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).

• NCBI Reference Sequences: current status, policy and new initiatives.

  PMID 18927115 · PMC2686572 · Nucleic acids research · 2009 · 7 claims · 5 setups

  Full-text index only

  RefSeq is a curated, non-redundant, explicitly linked database of nucleotide and protein sequences spanning genomes, transcripts and proteins across prokaryotes, eukaryotes and viruses

  microbial bacterial prokaryotic refseq spliced structural functional

• Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

  PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

  genome affymetrix antisense mirna computational microarray sage

• Recent segmental and gene duplications in the mouse genome.

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

  Full-text index only

  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

• 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

• HaploSNPer: a web-based allele and SNP detection tool.

  PMID 18307806 · PMC2288614 · BMC genetics · 2008 · 6 claims · 2 setups

  Full-text index only

  HaploSNPer is a web-based tool integrating BLASTN, CAP3/PHRAP, and QualitySNP into a single pipeline for allele and SNP detection from diploid and polyploid species

  sncg wheat est

• A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.

  PMID 34740326 · PMC8571832 · BMC genomics · 2021 · 8 claims · 7 setups

  Has reproduction · 95

  P. betacei P8084 has the largest sequenced genome in the Phytophthora genus (270 Mb)

  betacei predicted genome k-mer busco

• Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

  PMID 12702206 · PMC154576 · Genome biology · 2003 · 8 claims · 6 setups

  Full-text index only

  Segmental duplications comprise 3.53% (107.4/3,043.1 Mb) of the June 2002 human genome assembly

  genome refseq-annotated chromosome chromosome-wide e-pcr ambsnp

• Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

  PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

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  Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

  five cichlid pairwise lake low-coverage blastx multi-species

• Characterization of 954 bovine full-CDS cDNA sequences.

  PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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  954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

  bovine translated bflic sequence est primer-walking blastp

• Ensembl 2006.

  PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

  cow ensembl snps genome gene whole-genome pairwise

• CONSULT: accurate contamination removal using locality-sensitive hashing.

  PMID 34377979 · PMC8340999 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 90

  CONSULT uses locality-sensitive hashing to test whether query k-mers fall within a user-defined Hamming distance of a reference k-mer database, allowing inexact matching against tens of thousands of microbial species.

  tree gtdb kraken-ii genome k-mer genome-skim organelle

• Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

  PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups

  Has reproduction · 100

  NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.

  garlic pepper pear grapevine rna-seq mrna-seq transcriptome

• MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

  PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups

  Has reproduction · 50

  MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.

  bovine simulated cami trimming decontamination assembly

• Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

  PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

  Full-text index only

  Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

  orthologous random cattle aligned three-way pairwise bac

• A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

  PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups

  Full-text index only

  The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs

  carp randomly zebrafish reciprocal sequence microarray

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Ensembl 2008.

  PMID 18000006 · PMC2238821 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  The Ensembl regulatory build integrates multiple genome-wide functional genomics datasets to automatically annotate regulatory regions and assign putative functions across the genome.

  embryonic amniota multi-species individuals automated chip-chip comparative

• Ensembl 2007.

  PMID 17148474 · PMC1761443 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  Ensembl added 18 new chordate genomes this year, increasing total genomes available from 15 to 33, the largest yearly increase to date.

  low-coverage cow chicken genome genome standard customized