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 60

System / cell line: gene ✕ Assay: additional ✕ Clear

Seasonality of influenza A(H3N2) virus: a Hong Kong perspective (1997-2006).

PMID 18648550 · PMC2481298 · PloS one · 2008 · 7 claims · 4 setups

Full-text index only

Influenza A(H3N2) seasonality is largely explained by global viral migration, with similar viruses appearing in different countries at different times

influenza same hong gene maximum-likelihood protein-coding
Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

Has reproduction · 90

Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

tsitsikamma tethybacterales putative bin genome 16s multi-locus
Additional EFNB1 mutations in craniofrontonasal syndrome.

PMID 18627045 · PMC2774847 · American journal of medical genetics. Part A · 2008 · 8 claims · 4 setups

Full-text index only

Loss-of-function mutations in EFNB1 (Xq13.1) are the cause of CFNS in the majority of patients

lymphoblastoid cfns patients additional pcr multiplex molecular
A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

Full-text index only

A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

kidney same identified additional microarray significance fisher's
Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

Full-text index only

A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

lsl-krasg12d soft combined mfh microarray gene oncogenic
Gene expression study on peripheral blood identifies progranulin mutations.

PMID 18551524 · PMC2773201 · Annals of neurology · 2008 · 7 claims · 3 setups

Full-text index only

PGRN is highly expressed in peripheral blood (97th percentile of all array genes)

peripheral blood-derived microarray direct real-time
CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.

PMID 15796777 · PMC1274267 · BMC bioinformatics · 2005 · 8 claims · 2 setups

Full-text index only

CGMIM is a Perl program that text-mines OMIM entries to identify cancer-gene associations and genetically-related cancer type pairs.

omim automated manual
Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

Full-text index only

Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

biomedical refseq training independent text-mining data-mining candidate
EGASP: Introduction.

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

Full-text index only

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
Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis.

PMID 12396926 · PMC2730316 · Emerging infectious diseases · 2002 · 7 claims · 4 setups

Full-text index only

All 86 B. anthracis isolates tested share an identical 16S rRNA gene sequence, designated 16S type 6

bacillus clinical additional 16s nested comparative
Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

Full-text index only

Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

family additional unrelated mutant direct linkage targeted
Linking disease-associated genes to regulatory networks via promoter organization.

PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups

Full-text index only

Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks

orthologous eukaryotic genomatix pubmed promoter model additional
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

Full-text index only

Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

identified cst csts comparative coding exon
Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

Full-text index only

Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

postmortem genes gene proteins microarray protein-protein hierarchical
Patterns of somatic mutation in human cancer genomes.

PMID 17344846 · PMC2712719 · Nature · 2007 · 8 claims · 5 setups

Full-text index only

Systematic resequencing of a large gene family (protein kinases) across diverse cancers reveals a larger repertoire of cancer genes than previously anticipated

cancers additional computational combined targeted follow-up statistical
Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.

PMID 18269759 · PMC2291036 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

Full-text index only

The mouse Abp gene repertoire is twice as large as previously reported, comprising 30 Abpa and 34 Abpbg genes/pseudogenes

c57bl mus rodent genomic comparative pcr phylogenetic
A2TEA: Identifying trait-specific evolutionary adaptations.

PMID 37224329 · PMC10186066 · F1000Research · 2022 · 8 claims · 7 setups

Has reproduction · 90

A2TEA integrates gene family expansion analysis with differential expression data across species to identify genes that were targets of evolutionary adaptation to a given stress/treatment

user-provided multi-species genes sequences rna-seq orthologous phylogenetic
NETISCE: a network-based tool for cell fate reprogramming.

PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

Has reproduction · 85

NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

ascidian pluripotent drosophila signal fvs-finding sfa
The post-genomic era for a select few.

PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

Full-text index only

The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

takifugu physcomitrella coli vibrio comparative genetic dna-microarray
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

Full-text index only

GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence

Experiments

Seasonality of influenza A(H3N2) virus: a Hong Kong perspective (1997-2006).

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

Additional EFNB1 mutations in craniofrontonasal syndrome.

A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

Gene expression study on peripheral blood identifies progranulin mutations.

CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.

Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

EGASP: Introduction.

Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis.

Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

Linking disease-associated genes to regulatory networks via promoter organization.

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

Patterns of somatic mutation in human cancer genomes.

Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.

A2TEA: Identifying trait-specific evolutionary adaptations.

NETISCE: a network-based tool for cell fate reprogramming.

The post-genomic era for a select few.

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.