Biography
Dr. Ciaran Lee studied Genetics at University College Cork (UCC) and obtained his PhD in Molecular Medicine also at UCC. This was followed by two postdoctoral positions in the US at Georgia Institute of Technology and at Rice University. At Rice University he established and directed a Genome Engineering Core to develop genome engineering tools for treating human disease. He returned to UCC in 2019 to investigate the role of the gut microbiome in inflammation as a Marie Curie Fellow. In 2023 he was appointed as a Lecturer in the School of Biochemistry and Cell Biology at UCC.Research Interests
My research journey began as a PhD student designing Zinc Finger Nucleases to target cystic fibrosis causing mutations (ZFNs for CF correction). As a postdoc researcher I worked on developing CRISPR gene editing for treating sickle cell disease (CRISPR for SCD, CRISPR for SCD pre-clinical), developing systems for in vivo CRISPR gene editing (In vivo CRISPR, in vivo self-deleting CRISPR), applying in vivo CRISPR editing for inborn errors of metabolism (CRISPR for methylmalonic acidemia), and designing methods to improve the safety of gene editing tools (TRACE-seq, HiFi CRISPR, COSMID). Recently I developed a CRISPR based functional genomics approach to identify variants of interest in inflammatory disease (expression CROP-seq). My research focuses on developing gene editing tools for treating genetic diseases and cancer with an emphasis on novel CRISPR based techniques such as base editing, prime editing, and CRISPR transposases. I am also interested in the identification of modifier genes for inherited disorders, engineering synthetic microbes as living drugs, and mining microbial genomes for novel DNA modifying enzymes that can be harnessed to create the next generation of genome editing tools.Research Grants
| Project | Funding Body | Start Date | End Date | Award | |
|---|---|---|---|---|---|
| Bifidobacteria as a model system for host-microbe interaction - BIF-PROTECTS | Horizon 2020 | 01-APR-21 | 31-MAR-23 | €196,591.00 | |
| Cystinosis Gene Repair | Other: Not Listed | 01-OCT-10 | 30-SEP-12 | €146,258.00 |
Publications
Book Chapters
| Year | Publication | |
|---|---|---|
| (2022) | 'Identification and Validation of CRISPR/Cas9 Off-Target Activity in Hematopoietic Stem and Progenitor Cells' Park SH;Lee CM;Bao G; (2022) 'Identification and Validation of CRISPR/Cas9 Off-Target Activity in Hematopoietic Stem and Progenitor Cells' In: Nagarajan Kannan, Philip Beer (eds). Stem Cell Assays: Methods and Protocols. New York: Springer US. [DOI] [Details] | |
| (2017) | 'Design and validation of CRISPR/Cas9 systems for targeted gene modification in induced pluripotent stem cells' Lee, Ciaran M and Zhu, Haibao and Davis, Timothy H and Deshmukh, Harshahardhan and Bao, Gang (2017) 'Design and validation of CRISPR/Cas9 systems for targeted gene modification in induced pluripotent stem cells' In: In vitro mutagenesis. New York, NY: Humana Press. [Details] | |
| (2009) | 'Gene therapy and individualized medicine' Harrison P.;Flynn R.;Lee C. (2009) 'Gene therapy and individualized medicine' In: Predictive Diagnostics and Personalized Treatment: Dream or Reality. [Details] |
Peer Reviewed Journals
| Year | Publication | |
|---|---|---|
| (2024) | 'GH136-encoding gene (perB) is involved in gut colonization and persistence by Bifidobacterium bifidum PRL2010' Rizzo SM;Vergna LM;Alessandri G;Lee C;Fontana F;Lugli GA;Carnevali L;Bianchi MG;Barbetti M;Taurino G;Sgoifo A;Bussolati O;Turroni F;van Sinderen D;Ventura M; (2024) 'GH136-encoding gene (perB) is involved in gut colonization and persistence by Bifidobacterium bifidum PRL2010'. Microbial Biotechnology, 17 (2) [DOI] [Details] | |
| (2022) | 'Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus' Vaidyanathan S;Baik R;Chen L;Bravo DT;Suarez CJ;Abazari SM;Salahudeen AA;Dudek AM;Teran CA;Davis TH;Lee CM;Bao G;Randell SH;Artandi SE;Wine JJ;Kuo CJ;Desai TJ;Nayak JV;Sellers ZM;Porteus MH; (2022) 'Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus'. Molecular Therapy, 30 (1) [DOI] [Details] | |
| (2022) | 'Electroporation-Mediated Delivery of Cas9 Ribonucleoproteins Results in High Levels of Gene Editing in Primary Hepatocytes' Rathbone, T;Ates, I;Fernando, L;Addlestone, E;Lee, CM;Richards, VP;Cottle, RN (2022) 'Electroporation-Mediated Delivery of Cas9 Ribonucleoproteins Results in High Levels of Gene Editing in Primary Hepatocytes'. Crispr Journal, 5 :397-409 [DOI] [Details] | |
| (2022) | 'High-throughput Imaging of CRISPR- and Recombinant Adeno-associated Virus-induced DNA Damage Response in Human Hematopoietic Stem and Progenitor Cells' Allen, D;Weiss, LE;Saguy, A;Rosenberg, M;Iancu, O;Matalon, O;Lee, CR;Beider, K;Nagler, A;Shechtman, Y;Hendel, A (2022) 'High-throughput Imaging of CRISPR- and Recombinant Adeno-associated Virus-induced DNA Damage Response in Human Hematopoietic Stem and Progenitor Cells'. Crispr Journal, 5 :80-94 [DOI] [Details] | |
| (2021) | 'Development of beta-globin gene correction in human hematopoietic stem cells as a potential durable treatment for sickle cell disease' Lattanzi, A;Camarena, J;Lahiri, P;Segal, H;Srifa, W;Vakulskas, CA;Frock, RL;Kenrick, J;Lee, C;Talbott, N;Skowronski, J;Cromer, MK;Charlesworth, CT;Bak, RO;Mantri, S;Bao, G;DiGiusto, D;Tisdale, J;Wright, JF;Bhatia, N;Roncarolo, MG;Dever, DP;Porteus, MH (2021) 'Development of beta-globin gene correction in human hematopoietic stem cells as a potential durable treatment for sickle cell disease'. Science Translational Medicine, 13 [DOI] [Details] | |
| (2021) | 'In vivo genome editing at the albumin locus to treat methylmalonic acidemia' Schneller JL;Lee CM;Venturoni LE;Chandler RJ;Li A;Myung S;Cradick TJ;Hurley AE;Lagor WR;Bao G;Venditti CP; (2021) 'In vivo genome editing at the albumin locus to treat methylmalonic acidemia'. Molecular Therapy-Methods &Amp; Clinical Development, 23 [DOI] [Details] | |
| (2021) | 'TNF-alpha synergises with IFN-gamma to induce caspase-8-JAK1/2-STAT1-dependent death of intestinal epithelial cells' Woznicki, JA;Saini, N;Flood, P;Rajaram, S;Lee, CM;Stamou, P;Skowyra, A;Bustamante-Garrido, M;Regazzoni, K;Crawford, N;McDade, SS;Longley, DB;Aza-Blanc, P;Shanahan, F;Zulquernain, SA;McCarthy, J;Melgar, S;McRae, BL;Nally, K (2021) 'TNF-alpha synergises with IFN-gamma to induce caspase-8-JAK1/2-STAT1-dependent death of intestinal epithelial cells'. Cell Death &Amp; Disease, 12 [DOI] [Details] | |
| (2021) | 'The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells' Sharma R;Dever DP;Lee CM;Azizi A;Pan Y;Camarena J;Köhnke T;Bao G;Porteus MH;Majeti R; (2021) 'The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells'. Nature Communications, 12 (1) [DOI] [Details] | |
| (2020) | 'High-Efficiency, Selection-free Gene Repair in Airway Stem Cells from Cystic Fibrosis Patients Rescues CFTR Function in Differentiated Epithelia' Vaidyanathan, Sriram and Salahudeen, Ameen A and Sellers, Zachary M and Bravo, Dawn T and Choi, Shannon S and Batish, Arpit and Le, Wei and Baik, Ron and Kaushik, Milan P and Galper, Noah and others (2020) 'High-Efficiency, Selection-free Gene Repair in Airway Stem Cells from Cystic Fibrosis Patients Rescues CFTR Function in Differentiated Epithelia'. Cell Stem Cell, 26 (2):161-171 [Details] | |
| (2020) | 'Genome editing of donor-derived T-cells to generate allogenic chimeric antigen receptor-modified T cells: Optimizing $\alpha$$\beta$ T cell-depleted haploidentical hematopoietic stem cell transplantation' Wiebking, Volker and Lee, Ciaran M and Mostrel, Nathalie and Lahiri, Premanjali and Bak, Rasmus and Bao, Gang and Roncarolo, Maria Grazia and Bertaina, Alice and Porteus, Matthew H (2020) 'Genome editing of donor-derived T-cells to generate allogenic chimeric antigen receptor-modified T cells: Optimizing $\alpha$$\beta$ T cell-depleted haploidentical hematopoietic stem cell transplantation'. Haematologica, [Details] | |
| (2020) | 'Fine-mapping within eQTL credible intervals by expression CROP-seq' Pan, Yidan; Tian, Ruoyu; Lee, Ciaran M.; Bao, Gang; Gibson, Greg (2020) 'Fine-mapping within eQTL credible intervals by expression CROP-seq'. Biology Methods & Protocols, 5 (1):1-8 [DOI] [Full Text] [Details] | |
| (2020) | 'Site-Specific Post-translational Surface Modification of Adeno-Associated Virus Vectors Using Leucine Zippers' Thadani, Nicole N and Yang, Joanna and Moyo, Buhle and Lee, Ciaran M and Chen, Maria Y and Bao, Gang and Suh, Junghae (2020) 'Site-Specific Post-translational Surface Modification of Adeno-Associated Virus Vectors Using Leucine Zippers'. ACS Synthetic Biology, 9 (3):461-467 [Details] | |
| (2020) | 'AAV-CRISPR gene editing is negated by pre-existing immunity to Cas9' Li, Ang and Tanner, Mark R and Lee, Ciaran M and Hurley, Ayrea E and De Giorgi, Marco and Jarrett, Kelsey E and Davis, Timothy H and Doerfler, Alexandria M and Bao, Gang and Beeton, Christine and others (2020) 'AAV-CRISPR gene editing is negated by pre-existing immunity to Cas9'. Molecular Therapy, [Details] | |
| (2020) | 'CRISPR-based gene editing enables FOXP3 gene repair in IPEX patient cells' Goodwin, M.; Lee, E.; Lakshmanan, U.; Shipp, S.; Froessl, L.; Barzaghi, F.; Passerini, L.; Narula, M.; Sheikali, A.; Lee, Ciaran M.; Bao, G.; Bauer, C. S.; Miller, H. K.; Garcia-Lloret, M.; Butte, M. J.; Bertaina, A.; Shah, A.; Pavel-Dinu, M.; Hendel, A.; Porteus, M.; Roncarolo, M. G.; Bacchetta, R. (2020) 'CRISPR-based gene editing enables FOXP3 gene repair in IPEX patient cells'. Science Advances, 6 (19):1-17 [DOI] [Full Text] [Details] | |
| (2020) | 'Metabolic engineering generates a transgene-free safety switch for cell therapy' Wiebking V.;Patterson J.O.;Martin R.;Chanda M.K.;Lee C.M.;Srifa W.;Bao G.;Porteus M.H. (2020) 'Metabolic engineering generates a transgene-free safety switch for cell therapy'. Nature Biotechnology, [DOI] [Details] | |
| (2020) | 'Pitfalls in single clone crispr-cas9 mutagenesis to fine-map regulatory intervals' Tian, Ruoyu; Pan, Yidan; Etheridge, Thomas H. A.; Deshmukh, Harshavardhan; Gulick, Dalia; Gibson, Greg; Bao, Gang; Lee, Ciaran M. (2020) 'Pitfalls in single clone crispr-cas9 mutagenesis to fine-map regulatory intervals'. Genes, 11 (5):1-18 [DOI] [Full Text] [Details] | |
| (2020) | 'Tools for experimental and computational analyses of off-target editing by programmable nucleases' Bao, X. Robert; Pan, Yidan; Lee, Ciaran M.; Davis, Timothy H.; Bao, Gang (2020) 'Tools for experimental and computational analyses of off-target editing by programmable nucleases'. Nature Protocols, 16 :10-26 [DOI] [Full Text] [Details] | |
| (2019) | 'Optimization of CRISPR/Cas9 Delivery to Human Hematopoietic Stem and Progenitor Cells for Therapeutic Genomic Rearrangements' Lattanzi, Annalisa and Meneghini, Vasco and Pavani, Giulia and Amor, Fatima and Ramadier, Sophie and Felix, Tristan and Antoniani, Chiara and Masson, Cecile and Alibeu, Olivier and Lee, Ciaran and others (2019) 'Optimization of CRISPR/Cas9 Delivery to Human Hematopoietic Stem and Progenitor Cells for Therapeutic Genomic Rearrangements'. Molecular Therapy, 27 (1):137-150 [Details] | |
| (2019) | 'Therapeutically relevant engraftment of a CRISPR-Cas9-edited HSC-enriched population with HbF reactivation in nonhuman primates' Humbert O.;Radtke S.;Samuelson C.;Carrillo R.;Perez A.;Reddy S.;Lux C.;Pattabhi S.;Schefter L.;Negre O.;Lee C.;Bao G.;Adair J.;Peterson C.;Rawlings D.;Scharenberg A.;Kiem H. (2019) 'Therapeutically relevant engraftment of a CRISPR-Cas9-edited HSC-enriched population with HbF reactivation in nonhuman primates'. Science Translational Medicine, 11 (503) [DOI] [Details] | |
| (2019) | 'Gene correction for SCID-X1 in long-term hematopoietic stem cells' Pavel-Dinu, Mara and Wiebking, Volker and Dejene, Beruh T and Srifa, Waracharee and Mantri, Sruthi and Nicolas, Carmencita E and Lee, Ciaran and Bao, Gang and Kildebeck, Eric J and Punjya, Niraj and others (2019) 'Gene correction for SCID-X1 in long-term hematopoietic stem cells'. Nature communications, 10 (1):1-15 [Details] | |
| (2019) | 'Engineered materials for in vivo delivery of genome-editing machinery' Tong, Sheng and Moyo, Buhle and Lee, Ciaran M and Leong, Kam and Bao, Gang (2019) 'Engineered materials for in vivo delivery of genome-editing machinery'. Nature Reviews Materials, :1-12 [Details] | |
| (2019) | 'Highly efficient editing of the $\beta$-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease' Park, So Hyun and Lee, Ciaran M and Dever, Daniel P and Davis, Timothy H and Camarena, Joab and Srifa, Waracharee and Zhang, Yankai and Paikari, Alireza and Chang, Alicia K and Porteus, Matthew H and others (2019) 'Highly efficient editing of the $\beta$-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease'. Nucleic acids research, 47 (15):7955-7972 [Details] | |
| (2019) | 'Collagen-rich airway smooth muscle cells are a metastatic niche for tumor colonization in the lung' Lee, Yu-Cheng and Kurtova, Antonina V and Xiao, Jing and Nikolos, Fotis and Hayashi, Kazukuni and Tramel, Zoe and Jain, Antrix and Chen, Fengju and Chokshi, Mithil and Lee, Ciaran and others (2019) 'Collagen-rich airway smooth muscle cells are a metastatic niche for tumor colonization in the lung'. Nature communications, 10 (1):1-16 [Details] | |
| (2019) | 'A self-deleting AAV-CRISPR system for in vivo genome editing' Li, Ang and Lee, Ciaran M and Hurley, Ayrea E and Jarrett, Kelsey E and De Giorgi, Marco and Lu, Weiqi and Balderrama, Karol S and Doerfler, Alexandria M and Deshmukh, Harshavardhan and Ray, Anirban and others (2019) 'A self-deleting AAV-CRISPR system for in vivo genome editing'. Molecular Therapy-Methods \& Clinical Development, 12 :111-122 [Details] | |
| (2019) | 'Spatial control of in vivo CRISPR--Cas9 genome editing via nanomagnets' Zhu, Haibao and Zhang, Linlin and Tong, Sheng and Lee, Ciaran M and Deshmukh, Harshavardhan and Bao, Gang (2019) 'Spatial control of in vivo CRISPR--Cas9 genome editing via nanomagnets'. Nature biomedical engineering, 3 (2):126-136 [Details] | |
| (2019) | 'Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I' Gomez-Ospina, Natalia and Scharenberg, Samantha G and Mostrel, Nathalie and Bak, Rasmus O and Mantri, Sruthi and Quadros, Rolen M and Gurumurthy, Channabasavaiah B and Lee, Ciaran and Bao, Gang and Suarez, Carlos J and others (2019) 'Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I'. Nature communications, 10 (1):1-14 [Details] | |
| (2019) | 'Gene correction for SCID-X1 in long-term hematopoietic stem cells' Pavel-Dinu, Mara and Wiebking, Volker and Dejene, Beruh T and Srifa, Waracharee and Mantri, Sruthi and Nicolas, Carmencita E and Lee, Ciaran and Bao, Gang and Kildebeck, Eric J and Punjya, Niraj and others (2019) 'Gene correction for SCID-X1 in long-term hematopoietic stem cells'. Nature communications, 10 (1):1-15 [Details] | |
| (2018) | 'In Vivo Ryr 2 Editing Corrects Catecholaminergic Polymorphic Ventricular Tachycardia' Pan, Xiaolu and Philippen, Leonne and Lahiri, Satadru K and Lee, Ciaran and Park, So Hyun and Word, Tarah A and Li, Na and Jarrett, Kelsey E and Gupta, Rajat and Reynolds, Julia O and others (2018) 'In Vivo Ryr 2 Editing Corrects Catecholaminergic Polymorphic Ventricular Tachycardia'. Circulation Research, 123 (8):953-963 [Details] | |
| (2018) | 'A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells' Vakulskas, Christopher A and Dever, Daniel P and Rettig, Garrett R and Turk, Rolf and Jacobi, Ashley M and Collingwood, Michael A and Bode, Nicole M and McNeill, Matthew S and Yan, Shuqi and Camarena, Joab and others (2018) 'A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells'. Nature medicine, 24 (8) [Details] | |
| (2018) | 'Somatic editing of Ldlr with adeno-associated viral-CRISPR is an efficient tool for atherosclerosis research' Jarrett, Kelsey E and Lee, Ciaran and De Giorgi, Marco and Hurley, Ayrea and Gillard, Baiba K and Doerfler, Alexandria M and Li, Ang and Pownall, Henry J and Bao, Gang and Lagor, William R (2018) 'Somatic editing of Ldlr with adeno-associated viral-CRISPR is an efficient tool for atherosclerosis research'. Arteriosclerosis, thrombosis, and vascular biology, 38 (9):1997-2006 [Details] | |
| (2018) | 'Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity' Lee, Ciaran M and Davis, Timothy H and Bao, Gang (2018) 'Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity'. Experimental physiology, 103 (4):456-460 [Details] | |
| (2017) | 'CRISPR/Cas9-Based Genome Editing for Disease Modeling and Therapy: Challenges and Opportunities for Nonviral Delivery' Wang, Hong-Xia and Li, Mingqiang and Lee, Ciaran M and Chakraborty, Syandan and Kim, Hae-Won and Bao, Gang and Leong, Kam W (2017) 'CRISPR/Cas9-Based Genome Editing for Disease Modeling and Therapy: Challenges and Opportunities for Nonviral Delivery'. Chemical Reviews, 117 (15):9874-9906 [Details] | |
| (2017) | 'Genome editing for inborn errors of metabolism: advancing towards the clinic' Schneller, Jessica L and Lee, Ciaran M and Bao, Gang and Venditti, Charles P (2017) 'Genome editing for inborn errors of metabolism: advancing towards the clinic'. BMC medicine, 15 (1) [Details] | |
| (2017) | 'CD7-edited T cells expressing a CD7-specific CAR for the therapy of T-cell malignancies' Gomes-Silva, Diogo and Srinivasan, Madhuwanti and Sharma, Sandhya and Lee, Ciaran M and Wagner, Dimitrios L and Davis, Timothy H and Rouce, Rayne H and Bao, Gang and Brenner, Malcolm K and Mamonkin, Maksim (2017) 'CD7-edited T cells expressing a CD7-specific CAR for the therapy of T-cell malignancies'. Blood, 130 (3):285-296 [Details] | |
| (2017) | 'Somatic genome editing with CRISPR/Cas9 generates and corrects a metabolic disease' Jarrett, Kelsey E and Lee, Ciaran M and Yeh, Yi-Hsien and Hsu, Rachel H and Gupta, Rajat and Zhang, Min and Rodriguez, Perla J and Lee, Chang Seok and Gillard, Baiba K and Bissig, Karl-Dimiter and others (2017) 'Somatic genome editing with CRISPR/Cas9 generates and corrects a metabolic disease'. Scientific Reports, 7 [Details] | |
| (2017) | 'Efficient CRISPR/Cas9-mediated genome editing using a chimeric single-guide RNA molecule' Butt, Haroon and Eid, Ayman and Ali, Zahir and Atia, Mohamed AM and Mokhtar, Morad M and Hassan, Norhan and Lee, Ciaran M and Bao, Gang and Mahfouz, Magdy M (2017) 'Efficient CRISPR/Cas9-mediated genome editing using a chimeric single-guide RNA molecule'. Frontiers in Plant Science, 8 [Details] | |
| (2016) | 'A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood' Zhao, Jing and Akinsanmi, Idowu and Arafat, Dalia and Cradick, TJ and Lee, Ciaran M and Banskota, Samridhi and Marigorta, Urko M and Bao, Gang and Gibson, Greg (2016) 'A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood'. The American Journal of Human Genetics, 98 (2):299-309 [Details] | |
| (2016) | 'Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing' Lee, Ciaran M and Cradick, Thomas J and Fine, Eli J and Bao, Gang (2016) 'Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing'. Molecular Therapy, 24 (3):475-487 [Details] | |
| (2016) | 'Treating hemoglobinopathies using gene-correction approaches: promises and challenges' Cottle, Renee N and Lee, Ciaran M and Bao, Gang (2016) 'Treating hemoglobinopathies using gene-correction approaches: promises and challenges'. Human Genetics, 135 (9):993-1010 [Details] | |
| (2016) | 'Analysis of gene repair tracts from Cas9/gRNA double-stranded breaks in the human CFTR gene' Hollywood, Jennifer A and Lee, Ciaran M and Scallan, Martina F and Harrison, Patrick T (2016) 'Analysis of gene repair tracts from Cas9/gRNA double-stranded breaks in the human CFTR gene'. Scientific reports, 6 (1):1-7 [Details] | |
| (2016) | 'Streptococcus thermophilus CRISPR-Cas9 systems enable specific editing of the human genome' M\"uller, Maximilian and Lee, Ciaran M and Gasiunas, Giedrius and Davis, Timothy H and Cradick, Thomas J and Siksnys, Virginijus and Bao, Gang and Cathomen, Toni and Mussolino, Claudio (2016) 'Streptococcus thermophilus CRISPR-Cas9 systems enable specific editing of the human genome'. Molecular Therapy, 24 (3):636-644 [Details] | |
| (2016) | 'The Neisseria meningitidis CRISPR-Cas9 system enables specific genome editing in mammalian cells' Lee, Ciaran M and Cradick, Thomas J and Bao, Gang (2016) 'The Neisseria meningitidis CRISPR-Cas9 system enables specific genome editing in mammalian cells'. Molecular Therapy, 24 (3):645-654 [Details] | |
| (2015) | 'Controlled delivery of $\beta$-globin-targeting TALENs and CRISPR/Cas9 into mammalian cells for genome editing using microinjection' Cottle, Renee N and Lee, Ciaran M and Archer, David and Bao, Gang (2015) 'Controlled delivery of $\beta$-globin-targeting TALENs and CRISPR/Cas9 into mammalian cells for genome editing using microinjection'. Scientific reports, 5 [Details] | |
| (2015) | 'Efficient fdCas9 synthetic endonuclease with improved specificity for precise genome engineering' Aouida, Mustapha and Eid, Ayman and Ali, Zahir and Cradick, Thomas and Lee, Ciaran and Deshmukh, Harshavardhan and Atef, Ahmed and AbuSamra, Dina and Gadhoum, Samah Zeineb and Merzaban, Jasmeen and others (2015) 'Efficient fdCas9 synthetic endonuclease with improved specificity for precise genome engineering'. PLoS One, 10 (7) [Details] | |
| (2014) | 'COSMID: a web-based tool for identifying and validating CRISPR/Cas off-target sites' Cradick, Thomas J and Qiu, Peng and Lee, Ciaran M and Fine, Eli J and Bao, Gang (2014) 'COSMID: a web-based tool for identifying and validating CRISPR/Cas off-target sites'. Molecular Therapy-Nucleic Acids, 3 [Details] | |
| (2012) | 'Correction of the $\Delta$F508 Mutation in the Cystic Fibrosis Transmembrane Conductance Regulator Gene by Zinc-Finger Nuclease Homology-Directed Repair' Lee, Ciaran M and Flynn, Rowan and Hollywood, Jennifer A and Scallan, Martina F and Harrison, Patrick T (2012) 'Correction of the $\Delta$F508 Mutation in the Cystic Fibrosis Transmembrane Conductance Regulator Gene by Zinc-Finger Nuclease Homology-Directed Repair'. BioResearch Open Access, 1 (3):99-108 [Details] |
Other Journals
| Year | Publication | |
|---|---|---|
| (2020) | 'TRACE-Seq Reveals Clonal Reconstitution Dynamics of Gene Targeted Human Hematopoietic Stem Cells' Sharma, Rajiv and Dever, Daniel P and Lee, Ciaran M and Azizi, Armon and Pan, Yidan and Camarena, Joab and K\"ohnke, Thomas and Bao, Gang and Porteus, Matthew and Majeti, Ravindra (2020) 'TRACE-Seq Reveals Clonal Reconstitution Dynamics of Gene Targeted Human Hematopoietic Stem Cells' bioRxiv, . [Details] | |
| (2019) | 'Highly Efficient Repair of the $\Delta$F508 Mutation in Airway Stem Cells of Cystic Fibrosis Patients with Functional Rescue of the Differentiated Epithelia' Vaidyanathan, Sriram and Salahudeen, Ameen A and Sellers, Zachary M and Bravo, Dawn T and Choi, Shannon S and Batish, Arpit and Le, Wei and De La O, Sean and Kaushik, Milan P and Galper, Noah and others (2019) 'Highly Efficient Repair of the $\Delta$F508 Mutation in Airway Stem Cells of Cystic Fibrosis Patients with Functional Rescue of the Differentiated Epithelia' bioRxiv, . [Details] |
Conference Publications
| Year | Publication | |
|---|---|---|
| (2020) | In-Silico and Experimental Detection of Personalized CRISPR Off-Targets Pan, YD;Lee, C;Deshmukh, H;Bao, G (2020) In-Silico and Experimental Detection of Personalized CRISPR Off-Targets , pp.456-457 [Details] | |
| (2017) | MOLECULAR THERAPY Lattanzi, Annalisa and Meneghini, Vasco and Pavani, Giulia and Amor, Fatima and Antoniani, Chiara and Lee, Ciaran and Porteus, Matthew and Bao, Gang and Amendola, Mario and Mavilio, Fulvio and others (2017) Viral and Non-Viral Delivery of the CRISPR-Cas9 System in Human Hematopoietic Stem and Progenitor Cells MOLECULAR THERAPY , pp.299-299 [Details] | |
| (2017) | MOLECULAR THERAPY Park, So Hyun and Lee, Ciaran M and Zhang, Yankai and Sheehan, Vivien and Bao, Gang (2017) Gene Edited Hematopoietic Stem/Progenitor Cells for Treating Sickle Cell Disease MOLECULAR THERAPY , pp.178-178 [Details] | |
| (2017) | MOLECULAR THERAPY Lagor, William R and Jarrett, Kelsey E and Lee, Ciaran M and Yeh, Yi-Hsien and Hsu, Rachel H and Gupta, Rajat and Zhang, Min and Rodriguez, Perla and Bissig, Karl-Dimiter and Pownall, Henry J and others (2017) Somatic Genome Editing with AAV Vectors Generates and Corrects a Metabolic Disease MOLECULAR THERAPY , pp.14-14 [Details] | |
| (2017) | MOLECULAR THERAPY Wagner, Dimitrios L and Tashiro, Haruko and Shum, Thomas and Halder, Debopriyo and Gundry, Michael C and Brunetti, Lorenzo and Lee, Ciaran M and Shin, Benjamin H and Sauer, Tim and Mamonkin, Maksim and others (2017) A Single CRISPR-Mediated Knockout as Novel Suicide Switch and Selection Tool for Gene-Modified T Cells MOLECULAR THERAPY , pp.63-64 [Details] | |
| (2017) | Preclinical development of HBB gene correction in autologous hematopoietic stem and progenitor cells to treat severe sickle cell disease Dever, Daniel P and Camarena, Joab and Lee, Ciaran and Vakulskas, Christopher and Behlke, Mark and Bao, Gang and Porteus, Matthew (2017) Preclinical development of HBB gene correction in autologous hematopoietic stem and progenitor cells to treat severe sickle cell disease , pp.4620-4620 [Details] | |
| (2017) | MOLECULAR THERAPY Lee, Ciaran M and Park, So Hyun and Zhang, Yankai and Deshmukh, Harshavardhan and Cradick, TJ and Sheehan, Vivien and Bao, Gang (2017) Genome Editing Based Reactivation of Fetal Hemoglobin Expression in HSPCs for Treating Sickle Cell Disease MOLECULAR THERAPY , pp.305-305 [Details] | |
| (2016) | 131. Chromatin-Dependent Loci Accessibility Affects CRISPR-Cas9 Targeting Efficiency Lee, Ciaran M and Davis, Timothy H and Deshmukh, Harshavardhan and Bao, Gang (2016) 131. Chromatin-Dependent Loci Accessibility Affects CRISPR-Cas9 Targeting Efficiency [Details] | |
| (2016) | Therapeutic CRISPR/Cas9 genome editing for treating sickle cell disease Park, So Hyun and Lee, Ciaran M and Deshmukh, Harshavardhan and Bao, Gang (2016) Therapeutic CRISPR/Cas9 genome editing for treating sickle cell disease [Details] | |
| (2015) | Gene editing with crispr-cas9 for treating beta-hemoglobinopathies Lee, Ciaran and Bao, Gang and Porteus, Matthew H and Cornu, Tatjana and Miccio, Annarita and Cradick, Thomas and Cathomen, Toni and Lundberg, Ante and Mavilio, Fulvio (2015) Gene editing with crispr-cas9 for treating beta-hemoglobinopathies [Details] | |
| (2013) | 60 Permanent correction of> 80\% of disease-causing mutations in human CF cells Hollywood, Jennifer and Harrison, PT and Flynn, R and Lee, CM (2013) 60 Permanent correction of> 80\% of disease-causing mutations in human CF cells [Details] | |
| (2011) | Proceedings of The Physiological Society Hollywood, JA and Lee, CM and Flynn, R and Kaschig, K and Scallan, MF and Harrison, PT (2011) Correction of the Cystic Fibrosis Transmembrane Conductance Regulator in Cystic Fibrosis Epithelial Cells using Zinc Finger Nuclease Homology-Directed Repair Proceedings of The Physiological Society [Details] | |
| (2008) | Proceedings of The Physiological Society Lee, C and Flynn, R and Harrison, P (2008) Towards in vivo correction of the cftr $\Delta$F508 allele: design and synthesis of two zinc finger nucleases for homology-directed repair Proceedings of The Physiological Society [Details] |
Professional Activities
Patents
| Patent Number | Title | Granted | |
|---|---|---|---|
| AU2016225179C1 | Materials and methods for treatment of hemoglobinopathies | 05-MAY-22 |
Committees
| Committee | Function | From / To | |
|---|---|---|---|
| PhD External Examiner, Georgia Institute of Technology | External Examiner | / | |
| MSc External Examiner, Royal Holloway University London | External Examiner | / | |
| Graduate Studies, School of Biochemistry and Cell Biology | Member | 2023 / | |
| Emily's Entourage | Grant Reviewer | 2022 / 2022 | |
| European Research Council | Grant Reviewer | 2022 / 2022 | |
| Childrens Tumor Foundation | Grant Reviewer | 2019 / 2019 | |
| NIST Genome Editing Standards Workshop | Participant | 2016 / 2016 |
Employment
| Employer | Position | From / To | |
|---|---|---|---|
| University College Cork | Postdoctoral Fellow | 01-OCT-10 / 30-SEP-12 | |
| University College Cork | Senior Postdoc and Marie Curie Fellow | 01-JAN-19 / 30-JUN-23 | |
| Georgia Institute of Technology | Postdoctoral Fellow | 01-JUL-13 / 30-JUN-15 | |
| Rice University | Director Genome Editing Core | 01-JUL-15 / 18-DEC-18 |
Education
| Year | Institution | Qualification | Subject | |
|---|---|---|---|---|
| 2011 | University College Cork | PhD | Molecular Medicine | |
| 2006 | University College Cork | BSc | Genetics |
Journal Activities
| Journal | Role | To / From | |
|---|---|---|---|
| Frontiers In Genome Editing | Member of Editorial Board | 22-APR-22 - | |
| Gene Therapy | Peer Reviewer | - | |
| Scientific Reports | Peer Reviewer | - | |
| Acs Applied Materials & Interfaces | Peer Reviewer | - | |
| Acs Biomaterials Science & Engineering | Peer Reviewer | - | |
| Frontiers In Cellular And Infection Microbiology | Peer Reviewer | - | |
| Molecular Therapy | Peer Reviewer | - | |
| Nucleic Acids Research | Peer Reviewer | - | |
| Biotechnology And Bioengineering | Peer Reviewer | - | |
| Animal Biotechnology | Peer Reviewer | - | |
| Nature Protocols | Peer Reviewer | - | |
| Crispr Journal | Peer Reviewer | - |
Teaching Activities
Teaching Interests
Currently I teach and facilitate practical lab training sessions for postgraduate students in Advanced Cell and Gene Therapy (BC6005, BC6006, and BC6007). In addition, I teach and supervise 3rd year Biochemistry students for their Literature Review Project (BC3012) and 4th year Biochemistry students for their laboratory based 8-week Research Project (BC4012). I also contribute to serval other courses at the undergraduate (GN4003) and postgraduate level (BC6011, ML6005, and ML6006).Research Information
Internal Collaborators
| Name | Institute | Country | |
|---|---|---|---|
| Douwe van Sinderen | School of Microbiology, University College Cork | IRELAND | |
| Patrick Harrison | Dept. Physiology, University College Cork | IRELAND |
External Collaborators
| Name | Organisation / Institute | Country | |
|---|---|---|---|
| Francesca Bottacini | Munster Technical University | IRELAND | |
| Greg Gibson | Georgia Institute of Technology | U.S.A. | |
| Renee Cottle | Clemson University | U.S.A. | |
| Ayal Hendel | Bar Ilan University | ISRAEL | |
| Gang Bao | Rice University | U.S.A. |