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 62

System / cell line: chain ✕ Clear

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.

PMID 16790052 · PMC1534064 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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The Sequential Minimal Optimization (SMO) SVM algorithm was the best-performing classifier among 26 WEKA classifiers for predicting catalytic residues

benchmarking same pirsf pdb supervised wrapper sequence
Dyneins across eukaryotes: a comparative genomic analysis.

PMID 17897317 · PMC2239267 · Traffic (Copenhagen, Denmark) · 2007 · 8 claims · 6 setups

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Phylogenetic inference identified nine DHC families (two cytoplasmic, seven axonemal) and six IC families (one cytoplasmic)

predicted dhc non-redundant arabidopsis hmm-based bayesian tblastn
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
MODBASE, a database of annotated comparative protein structure models and associated resources.

PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

sequences chains template chain comparative pairwise ligand
Evaluation of the genetic polymorphism of Plasmodium falciparum P126 protein (SERA or SERP) and its influence on naturally acquired specific antibody responses in malaria-infected individuals living in the Brazilian Amazon.

PMID 18667071 · PMC2515332 · Malaria journal · 2008 · 8 claims · 4 setups

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Only two OR fragment types were identified in P. falciparum isolates from the Brazilian Amazon: OR-I (175 bp) and OR-II (199 bp)

falciparum pcr-amplified p126 sera nested agarose sequencing
A nonsense mutation in CRYGC associated with autosomal dominant congenital nuclear cataract in a Chinese family.

PMID 18618005 · PMC2447816 · Molecular vision · 2008 · 6 claims · 4 setups

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A heterozygous c.327C>A transversion in exon 3 of CRYGC causes a nonsense mutation (C109X) that cosegregates with autosomal dominant congenital nuclear cataract in a Chinese family.

genomic type family γc-crystallin pcr comparative clinical
Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

PMID 18616294 · PMC2646719 · Biochemistry · 2008 · 8 claims · 6 setups

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Both G[8,5-Me]T and T[5-Me,8]G intrastrand cross-links are strongly mutagenic in COS-7 and 293T mammalian cells

cos-7 293t synthetic pms2 shuttle primer steady-state
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

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38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

hg18 zebrafish bystander human-mouse comparative synteny orthologous
Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

PMID 19793394 · PMC2765450 · BMC genetics · 2009 · 8 claims · 4 setups

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The three-locus TaqI B-TaqI D-TaqI A haplotype at DRD2 constitutes a powerful genetic marker reflecting the most ancient dispersal of anatomically modern humans

genomic genotype rflp haplotype pcr-rflp hardy-weinberg pairwise
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

PMID 19758473 · PMC2745591 · BMC bioinformatics · 2009 · 8 claims · 8 setups

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None of 39 tested structural properties can be used as a sole classification criterion to separate neutral SNPs from disease mutations.

ensembl swissprot same structural foldx side
Novel approaches for identifying target antigens of autoreactive human B and T cells.

PMID 19763575 · PMC2845891 · Seminars in immunopathology · 2009 · 8 claims · 8 setups

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CD8+ T cells infiltrating MS brain and IM muscle tissue show clonal expansions consistent with antigen-driven selection

muscle brain morphologically autopsy cdr3-spectratyping single-cell immunohistochemistry
mtDNA G10398A variant in African-American women with breast cancer provides resistance to apoptosis and promotes metastasis in mice.

PMID 19763141 · PMC2909846 · Journal of human genetics · 2009 · 8 claims · 8 setups

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The G10398A cybrid shows slower proliferation and delayed cell cycle progression (G1 accumulation, decreased G2/M) compared to wild-type G10398 cybrid

blood mitochondria g10398a cybrid pcr cybrid spectrophotometric
The flexible pocketome engine for structural chemogenomics.

PMID 19727619 · PMC2975493 · Methods in molecular biology (Clifton, N.J.) · 2009 · 8 claims · 8 setups

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A comprehensive structural Pocketome combined with ensemble docking enables de novo, structure-based prediction of ligand binding poses and activities for new proteins and new chemical scaffolds.

pdb bacteriorhodopsin enr asn automated virtual energy-based
B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

ebv-transformed cloned rt-pcr southern sequence
DNA sequencing: bench to bedside and beyond.

PMID 17855400 · PMC2094077 · Nucleic acids research · 2007 · 8 claims · 7 setups

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DNA sequencing methods derived from Sanger's 1977 dideoxy method have dominated sequencing for 30 years despite being only incrementally refined.

bacteriophage double-stranded single-stranded cloned plus maxam-gilbert dideoxy
The UCSC Genome Browser Database: update 2009.

PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

chimp vertebrate mrnas genome genome-wide multiz blat
Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups

Has reproduction · 68

Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla

fecal horse dominant plasma shotgun taxonomic functional
Genetics of osteoarticular disorders, Florence, Italy, 22-23 February 2002.

PMID 12223106 · PMC128940 · Arthritis research · 2002 · 8 claims · 8 setups

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OP and OA are common, polygenic, multifactorial quantitative disorders influenced by both low-penetrance genetic variants and environmental factors

patients twin families dutch association magnetic genome-wide
Columba: an integrated database of proteins, structures, and annotations.

PMID 15801979 · PMC1087474 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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COLUMBA physically integrates data from twelve protein structure-related databases (PDB, KEGG, Swiss-Prot, CATH, SCOP, Gene Ontology, ENZYME, etc.) into a single PostgreSQL data warehouse.

pdb database sequence secondary
Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

monocyte-derived mdm mdms western p24 seldi-tof sds-page

Experiments

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.

Dyneins across eukaryotes: a comparative genomic analysis.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

MODBASE, a database of annotated comparative protein structure models and associated resources.

Evaluation of the genetic polymorphism of Plasmodium falciparum P126 protein (SERA or SERP) and its influence on naturally acquired specific antibody responses in malaria-infected individuals living in the Brazilian Amazon.

A nonsense mutation in CRYGC associated with autosomal dominant congenital nuclear cataract in a Chinese family.

Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

Novel approaches for identifying target antigens of autoreactive human B and T cells.

mtDNA G10398A variant in African-American women with breast cancer provides resistance to apoptosis and promotes metastasis in mice.

The flexible pocketome engine for structural chemogenomics.

B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

DNA sequencing: bench to bedside and beyond.

The UCSC Genome Browser Database: update 2009.

Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

Genetics of osteoarticular disorders, Florence, Italy, 22-23 February 2002.

Columba: an integrated database of proteins, structures, and annotations.

Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.