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).

• A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

  PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

  Full-text index only

  Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

  gria2 drosophila nova1 cd45 splicing sirna hits-clip

• Impact of short-read sequencing on the misassembly of a plant genome.

  PMID 33530937 · PMC7852129 · BMC genomics · 2021 · 7 claims · 6 setups

  Full-text index only

  Short-read tomato assembly has substantial high-coverage (0.6%, 5.1 Mb) and low-coverage (9.7%, 79.6 Mb) regions relative to background coverage

  tomato whole-genome cnv machine

• IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

  PMID 25406361 · PMC4274634 · RNA (New York, N.Y.) · 2015 · 8 claims · 6 setups

  Has reproduction · 30

  Existing ab initio assemblers (Cufflinks, Scripture) annotate at most one 3' boundary per terminal exon and therefore cannot assemble coexpressed tandem 3' UTR isoforms.

  mapped simulated rna-seq ict1 computational benchmarking 3'-seq

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

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

  Full-text index only

  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

• First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.

  PMID 41436027 · PMC12958814 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

  Full-text index only

  This study produced the first genome assemblies of Neotropical Bombus (Thoracobombus) species, B. pauloensis and B. pullatus

  pauloensis masked long-read k-mer novo

• polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

  PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.

  helicoverpa alternate contigs assemblies long-read short-read duplicate

• Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.

  PMID 33103064 · PMC7568946 · One health outlook · 2020 · 8 claims · 3 setups

  Has reproduction · 85

  An open-access pathogen surveillance database (NCBI Pathogen Detection) plus contributor Best Practices enables FAIR, interoperable genomic data across human, animal, food, and environmental sources for One Health surveillance.

  salmonella ncbi-pd illumina empirical coverage

• lncEvo: automated identification and conservation study of long noncoding RNAs.

  PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 61

  lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.

  chimp assembled pairwise raw bulk lncrna comparative

• Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43.

  PMID 34647802 · PMC8515887 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

  Has reproduction · 88

  The complete, chromosome-scale genome sequence of Porcisia hertigi (isolate C119, strain LV43) was assembled using combined short- and long-read sequencing technologies.

  porcisia hertigi parasite extraction short-read

• Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV763.

  PMID 34498918 · PMC8428246 · Microbiology resource announcements · 2021 · 7 claims · 7 setups

  Has reproduction · 80

  Complete chromosome-scale genome sequence of Leishmania (Mundinia) enriettii isolate CUR178, strain LV763 was assembled using combined short-read and long-read sequencing

  leishmania whole-genome long-read genome

• Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768.

  PMID 34498920 · PMC8428255 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

  Has reproduction · 78

  The complete genome sequence of Leishmania (Mundinia) orientalis, isolate LSCM4, strain LV768, was determined using combined short-read and long-read sequencing.

  leishmania orientalis culture extraction short-read

• A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.

  PMID 40323688 · PMC12584591 · The Journal of heredity · 2025 · 6 claims · 8 setups

  Has reproduction · 99

  This paper presents the first de novo, haplotype-resolved reference-quality genome assembly of Sebastes paucispinis (bocaccio rockfish).

  sebastes assembled pacbio omni-c k-mer

• Advances in the study of SR protein family.

  PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

  Full-text index only

  SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

  nuclear bovine drosophila caenorhabditis selex rna-binding splicing

• Of rats and men.

  PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups

  Full-text index only

  The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)

  rattus cftr fugu transgenic whole-genome comparative genome

• The UCSC genome browser database: update 2007.

  PMID 17142222 · PMC1669757 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser Database provides sequence and annotation data for 13 vertebrate and 19 invertebrate species as of September 2006.

  hg17 genome lines xenopus comparative snp linkage

• The UCSC Genome Browser database: update 2010.

  PMID 19906737 · PMC2808870 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  The UCSC Genome Browser provides a large database of publicly available sequence and annotation data with an integrated tool set for examining, comparing, aligning, and displaying genomes

  genome vertebrate individuals personal snp sequence genome-wide

• Ensembl's 10th year.

  PMID 19906699 · PMC2808936 · Nucleic acids research · 2010 · 8 claims · 8 setups

  Full-text index only

  Ensembl provides comprehensive gene annotation and integrated genomic resources (variation, regulation, comparative genomics) across a growing set of chordate genomes

  anole western genome cd4+ whole-genome gene cross-database

• Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.

  PMID 15826305 · PMC1087836 · BMC bioinformatics · 2005 · 8 claims · 3 setups

  Full-text index only

  Statistical Viewer is a plug-in package for Ensembl that displays disease study-specific linkage and/or association data as 2D plots within Ensembl's Contig View and Cyto View pages.

  genome decode ensembl marker-to-genome genetic-to-physical linkage

• Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

  PMID 19797407 · PMC2778335 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 7 setups

  Full-text index only

  ProSeq3 is a program with a graphic user interface that simplifies preparation and basic population genetic analysis of multigenic DNA polymorphism datasets

  software authors sequence polymorphism phylogenetic