Papers matching “transcriptome annotation” 23
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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 -
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 -
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 -
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 -
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 -
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 -
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 -
2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Sebastian Tiesmeyer, Niklas Müller‐Bötticher, Sergio Marco Salas, Paul Kießling, Paul M. Horn, Adrien Guillot, +7 more
9citations -
The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics
Shrey Parikh, Daniel C. Strobl, Sara Jiménez, Julia Beckmann, Lucas Arnoldt, Eljas Roellin, +19 more
1citations -
Utilizing gene co-expression networks with the rat kidney TXG-MAPr tool to enhance safety assessment, biomarker identification and human translation2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Steven J. Kunnen, Giulia Callegaro, Jeffrey J. Sutherland, Panuwat Trairatphisan, Hugo W van Kessel, Lukas S. Wijaya, +11 more
1citations -
Cellular context shapes the transcriptomic impact of somatic variants2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access
Peisen Sun, Peng Jia, Chuyuan Lou, Xiaona Li, Miaojing Li, Ruifen Zhang, +23 more
0citations -
Refining the transcriptional landscapes for distinct clades of virulent phages infecting pseudomonas aeruginosa2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Environmental Science Bacteriophages and microbial interactions Open access
Leena Putzeys, Laura Wicke, Maarten Boon, Vera van Noort, Jörg Vogel, Rob Lavigne
1citations -
Analysis of pre-symptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Amyotrophic Lateral Sclerosis Research Open access
Marina L. García‐Vaquero, Barbara Flix, Marcelo Henrique Neves Pereira, Lucile Palin, Tânia Monteiro Marques, Francisco Rodrigues Pinto, +4 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 -
Roles for the long non-coding RNA Pax6os1 / PAX6-AS1 in pancreatic beta cell identity and function2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Pancreatic function and diabetes Open access
Livia López–Noriega, Rebecca Callingham, Aida Martínez-Sánchez, Sameena Nawaz, Grazia Pizza, Nejc Haberman, +13 more
6citations -
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 -
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
23 results