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 145

System / cell line: full ✕ Assay: sequence ✕ Clear

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

full-length alternative refseq genome pairwise mitochondrial signal
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
A conversation with John Sulston.

PMID 14580111 · PMC2588810 · The Yale journal of biology and medicine · 2002 · 8 claims · 5 setups

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C. elegans, with about 1,000 cells, is an ideal model for studying how cells divide, communicate, differentiate, and undergo programmed death, bridging single-celled organisms and complex animals

elegans genomic survey lineage ablation physical
Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.

PMID 19034644 · PMC2728159 · Breast cancer research and treatment · 2009 · 7 claims · 5 setups

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Family history of breast cancer is not associated with all-cause mortality after breast cancer diagnosis in women without a known germline BRCA1/BRCA2 mutation.

women same breast structured cox germline
Comparing whole genomes using DNA microarrays.

PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.

genome saccharomyces mitochondrial sars array comparative resequencing
Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

PMID 15757514 · PMC1084347 · BMC microbiology · 2005 · 8 claims · 7 setups

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PSI-BLAST identified several novel homologies between LEE-encoded and Ysc-Yop-associated proteins

lee-encoded escc sepq escd psi-blast blastp domain
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
Hepatitis B virus genotypes/subgenotypes in voluntary blood donors in Makassar, South Sulawesi, Indonesia.

PMID 19691824 · PMC2732614 · Virology journal · 2009 · 7 claims · 5 setups

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HBV/B and HBV/C are the dominant genotypes among HBsAg-positive blood donors in Makassar

serum hbv pre-s genotype-specific nested complete
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

cynomolgus 3-year-old macaque est full-insert oligonucleotide
Novel dengue virus type 1 from travelers to Yap State, Micronesia.

PMID 16494770 · PMC3373118 · Emerging infectious diseases · 2006 · 8 claims · 5 setups

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DENV-1 responsible for the 2004 Yap State dengue outbreak was isolated from serum of 4 Japanese travelers returning from Yap

mosquito viral denv-1 full-length virus complete sequence
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
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
A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups

Has reproduction · 76

58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date

asfv b602l porcine sardinian whole-genome sanger haemoadsorption
Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

cdna image hbs1l ahi1 rt-pcr est northern
A potentially deleterious new CYP2C9 polymorphism identified in an African American patient with major hemorrhage on warfarin therapy.

PMID 19083245 · PMC2662477 · Blood cells, molecules & diseases · 2009 · 7 claims · 4 setups

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A new CYP2C9 coding polymorphism, G1078A (D360N) in exon 7, was identified in an African American patient who experienced major gastrointestinal hemorrhage on warfarin therapy

african index cyp2c9 study pyrosequencing pcr custom
Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

PMID 8601611 · PMC2120780 · The Journal of cell biology · 1996 · 8 claims · 7 setups

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Full-length cDNAs encoding occludin were cloned and sequenced from rat-kangaroo (potoroo), human, mouse, and dog

ptk2 t84 escherichia computational expression immunofluorescence immunoblotting
Empirical codon substitution matrix.

PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

orthologous million codon same pairwise empirical comparative
Mitochondrial diversity within modern human populations.

PMID 17439969 · PMC1888801 · Nucleic acids research · 2007 · 8 claims · 5 setups

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Modern humans show extremely low divergence from the mitochondrial consensus sequence, differing on average by only 21.6 nucleotide sites

full-length mitochondrial mtdna additional sequence site-by-site regional
Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

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NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

mandenka worldwide hapmap nat2 full snp analysis
Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

PMID 15115540 · PMC420239 · BMC genomics · 2004 · 6 claims · 3 setups

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Bioinformatic sequence comparison of 60,770 RIKEN FANTOM2 mouse cDNA clones identified 2,578 sequences with 70-85% identity to known human disease genes/proteins

riken medline sequence manual semi-automated

Experiments

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

A conversation with John Sulston.

Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.

Comparing whole genomes using DNA microarrays.

Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

Hepatitis B virus genotypes/subgenotypes in voluntary blood donors in Makassar, South Sulawesi, Indonesia.

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

Novel dengue virus type 1 from travelers to Yap State, Micronesia.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

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

A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

A potentially deleterious new CYP2C9 polymorphism identified in an African American patient with major hemorrhage on warfarin therapy.

Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

Empirical codon substitution matrix.

Mitochondrial diversity within modern human populations.

Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.