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 117

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

Characterization of 954 bovine full-CDS cDNA sequences.

PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

bovine translated bflic sequence est primer-walking blastp
HaploSNPer: a web-based allele and SNP detection tool.

PMID 18307806 · PMC2288614 · BMC genetics · 2008 · 6 claims · 2 setups

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HaploSNPer is a web-based tool integrating BLASTN, CAP3/PHRAP, and QualitySNP into a single pipeline for allele and SNP detection from diploid and polyploid species

sncg wheat est
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
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
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

lncap lncap-derived r1881-treated massively blast blat
GenBank.

PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

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GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

sapiens organisms genbank large-scale genome expressed blast
Bases and spaces: resources on the web for accessing the draft human genome.

PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

bac whole-genome draft submitted bac radiation initio
Identification and characterization of insect-specific proteins by genome data analysis.

PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

drosophila insect-core locusta insect-specific comparative est functional
Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

genomes longin plant phytolongin iterative phylogenetic genomic
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

est clustered sequences sequence est sequence orf
NEIBank: genomics and bioinformatics resources for vision research.

PMID 18648525 · PMC2480482 · Molecular vision · 2008 · 8 claims · 7 setups

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NEIBank is an integrated genomics and bioinformatics resource for vision research, combining EST/cDNA clone data, SAGE expression data, and eye disease gene databases.

dissected eye retina cdna est serial sequence
Compressing DNA sequence databases with coil.

PMID 18489794 · PMC2426707 · BMC bioinformatics · 2008 · 8 claims · 1 setups

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coil achieves higher compression ratio than state-of-the-art general-purpose compression tools on a large GenBank EST database file

large sequence
Insights into vertebrate evolution from the chicken genome sequence.

PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups

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Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals

red chicken whole-genome comparative synteny
More biology from the sequence.

PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

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The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

schizosaccharomyces chromosome genome cervical whole-genome sequence genome
Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

redundant mammalian genomic vertebrates blast pattern-hit tblastn
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

refseq tp53 tumor 154-gene est paired array
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

PMID 16845044 · PMC1538898 · Nucleic acids research · 2006 · 8 claims · 2 setups

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The ASPIC algorithm, using an optimization procedure that minimizes splice site predictions and transcript isoforms from multiple EST-genome alignments, outperforms other similar AS-prediction tools in sensitivity and selectivity

hnrpr specified comparative algorithm
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

PMID 16469098 · PMC1409804 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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AUGUSTUS+ extends the AUGUSTUS GHMM by combining intrinsic sequence information with extrinsic hints via an extended emission alphabet, so the GHMM jointly models the DNA sequence, gene structure, and hint collection.

chromosome genomic training ghmm-based sequence parameter
Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.

PMID 12546714 · PMC149328 · BMC genetics · 2003 · 8 claims · 5 setups

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A human oocyte-specific DNMT1 isoform (DNMT1o), driven by a novel upstream exon 1o, is expressed in mature oocytes and early embryos but not in somatic tissues

oocytes genomic fbhm population rt-pcr est direct
The gene guessing game.

PMID 11025532 · PMC2448377 · Yeast (Chichester, England) · 2000 · 8 claims · 6 setups

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Published methods for estimating human gene number diverge widely, from ~30,000 to over 140,000 genes.

genomic ests tetraodon genome cpg est comparative

Experiments

Characterization of 954 bovine full-CDS cDNA sequences.

HaploSNPer: a web-based allele and SNP detection tool.

Genome-wide survey of allele-specific splicing in humans.

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

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

GenBank.

Bases and spaces: resources on the web for accessing the draft human genome.

Identification and characterization of insect-specific proteins by genome data analysis.

Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

NEIBank: genomics and bioinformatics resources for vision research.

Compressing DNA sequence databases with coil.

Insights into vertebrate evolution from the chicken genome sequence.

More biology from the sequence.

Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.

The gene guessing game.