Via Google Scholar
Research
*co-first, #co-corresponding
95. Sami Nourreddine*, Yesh Doctor*, Amir Dailamy, Antoine Forget, Yi-Hung Lee, Becky Chinn, Hammza Khaliq, Benjamin Polacco, Monita Murlidharan, Emily Pan, Yifan Zhang, Alina Sigaeva, Jan Niklas Hansen, Jiahao Gao, Jillian A. Parker, Kirsten Obernier, Timothy Clark, Jake Y. Chen, Christian Metallo, Emma Lundberg, Trey Ideker, Nevan Krogan, Prashant Mali, "A perturbation cell atlas of human induced pluripotent stem cells," bioRxiv (preprint).
94. Susan M. Byrne, Stephen M. Burleigh, Robert Fragoza, Yue Jiang, Yiannis Saava, Ricky Pabon, Joseph Rainaldi, Andrew Portell, Prashant Mali, Adrian Briggs, "A novel engineered U7 small nuclear RNA scaffold greatly increases in vitro and in vivo ADAR-mediated programmable RNA base editing," bioRxiv (preprint).
93. Andrew Portell*, Kyle Ford*, Amanda Suhardjo, Joseph Rainaldi, Mark N. Bublik, Milan Sanghvi, Aditya Kumar, Madeleine K. Wing, Nathan D. Palmer, Duy An Le, Nikitha Kalahasti, Amir Dailamy, Prashant Mali, "Reprogramming adeno-associated virus tropism via displayed peptides tiling receptor ligands," bioRxiv (preprint).
92. Amir Dailamy*, Weiqi Lyu*, Sami Nourreddine, Joseph Rainaldi, Daniella McDonald, Rebecca Panwala, Alysson Muotri, Michael S. Breen, Kun Zhang, Prashant Mali, "Charting and probing the activity of ADARs in human development and cell-fate specification," Nature Communications (2024).
91. Yesh Doctor*, Milan Sanghvi*, Prashant Mali, "A manual for genome and transcriptome engineering," IEEE Reviews in Biomedical Engineering (2024).
90. Michael Tong, Nathan Palmer, Amir Dailamy, Aditya Kumar, Hammza Khaliq, Sangwoo Han, Emma Finburgh, Madeleine Wing, Camilla Hong, Yichen Xiang, Katelyn Miyasaki, Andrew Portell, Joseph Rainaldi, Amanda Suhardjo, Sami Nourreddine, Wei Leong Chew, Ester J. Kwon, Prashant Mali, "Robust genome and cell engineering via in vitro and in situ circularized RNAs," bioRxiv, Nature Biomedical Engineering (2024).
89. Kivilcim Ozturk, Rebecca Panwala, Jeanna Sheen, Kyle Ford, Nathan Payne, Andrew Portell, Dong-Er Zhang, Stephan Hutter, Torsten Haferlach, Trey Ideker, Prashant Mali#, Hannah Carter#, "Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS," bioRxiv, Cell Reports 43, pp. 114436 (2024).
92. Timothy Clark, Jillian Mohan, Leah Schaffer, Kirsten Obernier, Sadna Al Manir, Christopher P Churas, Amir Dailamy, Yesh Doctor, Antoine Forget, Jan Niklas Hansen, Mengzhou Hu, Joanna Lenkiewicz, Maxwell Adam Levinson, Charlotte Marquez, Sami Nourreddine, Justin Niestroy, Dexter Pratt, Gege Qian, Swathi Thaker, Jean-Christophe Belisle-Pipon, Cynthia Brandt, Jake Chen, Ying Ding, Samah Fodeh, Nevam Krogan, Emma Lundberg, Prashant Mali, Pamela Payne-Foster, Sarah Ratcliffe, Vardit Ravitsky, Andrej Sali, Wade Schulz, Trey Ideker, "Cell maps for artificial intelligence: AI-ready maps of human cell architecture from disease-relevant cell lines," bioRxiv (2024).
87. Yusuke Goto*, Keiichi Koshizuka*, Toshinori Ando, Hiroki Izumi, Xingyu Wu, Kuniaki Sato, Tomohiko Ishikawa, Kyle Ford, Xiaodong Feng, Zhiyong Wang, Nadia Arang, Michael M. Allevato, Ayush Kishore, Prashant Mali, J. Silvio Gutkind, "A kinome-wide synthetic lethal CRISPR/Cas9 screen reveals that mTOR inhibition prevents adaptive resistance to CDK4/CDK6 blockade in HNSCC," Cancer Research Communication (2024).
86. Dong Jun Park, Wooil Choi, Sakeef Sayeed, Robert A. Dorschner, Joseph Rainaldi, Kayla Ho, Jenny Kezios, John P. Nolan, Prashant Mali, Todd Costantini, Brian P. Elicieiri, "Defining the activity of pro-reparative extracellular vesicles in wound healing based on miRNA payloads and cell type-specific lineage mapping," Molecular Therapy (2024).
85. Michael M. Allevato, Sally Trinh, Keiichi Koshizuka, Daniela Nachmanson, Thien-Tu C. Nguyen, Yumi Yokoyama, Xingyu Wu, Allen Andres, Zhiyong Wang, Jeramie Watrous, Alfredo A. Molinolo, Prashant Mali, Olivier Harismendy, Mohit Jain, Robert Wild, J. Silvio Gutkind, "A genome-wide CRISPR screen reveals that antagonism of glutamine metabolism sensitizes head and neck squamous cell carcinoma to ferroptotic cell death," Cancer Letters 598, pp. 217089 (2024).
84. Karina Barbosa, Anagha Deshpande, Marlenne Perales, Ping Xiang, Rabi Murad, Akula Bala Pramod, Anna Minkina, Neil Robertson, Fiorella Schischlik, Xue Lei, Younguk Son, Adam Brown, Diana Amend, Irmela Jeremias, John G. Doench, R. Keith Humphries, Eytan Ruppin, Jay Shendure, Prashant Mali, Peter D. Adams, Aniruddha J. Deshpande, "Transcriptional control of leukemogenesis by the chromatin reader SGF29," Blood 143, pp. 697-712 (2024).
83. Shankar Subramaniam, Metin Akay, Mark Anastasio, Vasudev Bailey, David Boas, Paolo Bonato, Ashutosh Chilkoti, Jennifer Cochran, Vicki Colvin, Tejal Desai, James Duncan, Frederick Epstein, Stephanie Fraley, Cecilia Giachelli, Jane Grande-Allen, Jordan Green, X. Eduard Guo, Isaac B. Hilton, Jay Humphrey, Chris Johnson, George Karniadakis, Michael King, Robert Kirsch, Sanjay Kumar, Cato Laurencin, Song Li, Rick Lieber, Nigel Lovell, Prashant Mali, Susan Margulies, David Meaney, Brenda Ogle, Bernhard Palsson, Nicholas Peppas, Eric Perreault, Rick Rabbitt, Lori Setton, Lonnie Shea, Sanjeev Shroff, Kirk Shung, Andreas Tolias, Marjolein van der Meulen, Shyni Varghese, Gordana Vunjak-Novakovic, John White, Raymond Winslow, Jinayi Zhan, Kun Zhang, Charles Zukoski, Michael Miller, "Grand Challenges at the Interface of Engineering and Medicine," IEEE Engineering in Medicine and Biology 5, pp. 1-13 (2024).
82. Andrew Portell, Prashant Mali, "Mutation corrections in spinal muscular atrophy," Nature Biomedical Engineering 8, pp. 111-113 (2024).
81. Kyle Ford*, Brenton P. Munson*, Samson H. Fong*, Rebecca Panwala, Wai Keung Chu, Joseph Rainaldi, Nongluk Plongthongkum, Vinayagam Arunachalam, Jarek Kostrowicki, Dario Meluzzi, Jason F. Kreisberg, Kristen Jensen-Pergakes, Todd VanArsdale, Thomas Paul, Pablo Tamayo, Kun Zhang, Jadwiga Bienkowska#, Prashant Mali#, Trey Ideker#, "Multimodal Perturbation Analyses of Cyclin-dependent Kinases Reveal a Network of Synthetic Lethalities Associated with Cell Cycle Regulation and Transcriptional Regulation," Scientific Reports 13, pp. 7678 (2023).
80. Aditya Kumar#, Starry He, Prashant Mali#, "Systematic Discovery of Transcription Factors that Improve hPSC-derived Cardiomyocyte Maturation via Temporal Analysis of Bioengineered Tissues," APL Bioengineering 7, pp. 026109 (2023).
79. Brian J. Booth, Sami Nourreddine, Dhruva Katrekar, Yiannis Savva, Debojit Bose, Thomas J. Long, David J. Huss#, Prashant Mali#, "RNA editing: expanding the potential of RNA therapeutics," Molecular Therapy 31, pp. 1533-1549 (2023).
78. Michal K. Handzlik, Jivani M. Gengatharan, Katie E. Frizzi, Grace H. McGregor, Cameron Martino, Gibraan Rahman, Antonio Gonzalez, Ana M. Moreno, Courtney R. Green, Lucie S. Guernsey, Terry Lin, Patrick Tseng, Yoichiro Ideguchi, Regis J. Fallon, Amandine Chaix, Satchidananda Panda, Prashant Mali, Martina Wallace, Rob Knight, Marin L. Gantner, Nigel A. Calcutt, Christian M. Metallo, "Insulin-regulated serine and lipid metabolism driver peripheral neuropathy," Nature 614, pp. 118-124 (2023).
77. Nadia Arang, Simone Lubrano, Damiano C. Rigiracciolo, Daniela Nachmanson, Scott M. Lippman, Prashant Mali, Olivier Harismendy, J. Silvio Gutkind, "Whole-genome CRISPR screening identified PI3K/AKT as a downstream component of the oncogenic GNAQ-Focal Adhesion Kinase signaling circuitry," Journal of Biological Chemistry 299, pp. 102866 (2023).
76. Daniel Tabet, Victoria Parikh, Prashant Mali, Frederick P. Roth, Melina Claussnitzer, "Scalable functional assays for the interpretation of human genetic variation," Annual Reviews of Genetics 56, pp. 441-465 (2022).
75. Elizabeth H. Kellogg, Jonathan Gootenberg, Omar Abudayyeh, Alan S. L. Wong, James E. Dahlman, Audrone Lapinaite, Cameron Myhrvold, Chan C. Liu, Patrick D. Hsu, Prashant Mali, Lei S. Qi, "What are the current bottlenecks in developing and applying CRISPR technologies," Cell Systems 13, pp. 589-593 (2022).
74. Yichen Xiang, Dhruva Katrekar, Prashant Mali, "Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing," Methods 205, pp. 158-166 (2022).
73. Dhruva Katrekar, James Yen, Yichen Xiang, Anushka Saha, Dario Meluzzi, Yiannis Savva, Prashant Mali, "Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs," bioRxiv, Nature Biotechnology 40, pp. 938-945 (2022).
72. Michael Hu, Xin Y. Lei, John D. Larson, Melissa McAlonis, Kyle Ford, Daniella McDonald, Krystal Mach, Jessica M. Rusert, Robert J. Wechsler-Reya, Prashant Mali, "Integrated genome and tissue engineering enables screening of cancer vulnerabilities in physiologically relevant perfusable ex vivo cultures," Biomaterials 280, pp. 121276 (2022).
71. Dhruva Katrekar, Nathan Palmer, Yichen Xiang, Anushka Saha, Dario Meluzzi, Prashant Mali, "Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA base-editing activity, functionality and specificity," bioRxiv, eLife 11, e75555 (2022).
70. Udit Parekh, Daniella McDonald, Amir Dailamy, Yan Wu, Thekla Cordes, Kun Zhang, Ann Tipps, Christian Metallo, Prashant Mali, "Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas," bioRxiv, iScience 24, pp. 103149 (2021).
69. Amir Dailamy*, Udit Parekh*, Dhruva Katrekar, Aditya Kumar, Daniella McDonald, Ana Moreno, Pegah Bagheri, Tse Nga Ng, Prashant Mali, "Programmatic introduction of parenchymal cell types into blood vessel organoids," Stem Cell Reports 16, pp. 2432-2441 (2021).
68. Kyle Ford, Rebecca Panwala, Dai-Hua Chen, Andrew Portell, Nathan Palmer, Prashant Mali, "Peptide tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors," Cell Systems 12, pp. 1-17 (2021).
67. Ana M. Moreno, Fernando Aleman, Glaucilene F. Catroli, Matthew Hunt, Michael Hu, Amir Dailamy, Andrew Pla, Sarah A. Woller, Nathan Palmer, Udit Parekh, Daniella McDonald, Amanda J. Roberts, Vanessa Goodwill, Ian Dryden, Robert F. Hevner, Lauriane Delay, Gilson Goncalves dos Santos, Tony Yaksh#, Prashant Mali#, "Long-lasting analgesia via targeted in situ repression of Nav1.7 in mice," bioRxiv, Science Translational Medicine 13, eaay9056 (2021).
66. Kathleen Leeper, Kian Kalhor, Andyna Vernet, Amanda Graveline, George M. Church, Prashant Mali, Reza Kalhor, "Lineage barcoding in mice with homing CRISPR," Nature Protocols 16, 2088-2108 (2021).
65. Justine Paradis, Monica Acosta, Robert Saddawi-Konefka, Ayush Kishore, Simone Lubrano, Frederico Gomes, Nadia Arang, Manoela Tiago, Silvia Coma, Xingyu Wu, Kyle Ford, Chi-Ping Day, Glenn Merlino, Prashant Mali, Jonathan Pachter, Takami Sato, Andrew Aplin, J. Silvio Gutkind, "Synthetic Lethal Screens Reveal Co-Targeting FAK and MEK as a Multimodal Precision Therapy for GNAQ-Driven Uveal Melanoma," Clinical Cancer Research CCR-20-3363 (2021).
64. Daniella McDonald*, Yan Wu*, Amir Dailamy, Justin Tat, Udit Parekh, Dongxin Zhao, Michael Hu, Ann Tipps, Kun Zhang#, Prashant Mali#, "Defining the teratoma as a model for multi-lineage human development," Cell 183, pp. 1402-1419 (2020).
63. Lavina Sierra Tay*, Nathan Palmer*, Rebecca Panwala, Wei Leong Chew#, Prashant Mali#, "Translating CRISPR-Cas therapeutics: approaches and challenges," The CRISPR Journal 3, pp. 253-275 (2020).
62. Aditya Kumar#, Prashant Mali#, "Mapping regulators of cell fate determination: approaches and challenges," APL Bioengineering 4, 031501 (2020).
61. Celine J Rocca, Joseph N Rainaldi, Jay Sharma, Shi Yanmeng, Joseph H Haquang, Jens Luebeck, Prashant Mali, Stephanie Cherqui, "CRISPR/Cas9 mediated genetic correction of hematopoietic stem cells from patients with Friedreich's Ataxia," Molecular Therapy Methods and Clinical Development 28, pp. 1026-1036 (2020).
60. Ana M. Moreno*, Nathan Palmer*, Fernando Aleman, Genghao Chen, Andrew Pla, Ning Jiang, Wei Leong Chew, Mansun Law, Prashant Mali, "Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy," bioRxiv, Nature Biomedical Engineering 3, pp. 806-816 (2019).
59. Prashant Mali, "Humanizing transcriptome engineering," Cell 178, pp. 8-9 (2019).
58. Genghao Chen*, Dhruva Katrekar*, Prashant Mali, "RNA-guided adenosine deaminases - advances and challenges for therapeutic RNA editing," Biochemistry 58, pp. 1947-1957 (2019).
57. Dhruva Katrekar, Genghao Chen, Dario Meluzzi, Ashwin Ganesh, Atharv Worlikar, Yu-Ru Shih, Shyni Varghese, Prashant Mali, "In vivo RNA editing of point mutations via RNA-guided adenosine deaminases," bioRxiv, Nature Methods 16, pp. 239-242 (2019).
56. Kyle Ford*, Daniella McDonald*, Prashant Mali, "Functional genomics via CRISPR-Cas," Journal of Molecular Biology 431, pp. 48-65 (2019).
55. Anagha Deshpande, Bo Rui Chen, Luyi Zhao, Kelsey Saddoris, Mayuri Kerr, Nan Zhu, Prashant Mali, Aniruddha Deshpande, "Investigation of genetic dependencies using CRISPR-Cas9 competition assays," Journal of Visualized Experiments, 143, doi: 10.3791/58710 (2019).
54. Udit Parekh*, Yan Wu*, Dongxin Zhao, Atharv Worlikar, Neha Shah, Kun Zhang#, Prashant Mali#, "Mapping cellular reprogramming via pooled overexpression screens with paired fitness and single-cell sequencing readout," Cell Systems 7, pp. 548-555 (2018).
53. Michael Hu, Amir Dailamy, Xin Lei, Udit Parekh, Daniella McDonald, Aditya Kumar, Prashant Mali, "Facile engineering of long-term culturable ex vivo vascularized tissues using biologically derived matrices," Advanced Healthcare Materials 7, pp. 1800845 (2018).
52. Reza Kalhor, Kian Kalhor, Leo Mejia, Kathleen Leeper, Amanda Graveline, Prashant Mali, George M. Church, "Developmental barcoding of whole mouse via homing CRISPR," Science 31, eaat9804 (2018).
51. April Pawluk, Jia Chen, Weizhi Ji, Prashant Mali, "The future of genome editing," Cell 173, pp. 1311-1313 (2018).
50. Ana M. Moreno, Xin Fu, Jie Zhu, Dhruva Katrekar, Yu-Ru V. Shih, John Marlett, Jessica Cabotaje, Jasmine Tat, John Naughton, Leszek Lisowski, Shyni Varghese, Kang Zhang#, Prashant Mali#, "In situ gene therapy via AAV-CRISPR-Cas9 mediated targeted gene regulation," Molecular Therapy 26, pp. 1818-1827 (2018).
49. Dhruva Katrekar, Ana M. Moreno, Genghao Chen, Atharv Worlikar, Prashant Mali, "Oligonucleotide conjugated multi-functional adeno-associated viruses," Scientific Reports 8, pp. 3589 (2018).
48. Dongxin Zhao*, Mehmet G. Badur*, Jens Luebeck, Jose H. Magana, Amanda Birmingham, Roman Sasik, Christopher S. Ahn, Trey Ideker, Christian Metallo#, Prashant Mali#, "Combinatorial CRISPR-Cas9 metabolic screens reveal critical redox control points dependent on the KEAP1-NRF2 regulatory axis," Molecular Cell 69, pp. 699-708 (2018).
47. The malERA Refresh Consultative Panel on Basic Science and Enabling Technologies, "malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication," PLOS Medicine, https://doi.org/10.1371/journal/pmed.1002451 (2017).
46. Deepak Asudani, Marianna Yusupova, Prashant Mali, "Genome engineering via CRISPR-Cas systems: inserting the 'precision' in precision medicine," The Journal of Precision Medicine (2017).
45. Dhruva Katrekar*, Michael Hu*, Prashant Mali, "Advances in CRISPR-Cas based genome engineering," Current Opinion in Biomedical Engineering 1, pp. 78-86 (2017).
44. Dan Du, Assen Roguev, David E. Gordon, Meng Chen, Si-Han Chen, Michael Shales, John Paul Shen, Trey Ideker, Prashant Mali, Lei Qi, Nevan Krogan, "Genetic interaction mapping in mammalian cells using CRISPR interference," Nature Methods 14, pp. 577-580 (2017).
43. Ana Moreno, Prashant Mali, "Therapeutic genome engineering via CRISPR-Cas systems," WIREs System Biology and Medicine, e1380 (2017).
42. John Paul Shen*, Dongxin Zhao*, Roman Sasik*, Jens Luebeck, Amanda Birmingham, Ana Bojorquez-Gomez, Katherine Licon, Kristin Klepper, Daniel Pekin, Alex Beckett, Kyle Sanchez, Alex Thomas, Chih-Chung Kuo, Dan Du, Assen Roguev, Nathan E. Lewis, Aaron N. Chang, Jason F. Kreisberg, Nevan Krogan, Lei Qi, Trey Ideker#, Prashant Mali#, "Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions," Nature Methods 14, pp. 573-576 (2017).
41. Udit Parekh*, Marianna Yusupova*, Prashant Mali, "Genome engineering in human pluripotent stem cells," Current Opinion in Chemical Engineering 15, pp. 56-67 (2017).
40. Reza Kalhor, Prashant Mali#, George M. Church#, "Rapidly evolving homing CRISPR barcodes," Nature Methods 14, pp. 195-200 (2017).
39. Jennifer Doudna#, Prashant Mali#, "CRISPR-Cas: A laboratory manual," Cold Spring Harbor Laboratory Press, Book ISBN 978-1-621821-30-4 (2016).
Harvard University --------------------------------------------------------------------------------------------------------------------------------------------------------------
38. Wei Leong Chew, Mohammadsharif Tabebordbar, Jason K. E. Cheng, Prashant Mali, Elizabeth Y. Wu, Alex H. M. Ng, Kexian Zhu, Amy J. Wagers, George M. Church, "A multifunctional AAV-CRISPR-Cas9 and its host response," Nature Methods 13, pp. 868-874 (2016).
37. Luhan Yang, Adrian W. Briggs, Wei Leong Chew, Prashant Mali, Marc Guell, John Aach, Daniel B. Goodman, David Cox, Yinan Kan, Emal Lesha, Venkataramanan Soundarajan, Feng Zhang, George M. Church, "Engineering and optimising deaminase fusions for genome editing," Nature Communications 7, 13330 (2016).
36. Raj Chari*, Prashant Mali*,#, Mark Moosburner, George M. Church#, "Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach," Nature Methods 12, pp. 823-826 (2015).
35. Susan M. Byrne, Luis Ortiz, Prashant Mali, John Aach, George M. Church, "Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells,” Nucleic Acids Research 43, e21 (2015).
34. Susan M. Byrne, Prashant Mali, George M. Church, "Genome editing in human stem cells,” Methods in Enzymology 546, pp. 119-138 (2014).
33. Je Hyuk Lee*, Evan R Daugharthy*, Jonathan Scheiman, Reza Kalhor, Joyce L Yang, Thomas C Ferrante, Richard Terry, Sauveur SF Jeanty, Chao Li, Ryoji Amamoto, Derek T Peters, Brian M Turczyk, Adam H Marblestone, Samuel A Inverso, Amy Bernard, Prashant Mali, Xavier Rios, John Aach, George M. Church, “Highly multiplexed subcellular RNA sequencing In situ,” Science 343, pp. 1360-1363 (2014).
32. Luhan Yang, Prashant Mali, Caroline Kim-Kiselak, George M. Church, “CRISPR-Cas-mediated targeted genome editing in human cells,” Methods in Molecular Biology 1114 pp. 245-267 (2014).
31. John Aach, Prashant Mali, George M. Church, "CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes," bioRxiv, https://doi.org/10.1101/005074 (2014).
30. Prashant Mali*,#, Kevin M. Esvelt*,#, George M. Church, “Cas9 as a versatile tool for engineering biology,” Nature Methods 10, pp. 957-963 (2013).
29. Kevin M. Esvelt*, Prashant Mali*, Jonathan L. Braff, Mark Moosburner, Stephanie J. Yaung, George M. Church, “Orthogonal Cas9 proteins for RNA-guided gene regulation and editing,” Nature Methods 10, pp. 1116-1121 (2013).
28. Prashant Mali*, John Aach*, P. Benjamin Stranges, Kevin M. Esvelt, Mark Moosburner, Sriram Kosuri, Luhan Yang, George M. Church, "Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering," Nature Biotechnology 31, pp. 833-838 (2013).
27. Luhan Yang, Marc Guell, Susan Byrne, Joyce L. Yang, Alejandro De Los Angeles, Prashant Mali, John Aach, Caroline Kim-Kiselak, Adrian W Briggs, Xavier Rios, Po-Yi Huang, George Daley, George M. Church, "Optimization of scarless human stem cell genome editing," Nucleic Acids Research 41, pp. 9049-9061 (2013).
26. Sravanti Kusuma, Yu-I Shen, Donny Hanjaya-Putra, Prashant Mali, Linzhao Cheng, Sharon Gerecht, "Self-organized vascular networks from human pluripotent stem cells in a synthetic matrix," PNAS 110, pp.12601-12606 (2013).
25. Prashant Mali*, John Aach*, Je-Hyuk Lee, Daniel Levner, Lisa Nip, George M. Church, “Barcoding cells using cell-surface programmable DNA binding domains,” Nature Methods 10, pp.403-406 (2013).
24. James E. DiCarlo, Julie E. Norville, Prashant Mali, Xavier Rios, John Aach, George M. Church, “Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems,” Nucleic Acids Research 41, pp.4336-4343 (2013).
23. Prashant Mali*, Luhan Yang*, Kevin M. Esvelt, John Aach, Marc Guell, James E. DiCarlo, Julie E. Norville, George M. Church, “RNA-guided human genome engineering via Cas9,” Science 339, pp. 823-826 (2013).
22. Adrian W. Briggs, Xavier Rios, Raj Chari, Luhan Yang, Feng Zhang, Prashant Mali, George M. Church, "Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers," Nucleic Acids Research 40, e117 (2012).
Johns Hopkins University -----------------------------------------------------------------------------------------------------------------------------------------------------
21. Prashant Mali, Linzhao Cheng, “Human cell engineering: cellular reprogramming and genome editing,” Stem Cells 30, pp. 75-81 (2012).
20. Shyam B. Khatau, Sravanti Kusuma, Donny Hanjaya-Putra, Prashant Mali, Linzhao Cheng, Jerry SH Lee, Sharon Gerecht, Denis Wirtz, "The differential formation of the LINC-mediated perinuclear actin cap in pluripotent and somatic cells," PLoS ONE 7, pp. e36689 (2012).
19. Chunlin Zou, Bin-Kuan Chou, Sarah N Dowey, Kitman Tsang, Xiaosong Huang, Cyndi F Liu, Cory Smith, Jonathan Yen, Prashant Mali, Yu Alex Zhang, Linzhao Cheng, Zhaohui Ye, “Efficient derivation and genetic modifications of human pluripotent stem cells on engineered human feeder cell lines,” Stem Cells and Development 21, pp. 2298-2311 (2012).
18. Jizhong Zou*, Prashant Mali*, Xiaosong Huang, Sarah N. Dowey, and Linzhao Cheng, “Site specific gene correction of a mutated beta-globin gene in human iPS cells derived from an adult patient with sickle cell disease,” Blood 118, pp. 4599-4608 (2011).
17. Bin-Kuan Chou*, Prashant Mali*, Xiaosong Huang*, Zhaohui Ye, Sarah N. Dowey, Linda M.S. Resar, Chunlin Zou, Y. Alex Zhang, Jay Tong, and Linzhao Cheng, “Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures,” Cell Research 21, pp. 518-529 (2011).
16. Prashant Mali, Zhaohui Ye, Bin-Kuan Chou, Jonathan Yen, Linzhao Cheng, “An improved method for generating and identifying human induced pluripotent stem cells,” Methods in Molecular Biology 636, pp. 191-205 (2010).
15. Prashant Mali, Denis Wirtz, Peter C. Searson, “Interplay of RhoA and motility in the programmed spreading of daughter cells post mitosis,” Biophysical Journal 99, pp. 3526-3534 (2010).
14. Andrzej Swistowski, Jun Peng, Qiuyue Liu, Prashant Mali, Mahendra S. Rao, Linzhao Cheng, and Xianmin Zeng, "Efficient generation of functional dopaminergic neurons from human induced pluripotent stem cells under defined conditions," Stem Cells 28, pp. 1893-1904 (2010).
13. Joyce E. Ohm*, Prashant Mali*, Leander Van Neste*, David M. Berman, Liang Liang, Kurinji Pandiyan, Kimberly Briggs, Wei Zhang, Pedram Argani, Brian Simons, Wayne Yu, William Matsui, Wim Van Criekinge, Feyruz Rassool, Elias Zambidis, Kornel Schuebel, Leslie Cope, Jonathan Yen, Helai Mohammad, Linzhao Cheng, Stephen B. Baylin, “Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells,” Cancer Research 70, pp. 7662-7673 (2010).
12. Prashant Mali, Bin-Kuan Chou, Jonathan Yen, Zhaohui Ye, Jizhong Zou, Sarah Dowey, Robert A. Brodsky, Joyce E. Ohm, Wayne Yu, Stephen B. Baylin, Kosuke Yusa, Allan Bradley, David J. Meyers, Chandrani Mukherjee, Philip A. Cole, Linzhao Cheng, “Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes,” Stem Cells 28, pp. 713-720 (2010).
11. Zhaohui Ye*, Huichun Zhan*, Prashant Mali, Sarah Dowey, Donna M. Williams, Yoon-Young Jang, Chi V. Dang, Jerry L. Spivak, Alison R. Moliterno, Linzhao Cheng, "Human-induced pluripotent stem cells from blood cells of healthy donors and patients with acquired blood disorders," Blood 114, pp. 5473-5480 (2009).
10. Jizhong Zou, Morgan L. Maeder, Prashant Mali, Shondra M. Pruett-Miller, Stacey Thibodeau-Beganny, Bin-Kuan Chou, Guibin Chen, Zhaohui Ye, In-Hyun Park, George Q. Daley, Matthew H. Porteus, J. Keith Joung, Linzhao Cheng, "Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells," Cell Stem Cell 5, pp. 97-110 (2009).
9. Prashant Mali, Zhaohui Ye, Holly Hammond, Xiaobing Yu, Jeffery Lin, Guibin Chen, Jizhong Zhou, Linzhao Cheng, "Improved efficiency and pace of generating induced pluripotent stem cells from human adult and fetal fibroblasts," Stem Cells 26, pp. 1998-2005 (2008).
8. Xiaobing Yu, Jizhong Zhou, Zhaohui Ye, Holly Hammond, Guibin Chen, Akinori Tokunaga, Prashant Mali, Yue-Ming Li, Curt Civin, Nicholas Gaiano, Linzhao Cheng, "Notch signaling activation in human embryonic stem cells is required for embryonic, but not trophoblastic, lineage commitment," Cell Stem Cell 2, pp. 461-471 (2008).
7. Guibin Chen, Zhaohui Ye, Xiaobing Yu, Jizhong Zhou, Prashant Mali, Robert Brodsky, Linzhao Cheng, "Trophoblast differentiation defect in human embryonic stem cells lacking PIG-A and GPI-anchored cell-surface proteins," Cell Stem Cell 2, pp. 345-355 (2008).
6. Liuhong Cai*, Zhaohui Ye*, Betty Ying Zhou, Prashant Mali, Canquan Zhou, Linzhao Cheng, "Promoting human embryonic stem cell renewal or differentiation by modulating Wnt signal and culture conditions," Cell Research 17, pp. 62-72 (2007).
5. Prashant Mali, Linzhao Cheng, "Reprogramming somatic cells without fusion or ethical confusion," Regenerative Medicine 1, pp. 837-840 (2006).
4. Bridget Wildt*, Prashant Mali*, Peter C. Searson, "Electrochemical template synthesis of multisegment nanowires: fabrication and protein functionalization," Langmuir 22, pp. 10528-10534 (2006).
3. Prashant Mali*, Nirveek Bhattacharjee*, Peter C. Searson, "Electrochemically programmed release of biomolecules and nanoparticles," NanoLetters 6, pp. 1250-1253 (2006).
Indian Institute of Technology Bombay ---------------------------------------------------------------------------------------------------------------------------------
2. Prashant Mali*, Aniruddh Sarkar*, Rakesh K. Lal, "Facile fabrication of microfluidic systems using electron beam lithography," Lab on Chip 6, pp. 310-315 (2006).
1. Prashant Mali, Rakesh K. Lal, "The dnaSET: A novel device for single-molecule DNA sequencing," IEEE Transactions on Electron Devices 51, pp. 2004-2012 (2004).
*co-first, #co-corresponding
95. Sami Nourreddine*, Yesh Doctor*, Amir Dailamy, Antoine Forget, Yi-Hung Lee, Becky Chinn, Hammza Khaliq, Benjamin Polacco, Monita Murlidharan, Emily Pan, Yifan Zhang, Alina Sigaeva, Jan Niklas Hansen, Jiahao Gao, Jillian A. Parker, Kirsten Obernier, Timothy Clark, Jake Y. Chen, Christian Metallo, Emma Lundberg, Trey Ideker, Nevan Krogan, Prashant Mali, "A perturbation cell atlas of human induced pluripotent stem cells," bioRxiv (preprint).
94. Susan M. Byrne, Stephen M. Burleigh, Robert Fragoza, Yue Jiang, Yiannis Saava, Ricky Pabon, Joseph Rainaldi, Andrew Portell, Prashant Mali, Adrian Briggs, "A novel engineered U7 small nuclear RNA scaffold greatly increases in vitro and in vivo ADAR-mediated programmable RNA base editing," bioRxiv (preprint).
93. Andrew Portell*, Kyle Ford*, Amanda Suhardjo, Joseph Rainaldi, Mark N. Bublik, Milan Sanghvi, Aditya Kumar, Madeleine K. Wing, Nathan D. Palmer, Duy An Le, Nikitha Kalahasti, Amir Dailamy, Prashant Mali, "Reprogramming adeno-associated virus tropism via displayed peptides tiling receptor ligands," bioRxiv (preprint).
92. Amir Dailamy*, Weiqi Lyu*, Sami Nourreddine, Joseph Rainaldi, Daniella McDonald, Rebecca Panwala, Alysson Muotri, Michael S. Breen, Kun Zhang, Prashant Mali, "Charting and probing the activity of ADARs in human development and cell-fate specification," Nature Communications (2024).
91. Yesh Doctor*, Milan Sanghvi*, Prashant Mali, "A manual for genome and transcriptome engineering," IEEE Reviews in Biomedical Engineering (2024).
90. Michael Tong, Nathan Palmer, Amir Dailamy, Aditya Kumar, Hammza Khaliq, Sangwoo Han, Emma Finburgh, Madeleine Wing, Camilla Hong, Yichen Xiang, Katelyn Miyasaki, Andrew Portell, Joseph Rainaldi, Amanda Suhardjo, Sami Nourreddine, Wei Leong Chew, Ester J. Kwon, Prashant Mali, "Robust genome and cell engineering via in vitro and in situ circularized RNAs," bioRxiv, Nature Biomedical Engineering (2024).
89. Kivilcim Ozturk, Rebecca Panwala, Jeanna Sheen, Kyle Ford, Nathan Payne, Andrew Portell, Dong-Er Zhang, Stephan Hutter, Torsten Haferlach, Trey Ideker, Prashant Mali#, Hannah Carter#, "Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS," bioRxiv, Cell Reports 43, pp. 114436 (2024).
92. Timothy Clark, Jillian Mohan, Leah Schaffer, Kirsten Obernier, Sadna Al Manir, Christopher P Churas, Amir Dailamy, Yesh Doctor, Antoine Forget, Jan Niklas Hansen, Mengzhou Hu, Joanna Lenkiewicz, Maxwell Adam Levinson, Charlotte Marquez, Sami Nourreddine, Justin Niestroy, Dexter Pratt, Gege Qian, Swathi Thaker, Jean-Christophe Belisle-Pipon, Cynthia Brandt, Jake Chen, Ying Ding, Samah Fodeh, Nevam Krogan, Emma Lundberg, Prashant Mali, Pamela Payne-Foster, Sarah Ratcliffe, Vardit Ravitsky, Andrej Sali, Wade Schulz, Trey Ideker, "Cell maps for artificial intelligence: AI-ready maps of human cell architecture from disease-relevant cell lines," bioRxiv (2024).
87. Yusuke Goto*, Keiichi Koshizuka*, Toshinori Ando, Hiroki Izumi, Xingyu Wu, Kuniaki Sato, Tomohiko Ishikawa, Kyle Ford, Xiaodong Feng, Zhiyong Wang, Nadia Arang, Michael M. Allevato, Ayush Kishore, Prashant Mali, J. Silvio Gutkind, "A kinome-wide synthetic lethal CRISPR/Cas9 screen reveals that mTOR inhibition prevents adaptive resistance to CDK4/CDK6 blockade in HNSCC," Cancer Research Communication (2024).
86. Dong Jun Park, Wooil Choi, Sakeef Sayeed, Robert A. Dorschner, Joseph Rainaldi, Kayla Ho, Jenny Kezios, John P. Nolan, Prashant Mali, Todd Costantini, Brian P. Elicieiri, "Defining the activity of pro-reparative extracellular vesicles in wound healing based on miRNA payloads and cell type-specific lineage mapping," Molecular Therapy (2024).
85. Michael M. Allevato, Sally Trinh, Keiichi Koshizuka, Daniela Nachmanson, Thien-Tu C. Nguyen, Yumi Yokoyama, Xingyu Wu, Allen Andres, Zhiyong Wang, Jeramie Watrous, Alfredo A. Molinolo, Prashant Mali, Olivier Harismendy, Mohit Jain, Robert Wild, J. Silvio Gutkind, "A genome-wide CRISPR screen reveals that antagonism of glutamine metabolism sensitizes head and neck squamous cell carcinoma to ferroptotic cell death," Cancer Letters 598, pp. 217089 (2024).
84. Karina Barbosa, Anagha Deshpande, Marlenne Perales, Ping Xiang, Rabi Murad, Akula Bala Pramod, Anna Minkina, Neil Robertson, Fiorella Schischlik, Xue Lei, Younguk Son, Adam Brown, Diana Amend, Irmela Jeremias, John G. Doench, R. Keith Humphries, Eytan Ruppin, Jay Shendure, Prashant Mali, Peter D. Adams, Aniruddha J. Deshpande, "Transcriptional control of leukemogenesis by the chromatin reader SGF29," Blood 143, pp. 697-712 (2024).
83. Shankar Subramaniam, Metin Akay, Mark Anastasio, Vasudev Bailey, David Boas, Paolo Bonato, Ashutosh Chilkoti, Jennifer Cochran, Vicki Colvin, Tejal Desai, James Duncan, Frederick Epstein, Stephanie Fraley, Cecilia Giachelli, Jane Grande-Allen, Jordan Green, X. Eduard Guo, Isaac B. Hilton, Jay Humphrey, Chris Johnson, George Karniadakis, Michael King, Robert Kirsch, Sanjay Kumar, Cato Laurencin, Song Li, Rick Lieber, Nigel Lovell, Prashant Mali, Susan Margulies, David Meaney, Brenda Ogle, Bernhard Palsson, Nicholas Peppas, Eric Perreault, Rick Rabbitt, Lori Setton, Lonnie Shea, Sanjeev Shroff, Kirk Shung, Andreas Tolias, Marjolein van der Meulen, Shyni Varghese, Gordana Vunjak-Novakovic, John White, Raymond Winslow, Jinayi Zhan, Kun Zhang, Charles Zukoski, Michael Miller, "Grand Challenges at the Interface of Engineering and Medicine," IEEE Engineering in Medicine and Biology 5, pp. 1-13 (2024).
82. Andrew Portell, Prashant Mali, "Mutation corrections in spinal muscular atrophy," Nature Biomedical Engineering 8, pp. 111-113 (2024).
81. Kyle Ford*, Brenton P. Munson*, Samson H. Fong*, Rebecca Panwala, Wai Keung Chu, Joseph Rainaldi, Nongluk Plongthongkum, Vinayagam Arunachalam, Jarek Kostrowicki, Dario Meluzzi, Jason F. Kreisberg, Kristen Jensen-Pergakes, Todd VanArsdale, Thomas Paul, Pablo Tamayo, Kun Zhang, Jadwiga Bienkowska#, Prashant Mali#, Trey Ideker#, "Multimodal Perturbation Analyses of Cyclin-dependent Kinases Reveal a Network of Synthetic Lethalities Associated with Cell Cycle Regulation and Transcriptional Regulation," Scientific Reports 13, pp. 7678 (2023).
80. Aditya Kumar#, Starry He, Prashant Mali#, "Systematic Discovery of Transcription Factors that Improve hPSC-derived Cardiomyocyte Maturation via Temporal Analysis of Bioengineered Tissues," APL Bioengineering 7, pp. 026109 (2023).
79. Brian J. Booth, Sami Nourreddine, Dhruva Katrekar, Yiannis Savva, Debojit Bose, Thomas J. Long, David J. Huss#, Prashant Mali#, "RNA editing: expanding the potential of RNA therapeutics," Molecular Therapy 31, pp. 1533-1549 (2023).
78. Michal K. Handzlik, Jivani M. Gengatharan, Katie E. Frizzi, Grace H. McGregor, Cameron Martino, Gibraan Rahman, Antonio Gonzalez, Ana M. Moreno, Courtney R. Green, Lucie S. Guernsey, Terry Lin, Patrick Tseng, Yoichiro Ideguchi, Regis J. Fallon, Amandine Chaix, Satchidananda Panda, Prashant Mali, Martina Wallace, Rob Knight, Marin L. Gantner, Nigel A. Calcutt, Christian M. Metallo, "Insulin-regulated serine and lipid metabolism driver peripheral neuropathy," Nature 614, pp. 118-124 (2023).
77. Nadia Arang, Simone Lubrano, Damiano C. Rigiracciolo, Daniela Nachmanson, Scott M. Lippman, Prashant Mali, Olivier Harismendy, J. Silvio Gutkind, "Whole-genome CRISPR screening identified PI3K/AKT as a downstream component of the oncogenic GNAQ-Focal Adhesion Kinase signaling circuitry," Journal of Biological Chemistry 299, pp. 102866 (2023).
76. Daniel Tabet, Victoria Parikh, Prashant Mali, Frederick P. Roth, Melina Claussnitzer, "Scalable functional assays for the interpretation of human genetic variation," Annual Reviews of Genetics 56, pp. 441-465 (2022).
75. Elizabeth H. Kellogg, Jonathan Gootenberg, Omar Abudayyeh, Alan S. L. Wong, James E. Dahlman, Audrone Lapinaite, Cameron Myhrvold, Chan C. Liu, Patrick D. Hsu, Prashant Mali, Lei S. Qi, "What are the current bottlenecks in developing and applying CRISPR technologies," Cell Systems 13, pp. 589-593 (2022).
74. Yichen Xiang, Dhruva Katrekar, Prashant Mali, "Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing," Methods 205, pp. 158-166 (2022).
73. Dhruva Katrekar, James Yen, Yichen Xiang, Anushka Saha, Dario Meluzzi, Yiannis Savva, Prashant Mali, "Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs," bioRxiv, Nature Biotechnology 40, pp. 938-945 (2022).
72. Michael Hu, Xin Y. Lei, John D. Larson, Melissa McAlonis, Kyle Ford, Daniella McDonald, Krystal Mach, Jessica M. Rusert, Robert J. Wechsler-Reya, Prashant Mali, "Integrated genome and tissue engineering enables screening of cancer vulnerabilities in physiologically relevant perfusable ex vivo cultures," Biomaterials 280, pp. 121276 (2022).
71. Dhruva Katrekar, Nathan Palmer, Yichen Xiang, Anushka Saha, Dario Meluzzi, Prashant Mali, "Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA base-editing activity, functionality and specificity," bioRxiv, eLife 11, e75555 (2022).
70. Udit Parekh, Daniella McDonald, Amir Dailamy, Yan Wu, Thekla Cordes, Kun Zhang, Ann Tipps, Christian Metallo, Prashant Mali, "Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas," bioRxiv, iScience 24, pp. 103149 (2021).
69. Amir Dailamy*, Udit Parekh*, Dhruva Katrekar, Aditya Kumar, Daniella McDonald, Ana Moreno, Pegah Bagheri, Tse Nga Ng, Prashant Mali, "Programmatic introduction of parenchymal cell types into blood vessel organoids," Stem Cell Reports 16, pp. 2432-2441 (2021).
68. Kyle Ford, Rebecca Panwala, Dai-Hua Chen, Andrew Portell, Nathan Palmer, Prashant Mali, "Peptide tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors," Cell Systems 12, pp. 1-17 (2021).
67. Ana M. Moreno, Fernando Aleman, Glaucilene F. Catroli, Matthew Hunt, Michael Hu, Amir Dailamy, Andrew Pla, Sarah A. Woller, Nathan Palmer, Udit Parekh, Daniella McDonald, Amanda J. Roberts, Vanessa Goodwill, Ian Dryden, Robert F. Hevner, Lauriane Delay, Gilson Goncalves dos Santos, Tony Yaksh#, Prashant Mali#, "Long-lasting analgesia via targeted in situ repression of Nav1.7 in mice," bioRxiv, Science Translational Medicine 13, eaay9056 (2021).
66. Kathleen Leeper, Kian Kalhor, Andyna Vernet, Amanda Graveline, George M. Church, Prashant Mali, Reza Kalhor, "Lineage barcoding in mice with homing CRISPR," Nature Protocols 16, 2088-2108 (2021).
65. Justine Paradis, Monica Acosta, Robert Saddawi-Konefka, Ayush Kishore, Simone Lubrano, Frederico Gomes, Nadia Arang, Manoela Tiago, Silvia Coma, Xingyu Wu, Kyle Ford, Chi-Ping Day, Glenn Merlino, Prashant Mali, Jonathan Pachter, Takami Sato, Andrew Aplin, J. Silvio Gutkind, "Synthetic Lethal Screens Reveal Co-Targeting FAK and MEK as a Multimodal Precision Therapy for GNAQ-Driven Uveal Melanoma," Clinical Cancer Research CCR-20-3363 (2021).
64. Daniella McDonald*, Yan Wu*, Amir Dailamy, Justin Tat, Udit Parekh, Dongxin Zhao, Michael Hu, Ann Tipps, Kun Zhang#, Prashant Mali#, "Defining the teratoma as a model for multi-lineage human development," Cell 183, pp. 1402-1419 (2020).
63. Lavina Sierra Tay*, Nathan Palmer*, Rebecca Panwala, Wei Leong Chew#, Prashant Mali#, "Translating CRISPR-Cas therapeutics: approaches and challenges," The CRISPR Journal 3, pp. 253-275 (2020).
62. Aditya Kumar#, Prashant Mali#, "Mapping regulators of cell fate determination: approaches and challenges," APL Bioengineering 4, 031501 (2020).
61. Celine J Rocca, Joseph N Rainaldi, Jay Sharma, Shi Yanmeng, Joseph H Haquang, Jens Luebeck, Prashant Mali, Stephanie Cherqui, "CRISPR/Cas9 mediated genetic correction of hematopoietic stem cells from patients with Friedreich's Ataxia," Molecular Therapy Methods and Clinical Development 28, pp. 1026-1036 (2020).
60. Ana M. Moreno*, Nathan Palmer*, Fernando Aleman, Genghao Chen, Andrew Pla, Ning Jiang, Wei Leong Chew, Mansun Law, Prashant Mali, "Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy," bioRxiv, Nature Biomedical Engineering 3, pp. 806-816 (2019).
59. Prashant Mali, "Humanizing transcriptome engineering," Cell 178, pp. 8-9 (2019).
58. Genghao Chen*, Dhruva Katrekar*, Prashant Mali, "RNA-guided adenosine deaminases - advances and challenges for therapeutic RNA editing," Biochemistry 58, pp. 1947-1957 (2019).
57. Dhruva Katrekar, Genghao Chen, Dario Meluzzi, Ashwin Ganesh, Atharv Worlikar, Yu-Ru Shih, Shyni Varghese, Prashant Mali, "In vivo RNA editing of point mutations via RNA-guided adenosine deaminases," bioRxiv, Nature Methods 16, pp. 239-242 (2019).
56. Kyle Ford*, Daniella McDonald*, Prashant Mali, "Functional genomics via CRISPR-Cas," Journal of Molecular Biology 431, pp. 48-65 (2019).
55. Anagha Deshpande, Bo Rui Chen, Luyi Zhao, Kelsey Saddoris, Mayuri Kerr, Nan Zhu, Prashant Mali, Aniruddha Deshpande, "Investigation of genetic dependencies using CRISPR-Cas9 competition assays," Journal of Visualized Experiments, 143, doi: 10.3791/58710 (2019).
54. Udit Parekh*, Yan Wu*, Dongxin Zhao, Atharv Worlikar, Neha Shah, Kun Zhang#, Prashant Mali#, "Mapping cellular reprogramming via pooled overexpression screens with paired fitness and single-cell sequencing readout," Cell Systems 7, pp. 548-555 (2018).
53. Michael Hu, Amir Dailamy, Xin Lei, Udit Parekh, Daniella McDonald, Aditya Kumar, Prashant Mali, "Facile engineering of long-term culturable ex vivo vascularized tissues using biologically derived matrices," Advanced Healthcare Materials 7, pp. 1800845 (2018).
52. Reza Kalhor, Kian Kalhor, Leo Mejia, Kathleen Leeper, Amanda Graveline, Prashant Mali, George M. Church, "Developmental barcoding of whole mouse via homing CRISPR," Science 31, eaat9804 (2018).
51. April Pawluk, Jia Chen, Weizhi Ji, Prashant Mali, "The future of genome editing," Cell 173, pp. 1311-1313 (2018).
50. Ana M. Moreno, Xin Fu, Jie Zhu, Dhruva Katrekar, Yu-Ru V. Shih, John Marlett, Jessica Cabotaje, Jasmine Tat, John Naughton, Leszek Lisowski, Shyni Varghese, Kang Zhang#, Prashant Mali#, "In situ gene therapy via AAV-CRISPR-Cas9 mediated targeted gene regulation," Molecular Therapy 26, pp. 1818-1827 (2018).
49. Dhruva Katrekar, Ana M. Moreno, Genghao Chen, Atharv Worlikar, Prashant Mali, "Oligonucleotide conjugated multi-functional adeno-associated viruses," Scientific Reports 8, pp. 3589 (2018).
48. Dongxin Zhao*, Mehmet G. Badur*, Jens Luebeck, Jose H. Magana, Amanda Birmingham, Roman Sasik, Christopher S. Ahn, Trey Ideker, Christian Metallo#, Prashant Mali#, "Combinatorial CRISPR-Cas9 metabolic screens reveal critical redox control points dependent on the KEAP1-NRF2 regulatory axis," Molecular Cell 69, pp. 699-708 (2018).
47. The malERA Refresh Consultative Panel on Basic Science and Enabling Technologies, "malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication," PLOS Medicine, https://doi.org/10.1371/journal/pmed.1002451 (2017).
46. Deepak Asudani, Marianna Yusupova, Prashant Mali, "Genome engineering via CRISPR-Cas systems: inserting the 'precision' in precision medicine," The Journal of Precision Medicine (2017).
45. Dhruva Katrekar*, Michael Hu*, Prashant Mali, "Advances in CRISPR-Cas based genome engineering," Current Opinion in Biomedical Engineering 1, pp. 78-86 (2017).
44. Dan Du, Assen Roguev, David E. Gordon, Meng Chen, Si-Han Chen, Michael Shales, John Paul Shen, Trey Ideker, Prashant Mali, Lei Qi, Nevan Krogan, "Genetic interaction mapping in mammalian cells using CRISPR interference," Nature Methods 14, pp. 577-580 (2017).
43. Ana Moreno, Prashant Mali, "Therapeutic genome engineering via CRISPR-Cas systems," WIREs System Biology and Medicine, e1380 (2017).
42. John Paul Shen*, Dongxin Zhao*, Roman Sasik*, Jens Luebeck, Amanda Birmingham, Ana Bojorquez-Gomez, Katherine Licon, Kristin Klepper, Daniel Pekin, Alex Beckett, Kyle Sanchez, Alex Thomas, Chih-Chung Kuo, Dan Du, Assen Roguev, Nathan E. Lewis, Aaron N. Chang, Jason F. Kreisberg, Nevan Krogan, Lei Qi, Trey Ideker#, Prashant Mali#, "Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions," Nature Methods 14, pp. 573-576 (2017).
41. Udit Parekh*, Marianna Yusupova*, Prashant Mali, "Genome engineering in human pluripotent stem cells," Current Opinion in Chemical Engineering 15, pp. 56-67 (2017).
40. Reza Kalhor, Prashant Mali#, George M. Church#, "Rapidly evolving homing CRISPR barcodes," Nature Methods 14, pp. 195-200 (2017).
39. Jennifer Doudna#, Prashant Mali#, "CRISPR-Cas: A laboratory manual," Cold Spring Harbor Laboratory Press, Book ISBN 978-1-621821-30-4 (2016).
Harvard University --------------------------------------------------------------------------------------------------------------------------------------------------------------
38. Wei Leong Chew, Mohammadsharif Tabebordbar, Jason K. E. Cheng, Prashant Mali, Elizabeth Y. Wu, Alex H. M. Ng, Kexian Zhu, Amy J. Wagers, George M. Church, "A multifunctional AAV-CRISPR-Cas9 and its host response," Nature Methods 13, pp. 868-874 (2016).
37. Luhan Yang, Adrian W. Briggs, Wei Leong Chew, Prashant Mali, Marc Guell, John Aach, Daniel B. Goodman, David Cox, Yinan Kan, Emal Lesha, Venkataramanan Soundarajan, Feng Zhang, George M. Church, "Engineering and optimising deaminase fusions for genome editing," Nature Communications 7, 13330 (2016).
36. Raj Chari*, Prashant Mali*,#, Mark Moosburner, George M. Church#, "Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach," Nature Methods 12, pp. 823-826 (2015).
35. Susan M. Byrne, Luis Ortiz, Prashant Mali, John Aach, George M. Church, "Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells,” Nucleic Acids Research 43, e21 (2015).
34. Susan M. Byrne, Prashant Mali, George M. Church, "Genome editing in human stem cells,” Methods in Enzymology 546, pp. 119-138 (2014).
33. Je Hyuk Lee*, Evan R Daugharthy*, Jonathan Scheiman, Reza Kalhor, Joyce L Yang, Thomas C Ferrante, Richard Terry, Sauveur SF Jeanty, Chao Li, Ryoji Amamoto, Derek T Peters, Brian M Turczyk, Adam H Marblestone, Samuel A Inverso, Amy Bernard, Prashant Mali, Xavier Rios, John Aach, George M. Church, “Highly multiplexed subcellular RNA sequencing In situ,” Science 343, pp. 1360-1363 (2014).
32. Luhan Yang, Prashant Mali, Caroline Kim-Kiselak, George M. Church, “CRISPR-Cas-mediated targeted genome editing in human cells,” Methods in Molecular Biology 1114 pp. 245-267 (2014).
31. John Aach, Prashant Mali, George M. Church, "CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes," bioRxiv, https://doi.org/10.1101/005074 (2014).
30. Prashant Mali*,#, Kevin M. Esvelt*,#, George M. Church, “Cas9 as a versatile tool for engineering biology,” Nature Methods 10, pp. 957-963 (2013).
29. Kevin M. Esvelt*, Prashant Mali*, Jonathan L. Braff, Mark Moosburner, Stephanie J. Yaung, George M. Church, “Orthogonal Cas9 proteins for RNA-guided gene regulation and editing,” Nature Methods 10, pp. 1116-1121 (2013).
28. Prashant Mali*, John Aach*, P. Benjamin Stranges, Kevin M. Esvelt, Mark Moosburner, Sriram Kosuri, Luhan Yang, George M. Church, "Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering," Nature Biotechnology 31, pp. 833-838 (2013).
27. Luhan Yang, Marc Guell, Susan Byrne, Joyce L. Yang, Alejandro De Los Angeles, Prashant Mali, John Aach, Caroline Kim-Kiselak, Adrian W Briggs, Xavier Rios, Po-Yi Huang, George Daley, George M. Church, "Optimization of scarless human stem cell genome editing," Nucleic Acids Research 41, pp. 9049-9061 (2013).
26. Sravanti Kusuma, Yu-I Shen, Donny Hanjaya-Putra, Prashant Mali, Linzhao Cheng, Sharon Gerecht, "Self-organized vascular networks from human pluripotent stem cells in a synthetic matrix," PNAS 110, pp.12601-12606 (2013).
25. Prashant Mali*, John Aach*, Je-Hyuk Lee, Daniel Levner, Lisa Nip, George M. Church, “Barcoding cells using cell-surface programmable DNA binding domains,” Nature Methods 10, pp.403-406 (2013).
24. James E. DiCarlo, Julie E. Norville, Prashant Mali, Xavier Rios, John Aach, George M. Church, “Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems,” Nucleic Acids Research 41, pp.4336-4343 (2013).
23. Prashant Mali*, Luhan Yang*, Kevin M. Esvelt, John Aach, Marc Guell, James E. DiCarlo, Julie E. Norville, George M. Church, “RNA-guided human genome engineering via Cas9,” Science 339, pp. 823-826 (2013).
22. Adrian W. Briggs, Xavier Rios, Raj Chari, Luhan Yang, Feng Zhang, Prashant Mali, George M. Church, "Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers," Nucleic Acids Research 40, e117 (2012).
Johns Hopkins University -----------------------------------------------------------------------------------------------------------------------------------------------------
21. Prashant Mali, Linzhao Cheng, “Human cell engineering: cellular reprogramming and genome editing,” Stem Cells 30, pp. 75-81 (2012).
20. Shyam B. Khatau, Sravanti Kusuma, Donny Hanjaya-Putra, Prashant Mali, Linzhao Cheng, Jerry SH Lee, Sharon Gerecht, Denis Wirtz, "The differential formation of the LINC-mediated perinuclear actin cap in pluripotent and somatic cells," PLoS ONE 7, pp. e36689 (2012).
19. Chunlin Zou, Bin-Kuan Chou, Sarah N Dowey, Kitman Tsang, Xiaosong Huang, Cyndi F Liu, Cory Smith, Jonathan Yen, Prashant Mali, Yu Alex Zhang, Linzhao Cheng, Zhaohui Ye, “Efficient derivation and genetic modifications of human pluripotent stem cells on engineered human feeder cell lines,” Stem Cells and Development 21, pp. 2298-2311 (2012).
18. Jizhong Zou*, Prashant Mali*, Xiaosong Huang, Sarah N. Dowey, and Linzhao Cheng, “Site specific gene correction of a mutated beta-globin gene in human iPS cells derived from an adult patient with sickle cell disease,” Blood 118, pp. 4599-4608 (2011).
17. Bin-Kuan Chou*, Prashant Mali*, Xiaosong Huang*, Zhaohui Ye, Sarah N. Dowey, Linda M.S. Resar, Chunlin Zou, Y. Alex Zhang, Jay Tong, and Linzhao Cheng, “Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures,” Cell Research 21, pp. 518-529 (2011).
16. Prashant Mali, Zhaohui Ye, Bin-Kuan Chou, Jonathan Yen, Linzhao Cheng, “An improved method for generating and identifying human induced pluripotent stem cells,” Methods in Molecular Biology 636, pp. 191-205 (2010).
15. Prashant Mali, Denis Wirtz, Peter C. Searson, “Interplay of RhoA and motility in the programmed spreading of daughter cells post mitosis,” Biophysical Journal 99, pp. 3526-3534 (2010).
14. Andrzej Swistowski, Jun Peng, Qiuyue Liu, Prashant Mali, Mahendra S. Rao, Linzhao Cheng, and Xianmin Zeng, "Efficient generation of functional dopaminergic neurons from human induced pluripotent stem cells under defined conditions," Stem Cells 28, pp. 1893-1904 (2010).
13. Joyce E. Ohm*, Prashant Mali*, Leander Van Neste*, David M. Berman, Liang Liang, Kurinji Pandiyan, Kimberly Briggs, Wei Zhang, Pedram Argani, Brian Simons, Wayne Yu, William Matsui, Wim Van Criekinge, Feyruz Rassool, Elias Zambidis, Kornel Schuebel, Leslie Cope, Jonathan Yen, Helai Mohammad, Linzhao Cheng, Stephen B. Baylin, “Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells,” Cancer Research 70, pp. 7662-7673 (2010).
12. Prashant Mali, Bin-Kuan Chou, Jonathan Yen, Zhaohui Ye, Jizhong Zou, Sarah Dowey, Robert A. Brodsky, Joyce E. Ohm, Wayne Yu, Stephen B. Baylin, Kosuke Yusa, Allan Bradley, David J. Meyers, Chandrani Mukherjee, Philip A. Cole, Linzhao Cheng, “Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes,” Stem Cells 28, pp. 713-720 (2010).
11. Zhaohui Ye*, Huichun Zhan*, Prashant Mali, Sarah Dowey, Donna M. Williams, Yoon-Young Jang, Chi V. Dang, Jerry L. Spivak, Alison R. Moliterno, Linzhao Cheng, "Human-induced pluripotent stem cells from blood cells of healthy donors and patients with acquired blood disorders," Blood 114, pp. 5473-5480 (2009).
10. Jizhong Zou, Morgan L. Maeder, Prashant Mali, Shondra M. Pruett-Miller, Stacey Thibodeau-Beganny, Bin-Kuan Chou, Guibin Chen, Zhaohui Ye, In-Hyun Park, George Q. Daley, Matthew H. Porteus, J. Keith Joung, Linzhao Cheng, "Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells," Cell Stem Cell 5, pp. 97-110 (2009).
9. Prashant Mali, Zhaohui Ye, Holly Hammond, Xiaobing Yu, Jeffery Lin, Guibin Chen, Jizhong Zhou, Linzhao Cheng, "Improved efficiency and pace of generating induced pluripotent stem cells from human adult and fetal fibroblasts," Stem Cells 26, pp. 1998-2005 (2008).
8. Xiaobing Yu, Jizhong Zhou, Zhaohui Ye, Holly Hammond, Guibin Chen, Akinori Tokunaga, Prashant Mali, Yue-Ming Li, Curt Civin, Nicholas Gaiano, Linzhao Cheng, "Notch signaling activation in human embryonic stem cells is required for embryonic, but not trophoblastic, lineage commitment," Cell Stem Cell 2, pp. 461-471 (2008).
7. Guibin Chen, Zhaohui Ye, Xiaobing Yu, Jizhong Zhou, Prashant Mali, Robert Brodsky, Linzhao Cheng, "Trophoblast differentiation defect in human embryonic stem cells lacking PIG-A and GPI-anchored cell-surface proteins," Cell Stem Cell 2, pp. 345-355 (2008).
6. Liuhong Cai*, Zhaohui Ye*, Betty Ying Zhou, Prashant Mali, Canquan Zhou, Linzhao Cheng, "Promoting human embryonic stem cell renewal or differentiation by modulating Wnt signal and culture conditions," Cell Research 17, pp. 62-72 (2007).
5. Prashant Mali, Linzhao Cheng, "Reprogramming somatic cells without fusion or ethical confusion," Regenerative Medicine 1, pp. 837-840 (2006).
4. Bridget Wildt*, Prashant Mali*, Peter C. Searson, "Electrochemical template synthesis of multisegment nanowires: fabrication and protein functionalization," Langmuir 22, pp. 10528-10534 (2006).
3. Prashant Mali*, Nirveek Bhattacharjee*, Peter C. Searson, "Electrochemically programmed release of biomolecules and nanoparticles," NanoLetters 6, pp. 1250-1253 (2006).
Indian Institute of Technology Bombay ---------------------------------------------------------------------------------------------------------------------------------
2. Prashant Mali*, Aniruddh Sarkar*, Rakesh K. Lal, "Facile fabrication of microfluidic systems using electron beam lithography," Lab on Chip 6, pp. 310-315 (2006).
1. Prashant Mali, Rakesh K. Lal, "The dnaSET: A novel device for single-molecule DNA sequencing," IEEE Transactions on Electron Devices 51, pp. 2004-2012 (2004).
Patents
29. Prashant Mali, Michael Tong, "Zinc finger engineering," WO 2024107861 (2024).
28. Prashant Mali, Andrew Portell, Kyle Ford, Amanda Suhardjo, "Reprogramming tropism via displayed peptides tiling receptor-ligands," WO 2024055020 (2024).
27. Prashant Mali, Aditya Kumar, Ester Kwon, Katelyn Miyasaki, "In vitro and in vivo protein translation via in situ circularized RNAs," WO 2023154749 (2023).
26. Prashant Mali, Amir Dailamy, Udit Parekh, "Engineered Vascularized Organoids," US 20230174949 (2023).
25. Prashant Mali, Dhruva Katrekar, Lauren Hodge, Kyle M. Ford, Andrew Portell, "Modified viruses and viral particles, methods of making, and uses thereof," WO 2022212928 (2022).
24. Prashant Mali, Andrew Portell, Amir Dailamy, Aditya Kumar, "Ribozyme-activated RNA constructs and uses thereof," WO 2022150773 (2022).
23. Prashant Mali, Dhruva Katrekar, James Yen, "Programmable RNA editing in vivo via recruitment of endogenous ADARs," WO 2022147573 (2022).
22. Prashant Mali, Nathan Palmer, Aditya Kumar, Amanda Suhardjo, "Engineering immune orthogonal AAVs and immune stealth CRISPR-Cas," WO 2022120103 (2022).
21. Prashant Mali, Dhruva Katrekar, "Engineering circular guide-RNAs," WO 2021113264 (2021).
20. David Huss, Prashant Mali, Anupama Lakshmanan, Christopher Nye, Yiannis Savva, Liana Stein, Richard Sullivan, Rafael Ponce, "Therapeutic Editing," WO 2021113270 (2021).
19. Prashant Mali, Dhruva Katrekar, Thomas Morton, "Targeting transfer RNA for the suppression of nonsense mutations in messenger RNA," WO 2021142343 (2021).
18. Prashant Mali, Kyle M. Ford, Nathan Palmer, Rebecca Panwala, "Gene fragment overexpression screening methodologies, and uses thereof," WO 2021041953 (2021).
17. Prashant Mali, Udit Parekh, Yan Wu, Kun Zhang, "Methods for screening genetic perturbations," WO 20210108193 (2021).
16. Prashant Mali, Ana M. Moreno, "Long-lasting analgesis via targeted epigenetic repression," WO 2020210542 (2020).
15. Prashant Mali, Dhruva Katrekar, Dario Meluzzi, Genghao Chen, Kyle M. Ford, "RNA and DNA base editing via engineered ADAR recruitment," WO 2020051555 (2020).
14. Prashant Mali, Daniella McDonald, Kun Zhang, Yan Wu, Amir Dailamy, Udit Parekh, Michael Hu, "Novel method to engineer transplantable tissues," WO 20200010249 (2020).
13. Prashant Mali, Udit Parekh, Amir Dailamy, Xin Lei, Michael Hu, "Use of 3D-printed freestanding structures for ex vivo tissues," WO 2019226710 (2019).
12. Paul Mischel, Prashant Mali, Vineet Bafna, Kristen Turner, Viraj Deshpande, Doruk Beyter, "Methods of diagnosing and treating cancer targeting extrachromosomal DNA," WO 20180355416 (2018).
11. Prashant Mali, Ana Moreno, Nathan Palmer, "Engineering CRISPR-Cas9 Immune Stealth," WO 2018170015 (2018).
10. Prashant Mali, Dhruva Katrekar, "RNA targeting of point mutations via suppressor tRNAs and deaminases," WO 2018161032 (2018).
9. Prashant Mali, Dhruva Katrekar, Ana Moreno, "CRISPR-Cas genome engineering via modular AAV delivery system," WO 2018035503 (2018).
8. Kun Zhang, Prashant Mali, Yan Wu, Dongxin Zhao, "Efficient genetic screening method," WO 2018005691 (2018).
7. Reza Kalhor, Prashant Mali, George Church, "Engineered guide RNA sequences for in situ detection and sequencing," WO 2018085414 (2018).
6. George M. Church, Reza Kalhor, Prashant Mali, "Self-targeting guide RNAs in CRISPR system," WO 2017196768 (2017).
5. George M. Church, Kevin M. Esvelt, Prashant Mali, "Orthogonal Cas9 proteins for RNA-guided gene regulation and editing," WO 2015006294 (2015).
4. George M. Church, Prashant Mali, Kevin M. Esvelt, “RNA-guided transcriptional regulation,” US 20140356959 (2014).
3. Prashant Mali, George M. Church, Luhan Yang, "RNA-guided human genome engineering," US 20140342456 (2014).
2. George M. Church, Prashant Mali, “Polynucleotide-binding domains as a means of cell labeling, cell organization and polymer sequencing,” WO 2014028311 (2014).
1. Peter Searson, Nirveek Bhattacharjee, Prashant Mali, "Method and Device for Controlled Release of Biomolecules and Nanoparticles," US 20080067056 (2008).
29. Prashant Mali, Michael Tong, "Zinc finger engineering," WO 2024107861 (2024).
28. Prashant Mali, Andrew Portell, Kyle Ford, Amanda Suhardjo, "Reprogramming tropism via displayed peptides tiling receptor-ligands," WO 2024055020 (2024).
27. Prashant Mali, Aditya Kumar, Ester Kwon, Katelyn Miyasaki, "In vitro and in vivo protein translation via in situ circularized RNAs," WO 2023154749 (2023).
26. Prashant Mali, Amir Dailamy, Udit Parekh, "Engineered Vascularized Organoids," US 20230174949 (2023).
25. Prashant Mali, Dhruva Katrekar, Lauren Hodge, Kyle M. Ford, Andrew Portell, "Modified viruses and viral particles, methods of making, and uses thereof," WO 2022212928 (2022).
24. Prashant Mali, Andrew Portell, Amir Dailamy, Aditya Kumar, "Ribozyme-activated RNA constructs and uses thereof," WO 2022150773 (2022).
23. Prashant Mali, Dhruva Katrekar, James Yen, "Programmable RNA editing in vivo via recruitment of endogenous ADARs," WO 2022147573 (2022).
22. Prashant Mali, Nathan Palmer, Aditya Kumar, Amanda Suhardjo, "Engineering immune orthogonal AAVs and immune stealth CRISPR-Cas," WO 2022120103 (2022).
21. Prashant Mali, Dhruva Katrekar, "Engineering circular guide-RNAs," WO 2021113264 (2021).
20. David Huss, Prashant Mali, Anupama Lakshmanan, Christopher Nye, Yiannis Savva, Liana Stein, Richard Sullivan, Rafael Ponce, "Therapeutic Editing," WO 2021113270 (2021).
19. Prashant Mali, Dhruva Katrekar, Thomas Morton, "Targeting transfer RNA for the suppression of nonsense mutations in messenger RNA," WO 2021142343 (2021).
18. Prashant Mali, Kyle M. Ford, Nathan Palmer, Rebecca Panwala, "Gene fragment overexpression screening methodologies, and uses thereof," WO 2021041953 (2021).
17. Prashant Mali, Udit Parekh, Yan Wu, Kun Zhang, "Methods for screening genetic perturbations," WO 20210108193 (2021).
16. Prashant Mali, Ana M. Moreno, "Long-lasting analgesis via targeted epigenetic repression," WO 2020210542 (2020).
15. Prashant Mali, Dhruva Katrekar, Dario Meluzzi, Genghao Chen, Kyle M. Ford, "RNA and DNA base editing via engineered ADAR recruitment," WO 2020051555 (2020).
14. Prashant Mali, Daniella McDonald, Kun Zhang, Yan Wu, Amir Dailamy, Udit Parekh, Michael Hu, "Novel method to engineer transplantable tissues," WO 20200010249 (2020).
13. Prashant Mali, Udit Parekh, Amir Dailamy, Xin Lei, Michael Hu, "Use of 3D-printed freestanding structures for ex vivo tissues," WO 2019226710 (2019).
12. Paul Mischel, Prashant Mali, Vineet Bafna, Kristen Turner, Viraj Deshpande, Doruk Beyter, "Methods of diagnosing and treating cancer targeting extrachromosomal DNA," WO 20180355416 (2018).
11. Prashant Mali, Ana Moreno, Nathan Palmer, "Engineering CRISPR-Cas9 Immune Stealth," WO 2018170015 (2018).
10. Prashant Mali, Dhruva Katrekar, "RNA targeting of point mutations via suppressor tRNAs and deaminases," WO 2018161032 (2018).
9. Prashant Mali, Dhruva Katrekar, Ana Moreno, "CRISPR-Cas genome engineering via modular AAV delivery system," WO 2018035503 (2018).
8. Kun Zhang, Prashant Mali, Yan Wu, Dongxin Zhao, "Efficient genetic screening method," WO 2018005691 (2018).
7. Reza Kalhor, Prashant Mali, George Church, "Engineered guide RNA sequences for in situ detection and sequencing," WO 2018085414 (2018).
6. George M. Church, Reza Kalhor, Prashant Mali, "Self-targeting guide RNAs in CRISPR system," WO 2017196768 (2017).
5. George M. Church, Kevin M. Esvelt, Prashant Mali, "Orthogonal Cas9 proteins for RNA-guided gene regulation and editing," WO 2015006294 (2015).
4. George M. Church, Prashant Mali, Kevin M. Esvelt, “RNA-guided transcriptional regulation,” US 20140356959 (2014).
3. Prashant Mali, George M. Church, Luhan Yang, "RNA-guided human genome engineering," US 20140342456 (2014).
2. George M. Church, Prashant Mali, “Polynucleotide-binding domains as a means of cell labeling, cell organization and polymer sequencing,” WO 2014028311 (2014).
1. Peter Searson, Nirveek Bhattacharjee, Prashant Mali, "Method and Device for Controlled Release of Biomolecules and Nanoparticles," US 20080067056 (2008).