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 23

System / cell line: acid ✕ Assay: motif ✕ Clear

Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

h3n2 meme sequence entropy
What makes species unique? The contribution of proteins with obscure features.

PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

eukaryotic animal cerevisiae homo hmmpfam blast tblastn
Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr
A surrogate-based approach for post-genomic partner identification.

PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

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Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

biotinylated tnf-β analysis secondary phage sequence secondary
Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia.

PMID 15314077 · PMC2211936 · The Journal of experimental medicine · 2004 · 7 claims · 5 setups

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Five distinct sets of B-CLL patients express strikingly similar (stereotyped) BCRs sharing common H and L chain V region gene segments and similar CDR3 length, composition, and junctional residues.

b-cll sequence cd5+ igv blast phylogenetic
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

PMID 8903171 · PMC2626880 · Emerging infectious diseases · 1995 · 7 claims · 4 setups

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Romanian and Brazilian HIV-1 subtype F envelope C2-V3 sequences cluster into two related but distinct phylogenetic groups.

hiv-1 same brazilian phylogenetic bootstrap pruning
Natural history of S-adenosylmethionine-binding proteins.

PMID 16225687 · PMC1282579 · BMC structural biology · 2005 · 8 claims · 6 setups

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The last universal common ancestor (LUCA) of cellular life had between 10 and 20 SAM-binding proteins from at least 5 fold classes

arabidopsis nicotianamine rossmann-fold cyclopropane psi-blast pdbblast comparative
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
MEROPS: the peptidase database.

PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

archaean holotype c-x-c proteins comparative domain substrate
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence
Automatic discovery of cross-family sequence features associated with protein function.

PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

non-redundant same evolved eukaryotic self-supervised experiment self-organizing
Functional analysis of novel SNPs and mutations in human and mouse genomes.

PMID 19091009 · PMC2638150 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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FANS streamlines functional analysis of novel SNPs and mutations into a simplified, few-click, four-step procedure.

apoe 11-nucleotide sequence genomic manual automated exonic
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis
PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

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PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

natural aligned ns3 denv sequence pcp-consensus physicochemical
Innate immune modulation by RNA viruses: emerging insights from functional genomics.

PMID 18654572 · PMC7097543 · Nature reviews. Immunology · 2008 · 8 claims · 7 setups

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Influenza virus signals primarily through RIG-I to induce ISG expression, while West Nile virus signals through both RIG-I and MDA5 cooperatively.

embryonic liver brain serial gene-expression computational
IMGT, the international ImMunoGeneTics information system.

PMID 15608269 · PMC540019 · Nucleic acids research · 2005 · 8 claims · 6 setups

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IMGT is a high-quality integrated knowledge resource for immunoglobulins (IG), T cell receptors (TR), MHC, and related proteins of the immune system (RPI) across vertebrate species

igh mhc pairs automated junction structure
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

genomic red computational abo sequencing blood

Experiments

Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

What makes species unique? The contribution of proteins with obscure features.

Genetic diversity among five T4-like bacteriophages.

Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

A surrogate-based approach for post-genomic partner identification.

Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

Natural history of S-adenosylmethionine-binding proteins.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

MEROPS: the peptidase database.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

Automatic discovery of cross-family sequence features associated with protein function.

Functional analysis of novel SNPs and mutations in human and mouse genomes.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

Innate immune modulation by RNA viruses: emerging insights from functional genomics.

IMGT, the international ImMunoGeneTics information system.

Web-based resources for comparative genomics.

ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.