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 269

System / cell line: target ✕ Clear

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

Full-text index only

MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Genomics: applications in mechanism elucidation.

PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

Full-text index only

Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

extract panel saccharomyces inbred affinity cytotoxicity genome-wide
Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

PMID 19057677 · PMC2585813 · PLoS genetics · 2008 · 7 claims · 8 setups

Full-text index only

Genome-wide siRNA screening identified 92 novel genes that support melanin production in human melanocytes with a low false discovery rate.

mnt-1 melanocyte melanocytes genome-wide secondary quantitative
Genetical genomics: spotlight on QTL hotspots.

PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

Full-text index only

Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

adipose saccharomyces genome-wide permutation gene
SNP-specific extraction of haplotype-resolved targeted genomic regions.

PMID 18611953 · PMC2528194 · Nucleic acids research · 2008 · 6 claims · 4 setups

Full-text index only

SNP-specific extraction isolates haploid genomic DNA flanking targeted SNPs by hybridizing an allele-specific oligo, enzymatically extending it with biotinylated nucleotides, and capturing the tagged allele with streptavidin-coated magnetic particles.

genomic diploid quantitative sanger low
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.

PMID 18487273 · PMC2447794 · Nucleic acids research · 2008 · 8 claims · 7 setups

Full-text index only

PolySearch supports more than 50 different classes of queries against nearly a dozen types of text, abstract, or bioinformatic databases

manually biomedical text feature real-life
Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

Full-text index only

Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

tumor-derived tumor lash gene cytotoxicity sirna ribozyme
A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

Full-text index only

FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

chimpanzee hepg2 promoters liver quantitative western sirna
Evolutionary trace annotation of protein function in the structural proteome.

PMID 20036248 · PMC2831211 · Journal of molecular biology · 2010 · 8 claims · 7 setups

Full-text index only

ET-ranked residue clusters can be used to build 3D templates that predict GO function in enzymes and non-enzymes alike, without prior knowledge of functional mechanism.

structural pdb pairs annotated evolutionary template support
SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

Full-text index only

SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

embryonic hesc small sequence adapter
Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

PMID 20008508 · PMC2836564 · Nucleic acids research · 2010 · 8 claims · 6 setups

Full-text index only

Most TEs insert within specific 'hotspots' along the targeted TE rather than uniformly.

genome sequences unique nested chi-square position-specific
Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

PMID 19997482 · PMC2776985 · PLoS computational biology · 2009 · 7 claims · 4 setups

Full-text index only

An ILP formulation of the Boolean pathway optimization problem fits phosphoproteomic data faster and more efficiently than the previously used genetic algorithm (GA) approach.

hepg2 computational same bead-based integer comparative
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

Full-text index only

A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

genome affymetrix antisense mirna computational microarray sage
Structure of protein interaction networks and their implications on drug design.

PMID 19876376 · PMC2760708 · PLoS computational biology · 2009 · 8 claims · 6 setups

Full-text index only

Budding yeast and human PINs are scale-rich and configured as highly optimized tolerance (HOT) networks similar to Internet router-level topology, rather than scale-free networks formed by preferential attachment.

budding pin yeast protein-protein graph-theoretic gene
The role of medical structural genomics in discovering new drugs for infectious diseases.

PMID 19855826 · PMC2756625 · PLoS computational biology · 2009 · 8 claims · 6 setups

Full-text index only

Structure-based drug design using X-ray/NMR protein structures has contributed to the development of numerous approved and improved therapeutics.

bacteria plasmodium candidate burkholderia high-throughput animal compound-target
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

Full-text index only

A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

macrophage hela vaccinia bacillus gene protein-protein comparative
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

Full-text index only

Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

gria2 drosophila nova1 cd45 splicing sirna hits-clip
A survey of integral alpha-helical membrane proteins.

PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

Full-text index only

An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.

pfam-a organisms 34-genome integral transmembrane comparative sequence
Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

Full-text index only

159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

pooled sequenced analysis predicted small bioinformatic qrt-pcr
Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.

PMID 19682357 · PMC2782262 · BMC microbiology · 2009 · 8 claims · 5 setups

Full-text index only

The RCA assay correctly identified all ERG11 mutations in eight 'reference' azole-resistant C. albicans isolates with known mutations.

clinical pcr template padlock sequencing antifungal

Experiments

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Genomics: applications in mechanism elucidation.

Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

Genetical genomics: spotlight on QTL hotspots.

SNP-specific extraction of haplotype-resolved targeted genomic regions.

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.

Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

Evolutionary trace annotation of protein function in the structural proteome.

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

Structure of protein interaction networks and their implications on drug design.

The role of medical structural genomics in discovering new drugs for infectious diseases.

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

A survey of integral alpha-helical membrane proteins.

Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.