CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool

Fiji: an open-source platform for biological-image analysis

Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116

Multiplex Genome Engineering Using CRISPR/Cas Systems

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339

The Human Genome Browser at UCSC

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400

RNA-Guided Human Genome Engineering via Cas9

Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210

DNA targeting specificity of RNA-guided Cas9 nucleases

Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741

Efficient genome editing in zebrafish using a CRISPR-Cas system

Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937

Genome editing with engineered zinc finger nucleases

Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S., & Gregory, P. D. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2842 · Cited by 2,285

A TALE nuclease architecture for efficient genome editing

Miller, J. C., Tan, S., Qiao, G., Barlow, K. A., Wang, J., Xia, D. F., Meng, X., Paschon, D. E., Leung, E., Hinkley, S. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1755 · Cited by 2,098

Сложность обнаружения гомологичной рекомбинации, опосредованной CRISPR/Cas9, у Danio rerio

Pi, Y., He, K. Z., Zhang, W. Q., Dong, Z., Jiang, F., Jiang, K., & Guo, S. (2020) · Molecular Biology · doi:10.31857/s0026898420030131

Optimization of de novo 10-hydroxygeraniol production in Saccharomyces cerevisiae

Davies, M. E. (2019) · Spectrum Research Repository (Concordia University)

Cystic proliferation of embryonic germ stem cells is necessary to reproductive success and normal mating behavior in medakaPreprint

Padilla, L. F. A., Castañeda-Cortés, D. C., da Rosa, I. F., Nóbrega, R. H., & Fernandino, J. I. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.30.274480

IN VITRO GENERATION OF HUMAN RETINAL GANGLION CELLS VIA DIRECT CONVERSION AND STEM CELL DIFFERENTIATION

Sluch, V. M. (2015)

Functional and structural characterization of LysM proteins in interactions between fungi and plants

Tian, H. (2020) · doi:10.18174/525407

IFN-λ4 may contribute to HCV persistence by increasing ER stress and enhancing IRF1 signalingPreprint

Onabajo, O. O., Wang, F., Lee, M., Flórez-Vargas, O., Obajemu, A. A., Castro, M. A. A., Tanikawa, C., Vargas, J. M., Liao, S.-F., Song, C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.28.359398

Template-independent genome editing and repairing correct frameshift disease in vivoPreprint

Liu, L., Li, K., Zou, L., Hou, H., Hu, Q., Liu, S., Wang, S., Wang, Y., Li, J., Song, C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.13.381160

Evaluation of genetic engineering and genome editing tools to develop multifactorial reproductive sterility or killing sperm systems for the improvement of the Sterile Insect Technique

Eckermann, K. N. (2020) · doi:10.53846/goediss-8321

Translational Research Using CRISPR/Cas

Tyagi, A., Sharma, S. B., Vats, S., Ali, S., Kumar, S., Gulzar, N., & Deshmukh, R. (2020) · Concepts and strategies in plant sciences · doi:10.1007/978-3-030-42022-2_8

Myeloid leukemia vulnerabilities at CTCF-enriched long noncoding RNA lociPreprint

Ng, M. S. W., Verboon, L., Issa, H., Bhayadia, R., Alejo-Valle, O., Borchert, D., Schuschel, K., Regényi, E., Reinhardt, D., Yaspo, M., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-727909/v1

Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafishPreprint

Nieścierowicz, K., Pryszcz, L. P., Navarrete, C., Tralle, E., Kasprzyk, M. E., Nahia, K. A., Misztal, K., Bochtler, M., & Winata, C. L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.26.457081

Genetic causes and stem-cell-based therapeutic strategies in neuromuscular diseases

Guo, L. (2021) · Research Publications (Maastricht University) · doi:10.26481/dis.20210623lg

Ultra-deep sequencing reveals no evidence of oncogenic mutations or enrichment by ex vivo CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cellsPreprint

Cromer, M. K., Barsan, V. V., Jaeger, E. B., Wang, M., Hampton, J. P., Chen, F., Kennedy, D., Khrebtukova, I., Granat, A., Truong, T., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.27.466166

Generation of 3X FLAG-tagged human embryonic stem cell (hESC) line to study WNT-induced β-catenin DNA interactions (HVRDe009-A-2)

Cutts, J., Kostes, W., & Brafman, D. A. (2021) · Stem Cell Research · doi:10.1016/j.scr.2021.102586

Contribution à la synthèse organique induite par laser : synthèse de composés soufrés : cycloadditions sur les énones

Lemaire, F. (1990) · OpenGrey (Institut de l'Information Scientifique et Technique)

Faculty Opinions recommendation of A transient reporter for editing enrichment (TREE) in human cells.

Suh, Y. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736464519.793579914

A centromeric RNA-associated protein complex affects germ line development in Drosophila melanogasterPreprint

Höcker, S., Akan, I. S., Simon, A. M., Yildirim, K., Kenéz, L. A., Lohmann, I., & Erhardt, S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.05.479222

Application of CRISPR-Based Technology in Plant Gene Editing and Agricultural Engineering

Zhang, Z., Wang, P., & Liu, J. (2022) · Springer eBooks · doi:10.1007/978-981-16-8504-0_5

Imaging tools generated by CRISPR/Cas9 tagging reveal cytokinetic diversity in mammalian cellsPreprint

Husser, M. C., Ozugergin, I., Resta, T., Martin, V. J. J., & Piekny, A. J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.14.484313

Computational Tools for Target Design and Analysis

Hwang, G., & Bae, S. (2022) · Wiley eBooks · doi:10.1002/9781119671404.ch5 · Cited by 1

FCHO controls AP2’s critical endocytic roles through a PtdIns4,5P 2 membrane-dependent switchPreprint

Zaccai, N. R., Kadlecová, Z., Dickson, V. K., Korobchevskaya, K., Kamenický, J., Kovtun, O., Umasankar, P. K., Wrobel, A. G., Kaufman, J. G. G., Gray, S. R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.02.486817

Investigación de la Leucemia Mieloide Aguda mediante el desarrollo de modelos in vitro e in vivo

Romero, E. G. (2022) · doi:10.4995/thesis/10251/181891

Peer Review #2 of "Mitochondrial complex I deficiency leads to the retardation of early embryonic development in Ndufs4 knockout mice (v0.1)"

(2017) · PeerJ · doi:10.7287/peerj.3339v0.1/reviews/2

Optimized sgRNA Design by Deep Learning to Balance the Off-Target Effects and On-Target Activity of CRISPR/Cas9Preprint

Lan, J., Cui, Y., Wang, X., Song, G., & Lou, J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.04.976340

Mês Nacional de Conscientização da Fibrose Cística no Brasil

. (2019) · Visão Acadêmica · doi:10.5380/acd.v20i3.1.69506

Faculty Opinions recommendation of Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming.

Chiang, C. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734885407.793555754

Faculty Opinions recommendation of Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish.

Cayouette, M. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.735399153.793558375

Peer Review #1 of "Mitochondrial complex I deficiency leads to the retardation of early embryonic development in Ndufs4 knockout mice (v0.1)"

(2017) · PeerJ · doi:10.7287/peerj.3339v0.1/reviews/1

Peer Review #1 of "Identification of high-efficiency 3′GG gRNA motifs in indexed FASTA files with ngg2 (v0.1)"

(2015) · PeerJ Computer Science · doi:10.7287/peerj-cs.33v0.1/reviews/1

Faculty Opinions recommendation of DeepCRISPR: optimized CRISPR guide RNA design by deep learning.

Conboy, I. M. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733509871.793553954

Peer Review #2 of "Identification of high-efficiency 3′GG gRNA motifs in indexed FASTA files with ngg2 (v0.1)"

(2015) · PeerJ Computer Science · doi:10.7287/peerj-cs.33v0.1/reviews/2

Peer Review #3 of "Mitochondrial complex I deficiency leads to the retardation of early embryonic development in Ndufs4 knockout mice (v0.1)"

(2017) · PeerJ · doi:10.7287/peerj.3339v0.1/reviews/3

4 CRISPR-Based Genome Engineering in Human Stem Cells

Garcia, T. Y., & Lamba, D. A. (2017) · CRC Press eBooks · doi:10.1201/9781315402185-5

Complexity of Detecting CRISPR/Cas9-Mediated Homologous Recombination in Zebrafish

Pi, Y., He, K. Z., Zhang, W. Q., Dong, Z., Jiang, F., Jiang, K., & Guo, S. (2020) · Molecular Biology · doi:10.1134/s0026893320030139

Faculty Opinions recommendation of Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.

Wang, H. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.726081204.793558122

Genome Editing

Murata, K., Kinoshita, M., Naruse, K., Tanaka, M., & Kamei, Y. (2019) · doi:10.1002/9781119575399.ch7

CRISPR/Cas9 Genome Editing: Future Treatment of Duane Retraction Syndrome

Zulfikar, M. R., Renesteen, E., & Wardhani, B. W. K. (2022) · Pharmaceutical Sciences and Research · doi:10.7454/psr.v9i1.1231

Epigenetic-focused CRISPR/Cas9 screen identifies ASH2L as a regulator of glioblastoma cell survivalPreprint

Ozyerli‐Goknar, E., Kala, E. Y., Aksu, A. C., Bulut, İ., Cingöz, A., Nizamuddin, S., Biniossek, M. L., Seker-Polat, F., Morova, T., Aztekin, C., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.17.504245

Synthetic biology tools for transcriptional activation and regulation of biosynthetic gene clusters in filamentous fungi

Mózsik, L. (2022) · doi:10.33612/diss.240014510

Targeted Manipulation of Histone Modification in Medaka Embryos

Fukushima, H. S., Takeda, H., & Nakamura, R. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2724-2_20

Early eye and forebrain development are facilitated by Bone Morphogenetic Protein antagonismPreprint

Bulk, J., Kyrychenko, V., Rensinghoff, P., & Heermann, S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.01.518698

Pcz1 regulates growth, conidiation, conidial germination, and production of penicillin in the filamentous fungus Penicillium rubens (formerly Penicillium chrysogenum)Preprint

Gil-Durán, C., Palma, D., Marcano, Y., Levicán, G. J., Vaca, I., & Chávez, R. (2023) · Research Square · doi:10.21203/rs.3.rs-2420194/v1

Elucidating the molecular pathology of DEPDC5 mutation induced mTOR-hyperactivation associated with epilepsy and autism spectrum disorder

Jones, M. (2022) · Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) · doi:10.21248/gups.71574

Increasing methionine content of soybean using CRISPR/Cas9 and developing machine learning predictive models

Tukuli, A. R. (2022) · MOspace Institutional Repository (University of Missouri) · doi:10.32469/10355/93992

Temporal and clonal characterization of neural stem cell niche recruitment in the medaka neuromast

Onistschenko, J., Kaminsky, S., Vázquez-Marín, J., Groß, K., Wang, T., Seleit, A., Dörr, M., & Centanin, L. (2023) · Cells and Development · doi:10.1016/j.cdev.2023.203837

The involvement of RS2Z proteins in tomato heat stress response and thermotolerance

Rosenkranz, R. R. E. (2023) · doi:10.21248/gups.73855

Data from Deficiency of the Polycomb Protein RYBP and TET Methylcytosine Oxidases Promotes Extensive CpG Island Hypermethylation and Malignant Transformation

Cui, W., Huang, Z., Jin, S., Johnson, J. S., Lau, K. H., Hostetter, G. H., & Pfeifer, G. P. (2023) · doi:10.1158/0008-5472.c.6769325

An atypical endomembrane localized CNL-type immune receptor with a conserved deletion in the N-terminal signaling domain functions in cell death and immunityPreprint

Sunil, S., Beeh, S., Stöbbe, E., Fischer, K., Wilhelm, F., Meral, A., Paris, C., Teasdale, L. C., Jiang, Z., Zhang, L., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.04.556214

Human skeletal muscle organoids model fetal myogenesis and sustain uncommitted PAX7 myogenic progenitorsPreprint

Mavrommatis, L., Jeong, H., Kindler, U., Gomez‐Giro, G., Kienitz, M., Stehling, M., Psathaki, O. E., Zeuschner, D., Bixel, M. G., Han, D., et al. (2023) · eLife · doi:10.7554/elife.87081.2

Characterization of a Novel LncRNA(LincRNA-Abcc10) in Northern Pike( Esox Lucius)Preprint

Shunzhe, W., Wang, S., Yang, Q., Liu, Y., Liu, Y., Wang, Y., Sun, H., Zhang, J., Li, J., & Wanlong, L. (2023) · SSRN Electronic Journal · doi:10.2139/ssrn.4579001

Streamlined generation of CRISPR/Cas9-mediated single-cell knockout clones in murine cell linesPreprint

Hub, T., Cornean, A., Kellen, R., Thomas, F., Freichel, M., & Rebekka, M. W. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.20.563250

Conditional Chemoconnectomics: A Set of Libraries Targeting All Chemical Transmission Corresponding Genes EfficientlyPreprint

Mao, R., Yu, J., Deng, B., Dai, X., Du, Y., Du, S., Zhang, W., & Rao, Y. (2023) · eLife · doi:10.7554/elife.91927.1

Data Visualization of CRISPR-Cas9 Guide RNA Design Tools

Jain, Y., Izzath, F. A. M., Wilson, L. O. W., & Bauer, D. C. (2024) · Studies in health technology and informatics · doi:10.3233/shti231069

Unraveling the molecular mechanisms involved in plant growth promotion and soil bacterial community modulation by Pantoea agglomerans 33.1

Ferreira, A. A. O. (2023) · doi:10.11606/d.11.2023.tde-14032024-105801

Cereal crop genome editing tools and their applications to sustainable agriculture

Elarabi, N. I., Hesham, A. E., EL-BELTAGI, H. S., Adel Abdel-Sabour, R. E. Z. K., Shalaby, T., Al-Saikhan, M. S., Mohamed, A. A., & Abdelhadi, A. A. (2024) · Notulae Botanicae Horti Agrobotanici Cluj-Napoca · doi:10.15835/nbha52113494

Additional file 14 of High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes)

Inoue, Y., Suzuki, Y., Kunishima, Y., Washio, T., Morishita, S., & Takeda, H. (2023) · Figshare · doi:10.6084/m9.figshare.24002880

Additional file 13 of High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes)

Inoue, Y., Suzuki, Y., Kunishima, Y., Washio, T., Morishita, S., & Takeda, H. (2023) · Figshare · doi:10.6084/m9.figshare.24002877

Additional file 23 of A Cas9-mediated adenosine transient reporter enables enrichment of ABE-targeted cells

Brookhouser, N., Nguyen, T., Tekel, S. J., Standage-Beier, K., Wang, X., & Brafman, D. A. (2020) · Figshare · doi:10.6084/m9.figshare.13467915

Additional file 2 of Molecular characterization of breast cancer cell pools with normal or reduced ability to respond to progesterone: a study based on RNA-seq

Eduardo, M. B., Keller, I., Schuster, N., Aebi, S. P., & Jaggi, R. B. (2023) · Figshare · doi:10.6084/m9.figshare.23902893

Additional file 8 of High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes)

Inoue, Y., Suzuki, Y., Kunishima, Y., Washio, T., Morishita, S., & Takeda, H. (2023) · Figshare · doi:10.6084/m9.figshare.24002859

Additional file 2 of Homology-independent targeted insertion (HITI) enables guided CAR knock-in and efficient clinical scale CAR-T cell manufacturing

Balke‐Want, H., Keerthi, V., Gkitsas-Long, N., Mancini, A. G., Kurgan, G., Fowler, C., Xu, P., Liu, X., Asano, K., Patel, S., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23583513

Generation of a PPM1A-deficient human induced pluripotent stem cell line using CRISPR-Cas9 technology

Guo, X., Zhao, K., Zhang, Y., Zhou, T., & Pan, G. (2024) · Stem Cell Research · doi:10.1016/j.scr.2024.103420

Prime Editing in vivo: Correcting the Leptin Receptor of db/db MicePreprint

Lee, K., Xu, Y., Geng, B., Kim, J. S., Kellon, N., He, M., Zhang, Z., Li, D., Gouchoe, D. A., & Hua Zhu, C. (2024) · doi:10.22541/au.171507305.55377808/v1

Prime editing‐mediated correction of the leptin receptor in muscle cells of db/db mice

Lee, K. E., Xu, Y., Geng, B., Kim, J. S., Kellon, N., He, Z., Zhang, Z., Li, D., Gouchoe, D. A., & Hua Zhu, C. (2024) · Biotechnology Journal · doi:10.1002/biot.202300676

Co-expression of the AsCas12a ultra variant, a T7 RNA Polymerase and a cytosine base editor greatly increases transfection and editing rates in Leishmania speciesPreprint

May, N. H., Schmid, A., Meiser, E., & Beneke, T. (2024) · eLife · doi:10.7554/elife.97437.1

Altered thymic niche synergistically drives the massive proliferation of malignant thymocytes

Tsingos, E., Dick, A. M., & Bajoghli, B. (2025) · eLife · doi:10.7554/elife.101137.3

Optimization of gene knockout approaches and practical solutions to sgRNA selection challenges in hPSCs with inducible Cas9 systemPreprint

Ni, J., Gong, J., Ran, Y., Bai, R., Huang, P., Zheng, Z., Zhou, M. R., You, Y., Lan, F., & Liu, X. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.09.602644

Generation of Knockout Human PSCs Using CRISPR/Cas9 Editing with a Donor Template

Shan, Y., Ma, N., & Liao, B. (2024) · Neuromethods · doi:10.1007/978-1-0716-3999-3_6

Many erroneous noncoding transcripts in cancer cells can highly specifically regulate cancer-related genes and pathwaysPreprint

He, S., Xiong, W., Huo, J.-P., Lin, J., Li, J., & Zhu, H. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.13.603398

Progress and Prospects in CRISPR Genome Engineering Nucleases

Surendranath, K., Akram, K., Kanagaraj, R., Savash, M., Khan, S., Pantuzcek, J., Karri, M., Guha, S., Rangan, S. L., Kour, E., et al. (2024) · Springer eBooks · doi:10.1007/978-981-97-1777-4_4

Codon usage and expression-based features significantly improve prediction of CRISPR efficiency

Bergman, S., & Tuller, T. (2024) · npj Systems Biology and Applications · doi:10.1038/s41540-024-00431-8 · Cited by 2

Generation of RAB4A homozygous knockout induced pluripotent stem cell (iPSC) line

wang, R., & Shen, Q. X. (2024) · Stem Cell Research · doi:10.1016/j.scr.2024.103556

Positional information drives distinct traits in transcriptomically identified neuronal typesPreprint

Shainer, I., Kappel, J. M., Laurell, E., Donovan, J. C., Schneider, M., Kuehn, E., Arnold-Ammer, I., Stemmer, M., Larsch, J., & Baier, H. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.15.613138

Prosapip1 in the dorsal hippocampus mediates synaptic protein composition, long-term potentiation, and spatial memoryPreprint

Hoisington, Z. W., Gangal, H., Phamluong, K., Shukla, C., Ehinger, Y., Moffat, J. J., Homanics, G. E., Wang, J., & Dorit Ron, A. (2024) · eLife · doi:10.7554/elife.100653.1

Altered thymic niche synergistically drives the massive proliferation of malignant thymocytesPreprint

Tsingos, E., Dick, A. M., & Bajoghli, B. (2024) · eLife · doi:10.7554/elife.101137

Altered thymic niche synergistically drives the massive proliferation of malignant thymocytesPreprint

Tsingos, E., Dick, A. M., & Bajoghli, B. (2024) · eLife · doi:10.7554/elife.101137.1

Understanding the Development of Compensatory Pathways in a Mutant Malaria Parasite Harbouring Hypomorphic Allele of Plant-Like Kinases

Choudhury, H., Sharma, M. D., Gangwar, U., Siddiqui, N., & Bansal, A. (2024) · Journal of Visualized Experiments · doi:10.3791/67079

Cytosolic Carboxypeptidase 5 maintains mammalian ependymal multicilia to ensure proper homeostasis and functions of the brainPreprint

Dad, R., Wang, Y., Fang, C., Chen, Y., Zhang, Y., Zhang, Y., Pan, X., Zhang, X., Swanekamp, E., Patel, K., et al. (2024) · eLife · doi:10.1101/2024.12.30.630763

CRISPR/Cas9-mediated generation of a homozygous CRB2 knockout H1 human embryonic stem cell line

Zhang, L., Zhang, F., & Yao, M. (2025) · Stem Cell Research · doi:10.1016/j.scr.2025.103677

Improved base editing and functional screening in Leishmania via co-expression of the AsCas12a ultra variant, a T7 RNA Polymerase, and a cytosine base editorPreprint

May, N. H., Cao, N. A., Schmid, A., Link, F., Arias-del-Angel, J. A., Meiser, E., & Beneke, T. (2025) · eLife · doi:10.7554/elife.97437.2

Cytosolic Carboxypeptidase 5 maintains mammalian ependymal multicilia to ensure proper homeostasis and functions of the brainPreprint

Dad, R., Wang, Y., Fang, C., Chen, Y., Zhang, Y., Zhang, Y., Pan, X., Zhang, X., Swanekamp, E., Patel, K., et al. (2025) · eLife · doi:10.7554/elife.105577

Cytosolic Carboxypeptidase 5 maintains mammalian ependymal multicilia to ensure proper homeostasis and functions of the brainPreprint

Dad, R., Wang, Y., Fang, C., Chen, Y., Zhang, Y., Pan, X., Zhang, X., Swanekamp, E., Patel, K., Wolf, M. T. F., et al. (2025) · eLife · doi:10.7554/elife.105577.1

Targeted Base Editing in Rice Using Target-AID

Nguyen, S. M., Taoka, K.-I., & Nishida, K. (2025) · Springer protocols handbooks/Springer protocols · doi:10.1007/978-1-0716-4358-7_1

Prosapip1 in the dorsal hippocampus mediates synaptic protein composition, long-term potentiation, and spatial memoryPreprint

Hoisington, Z. W., Gangal, H., Phamluong, K., Shukla, C., Ehinger, Y., Moffat, J. J., Homanics, G. E., Wang, J., & Dorit Ron, A. (2025) · eLife · doi:10.7554/elife.100653.2 · Cited by 1

CRISPR/Cas-mediated mRNA knockdown in the embryos of Xenopus tropicalis

Lin, X., Zhou, Y., Meng, K., Yang, J., Zhang, H., Lin, J.-H., Wu, H., Wang, X., Zhao, H., Feng, S., et al. (2025) · Cell & Bioscience · doi:10.1186/s13578-025-01397-8

Contextual Statistical Evaluation of Selected CRISPR-Cas9 Recurrent Deep Learning Models Predicting Off-Target Activities for K562 and Hek293 Cell Lines

Powierża, M., Łaczmański, Ł., & Huk, M. (2025) · Lecture notes in computer science · doi:10.1007/978-981-96-6008-7_17

Two iPSC lines with a heterozygous frameshift mutation in the floating-harbour syndrome locus of the SRCAP gene

Rhode, J. M., Edwards, S., Tzvetkova, A., Jensen, L. R., Hossain, M. F., Nowack, B., Hagenau, L., & Kuss, A. W. (2025) · Stem Cell Research · doi:10.1016/j.scr.2025.103730

CRISPR-Cas9 repair complexity in Drosophila melanogaster : NHEJ-induced deletions and HDR variability in the bantam microRNA genePreprint

Sousa, P. D., Houbron, É., Seitz, H., & Busseau, I. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.29.656857

Altered thymic niche synergistically drives the massive proliferation of malignant thymocytesPreprint

Tsingos, E., Dick, A. M., & Bajoghli, B. (2025) · eLife · doi:10.7554/elife.101137.2

Weighted Off-target and Efficiency Scoring Reveal Genome Composition-Dependent Optimal CRISPR/Cas9 Guide DesignPreprint

Krishna, Y. K. Y. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.13.670047

Transcriptional regulation of Ligase IV by an intronic regulatory element directs thymocyte development

Estrada, M. D., Gebhardt, C. J., Salem, M. A., Rau, C. N., Sharma, K., Glynn, R. A., Bassing, C. H., Oltz, E. M., & Collins, P. L. (2025) · Genes and Immunity · doi:10.1038/s41435-025-00353-3 · Cited by 1

High-Throughput Generation of Pichia pastoris Knock-Out Strains by Using CRISPR/Cas9

Smirnov, K., Rieder, L., & Glieder, A. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4779-0_24

An Ehrlich-inspired retrobiosynthesis of pharmaceutical scaffoldsPreprint

Rumpl, A. E. C., Kowalski, D., Goodhew, J. R., Hirano, M., Bogucki, L., Rosa, C. A., Lachance, M., & Pyne, M. E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.10.687684

Optimization of gene knockout approaches and sgRNA selection in hPSCs with inducible Cas9 expression

Ni, J., Gong, J., Ran, Y., Bai, R., Huang, P., Zheng, Z., Zhou, M. R., Lan, F., Gu, W., & Liu, X. (2025) · Scientific Reports · doi:10.1038/s41598-025-24184-4

Serotonin receptor 4 in the ventral CA3 regulates agomelatine-induced anxiolytic-like behaviors.

Liu, X.-H., Naveed, M., Hu, X.-Y., Zhu, L.-L., Meng, F., Zhou, Q.-G., & Zhang, J. (2025) · Acta Pharmacologica Sinica · doi:10.1038/s41401-025-01692-7

Designing of guide RNA for CRISPR gene editing: A web-based foundational approach

Okemo, P., & Henry, R. J. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-29281-1.00012-5

Additional file 2 of A Cas9-mediated adenosine transient reporter enables enrichment of ABE-targeted cells

Brookhouser, N., Nguyen, T., Tekel, S. J., Standage-Beier, K., Wang, X., & Brafman, D. A. (2020) · Figshare · doi:10.6084/m9.figshare.13467917

Additional file 12 of A Cas9-mediated adenosine transient reporter enables enrichment of ABE-targeted cells

Brookhouser, N., Nguyen, T., Tekel, S. J., Standage-Beier, K., Wang, X., & Brafman, D. A. (2020) · Figshare · doi:10.6084/m9.figshare.13467891

Additional file 15 of A Cas9-mediated adenosine transient reporter enables enrichment of ABE-targeted cells

Brookhouser, N., Nguyen, T., Tekel, S. J., Standage-Beier, K., Wang, X., & Brafman, D. A. (2020) · Figshare · doi:10.6084/m9.figshare.13467897

Additional file 7 of High-fat diet in early life triggers both reversible and persistent epigenetic changes in the medaka fish (Oryzias latipes)

Inoue, Y., Suzuki, Y., Kunishima, Y., Washio, T., Morishita, S., & Takeda, H. (2023) · Figshare · doi:10.6084/m9.figshare.24002856

CRISPcut: A novel tool for designing optimal sgRNAs for CRISPR/Cas9 based experiments in human cells

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Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites

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CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization

Zhu, H., Misel, L., Graham, M., Robinson, M. L., & Liang, C. (2016) · Scientific Reports · doi:10.1038/srep25516 · Cited by 38

CasOT: A genome-wide cas9/gRNA off-target searching tool

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Computational Prediction of CRISPR/Cas9 Target Sites Reveals Potential Off-Target Risks in Human and Mouse

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