Selected publications

Full list of publications and preprints

  1. Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells
    Liang W*, Muller S*, Hart SK, Wessels H, Mendez-Mancilla A, Sookdeo A, Choi O, Caragine CM, Corman A, Lu L, Kolumba O, Williams B, Sanjana NE. Cell (2024).
  2. Deciphering the impact of genomic variation on function
    IGVF Consortium (including Morris JA, Caragine C, Sanjana NE). Nature (2024).
  3. Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes
    Megagiannis P*, Mei Y*, Yan RE, Yuan L, Wilde JJ, Eckersberg H, Suresh R, Tan X, Chen H, Farmer WT, Cha K, Le PU, Catoire H, Rochefort D, Kwan T, Yee BA, Dion P, Krishnaswamy A, Cloutier JF, Stifani S, Petrecca K, Yeo GW, Murai KK, Feng G, Rouleau GA, Ideker T#, Sanjana NE, Zhou Y#. Cell Reports (2024).
  4. Low copy CRISPR-Cas13d mitigates collateral RNA cleavage
    Hart SK, Wessels H, Mendez-Mancilla A, Muller S, Drabavicius G, Choi O, Sanjana NE. bioRxiv preprint (2024).
  5. Genome-wide CRISPR screens in spheroid culture reveal that the tumor suppressor LKB1 inhibits growth via the PIKFYVE lipid kinase
    Ferrarone J, Thomas J, Unni AM, Zheng Y, Nagiec MJ, Gardner E, Mashadova O, Li K, Koundouros N, Montalbano A, Mustafa M, Cantley LC, Blenis J, Sanjana NE, Varmus H. PNAS (2024).
    bioRxiv preprint
  6. Enhancer-targeted CRISPR-activation rescues haploinsufficient autism susceptibility genes
    Chen GT, Nair G, Osorio AJ, Holley SM, Ghassemzadeh K, Gonzalez JG, Lu C, Sanjana NE, Cepeda C, Geschwind D. bioRxiv preprint (2024).
  7. Non-linear transcriptional responses to gradual modulation of transcription factor dosage
    Domingo J, Minaeva M, Morris JA, Ziosi M, Sanjana NE, Lappalainen T. bioRxiv preprint (2024).
  8. 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 (2023).
    Press coverage: Top 25 most read Health Sci articles in 2023
  9. Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis
    Morris JA, Sun JS, Sanjana NE. Trends in Genetics (2023).
  10. Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction
    Shi X*, Lu C*, Corman A*, Nikish A, Zhou Y, Platt RJ, Iossifov I, Zhang F, Pan JQ#, Sanjana NE#. American Journal of Human Genetics (2023).
  11. 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 H, Sanjana NE, Knowles DA. bioRxiv preprint (2023).
  12. The Impact of Genomic Variation on Function (IGVF) Consortium
    IGVF Consortium, Morris JA, Caragine C, Sanjana NE. arXiv preprint (2023).
  13. Prediction of on-target and off-target activity of CRISPR–Cas13d guide RNAs using deep learning
    Wessels H*, Stirn A*, Méndez-Mancilla A, Kim EJ, Hart SK, Knowles DA#, Sanjana NE#. Nature Biotechnology (2023).
  14. 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 (2023).
    bioRxiv preprint
    Press coverage: Nature Genetics, Nature Reviews Genetics, National Science Foundation, Drug Target Review
  15. Genome-wide CRISPR/Cas9 screens reveal shared and cell-specific mechanisms of resistance to SHP2 inhibition
    Wei W, Geer MJ, Guo X, Dolgalev I, Sanjana NE, Neel BG. Journal of Experimental Medicine (2023).
    bioRxiv preprint
  16. Faithful heteroscedastic regression with neural networks
    Stirn A, Wessels H, Schertzer M, Pereira L, Sanjana NE, Knowles DA. AISTATS (2023).
    arXiv preprint
  17. Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq
    Wessels H*, Mendez-Mancilla A*, Hao Y, Papalexi E, Mauck WM, Lu L, Morris JA, Mimitou EP, Smibert P, Sanjana NE#, Satija R#. Nature Methods (2022).
    bioRxiv preprint
  18. Expanding the scope of bacterial CRISPR activation with PAM-flexible dCas9 variants
    Kiattisewee C*, Karanjia AV*, Legut M, Daniloski Z, Koplik SE, Nelson J, Kleinstiver BP, Sanjana NE, Carothers JM#, Zalatan JG#. ACS Synthetic Biology (2022).
    bioRxiv preprint
  19. Cancer genes disfavoring T cell immunity identified via integrated systems approach
    Kishton RJ*, Patel SJ*, Decker AK, Vodnala SK, Cam M, Yamamoto TN, Patel Y, Sukumar M, Yu Z, Ji M, Henning AN, Gurusamy D, Palmer DC, Stefanescu RA, Girvin AT, Lo W, Pasetto A, Malekzadeh P, Deniger DC, Wood KC, Sanjana NE, Restifo NP. Cell Reports (2022).
    bioRxiv preprint
  20. Recurrent somatic mutations as predictors of immunotherapy response
    Gajic Z, Deshpande A, Legut M, Imieliński M#, Sanjana NE#. Nature Communications (2022).
    Gitlab repo
  21. A genome-scale screen for synthetic drivers of T cell proliferation
    Legut M, Gajic Z, Guarino M, Daniloski Z, Rahman JA, Xue X, Lu C, Lu L, Mimitou EP, Hao S, Davoli T, Diefenbach C, Smibert P, Sanjana NE. Nature (2022).
    Press coverage: New England Journal of Medicine, Nature Reviews Cancer
  22. The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes
    Garipler G*, Lu C*, Morrissey A, Lopez-Zepeda LS, Pei Y, Vidal SE, Petisco Fiore APZ, Aydin B, Stadtfeld M, Ohler U, Mahony S, Sanjana NE#, Mazzoni EO#. Cell Reports (2022).
    bioRxiv preprint
  23. CRISPR in cancer biology and therapy
    Katti A*, Diaz BJ*, Caragine CM*, Sanjana NE#, Dow LE#. Nature Reviews Cancer (2022).
  24. Autism genes converge on asynchronous development of shared neuron classes
    Paulsen B*, Velasco S*, Kedaigle AJ*, Pigoni M*, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, Abbate C, Tucewicz A, Smith SN, Albanese A, Barrett L, Sanjana NE, Shi X, Chung K, Lage K, Boyden ES, Regev A, Levin JZ, Arlotta P. Nature (2022).
    bioRxiv preprint
  25. The molecular biologists’ ever-expanding toy box
    McCord RP, Taipale M, Teichmann S, Vorhees R, Wan Y, Dekker C, Sanjana NE. Molecular Cell (2022).
  26. Automated design of CRISPR prime editors for 56,000 human pathogenic variants
    Morris JA*, Rahman JA*, Guo X, Sanjana NE. iScience (2021).
    bioRxiv preprint
  27. Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens
    Guo X, Rahman JA, Wessels H, Méndez-Mancilla A, Haro D, Chen X, Sanjana NE. Cell Genomics (2021).
    bioRxiv preprint
  28. Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus
    Kasela S, Daniloski Z, Bollepalli S, Jordan TX, tenOever B, Sanjana NE, Lappalainen T. Genome Biology (2021).
    medRxiv preprint
  29. Open science is good for science (and for you)
    Sanjana NE. Nature Reviews Molecular Cell Biology (2021).
  30. Chemically modified guide RNAs enhance CRISPR-Cas13 knockdown in human cells
    Méndez-Mancilla A*, Wessels H*, Legut M, Kadina A, Mabuchi M, Walker J, Robb GB, Holden K, Sanjana NE. Cell Chemical Biology (2022).
    bioRxiv preprint
  31. Tracking cell lineages to improve research reproducibility
    Zaaijer S*, Groen SC*, Sanjana NE. Nature Biotechnology (2021).
  32. Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens
    Liscovitch-Brauer N*, Montalbano A*, Deng J, Méndez-Mancilla A, Wessels H, Moss NG, Kung C, Sookdeo A, Guo X, Geller E, Jaini S, Smibert P, Sanjana NE. Nature Biotechnology (2021).
    bioRxiv preprint
  33. Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
    Sorek M, Oweis W, Nissim-Rafinia M, Maman M, Simon S, Hession CC, Adiconis X, Simmons SK, Sanjana NE, Shi X, Lu C, Pan JQ, Xu X, Pouladi ML, Ellerby LM, Zhang F, Levin JZ, Meshorer E. Genome Biology (2021).
    bioRxiv preprint
  34. The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types
    Daniloski Z*, Jordan TX*, Ilmain JK, Guo X, Bhabha G, tenOever BR#, Sanjana NE#. eLife (2021).
    bioRxiv preprint
  35. Identification of required host factors for SARS-CoV-2 infection in human cells
    Daniloski Z*, Jordan TX*, Wessels HH, Hoagland DA, Kasela S, Legut M, Maniatis S, Mimitou EP, Lu L, Geller E, Danziger O, Rosenberg BR, Phatnani H, Smibert P, Lappalainen T, tenOever BR#, Sanjana NE#. Cell (2021).
    Press coverage: Nature Reviews Genetics, Nature Reviews Molecular Cell Biology, Trends in Genetics, CNBC, GenomeWeb, ScienceDaily, Cell
  36. CRISPR-Decryptr reveals cis-regulatory elements from noncoding perturbation screens
    Rasmussen AW, Äijö T, Gabitto MI, Carriero N, Sanjana NE, Skok J, and Bonneau R. bioRxiv preprint (2020).
  37. Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy
    Lek A, Zhang Y, Woodman KG, Huang S, DeSimone AM, Cohen J, Ho V, Conner J, Mead L, Kodani A, Pakula A, Sanjana NE, King OD, Jones PL, Wagner KR, Lek M, Kunkel LM. Science Translational Medicine (2020).
  38. Massively parallel Cas13 screens reveal principles for guide RNA design
    Wessels H*, Méndez-Mancilla A*, Guo X, Legut M, Daniloski Z, Sanjana NE. Nature Biotechnology (2020).
    Journal cover | bioRxiv preprint
  39. High-throughput screens of PAM-flexible Cas9 variants for gene knock-out and transcriptional modulation
    Legut M*, Daniloski Z*, Xue X, McKenzie D, Guo X, Wessels H, Sanjana NE. Cell Reports (2020).
    Journal cover | bioRxiv preprint
  40. Generation of a knock-in MAP2-tdTomato reporter human embryonic stem cell line with inducible expression of NEUROG2/1
    Lu C, Sanjana NE. Stem Cell Research (2019).
  41. Immunomagnetic cell sorting
    Legut M, Sanjana NE. Nature Biomedical Engineering (2019).
  42. Identification of cancer drivers at CTCF insulators in 1,962 whole genomes
    Liu C*, Martinez-Fundichely A*, Diaz B*, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E, Sanjana NE, Khurana E. Cell Systems (2019).
  43. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
    Mimitou E, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, Satija R, Sanjana NE, Koralov S, Smibert P. Nature Methods (2019).
    bioRxiv preprint
  44. Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons
    Lu C*, Shi X*, Allen A*, Baez-Nieto D*, Nikish A, Sanjana NE, Pan JQ. FASEB Journal (2019).
  45. A genome-wide net to catch and understand cancer
    Sanjana NE. Science Translational Medicine (2018).
    Journal cover
  46. GFAP mutations in astrocytes impair oligodendrocyte progenitor proliferation and myelination in an hiPSC model of Alexander disease
    Li L, Tian E, Chen X, Chao J, Klein J, Qu Q, Sun G, Sun G, Huang Y, Warden CD, Ye P, Feng L, Li X, Cui Q, Sultan A, Douvaras P, Fossati V, Sanjana NE, Riggs AD, Shi Y. Cell Stem Cell (2018).
  47. Two Angelman families with unusually advanced neurodevelopment carry a start codon variant in the most highly expressed UBE3A isoform
    Sadhwani A*, Sanjana NE*, Willen JM*, Calculator SN, Black ED, Bean LJH, Li H, Tan WH. American Journal of Medical Genetics (2018).
  48. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments
    Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan G, Zhang F, Concordet J, Pinello L. Nature Protocols (2018).
    bioRxiv preprint
  49. Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons
    Tekin H, Simmons S, Cummings B, Gao L, Adiconis X, Hession CC, Ghoshal A, Dionne D, Choudhury SR, Yesilyurt V, Sanjana NE, Shi X, Lu C, Heidenreich M, Pan JQ, Levin JZ, Zhang F. Nature Biomedical Engineering (2018).
  50. Target discovery for precision medicine using high-throughput genome engineering
    Guo X, Chitale P, Sanjana NE. Advances in Experimental Medicine and Biology (2017).
  51. High-throughput approaches to pinpoint function within the noncoding genome
    Montalbano A*, Canver MC*, Sanjana NE. Molecular Cell (2017).
  52. GUIDES: sgRNA design for loss-of-function screens
    Meier JA, Zhang F, Sanjana NE. Nature Methods (2017).
    GUIDES website | Github repo | bioRxiv preprint
  53. Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood
    Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, Zhang F. Nature (2017).
  54. Identification of essential genes for cancer immunotherapy
    Patel S*#, Sanjana NE*#, Kishton R, Eidizadeh A, Vodnala SK, Cam M, Gartner JJ, Jia L, Steinberg SM, Yamamoto TN, Merchant AS, Mehta GU, Chichura A, Shalem O, Tran E, Eil R, Sukumar M, Guijarro EP, Day C, Robbins P, Feldman S, Merlino G, Zhang F, Restifo NP#. Nature (2017).
  55. Genome-scale CRISPR screens
    Sanjana NE. Analytical Biochemistry (2017).
  56. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening
    Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F. Nature Protocols (2017).
    bioRxiv preprint
  57. Transcription control by the ENL YEATS domain in acute leukaemia
    Erb MA, Scott TG, Li BE, Xie H, Paulk J, Seo HS, Souza A, Roberts JM, Dastjerdi S, Buckley DL, Sanjana NE, Shalem O, Nabeet B, Zeid R, Offei-Addo NK, Dhe-Paganon S, Zhang F, Orkin SH, Winter GE, Bradner JE. Nature (2017).
  58. Multiscale genome engineering: Genome-wide screens and targeted approaches
    Sanjana NE. Genomes Editing in the Neurosciences (2017).
  59. Genome-scale networks link neurodegenerative disease genes to α-synuclein through specific molecular pathways
    Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis B, Schondorf DC, Barrasa I, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S. Cell Systems (2017).
  60. High-resolution interrogation of functional elements in the noncoding genome
    Sanjana NE*#, Wright JB*, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F#. Science (2016).
    bioRxiv preprint
  61. CRISPR screens to discover functional noncoding elements
    Wright JB, Sanjana NE. Trends in Genetics (2016).
  62. Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks
    Honegger T, Thielen MI, Feizi S, Sanjana NE, Voldman J. Scientific Reports (2016).
  63. The Genome Project-Write
    Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. Science (2016).
  64. Hypoxia as a therapy for mitochondrial disease
    Jain IH, Zazzeron L, Goli R, Alexa K, Schatzman-Bone S, Dhillon H, Goldberger O, Peng J, Shalem O, Sanjana NE, Zhang F, Goesslin W, Zapol W, Mootha VK. Science (2016).
  65. Mice with Shank3 mutations associated with ASD and schizophrenia display both shared and distinct defects
    Zhou Y, Kaiser T, Monteiro P, Zhang X, Van der Goes MS, Wang D, Barak B, Zeng M, Li C, Lu C, Wells M, Amaya A, Nguyen S, Lewis N, Sanjana NE, Zhou Y, Zhang M, Zhang F, Fu Z, Feng G. Neuron (2016).
  66. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis
    Canver MC*, Smith EC*, Sher F*, Pinello L*, Sanjana NE*, Shalem S, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan G, Zhang F, Orkin SH & Bauer DE. Nature (2015).
  67. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks
    Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A. Cell (2015).
  68. High-throughput functional genomics using CRISPR/Cas9,
    Shalem O, Sanjana NE, Zhang F. Nature Reviews Genetics (2015).
    Journal cover
  69. A genome-wide CRISPR screen in a mouse model of tumor growth and metastasis,
    Chen S*, Sanjana NE*, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp P. Cell (2015).
    Press coverage: Science, Nature Genetics, Nature Reviews Genetics, Cancer Discovery, F1000 Prime, National Institutes of Health Research Matters newsletter, AAAS EurekAlert!, Science Daily, Lung Cancer News Today, GenomeWeb,BioOptics World, Broad Institute News Office, Cell Press.
  70. Rapid neurogenesis through transcriptional activation in human stem cells,
    Busskamp V*, Lewis NE*, Guye P*, Ng AHM, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Stadler M, Weiss R, Church GM. Molecular Systems Biology (2014).
  71. Improved lentiviral vectors and genome-wide libraries for CRISPR screening
    Sanjana NE*, Shalem O*, Zhang F. Nature Methods (2014).
    Companion web site | bioRxiv preprint
  72. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites
    Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A. Cell Reports (2014).
  73. Genome-scale CRISPR-Cas9 knockout screening in human cells
    Shalem O*, Sanjana NE*, Hartenian E, Shi X, Scott DA, Mikkelsen T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F. Science (2014).
    Companion web site
    Press coverage: Science, Nature, Nature Genetics, Nature Methods, Nature Biotechnology, MIT News Office, Broad Institute News Office, Genetic Engineering & Biotech News, The Scientist (1) (2), Bioscience Technology, Red Orbit, Que! (Spanish), Addgene
  74. Activity-dependent A-to-I RNA editing in rat cortical neurons
    Sanjana NE, Levanon EY, Hueske EA, Ambrose JM, Li JB. GENETICS 192, 281-7 (2012).
    Journal cover
  75. A transcription activator-like effector toolbox for genome engineering
    Sanjana NE*, Cong L*, Zhou Y*, Cunniff MM, Feng G, Zhang F. Nature Protocols 7, 171-192 (2012).
    companion web site
  76. The wanderlust of newborn neocortical interneurons
    Scott BB, Sanjana NE. Journal of Neuroscience 29, 7114-7115 (2009).
  77. A fast flexible ink-jet printing method for patterning dissociated neurons in culture
    Sanjana NE*, Fuller SB*. Journal of Neuroscience Methods 136, 151-163 (2004).
    companion web site
    Press coverage: MIT News Office
  78. Bayesian models of inductive generalization
    Sanjana NE, Tenenbaum JB , Advances in Neural Information Processing Systems 15, 51-58 (2003).
* = co-first author

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