Publications
2025
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pC-SAC: Method for High-Resolution 3D Genome Reconstruction from Low-Resolution Hi-C Data
J. Carlos Angel, Narjis El Amraoui, Gamze Gürsoy. Nucleic Acids Research [in press].
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Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability
Bai D, Cao Z, Attada N, Song J, Zhu C. Nature Methods.
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Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers
Caragine CM, Le VT, Mustafa M, Diaz BJ, Morris JA, Müller S, Mendez-Mancilla A, Geller E, Liscovitch-Brauer N, Sanjana NE. Nature Communications.
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Precise RNA targeting with CRISPR-Cas13d
Hart SK, Müller S, Wessels HH, Méndez-Mancilla A, Drabavicius G, Choi O, Sanjana NE. Nature Biotechnology.
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Single-cell mapping of regulatory DNA:Protein interactions
Chi WY, Yoon SH, Mekerishvili L, Ganesan S, Potenski C, Izzo F, Landau D, Raimondi I. bioRxiv [Preprint].
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. Cell.
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Paired CRISPR screens to map gene regulation in cis and trans
Xue X, Gajic ZZ, Caragine CM, Legut M, Walker C, Kim JYS, Wang X, Yan RE, Wessels HH, Lu C, Bapodra N, Gürsoy G, Sanjana NE. bioRxiv [Preprint].
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Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling
Yan RE, Corman A, Katgara L, Wang X, Xue X, Gajic ZZ, Sam R, Farid M, Friedman SM, Choo J, Raimondi I, Ganesan S, Katsevich E, Greenfield JP, Dahmane N, Sanjana NE. Nature Biotechnology.
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A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data
Park C, Mani S, Beltran-Velez N, Maurer K, Huang T, Li S, Gohil S, Livak KJ, Knowles DA, Wu CJ, Azizi E. Genome Research.
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Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome
Ganesan S, Murray RM, Sotelo J, Eton EO, Takashima K, Botella T, Beattie K, Indart AC, Chraiki N, Croizier C, Izzo F, Potenski C, Marro S, Wu Z, Gao S, Young NS, Blair JD, Satija R, Terrier B, Heiblig M, Papapetrou EP, Sujobert P, Kosmider O, Beck DB, Landau DA. bioRxiv [Preprint].
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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. Nature Genetics.
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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. Nature Medicine.
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Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts
Yuan DJ, 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 DA. bioRxiv [Preprint].
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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. Nature Communications.
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Low copy CRISPR-Cas13d mitigates collateral RNA cleavage
Hart SK, Wessels HH, Méndez-Mancilla A, Müller S, Drabavicius G, Choi O, Sanjana NE. bioRxiv [Preprint]
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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. Nature.
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Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis
Morris JA, Sun JS, Sanjana NE. Trends in Genetics [Review].
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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. Cancer Discovery.
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. Nature Communications.
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Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox
Schertzer MD, Stirn A, Isaev K, Pereira L, Das A, Harbison C, Park SH, Wessels HH, Sanjana NE, Knowles DA. bioRxiv [Preprint].
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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. Science.