| A sandbox for prediction and integration of DNA, RNA, and proteins in single cells MD Luecken, DB Burkhardt, R Cannoodt, C Lance, A Agrawal, H Aliee, ... Thirty-fifth Conference on Neural Information Processing Systems Datasets …, 2021 | 105 | 2021 |
| Restoration of patterned vision with an engineered photoactivatable G protein-coupled receptor MH Berry, A Holt, J Levitz, J Broichhagen, BM Gaub, M Visel, C Stanley, ... Nature communications 8 (1), 1862, 2017 | 86 | 2017 |
| CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data CZI Cell Science Program, S Abdulla, B Aevermann, P Assis, S Badajoz, ... Nucleic Acids Research 53 (D1), D886-D900, 2025 | 69 | 2025 |
| A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting NC Lammers, YJ Kim, J Zhao, HG Garcia Current opinion in cell biology 67, 147-157, 2020 | 67 | 2020 |
| Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing J Liu, V Tran, VNP Vemuri, A Byrne, M Borja, YJ Kim, S Agarwal, R Wang, ... Life science alliance 6 (1), 2023 | 54 | 2023 |
| Zebrahub–Multimodal zebrafish developmental atlas reveals the State-transition dynamics of late-vertebrate pluripotent axial progenitors M Lange, A Granados, S VijayKumar, J Bragantini, S Ancheta, ... BioRxiv, 2023.03. 06.531398, 2023 | 46 | 2023 |
| Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage J Liu, D Hansen, E Eck, YJ Kim, M Turner, S Alamos, HG Garcia PLoS computational Biology, 2021 | 34 | 2021 |
| Lighting up the central dogma for predictive developmental biology HG Garcia, A Berrocal, YJ Kim, G Martini, J Zhao Current topics in developmental biology 137, 1-35, 2020 | 22 | 2020 |
| Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer YJ Kim, K Rhee, J Liu, S Jeammet, MA Turner, SJ Small, HG Garcia Elife 11, e73395, 2022 | 20 | 2022 |
| Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis E Mennillo, YJ Kim, G Lee, I Rusu, RK Patel, LC Dorman, E Flynn, S Li, ... Nature Communications 15 (1), 1493, 2024 | 17* | 2024 |
| Optogenetic dissection of transcriptional repression in a multicellular organism J Zhao, NC Lammers, S Alamos, YJ Kim, G Martini, HG Garcia Nature Communications 15 (1), 9263, 2024 | 6 | 2024 |
| A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors M Lange, A Granados, S VijayKumar, J Bragantini, S Ancheta, YJ Kim, ... Cell 187 (23), 6742-6759. e17, 2024 | 3 | 2024 |
| Dysregulation of CD4+ and CD8+ resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis JY He, YJ Kim, E Mennillo, I Rusu, J Bain, AA Rao, C Andersen, K Law, ... Journal for ImmunoTherapy of Cancer 12 (4), 2024 | 3 | 2024 |
| Tutorial: guidelines for manual cell type annotation of single-cell multi-omics datasets using interactive software YJ Kim, A Tarashansky, K Liang, M Urisko, L Dorman, M Borja, N Neff, ... bioRxiv, 2023.07. 11.548639, 2023 | 2 | 2023 |
| Single-nucleus RNA sequencing provides insights into the GL261-GSC syngeneic mouse model of glioblastoma L Garcia-Vicente, M Borja, V Tran, A Alvarez-Vazquez, ... bioRxiv, 2023.10. 26.564166, 2023 | 2 | 2023 |
| Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis YJ Kim, S VijayKumar, B Iovino, A Granados, S Ancheta, X Zhao, ... bioRxiv, 2024.10. 18.618987, 2024 | | 2024 |
