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).

• Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

  PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

  Has reproduction · 87

  TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

  testseta bprna-new ts-inter individual jaccard pca ensemble

• Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

  PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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  The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

  genome seven genes computational cage comparative

• Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

  PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups

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  An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes

  genome training svm support leave-one-out sensitivity

• Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

  PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.

  boars lwd lws pig whole-genome genetic genome-wide

• Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions.

  PMID 42258536 · PMC13244158 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  RADIAnT is a reads-to-interactions computational pipeline for analyzing RNA–DNA ligation data

  embryonic k562 mesc endothelial grid-seq radicl-seq red-c

• 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

• Hobbes: optimized gram-based methods for efficient read alignment.

  PMID 22199254 · PMC3315303 · Nucleic acids research · 2012 · 8 claims · 4 setups

  Has reproduction · 83

  Hobbes, a gram-based short-read mapper supporting Hamming and edit distance, is faster than all other read-mapping programs tested while maintaining high mapping quality.

  genome hg18 example reference read-mapping character-substitution algorithmic

• Mutations in alpha-tubulin cause abnormal neuronal migration in mice and lissencephaly in humans.

  PMID 17218254 · PMC1885944 · Cell · 2007 · 8 claims · 8 setups

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  A semidominant ENU-induced S140G mutation in α-1 tubulin (Tuba1) causes hyperactivity and impaired neuronal migration in Jna/+ mice

  enu-mutagenized jna cell-free hippocampus locomotor qtl gtp-binding

• A computational screen for type I polyketide synthases in metagenomics shotgun data.

  PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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  Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

  predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds

• Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.

  PMID 19694819 · PMC4286260 · Genes, brain, and behavior · 2009 · 6 claims · 6 setups

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  A family-based clustering strategy using neurocognitive test scores (CPT, WCST) can identify more homogeneous subgroups of schizophrenia families for genetic association analysis

  multiplex affected subjects cluster-specific family-based continuous wisconsin

• WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.

  PMID 41911220 · PMC13048486 · PLoS computational biology · 2026 · 8 claims · 5 setups

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  WEPP is a pathogen-agnostic pipeline that uses phylogenetic placement of sequencing reads onto mutation-annotated trees (MATs) to identify candidate haplotypes and estimate their abundances

  sars-cov-2 mutation-annotated simulated synthetic real-world

• Natural clines and human management impact the genetic structure of Algerian honey bee populations.

  PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups

  Has reproduction · 55

  Algerian honey bees show no significant admixture from European reference honey bee populations

  haploid combined ld-pruned algerian whole-genome variant principal

• PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.

  PMID 41919010 · PMC13034549 · Bioinformatics advances · 2026 · 8 claims · 7 setups

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  PeakPrime is a reproducible Nextflow pipeline that calls 3′ RNA-seq coverage peaks (MACS2), selects exonic windows, designs strand-appropriate primers (Primer3), and screens specificity (Bowtie2)

  imr-32 universal candidate 10m-read rna-seq targeted quantitative

• Identification of novel DNA sequence motifs that modulate transcription in T cells.

  PMID 41514212 · PMC12879379 · BMC genomics · 2026 · 8 claims · 8 setups

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  Identified 2,036 novel DNA motifs enriched in regulatory regions of T-cell-specific genes

  t-cell non-t-cell cd4+ sequences rna-seq dnase-seq h3k27ac

• Web-based resources for comparative genomics.

  PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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  Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

  yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood

• A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.

  PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date

  pigs sscrofa11.1 pig domestic whole-genome tandem repeat

• Computational analysis of splicing errors and mutations in human transcripts.

  PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

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  Retained introns are significantly shorter than constitutively spliced introns

  refseq genes intron exon computational splice prediction

• Modeling nascent transcription from chromatin landscape and structure with CLASTER.

  PMID 41691282 · PMC13011747 · Genome biology · 2026 · 7 claims · 8 setups

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  CLASTER, a deep neural network combining chromatin landscape tracks and 3D contact maps, accurately predicts kilobasepair-resolution nascent RNA (EU-seq) profiles in a DNA-sequence-agnostic manner

  embryonic mescs chromatin k562 eu-seq chip-seq micro-c

• Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

  PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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  The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

  tlr4 mus chimpanzee baboon genomic coding sequence