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 73

System / cell line: domain ✕ Assay: alignment ✕ Clear

Bioinformatic mapping of AlkB homology domains in viruses.

PMID 15627404 · PMC544882 · BMC genomics · 2005 · 8 claims · 8 setups

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AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, mainly within a subgroup of the Flexiviridae family.

ncbi 146-sequence representative hel psi-blast pfam profile
Pseudofam: the pseudogene families database.

PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

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Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

eukaryotic over pseudogenes pseudogene blast family sequence
The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.

PMID 14519199 · PMC328453 · Genome biology · 2003 · 8 claims · 5 setups

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Sequence-profile (PSI-BLAST) searches unify archaeal Alba with eukaryotic RNase P/MRP subunits Rpp20/Pop7 and Rpp25, and with the ciliate macronuclear-development protein Mdp2, into a single Alba superfamily.

archaeal eukaryotic alba sulfolobus psi-blast sequence phylogenetic
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
Phylogenetic analysis of RhoGAP domain-containing proteins.

PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

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RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

rhogap aligned bayesian domain sequence maximum bayesian
A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

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PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

pax6 brain yeast sequence yeast semi-quantitative
The UCSC Proteome Browser.

PMID 15608236 · PMC540054 · Nucleic acids research · 2005 · 8 claims · 5 setups

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The UCSC Proteome Browser is tightly integrated with the UCSC Genome Browser, giving users simultaneous access to genome and proteome data.

swiss-prot sequence domain isoelectric
Computational comparison of two mouse draft genomes and the human golden path.

PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

newly genome chromosome genomic blat blastn repeat
Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

PMID 16022726 · PMC1187884 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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466 Tetraodon GPCRs (Tnig-GPCRs) were identified genome-wide, of which 457 had not been previously reported

tetraodon tnig-gpcr non-rhodopsin-like domain sequence transmembrane
Identifying repeat domains in large genomes.

PMID 16507140 · PMC1431705 · Genome biology · 2006 · 7 claims · 5 setups

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A repeat domain graph, built using a modified A-Bruijn graph framework, decomposes a repeat library into shared repeat domains and reveals the mosaic structure of repeat families.

repbase elegans concatenated repeat comparative dot
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

dog predicted ace3 panel blast sequence homology
Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

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The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

turmoil-1 rrm elegans predicted pairwise maximum genome-wide
Sequence similarity network reveals common ancestry of multidomain proteins.

PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

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Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

curated complete well-studied sequence alignment domain
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
Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

tlr4 mus chimpanzee baboon genomic coding sequence
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

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About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

predicted non-masked genome interpro hmm tblastn inter-species
ECgene: genome annotation for alternative splicing.

PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

brca2 rgs17 organs cdna genomic genome transcript
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
Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.

PMID 17517123 · PMC1899181 · BMC genomics · 2007 · 8 claims · 4 setups

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A new method combining known LRR structures, multiple sequence alignment, and secondary structure prediction identifies and aligns LRRs in TLRs more accurately than PFAM/InterPro/SMART

tlrs lrr-containing tlr2 mammalian comparative structural secondary
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

Bioinformatic mapping of AlkB homology domains in viruses.

Pseudofam: the pseudogene families database.

The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.

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

Phylogenetic analysis of RhoGAP domain-containing proteins.

A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

The UCSC Proteome Browser.

Computational comparison of two mouse draft genomes and the human golden path.

Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

Identifying repeat domains in large genomes.

Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

Sequence similarity network reveals common ancestry of multidomain proteins.

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

Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

ECgene: genome annotation for alternative splicing.

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

Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.

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