Selected publications

Full list of publications and preprints

  1. Lu C*, Garipler G*, Dai C*, Roush T, Salome-Correa J, Martin A, Liscovitch-Brauer N, Mazzoni EO#, Sanjana NE#. Nature Communications (2023).
  2. Morris JA, Sun JS, Sanjana NE. Trends in Genetics (2023).
  3. Ferrarone J, Thomas J, Unni A, Zheng Y, Nagiec M, Gardner E, Mashadova O, Li K, Koundouros N, Montalbano A, Mustafa M, Cantley L, Blenis J, Sanjana N, Varmus H. bioRxiv preprint (2023).
  4. 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).
  5. Schertzer MD, Stirn A, Isaev K, Pereira L, Das A, Harbison C, Park SH, Wessels H, Sanjana NE, Knowles DA. bioRxiv preprint (2023).
  6. IGVF Consortium, Morris JA, Caragine C, Sanjana NE. arXiv preprint (2023).
  7. Wessels H*, Stirn A*, Méndez-Mancilla A, Kim EJ, Hart SK, Knowles DA#, Sanjana NE#. Nature Biotechnology (2023).
  8. 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
  9. Wei W, Geer MJ, Guo X, Dolgalev I, Sanjana NE, Neel BG. Journal of Experimental Medicine (2023).
    bioRxiv preprint
  10. Stirn A, Wessels H, Schertzer M, Pereira L, Sanjana NE, Knowles DA. AISTATS (2023).
    arXiv preprint
  11. 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
  12. 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
  13. 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
  14. Gajic Z, Deshpande A, Legut M, Imieliński M#, Sanjana NE#. Nature Communications (2022).
    Gitlab repo
  15. 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).
  16. 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
  17. Katti A*, Diaz BJ*, Caragine CM*, Sanjana NE#, Dow LE#. Nature Reviews Cancer (2022).
  18. 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
  19. McCord RP, Taipale M, Teichmann S, Vorhees R, Wan Y, Dekker C, Sanjana NE. Molecular Cell (2022).
  20. Morris JA*, Rahman JA*, Guo X, Sanjana NE. iScience (2021).
    bioRxiv preprint
  21. Guo X, Rahman JA, Wessels H, Méndez-Mancilla A, Haro D, Chen X, Sanjana NE. Cell Genomics (2021).
    bioRxiv preprint
  22. Kasela S, Daniloski Z, Bollepalli S, Jordan TX, tenOever B, Sanjana NE, Lappalainen T. Genome Biology (2021).
    medRxiv preprint
  23. Sanjana NE. Nature Reviews Molecular Cell Biology (2021).
  24. 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
  25. Zaaijer S*, Groen SC*, Sanjana NE. Nature Biotechnology (2021).
  26. 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
  27. 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
  28. Daniloski Z*, Jordan TX*, Ilmain JK, Guo X, Bhabha G, tenOever BR#, Sanjana NE#. eLife (2021).
    bioRxiv preprint
  29. 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).
  30. Rasmussen AW, Äijö T, Gabitto MI, Carriero N, Sanjana NE, Skok J, and Bonneau R. bioRxiv preprint (2020).
  31. 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).
  32. Wessels H*, Méndez-Mancilla A*, Guo X, Legut M, Daniloski Z, Sanjana NE. Nature Biotechnology (2020).
    Journal cover | bioRxiv preprint
  33. Legut M*, Daniloski Z*, Xue X, McKenzie D, Guo X, Wessels H, Sanjana NE. Cell Reports (2020).
    Journal cover | bioRxiv preprint
  34. Lu C, Sanjana NE. Stem Cell Research (2019).
  35. Legut M, Sanjana NE. Nature Biomedical Engineering (2019).
  36. 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).
  37. 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
  38. Lu C*, Shi X*, Allen A*, Baez-Nieto D*, Nikish A, Sanjana NE, Pan JQ. FASEB Journal (2019).
  39. Sanjana NE. Science Translational Medicine (2018).
    Journal cover
  40. 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).
  41. Sadhwani A*, Sanjana NE*, Willen JM*, Calculator SN, Black ED, Bean LJH, Li H, Tan WH. American Journal of Medical Genetics (2018).
  42. 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
  43. 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).
  44. Guo X, Chitale P, Sanjana NE. Advances in Experimental Medicine and Biology (2017).
  45. Montalbano A*, Canver MC*, Sanjana NE. Molecular Cell (2017).
  46. Meier JA, Zhang F, Sanjana NE. Nature Methods (2017).
    GUIDES website | Github repo | bioRxiv preprint
  47. 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).
  48. 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).
  49. Sanjana NE. Analytical Biochemistry (2017).
  50. Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F. Nature Protocols (2017).
    bioRxiv preprint
  51. 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).
  52. Sanjana NE. Genomes Editing in the Neurosciences (2017).
  53. 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).
  54. Sanjana NE*#, Wright JB*, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F#. Science (2016).
    bioRxiv preprint
  55. Wright JB, Sanjana NE. Trends in Genetics (2016).
  56. Honegger T, Thielen MI, Feizi S, Sanjana NE, Voldman J. Scientific Reports (2016).
  57. 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).
  58. 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).
  59. 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).
  60. 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).
  61. 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).
  62. Shalem O, Sanjana NE, Zhang F. Nature Reviews Genetics (2015).
    Journal cover
  63. 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).
  64. 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).
  65. Sanjana NE*, Shalem O*, Zhang F. Nature Methods (2014).
    Companion web site | bioRxiv preprint
  66. 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).
  67. 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
  68. Sanjana NE, Levanon EY, Hueske EA, Ambrose JM, Li JB. GENETICS 192, 281-7 (2012).
    Journal cover
  69. Sanjana NE*, Cong L*, Zhou Y*, Cunniff MM, Feng G, Zhang F. Nature Protocols 7, 171-192 (2012).
    companion web site
  70. Scott BB, Sanjana NE. Journal of Neuroscience 29, 7114-7115 (2009).
  71. Sanjana NE*, Fuller SB*. Journal of Neuroscience Methods 136, 151-163 (2004).
    companion web site
    Press coverage: MIT News Office
  72. Sanjana NE, Tenenbaum JB , Advances in Neural Information Processing Systems 15, 51-58 (2003).
* = co-first author