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 8

System / cell line: training ✕ Assay: screening ✕ Clear

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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The IAB algorithm (integration of ANN and BLAST) identifies genome-wide specific oligos much faster than pure BLAST search while maintaining comparable success rate and cross homology

tigr xanthomonas xcc ann wu-blast whole-genome
Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.

PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups

Has reproduction · 63

Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA

clinical nicu genomic maldi-tof pbp2a cefoxitin
Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.

PMID 35197930 · PMC8859149 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups

Has reproduction · 85

Robust Rank Aggregation (RRA) can integrate DEG lists from multiple independent RIF microarray datasets to identify robust DEGs.

endometrium integrated robust ppi microarray robust gene
Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups

Has reproduction · 48

A hybrid signature combining the Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).

metabric scan-b gene rna-seq feature
Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

muscle-specific bovine refseq cardiac novo est blastn
A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

Full-text index only

A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

duke nci-60 mayo spanish gene cdna igvh
Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

Has reproduction · 87

TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

testseta bprna-new ts-inter individual jaccard pca ensemble
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.

PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 7 setups

Has reproduction · 97

TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.

aortic brown genes training wgcna biological gsva

Experiments

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.

Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.

Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.