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).

• Evaluating native-like structures of RNA-protein complexes through the deep learning method.

  PMID 36828844 · PMC9958188 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 67

  DRPScore identifies native-like RNA-protein structures with higher success rates than ITScore-PR, DARS-RNP, and 3dRPC across bound and unbound testing sets.

  bound-bound unbound-bound unbound-unbound bacillus structure interface secondary

• Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.

  PMID 24555103 · PMC3892923 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 71

  The distance between consecutive backbone Cα atoms in high-quality structures is normally distributed with mean 3.8 Å and standard deviation 0.04 Å, justifying a reference state in which all consecutive Cα atoms are 3.8 Å apart.

  top100h decoys i-tasser non-homologous statistical rdcc comparative

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 8 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign is the first RNA sequence/structure pairwise alignment algorithm based on incremental ensemble mountain distance, running in O(n^3) time and O(n^2) space for two sequences of length n.

  sequences sequence trna target pairwise global single

• Ab initio identification of human microRNAs based on structure motifs.

  PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

  genome mirna hairpins chromosome secondary linear five-fold

• Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans.

  PMID 19860882 · PMC2775748 · BMC genetics · 2009 · 8 claims · 8 setups

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  A set of 47 SNPs selected via the 4gen pairwise F_ST approach serves as an ASM panel distinguishing four continental groups (African, Eurasian, Asian/Oceanian, Native American)

  ycc individuals hgdp-ceph asm snp structure pairwise

• 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

• TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

  PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

  Full-text index only

  TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

  scop-derived malt nr-70 scop profile-based dali remote

• In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

  PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups

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  Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip

  canine tissues hg-u133a probes microarray sequence ortholog

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• Optimisation of the core subset for the APY approximation of genomic relationships.

  PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups

  Has reproduction · 85

  APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.

  simulated real genotyped gblup population

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

  PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

  user-submitted string pubmed protein-coding gene hierarchical text-mining

• A general definition and nomenclature for alternative splicing events.

  PMID 18688268 · PMC2467475 · PLoS computational biology · 2008 · 6 claims · 4 setups

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  Existing AS nomenclatures (Malko et al.'s 5-letter strings, Nagasaki et al.'s bit matrices, and the ASD/ATD/AEdb system) are redundant, ambiguous, or incapable of representing complex or large splicing variations.

  refseq reference metazoan example computational comparative

• Systematic identification of pseudogenes through whole genome expression evidence profiling.

  PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

  genome ensembl vega celera spliced protein-to-genome pseudogene

• Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

  PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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  MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

  genome tissues novo pairwise rt-pcr

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant

• Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices.

  PMID 18398479 · PMC2276316 · PloS one · 2008 · 8 claims · 6 setups

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  The first singular component of a PSSM acts to disfavor substitutions, penalizing potentially functionally important residues at conserved sites more severely.

  representative pfam pdb right psi-blast hidden singular

• The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

  PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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  3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

  bovine cow coding blast-based ensembl gene

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• 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