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).

• TiSMeD: A tissue-specific methylation and expression database for biomarker and translational applications.

  PMID 41883585 · PMC13011251 · Molecular therapy. Nucleic acids · 2026 · 8 claims · 8 setups

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  TiSMeD integrates 6,782 methylomes, 16,894 transcriptomes, and 241 proteomes across 48 normal human tissues into a searchable database

  normal plasma case-control tcga methylation transcriptome proteomics

• SMART: spatial multi-omic aggregation using graph neural networks and metric learning.

  PMID 41896208 · PMC13031631 · Nature communications · 2026 · 8 claims · 5 setups

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  SMART accurately identifies spatial regions of anatomical structures and is compatible with spatial datasets of any type and number of omics layers

  simulated lymph brain spleen simulated spatial multi-section

• Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma.

  PMID 41916296 · PMC13130669 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Immune and stromal heterogeneity, rather than genetic variation, are primary drivers of gene expression ITH in iCCA

  multi-region icca four lihv bulk hallmark single-cell

• A sequence knowledge-guided deep learning method for single-cell multi-omics translation.

  PMID 41975483 · PMC13185235 · Genome biology · 2026 · 7 claims · 7 setups

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  scProTrans, a deep learning framework combining sequence knowledge (dna2vec gene embeddings, ProtT5 protein embeddings) with a cross-omics attention mechanism, translates single-cell transcriptome data into proteome profiles

  multi-omics pbmcs datasets fully cite-seq cross-technology tri-omics

• A high-resolution spatial map of cilia-associated proteins in the human fallopian tube.

  PMID 42010243 · PMC13096173 · Nature communications · 2026 · 6 claims · 7 setups

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  310 genes show elevated expression in the human fallopian tube compared to other tissues, the majority associated with motile cilium structure/function.

  fallopian ft-elevated tma comparison bulk single-cell gene

• A 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights.

  PMID 42013851 · PMC13198309 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  A 15-layer multi-omics atlas of 159 primary gastric adenocarcinomas and 30 matched normal adjacent tissues was generated, including previously unprofiled layers such as glycoproteomics, XL-MS-based PPI mapping, metabolomics, and tumor microbiome data

  gastric whole-exome methylation sequencing

• pmid-42030938

  PMID 42030938 · PMC13198283 · 8 claims · 8 setups

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  A multiomic (snRNA-seq, snATAC-seq, WGS, CODEX) atlas defines a core set of pHGG neoplastic cell states shared across molecular subtypes

  phgg neoplastic fetal single-nucleus whole-genome codex

• pmid-42050691

  PMID 42050691 · PMC13126711 · 8 claims · 8 setups

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  GLYATL1 expression is upregulated in AI-resistant breast cancer cell models and in patients undergoing AI therapy

  mcf7 lysates rna-sequencing atac-sequencing epic

• The AICL-KLRF1 axis supports CD4-CD8 T cell communication and cytokine competence in pre-exhausted CD8(+) T cells.

  PMID 41851343 · PMC13121605 · EMBO reports · 2026 · 8 claims · 8 setups

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  Progressive expression of KLRB1, KLRG1, GPR56, and KLRF1 tracks CD8+ T cell differentiation stages (TN, TCM, TEM, TEMRA), mirroring the pattern previously shown in CD4+ T cells

  unstimulated cd3+-enriched enriched cd8+ flow sorting-based spatial

• Bioinformatics methods for learning radiation-induced lung inflammation from heterogeneous retrospective and prospective data.

  PMID 19704920 · PMC2688763 · Journal of biomedicine & biotechnology · 2009 · 8 claims · 3 setups

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  Kernel-based methods (e.g., SVM) can capture nonlinear dose-volume interactions relevant to predicting radiation pneumonitis

  nsclc inoperable blood retrospective prospective 3-way

• Identification of disease markers in human cerebrospinal fluid using lipidomic and proteomic methods.

  PMID 16410651 · PMC3851111 · Disease markers · 2006 · 8 claims · 3 setups

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  Lipids comprise the bulk of the dry mass of the brain and serve structural, insulating, energy-storage, and signaling/inflammatory-mediator roles.

  brain cerebrospinal electrospray liquid selected

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

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  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• Genomic and proteomic techniques applied to reproductive biology.

  PMID 11574051 · PMC138959 · Genome biology · 2001 · 8 claims · 8 setups

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  Knockout of the E6-AP (UBE3A) gene reduces testis and prostate size in male mice and compromises estradiol action in females

  e6-ap fgf9-deficient jsd one-cell gene germ-cell interference

• Back to basics.

  PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

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  Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

  chromosome pendrin yeast carbonic genome gene mudpit

• Harnessing the HGP of public health.

  PMID 15176090 · PMC1241998 · Environmental health perspectives · 2004 · 8 claims · 7 setups

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  The tombusvirus p19 protein selectively recognizes and sequesters short (21-22 nucleotide) silencing siRNAs, discriminating them from longer siRNAs by measuring siRNA length via tryptophan-mediated end-stacking interactions

  carnation cirv blood rice x-ray site-directed mass

• International sequencing consortium.

  PMID 15174459 · PMC1315987 · Environmental health perspectives · 2004 · 8 claims · 6 setups

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  The p19 viral silencing-suppressor protein selectively recognizes short (21-22 nt) silencing siRNAs by measuring duplex length, using tryptophan residues (Trp39, Trp42) as molecular calipers that stack against the siRNA end base pairs.

  cirv blood sampled rice x-ray site-directed mass

• Toxoplasma: the next 100years.

  PMID 18672085 · PMC2596634 · Microbes and infection · 2008 · 8 claims · 8 setups

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  Micronemes, rhoptries, and dense granules are specialized secretory organelles that mediate T. gondii host cell invasion and remodeling

  gondii mammalian cdna affymetrix sage

• Defining the proteome.

  PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups

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  Integration of multi-omics data is an important step toward a systems-biology approach to the proteome

  brain chicken bacillus yeast proteome proteomics two-dimensional

• Fatty acid synthesis suppresses dietary polyunsaturated fatty acid use.

  PMID 38167725 · PMC10762034 · Nature communications · 2024 · 7 claims · 8 setups

  Has reproduction · 94

  FASN activity critically determines the use/incorporation of dietary PUFA into complex lipids in mice and humans

  index nash patient-derived hek293t lipidomics 14c-acetate cycloheximide

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups

  Has reproduction · 66

  Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level

  prostate bulk weighted reverse