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 28

System / cell line: species ✕ Assay: novel ✕ Clear

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

PMID 18203199 · PMC2578871 · American journal of medical genetics. Part A · 2008 · 6 claims · 8 setups

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Two novel homozygous missense mutations in BBS5 (p.Gly72Ser and p.Thr183Ala) were identified in non-Caucasian BBS patients (Somali and Sri Lankan)

genomic somali sri ethnically dhplc snp sanger
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
Comparative genomics.

PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed
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
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

Has reproduction · 63

>700 tissue-specific transcriptomes generated from w1118 and 141 DGRP Drosophila lines, forming a circadian gene expression atlas

w1118 dgrp drosophila dgrp-796 bulk high uas-rnai
The nuclear pore complex.

PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

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NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a
Molecular characterization of retinitis pigmentosa in Saudi Arabia.

PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups

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The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.

blood-derived families pcr-amplified ethnically genome-wide linkage bidirectional
Human stool contains a previously unrecognized diversity of novel astroviruses.

PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups

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Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1

stool consensus-pcr-positive negative one consensus specific sanger
Genome informatics: taming the avalanche of genomic data.

PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

genes arabidopsis genome vertebrate comparative conservation whole-genome
Population genomics: diversity and virulence in the Neisseria.

PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups

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Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria

neisseria meningitidis meningococcal multi-locus microarray genome
SARS--beginning to understand a new virus.

PMID 15035025 · PMC7097337 · Nature reviews. Microbiology · 2003 · 8 claims · 8 setups

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A previously unknown coronavirus (SARS-CoV) was isolated from FRhK-4 and Vero E6 cells inoculated with clinical specimens from SARS patients and identified as the causative agent of SARS

frhk-4 macaques sars-cov coronavirus virus infection whole-genome
The EH1 motif in metazoan transcription factors.

PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

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There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

homeobox-containing forkhead-containing complete combined meme hmm logistic
AgBase: a functional genomics resource for agriculture.

PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups

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AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.

pasteurella chicken maize gene proteogenomic mudpit differential
Ab initio identification of human microRNAs based on structure motifs.

PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

genome mirna hairpins chromosome secondary linear five-fold
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

PMID 19686598 · PMC2736583 · BMC medical genetics · 2009 · 8 claims · 7 setups

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DGGE screening of the non-duplicated PKD1 region detects likely pathogenic mutations in Czech ADPKD patients

genomic pcr polycystin-1 czech denaturing sanger family
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

Has reproduction · 86

CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

tissues predicted tss-enhancer cattle cage extraction coexpression
The DNA sequence and analysis of human chromosome 13.

PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

chromosome rpci-11 genomic comparative fluorescence

Experiments

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Comparative genomics.

NEIBank: genomics and bioinformatics resources for vision research.

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

The nuclear pore complex.

Molecular characterization of retinitis pigmentosa in Saudi Arabia.

Human stool contains a previously unrecognized diversity of novel astroviruses.

Genome informatics: taming the avalanche of genomic data.

Population genomics: diversity and virulence in the Neisseria.

SARS--beginning to understand a new virus.

The EH1 motif in metazoan transcription factors.

AgBase: a functional genomics resource for agriculture.

Ab initio identification of human microRNAs based on structure motifs.

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

The DNA sequence and analysis of human chromosome 13.