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).

Publications 1.3k Datasets 392.5k Experiments 19

System / cell line: sequences ✕ Assay: masked ✕ Clear

Retentive Network promotes efficient RNA language modeling of long sequences.

PMID 41814064 · PMC13111708 · Communications biology · 2026 · 8 claims · 6 setups

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RNAret, a RetNet-based RNA language model with O(n) complexity, achieves training parallelism and low computational overhead while processing long RNA sequences

million rnacentral mirtarraw rnastralign self-supervised t-sne mirna-mrna
Separating selection from mutation in antibody language models.

PMID 41944291 · PMC13056363 · eLife · 2026 · 8 claims · 6 setups

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Masked antibody language models such as AbLang2 are biased by nucleotide-level mutation processes (germline memorization, codon table, SHM rate variation)

single nine antibody reconstructed masked-site correlation functional
Advancing codon language modeling with synonymous codon constrained masking.

PMID 41736545 · PMC12956333 · Nucleic acids research · 2026 · 8 claims · 7 setups

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SynCodonLM introduces synonymous codon-constrained masking, restricting masked-codon prediction to only synonymous codon options via logit masking before softmax

cds syncodonlm escherichia rscu masked t-sne pca
A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

PMID 15626332 · PMC5172250 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 6 setups

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Repeats of different copy number have distinct probabilities of appearance in shotgun data, which can be modeled statistically to define recognition thresholds (MDRs) at different shotgun coverages.

simulated same repeat whole-genome genome
BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.

PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups

Has reproduction · 50

BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length

rfam plant lncrna-mirna sequences unsupervised mirna-lncrna length-binned
PigGIS: Pig Genomic Informatics System.

PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

million pig matched wgs blastx repeat sequence
Computational comparison of two mouse draft genomes and the human golden path.

PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

newly genome chromosome genomic blat blastn repeat
Pegasys: software for executing and integrating analyses of biological sequences.

PMID 15096276 · PMC406494 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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Pegasys is a flexible, modular, customizable software system for executing and integrating heterogeneous biological sequence analysis tools

eukaryotic formatted genomic input initio sequence gene
Recent segmental and gene duplications in the mouse genome.

PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

genome gene ensembl-annotated chromosome pairwise gene blat
CEAS: cis-regulatory element annotation system.

PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

genome genomic chip-chip repeat-masked conservation
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

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About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

predicted non-masked genome interpro hmm tblastn inter-species
A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

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PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

genomic genome extracted pairwise online genome-wide
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

sus pig concatenated three-species whole-genome repeat comparative
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

orthologous randomized high-score promoters pssm-based comparative motif
Comprehensive benchmarking of large language models for RNA secondary structure prediction.

PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

Has reproduction · 88

Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.

archiveii bprna large-scale secondary cross-family self-supervised
The Chromosome-Scale Genome Assembly of the Redlip Blenny, Ophioblennius macclurei (Blenniidae).

PMID 41378738 · PMC12758960 · Genome biology and evolution · 2026 · 8 claims · 12 setups

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A chromosome-scale genome assembly of O. macclurei was generated (529.6 Mb, scaffold N50 23.7 Mb, GC 43.49%) using ONT long reads, Illumina short reads, and Hi-C scaffolding.

blood muscle tissues assembled oxford illumina hi-c
Evaluating the performance of ancient DNA genetic relatedness estimation methods using high-fidelity pedigree simulations.

PMID 41796349 · PMC13081257 · Genome biology · 2026 · 8 claims · 5 setups

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BADGER, an automated snakemake pipeline, was developed to simulate high-fidelity pedigrees and raw ancient DNA sequence data for benchmarking genetic relatedness methods

genomes simulated pedigree ancient read
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis
Predicting failure rate of PCR in large genomes.

PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

genomic genome pcr combined large-scale exact-match mismatch-tolerant

Experiments

Retentive Network promotes efficient RNA language modeling of long sequences.

Separating selection from mutation in antibody language models.

Advancing codon language modeling with synonymous codon constrained masking.

A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.

PigGIS: Pig Genomic Informatics System.

Computational comparison of two mouse draft genomes and the human golden path.

Pegasys: software for executing and integrating analyses of biological sequences.

Recent segmental and gene duplications in the mouse genome.

CEAS: cis-regulatory element annotation system.

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

Comprehensive benchmarking of large language models for RNA secondary structure prediction.

The Chromosome-Scale Genome Assembly of the Redlip Blenny, Ophioblennius macclurei (Blenniidae).

Evaluating the performance of ancient DNA genetic relatedness estimation methods using high-fidelity pedigree simulations.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

Predicting failure rate of PCR in large genomes.