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Population-scale cellular GUIDE-seq-2 and biochemical CHANGE-seq-R profiles reveal human genetic variation frequently affects Cas9 off-target activity

2025-02-12 | Preprint
Contributors: Shengdar Tsai; Cicera Lazzarotto; Yichao Li; Ashley R. Flory; Jacqueline Chyr; Muyu Yang; Varun Katta; Elizabeth Urbina; GaHyun Lee; Rachael Wood et al.
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Crossref

CHANGE-seq-BE enables simultaneously sensitive and unbiasedin vitroprofiling of base editor genome-wide activity

2024-03-30 | Preprint
Contributors: Cicera R. Lazzarotto; Varun Katta; Yichao Li; Elizabeth Urbina; GaHyun Lee; Shengdar Q. Tsai
Source: check_circle
Crossref

In vivo engineered B cells secrete high titers of broadly neutralizing anti-HIV antibodies in mice

Nature Biotechnology
2022 | Journal article
EID:

2-s2.0-85131526338

Part of ISSN: 15461696 10870156
Contributors: Nahmad, A.D.; Lazzarotto, C.R.; Zelikson, N.; Kustin, T.; Tenuta, M.; Huang, D.; Reuveni, I.; Nataf, D.; Raviv, Y.; Horovitz-Fried, M. et al.
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Shengdar Q. Tsai via Scopus - Elsevier

Prediction and validation of hematopoietic stem and progenitor cell off-target editing in transplanted rhesus macaques

Molecular Therapy
2022 | Journal article
EID:

2-s2.0-85114667768

Part of ISSN: 15250024 15250016
Contributors: AlJanahi, A.A.; Lazzarotto, C.R.; Chen, S.; Shin, T.-H.; Cordes, S.; Fan, X.; Jabara, I.; Zhou, Y.; Young, D.J.; Lee, B.-C. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Production and characterization of virus-free, CRISPR-CAR T cells capable of inducing solid tumor regression

Journal for ImmunoTherapy of Cancer
2022 | Journal article
EID:

2-s2.0-85138151779

Part of ISSN: 20511426
Contributors: Mueller, K.P.; Piscopo, N.J.; Forsberg, M.H.; Saraspe, L.A.; Das, A.; Russell, B.; Smerchansky, M.; Cappabianca, D.; Shi, L.; Shankar, K. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Base editing of haematopoietic stem cells rescues sickle cell disease in mice

Nature
2021 | Journal article
EID:

2-s2.0-85107300538

Part of ISSN: 14764687 00280836
Contributors: Newby, G.A.; Yen, J.S.; Woodard, K.J.; Mayuranathan, T.; Lazzarotto, C.R.; Li, Y.; Sheppard-Tillman, H.; Porter, S.N.; Yao, Y.; Mayberry, K. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

CRISPR-targeted MAGT1 insertion restores XMEN patient hematopoietic stem cells and lymphocytes

Blood
2021 | Journal article
EID:

2-s2.0-85121927812

Part of ISSN: 15280020 00064971
Contributors: Brault, J.; Liu, T.; Bello, E.; Liu, S.; Sweeney, C.L.; Meis, R.J.; Koontz, S.; Corsino, C.; Choi, U.; Vayssiere, G. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq

Nature Protocols
2021 | Journal article
EID:

2-s2.0-85119140522

Part of ISSN: 17502799 17542189
Contributors: Malinin, N.L.; Lee, G.H.; Lazzarotto, C.R.; Li, Y.; Zheng, Z.; Nguyen, N.T.; Liebers, M.; Topkar, V.V.; Iafrate, A.J.; Le, L.P. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity

Science Translational Medicine
2021 | Journal article
EID:

2-s2.0-85119933474

Part of ISSN: 19466242 19466234
Contributors: Prinzing, B.; Zebley, C.C.; Petersen, C.T.; Fan, Y.; Anido, A.A.; Yi, Z.; Nguyen, P.; Houke, H.; Bell, M.; Haydar, D. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Disease severity impacts plerixafor-mobilized stem cell collection in patients with sickle cell disease

Blood Advances
2021 | Journal article
EID:

2-s2.0-85106706093

Part of ISSN: 24739537 24739529
Contributors: Leonard, A.; Sharma, A.; Uchida, N.; Stroncek, D.; Panch, S.R.; West, K.; Molloy, E.; Hughes, T.E.; Hauffe, S.; Taylor, T. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Easy-Prime: a machine learning–based prime editor design tool

Genome Biology
2021 | Journal article
EID:

2-s2.0-85112799257

Part of ISSN: 1474760X 14747596
Contributors: Li, Y.; Chen, J.; Tsai, S.Q.; Cheng, Y.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Enhanced homology-directed repair for highly efficient gene editing in hematopoietic stem/progenitor cells

Blood
2021 | Journal article
EID:

2-s2.0-85105594152

Part of ISSN: 15280020 00064971
Contributors: De Ravin, S.S.; Brault, J.; Meis, R.J.; Liu, S.; Li, L.; Pavel-Dinu, M.; Lazzarotto, C.R.; Liu, T.; Koontz, S.M.; Choi, U. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Human genetic diversity alters therapeutic gene editing off-target outcomes

bioRxiv
2021 | Other
EID:

2-s2.0-85136910755

Part of ISSN: 26928205
Contributors: Cancellieri, S.; Zeng, J.; Lin, L.Y.; Tognon, M.; Nguyen, M.A.; Lin, J.; Bombieri, N.; Maitland, S.A.; Ciuculescu, M.-F.; Katta, V. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

In vivo engineered B cells retain memory and secrete high titers of anti-HIV antibodies in mice

bioRxiv
2021 | Other
EID:

2-s2.0-85106601219

Part of ISSN: 26928205
Contributors: Nahmad, A.D.; Lazzarotto, C.R.; Zelikson, N.; Kustin, T.; Tenuta, M.; Huang, D.; Reuveni, I.; Horovitz-Fried, M.; Dotan, I.; Rosin-Arbesfeld, R. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression

Genome Biology
2021 | Journal article
EID:

2-s2.0-85102601239

Part of ISSN: 1474760X 14747596
Contributors: Gao, P.; Lyu, Q.; Ghanam, A.R.; Lazzarotto, C.R.; Newby, G.A.; Zhang, W.; Choi, M.; Slivano, O.J.; Holden, K.; Walker, J.A. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Production and characterization of virus-free, CRISPR-CAR T cells capable of inducing solid tumor regression

bioRxiv
2021 | Other
EID:

2-s2.0-85123493655

Part of ISSN: 26928205
Contributors: Mueller, K.P.; Piscopo, N.J.; Forsberg, M.H.; Saraspe, L.A.; Das, A.; Russell, B.; Smerchansky, M.; Shi, L.; Shankar, K.; Ali, A. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

The NIH Somatic Cell Genome Editing program

Nature
2021-04-08 | Journal article
Contributors: Krishanu Saha; Erik J. Sontheimer; P. J. Brooks; Melinda R. Dwinell; Charles A. Gersbach; David R. Liu; Stephen A. Murray; Shengdar Q. Tsai; Ross C. Wilson; Daniel G. Anderson et al.
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BCL11A enhancer–edited hematopoietic stem cells persist in rhesus monkeys without toxicity

Journal of Clinical Investigation
2020 | Journal article
EID:

2-s2.0-85097113609

Part of ISSN: 15588238 00219738
Contributors: Demirci, S.; Zeng, J.; Wu, Y.; Uchida, N.; Shen, A.H.; Pellin, D.; Gamer, J.; Yapundich, M.; Drysdale, C.; Bonanno, J. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity

Nature Biotechnology
2020 | Journal article
EID:

2-s2.0-85092252245

Part of ISSN: 15461696 10870156
Contributors: Lazzarotto, C.R.; Malinin, N.L.; Li, Y.; Zhang, R.; Yang, Y.; Lee, G.H.; Cowley, E.; He, Y.; Lan, X.; Jividen, K. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression

bioRxiv
2020 | Other
EID:

2-s2.0-85098891322

Part of ISSN: 26928205
Contributors: Gao, P.; Lyu, Q.; Ghanam, A.R.; Lazzarotto, C.R.; Newby, G.A.; Zhang, W.; Choi, M.; Slivano, O.J.; Holden, K.; Walker, J.A. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Safe and efficient peripheral blood stem cell collection in patients with sickle cell disease using plerixafor

Haematologica
2020 | Journal article
EID:

2-s2.0-85085878157

Part of ISSN: 15928721 03906078
Contributors: Uchida, N.; Leonard, A.; Stroncek, D.; Panch, S.R.; West, K.; Molloy, E.; Hughes, T.E.; Hauffe, S.; Taylor, T.; Fitzhugh, C. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Validation and long-term follow up of CD33 off-targets predicted in vitro and in silico using error-corrected sequencing in rhesus macaques

bioRxiv
2020 | Other
EID:

2-s2.0-85102604089

Part of ISSN: 26928205
Contributors: AlJanahi, A.A.; Lazzarotto, C.R.; Chen, S.; Shin, T.-H.; Cordes, S.; Jabara, I.; Zhou, Y.; Young, D.; Lee, B.-C.; Yu, K.-R. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Zebrafish dscaml1 deficiency impairs retinal patterning and oculomotor function

Journal of Neuroscience
2020 | Journal article
EID:

2-s2.0-85077475196

Part of ISSN: 15292401 02706474
Contributors: Ma, M.; Ramirez, A.D.; Wang, T.; Roberts, R.L.; Harmon, K.E.; Schoppik, D.; Sharma, A.; Kuang, C.; Goei, S.L.; Gagnon, J.A. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Genome editing of HBG1 and HBG2 to induce fetal hemoglobin

Blood Advances
2019 | Journal article
EID:

2-s2.0-85074951547

Part of ISSN: 24739537 24739529
Contributors: Métais, J.-Y.; Doerfler, P.A.; Mayuranathan, T.; Bauer, D.E.; Fowler, S.C.; Hsieh, M.M.; Katta, V.; Keriwala, S.; Lazzarotto, C.R.; Luk, K. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Highly efficient therapeutic gene editing of human hematopoietic stem cells

Nature Medicine
2019 | Journal article
EID:

2-s2.0-85063430214

Part of ISSN: 1546170X 10788956
Contributors: Wu, Y.; Zeng, J.; Roscoe, B.P.; Liu, P.; Yao, Q.; Lazzarotto, C.R.; Clement, K.; Cole, M.A.; Luk, K.; Baricordi, C. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Safe and Efficient Peripheral Blood Stem Cell Collection in Patients with Sickle Cell Disease Using Plerixafor

SSRN
2019 | Other
EID:

2-s2.0-85110511813

Part of ISSN: 15565068
Contributors: Uchida, N.; Leonard, A.; Stroncek, D.; Panch, S.R.; West, K.; Molloy, E.; Hughes, T.E.; Hauffe, S.; Taylor, T.; Fitzhugh, C. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Zebrafish Dscaml1 is Essential for Retinal Patterning and Function of Oculomotor Subcircuits

bioRxiv
2019 | Other
EID:

2-s2.0-85095657196

Part of ISSN: 26928205
Contributors: Ma, M.; Ramirez, A.D.; Wang, T.; Roberts, R.L.; Harmon, K.E.; Schoppik, D.; Sharma, A.; Kuang, C.; Goei, S.L.; Gagnon, J.A. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

High levels of AAV vector integration into CRISPR-induced DNA breaks

Nature Communications
2019-09-30 | Journal article
Contributors: Killian S. Hanlon; Benjamin P. Kleinstiver; Sara P. Garcia; Mikołaj P. Zaborowski; Adrienn Volak; Stefan E. Spirig; Alissa Muller; Alexander A. Sousa; Shengdar Q. Tsai; Niclas E. Bengtsson et al.
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Genetic Inactivation of CD33 in Hematopoietic Stem Cells to Enable CAR T Cell Immunotherapy for Acute Myeloid Leukemia

Cell
2018 | Journal article
EID:

2-s2.0-85047396504

Part of ISSN: 10974172 00928674
Contributors: Kim, M.Y.; Yu, K.-R.; Kenderian, S.S.; Ruella, M.; Chen, S.; Shin, T.-H.; Aljanahi, A.A.; Schreeder, D.; Klichinsky, M.; Shestova, O. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

In vivo CRISPR editing with no detectable genome-wide off-target mutations

Nature
2018 | Journal article
EID:

2-s2.0-85053496364

Part of ISSN: 14764687 00280836
Contributors: Akcakaya, P.; Bobbin, M.L.; Guo, J.A.; Malagon-Lopez, J.; Clement, K.; Garcia, S.P.; Fellows, M.D.; Porritt, M.J.; Firth, M.A.; Carreras, A. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

In vivo CRISPR-Cas gene editing with no detectable genome-wide off-target mutations

bioRxiv
2018 | Other
EID:

2-s2.0-85095643883

Part of ISSN: 26928205
Contributors: Akcakaya, P.; Bobbin, M.L.; Guo, J.A.; Lopez, J.M.; Clement, M.K.; Garcia, S.P.; Fellows, M.D.; Porritt, M.J.; Firth, M.A.; Carreras, A. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Illuminating the genome-wide activity of genome editors for safe and effective therapeutics

Genome Biology
2018-12 | Journal article
Contributors: Yong Cheng; Shengdar Q. Tsai
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Defining CRISPR–Cas9 genome-wide nuclease activities with CIRCLE-seq

Nature Protocols
2018-11-19 | Journal article
Contributors: Cicera R. Lazzarotto; Nhu T. Nguyen; Xing Tang; Jose Malagon-Lopez; Jimmy A. Guo; Martin J. Aryee; J. Keith Joung; Shengdar Q. Tsai
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Crossref
grade
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Discovering the Genome-Wide Activity of CRISPR-Cas Nucleases

ACS Chemical Biology
2018-02-16 | Journal article
Contributors: Shengdar Q. Tsai
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Crossref
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Challenges for Sensitive Quantification of Gene Editing “Off-Target” Activity

Small Methods
2017 | Journal article
EID:

2-s2.0-85070858939

Part of ISSN: 23669608
Contributors: Tsai, S.Q.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

CIRCLE-seq: A highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets

Nature Methods
2017 | Journal article
EID:

2-s2.0-85018272560

Part of ISSN: 15487105 15487091
Contributors: Tsai, S.Q.; Nguyen, N.T.; Malagon-Lopez, J.; Topkar, V.V.; Aryee, M.J.; Joung, J.K.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Nodal patterning without lefty inhibitory feedback is functional but fragile

eLife
2017 | Journal article
EID:

2-s2.0-85040948779

Part of ISSN: 2050084X
Contributors: Rogers, K.W.; Lord, N.D.; Gagnon, J.A.; Pauli, A.; Zimmerman, S.; Aksel, D.C.; Reyon, D.; Tsai, S.Q.; Joung, J.K.; Schier, A.F.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Towards safe therapy for immunodeficiency

Nature Biomedical Engineering
2017 | Journal article
EID:

2-s2.0-85037837585

Part of ISSN: 2157846X
Contributors: Tsai, S.Q.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases

Nature Reviews Genetics
2016 | Journal article
EID:

2-s2.0-84964253170

Part of ISSN: 14710064 14710056
Contributors: Tsai, S.Q.; Joung, J.K.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells

Nature Biotechnology
2016 | Journal article
EID:

2-s2.0-84981347695

Part of ISSN: 15461696 10870156
Contributors: Kleinstiver, B.P.; Tsai, S.Q.; Prew, M.S.; Nguyen, N.T.; Welch, M.M.; Lopez, J.M.; McCaw, Z.R.; Aryee, M.J.; Joung, J.K.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects

Nature
2016 | Journal article
EID:

2-s2.0-84963941043

Part of ISSN: 14764687 00280836
Contributors: Kleinstiver, B.P.; Pattanayak, V.; Prew, M.S.; Tsai, S.Q.; Nguyen, N.T.; Zheng, Z.; Joung, J.K.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Open-source guideseq software for analysis of GUIDE-seq data

Nature Biotechnology
2016 | Journal article
EID:

2-s2.0-84969802813

Part of ISSN: 15461696 10870156
Contributors: Tsai, S.Q.; Topkar, V.V.; Joung, J.K.; Aryee, M.J.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition

Nature Biotechnology
2015 | Journal article
EID:

2-s2.0-84949791988

Part of ISSN: 15461696 10870156
Contributors: Kleinstiver, B.P.; Prew, M.S.; Tsai, S.Q.; Nguyen, N.T.; Topkar, V.V.; Zheng, Z.; Joung, J.K.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Continuous directed evolution of DNA-binding proteins to improve TALEN specificity

Nature Methods
2015 | Journal article
EID:

2-s2.0-84959102577

Part of ISSN: 15487105 15487091
Contributors: Hubbard, B.P.; Badran, A.H.; Zuris, J.A.; Guilinger, J.P.; Davis, K.M.; Chen, L.; Tsai, S.Q.; Sander, J.D.; Joung, J.K.; Liu, D.R.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Dimeric CRISPR RNA-Guided FokI-dCas9 Nucleases Directed by Truncated gRNAs for Highly Specific Genome Editing

Human Gene Therapy
2015 | Journal article
EID:

2-s2.0-84937575600

Part of ISSN: 15577422 10430342
Contributors: Wyvekens, N.; Topkar, V.V.; Khayter, C.; Joung, J.K.; Tsai, S.Q.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

Nature
2015 | Journal article
EID:

2-s2.0-84937908208

Part of ISSN: 14764687 00280836
Contributors: Kleinstiver, B.P.; Prew, M.S.; Tsai, S.Q.; Topkar, V.V.; Nguyen, N.T.; Zheng, Z.; Gonzales, A.P.W.; Li, Z.; Peterson, R.T.; Yeh, J.-R.J. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Genome editing in human cells using CRISPR/Cas nucleases

Current Protocols in Molecular Biology
2015 | Journal article
EID:

2-s2.0-85016241108

Part of ISSN: 19343647 19343639
Contributors: Wyvekens, N.; Tsai, S.Q.; Joung, J.K.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

Nature Biotechnology
2015 | Journal article
EID:

2-s2.0-84923266604

Part of ISSN: 15461696 10870156
Contributors: Tsai, S.Q.; Zheng, Z.; Nguyen, N.T.; Liebers, M.; Topkar, V.V.; Thapar, V.; Wyvekens, N.; Khayter, C.; Iafrate, A.J.; Le, L.P. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

Nature Genetics
2015 | Journal article
EID:

2-s2.0-84929134273

Part of ISSN: 15461718 10614036
Contributors: Liao, J.; Karnik, R.; Gu, H.; Ziller, M.J.; Clement, K.; Tsankov, A.M.; Akopian, V.; Gifford, C.A.; Donaghey, J.; Galonska, C. et al.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier

Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity

Nature Methods
2014 | Journal article
EID:

2-s2.0-84897954502

Part of ISSN: 15487105 15487091
Contributors: Guilinger, J.P.; Pattanayak, V.; Reyon, D.; Tsai, S.Q.; Sander, J.D.; Joung, J.K.; Liu, D.R.
Source: Self-asserted source
Shengdar Q. Tsai via Scopus - Elsevier
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