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).

Publications 1.3k Datasets 392.5k Experiments 35

System / cell line: same ✕ Assay: structure ✕ Clear

Oligomeric protein structure networks: insights into protein-protein interactions.

PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

non-redundant same known complexes structure hub comparison
Structural evolution of the protein kinase-like superfamily.

PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

bank representative same kinase comparative manual structure-annotated
Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

PMID 18769673 · PMC2518838 · PloS one · 2008 · 8 claims · 6 setups

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The protein sequence-structure map behaves as a noisy digital communication channel whose capacity C exceeds the transmission rate R for native structures, satisfying Shannon's noisy channel theorem

chains pdbselect25 same single-domain statistical channel negative
Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

PMID 16093549 · PMC1184218 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Created the Mammalian Orthologous Intron Database (MOID) containing orthologous introns of human, mouse and rat identified via conserved reading-frame position

introns ribosomal rrna comparative orthologous pairwise
Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes.

PMID 16091150 · PMC1208870 · BMC cancer · 2005 · 7 claims · 5 setups

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Three of the five DNA repair genes (MRE11A, RAD50, XRCC4) do not conform to a contiguous haplotype block structure; instead SNPs in high LD can be non-contiguous, fitting a more flexible LD group paradigm

unrelated same haplotype caucasian snp haplotype group
Using ESTs to improve the accuracy of de novo gene prediction.

PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome

elegans genome chromosome novo gene partial
In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

hmlh1 same cos-7 hela ese splice minigene
Information extraction from full text scientific articles: where are the keywords?

PMID 12775220 · PMC166134 · BMC bioinformatics · 2003 · 8 claims · 5 setups

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The keyword content of the five article sections (A, I, M, R, D) is heterogeneous, i.e., different sections carry different kinds of information.

corpus same articles keyword validation qualitative
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
Iterative pruning PCA improves resolution of highly structured populations.

PMID 19930644 · PMC2790469 · BMC bioinformatics · 2009 · 7 claims · 7 setups

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ipPCA is a novel algorithm that assigns individuals to subpopulations and infers the total number of subpopulations (K) present in genotypic data

simulated hapmap cattle shriver's simulated snp comparative
Genome sequences and great expectations.

PMID 11178275 · PMC150431 · Genome biology · 2001 · 8 claims · 3 setups

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Function is known or can be predicted for an average of 62% of proteins across 31 analyzed genomes.

complete annotated haemophilus automated benchmarking temporal
Predictive genomics of cardioembolic stroke.

PMID 19064790 · PMC2752697 · Stroke · 2009 · 8 claims · 4 setups

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A Bayesian network multivariate model achieves 86% predictive accuracy (AUC) for cardioembolic stroke on fitted values

blood-derived gasros same custom bayesian roc
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
Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.

PMID 35348734 · PMC9756952 · Nucleic acids research · 2022 · 7 claims · 6 setups

Has reproduction · 91

A nascent intermediate central helix forms in the yxjA riboswitch that is mutually exclusive with both the aptamer's P1 helix and the expression platform's intrinsic terminator hairpin.

coli yxja refolded flow bulk cotranscriptional
Genetic analysis of the GLUT10 glucose transporter (SLC2A10) polymorphisms in Caucasian American type 2 diabetes.

PMID 16336637 · PMC1325051 · BMC medical genetics · 2005 · 7 claims · 5 setups

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GLUT10 (SLC2A10) is a facilitative glucose transporter gene mapped within the T2DM-linked chromosome 20q12-13.1 region

caucasian same subjects xenopus snp linkage haplotype
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

PMID 16105176 · PMC1201154 · BMC structural biology · 2005 · 8 claims · 5 setups

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Interaction patterns across obligatory and non-obligatory interfaces are different, with obligatory contacts predominantly non-polar

pdb obligatory same psi-blast solvent residue
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
Conservation, variability and the modeling of active protein kinases.

PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

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A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

active-conformation same chak rio2 sequence-order pairwise structural
Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

PMID 18929582 · PMC2599865 · Mutation research · 2008 · 8 claims · 5 setups

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Overall MSY1 mutation frequencies in sperm (2.68%) and blood (1.88%) are not significantly different

sperm donor hgr1b3 single-molecule fluorescent radioactive
Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

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Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr

Experiments

Oligomeric protein structure networks: insights into protein-protein interactions.

Structural evolution of the protein kinase-like superfamily.

Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes.

Using ESTs to improve the accuracy of de novo gene prediction.

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

Information extraction from full text scientific articles: where are the keywords?

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

Iterative pruning PCA improves resolution of highly structured populations.

Genome sequences and great expectations.

Predictive genomics of cardioembolic stroke.

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

Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.

Genetic analysis of the GLUT10 glucose transporter (SLC2A10) polymorphisms in Caucasian American type 2 diabetes.

Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

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

Conservation, variability and the modeling of active protein kinases.

Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.