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).

• Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

  PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

  pcr-amplified same sequence luciferase bioluminometric bati comparison

• The signal in the genomes.

  PMID 16683016 · PMC1447653 · PLoS computational biology · 2006 · 7 claims · 3 setups

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  A high breakpoint reuse rate in the output of rearrangement algorithms indicates loss of historical signal, not good evidence for genomic fragile regions

  simulated genome

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

  PMID 16822311 · PMC1553470 · Retrovirology · 2006 · 8 claims · 6 setups

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  CTLL cells stably expressing wild-type Tax (CTLL/WT) show higher aneuploidy than a CREB-transactivation-deficient Tax clone (CTLL/703)

  ctll gene promoter metaphase microarray bioinformatics

• Promoting human promoters.

  PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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  A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

  gene liver cycle genes computational expression time-course

• A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

  PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups

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  A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability

  hela candidate screen genome-wide propidium sirna

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.

  grch38 homogeneous per single single-cell clustering cell-type

• Comparing cellular proteomes by mass spectrometry.

  PMID 19886975 · PMC2784314 · Genome biology · 2009 · 8 claims · 6 setups

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  MS-based proteomics combined with cryo-electron tomography (CET) enables determination of absolute and relative protein abundances and localization

  leptospira saccharomyces specified shotgun selected cryo-electron

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  H. caudiculatum (lower canopy) exhibits about twice as many differentially expressed genes as H. dentatum (upper canopy), with a higher proportion of both increased and decreased gene abundance during dehydration.

  hymenophyllum dark-adapted annotated differentially bulk relative chlorophyll

• Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

  PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 80

  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

  PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups

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  P. falciparum encodes substantially more membrane transport proteins than originally annotated

  falciparum genome-wide bioinformatic quantification

• The protein-phosphatome of the human malaria parasite Plasmodium falciparum.

  PMID 18793411 · PMC2559854 · BMC genomics · 2008 · 8 claims · 8 setups

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  P. falciparum possesses 27 putative protein phosphatase sequences across the four major PP families (PPP, PPM, PTP, NIF), plus 7 additional sequences predicted to dephosphorylate non-protein substrates, totaling 34.

  sapiens ppp-domain metallophosphatase pf14_0142 hmm sequence neighbour-net

• RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

  PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 41

  Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

  pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative

• Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

  PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

  Has reproduction · 87

  NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

  lines bulk single-cell housekeeping bulk pca single-sample

• Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

  PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 6 claims · 8 setups

  Has reproduction

  A deep learning WSI cluster (three-class mini batch K-means on Inception V3 features) is associated with overall survival (P<0.001) and is an independent prognostic predictor (P=0.031) in BLCA.

  tcga-blca blca tcga deep transfer-learning neural-network

• Identity rather than 3D position informs splicing of rare introns in the human genome.

  PMID 41561379 · PMC12814444 · iScience · 2026 · 8 claims · 7 setups

  Has reproduction · 98

  Splicing efficiency depends on intron identity rather than nuclear (SPAD) position; despite shared SPAD proximity, major-like and minor-like introns are less efficiently spliced than major and minor introns

  k562 reference intron-class-containing hi-c tsa-seq damid-seq

• Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.

  PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups

  Has reproduction · 63

  The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.

  balb cl-sl donovani experimental transgenic genome

• Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

  PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

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  HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

  plasma proviral cloned pbmc hiv-1 nested clonal