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).

• The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance.

  PMID 41124349 · PMC12774589 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

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  R. solani isolates AG8-1 and AG8-3 each possess 2 distinct nuclear haplotypes, each ~50 Mbp assembled into 16 chromosomes

  solani ag8-1 rhizoctonia annotated pacbio hi-c stranded

• ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.

  PMID 41243977 · PMC12807738 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  ATACdb 2.0 expands data scale, adding mouse chromatin accessibility data and substantially expanding human samples, plus pseudo-bulk ATAC-seq profiles built from scATAC-seq data to increase cell type diversity

  geo scatac-ref bulk scatac-seq h3k27ac

• Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

  PMID 41371963 · PMC12758400 · Genome research · 2026 · 8 claims · 6 setups

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  GSC-like and CySC-like cells isolated from upd tumor testes are transcriptionally comparable to wild-type GSC/early-spermatogonia and CySC clusters, respectively

  upd gsc-like wild-type scrna-seq differential gene

• Predicting the effect of CRISPR-Cas9-based epigenome editing.

  PMID 41524535 · PMC12795505 · eLife · 2026 · 8 claims · 6 setups

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  Machine learning (CNN and ridge regression) models trained on histone PTM ChIP-seq and RNA-seq data from 13 ENCODE cell types accurately predict endogenous gene expression, with transcriptome-wide correlations of ~0.70-0.79 for most cell types

  hek293t k562 computational chip-seq rna-seq mnase-seq

• Differentiation in the human urothelia is defined by distinct alternative polyadenylation.

  PMID 41533515 · PMC12937501 · Cell reports · 2026 · 8 claims · 8 setups

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  APA introduces a major layer of transcriptomic diversity during urothelial differentiation, largely independent of changes in mRNA levels

  urothelial urothelial-specific ureter hek293t single-cell poly fluorescence

• Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA.

  PMID 41535307 · PMC12913623 · Nature communications · 2026 · 8 claims · 8 setups

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  e2MPRA, combining lentiviral integration-based MPRA with CUT&Tag or ATAC-seq, enables simultaneous measurement of regulatory activity, protein binding, and epigenetic modification of the same synthetic CRE sequences.

  hepg2 lentimpra atac-seq h3k27ac

• CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

  PMID 41555433 · PMC12903630 · Genome biology · 2026 · 8 claims · 8 setups

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  CLAMP, a chromatin-accessibility language model, predicts protein-mediated chromatin loops across 10 species, 18 proteins, and 24 cell types with superior performance versus existing methods.

  species gm12878 types chromatin cross-protein cross-cell-type

• Redefinition of the toll-like receptor repertoire in Ciona robusta through genomic, structural, and expression analyses.

  PMID 41568004 · PMC12816324 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 8 setups

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  CiTLR13 is a redundant annotation of CiTLR1 (same genomic locus, >94% sequence identity), so it is not a distinct TLR gene

  ciona six lrr tlr blastp domain nucleotide

• ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

  PMID 41592570 · PMC13069865 · Cell genomics · 2026 · 8 claims · 7 setups

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  ChromBERT is pre-trained via masked reconstruction on the Cistrome-Human-6K dataset (6,391 cistromes, 991 transcription regulators) to learn genome-wide interaction syntax of transcription regulators

  lines chromosome embryonic transcription chip-seq chromhmm hi-c

• Expression spectrum of TE-driven transcripts in human adult tissues.

  PMID 41593763 · PMC12924553 · Genome biology · 2026 · 8 claims · 8 setups

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  TE-driven transcripts are broadly expressed across human adult tissues and contribute to both housekeeping and tissue-specific gene regulation

  tissues paired sequences genome bulk differential chip-seq

• Substantial unannotated noncoding transcripts in tumors may transcriptionally regulate cancer-related genes.

  PMID 41606598 · PMC12924361 · BMC biology · 2026 · 8 claims · 8 setups

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  Many unannotated genes and transcripts (MSTRG/UNTs) are pervasively generated and significantly differentially expressed in cancer cell lines and tissues across four tumor types (lung, liver, stomach, colon)

  cancer a549 unt bulk chip-seq computational

• Resolving clonal evolution and selection of extrachromosomal DNA at single-cell resolution.

  PMID 41606654 · PMC12853921 · Genome biology · 2026 · 7 claims · 8 setups

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  ecSingle, a computational method integrating allelic imbalance (BAF deviation) and outlier expression from scRNA-seq, can identify oncogene-carrying ecDNA at single-cell resolution.

  colo320dm glioblastoma medulloblastoma ce26 scrna-seq whole-genome long-read

• Pharmacological perturbation of splicing elicits SMG1 reduction: Implications for cancer therapy.

  PMID 41623476 · PMC12857400 · iScience · 2026 · 7 claims · 12 setups

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  Splicing-modulatory drugs MS023 and indisulam act as inadvertent NMD inhibitors by downregulating SMG1 protein levels

  4t1 tumor-draining arst panc02 mts tumor ifn-γ

• Systematic transcriptome analysis reveals the function of alternative promoters in hematopoietic lineages.

  PMID 41650962 · PMC12985389 · Stem cell reports · 2026 · 8 claims · 8 setups

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  Analysis of 532 RNA-seq datasets constructed a high-resolution promoter activity landscape across hematopoietic lineages

  hematopoietic major monocytes candidate rna-seq h3k4me3 motif

• The gene expression landscape of disease genes.

  PMID 41664080 · PMC12983648 · Genome biology · 2026 · 8 claims · 8 setups

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  In tissues and cell types with established disease relevance, disease genes show higher and more specific gene expression than control genes

  gtex pubmed tabula archs4 differential magma anderson-darling

• Predictive modeling of molecular activity underlying physical cell-cell interactions.

  PMID 41672069 · PMC12946745 · Cell reports methods · 2026 · 8 claims · 5 setups

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  Gloss, an overlapping group lasso regression combining single-gene and curated pathway features, predicts LIPSTIC interaction intensity from scRNA-seq data

  tumor intestine mediastinal organs lipsticv1 ulipstic cite-seq

• Development of a potent monoclonal antibody for treatment of human metapneumovirus infections.

  PMID 41680141 · PMC13013820 · Nature communications · 2026 · 8 claims · 8 setups

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  4F11 is a highly potent neutralizing mAb against HMPV with in vitro and in vivo efficacy

  splenocytes vero recombinant hmpv fluorescent plaque biolayer

• Global reorganization of genome architecture at the transition to gametogenesis.

  PMID 41721019 · PMC12999497 · Nature structural & molecular biology · 2026 · 8 claims · 8 setups

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  Premeiotic gonadal germ cells display a distinct chromosome and genome architecture concomitant with commitment to gametogenesis, involving separation of individual chromosomes, peripheral centromere anchoring, reduced interchromosomal interactions and disentangled chromosome ends

  e13.5 e9.5 gonadal facs-sorted transmission immunofluorescence minor

• SLC25A37 as a novel therapeutic target for benign prostatic hyperplasia: integrative analyses of single-cell RNA sequencing and genome-wide association studies.

  PMID 41726128 · PMC12917586 · Open medicine (Warsaw, Poland) · 2026 · 8 claims · 8 setups

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  SLC25A37 is causally associated with increased BPH risk, supported by MR, Bayesian colocalization, and reverse MR analyses

  prostate gwas eqtl bph single-cell mendelian bayesian

• Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.

  PMID 41735611 · PMC13095655 · Nature structural & molecular biology · 2026 · 6 claims · 7 setups

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  TADs and large-scale chromatin structures remain largely unchanged during sex determination, suggesting a preformed configuration

  facs-sorted same integrated fgf9 hi-c chip-seq metaloci