| A Python library for probabilistic analysis of single-cell omics data A Gayoso, R Lopez, G Xing, P Boyeau, V Valiollah Pour Amiri, J Hong, ... Nature biotechnology 40 (2), 163-166, 2022 | 284 | 2022 |
| Functional interpretation of single cell similarity maps D DeTomaso, MG Jones, M Subramaniam, T Ashuach, CJ Ye, N Yosef Nature communications 10 (1), 4376, 2019 | 190 | 2019 |
| The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination F Wimmers, M Donato, A Kuo, T Ashuach, S Gupta, C Li, M Dvorak, ... Cell 184 (15), 3915-3935. e21, 2021 | 161 | 2021 |
| MultiVI: deep generative model for the integration of multimodal data T Ashuach, MI Gabitto, RV Koodli, GA Saldi, MI Jordan, N Yosef Nature Methods 20 (8), 1222-1231, 2023 | 96 | 2023 |
| Identification and massively parallel characterization of regulatory elements driving neural induction F Inoue, A Kreimer, T Ashuach, N Ahituv, N Yosef Cell stem cell 25 (5), 713-727. e10, 2019 | 94 | 2019 |
| lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements MG Gordon, F Inoue, B Martin, M Schubach, V Agarwal, S Whalen, ... Nature protocols 15 (8), 2387-2412, 2020 | 78 | 2020 |
| MPRAnalyze: statistical framework for massively parallel reporter assays T Ashuach, DS Fischer, A Kreimer, N Ahituv, FJ Theis, N Yosef Genome biology 20, 1-17, 2019 | 67 | 2019 |
| PeakVI: A deep generative model for single-cell chromatin accessibility analysis T Ashuach, DA Reidenbach, A Gayoso, N Yosef Cell reports methods 2 (3), 2022 | 52 | 2022 |
| Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation A Kreimer, T Ashuach, F Inoue, A Khodaverdian, C Deng, N Yosef, ... Nature communications 13 (1), 1504, 2022 | 23 | 2022 |
| GeneFishing to reconstruct context specific portraits of biological processes K Liu, E Theusch, Y Zhou, T Ashuach, AC Dose, PJ Bickel, MW Medina, ... Proceedings of the National Academy of Sciences 116 (38), 18943-18950, 2019 | 10 | 2019 |
| Functional interpretation of single cell similarity maps. Nat. Commun. 10, 4376 D DeTomaso, MG Jones, M Subramaniam, T Ashuach, CJ Ye, N Yosef | 8 | 2019 |
| Massively parallel characterization of regulatory dynamics during neural induction F Inoue, A Kreimer, T Ashuach, N Ahituv, N Yosef BioRxiv, 370452, 2018 | 6 | 2018 |
| Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements MG Gordon, F Inoue, B Martin, M Schubach, V Agarwal, S Whalen, ... Nature protocols 16 (7), 3736, 2021 | 4 | 2021 |
| Hepatitis C virus infects and perturbs liver stem cells NL Meyers, T Ashuach, DE Lyons, MM Khalid, CR Simoneau, AL Erickson, ... Mbio 14 (6), e01318-23, 2023 | 2 | 2023 |
| NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids CR Simoneau, PY Chen, GK Xing, MM Khalid, NL Meyers, JM Hayashi, ... BioRxiv, 2022 | 2 | 2022 |
| Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework J Liu, T Ashuach, F Inoue, N Ahituv, N Yosef, A Kreimer Nucleic Acids Research 52 (4), 1613-1627, 2024 | 1 | 2024 |
| Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans F Wimmers, M Donato, A Kuo, T Ashuach, S Gupta, C Li, M Dvorak, ... MedRxiv, 2021.05. 24.21253087, 2021 | 1 | 2021 |
| Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation W DeGroat, F Inoue, T Ashuach, N Yosef, N Ahituv, A Kreimer bioRxiv, 2024.05. 22.595375, 2024 | | 2024 |
| Best practices for perturbation MPRA–a computational evaluation framework of sequence design strategies J Liu, T Ashuach, F Inoue, N Ahituv, N Yosef, A Kreimer bioRxiv, 2023 | | 2023 |
| Methodology and Applications for studying the Heterogeneity and Sequence Determinants of cis-Regulatory Elements T Ashuach University of California, Berkeley, 2022 | | 2022 |
