Publications

SVG file icon

Barcoding Notch signaling in the developing brain
Siniscalco, A.M., Perera, R.P., Greenslade, J.M., Masters, A., Doll, H.M., Raj, B. (2024) biorxiv. Link

Tracing developmental lineages
Raj, B. (2023) Nature Methods. 20(12):1852-1854. Link

Prior to Raj lab at UPenn

Emergence of neuronal diversity during vertebrate brain development
Raj, B.
, Farrell, J.A., Liu, J., El Kholtei, J., Carte, A.N., Navajas Acedo, J., Du, L.Y., McKenna, A., Relić, Đ., Leslie, J.M., Schier, A.F. (2020) Neuron. 108(6):1058-1074
Learn More

Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT
Raj, B., Gagnon, J.A., Schier, A.F. (2018) Nature Protocols. 13(11):2685-2713
Learn More

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain
Raj, B., Wagner, D.E.*, McKenna, A.*, Pandey, S., Klein, A.M., Shendure, J., Gagnon, J.A., Schier, A.F. (2018) Nature Biotechnology. 36(5):442-50
Learn More

Featured as 2018 Breakthrough of the Year by Science
Named as 2018 Method to Watch by Nature Methods

Prior Research in Alternative Splicing

Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons
Gonatopoulos-Pournatzis, T., Wu, M., Braunschweig, U., Roth, J., Han, H., Best, A.J., Raj, B., Aregger, M., O'Hanlon, D., Ellis, J.D., Calarco, J.A., Moffat, J., Gingras, A.C., Blencowe, B.J. (2018) Molecular Cell. 72(3):510-524
Learn More

An alternative splicing event amplifies evolutionary differences between vertebrates
Gueroussov, S., Gonatopoulos-Pournatzis, T., Irimia, M., Raj, B., Yuan-Lin, Z., Gingras, A.-C., Blencowe, B.J. (2015) Science. 349(6250):868-73
Learn More

Alternative splicing in the mammalian nervous system: recent insights into mechanisms and functional roles
Raj, B. and Blencowe, B.J+. (2015) Neuron. 87(1):14-27
Learn More

A highly conserved program of neuronal microexons is misregulated in autistic brain
Irimia, M., Weatheritt, R.J.*, Ellis, J.*, Parikshak, N.N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O’Hanlon, D., Barrios-Rodiles, M., Wrana, J.L., Roth, F., Geschwind, D., Blencowe, B.J. (2014) Cell. 159(7): 1511-23
Learn More

Global regulatory mechanism underlying the activation of an exon network required for neurogenesis
Raj, B.
, Irimia, M., Braunschweig, U., Sterne-Weiler, T., O’Hanlon, D., Yuan-Lin, Z., Chen, G.I., Easton, L., Ule, J., Gingras, A.-C., Eyras, E. and Blencowe, B.J. (2014) Molecular Cell. 56(1): 90-103
Learn More

Cross-regulation between an alternative splicing regulator and a transcription repressor controls neurogenesis
Raj, B.
, O’Hanlon, D., Vessey, J.P., Pan, Q., Ray, D., Buckley, N.J., Miller, F.D., and Blencowe, B.J. (2011) Molecular Cell. 43(5): 843-50
Learn More

Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein
Calarco, J.A., Superina, S., O’Hanlon, D., Gabut, M., Raj, B., Pan, Q., Skalska, U., Clarke, L., Gelinas, D., van der Kooy, D., Zhen, M., Ciruna, B., and Blencowe, B.J. (2009) Cell. 138(5): 898-910
Learn More