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).

• Adaptive history of single copy genes highly expressed in the term human placenta.

  PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

  term single same lists microarray comparative site

• Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.

  PMID 41253754 · PMC12627582 · Nature communications · 2025 · 7 claims · 8 setups

  Has reproduction · 10

  Fetal Gli1+ cells (including cells outside the cartilage) are the precursors of postnatal long-lived chondroprogenitors and give rise to most growth-plate chondrocytes juvenile/adult.

  fetal left-cart-p21moe growth gli1creer single-nuclei bulk cre-based

• Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

  PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups

  Has reproduction · 83

  scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach

  liver hepatocyte detected adipose single-cell differential protein-protein

• Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

  PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 7 setups

  Has reproduction · 80

  After long-term ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin locations, most prominently centromeric satellite/micro-satellite DNA.

  pbmc single cd4 flip-seq mip-seq prip-seq

• Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model.

  PMID 36321803 · PMC9708074 · eLife · 2022 · 7 claims · 5 setups

  Has reproduction · 72

  Follicle cell-specific Lgl knockdown (Lgl-KD) causes loss of apical-basal polarity and invasive multilayering of the follicular epithelium without long-distance metastasis

  drosophila single-cell bulk immunofluorescence

• Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

  PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

  interscapular ibat bat single-nucleus qpcr western

• Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.

  PMID 34719737 · PMC8629906 · Cellular and molecular life sciences : CMLS · 2021 · 7 claims · 8 setups

  Has reproduction · 50

  VAP-1 is expressed on a subset of human HSC and on bone marrow vasculature, forming a hematogenic niche.

  facs-sorted sorted cd34+ bulk single-cell flow

• The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

  PMID 15740614 · PMC555937 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Edge-Betweenness clustering separates protein interaction graphs into subgraphs whose GO term distributions show significant correlations, revealing biologically meaningful functional modules.

  interaction yeast edge-betweenness chi-squared robustness

• Polyploidy and the petal transcriptome of Gossypium.

  PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

  Has reproduction · 51

  Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

  petal rna-seq commonly polyploid rna-seq read universal

• Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

  PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 6 setups

  Has reproduction · 94

  EiaD is a reproducible, versioned pan-eye and body RNA-seq transcriptome dataset built from 916 eye and 1375 GTEx samples via a Snakemake pipeline output as a single SQLite database.

  eye-related body eiad fetal bulk differential term

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular

• PubMatrix: a tool for multiplex literature mining.

  PMID 14667255 · PMC317283 · BMC bioinformatics · 2003 · 8 claims · 3 setups

  Full-text index only

  PubMatrix is a web-based CGI tool that queries PubMed with two lists of terms (search terms vs modifier terms) and returns a matrix of pairwise co-occurrence frequency counts

  pubmed ovarian genome literature cdna

• Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation.

  PMID 37311769 · PMC10264453 · Nature communications · 2023 · 7 claims · 8 setups

  Has reproduction · 69

  Porcine kidney xenografts transplanted into NHPs show only modest growth over time.

  yucatan cynomolgus nhp parathyroid bulk serial plasma

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.

  PMID 17982171 · PMC2238866 · Nucleic acids research · 2008 · 6 claims · 5 setups

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  StellaBase Disease houses homology data for 155,904 invertebrate isoforms of human disease genes across four model systems, including 14,874 predicted Nematostella genes

  nematostella blastp est snp

• Cohesin regulates alternative splicing.

  PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

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  Cohesin regulates alternative splicing independently of its effects on transcription.

  hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  ChIRP-MS identifies 309 host proteins that bind SARS-CoV-2 RNA during active infection across Huh7.5 and Vero E6 cells.

  huh7.5 host lung chirp-ms chirp-rna-seq sds-page