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 473

System / cell line: sites ✕ Clear

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.

PMID 19638617 · PMC2889494 · Science signaling · 2009 · 8 claims · 6 setups

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Pathway reconstruction can be modeled as a prize-collecting Steiner tree problem, balancing penalties for excluding terminal nodes against costs for including edges, controlled by a parameter β.

saccharomyces phosphoproteomic expression curated
Computational identification of transcriptional regulatory elements in DNA sequence.

PMID 16855295 · PMC1524905 · Nucleic acids research · 2006 · 8 claims · 3 setups

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Weight matrix (PWM/PSSM) models of TF binding sites are grounded in biophysical theory of protein-DNA interactions, with position weights corresponding to log-odds contributions to binding free energy

saccharomyces generic pwm-based pwm
The stem cell population of the human colon crypt: analysis via methylation patterns.

PMID 17335343 · PMC1808490 · PLoS computational biology · 2007 · 8 claims · 3 setups

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A coalescent-based, full probabilistic model with MCMC Bayesian inference provides a more powerful alternative to prior forward-simulation approaches for analyzing methylation pattern data from crypts.

colon computational simulated bisulfite coalescent posterior
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.

PMID 33662629 · PMC9801043 · Genomics, proteomics & bioinformatics · 2022 · 8 claims · 8 setups

Has reproduction · 50

DeeReCT-APA quantitatively predicts the usage of all competing PASs of a gene simultaneously, rather than casting the problem as pairwise comparison like prior methods.

fibroblast genomic same 3'-region 3'-mrna deep
CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

PMID 34210356 · PMC8247108 · Genome biology · 2021 · 7 claims · 2 setups

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A centralised hub model built on the CLIMB compute infrastructure (CLIMB-COVID) can integrate SARS-CoV-2 genomic sequencing data and sample metadata from a decentralised, autonomous network of sequencing sites into a single canonical dataset.

sars-cov-2 whole-genome pcr
Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas.

PMID 35073255 · PMC8828049 · eLife · 2022 · 8 claims · 7 setups

Has reproduction · 57

Prokaryotic community similarity follows a significant U-shape relationship over geographic distance up to 4000 km, decreasing within biotas but increasing across biotas after a tipping point of 1760-1920 km

soil grassland 16s plant soil
GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.

PMID 35087491 · PMC8787282 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

Has reproduction · 50

GAL08 is a dominant bacterial clade in Dewar Creek hot spring sediment, comprising up to 29.2% of the microbial community by relative read abundance

hot 16s gal08 16s qpcr single-cell
Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

Has reproduction · 98

Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

hg38 hela hek293t induced genome-wide high-throughput chip-seq
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups

Has reproduction · 98

maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors

lines hepg2 types single chip-seq omni-atac-seq atac-seq
Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.

PMID 35714765 · PMC9283944 · The Journal of biological chemistry · 2022 · 8 claims · 4 setups

Has reproduction · 80

Genome-wide Ψ mapping using HydraPsiSeq and small RNA Ψ-seq identifies Ψ sites on snoRNA, 7SL RNA, vtRNA, SL RNA, and tRNA in T. brucei

brucei hydrapsiseq small primer
Genome informatics: taming the avalanche of genomic data.

PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

genes arabidopsis genome vertebrate comparative conservation whole-genome
Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

orthologues repair case-control phosphorylation cross-species database
Antibody binding loop insertions as diversity elements.

PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

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A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

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The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
Accurate splice site prediction using support vector machines.

PMID 18269701 · PMC2230508 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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Weighted degree (WD) kernel SVMs outperform Markov Chains, GeneSplicer and SpliceMachine for genome-wide splice site recognition

nn269 dgsplicer caenorhabditis arabidopsis svm genome-wide
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

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miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

major tissues conserved predicted quantitative bead-based microarray
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

inhbb cloned same fresh-frozen rnase masscleave clonal
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

embryonic neural t-cells mm8 chip-seq chip-chip pwm
Novel transglutaminase-1 mutations and genotype-phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA.

PMID 18948357 · PMC3044481 · Journal of medical genetics · 2009 · 8 claims · 6 setups

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TGM1 germline mutations were identified in 55% (57/104) of patients with ARCI

arci unrelated dog direct sequence blast
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

Experiments

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.

Computational identification of transcriptional regulatory elements in DNA sequence.

The stem cell population of the human colon crypt: analysis via methylation patterns.

DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas.

GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.

Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.

Genome informatics: taming the avalanche of genomic data.

Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

Antibody binding loop insertions as diversity elements.

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

Accurate splice site prediction using support vector machines.

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

Novel transglutaminase-1 mutations and genotype-phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.