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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 -
Unveiling the Impact of Microglial Cells in Alzheimer's Disease Pathogenesis: Insights from Single-Cell RNA-seq Analysis and In Vivo Validation2024 Research Square preprint Neuroscience Neuroinflammation and Neurodegeneration Mechanisms Open access
Nima Sanadgol, Adib Miraki Feriz, Laya Ravanjoo, Mohammad Haddadi, Cordian Beyer, Adib Zendedel, +1 more
0citations -
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Daniel Osorio, Anna Capasso, S. Gail Eckhardt, Uma P. Giri, Alexander J. Somma, Todd M. Pitts, +8 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 -
CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data2024 arXiv (Cornell University) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Ping‐Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien‐Yu Chen, +3 more
0citations -
Single-Cell Integration and Multi-Modal Profiling Reveals Phenotypes and Spatial Organization of Neutrophils in Colorectal Cancer2025 SSRN Electronic Journal preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Valentin Marteau, Niloofar Nemati, Kristina Handler, Deeksha Raju, Alexander Kirchmair, Dietmar Rieder, +37 more
0citations -
Integrative learning of disentangled representations from single-cell RNA-sequencing datasets2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Claudio Novella-Rausell, Dorien J.M. Peters, Ahmed Essam Mahfouz
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 Single-Cell Level Comparison of Human Inner Ear Organoids and the Human Cochlea and Vestibular Organs2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Hearing, Cochlea, Tinnitus, Genetics Open access
Wouter H. van der Valk, Edward S. A. van Beelen, Matthew R. Steinhart, Carl A. Nist-Lund, John C.M.J. de Groot, Peter Paul G. van Benthem, +2 more
2citations -
Identification of endothelial-to-mesenchymal transition gene signatures in single-cell transcriptomics of human atherosclerotic tissue2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access
Lotte Slenders, Marian Wesseling, Arjan Boltjes, Daniek Kapteijn, Marie A.C. Depuydt, Koen H.M. Prange, +8 more
6citations -
Single-Cell Resolution of Cellular Damage Illuminates Disease Progression2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Tsimafei Padvitski, Paula Unger Avila, He Chen, Fabian Braun, David Unnersjö‐Jess
1citations -
Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Tendon Structure and Treatment Open access
Jolet Y. Mimpen, Mathew J. Baldwin, Claudia Paul, Lorenzo Ramos‐Mucci, Alina Kurjan, C. Cohen, +9 more
5citations -
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 -
Microfluidic single-cell scale-down bioreactors: A proof-of-concept for the growth of Corynebacterium glutamicum at oscillating pH values2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Engineering Fluid Dynamics and Mixing Open access
Sarah Täuber, Luisa Blöbaum, Valentin Steier, Marco Oldiges, Alexander Grünberger
2citations -
Identifying commonalities between cell lines and tumors at the single cell level using Sobolev Alignment of deep generative models2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Soufiane M. C. Mourragui, Joseph C. Siefert, Marcel J. T. Reinders, Marco Loog, Lodewyk F.A. Wessels
2citations -
Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Rose Yinghan Behncke, +27 more
5citations -
PILOT-GM-VAE: Patient-Level Analysis of single cell Disease Atlas with Optimal Transport of Gaussian Mixture Variational Autoencoders2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Mehdi Joodaki, Mina Shaigan, James Shiniti Nagai, Tiago Maié, Christoph Kuppe, Ivan G. Costa
0citations -
Single cell trajectory analysis of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access
Chaido Ori, Meshal Ansari, Ilias Angelidis, Fabian Joachim Theis, Herbert B. Schiller, Micha Drukker
2citations -
OX40 agonism enhances efficacy of PD-L1 checkpoint blockade by shifting the cytotoxic T cell differentiation spectrum2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access
Guillaume Beyrend, Tetje Cornelia van der Sluis, Esmé T.I. van der Gracht, Tamim Abdelaal, Simon P. Jochems, Robert A. Belderbos, +16 more
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 -
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, +18 more
0citations -
Integrating cell interaction with transcript factors to obtain a robust gene panel for prognostic prediction and therapies in cholangiocarcinoma2022 Research Square preprint Medicine Cholangiocarcinoma and Gallbladder Cancer Studies Open access
Tingjie Wang, Chuanrui Xu, Dan Xu, Xiaofei Yang, Yaxin Liu, Xiujuan Li, +4 more
0citations