Library · Biology & lab methods
What CRISPR-Cas9 Gene Editing got wrong, from 67 theses
Summary written by a model from the records below: CRISPR-Cas9 gene editing experiments frequently encounter technical obstacles including poor delivery efficiency, lack of cleavage activity, and failed homology-directed repair integrations. Researchers also repeatedly report cellular toxicity, lethality when knocking out essential genes, and clonal heterogeneity that prompt shifts toward alternative modalities such as ribonucleoprotein complexes or CRISPR interference. These records come from graduate theses, 2021 to 2026, each labeled with its degree where the repository states it, and each links to its thesis. They were extracted by language models reading the full text, so treat each as a lead to read, not a verdict.
Plus 10 problems the authors left open, listed at the end.
Failure modes, by theses reporting them
Select a mode to jump to its records.
Homology directed repair and knock in donor integration suffer from low efficiency or complete failure
Multiple attempts to insert tags, point mutations, or larger transgenes into mammalian cells, embryos, and non-model systems yielded zero edited clones or failed to achieve germline transmission. Researchers repeatedly abandoned direct knock-in strategies due to deficient homologous recombination machinery, off-target integrations, and low on-target guide activity.
Tried and failed
CRISPR knock-in of degradation tag system applied to endogenous loci in difficult cell lines. Reason: low transfection efficiency and poor clone survival during selection
YAP and TAZ have Functionally Redundant Roles in Uveal Melanoma · MIT · PhD
Tried and failed
single-vector CRISPR knock-in and knockout gene replacement applied to human embryonic stem cell lines. Reason: Target cells failed to replace wild-type alleles with the mutant knock-in construct.
Cell cycle remodelling during human embryonic stem cell differentiation · Imperial · PhD
Tried and failed
CRISPR-Cas9 endogenous fluorescent tagging of essential genes applied to pluripotency transcription factor endogenous locus. Reason: Off-target integration occurred, and biallelic targeting led to cell death or loss of pluripotency
The Regulation of Transcription Factors Binding Site Occupancies by Their Concentrations · EPFL · PhD
Tried and failed
CRISPR/Cas9 homology-directed repair applied to human embryonic stem cell knock-in. Outcome: no signal. Reason: Zero of 192 sequenced clones showed successful incorporation of the target point mutation across three attempts
Clinical and cellular characterisation of HNF1A transcription factor variants in people with young-onset diabetes · Imperial · PhD
Tried and failed
CRISPR-Cas9 homology-directed repair with short donor templates applied to human B cell line gene editing. Outcome: no signal. Reason: extremely low or absent homology-directed repair efficiency yielding zero knock-in clones across hundreds screened
Investigating the effects of a novel ITP patient derived PRKDC mutation in a human B cell line. · Imperial · PhD
Tried and failed
CRISPR-Cas9 knock-in editing applied to candidate QTL variant validation. Reason: failed to generate edited mutants
Understanding complex behavior in C. elegans through natural variation · UT Austin · PhD
Considered and rejected
Considered and rejected: Homology-directed repair (HDR) via endonucleases (CRISPR/Cas9) at endogenous mutant loci in FA HSCs due to lack of functional homologous recombination machinery and low efficiency/error-prone nature of alternative repair pathways
Targeting Lnk (sh2b3) To Expand Healthy And Fanconi Anemia Human Hematopoietic Stem And Progenitor Cells · Penn · PhD
Considered and rejected
Considered and rejected: Rejected direct CRISPR/Cas9 HDR mutagenesis in parental cells due to inefficient editing and p53 activation by double-strand breaks; adopted a multi-step LSL-knockin intermediate instead
Mutagenese des endogenen TP53-Lokus durch CRISPR/Cas9-vermittelte homologe Rekombination & Base Editing in Lungenkarzinomzellen Mutagenesis of the endogenous TP53-locus via CRISPR/Cas9-mediated homology-directed repair & Base Editing in lung cancer cells · University of Marburg · PhD
Considered and rejected
Considered and rejected: CRISPR-Cas9 knock-in of KRAS-G12V in ID8 cells using Kras guide 6 was abandoned due to low on-target guide efficiency
Targeting NAD+ metabolism in ovarian cancer · Imperial · PhD
Tried and failed
CRISPR Cas9 homology directed domain swap applied to murine zygote genome editing. Reason: Targeted knock-in failed to achieve germline transmission in founder animals
Biological Characterization of Differential Function and Activation Between Closely-Related TGFβ Family Ligands · Harvard · PhD
Tried and failed
CRISPR-Cas9 with single-stranded oligonucleotide knock-in applied to generating point mutation mouse founder lines. Reason: failed to yield viable knock-in founder lines across multiple loci
Modeling Autism Spectrum Disorder: Fragile X syndrome and Rett syndrome · MIT · PhD
Tried and failed
CRISPR-Cas9-mediated pronuclear microinjection of linearized plasmids applied to large transgene knock-in at safe-harbor loci. Outcome: no signal. Reason: Achieved zero successful genomic integration events in generated offspring despite using purified Cas9 protein.
Metabolic regulation of hierarchical decisions in the bone mesenchymal lineage · Imperial · PhD
Considered and rejected
Considered and rejected: Generating an inducible Mrgprb4Cre-ERT2 line via CRISPR/Cas9 was abandoned after multiple failed insertion attempts over two years.
A Critical Role For Mrgprb4 Touch Neurons In A Skin-Brain Pathway For Stress Resilience · Penn · PhD
Tried and failed
CRISPR/Cas9 N-terminal tag knock-in applied to endogenous gene tagging in Drosophila. Reason: Multiple tested gRNA combinations failed to yield successful integration
Cell-specific spindle alignment in epithelial tissue via RASSF proteins · Imperial · PhD
Tried and failed
CRISPR-Cas9 endogenous fluorescent tagging with degron insertion applied to endogenous gene tagging in nematodes. Reason: None
Investigating cohesin’s role in developmental gene regulation using the model organism C. elegans · Imperial · PhD
Plasmid and viral vector delivery methods underperform compared to direct ribonucleoprotein electroporation
Transfection of large plasmids and transduction with lentiviral vectors frequently failed due to low titers, poor delivery efficiency, and severe cytotoxicity during nucleofection. Consequently, electroporation of pre-assembled Cas9 ribonucleoprotein complexes consistently outperformed plasmid delivery and nanoparticle formulations while reducing off-target and integration risks.
Lost to a baseline
Convective microfluidic transfection of large multicistronic CRISPR/Cas9 plasmids into iPSCs performed no better than standard Lipofectamine Stem (<1% efficiency).
Microfluidic Cell Processing for Personalized and Regenerative Medicine · Georgia Tech · PhD
Lost to a baseline
HDT-CRISPR-AuNP induced far lower gene editing and HDR integration frequencies than electroporated Cas9 RNP + HDT positive controls across Jurkats, T cells, and CD34+ cells.
Non-viral Gold Nanoparticle Mediated Delivery of CRISPR-Cas9 Ribonucleoprotein and Long DNA Transgenes into Primary Blood Cells · University of Washington · PhD
Lost to a baseline
Electroporation of 100 pmol free Cas9 RNP achieved 47.8 ± 15.3% editing in CD34+ HSPCs compared to 13.23 ± 0.12% for 3rd gen CRISPR-AuNP.
Development of Third-Generation Gold Nanoparticles (CRISPR-AuNP) for Enhanced CRISPR Delivery to Hematopoietic Stem and Progenitor Cells · University of Washington · PhD
Considered and rejected
Considered and rejected: Cas9-EGFP fusion protein was rejected due to much lower gene-editing efficiency in HSPCs/iPSCs compared to fluorophore-labeled CRISPR/Cas9-gRNA RNP complexes.
Establishment of a patient-specific iPSC model of stepwise leukemogenesis in severe congenital neutropenia · Tübingen · PhD
Considered and rejected
Considered and rejected: Co-transducing cells with two separate lentiviruses for CRISPR validation was rejected in favor of generating stable Cas9-expressing cell lines due to low efficiency.
Targeting Telomerase Overexpression by Synthetic Dosage Lethality · Saskatchewan · PhD
Considered and rejected
Considered and rejected: Rejected lentiviral CRISPR/Cas9 delivery in CD34+ cells due to low editing efficiency and oversized 15.8 kb vector
Enhancing human NK cell development: from UCB-CD34+ cells to functional NK cells · Imperial · PhD
Considered and rejected
Considered and rejected: Rejected TransIT-X2, Lipofectamine 3000, and Lonza Nucleofector electroporation for CRISPR/Cas9 plasmid delivery in Caco-2 cells due to lower transfection efficiency compared to Lipofectamine 2000.
Conditions-specific quantitative network rewiring of colon cancer-associated KRAS mutations in Caco-2 cell line · University College Dublin · PhD
Considered and rejected
Considered and rejected: Rejected plasmid-based CRISPR-Cas9 (pSpCas9(BB)-2A-GFP) expression due to potential prolonged Cas9 toxicity/off-target effects and low transfection efficiency, switching to RNP delivery.
RUNDC1 Regulates Proinsulin/Insulin Trafficking and TGN Exit · University of Washington · PhD
Lost to a baseline
Electroporation of free Cas9 RNP achieved 76.5 ± 5.5% editing vs 52.7 ± 13.5% for electroporated 2nd gen CRISPR-AuNP.
Development of Third-Generation Gold Nanoparticles (CRISPR-AuNP) for Enhanced CRISPR Delivery to Hematopoietic Stem and Progenitor Cells · University of Washington · PhD
Tried and failed
all-in-one lentiviral delivery of Cas9 and gRNA applied to pooled genome-wide CRISPR knockout screen. Reason: Low viral titers resulted in poor infection efficiency requiring infeasibly high lentivirus volumes.
Discovery of cancer vulnerabilities in gene expression regulation pathway · Harvard · PhD
Tried and failed
CRISPR knock-in delivery via nucleofection applied to cancer cell lines. Reason: Severe nucleofection-induced cytotoxicity prevented survival and clonal expansion of stably edited cells.
Identifying the transcriptional drivers of dormancy in luminal A breast cancer · Imperial · PhD
Considered and rejected
Considered and rejected: Rejected lentiviral delivery of CRISPR-Cas9-Cre due to genomic integration risks, gene silencing, and toxicity from permanent Cre expression, selecting adenoviral delivery instead.
Phosphorylierung der p53 H1-Helix: Rolle für Tumorsuppression und Tumorigenese p53 H1 helix phosphorylation: Role in tumor suppression and tumorigenesis · University of Marburg · PhD
Considered and rejected
Considered and rejected: Rejected plasmid-based CRISPR Cas9 delivery to avoid risk of genomic integration and off-target effects, opting instead for Cas9 protein/crRNA delivery.
Targeting oncogenic microRNAs in malignant germ cell tumours. · Cambridge · PhD
Considered and rejected
Considered and rejected: Rejected plasmid-based delivery of CRISPR-Cas9 constructs in favor of RNP complexes due to zero recovery of edited knock-in colonies.
Dissecting functional diversities of human sensory neuron subsets to develop a new humanized platform for pain therapy · Johns Hopkins · PhD
Double strand break induction and essential gene knockouts cause severe cytotoxicity and lethality
Generating complete gene disruptions or dense double-strand breaks frequently resulted in massive cell death, larval mortality, and failure to establish stable clonal knockout lines. To avoid lethality caused by targeting essential genes or triggering DNA damage responses, investigations routinely abandoned wild-type Cas9 cleavage in favor of CRISPR interference or RNA knockdown.
Tried and failed
homozygous gene knockout using CRISPR/Cas9 applied to human induced pluripotent stem cells. Reason: loss of target gene caused lethality and low cell viability
Investigating the role of sall4 during human cranial neural crest cells specification · Imperial · PhD
Considered and rejected
Considered and rejected: Rejected using CRISPR-Cas9 targeting alpha satellites to study centromeric DDR because generating tens of thousands of breaks per centromere exceeds physiological signaling thresholds.
Investigating the role of homologous recombination at human centromeres · Oxford · PhD
Tried and failed
CRISPR-Cas9 gene knockout applied to essential gene in cancer cell lines. Reason: Complete knockout resulted in cell lethality, preventing generation of stable clonal knockout lines.
Elucidating the mechanism of Dock7-mediated AKT activation, cellular transformation, and cancer cell survival · Cornell · PhD
Tried and failed
dual gRNA CRISPR-Cas9 knockout with antibiotic selection applied to cancer cell lines. Reason: specific gRNA pair co-transfections caused complete cell death post-transfection
The Role of RAD51AP1 in Drug Resistance in Glioblastoma Cells · Harvard · Master's
Tried and failed
CRISPR-Cas9 knockout of essential proteasome subunits applied to human cell line gene knockout. Reason: Knocking out the 5'-end of essential proteasomal catalytic subunits resulted in complete cell lethality.
Immunoproteasomes in microglial activation and inflammation · Imperial · Master's
Considered and rejected
Considered and rejected: Rejected using sgRNA-mediated CRISPR knockout of PNUTS in TREx-RTA-BCBL1 cells due to high cytotoxicity, adopting inducible shRNA knockdown instead.
The PNUTS-PP1 Complex Acts as an Intrinsic Barrier to Kaposi's Sarcoma Associated Herpesvirus Gene Expression and Replication · UT Southwestern · PhD
Considered and rejected
Considered and rejected: Rejected CRISPR/Cas9 gene knockout in favor of shRNA knockdown because CRISPR requires mutating both alleles for complete knockout while shRNA provides efficient stable knockdown and avoids potential lethality of complete PDX1 loss.
Defining a Role for the Parahox Gene PDX1 in Colorectal Cancer · Johns Hopkins · Master's
Considered and rejected
Considered and rejected: Rejected standard CRISPR knockout in favor of CRISPRi (dCas9-KRAB) for validating essential metabolic and UFMylation genes (UFSP2, G6PD) to avoid double-strand break lethality.
Investigating the cellular response to folate depletion · Harvard · PhD
Considered and rejected
Considered and rejected: Standard knockout-oriented CRISPR-Cas9 was rejected in favor of CRISPRi because complete ablation of essential epigenetic modifiers causes generic cell lethality rather than reflecting regulatory and environmental perturbations.
Considered and rejected
Considered and rejected: Rejected using CRISPR-Cas9 for high-MOI guide pooling in favor of CRISPRi with dCas9-KRAB to avoid cellular toxicity caused by excessive double-stranded breaks.
Investigating human disease mechanisms through population genetics and experimental genetic screens · Harvard · PhD
Considered and rejected
Considered and rejected: CRISPR-Cas9 knockout was rejected in favour of RNAi knockdown to avoid potential lethality and non-viable phenotypes from complete CBB cycle disruption
The significance of non-foliar photosynthesis on development and nutritional value in tomato fruit · Nottingham · PhD
Tried and failed
CRISPR-based transgenic strain generation via microinjection applied to mosquito population control target genes. Reason: Severe larval mortality prevented the establishment of viable transgenic lines across multiple microinjection attempts.
Expanding the flexibility of genome editing approaches for population control of the malaria mosquito · Imperial · PhD
Target DNA cleavage fails due to inactive guide RNAs and low cutting efficiency
Several targeted loci remained completely unedited because designed or published guide RNAs exhibited negligible cleavage activity in genomic assays. Similar lack of cleavage occurred across varied nuclease ratios, miniature Cas orthologs, and recombineering protocols despite verified vector expression.
Tried and failed
CRISPR-Cas9 targeted DNA cleavage using specific sgRNA applied to embryonic stem cell genome editing. Outcome: no signal. Reason: Specific guide RNA design exhibited low cleavage efficiency at the target chromosomal locus
Mechanism of recurrent DNA break clusters (RDCs) generation in mouse and human cells · Harvard · PhD
Tried and failed
CRISPR activation targeting promoter with few sgRNAs applied to endogenous gene transcription in stem cells. Outcome: no signal. Reason: two promoter-targeting sgRNAs were insufficient to induce transcription compared to dense enhancer targeting
Poising and connectivity of enhancers upon naïve-to-primed transition in human embryonic stem cells (hESCs) · Imperial · PhD
Tried and failed
lentiviral CRISPR-Cas9 gene editing applied to hematopoietic stem and progenitor cells. Outcome: no signal. Reason: transduction occurred based on reporter expression but failed to produce detectable genomic DNA cleavage
Enhancing human NK cell development: from UCB-CD34+ cells to functional NK cells · Imperial · PhD
Tried and failed
CRISPR-Cas9 target cleavage applied to in vivo embryonic genomic DNA. Outcome: no signal. Reason: The designed guide RNA showed negligible cleavage activity resulting in an undetectable mutation rate.
Expanding the flexibility of genome editing approaches for population control of the malaria mosquito · Imperial · PhD
Tried and failed
CRISPR-Cas9 locus deletion applied to cancer cell microRNA clusters. Outcome: no signal. Reason: poor cutting efficiency detected in mismatch cleavage assays
Targeting oncogenic microRNAs in malignant germ cell tumours. · Cambridge · PhD
Tried and failed
CRISPR-Cas9 disruption with published guide RNAs applied to transcription factor binding motif editing. Reason: previously published guide RNAs failed to yield viable edited cell models at the target locus
Transcripts and transcription at an estrogen regulated enhancer of CCND1 · Imperial · PhD
Tried and failed
engineered miniature CRISPR-Cas nucleases applied to reporter gene disruption in mammalian cells. Outcome: no signal. Reason: miniature Cas nucleases exhibited insufficient cleavage activity across varied nuclease-to-guide ratios
AAV TRANSDUCTION TRACING IN HEMATOPOIETIC CELLS BY TARGETED SCARRING OF GENOMIC SAFE HARBORS · Harvard · Master's
Tried and failed
CRISPR-Cas mediated recombineering of viral genomes applied to bacteriophage receptor binding proteins. Outcome: did not generalise. Reason: extremely low recombinant recovery across multiple Cas systems with inconsistent counterselection efficacy
ENGINEERING BACTERIOPHAGE FOR IMPROVED BIOSENSING & THERAPEUTICS · Cornell · PhD
Tried and failed
CRISPR-Cas9 targeted genome editing applied to single-nucleotide polymorphism introduction in yeast. Reason: guide RNAs targeting specific candidate loci were ineffective, requiring fallback to counterselectable marker-based mutagenesis
On Pleiotropy and Evolutionary Dynamics in the Budding Yeast Saccharomyces cerevisiae · Harvard · PhD
Tried and failed
dual viral vector CRISPR Cas9 gene editing applied to primary alveolar epithelial cells in vitro. Outcome: no signal. Reason: genomic DNA remained unedited across passages despite high vector expression efficiency
Clonal isolation produces clone to clone heterogeneity and phenotypic compensation artifacts
Deriving single-cell knockout clones resulted in discordant phenotypes, karyotypic transcriptional drift, and selective outgrowth of unedited cells. Additionally, cellular activation requirements and non-targeting control evasion of double-strand break toxicity introduced substantial artifacts into pooled screens and functional assays.
Considered and rejected
Considered and rejected: Switched from Cas9 double-strand break deletion to CRISPRi interference because low editing frequency and sorting artifacts prevented bulk proteomic profiling.
Life without Replication in Bacillus subtilis · Leibniz Universität Hannover · PhD
Considered and rejected
Considered and rejected: Decided against using wild-type Cas9 double-strand breaks for knockout pipelines due to in-frame indels and slow clonal passaging, recommending CRISPRi/CRISPR-off instead.
Consequences and Limits of Cell-Cell Communication in Airway Immune Responses · MIT · PhD
Considered and rejected
Considered and rejected: Rejected classic single-colony CRISPR-Cas9 knockout for SNV modeling due to unpredictable karyotype-driven transcriptional drift and low (4%) editing efficiency.
Dissecting the contribution of non-coding regulatory mutations to hormone-dependent breast cancer evolution · Imperial · PhD
Tried and failed
CRISPR knockout clone generation applied to tumorigenesis xenograft models. Outcome: did not generalise. Reason: different single-cell derived knockout clones showed discordant in vivo tumorigenic capacity despite identical targeting
SMARCB1 Maintains Lineage Fidelity in Clear Cell Renal Cell Carcinoma · Cambridge · PhD
Tried and failed
non-targeting sgRNA controls in pooled screens applied to pluripotent stem cell CRISPR screens. Reason: Non-targeting controls evade Cas9 double-strand break toxicity, causing inflated relative abundance compared to cut-inducing guides.
Controlling Cell Fate During Directed Differentiation of Human Beta Cells · Harvard · PhD
Considered and rejected
Considered and rejected: Rejected constitutive lentiCRISPR-v2 knockout system due to Cas9 off-target effects and clone-to-clone variability during clonal selection, switching to an inducible Tet-on iCas9 multiplex system
The role of the YTHDF m6A readers in neuroblastoma · University of Trento · PhD
Considered and rejected
Considered and rejected: Rejected ID2 in vivo testing after initial screen because pan-T cell activation required for CRISPR/Cas9 editing caused premature differentiation away from the naive phenotype before knockout could take effect
T cell evolution in the blood and organs during acute graft-versus-host disease · Harvard · PhD
Considered and rejected
Considered and rejected: Rejected the generation of CRISPR/Cas9 knockout clones directly from a heterogeneous pool of transduced cells without first isolating and validating a well-characterised single-cell Cas9-expressing clone.
Identifying and characterising new targets of inflammatory caspases · Imperial · PhD
Nuclease expression systems cause host toxicity and suffer from leaky basal activity
Expression of active Cas nucleases or catalytically dead variants caused severe growth defects and toxicity in host bacteria, insect tissues, and mammalian cell lines. In addition, inducible platforms frequently exhibited promoter leakiness that led to unintended basal editing or lethality under selective growth conditions.
Tried and failed
split crRNA-tracrRNA inducible expression system applied to conditional CRISPR Cas9 genome editing. Reason: leaky basal expression caused unintended editing with no increase upon induction
Single-Cell Lineage Tracing Of Cancer Metastasis · Penn · PhD
Considered and rejected
Considered and rejected: CRISPRi dCas9 knockdown in 786O cells abandoned for in vivo experiments due to dCas9-induced growth defects and outgrowth of unedited cells.
Pbaf-Associated Circadian Lncrna Adirf-As1 Regulates Renal Clear Cell Tumorigenesis · Penn · PhD
Considered and rejected
Considered and rejected: Rejected dCas9/CRISPRi-based sgRNA mismatch tuning library due to immunogenicity concerns and off-target risks from constitutive dCas9 expression
Dissecting the impact of chimeric antigen receptor expression levels on T cell behaviour and response · Oxford · PhD
Tried and failed
constitutive nuclease expression for genome editing applied to cyanobacterial CRISPR genome engineering. Outcome: worse than baseline. Reason: Constitutive Cas12a expression caused reduced transformation efficiency compared to inducible expression.
Engineering the membrane rotor ring of ATP synthases involved in photosynthesis · Imperial · Doctorate
Considered and rejected
Considered and rejected: CRISPR-Cas9-mediated gene editing rejected because Cas9 expression was toxic to Clostridium immunis.
The Host and Microbial Determinants of Activity by Commensal Clostridium immunis · Duke · PhD
Considered and rejected
Considered and rejected: Rejected constitutive two-plasmid CRISPRi system (dCas9 on single-copy, gRNA on multi-copy) due to severe growth inhibition on methanol
Engineering and evolving glyoxylate utilization in Ethylmalonyl-CoA Pathway-deficient Methylobacterium extorquens PA1 for the production of crotonate from methanol · University of Marburg · Doctorate
Considered and rejected
Considered and rejected: Single-plasmid CRISPRi design with inducible dCas9 and constitutive gRNA expression due to persistent lethality on methanol in Δccr and ΔphaC strains from promoter leakiness
Engineering and evolving glyoxylate utilization in Ethylmalonyl-CoA Pathway-deficient Methylobacterium extorquens PA1 for the production of crotonate from methanol · University of Marburg · Doctorate
Tried and failed
heterologous catalytic dead CRISPR nuclease expression applied to bacterial host strain. Outcome: unstable. Reason: protein expression induced substantial host toxicity independent of guide RNA presence or selection
Massively-parallel characterization of CRISPR nuclease binding and applications in the creation of CRISPR-based gene circuits · Cornell · PhD
Considered and rejected
Considered and rejected: Abandoned UAS-Cas9 fat-body CRISPR knockout due to baseline Cas9-induced tissue toxicity under Cg-GAL4.
Dissecting Slit Signaling: Regulating Stem Cells, Proteolytic Cleavage and its Emerging Roles in Metabolism · University of Nevada, Reno · PhD
Engineered Cas variants and novel effector fusions underperform standard CRISPR tools
Novel engineered Cas variants and modified epigenetic effectors consistently showed weaker transcriptional repression than standard dCas9-KRAB or wild-type dCas9 systems. Direct nuclease fusions and alternative orthologs also failed to reproduce the robust gene silencing or activation achieved by established baselines.
Lost to a baseline
dSaCas9 and dLbCas12a CRISPRoff yielded less efficient gene silencing than dSpCas9 CRISPRoff
Elucidating Gene Regulatory Roles of DNA Modifications and Active DNA Demethylation Pathways · Penn · PhD
Lost to a baseline
PAM-flexible dCas9 variants (dxCas9-NG, dSpRY) exhibited weaker CRISPRi repression (5 to 30-fold) compared to wild-type dCas9 (~95-fold repression).
Synthetic CRISPR Tools for Information Processing in Bacteria · University of Washington · PhD
Lost to a baseline
dCas9-mediated CRISPRi targeting hisA failed to inhibit cell growth on minimal medium lacking histidine (cells remained viable), whereas Type IV-A1 CRISPRi completely suppressed growth (auxotrophy).
Characterization of Type IV-A1 CRISPR-interference on gene expression and plasmid replication · University of Marburg · PhD
Lost to a baseline
CRISPR-Cas-mediated HMR recruitment showed undetectable Trp1 gene silencing, failing to reproduce the strong silencing growth defect achieved by Gal4DBD-Yif1 baseline.
CRISPR-Cas Tools for Engineering Genome Structure and Gene Expression · University of Washington · PhD
Left open by the authors
Problems the authors named and did not get to.
Left open
Validate Cdh1 overexpression conclusions in human embryonic stem cells using CRISPR-mediated activation instead of the DHFR-TMP stabilization system. Blocker: Requires wet lab facilities, cell culture, and CRISPR genetic engineering apparatus.
Cell cycle remodelling during human embryonic stem cell differentiation · Imperial · PhD
Left open
Titrate Cas9 editing rates and optimize target site architecture to minimize multi-target deletions in the lineage tracing array. Blocker: Requires wet lab cell culture, CRISPR-Cas9 induction, and sequencing experiments
Single-Cell Lineage Tracing Of Cancer Metastasis · Penn · PhD
Left open
Generate chimeric CRISPR-Cas9 variants combining SpRY with hyperactive mutations and test cleavage efficiency and fidelity. Blocker: Requires a molecular biology wet lab to engineer, express, and assay Cas9 variants
Overcoming the limitations of CRISPR-based genome editing with kinetics-guided cryo-EM · UT Austin · PhD
Left open
Capture EBV episomes from spontaneous LCL lines exhibiting poor CRISPR/Cas9 editing and low proliferation. Blocker: Requires wet lab facilities, cell culture, CRISPR delivery, and biological samples (sLCL-B lines).
Investigating the germinal centre biology of an authentic Epstein-Barr virus strain · Imperial · PhD
Left open
Perturb candidate poised enhancers during the naïve-to-primed hESC transition using the optimized iCRISPRa system to assess gene activation effects. Blocker: Requires a wet lab, cell culture (hESCs), and experimental iCRISPRa assays.
Poising and connectivity of enhancers upon naïve-to-primed transition in human embryonic stem cells (hESCs) · Imperial · PhD
Left open
Perform CRISPR-Cas9 loss-of-function mutations or overexpression of candidate genes to functionally validate identified chemoresistant transcriptomic signatures. Blocker: Requires a wet-lab environment, cell cultures, and CRISPR-Cas9 experimental assays.
Clonal deconvolution of transcriptomic signatures and their spatial organisation in a mouse model of breast cancer · Cambridge · PhD
Left open
Use CRISPR/Cas9 to create catalytically dead HDAC7 mutants to determine direct versus indirect deacetylation of targets and histones. Blocker: Requires wet-lab experiments, cell culturing, CRISPR/Cas9 genome editing, and biochemical assays.
Role Of Pre-Mrna Alternative Splicing In Protein Diversity And Epigenetics · Penn · PhD
Left open
Perform CRISPR-mediated enhancer screens across multi-gene GRBs or TADs during developmental transitions to validate predicted target and bystander gene responsiveness. Blocker: Requires wet lab experimentation with CRISPR/Cas9 systems in cell cultures during developmental transitions.
Responsiveness of genes to long-range transcriptional regulation · Imperial · PhD
Left open
Functionally validate candidate epigenetic regulators identified from the CRISPRi screen in primordial germ cell development models. Blocker: Requires a wet lab with mouse stem cell culture, genetic manipulation tools (CRISPRi), and differentiation assays
Left open
Use CRISPR/Cas9 endogenous engineering to insert primary GCAUG motifs into introns of secondary-motif-regulated candidates like Cd47 to test developmental timing impacts. Blocker: Requires a molecular biology wet lab and CRISPR/Cas9 cell engineering apparatus.
Who has worked on this
Authors of the public theses cited on this page, most-cited first.
- Alina Schrodt · University of Marburg · Doctorate · 2026
Engineering and evolving glyoxylate utilization in Ethylmalonyl-CoA Pathway-deficient Methylobacterium extorquens PA1 for the production of crotonate from methanol - Karthikeya Srinivasa Varma Gottimukkala · University of Washington · PhD · 2025
Development of Third-Generation Gold Nanoparticles (CRISPR-AuNP) for Enhanced CRISPR Delivery to Hematopoietic Stem and Progenitor Cells - Liangdao Li · Cornell · PhD · 2024
EFFICIENT GENERATION OF PRIMORDIAL GERM CELLS AND CRISPR PERTURBATION SCREENS IDENTIFY EPIGENETIC REGULATORS IMPACTING PRIMORDIAL GERM CELL DEVELOPMENT - Ines Ullmo · Imperial · PhD · 2023
Enhancing human NK cell development: from UCB-CD34+ cells to functional NK cells - Joseph Padgett · Imperial · PhD · 2023
Cell cycle remodelling during human embryonic stem cell differentiation - Monica Della Rosa · Imperial · PhD · 2022
Poising and connectivity of enhancers upon naïve-to-primed transition in human embryonic stem cells (hESCs) - Kamen Simeonov · Penn · PhD · 2022
Single-Cell Lineage Tracing Of Cancer Metastasis - Shivani Bailey · Cambridge · PhD · 2021
Targeting oncogenic microRNAs in malignant germ cell tumours. - Nace Kranjc · Imperial · PhD · 2021
Expanding the flexibility of genome editing approaches for population control of the malaria mosquito - Chau Vuong · University of Washington · PhD · 2026
RUNDC1 Regulates Proinsulin/Insulin Trafficking and TGN Exit - Alexander Williams · Nottingham · PhD · 2026
The significance of non-foliar photosynthesis on development and nutritional value in tomato fruit - Martina Demurtas · Imperial · PhD · 2025
Investigating the role of sall4 during human cranial neural crest cells specification
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