Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

  PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

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  A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

  tcga-blca blca paired wgcna differential machine

• CDK4/6 inhibition mitigates chemotherapy-induced expansion of TP53-mutant clonal hematopoiesis.

  PMID 41814002 · PMC12987733 · Nature genetics · 2026 · 7 claims · 6 setups

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  Trilaciclib reduces chemotherapy-induced expansion of DDR-gene (TP53, PPM1D, CHEK2) clonal hematopoiesis across four randomized clinical trials and diverse chemotherapy regimens

  peripheral c57bl bone deep competitive flow

• A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

  PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

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  MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

  crc epithelial rcrc tcga-read scrna-seq copy gene

• Interpretable learning of temporal cellular dynamics from single-cell data.

  PMID 41875867 · PMC13030976 · Cell reports methods · 2026 · 7 claims · 7 setups

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  NeuroVelo couples a linear latent phase-space projection with a non-linear neural ODE, using RNA velocity as a physics-informed loss penalty, to jointly model cellular dynamics and enable gene-level interpretability

  gastrulation bone pancreatic cancer scrna-seq chip-seq computational

• Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing.

  PMID 41875869 · PMC13030979 · Cell reports methods · 2026 · 8 claims · 8 setups

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  Nuclei isolation protocol is a critical experimental variable shaping snRNA-seq data quality and biological interpretation

  cortex brain cortical snrna-seq snrna-seq bright-field nuclei

• ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.

  PMID 41888873 · PMC13154904 · Genome biology · 2026 · 8 claims · 6 setups

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  ImmuSeeker leverages the phylogenetic structure of HLA/KIR alleles in its alignment and filtering strategy to improve accuracy and robustness of immune gene signature detection

  a549 rna-seq covid-19 autoimmune bulk iso-seq rna-seq

• Stage-specific epigenetic priming amplifies gene activation during lineage commitment.

  PMID 41894493 · PMC13025117 · Science advances · 2026 · 8 claims · 8 setups

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  Full-body Msl1 knockout causes embryonic lethality by E10.5, with morphological/developmental delay detectable already at E8.5

  embryos e9.5 mesc-derived bright-field western 10x

• Dissecting host stress responses for predictable heterologous gene expression in E. coli.

  PMID 41909945 · PMC13034041 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  Excessive heterologous mRNA triggers a cold shock response that controls mRNA stability (cspA–I, deaD)

  coli combined rna-seq independent flow

• Boolean logic links chromatin accessibility states to gene expression variability across cell types.

  PMID 41909952 · PMC13148175 · Nucleic acids research · 2026 · 7 claims · 4 setups

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  ocrRBBR infers interpretable Boolean rules from combinations of accessible OCRs that explain gene expression variability across cell types

  immune genes atac-seq bulk hi-c

• Genetic diversity and regulatory features of human-specific NOTCH2NL duplications.

  PMID 41916274 · PMC13261667 · Cell genomics · 2026 · 8 claims · 7 setups

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  NOTCH2NL-like duplications occurred independently and recurrently across great ape lineages, but protein-coding NOTCH2NL copies emerged only in humans, ~2.2-3.7 mya

  nonhuman intronic t2t-chm13 dorsal long-read maximum duplicon

• Single-cell spatial transcriptomics reveals tumor microenvironment heterogeneity in primary and lymph node-metastatic small cell lung cancer.

  PMID 41916294 · PMC13130650 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Three malignant subclusters (C5, C6, C9) are enriched in LNM tumors and display distinct metabolic and angiogenic programs alongside spatial immune exclusion

  pt-lnm spatial single-cell multi-organ single-cell multiplex h&e

• Histone methyl-transferase G9a inhibition boosts the efficacy of immune checkpoint inhibitors in experimental hepatocellular carcinoma.

  PMID 41923620 · PMC13130624 · Cell reports. Medicine · 2026 · 7 claims · 8 setups

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  G9a expression inversely correlates with gene signatures predictive of favorable ICI response across multiple HCC patient cohorts

  tcga advanced nm53 plc bulk single-cell rt-qpcr

• pmid-41933176

  PMID 41933176 · PMC13223204 · 8 claims · 8 setups

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  Treg cluster proportions do not significantly differ between GDM and healthy control patients

  sorted pbmcs treg gdm-patient single-cell mass gene

• Transcriptomic analysis of the highly derived radial body plan of a sea urchin.

  PMID 24696402 · PMC4007537 · 7 claims · 7 setups

  Has reproduction · 68

  A de novo reference transcriptome for Heliocidaris erythrogramma spanning larval, metamorphic, and postmetamorphic stages provides a genomic resource for studying radial body plan evolution.

  sea heliocidaris panther novo rna-seq principal

• Early days: genomics and human responses to infection.

  PMID 16679048 · PMC7108404 · Current opinion in microbiology · 2006 · 8 claims · 8 setups

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  DNA microarray-based transcript profiling of primate/human responses to infection has begun to yield new insights into host-pathogen interactions but is limited by unresolved methodological challenges.

  peripheral liver gastric brain microarray

• Reducing language barriers, promoting information absorption, and communication using fanyi.

  PMID 39039634 · PMC11332769 · Chinese medical journal · 2024 · 7 claims · 3 setups

  Has reproduction · 67

  The fanyi R package retrieves gene information from NCBI and translates it into multiple languages using AI-driven online translation services

  pbmcs airway gene single-cell bulk functional

• Elderly Japanese women with cervical carcinoma show higher proportions of both intermediate-risk human papillomavirus types and p53 mutations.

  PMID 10098748 · PMC2362249 · British journal of cancer · 1999 · 8 claims · 3 setups

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  HPV DNA was detected in 44 of 46 (96%) cervical carcinomas from elderly women

  cervical paraffin-embedded pcr-based pcr-single-strand immunohistochemistry

• Detection of an Ala601Thr mutation of plasminogen gene in 3 out of 36 Korean patients with deep vein thrombosis.

  PMID 12692411 · PMC3055032 · Journal of Korean medical science · 2003 · 7 claims · 3 setups

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  Dysplasminogenemia was identified in 3 of 36 (8.3%) unrelated Korean DVT patients.

  plasma genomic amidolytic immunoturbidimetric pcr

• Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes.

  PMID 16202172 · PMC1260020 · BMC medical genetics · 2005 · 8 claims · 3 setups

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  HA-1 allele and genotype frequencies were determined in 131 unrelated Italian subjects (HA-1H=0.43, HA-1R=0.57), consistent with Hardy-Weinberg equilibrium and prior North American Caucasian data.

  genomic sequence-specific direct melting

• Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

  PMID 16925837 · PMC1810552 · Genome biology · 2006 · 6 claims · 3 setups

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  Promoter predictors that combine promoter prediction with gene prediction (N-SCAN, Fprom) achieve better performance than pure ab initio promoter predictors, mainly by reducing the promoter search space and false positives

  genome encode computational tss manual