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).

• Polymorphix: a sequence polymorphism database.

  PMID 15608242 · PMC540030 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  Polymorphix is an ACNUC-structured database that organizes EMBL/GenBank sequences into within-species homologous sequence families using similarity and bibliographic criteria, with alignments, outgroups and phylogenetic trees provided.

  eukaryotic clustered consensus aligned sequence blast phylogenetic

• Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines.

  PMID 18005451 · PMC2216041 · BMC bioinformatics · 2007 · 8 claims · 5 setups

  Full-text index only

  Parepro, an SVM-based method integrating three attribute sets (RD, MI, IE) derived from evolutionary and residue-property information, predicts whether an nsSNP is deleterious or neutral.

  sequences target svm benchmark homology

• Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

  PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

  Full-text index only

  Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

  organisms cide cideb hmmer tblastn sequence

• GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

  PMID 16845010 · PMC1538901 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  GeneAlign predicts coding exons by using signal detection (GeneSplicer/WMM) combined with CORAL, a heuristic linear-time alignment tool, to align candidate signal-flanked regions against annotated exons of a homologous organism's genes

  homologous human-mouse same gene comparative parameter micro-exon

• 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

• EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

  PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

  sequences homologous proteins coding pairwise single sequence

• GeneSeer: a sage for gene names and genomic resources.

  PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

  Full-text index only

  GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

  sofar clusters rnai gene blast sequence shrna

• The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment.

  PMID 25506420 · PMC4257144 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 42

  The EPD between Cβ atoms of consecutive residues provides unique signatures of amino acid pair types and can discriminate native from decoy protein structures.

  non-homologous same pisces structures finite-difference electrostatic sequence-distance

• Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

  PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

  Full-text index only

  ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

  paralogous human-mouse duplicated comparative ortholog binomial

• A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

  PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

  Full-text index only

  PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

  genomic genome extracted pairwise online genome-wide

• FeatureScan: revealing property-dependent similarity of nucleotide sequences.

  PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

  Full-text index only

  FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

  randomly fully same chimpanzee signal-theoretic featurescan blast

• Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

  PMID 18637199 · PMC2483709 · BMC microbiology · 2008 · 8 claims · 5 setups

  Full-text index only

  A RecA- phenotype increases genetic stability and may help restrict ongoing genome evolution of BCG substrains while maintaining protective efficacy

  bovis bcg genomic cell-free allelic southern sequencing

• Sequence similarity network reveals common ancestry of multidomain proteins.

  PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

  curated complete well-studied sequence alignment domain

• Developments in CORG: a gene-centric comparative genomics resource.

  PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

  Full-text index only

  CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

  upstream gene overlapping c-fos pairwise sequence comparative

• SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

  PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

  Full-text index only

  Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

  genomic cdna known sequence homology transcript

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

  PMID 15804363 · PMC1079826 · BMC genomics · 2005 · 7 claims · 7 setups

  Full-text index only

  Predicted solubility in E. coli (via CV-CV') depends on hydrolase size, phylogenetic origin, homologous family, and superfamily

  lipase bacterial small genera cv-cv correlation grouped

• Bioinformatic mapping of AlkB homology domains in viruses.

  PMID 15627404 · PMC544882 · BMC genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, mainly within a subgroup of the Flexiviridae family.

  ncbi 146-sequence representative hel psi-blast pfam profile

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

  Full-text index only

  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene

• A survey of integral alpha-helical membrane proteins.

  PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.

  pfam-a organisms 34-genome integral transmembrane comparative sequence