| The specious art of single-cell genomics T Chari, L Pachter PLOS Computational Biology 19 (8), e1011288, 2023 | 285 | 2023 |
| RNA velocity unraveled G Gorin, M Fang, T Chari, L Pachter PLOS Computational Biology 18 (9), e1010492, 2022 | 133 | 2022 |
| Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types T Chari, B Weissbourd, J Gehring, A Ferraioli, L Leclère, M Herl, F Gao, ... Science Advances 7 (48), eabh1683, 2021 | 75 | 2021 |
| Genome organization around nuclear speckles drives mRNA splicing efficiency P Bhat, A Chow, B Emert, O Ettlin, SA Quinodoz, M Strehle, Y Takei, ... Nature, 1-9, 2024 | 56 | 2024 |
| Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data M Carilli, G Gorin, Y Choi, T Chari, L Pachter Nature Methods 21 (8), 1466-1469, 2024 | 16 | 2024 |
| Spectral neural approximations for models of transcriptional dynamics G Gorin, M Carilli, T Chari, L Pachter Biophysical Journal 123 (17), 2892-2901, 2024 | 15 | 2024 |
| Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types T Chari, B Weissbourd, J Gehring, A Ferraioli, L Leclère, M Herl, F Gao, ... BioRxiv, 2021.01. 22.427844, 2021 | 13 | 2021 |
| Biophysically interpretable inference of cell types from multimodal sequencing data T Chari, G Gorin, L Pachter Nature Computational Science 4 (9), 677-689, 2024 | 6 | 2024 |
| Whole-animal multiplexed singlecell RNA-seq reveals transcriptional shifts across Clytia medusa cell types. Sci Adv. 2021; 7: eabh1683 T Chari, B Weissbourd, J Gehring, A Ferraioli, L Leclère, M Herl | 6 | |
| Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression. L Luebbert, DK Sullivan, M Carilli, KE Hjörleifsson, AV Winnett, T Chari, ... bioRxiv: The Preprint Server for Biology, 2023 | 5 | 2023 |
| Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX K Jackson, AS Booeshaghi, Á Gálvez-Merchán, L Moses, T Chari, ... bioRxiv, 2023.06. 28.546949, 2023 | 2 | 2023 |
| Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression L Luebbert, DK Sullivan, M Carilli, KE Hjörleifsson, AV Winnett, T Chari, ... bioRxiv, 2023.12. 11.571168, 2024 | 1 | 2024 |
| Identification of spatial homogeneous regions in tissues with concordex KC Jackson, AS Booeshaghi, Á Gálvez-Merchán, L Moses, T Chari, A Kim, ... bioRxiv, 2023.06. 28.546949, 2024 | | 2024 |
| Stochastic Modeling of Biophysical Responses to Perturbation T Chari, G Gorin, L Pachter bioRxiv, 2024 | | 2024 |
| Perturbing the Genome: From Bench to Biophysics T Chari California Institute of Technology, 2024 | | 2024 |
| Mechanistic modeling with a variational autoencoder for multimodal single-cell RNA sequencing data Supplementary Material M Carilli, G Gorin, Y Choi, T Chari, L Pachter | | 2023 |
| Biophysically informed modeling for mapping the effects of genetic and environmental perturbation on cell states T Chari, G Gorin, L Pachter APS March Meeting Abstracts 2023, N00. 303, 2023 | | 2023 |
| Spectral neural approximations for models of transcriptional dynamics Supplementary Material G Gorin, M Carilli, T Chari, L Pachter | | 2022 |
| The Split Senate T Chari, L Pachter | | 2021 |
| Betamethasone Phosphate Drug Delivery by Biodegradable Ocular Implant T Chari, C Li, R Varghese, Q Yang | | 2017 |
