Papers matching “transcriptome annotation” 83
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De novo transcriptome assembly and annotation of the common freshwater amphipod (Gammarus pulex) a valuable resource for ecotoxicogenomics2025 Scientific Data data-paper Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Camilo Escobar-Sierra, Sameer Hassan, Fabian G. Weichert, Henrik Aronsson, Kathrin P. Lampert, Henner Hollert, +2 more
2citations -
GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data2025 iScience article 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
1citations -
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 -
EchoGO: Traceable Functional Interpretation Across Annotation Contexts2026 Zenodo (CERN European Organization for Nuclear Research) software Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Camilo Escobar-Sierra, Felix Langschied, Angelina Miller, Pedro A. Inostroza
0citations -
MACA: Marker-based automatic cell-type annotation for single cell expression data2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Yang Xu, Simon J. Baumgart, Christian M. Stegmann, Sikander Hayat
2citations -
SwarmMAP: swarm learning for decentralized cell type annotation in single cell sequencing data2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Fu Zhu, Rafael Kramann, Sikander Hayat, +1 more
2citations -
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 -
SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Oliver Lester Saldanha, Vivien Goepp, Hyojin Kim, Jie Ping Zhu, Rafael Kramann, Sikander Hayat, +1 more
1citations -
Resolving the immune response across clonal cancer evolution in situ with Atera whole transcriptome profiling2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Shaocheng Wu, Mohita Mahajan, Maarten van der Linde, Chunfang Zhu, Robert B. West, David G.P. van IJzendoorn, +1 more
1citations -
Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information2020 Nature Communications article Biochemistry, Genetics and Molecular Biology RNA Research and Splicing Open access
Sebastian Guelfi, Karishma D’Sa, Juan Antonio Botía, Jana Vandrovcová, Regina Hertfelder Reynolds, David Zhang, +94 more
39citations -
The genome of the "Sea Vomit" Didemnum vexillum2020 Research Square preprint Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Ernesto Parra-Rincón, Cristian A. Velandia-Huerto, Jörg Fallmann, Adriaan Gittenberger, Federico D. Brown, Peter Florian Stadler, +1 more
1citations -
EchoGO validation and reproducibility compendium2026 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Camilo Escobar-Sierra, Felix Langschied, Angelina Miller, Pedro A. Inostroza
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 -
1381 Deciphering the role of immune cell communities in the initiation and progression of human colorectal cancer2024 Regular and Young Investigator Award Abstracts conference-abstract Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
S. Engels, Ana Marta Sequeira, Marieke E. Ijsselsteijn, Benedetta Manzato, Hao Dang, Jurjen J. Boonstra, +5 more
0citations -
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering2026 Nature Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Jieran Sun, Kirti Biharie, Peiying Cai, Niklas Müller‐Bötticher, Paul Kießling, Meghan A. Turner, +47 more
9citations -
A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Magda Grudniewska, Dorien J.M. Peters, Ahmed Essam Mahfouz
5citations -
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 -
Analytical choices drive toxicogenomic potency estimates: a systematic evaluation of transcriptomic points of departure2026 Toxicological Sciences article Biochemistry, Genetics and Molecular Biology Carcinogens and Genotoxicity Assessment Open access
Imke B. Bruns, Dayna R. Schultz, Emmanuel Demuynck, Friedel Dewulf, Ioannis Theologidis, Steven J. Kunnen, +12 more
0citations -
An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Celeste E Cohen, Antonio Párraga-Leo, Leticia Rodríguez-Montes, Christina E. Kim, Marie Moullet, Ana Paredes, +49 more
0citations -
A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery2023 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Magda Grudniewska, Dorien J.M. Peters, Ahmed Essam Mahfouz
38citations -
Non-target molecular network and putative genes of flavonoid biosynthesis in Erythrina velutina Willd., a Brazilian semiarid native woody plant2022 Frontiers in Plant Science article Biochemistry, Genetics and Molecular Biology Plant Gene Expression Analysis Open access
Daisy Sotero Chacon, Marlon Dias Mariano Santos, Bernardo Bonilauri, Johnatan Vilasboa, Cibele Tesser da Costa, Ivanice Bezerra da Silva, +18 more
12citations