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 27

System / cell line: in-silico ✕ Assay: small ✕ Clear

Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups

Has reproduction · 80

A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence

peripheral genes overlapping neutrophil-related microarray weighted kegg
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

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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
Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

Has reproduction · 64

L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

elegans small small sequencing lifespan
Prediction of specificity-determining residues for small-molecule kinase inhibitors.

PMID 19032760 · PMC2655090 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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S-Filter is a novel method combining sequence and structural information (within PFAAT) to predict specificity-determining residues and selectivity profiles for small-molecule kinase inhibitors

panel kinase-inhibitor sequence erk2 caliper radiometric solvent
Genome-wide reprogramming of sRNA and lncRNA in the epigenetic regulation following interspecific hybridization in the Brassica species.

PMID 41668146 · PMC12892563 · Molecular horticulture · 2026 · 6 claims · 5 setups

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Regulatory differences in sRNAs between the two F1 hybrids are mainly driven by maternal inheritance, with Hybrid-sh showing more maternal influence and Hybrid-yh showing transgressive regulation

brassica s70 small strand-specific atac-seq
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

Has reproduction · 91

175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

one sinensis small-molecular-weight leaves small genome mirna
A small-cell lung cancer genome with complex signatures of tobacco exposure.

PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

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22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

nci-h209 sclc lu-135 massively pcr multiplex
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

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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
Protocadherin 20 Is a POU Class 2 Homeobox 3 Target Gene Required for Proper Tuft Cell Microvillus Organization.

PMID 41619969 · PMC13051935 · Cellular and molecular gastroenterology and hepatology · 2026 · 8 claims · 8 setups

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POU2F3 ChIP-seq in isolated murine tuft cells identifies high-confidence POU2F3 binding sites/target genes enriched at gene promoters and the POU consensus motif

facs-isolated pou2f3 duodenal non-small-cell chip-seq novo bulk
How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

PMID 15804363 · PMC1079826 · BMC genomics · 2005 · 7 claims · 7 setups

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Predicted solubility in E. coli (via CV-CV') depends on hydrolase size, phylogenetic origin, homologous family, and superfamily

lipase bacterial small genera cv-cv correlation grouped
MirDIP 5.2: tissue context annotation and novel microRNA curation.

PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

Has reproduction · 89

mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

mirnas disease novel type mirna small bulk
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

Has reproduction · 55

352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

endometrial degs hub decidua microarray wgcna machine
Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.

PMID 42166739 · PMC13242923 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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SAMI is a UMI-aware, Singularity-contained Nextflow pipeline that detects splicing events diverging from transcript annotations directly from raw FASTQ files.

seraseq simulated small processed targeted simulated computation
Finding the needle in the haystack: why high-throughput screening is good for your health.

PMID 12100740 · PMC138735 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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HTS is essential for finding lead compounds, especially for novel targets whose active-site structure is unknown

raf-1 mitotic mutant tumor biochemical cell-based conformational
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

3'-utr mirbase hapmap comparative snp mirna
Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

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10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

aorta cardiovascular peripheral blood methylation mirna expression
TEMP: a computational method for analyzing transposable element polymorphism in populations.

PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

Has reproduction · 61

TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

drosophila five four melanogaster simulated comparative whole-genome
Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

PMID 19842929 · PMC2923222 · Pharmacogenomics · 2009 · 8 claims · 8 setups

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Approximately 15-20% of nonsynonymous variants in membrane transporters exhibit reduced function

abc hek293 expressing sophie computational transporter transport
miRGen 2.0: a database of microRNA genomic information and regulation.

PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

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miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

lung organ malme embryonic polii small nucleosome
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

Has reproduction · 71

AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

aml hovon cancer tcga bulk consensus machine

Experiments

Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

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

Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

Prediction of specificity-determining residues for small-molecule kinase inhibitors.

Genome-wide reprogramming of sRNA and lncRNA in the epigenetic regulation following interspecific hybridization in the Brassica species.

Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

A small-cell lung cancer genome with complex signatures of tobacco exposure.

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

Protocadherin 20 Is a POU Class 2 Homeobox 3 Target Gene Required for Proper Tuft Cell Microvillus Organization.

How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

MirDIP 5.2: tissue context annotation and novel microRNA curation.

Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.

Finding the needle in the haystack: why high-throughput screening is good for your health.

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

TEMP: a computational method for analyzing transposable element polymorphism in populations.

Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

miRGen 2.0: a database of microRNA genomic information and regulation.

Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.