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).

• Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

  PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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  41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

  genome transcriptome gene genes full-length genome cdna

• Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

  PMID 18443592 · PMC2742198 · Nature genetics · 2008 · 8 claims · 8 setups

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  Osteoglycin (Ogn) is a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM

  heart ogn cos-1 neonatal eqtl quantitative genome-wide

• MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

  PMID 24599324 · PMC3944147 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 29

  MOSAIK is the only aligner that consistently aligns reads from all major sequencing platforms (Illumina, AB SOLiD, Roche 454, Ion Torrent, Pacific Biosciences SMRT) using the same algorithmic approach.

  simulated million coli illumina short-read mapping neural-network

• Multi-context seeds enable fast and high-accuracy read mapping.

  PMID 41764549 · PMC13059148 · Genome biology · 2026 · 7 claims · 5 setups

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  Multi-context seeds (MCS) allow storage of seeds with different lengths in the same index structure by splitting hash bits among strobes, enabling full and partial matches

  simulated chm13 same sequence seed simulated

• Candidates for Balancing Selection in Leishmania donovani Complex Parasites.

  PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups

  Has reproduction · 64

  Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)

  infantum donovani snp populations whole-genome read admixture

• EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

  PMID 35561186 · PMC9113274 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 5 setups

  Has reproduction · 49

  EDGE COVID-19 (EC-19) is a web-based platform that automates QC, reference-based variant/consensus calling, lineage determination, and submission of SARS-CoV-2 genomes and metadata to GenBank, GISAID and INSDC for both Illumina and ONT data.

  sars-cov-2 srr illumina ont amplicon lineage cross-workflow

• A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

  PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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  Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

  individuals sequence resequencing snps targeted sequence genotype

• Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.

  PMID 42206012 · PMC13202175 · NAR genomics and bioinformatics · 2026 · 8 claims · 7 setups

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  AVITI and NovaSeq X Plus are highly comparable overall for variant-calling performance in WGS

  tumor mm1s aviti chr20 whole-genome pacbio small

• MitoVariome: a variome database of human mitochondrial DNA.

  PMID 19958475 · PMC2788364 · BMC genomics · 2009 · 8 claims · 5 setups

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  MitoVariome is a web-based, integrated variome database for human mitochondrial DNA that unifies sequence variation, haplogroup, and disease annotation information not jointly available in prior databases (MITOMAP, mtDB, Mitome, MitoRes).

  mitochondrial korean sequence short restriction

• Telomere-to-telomere assembly of a complete human X chromosome.

  PMID 32663838 · PMC7484160 · Nature · 2020 · 8 claims · 8 setups

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  Produced the first gapless, telomere-to-telomere assembly of a human chromosome (the X chromosome) using the CHM13 cell line

  chm13htert chm13 ultra-long-read pacbio linked-read

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• 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

• Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

  PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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  The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

  chimpanzee retrofitted primate aspm tar restriction genomic

• Cancer genome standards for long-read sequencing using cancer cell line mixtures.

  PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

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  Long-read variant calling tools achieve recall rates comparable to short-read gold standards

  colo829 same whole-genome short-read 5mc