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).

• The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.

  PMID 18796526 · PMC2566872 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  Some common scoring schemes tend to overextend alignments, generating spurious alignment flanks up to hundreds of bp/amino acids in length

  pseudo-random mitochondrial numts human-fugu monte blast smith-waterman

• Heterogeneous genomic molecular clocks in primates.

  PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

  Full-text index only

  Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

  baboon chimpanzee same human-chimpanzee relative phylogenetic four-species

• The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

  PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

  Full-text index only

  Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

  genome sds chimpanzee colinear comparative interspecific genomic

• SARS-CoV genome polymorphism: a bioinformatics study.

  PMID 16144519 · PMC5172477 · Genomics, proteomics & bioinformatics · 2005 · 8 claims · 6 setups

  Full-text index only

  SARS-CoV isolates can be classified into groups/subgroups based on the number and distribution of SNVs and INDELs relative to a 'profile' sequence, and this classification aligns with phylogenetic tree relationships and epidemiological spread.

  sars-cov annotated spike whole-genome positional codon

• A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

  PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

  Full-text index only

  PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

  pax6 brain yeast sequence yeast semi-quantitative

• Compression of structured high-throughput sequencing data.

  PMID 24260313 · PMC3832420 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 43

  Leveraging an explicit data schema (separate field encoding, field modeling, template compression, domain modeling) enables stronger compression of HTS alignment data than general-purpose compression of serialized bytes.

  benchmark ten rna-seq exome genome

• Evolutionary distance estimation and fidelity of pair wise sequence alignment.

  PMID 15840174 · PMC1087827 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  Evolutionary distance estimation is relatively unaffected by alignment error as long as 50% or more of homologous sites remain identical between sequences

  simulated simulated sequence indel

• Genome assembly comparison identifies structural variants in the human genome.

  PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

  Full-text index only

  Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

  genome ceph unrelated individuals whole-genome pcr quantitative

• 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

• Heterotachy in mammalian promoter evolution.

  PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

  Full-text index only

  The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

  promoter ancient chimpanzee comparative ancient micro-indel

• Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

  PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

  Full-text index only

  Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

  genome full-length ~3x10^7 isoform whole-genome full-length polysome

• Integrative functional genomics.

  PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

  yeast tissue-cultured mammalian genomic comparative targeted chip-chip

• 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

• How accurately is ncRNA aligned within whole-genome multiple alignments?

  PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups

  Full-text index only

  MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.

  genome vertebrate nonhuman genomic sequence whole-genome covariance

• Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

  PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

  Full-text index only

  Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

  5'-flanking upstream transiently genomic comparative tfbs promoter-reporter

• Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.

  PMID 18757892 · PMC2553571 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  3'-most (L type) poly(A) sites are more conserved than upstream F/M type sites, while intronic (C/H type) sites are the least conserved

  consensus poly comparative transposable

• Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

  PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

  genome insect yy1-related zinc blast sequence synonymous

• Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

  PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

  Full-text index only

  LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

  surgically tryptic set lysates lc-ms mascot immunohistochemistry

• 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

• Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

  PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

  Has reproduction · 95

  Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

  solar saltern combined individual metagenomic taxonomic functional