Biancalani, Tommaso

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

Biancalani, T., Scalia, G., Buffoni, L., Avasthi, R., Lu, Z., Sanger, A., Tokcan, N., Vanderburg, C. R., Segerstolpe, Å., Zhang, M., et al. (2021) · Nature Methods

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 931

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

HuBMAP Consortium, Writing Group, Snyder, M. P., Lin, S., Posgai, A., Atkinson, M., Regev, A., Rood, J., Rozenblatt-Rosen, O., Gaffney, L., et al. (2019) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 595

A multimodal cell census and atlas of the mammalian primary motor cortex

BRAIN Initiative Cell Census Network (BICCN), BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, Callaway, E. M., Dong, H.-W., Ecker, J. R., Hawrylycz, M. J., Huang, Z. J., Lein, E. S., Ngai, J., Osten, P., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 522

Molecular logic of cellular diversification in the mouse cerebral cortex

Di Bella, D. J., Habibi, E., Stickels, R. R., Scalia, G., Brown, J., Yadollahpour, P., Yang, S. M., Abbate, C., Biancalani, T., Macosko, E. Z., et al. (2021) · Nature

Single-cell and spatial transcriptomicsNeurogenesis and neuroplasticity mechanisms

Cited by 464

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 398

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Yao, Z., Liu, H., Xie, F., Fischer, S., Booeshaghi, A. S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Pinto-Duarte, A., Bartlett, A., et al. (2020) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 397

Escapement mechanisms and the conversion of disequilibria; the engines of creation

Branscomb, E., Biancalani, T., Goldenfeld, N., & Russell, M. (2017) · Physics Reports

Advanced Thermodynamics and Statistical MechanicsOrigins and Evolution of Life

Cited by 96

Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA

Kobayashi-Kirschvink, K. J., Comiter, C. S., Gaddam, S., Joren, T., Grody, E. I., Ounadjela, J. R., Zhang, K., Ge, B., Kang, J. W., Xavier, R. J., et al. (2024) · Nature Biotechnology

Spectroscopy Techniques in Biomedical and Chemical ResearchSingle-cell and spatial transcriptomics

Cited by 93

Noise-Induced Mechanism for Biological Homochirality of Early Life Self-Replicators

Jafarpour, F., Biancalani, T., & Goldenfeld, N. (2015) · Physical Review Letters

Origins and Evolution of LifeEvolution and Genetic Dynamics

Cited by 86

Noise-induced symmetry breaking far from equilibrium and the emergence of biological homochirality

Jafarpour, F., Biancalani, T., & Goldenfeld, N. (2017) · Physical Review E

Origins and Evolution of Lifestochastic dynamics and bifurcation

Cited by 50

Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages

Heimberg, G., Kuo, T., DePianto, D., Heigl, T., Diamant, N., Salem, O., Scalia, G., Biancalani, T., Turley, S., Rock, J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 40

regLM: Designing realistic regulatory DNA with autoregressive language models

Lal, A., Garfield, D., Biancalani, T., & Eraslan, G. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 6