Publications

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

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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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