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74 Articles

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Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization
Berackey, B. T., Tan, Z., Wu, G., Das, S. C., Li, R., Esser, B., Ye, Q., Nafisi, M., Park, S. S., Sequeira Mendieta, P. A., Berry, J., Mamdani, F., Zhu, Q., Holmes, T. C., Li, D., Wang, T., Behrens, M. M., Ren, B., Ecker, J. R., Bintu, B., Xu, X.
10.64898/2025.12.02.691876 — Posted: 2025-12-05
multiVIB: A unified probabilistic contrastive learning framework for atlas-scale integration of single-cell multi-omics data
Xu, Y., Fleming, S. J., Wang, B., Schoenbeck, E. G., Babadi, M., Huo, B.-X.
10.1101/2025.11.29.691308 — Posted: 2025-12-01
Fast Optimization of Robust Transcriptomics Embeddings using Probabilistic Inference Autoencoder Networks for multi-Omics
Wang, N., Turner, D., Feinberg, H., Nieto Caballero, V. E., Yuan, D., Scott, N., Cardenas, C., DeBerardine, M., Dan, S., Caceres, L., Schembri, J., Yao, Z., Lee, C., Pillow, J. W., Krienen, F. M.
10.1101/2025.11.16.686778 — Posted: 2025-11-27
A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia
Hewitt, M. N., Turner, M. A., Johansen, N., McMillen, D. A., Dan, S., DeBerardine, M., Ruiz, A., Huang, M., Quon, J., Fu, Y., Kapen, I., Barta, S., Martin, N., Cuevas, N. V., Olsen, P., Nagra, J., Campos, J., VanNess, M. M., Ransford, S., Juneau, Z., Hastings, S., Ching, L., Kunst, M., Basu, S., Hollt, T., Li, C., Lelieveldt, B., Yazdani, F., Zhang, Q., Levandowski, K., Feng, G., Rosen, B., Glasser, M. F., Hayashi, T., Garcia, A. D., Kana, O., Maltzer, Z. M., Campagnola, L., Jarsky, T., Kruse, L., Freiwald, W., Keene, C. D., Van Essen, D. C., Ariza, J., Waters, J., Krienen, F. M., Bakken, T. E
10.1101/2025.11.22.688128 — Posted: 2025-11-24
Spatial patterning of transcriptional and regulatory programs in the primate subcortex
Dan, S., Turner, M. A., DeBerardine, M., Caceres, L., Nieto, V. E., Schembri, J., Levandowski, K., Cardenas, C., Wang, N., Li, C., Basu, S., Zheng, H., Liu, X., Hollt, T., Feliciano, J., Zhang, Q., Nakamoto, R., McMillen, D. A., Martin, N., Cuevas, N. V., Olsen, P., Nagra, J., Campos, J., VanNess, M. M., Waters, J., Ransford, S., Juneau, Z., Hastings, S., Barta, S., Ruiz, A., Ariza, J., Raphael, B. J., Zeng, H., Lein, E. S., Lelieveldt, B., Feng, G., Long, B., Krienen, F. M.
10.1101/2025.11.22.689869 — Posted: 2025-11-24
Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism
Yuan, G., Suresh, V., Wigdor, E., Hao, Y., Leonard, R., Steyert, M., Griffiths, M., Evans, C., Rohani, N., Weiss, J., Lassen, F. H., Schafer, N., Dong, S., Palmer, D. S., Sanders, S. J., Nowakowski, T. J.
10.1101/2025.11.05.686845 — Posted: 2025-11-07
A three-dimensional histological cell atlas of the developing human brain
Jayakumar, J., Sivaprakasam, M., Verma, R., Bota, M., Joseph, J., Mulay, S., Kumutha, J., Srinivasan, C., S, S., S, L., Kumar, H. E., Bhaduri, A., Nowakowski, T. J., Roy, P. K., Savoia, S., Banerjee, S., Tward, D., Mitra, P. P.
10.1101/2024.12.17.628811 — Posted: 2024-12-18
Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development
Gao, Y., van Velthoven, C. T. J., Lee, C., Thomas, E. D., Bertagnolli, D., Carey, D., Casper, T., Chakka, A. B., Chakrabarty, R., Clark, M., Desierto, M. J., Ferrer, R., Gloe, J., Goldy, J., Guilford, N., Guzman, J., Halterman, C. R., Hirschstein, D., Ho, W., James, K., McCue, R., Meyerdierks, E., Nguy, B., Pena, N., Pham, T., Shapovalova, N. V., Sulc, J., Torkelson, A., Tran, A., Tung, H., Wang, J., Ronellenfitch, K., Levi, B., Hawrylycz, M. J., Pagan, C., Dee, N., Smith, K. A., Tasic, B., Yao, Z., Zeng, H.
10.1101/2024.10.02.616246 — Posted: 2024-10-06
A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development
Sonthalia, S., Li, G., Blanco, X. M., Casella, A., Liu, J., Stein-O'Brien, G., Caffo, B., Adkins, S., Orvis, J., Hertzano, R., Mahurkar, A., Gillis, J. A., Werner, J., Ma, S., Micali, N., Sestan, N., Rakic, P., Baro, G. S., Ament, S. A., Colantuoni, C.
10.1101/2024.02.26.581612 — Posted: 2024-08-07
Molecular and cellular dynamics of the developing human neocortex at single-cell resolution
Wang, L., Wang, C., Moriano, J. A., Chen, S., Zuo, G., Cebrian-Silla, A., Zhang, S., Mukhtar, T., Wang, S., Song, M., de Oliveira, L. G., Bi, Q., Augustin, J. J., Ge, X., Paredes, M. F., Huang, E. J., Alvarez-Buylla, A., Duan, X., Li, J., Kriegstein, A. R.
10.1101/2024.01.16.575956 — Posted: 2024-08-04

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