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 · 67
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.
PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups
binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)
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Has reproduction · 89
Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.
PMID 36882868 · PMC9991879 · BMC medicine · 2023 · 8 claims · 6 setups
Vaccination programmes with earlier start dates yield the most health benefits and lowest ICERs compared to late-starting programmes
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Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping.
PMID 12529185 · PMC149347 · BMC bioinformatics · 2003 · 5 claims · 4 setups
OSLEM (Optimal Step Length EM), which approximates an optimal step length via a fixed-point search (D_N = D_{N-1} + λ(D_preN - D_{N-1})), runs about twice as fast as standard EM while producing the same haplotype frequency estimates.
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Evolutionary algorithms for the selection of single nucleotide polymorphisms.
PMID 12875658 · PMC183839 · BMC bioinformatics · 2003 · 8 claims · 3 setups
Evolutionary algorithms are well suited to multiobjective optimization problems with large, intractable search spaces such as SNP selection, unlike exact methods (exhaustive enumeration) or single-objective search techniques (tabu search, simulated annealing).
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YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
PMID 15929789 · PMC1175843 · BMC bioinformatics · 2005 · 7 claims · 3 setups
YANA integrates METATOOL to provide a graphical, platform-independent front-end for editing, calculating, visualizing, and comparing elementary flux modes, with SBML support.
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Genomics: applications in mechanism elucidation.
PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups
Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.
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Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
PMID 16925837 · PMC1810552 · Genome biology · 2006 · 6 claims · 3 setups
Promoter predictors that combine promoter prediction with gene prediction (N-SCAN, Fprom) achieve better performance than pure ab initio promoter predictors, mainly by reducing the promoter search space and false positives
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pTARGET: a web server for predicting protein subcellular localization.
PMID 16844995 · PMC1538910 · Nucleic acids research · 2006 · 7 claims · 3 setups
pTARGET web server predicts nine distinct subcellular localizations in eukaryotic non-plant proteins using an algorithm based on location-specific Pfam domain occurrence patterns and amino acid composition (AAC)
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Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.
PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups
About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population
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MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.
PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups
A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs
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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
SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.
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Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.
PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups
PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301
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Has reproduction · 57
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
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
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Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.
PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups
Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)
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The promise and reality of personal genomics.
PMID 19723346 · PMC2768970 · Genome biology · 2009 · 7 claims · 6 setups
Despite being the most complete and accurate individually sequenced human genome to date, AK1 sequencing still misses a substantial fraction of variants, showing sequencing technology remains far from complete/reliable.