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).

• Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

  PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq

  liver-derived muscle heart pooled 10x oxford hi-c

• SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

  PMID 15961730 · PMC1151590 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  SW-ARRAY, an adaptation of the Smith-Waterman dynamic programming algorithm, provides a sensitive and robust method for identifying copy-number changes in array CGH data

  chromosome 16p array probe-by-probe sw-array

• 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

• 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

• Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

  PMID 16469098 · PMC1409804 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  AUGUSTUS+ extends the AUGUSTUS GHMM by combining intrinsic sequence information with extrinsic hints via an extended emission alphabet, so the GHMM jointly models the DNA sequence, gene structure, and hint collection.

  chromosome genomic training ghmm-based sequence parameter

• A genome annotation-driven approach to cloning the human ORFeome.

  PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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  Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

  chromosome pooled t-tailed naga comparative rt-pcr sanger

• Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

  PMID 19956714 · PMC2776354 · PloS one · 2009 · 8 claims · 5 setups

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  3,019 CNVs (2,381 autosomal, 638 X chromosome) were identified across 985 Caucasian and 692 Asian individuals using the Affymetrix 500K array

  same caucasian cau autosomal snp copy population

• Pathogenesis of vestibular schwannoma in ring chromosome 22.

  PMID 19772601 · PMC2758865 · BMC medical genetics · 2009 · 8 claims · 7 setups

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  Tumours in ring chromosome 22 patients arise from the combination of loss of the ring chromosome (first hit) and a pathogenic somatic NF2 mutation on the remaining chromosome 22 (second hit)

  peripheral schwann skin-biopsy vestibular karyotyping fish array

• NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

  PMID 41710890 · PMC12909245 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  Dysidea avara has a chromosome-level genome assembly of 575 Mb, N50 41 Mb, 162 scaffolds, and 15 chromosomes.

  dysidea avara translated nlrs long-read hi-c genome

• ZFHX4 is necessary for dopaminergic neuron differentiation and controls cell cycle by regulating LIN28A.

  PMID 42208531 · PMC13261933 · Stem cell reports · 2026 · 8 claims · 8 setups

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  ZFHX4 is a super-enhancer-controlled transcription factor induced during mDAN specification

  ipsc-derived smnpcs postmortem cut&tag bulk shrna

• Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes.

  PMID 41526351 · PMC12796357 · Nature communications · 2026 · 8 claims · 8 setups

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  Cardiomyocyte (CM)-specific Hi-C data detect substantially more and stronger promoter-interacting domains (PIDs) for CM marker genes than bulk cardiac tissue Hi-C data

  non-failing cardiac nf-lv-cm biological hi-c fluorescence-activated chip-seq

• Temporal multiomics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation.

  PMID 41545424 · PMC12920657 · Scientific data · 2026 · 8 claims · 8 setups

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  Generated a high-resolution, time-resolved multi-omics dataset (RNA-seq, ribosome profiling, and quantitative proteomics) tracking mRNA, translation, and protein dynamics across hESC differentiation into definitive endoderm and polyhormonal pancreatic cells

  hesc-derived rues2 extracted star-aligned rna-seq ribosome quantitative

• The genome sequence of the Mediterranean Skipper, Gegenes nostrodamus (Fabricius, 1793) (Lepidoptera: Hesperiidae).

  PMID 41908929 · PMC13019046 · Wellcome open research · 2026 · 6 claims · 7 setups

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  A chromosome-level genome assembly was generated for Gegenes nostrodamus (Mediterranean Skipper) as part of Project Psyche.

  gegenes pacbio hi-c k-mer

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

  Has reproduction · 91

  A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

  yeonsan ogye_1.1 locus tissues whole-genome genome structural

• Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

  PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

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  Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

  poodle dogs y-chromosome blast pcr nested

• Novel mutations in the ZEB1 gene identified in Czech and British patients with posterior polymorphous corneal dystrophy.

  PMID 17437275 · PMC2696796 · Human mutation · 2007 · 7 claims · 5 setups

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  Four novel pathogenic ZEB1 mutations (two deletions, one nonsense, one duplication, all in exon 7) were identified in four of ten unrelated Czech/British PPCD families

  peripheral genomic six individuals sequencing pcr microsatellite

• Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

  PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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  Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

  families genes individuals kidney genome-wide sanger resequencing

• Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

  PMID 15850495 · PMC1090572 · BMC genetics · 2005 · 8 claims · 6 setups

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  Haplotype block definitions based on LD measures (Definitions 1, 2, 3, 5) produce fewer, shorter blocks with limited sequence coverage compared to the haplotype diversity-based method (Definition 4)

  unrelated same snps haplotype snp haplotype pairwise

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Transcriptional landscape of repetitive elements in normal and cancer human cells.

  PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 76

  RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

  chromosomes lines imr-90 prostate simulated pol chip-seq