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).

• Analysis of sequence conservation at nucleotide resolution.

  PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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  SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

  encode population comparative snp functional

• Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

  PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

  Has reproduction · 95

  Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

  embryonic escs dem-cgis demg methylation chip-seq gene

• Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes.

  PMID 18828897 · PMC2760871 · Genome biology · 2008 · 8 claims · 8 setups

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  The overlap between phosphoproteomes of six eukaryotes (human, mouse, fly, yeast, plant, zebrafish) is significantly greater than expected by chance.

  liver fruit yeast plant high-throughput comparative

• Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

  PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

  genome functional registered omim comparative kendall's homology

• Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

  PMID 17567995 · PMC1891336 · Genome research · 2007 · 7 claims · 3 setups

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  Four different alignment methods show large-scale consistency but substantial differences in small-scale rearrangements, sensitivity, and specificity.

  mammalian aligned constrained sequence evolutionary comparative

• Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

  PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

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  Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

  normal genome-wide same omim microarray sage computational

• Genomic views of distant-acting enhancers.

  PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups

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  Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.

  genome patients embryos ret gwas targeted transgenic

• Ontological Discovery Environment: a system for integrating gene-phenotype associations.

  PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups

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  ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems

  strains integrated bipartite phish gene differential pairwise

• Genome-wide identification of human functional DNA using a neutral indel model.

  PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

  chromosome human-mouse genome individual whole-genome probabilistic comparative

• The Edinburgh human metabolic network reconstruction and its functional analysis.

  PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups

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  EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.

  enzyme emp kegg humancyc genome literature-based comparative

• Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

  PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 75

  All three mouse models (hAβ-KI, 5xFAD, APP/PS1) share more differentially expressed genes, GO biological processes, and KEGG pathways with LOAD than with EOAD patients.

  haβ-ki models degs app bulk functional master

• Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

  PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

  est gene worm fly blat-based transcription comparative

• Organization of physical interactomes as uncovered by network schemas.

  PMID 18949022 · PMC2561054 · PLoS computational biology · 2008 · 7 claims · 5 setups

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  A computational procedure can systematically identify 'emergent' network schemas that are both recurrent and over-represented relative to randomized networks preserving lower-order subschema distributions

  cerevisiae sapiens uncharacterized network cross-species functional

• A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

  PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

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  Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

  genes hela proteins worm co-expression quantitative functional

• SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells.

  PMID 32770939 · PMC7430845 · BMC genomics · 2020 · 8 claims · 5 setups

  Has reproduction · 94

  SOX10 binds preferentially at proximal promoter elements directly over TSSs in Schwann cells in vivo, identifying candidate SOX10-regulated promoters.

  sciatic schwann differentiating tn5prime chip-seq gene

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

  PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups

  Has reproduction · 75

  XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations

  vietnamese indica subpopulation whole-genome whole-genome xp-clr fst

• Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

  PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)

  preimplantation single uniparental embryos rna-seq paired gene

• Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

  PMID 12702206 · PMC154576 · Genome biology · 2003 · 8 claims · 6 setups

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  Segmental duplications comprise 3.53% (107.4/3,043.1 Mb) of the June 2002 human genome assembly

  genome refseq-annotated chromosome chromosome-wide e-pcr ambsnp

• Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

  PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups

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  FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements

  cerevisiae elegans randomized computational randomized microarray