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 3k

Assay: gene ✕ Clear

EGASP: Introduction.

PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups

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Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.

genome computational manual rt-pcr
Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

transmembrane simulated age duplicate maximum kernel monte
Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans.

PMID 16848906 · PMC1543620 · Molecular pain · 2006 · 8 claims · 5 setups

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COMT SNP5 (rs740603, intron 1) shows significant association with maximum post-operative pain rating

surgical candidate haplotype allele
CRSD: a comprehensive web server for composite regulatory signature discovery.

PMID 16845073 · PMC1538777 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CRSD is a comprehensive web server integrating six large-scale databases (UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway, GO) plus two newly constructed genome-wide databases (MRS and TRS) for composite regulatory signature discovery

gene 3'-utr promoter user-submitted genome-wide microrna binding
VIRGO: computational prediction of gene functions.

PMID 16845022 · PMC1538839 · Nucleic acids research · 2006 · 8 claims · 6 setups

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VIRGO constructs a functional linkage network (FLN) from gene expression and molecular interaction data, labels genes with GO annotations, and propagates these labels to predict functions of unlabelled genes

cerevisiae sapiens leave-one-out gene protein-protein
Independent component analysis reveals new and biologically significant structures in micro array data.

PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

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ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

acute serum-stimulated head aml microarray clust term
Promoting human promoters.

PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

gene liver cycle genes computational expression time-course
Adaptively inferring human transcriptional subnetworks.

PMID 16760900 · PMC1681499 · Molecular systems biology · 2006 · 8 claims · 7 setups

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A multivariate linear spline (MARS-based) model correlating PWM binding scores with log expression ratios can identify active cis-motif combinations in mammalian promoters without requiring gene clustering.

liver proximal hela predicted microarray computational novo
Insights into the physiology of childbirth using transcriptomics.

PMID 16752954 · PMC1475648 · PLoS medicine · 2006 · 7 claims · 4 setups

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Labor results in a change in the transcriptome in each component of the uterus studied

uterine lower microarray quantitative re-analysis
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

non-identical gene3d cath whole-gene domain transmembrane
Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

gastrointestinal ls174t pl3 msi gene rt-pcr rad51
Systems biology and the host response to viral infection.

PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

lung cd4 rhesus kshv microarray quantitative genomic
Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis.

PMID 18047719 · PMC2099488 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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Deconvoluting gene expression variance into technical (Gaussian, ~6.5% relative SD) and biological components identifies hypervariable (HV) genes that reflect true biological response to infection without requiring replicates

urothelial clustered genome-wide confocal k-means
Narcisse: a mirror view of conserved syntenies.

PMID 17981845 · PMC2238891 · Nucleic acids research · 2008 · 8 claims · 4 setups

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Narcisse is a database/web tool providing an integrated, multi-level comparative analysis of sequence similarities and conserved chromosomal segments (syntenies) across animal, plant, fungal and bacterial completely sequenced genomes.

annotated genome pairwise pairs sequence nucleic-level conserved
OPTIC: orthologous and paralogous transcripts in clades.

PMID 17933761 · PMC2238935 · Nucleic acids research · 2008 · 6 claims · 7 setups

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OPTIC is a database providing gene predictions and orthology assignments for three clades: amniotes (human, dog, mouse, opossum, platypus, chicken), 12 Drosophila species, and 4 Caenorhabditis nematodes.

drosophila translated gene orthologous homology-based all-against-all tree-based
Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

PMID 17888167 · PMC2082044 · BMC genomics · 2007 · 8 claims · 6 setups

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A proposed coupled two-way clustering (CTWC/SPC) method combined with a GO-based functional concept consistency score can identify compact, robust gene subsets that define clinically meaningful DLBCL subtypes

dlbcl identified microarray oligonucleotide coupled
Use of functional genomics to understand influenza-host interactions.

PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

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Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

hela a549 lung texas cdna microarray infection
Genomic and proteomic profiling II: comparative assessment of gene expression profiles in leiomyomas, keloids, and surgically-induced scars.

PMID 17718906 · PMC2039739 · Reproductive biology and endocrinology : RB&E · 2007 · 7 claims · 4 setups

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1124 transcripts (1103 genes; 732 over-expressed, 371 under-expressed) are differentially expressed in leiomyomas compared to keloids/incisional scars

keloid leiomyoma microarray quantitative
Genomic expression during human myelopoiesis.

PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

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An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

myeloid same cd34+ gene microarray unsupervised sam
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype

Experiments

EGASP: Introduction.

Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans.

CRSD: a comprehensive web server for composite regulatory signature discovery.

VIRGO: computational prediction of gene functions.

Independent component analysis reveals new and biologically significant structures in micro array data.

Promoting human promoters.

Adaptively inferring human transcriptional subnetworks.

Insights into the physiology of childbirth using transcriptomics.

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

Systems biology and the host response to viral infection.

Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis.

Narcisse: a mirror view of conserved syntenies.

OPTIC: orthologous and paralogous transcripts in clades.

Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

Use of functional genomics to understand influenza-host interactions.

Genomic and proteomic profiling II: comparative assessment of gene expression profiles in leiomyomas, keloids, and surgically-induced scars.

Genomic expression during human myelopoiesis.

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.