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).
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Network inference and network response identification: moving genome-scale data to the next level of biological discovery.
PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups
Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability
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Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics.
PMID 18783599 · PMC2559821 · Theoretical biology & medical modelling · 2008 · 8 claims · 2 setups
Probability landscapes permit systematic detection, analysis, and utilization of feature context-dependency in genomic data.
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Ensembl 2005.
PMID 15608235 · PMC540092 · Nucleic acids research · 2005 · 8 claims · 4 setups
Ensembl's automatic gene build system can flexibly and reliably annotate a wide variety of genomes with limited species-specific evidence.
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Environmental genome project: focusing on differences to understand the whole.
PMID 12460813 · PMC1241127 · Environmental health perspectives · 2002 · 8 claims · 4 setups
The EGP has generated a working list of more than 550 environmentally responsive genes involved in pathways such as metabolism, DNA repair, and cell cycle control as candidates for SNP resequencing.
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Characterizing natural variation using next-generation sequencing technologies.
PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups
Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.
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Has reproduction · 59
WASP: a versatile, web-accessible single cell RNA-Seq processing platform.
PMID 33736596 · PMC7977290 · BMC genomics · 2021 · 7 claims · 7 setups
WASP is a software platform for processing Drop-Seq-based scRNA-seq data generated with ddSEQ or 10x protocols, combining a Snakemake pre-processing pipeline with an R Shiny post-processing application.
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Comprehensive splice-site analysis using comparative genomics.
PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups
Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.
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Has reproduction · 96
A bioinformatic pipeline for simulating viral integration data.
PMID 35496474 · PMC9046613 · Data in brief · 2022 · 7 claims · 3 setups
A snakemake-based pipeline was developed to simulate integration of a viral or vector genome into a host genome, including sub-genomic fragment integration, structural variation, and host-site deletions.
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Has reproduction
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.
PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups
Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types
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mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.
PMID 16381973 · PMC1347373 · Nucleic acids research · 2006 · 8 claims · 3 setups
mtDB is a comprehensive, actively maintained database of published human mitochondrial genome sequences, providing a common resource for population genetics and medical research
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SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.
PMID 15774022 · PMC1274256 · BMC bioinformatics · 2005 · 7 claims · 3 setups
SNPHunter allows ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data (physical position, function class, flanking sequences at user-defined lengths, heterozygosity) from NCBI dbSNP
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Has reproduction · 68
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.
PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups
A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.
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Expression profiling of drug response--from genes to pathways.
PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups
Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.
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Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups
PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores
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Has reproduction · 49
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.
PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups
oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.