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 17

System / cell line: domains ✕ Assay: transmembrane ✕ Clear

A survey of integral alpha-helical membrane proteins.

PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.

pfam-a organisms 34-genome integral transmembrane comparative sequence
Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

PMID 16288662 · PMC1322226 · BMC evolutionary biology · 2005 · 7 claims · 5 setups

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Proteins with extended coiled-coil domains (>250 amino acids) are largely absent from bacterial genomes but present in archaea and eukaryotes.

proteomes predicted long prokaryotic coiled-coil all-against-all sequence
A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

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Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

washed platelets tryptic hek293t lc-ms free longsage
Coverage of whole proteome by structural genomics observed through protein homology modeling database.

PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

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FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

orfs predicted modeled representative homology transmembrane intrinsic
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

chicken comparative amino 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
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.

PMID 17349043 · PMC1829165 · BMC bioinformatics · 2007 · 8 claims · 6 setups

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A combined target-selection approach — pursuing both structurally uncharacterised domain families and additional targets from large structurally characterised superfamilies — is essential for comprehensive structural coverage of the genomes.

sp-trembl hmm-based domain computational
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

PMID 15784611 · PMC1069129 · Nucleic acids research · 2005 · 7 claims · 8 setups

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Position-specific phylogenetic features describing evolutionary conservation at a site (e.g. SIFT score, normalized site entropy, residue frequency change) are the best individual discriminators of disease-causing versus neutral GPCR mutations.

dbsnp gpcr transmembrane sequence six-frame sift logistic
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.

PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups

Has reproduction · 95

transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms

piper assembled longum predicted rna-seq novo transcriptome
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

hamster testis predicted cdna northern comparative
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

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The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

healthy mrp1 population novo population functional
LOCATE: a mammalian protein subcellular localization database.

PMID 17986452 · PMC2238969 · Nucleic acids research · 2008 · 8 claims · 6 setups

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LOCATE is a curated, web-accessible database housing membrane organization and subcellular localization data for mouse and human proteins.

hela proteome indirect automated computational
Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

PMID 19880432 · PMC2780955 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 8 claims · 5 setups

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Identified 23,241 human genes transcribed into protein-coding mRNAs using full-length cDNA and 5'-EST sequence data

tissues genome full-length genes full-length genome orf
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

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An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

anopheles gambiae reanocds05 initio full-length rt-pcr
Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

PMID 17668063 · PMC1925147 · PloS one · 2007 · 8 claims · 7 setups

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Mutations in UBIAD1 are causal for Schnyder crystalline corneal dystrophy

pedigrees pedigree genomic ubiad1 microsatellite fine direct
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

genome full-length ~3x10^7 isoform whole-genome full-length polysome

Experiments

A survey of integral alpha-helical membrane proteins.

Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

Coverage of whole proteome by structural genomics observed through protein homology modeling database.

Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

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

Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.

Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

LOCATE: a mammalian protein subcellular localization database.

Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.