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 47

System / cell line: comparison ✕ Assay: bioinformatic ✕ Clear

IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

PMID 11056671 · PMC17813 · Arthritis research · 2000 · 8 claims · 5 setups

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Somatically mutated IgVH genes with amino acid deletions and mixed IgV molecules were found in all three anatomical regions, suggesting a novel pathway for generating (auto)antibody specificities

synovial same cryosections formalin-fixed cdna seminested double
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

genome genomic chromosome randomization
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Proteomics as a tool for biomarker discovery.

PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

serum laser ovarian seldi-tof two-dimensional gene
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

reference unigene ensembl normal tandem polymorphism gene
Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr
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
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
Evidence for a minimal eukaryotic phosphoproteome?

PMID 17712425 · PMC1945084 · PloS one · 2007 · 8 claims · 3 setups

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Divergence in eukaryotic kinases at the primary sequence level is not reflected at the level of substrate phosphorylation.

lysates lysate pepchip peptide labelling statistical
Immunopathogenic interaction of environmental triggers and genetic susceptibility in diabetes: is epigenetics the missing link?

PMID 19033405 · PMC2584121 · Diabetes · 2008 · 8 claims · 3 setups

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Epigenetic modification of histones and DNA provides a plausible common mechanism linking environmental triggers to genetic susceptibility regions in autoimmune type 1 diabetes.

lymphocytes genetic nonobese chip-on-chip bioinformatic congenic
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

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MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical
Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

PMID 15867095 · PMC2213188 · The Journal of experimental medicine · 2005 · 7 claims · 6 setups

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IgVH genes have evolved precise placement of coding-strand Cs so that AID-induced C-to-T mutations are predominantly silent, especially in the CDRs.

igvh germline non-igv immunogenetics flow cdna bioinformatic
Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

Has reproduction · 73

Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

peripheral overlapping geo pbmcs bulk kegg protein-protein
Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

Has reproduction · 81

A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

lung sequencing assembled deer high-throughput metagenomic reference
Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

Has reproduction · 50

Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

sars-cov-2 publicly simulated simulated amplicon-based variant
Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

PMID 12697062 · PMC156599 · BMC genetics · 2003 · 8 claims · 6 setups

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Rabbit MYOC encodes a 490 amino acid, 54,882-Da protein that is 84% identical overall to human myocilin

rabbit gtm66 myoc myocilin cdna sds-page transfection
Genetic variation of SARS coronavirus in Beijing Hospital.

PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups

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113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain

clinical extracted rna-derived cloned nested screening direct
COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

PMID 15756302 · PMC2673054 · European journal of human genetics : EJHG · 2005 · 8 claims · 4 setups

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COMP mutations were identified in 78% of families referred with PSACH

genomic sequence subset pcr bidirectional sequence

Experiments

IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

Proteomics as a tool for biomarker discovery.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

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

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

Evidence for a minimal eukaryotic phosphoproteome?

Immunopathogenic interaction of environmental triggers and genetic susceptibility in diabetes: is epigenetics the missing link?

Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

Genetic variation of SARS coronavirus in Beijing Hospital.

COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.