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).

• Cell atlases and the developmental foundations of the phenotype.

  PMID 41662466 · PMC12904592 · PLoS computational biology · 2026 · 8 claims · 6 setups

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  There is a proportional relationship between average developmental similarity (⟨simD⟩) and average phenotypic similarity (⟨simP⟩) across genes, supporting the D–P rule on average

  caenorhabditis gene elegans single-cell phenotype non-negative

• Biphasic expression of thyroid hormone receptor TRβ1 in mammalian retina and anterior ocular tissues.

  PMID 37033230 · PMC10076699 · Frontiers in endocrinology · 2023 · 7 claims · 8 setups

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  TRβ1 shows a biphasic, late-peaking expression profile in retina that contrasts with the early embryonic peak of TRβ2

  retina fetal retinal cones rna-seq lacz immunofluorescence

• GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

  PMID 18795106 · PMC2532782 · Experimental diabetes research · 2008 · 6 claims · 4 setups

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  GeneSpeed Beta Cell is an online genomics data repository allowing simultaneous multiexperiment viewing and multidimensional (Boolean intersection/union) querying of pancreas- and islet-relevant datasets, integrated with GeneSpeed's domain-based gene categorization.

  embryonic pancreatic panel pituitary affymetrix

• Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

  PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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  Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

  chinese tissues skeletal pk15 full-length real-time gfp

• Two committees tackle toxicogenomics.

  PMID 12501852 · PMC1241123 · Environmental health perspectives · 2002 · 8 claims · 8 setups

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  NIEHS funded a $37 million, five-year Toxicogenomics Research Consortium (TRC) linking the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to coordinate gene-expression research on environmental health effects.

  strains nervous mice liver microarray gene toxicogenomic

• De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.

  PMID 24586345 · PMC3929608 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 59

  A de novo transcriptome for Calanus finmarchicus was assembled from six developmental-stage libraries, yielding 206,041 contigs and a reference set of 96,090 unique comps, representing a new molecular resource for this species.

  calanus pooled raw combined bulk extraction read

• Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

  PMID 18834967 · PMC2561938 · American journal of human genetics · 2008 · 7 claims · 6 setups

  Has reproduction · 70

  Heterozygous CHD7 mutations cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome without the CHARGE phenotype.

  ihh additional chd7 sanger targeted rt-pcr

• Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

  PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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  Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

  saliva amplified extracted differentially genome quality extraction

• Have microarrays failed to deliver for developmental biology?

  PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

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  Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

  drosophila caenorhabditis developing xenopus cdna genome-wide microarray

• Alternative splicing dynamics during human cardiac development in vivo and in vitro.

  PMID 41483812 · PMC12925949 · Stem cell reports · 2026 · 8 claims · 8 setups

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  iPSC-CMs globally resemble prenatal cardiac cells at both the transcriptional and splicing levels

  ipsc-cms heart bulk ipsc-cm immunofluorescence single-cell bulk

• Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

  PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups

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  Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.

  perfused lung microarray principal wilcoxon

• Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

  PMID 17486137 · PMC2673710 · Molecular systems biology · 2007 · 8 claims · 7 setups

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  Global MudPIT-based proteomic profiling across six mouse lung developmental time points (E13.5–P56) identifies thousands of proteins and captures developmental/cell-biological expression patterns.

  lung analysis embryonic homologues shotgun microarray k-nearest

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental

• Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.

  PMID 41159380 · PMC12979040 · Neuro-oncology · 2026 · 8 claims · 8 setups

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  A unified UMAP-based transcriptomic landscape built from 888 medulloblastoma and 370 ependymoma tumors reveals distinct clusters corresponding to known and novel molecular subtypes.

  medulloblastoma ependymoma healthy shh bulk fusion copy

• Integromics: challenges in data integration.

  PMID 12186644 · PMC139396 · Genome biology · 2002 · 8 claims · 7 setups

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  There is no simple solution to database integration in genomics/bioinformatics

  lines molecular gene monsanto high-throughput cluster-correlation microarray

• Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

  PMID 41612263 · PMC12924552 · BMC biology · 2026 · 8 claims · 6 setups

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  Profiling gene expression across 26 life stages of A. millepora and building an interactive Shiny-based tool (DEView) enables comprehensive visualisation of developmental transcriptomic data.

  acropora millepora bulk differential pca

• Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

  PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

  breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence

• MYC-induced USP10 stabilizes SOX4 to promote thymocyte proliferation and leukemia onset in mice.

  PMID 41927540 · PMC13216311 · Nature communications · 2026 · 8 claims · 8 setups

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  USP10 is dynamically expressed in thymocytes, peaking during proliferative stages of T cell development in both mouse and human

  thymocytes thymocyte t-all lin dub rt-qpcr single-cell

• Spatiotemporal dynamics of ecto-5'-nucleotidase (CD73) in mouse retina under physiological conditions.

  PMID 41560519 · PMC12912271 · Development (Cambridge, England) · 2026 · 8 claims · 6 setups

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  CD73 expression in the neural retina is restricted to the rod-photoreceptor lineage and becomes robustly detectable from postnatal day (P) 3 onward, persisting into adulthood.

  cd73-bac-egfp cd73-creert2 scrna-seq cd73-knockout immunofluorescence genetic whole-mount

• Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression.

  PMID 17997606 · PMC2065881 · PLoS genetics · 2007 · 8 claims · 5 setups

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  NR genes are predominantly expressed during organogenesis rather than early embryogenesis

  danio zebrafish coregulator rt-pcr whole-mount phylogenetic