CRISPR screen

Compact CRISPR-based genetic circuitry using a miniature genome-integrated Cas12m protein

A genome-integrated Cas12m in E. coli shows no measurable growth cost, reverses repression faster than dCas9, and supports NOT gates, a two-layer buffer and a two-pathway pigment circuit.

Thermodynamic Quality Control Reshapes Spatially Resolved Metabolic Flux Predictions in Prostate Cancer

Quality-controlled, cycle-certified E-Flux Human-GEM models of twelve regions from one prostate tumor curb implementation-driven flux inflation and show predicted metabolic similarity tracks spatial region, not histology.

Integrating Genetic Domestication and Model-Guided Kill-Switch Engineering in a Non-Model Bacterial Therapeutic

Host-measured parts and inducible systems for Brucella melitensis ΔvjbR guided a modeled Cas9 kill-switch, which cut mouse liver bacterial burden by about 91% at 30 mg/kg doxycycline.

PIE: Generalizing perturbation effects across unseen perturbations, contexts and datasets

Predicting differentially expressed genes and expression shifts per condition from database embeddings plus per-gene evidence, PIE reaches 1.2–3.2 times the best baseline's AUPRC on unseen contexts, perturbations and datasets.

STAR Suite: Transcriptomics processing in a single binary through AI-assisted development

Open-source STAR binary for five transcriptomic assays runs 3.9- to 6.2-fold faster than Cell Ranger 9.0.1 for scRNA-seq and Perturb-seq, 17- to 41-fold for Flex, with closely concordant counts.

SCALE: Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction

A set-aware latent transport model predicts treated cell populations from unpaired controls, keeps perturbation-specific signal in CRISPR, drug and cytokine data, and guided a cytokine choice tested in three donors.

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

Genome-scale CRISPRi perturb-seq in 22 million primary human CD4+ T cells maps stimulation-specific regulators and links perturbation signatures to T cell states and autoimmune genetics.

Systematic multivariate analysis of chromatin complex dependencies reveals Set1C/COMPASS as a melanoma-enriched epigenetic vulnerability

Complex-level DepMap dependency modeling across 42 cancer types nominates Set1C/COMPASS as melanoma-enriched; CXXC1 knockdown lowers H3K4me3, curbs proliferation, and suppresses MYC/E2F programs in responsive melanoma lines.

mV2G: a multiomic atlas for tissue-specific variant-to-gene prioritization

A web atlas counts evidence from 24 types for 188,634,118 variant-gene pairs across 50 human tissues; 1,530,420 pairs pass a high-confidence cutoff, 87% of them tissue-specific.

Pan-cancer proteogenomic interrogation of the Ubiquitin Proteasome System

Proteogenomic analysis of up to 11 CPTAC cohorts shows ubiquitin-proteasome proteins often diverge from transcripts; TP53-mutant tumors elevate UBR5 protein, while TRIM28 prognosis is lineage-dependent.

Genome-wide functional genomics screens identify therapeutic vulnerabilities for lymphangioleiomyomatosis

Differentiating TSC2-null human pluripotent stem cells into neural crest cells models lymphangioleiomyomatosis and reveals TWIST1 and SUN4 as synthetic lethal targets whose antisense knockdown eradicates mouse allograft tumors.

An integrated, scaled approach to resolve TSC2 variants of uncertain significance

Abundance scores for 8,891 TSC2 missense variants, plus mTOR pathway activity scores for 391, were calibrated to ACMG/AMP evidence. They putatively reclassify 212 of 276 clinical-cohort missense VUS.

Kinome-wide CRISPR/Cas9-knockout screening reveals critical protein kinases in vasopressin V2-receptor signaling

A kinome-wide CRISPR knockout screen in a mouse collecting duct Aqp2-GFP reporter line found 26 kinases shaping vasopressin-driven Aqp2 transcription, including Dyrk1a, Stk11 and TGF-β receptors.

Galvanin (TMEM154) is an electric-field sensor for directed cell migration

A CRISPRi migration screen in neutrophil-like HL-60 cells identified Galvanin (TMEM154), a single-pass membrane protein whose negatively charged ectodomain electrophoreses anodally to steer cathodal electrotaxis.

Divalent siRNA for prion disease

Divalent siRNA 2439-s4 lowers human PrP to 17% residual in transgenic mouse brain after one dose, and a separate mouse Prnp-targeting siRNA extends survival in prion-infected mice.

Cross-species meta-analysis reveals determinants of homing gene drive performance

Across nearly one million progeny from 10 species, species best predicts homing drive inheritance, while promoter, parent sex and maternal deposition each explain little of the inheritance variation.

Novel reporter of the PINK1-Parkin mitophagy pathway identifies its damage sensor in the import gate

A HaloTagged MFN2 reporter enabled CRISPRi screens showing diverse mitochondrial damage activates PINK1-Parkin via membrane potential loss, with TOM retaining PINK1 when TIM23 is blocked.

edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets

edgeR v4 adds a continuous negative binomial for fractional counts, bias-corrected quasi-likelihood for small counts, C-based fitting, and new transcript, exon, methylation and fold-change-threshold analyses.

Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT

Perturb-DBiT co-sequences spatial transcriptomes and gRNAs on one tissue section, supporting genome-wide in vivo CRISPR screens in FFPE and fresh-frozen tumors across three cancer models.

An epigenetic barrier sets the timing of human neuronal maturation

Chromatin regulators including EZH2, EHMT1/2, and DOT1L establish an epigenetic barrier in human neural progenitors that poises maturation genes and sets the protracted pace of cortical neuron maturation.

An encyclopedia of enhancer-gene regulatory interactions in the human genome

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

Effective gene expression prediction from sequence by integrating long-range interactions

Enformer, a sequence-based transformer integrating elements up to 100 kb away, lifts held-out gene expression prediction (correlation 0.81 to 0.85 versus Basenji2) and variant effect prediction.

Improved methods and optimized design for CRISPR Cas9 and Cas12a homology-directed repair

Empirical ssODN design rules for Cas9, Cas9 D10A and Cas12a HDR, plus end-modified donors and an NHEJ-inhibiting small molecule, raise HDR up to 10-fold.

Efficient immune cell genome engineering with improved CRISPR editing tools

Doxycycline-inducible dual-color Cas9, purified lentivirus, puromycin-selected nickase HDR, integrase-deficient lentiviral HDR delivery and an all-in-one CRISPRa vector enable editing of macrophage and Jurkat T cells.

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

Inserting theophylline aptamers into the sgRNA yields ligand-activated and ligand-deactivated guides that tune CRISPRi in E. coli over 11x to 13x dynamic ranges, enabling two-ligand multiplexing.

Inhibition of p53 improves CRISPR/Cas-mediated precision genome editing

Cas9-induced double-strand breaks trigger p53/p21/RB1-dependent G1 arrest in RPE-1 cells; transient p53 inhibition via MDM2 markedly raises homologous recombination precision editing efficiency.