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Prashant Mali, Ph.D. - Publications

Affiliations: 
2011 Johns Hopkins University, Baltimore, MD 
Area:
Biomedical Engineering, Human Development, Genetics, Cell Biology
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68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Barbosa K, Deshpande A, Perales ME, Xiang P, Murad R, Pramod AB, Minkina A, Robertson NA, Schischlik F, Lei X, Sun Y, Brown A, Amend D, Jeremias I, Doench JG, ... ... Mali P, et al. TRANSCRIPTIONAL CONTROL OF LEUKEMOGENESIS BY THE CHROMATIN READER SGF29. Blood. PMID 38048593 DOI: 10.1182/blood.2023021234  0.507
2023 Ford K, Munson BP, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, ... ... Mali P, et al. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Scientific Reports. 13: 7678. PMID 37169829 DOI: 10.1038/s41598-023-33329-2  0.759
2023 Booth BJ, Nourreddine S, Katrekar D, Savva Y, Bose D, Long TJ, Huss DJ, Mali P. RNA Editing: Expanding the Potential of RNA Therapeutics. Molecular Therapy : the Journal of the American Society of Gene Therapy. PMID 36620962 DOI: 10.1016/j.ymthe.2023.01.005  0.778
2022 Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M. Scalable Functional Assays for the Interpretation of Human Genetic Variation. Annual Review of Genetics. PMID 36055970 DOI: 10.1146/annurev-genet-072920-032107  0.5
2022 Xiang Y, Katrekar D, Mali P. Methods For Recruiting Endogenous And Exogenous ADAR Enzymes For Site-Specific RNA Editing. Methods (San Diego, Calif.). PMID 35779766 DOI: 10.1016/j.ymeth.2022.06.011  0.317
2021 Leeper K, Kalhor K, Vernet A, Graveline A, Church GM, Mali P, Kalhor R. Lineage barcoding in mice with homing CRISPR. Nature Protocols. PMID 33692551 DOI: 10.1038/s41596-020-00485-y  0.775
2020 McDonald D, Wu Y, Dailamy A, Tat J, Parekh U, Zhao D, Hu M, Tipps A, Zhang K, Mali P. Defining the Teratoma as a Model for Multi-lineage Human Development. Cell. PMID 33152263 DOI: 10.1016/j.cell.2020.10.018  0.407
2020 Kumar A, Mali P. Mapping regulators of cell fate determination: Approaches and challenges. Apl Bioengineering. 4: 031501. PMID 32637855 DOI: 10.1063/5.0004611  0.338
2020 Rocca CJ, Rainaldi JN, Sharma J, Shi Y, Haquang JH, Luebeck J, Mali P, Cherqui S. CRISPR-Cas9 Gene Editing of Hematopoietic Stem Cells from Patients with Friedreich's Ataxia. Molecular Therapy. Methods & Clinical Development. 17: 1026-1036. PMID 32462051 DOI: 10.1016/J.Omtm.2020.04.018  0.781
2019 Moreno AM, Palmer N, Alemán F, Chen G, Pla A, Jiang N, Leong Chew W, Law M, Mali P. Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy. Nature Biomedical Engineering. PMID 31332341 DOI: 10.1038/S41551-019-0431-2  0.328
2019 Mali P. Humanizing Transcriptome Engineering. Cell. 178: 8-9. PMID 31251918 DOI: 10.1016/J.Cell.2019.06.009  0.412
2019 Chen G, Katrekar D, Mali P. RNA-Guided Adenosine Deaminases: Advances and Challenges for Therapeutic RNA Editing. Biochemistry. PMID 30943016 DOI: 10.1021/Acs.Biochem.9B00046  0.418
2019 Katrekar D, Chen G, Meluzzi D, Ganesh A, Worlikar A, Shih YR, Varghese S, Mali P. In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nature Methods. PMID 30737497 DOI: 10.1038/S41592-019-0323-0  0.405
2019 Deshpande A, Chen BR, Zhao L, Saddoris K, Kerr M, Zhu N, Mali P, Deshpande AJ. Investigation of Genetic Dependencies Using CRISPR-Cas9-based Competition Assays. Journal of Visualized Experiments : Jove. PMID 30663717 DOI: 10.3791/58710  0.428
2018 Parekh U, Wu Y, Zhao D, Worlikar A, Shah N, Zhang K, Mali P. Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout. Cell Systems. PMID 30448000 DOI: 10.1016/J.Cels.2018.10.008  0.448
2018 Hu M, Dailamy A, Lei XY, Parekh U, McDonald D, Kumar A, Mali P. Facile Engineering of Long-Term Culturable Ex Vivo Vascularized Tissues Using Biologically Derived Matrices. Advanced Healthcare Materials. e1800845. PMID 30369101 DOI: 10.1002/Adhm.201800845  0.334
2018 Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM. Developmental barcoding of whole mouse via homing CRISPR. Science (New York, N.Y.). PMID 30093604 DOI: 10.1126/Science.Aat9804  0.771
2018 Ford K, McDonald D, Mali P. Functional Genomics via CRISPR-Cas. Journal of Molecular Biology. PMID 29959923 DOI: 10.1016/J.Jmb.2018.06.034  0.367
2018 Moreno AM, Fu X, Zhu J, Katrekar D, Shih YV, Marlett J, Cabotaje J, Tat J, Naughton J, Lisowski L, Varghese S, Zhang K, Mali P. In Situ Gene Therapy via AAV-CRISPR-Cas9-Mediated Targeted Gene Regulation. Molecular Therapy : the Journal of the American Society of Gene Therapy. PMID 29754775 DOI: 10.1016/J.Ymthe.2018.04.017  0.461
2018 Katrekar D, Moreno AM, Chen G, Worlikar A, Mali P. Oligonucleotide conjugated multi-functional adeno-associated viruses. Scientific Reports. 8: 3589. PMID 29483550 DOI: 10.1038/S41598-018-21742-X  0.364
2018 Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Molecular Cell. 69: 699-708.e7. PMID 29452643 DOI: 10.1016/J.Molcel.2018.01.017  0.309
2018 Shen JP, Zhao D, Munson B, Birmingham A, Sasik R, Bojorquez-Gomez A, Licon K, Klepper K, Beckett A, Sanchez KS, Mali P, Ideker T. Abstract 3299: High-throughput combinatorial CRISPR-Cas9 gene knockout reveals most genetic interactions are context dependent Cancer Research. 78: 3299-3299. DOI: 10.1158/1538-7445.Am2018-3299  0.369
2017 Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G. Corrigendum: Engineering and optimising deaminase fusions for genome editing. Nature Communications. 8: 16169. PMID 28991237 DOI: 10.1038/Ncomms16169  0.736
2017 Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nature Methods. PMID 28481362 DOI: 10.1038/Nmeth.4286  0.404
2017 Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, ... ... Mali P, et al. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nature Methods. PMID 28319113 DOI: 10.1038/Nmeth.4225  0.6
2017 Moreno AM, Mali P. Therapeutic genome engineering via CRISPR-Cas systems. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 28198142 DOI: 10.1002/Wsbm.1380  0.412
2017 Kalhor R, Mali P, Church GM. Rapidly evolving homing CRISPR barcodes. Nature Methods. 14: 195-200. PMID 27918539 DOI: 10.1038/Nmeth.4108  0.805
2017 Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Kreisberg J, Ideker T, Mali P. Abstract PR08: Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-Pr08  0.405
2017 Shen JP, Zhao D, Sasik R, Luebeck J, Bojorquez-Gomez A, Licon K, Ideker T, Mali P. Abstract 3039: Combinatorial CRISPR-Cas9 gene knockout to enable genetic interaction mapping in human cells Cancer Research. 77: 3039-3039. DOI: 10.1158/1538-7445.Am2017-3039  0.383
2017 Parekh U, Yusupova M, Mali P. Genome engineering in human pluripotent stem cells Current Opinion in Chemical Engineering. 15: 56-67. DOI: 10.1016/J.Coche.2016.12.002  0.456
2017 Katrekar D, Hu M, Mali P. Advances in CRISPR-Cas based genome engineering Current Opinion in Biomedical Engineering. 1: 78-86. DOI: 10.1016/J.Cobme.2017.04.001  0.391
2016 Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G. Engineering and optimising deaminase fusions for genome editing. Nature Communications. 7: 13330. PMID 27804970 DOI: 10.1038/Ncomms13330  0.774
2016 Chew WL, Tabebordbar M, Cheng JK, Mali P, Wu EY, Ng AH, Zhu K, Wagers AJ, Church GM. A multifunctional AAV-CRISPR-Cas9 and its host response. Nature Methods. 13: 868-74. PMID 27595405 DOI: 10.1038/Nmeth.3993  0.55
2015 Chari R, Mali P, Moosburner M, Church GM. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nature Methods. 12: 823-6. PMID 26167643 DOI: 10.1038/Nmeth.3473  0.573
2015 Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Research. 43: e21. PMID 25414332 DOI: 10.1093/Nar/Gku1246  0.589
2015 Mali P. DNA Editing: A Primer Blood. 126. DOI: 10.1182/Blood.V126.23.Sci-16.Sci-16  0.437
2014 Byrne SM, Mali P, Church GM. Genome editing in human stem cells. Methods in Enzymology. 546: 119-38. PMID 25398338 DOI: 10.1016/B978-0-12-801185-0.00006-4  0.633
2014 Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, ... Mali P, et al. Highly multiplexed subcellular RNA sequencing in situ. Science (New York, N.Y.). 343: 1360-3. PMID 24578530 DOI: 10.1126/Science.1250212  0.781
2014 Yang L, Mali P, Kim-Kiselak C, Church G. CRISPR-Cas-mediated targeted genome editing in human cells. Methods in Molecular Biology (Clifton, N.J.). 1114: 245-67. PMID 24557908 DOI: 10.1007/978-1-62703-761-7_16  0.697
2013 Mali P, Esvelt KM, Church GM. Cas9 as a versatile tool for engineering biology. Nature Methods. 10: 957-63. PMID 24076990 DOI: 10.1038/Nmeth.2649  0.745
2013 Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nature Methods. 10: 1116-21. PMID 24076762 DOI: 10.1038/nmeth.2681  0.744
2013 Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. Optimization of scarless human stem cell genome editing. Nucleic Acids Research. 41: 9049-61. PMID 23907390 DOI: 10.1093/Nar/Gkt555  0.674
2013 Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotechnology. 31: 833-8. PMID 23907171 DOI: 10.1038/Nbt.2675  0.797
2013 Kusuma S, Shen YI, Hanjaya-Putra D, Mali P, Cheng L, Gerecht S. Self-organized vascular networks from human pluripotent stem cells in a synthetic matrix. Proceedings of the National Academy of Sciences of the United States of America. 110: 12601-6. PMID 23858432 DOI: 10.1073/pnas.1306562110  0.5
2013 Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM. Barcoding cells using cell-surface programmable DNA-binding domains. Nature Methods. 10: 403-6. PMID 23503053 DOI: 10.1038/Nmeth.2407  0.591
2013 DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Research. 41: 4336-43. PMID 23460208 DOI: 10.1093/Nar/Gkt135  0.799
2013 Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science (New York, N.Y.). 339: 823-6. PMID 23287722 DOI: 10.1126/Science.1232033  0.806
2012 Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM. Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Research. 40: e117. PMID 22740649 DOI: 10.1093/Nar/Gks624  0.636
2012 Khatau SB, Kusuma S, Hanjaya-Putra D, Mali P, Cheng L, Lee JS, Gerecht S, Wirtz D. The differential formation of the LINC-mediated perinuclear actin cap in pluripotent and somatic cells. Plos One. 7: e36689. PMID 22574215 DOI: 10.1371/Journal.Pone.0036689  0.488
2012 Zou C, Chou BK, Dowey SN, Tsang K, Huang X, Liu CF, Smith C, Yen J, Mali P, Zhang YA, Cheng L, Ye Z. Efficient derivation and genetic modifications of human pluripotent stem cells on engineered human feeder cell lines. Stem Cells and Development. 21: 2298-311. PMID 22225458 DOI: 10.1089/Scd.2011.0688  0.757
2012 Mali P, Cheng L. Concise review: Human cell engineering: cellular reprogramming and genome editing. Stem Cells (Dayton, Ohio). 30: 75-81. PMID 21905170 DOI: 10.1002/Stem.735  0.642
2012 Shah SN, Kerr C, Cope L, Mali P, Zambidis E, Lui C, Hillion J, Belton A, Huso D, Resar L. Abstract 429: The high mobility group A1 oncogene enhances cellular reprogramming to a pluripotent stem-like cell Cancer Research. 72: 429-429. DOI: 10.1158/1538-7445.Am2012-429  0.464
2011 Zou J, Mali P, Huang X, Dowey SN, Cheng L. Site-specific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease. Blood. 118: 4599-608. PMID 21881051 DOI: 10.1182/Blood-2011-02-335554  0.572
2011 Chou BK, Mali P, Huang X, Ye Z, Dowey SN, Resar LM, Zou C, Zhang YA, Tong J, Cheng L. Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures. Cell Research. 21: 518-29. PMID 21243013 DOI: 10.1038/Cr.2011.12  0.746
2010 Mali P, Wirtz D, Searson PC. Interplay of RhoA and motility in the programmed spreading of daughter cells postmitosis. Biophysical Journal. 99: 3526-34. PMID 21112276 DOI: 10.1016/J.Bpj.2010.10.006  0.386
2010 Ohm JE, Mali P, Van Neste L, Berman DM, Liang L, Pandiyan K, Briggs KJ, Zhang W, Argani P, Simons B, Yu W, Matsui W, Van Criekinge W, Rassool FV, Zambidis E, et al. Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells. Cancer Research. 70: 7662-73. PMID 20841480 DOI: 10.1158/0008-5472.Can-10-1361  0.613
2010 Swistowski A, Peng J, Liu Q, Mali P, Rao MS, Cheng L, Zeng X. Efficient generation of functional dopaminergic neurons from human induced pluripotent stem cells under defined conditions. Stem Cells (Dayton, Ohio). 28: 1893-904. PMID 20715183 DOI: 10.1002/Stem.499  0.58
2010 Mali P, Ye Z, Chou BK, Yen J, Cheng L. An improved method for generating and identifying human induced pluripotent stem cells. Methods in Molecular Biology (Clifton, N.J.). 636: 191-205. PMID 20336524 DOI: 10.1007/978-1-60761-691-7_12  0.739
2010 Mali P, Chou BK, Yen J, Ye Z, Zou J, Dowey S, Brodsky RA, Ohm JE, Yu W, Baylin SB, Yusa K, Bradley A, Meyers DJ, Mukherjee C, Cole PA, et al. Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells (Dayton, Ohio). 28: 713-20. PMID 20201064 DOI: 10.1002/Stem.402  0.757
2010 Huang X, Chou B, Mali P, Ye Z, Dowey SN, Cheng L. Human IPS Cells Generated From Adult Peripheral Blood Cells and Purified CD34+ Cells by a Non-Integrating Plasmid. Blood. 116: 1589-1589. DOI: 10.1182/Blood.V116.21.1589.1589  0.743
2009 Ye Z, Zhan H, Mali P, Dowey S, Williams DM, Jang YY, Dang CV, Spivak JL, Moliterno AR, Cheng L. Human-induced pluripotent stem cells from blood cells of healthy donors and patients with acquired blood disorders Blood. 114: 5473-5480. PMID 19797525 DOI: 10.1182/Blood-2009-04-217406  0.745
2009 Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, Chou BK, Chen G, Ye Z, Park IH, Daley GQ, Porteus MH, Joung JK, Cheng L. Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell. 5: 97-110. PMID 19540188 DOI: 10.1016/J.Stem.2009.05.023  0.762
2009 Ye Z, Zhan H, Mali P, Dowey S, Williams D, Jang Y, Van Dang C, Spivak JL, Moliterno AR, Cheng L. Hematopoiesis of Human Induced Pluripotent Stem Cells Derived From Blood Cells of Healthy Donors and Patients with the JAK2-V617F Somatic Mutation. Blood. 114: 812-812. DOI: 10.1182/Blood.V114.22.812.812  0.746
2008 Mali P, Ye Z, Hommond HH, Yu X, Lin J, Chen G, Zou J, Cheng L. Improved efficiency and pace of generating induced pluripotent stem cells from human adult and fetal fibroblasts. Stem Cells (Dayton, Ohio). 26: 1998-2005. PMID 18511599 DOI: 10.1634/Stemcells.2008-0346  0.748
2008 Yu X, Zou J, Ye Z, Hammond H, Chen G, Tokunaga A, Mali P, Li YM, Civin C, Gaiano N, Cheng L. Notch signaling activation in human embryonic stem cells is required for embryonic, but not trophoblastic, lineage commitment. Cell Stem Cell. 2: 461-71. PMID 18462696 DOI: 10.1016/J.Stem.2008.03.001  0.72
2008 Chen G, Ye Z, Yu X, Zou J, Mali P, Brodsky RA, Cheng L. Trophoblast differentiation defect in human embryonic stem cells lacking PIG-A and GPI-anchored cell-surface proteins. Cell Stem Cell. 2: 345-55. PMID 18397754 DOI: 10.1016/J.Stem.2008.02.004  0.736
2007 Cai L, Ye Z, Zhou BY, Mali P, Zhou C, Cheng L. Promoting human embryonic stem cell renewal or differentiation by modulating Wnt signal and culture conditions. Cell Research. 17: 62-72. PMID 17211448 DOI: 10.1038/Sj.Cr.7310138  0.755
2006 Mali P, Cheng L. Reprogramming somatic cells without fusion or ethical confusion Regenerative Medicine. 1: 837-840. DOI: 10.2217/17460751.1.6.837  0.614
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