell sequencing data2025 IEEE Pacific Visualization Conference (PacificVis) conference-paper Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Soumyadeep Basu, Morgan E. Wirthlin, Jeroen Eggermont, Thomas Kroes, Boudewijn P. F. Lelieveldt, Ed S. Lein, +2 more
1citations -
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 -
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data2022 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 1 patent
Daniel Dimitrov, Dénes Türei, Martín Garrido‐Rodríguez, Paul L Burmedi, James Shiniti Nagai, Charlotte Boys, +7 more
670citations -
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 phenotype-driven data and drug repurposing strategy used to identify potential treatments targeting chondrocyte hypertrophy in osteoarthritis2025 Biomedicine & Pharmacotherapy article Medicine Osteoarthritis Treatment and Mechanisms Open access
Judith Veldman, Mauricio N. Ferrao Blanco, Nicole Kops, Wendy J. L. M. Koevoet, Eric M. Bindels, Gregory van Beek, +5 more
1citations -
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 -
Utility of Extrapolating Human S1500+ Genes to the Whole Transcriptome: Tunicamycin Case Study2020 Bioinformatics and Biology Insights article Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Deepak Mav, Dhiral P. Phadke, Michele R. Balik-Meisner, Bruce Alex Merrick, Scott S. Auerbach, Marije Niemeijer, +7 more
10citations -
Evidence That Non-Syndromic Familial Tall Stature Has an Oligogenic Origin Including Ciliary Genes2021 Frontiers in Endocrinology article Biochemistry, Genetics and Molecular Biology Genomics and Rare Diseases Open access
Birgit Weiß, Birgit Eberle, Ralph Roeth, Christiaan de Bruin, Julian C. K. Lui, Nagarajan Paramasivam, +5 more
7citations -
Integrating multi-omics technologies to decipher microbiome functions2026 Nature Communications review Biochemistry, Genetics and Molecular Biology Gut microbiota and health Open access
Tim Van Den Bossche, Eunice Lazau, Velma T. E. Aho, J. Alfredo Blakeley‐Ruiz, Maximilian Wolf, Benoit Josef Kunath, +39 more
2citations -
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