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 37

System / cell line: experimental ✕ Assay: comparison ✕ Clear

Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs.

PMID 16261191 · PMC1246807 · PLoS computational biology · 2005 · 7 claims · 7 setups

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A comprehensive stoichiometric model of the MAP was built comprising 197 metabolites, 219 reactions, and 28 proteins

stoichiometric map tuberculosis flux systematic drug
Using multiple alignments to improve seeded local alignment algorithms.

PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups

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Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone

alignment query leave-one-species-out seeded
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

PMID 35729113 · PMC9213456 · Nature communications · 2022 · 7 claims · 5 setups

Has reproduction · 84

Developed a python-based, scalable model creation and simulation pipeline that converts structured text files into an SBML-standard model and is high-performance/cloud-computing ready.

sparced mcf10a deterministic hybrid comparison
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
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.

PMID 34742227 · PMC8572424 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 7 setups

Has reproduction · 53

Current effective population size for all four farmed fish populations is small (≤50 fish), potentially threatening breeding-programme sustainability

turbot gilthead european common rad linkage computer
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

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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
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

genome sequences automatic manual sequence
Mutation analysis in the long isoform of USH2A in American patients with Usher Syndrome type II.

PMID 19881469 · PMC4511341 · Journal of human genetics · 2009 · 8 claims · 6 setups

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Screening all 72 exons of USH2A (long isoform) identifies significantly more mutations than screening only the short-isoform exons 1-21

genomic ush2 ush2a sscp audiological ophthalmological
Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.

PMID 35726533 · PMC9542029 · Molecular ecology · 2022 · 7 claims · 8 setups

Has reproduction · 93

Italian sparrow testis exhibits extensive transgressive gene expression relative to both parental species

testis ovary house differentially bulk gene protein-protein
Oligomeric protein structure networks: insights into protein-protein interactions.

PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

non-redundant same known complexes structure hub comparison
Columba: an integrated database of proteins, structures, and annotations.

PMID 15801979 · PMC1087474 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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COLUMBA physically integrates data from twelve protein structure-related databases (PDB, KEGG, Swiss-Prot, CATH, SCOP, Gene Ontology, ENZYME, etc.) into a single PostgreSQL data warehouse.

pdb database sequence secondary
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

pre-selected pre-tabulated genes ranked kegg expression text-mining
CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

genome random cd4+ six average mutual chip-seq
Increase in endoplasmic reticulum stress-related proteins and genes in adipose tissue of obese, insulin-resistant individuals.

PMID 18567819 · PMC2518495 · Diabetes · 2008 · 8 claims · 3 setups

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UPR/ER stress-related proteins (calreticulin, PDI A3, glutathione-S-transferase P) are upregulated in adipose tissue of obese versus lean humans

subcutaneous same adipose two-dimensional western real-time
The European Bioinformatics Institute's data resources: towards systems biology.

PMID 15608238 · PMC539980 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Since 2003 the EBI has launched new databases covering protein-protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI)

proteins varies vertebrate newly macromolecular microarray protein-protein
A global database for modeling tumor-immune cell communication.

PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

Has reproduction · 66

TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

pubmed scrna-seq tcga basal manual scrna-seq bulk
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

PMID 24715956 · PMC3962008 · F1000Research · 2013 · 8 claims · 6 setups

Has reproduction · 67

Cyrface is a Cytoscape app/Java library providing a general interface from Cytoscape (Java) to any R function or package.

cytoscape generated prior-knowledge iris software datarail logic
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
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

PMID 18053250 · PMC2246260 · Genome biology · 2007 · 8 claims · 4 setups

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Loss-of-function phenotypes in yeast are predictable from a gene's connections in a functional gene network via guilt-by-association.

saccharomyces guilt-by-association comparison network-guided
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide

Experiments

Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs.

Using multiple alignments to improve seeded local alignment algorithms.

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

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

Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.

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

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

Mutation analysis in the long isoform of USH2A in American patients with Usher Syndrome type II.

Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.

Oligomeric protein structure networks: insights into protein-protein interactions.

Columba: an integrated database of proteins, structures, and annotations.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

Increase in endoplasmic reticulum stress-related proteins and genes in adipose tissue of obese, insulin-resistant individuals.

The European Bioinformatics Institute's data resources: towards systems biology.

A global database for modeling tumor-immune cell communication.

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

Promoting human promoters.

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.