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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Has reproduction
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.
PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups
Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.
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Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.
PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups
Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.
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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 · 45
RNA structure maps across mammalian cellular compartments.
PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups
icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.
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InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.
PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups
InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM
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Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.
PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups
Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).
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MutDB: update on development of tools for the biochemical analysis of genetic variation.
PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups
MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)
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Human chromosome 7: DNA sequence and biology.
PMID 12690205 · PMC2882961 · Science (New York, N.Y.) · 2003 · 6 claims · 2 setups
Presents the DNA sequence and annotation of the entire human chromosome 7
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The Edinburgh human metabolic network reconstruction and its functional analysis.
PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups
EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.
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Has reproduction · 70
Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.
PMID 36450752 · PMC9712620 · Nature communications · 2022 · 8 claims · 8 setups
AR enhancer/chromatin binding usage is highly heterogeneous between primary prostate tumors, with <5% of all AR binding sites shared by half of tumors analyzed.
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Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.
PMID 17537826 · PMC1933130 · Nucleic acids research · 2007 · 7 claims · 5 setups
StSNP integrates dbSNP, PDB, KEGG, and NCBI Entrez data into a single web server for nsSNP analysis
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Has reproduction · 63
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.
PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups
More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes
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Filtering high-throughput protein-protein interaction data using a combination of genomic features.
PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups
A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.
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Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.
PMID 15673719 · PMC548352 · Nucleic acids research · 2005 · 8 claims · 5 setups
Presence of CENP-B box elements is required for efficient de novo centromere formation in HAC vectors
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Has reproduction · 61
TEMP: a computational method for analyzing transposable element polymorphism in populations.
PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups
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.