Publications
2024
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Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells
Liang WW, Müller S, Hart SK, Wessels HH, Méndez-Mancilla A, Sookdeo A, Choi O, Caragine CM, Corman A, Lu L, Kolumba O, Williams B, Sanjana NE. Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells. Cell. 2024 Nov.
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Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution
Schiffman JS, D'Avino AR, Prieto T, Pang Y, Fan Y, Rajagopalan S, Potenski C, Hara T, Suvà ML, Gawad C, Landau DA. Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution. Nat Genet. 2024 Oct.
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Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment
Widman AJ, Shah M, Frydendahl A, Halmos D, Khamnei CC, Øgaard N, Rajagopalan S, Arora A, Deshpande A, Hooper WF, Quentin J, Bass J, Zhang M, Langanay T, Andersen L, Steinsnyder Z, Liao W, Rasmussen MH, Henriksen TV, Jensen SØ, Nors J, Therkildsen C, Sotelo J, Brand R, Schiffman JS, Shah RH, Cheng AP, Maher C, Spain L, Krause K, Frederick DT, den Brok W, Lohrisch C, Shenkier T, Simmons C, Villa D, Mungall AJ, Moore R, Zaikova E, Cerda V, Kong E, Lai D, Malbari MS, Marton M, Manaa D, Winterkorn L, Gelmon K, Callahan MK, Boland G, Potenski C, Wolchok JD, Saxena A, Turajlic S, Imielinski M, Berger MF, Aparicio S, Altorki NK, Postow MA, Robine N, Andersen CL, Landau DA. Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment. Nat Med. 2024 Jun.
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Disentangling oncogenic amplicons in esophageal adenocarcinoma
Ng AWT, McClurg DP, Wesley B, Zamani SA, Black E, Miremadi A, Giger O, Hoopen RT, Devonshire G, Redmond AM, Grehan N, Jammula S, Blasko A, Li X, Aparicio S, Tavaré S; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium; Nowicki-Osuch K, Fitzgerald RC. Disentangling oncogenic amplicons in esophageal adenocarcinoma. Nat Commun. 2024 May.
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Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts (preprint)
Yuan, D. J., Zinno, J., Botella, T., Dhingra, D., Wang, S., Hawkins, A., Swett, A., Sotelo, J., Raviram, R., Hughes, C., Potenski, C., Yokoyama, A., Kakiuchi, N., Ogawa, S., & Landau, D. A. (2024). Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts. bioRxiv [Preprint]. 2024 May.
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Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms
Dunbar AJ, Bowman RL, Park YC, O'Connor K, Izzo F, Myers RM, Karzai A, Zaroogian Z, Kim WJ, Fernández-Maestre I, Waarts MR, Nazir A, Xiao W, Codilupi T, Brodsky M, Farina M, Cai L, Cai SF, Wang B, An W, Yang JL, Mowla S, Eisman SE, Hanasoge Somasundara AV, Glass JL, Mishra T, Houston R, Guzzardi E, Martinez Benitez AR, Viny AD, Koche RP, Meyer SC, Landau DA, Levine RL. Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms. Cancer Discov. 2024 May.
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Low copy CRISPR-Cas13d mitigates collateral RNA cleavage
Hart, S. K., Wessels, H.-H., Méndez-Mancilla, A., Müller, S., Drabavicius, G., Choi, O., & Sanjana, N. E. (2024). Low copy CRISPR-Cas13d mitigates collateral RNA cleavage. 2024 May.
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Mapping genotypes to chromatin accessibility profiles in single cells
Izzo F, Myers RM, Ganesan S, Mekerishvili L, Kottapalli S, Prieto T, Eton EO, Botella T, Dunbar AJ, Bowman RL, Sotelo J, Potenski C, Mimitou EP, Stahl M, El Ghaity-Beckley S, Arandela J, Raviram R, Choi DC, Hoffman R, Chaligné R, Abdel-Wahab O, Smibert P, Ghobrial IM, Scandura JM, Marcellino B, Levine RL, Landau DA. Mapping genotypes to chromatin accessibility profiles in single cells. Nature. 2024 May.
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Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome (preprint)
Ganesan, S., Murray, R. M., Sotelo, J., Eton, E. O., Takashima, K., Botella, T., Beattie, K., Indart, A. C., Chraiki, N., Croizier, C., Izzo, F., Potenski, C., Marro, S., Wu, Z., Gao, S., Young, N. S., Blair, J. D., Satija, R., Terrier, B., … Landau, D. A. (2024). Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome. bioRxiv [Preprint]. 2024 May.
2023
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Essential transcription factors for induced neuron differentiation
Lu C, Garipler G, Dai C, Roush T, Salome-Correa J, Martin A, Liscovitch-Brauer N, Mazzoni EO, Sanjana NE. Essential transcription factors for induced neuron differentiation. Nat Commun. 2023 Dec.
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DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data (preprint)
Park C, Mani S, Beltran-Velez N, Maurer K, Gohil S, Li S, Huang T, Knowles DA, Wu CJ, Azizi E. DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. bioRxiv [Preprint]. 2023 Nov.
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Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox (preprint)
Schertzer MD, Stirn A, Isaev K, Pereira L, Das A, Harbison C, Park SH, Wessels HH, Sanjana NE, Knowles DA. Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. bioRxiv [Preprint]. 2023 Sep.
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Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens
Morris JA, Caragine C, Daniloski Z, Domingo J, Barry T, Lu L, Davis K, Ziosi M, Glinos DA, Hao S, Mimitou EP, Smibert P, Roeder K, Katsevich E, Lappalainen T, Sanjana NE. Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens. Science. 2023 May.