Author
University of California, BerkeleyORCID 0000-0002-1489-8339Unclaimed ORCID profile · follow to get notified of new preprints
8 papers
Recent·Most cited
Hector Roux de Bézieux, Kelly Street, Stephan Fischer, Koen Van den Berge, Rebecca K. Chance, Davide Risso, Jesse A Gillis, John Ngai, Elizabeth A. Purdom, Sandrine Dudoit
Dune improves replicability of cell type discovery in scRNA-Seq by optimizing the trade-off between cluster resolution and cross-dataset consistency.
BMC Bioinformatics · May 24, 2024Peer-reviewedBioinformatics
Koen Van den Berge, Hsin-Jung Chou, Hector Roux de Bézieux, Kelly Street, Davide Risso, John Ngai, Sandrine Dudoit
The paper benchmarks ATAC-seq normalization methods and shows that GC-content effects must be accounted for to improve downstream analysis accuracy.
Cell Reports Methods · Nov 1, 2022Peer-reviewedBioinformatics
Hector Roux de Bézieux, Leandro Lima, Fanny Perraudeau, Arnaud Mary, Sandrine Dudoit, Laurent Jacob
CALDERA improves bacterial GWAS by testing subgraphs of De Bruijn graphs, enhancing power and interpretability while managing computational complexity.
Bioinformatics · Apr 14, 2022Peer-reviewedGenetics
Martin Kinisu, Yong Jin Choi, Claudia Cattoglio, Ke Liu, Hector Roux de Bézieux, Raeline Valbuena, Nicole Pum, Sandrine Dudoit, Haiyan Huang, Zhenyu Xuan, Sang Yong Kim, Lin He
This study identifies Klf5 as a key regulator of bi-potential cell fate in mouse preimplantation embryos by controlling both ICM and TE specification genes.
Cell Reports · Nov 1, 2021Peer-reviewedDevelopmental Biology
Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S. Adkins, Andrew I. Aldridge, Seth A. Ament, Anna Bartlett, M. Margarita Behrens, Koen Van den Berge, Darren Bertagnolli, Hector Roux de Bézieux, Tommaso Biancalani, A. Sina Booeshaghi, Héctor Corrada Bravo, , Eran A. Mukamel
The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.
Nature · Oct 6, 2021Peer-reviewedNeuroscience
Hector Roux de Bézieux, Koen Van den Berge, Kelly Street, Sandrine Dudoit
The paper introduces a method to infer and compare cell trajectories across multiple conditions, detecting differences in progression, population structure, and gene expression.
bioRxiv · Mar 9, 2021 · PreprintBioinformatics
David H. Brann, Tatsuya Tsukahara, Caleb Weinreb, Marcela Lipovsek, Koen Van den Berge, Boying Gong, Rebecca K. Chance, Iain C. Macaulay, Hsin-Jung Chou, Russell B. Fletcher, Diya Das, Kelly Street, Hector Roux de Bézieux, Yoon-Gi Choi, Davide Risso, , Sandeep Robert Datta
The paper identifies non-neuronal cell types in the olfactory system expressing SARS-CoV-2 entry genes, suggesting indirect mechanisms for COVID-19-associated anosmia.
Science Advances · Jul 24, 2020Peer-reviewedNeuroscience
Koen Van den Berge, Hector Roux de Bézieux, Kelly Street, Wouter Saelens, Robrecht Cannoodt, Yvan Saeys, Sandrine Dudoit, Lieven Clement
The paper introduces a generalized additive model framework for trajectory-based differential expression analysis in single-cell RNA-seq data, enabling flexible inference of within and between lineage gene expression differences.
Nature Communications · Mar 5, 2020Peer-reviewedBioinformatics