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).

• FeatureScan: revealing property-dependent similarity of nucleotide sequences.

  PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

  randomly fully same chimpanzee signal-theoretic featurescan blast

• Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

  PMID 17634103 · PMC1947971 · BMC genomics · 2007 · 8 claims · 4 setups

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  A closed-form approximation to the F-test non-centrality parameter (NCP) incorporating genetic model parameters (disease allele frequency, marker allele frequency, prevalence, genotype relative risk, sample size, genetic model, number of pools/replicates, machine variability) can be used to compute power for DNA pooling association studies

  modeled analytic factorial power

• A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

  PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups

  Has reproduction · 95

  RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA

  tcga er+ ccle computational spearman correlation gene

• Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

  PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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  Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

  orthologous random cattle aligned three-way pairwise bac

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

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  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence

• Computing Ka and Ks with a consideration of unequal transitional substitutions.

  PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups

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  MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias

  simulated pairs human-mouse human-dog computer comparative

• Uncertainty in the mating strategy of honeybees causes bias and unreliability in the estimates of genetic parameters.

  PMID 38632535 · PMC11022492 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 3 setups

  Has reproduction · 98

  The most precise estimates of genetic parameters and genetic trends are obtained when breeding queens are mated with drones of a single DPQ that is correctly assigned in the pedigree (SS mating).

  simulated simulation sensitivity

• 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

• Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

  PMID 16469098 · PMC1409804 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  AUGUSTUS+ extends the AUGUSTUS GHMM by combining intrinsic sequence information with extrinsic hints via an extended emission alphabet, so the GHMM jointly models the DNA sequence, gene structure, and hint collection.

  chromosome genomic training ghmm-based sequence parameter

• Using ESTs to improve the accuracy of de novo gene prediction.

  PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome

  elegans genome chromosome novo gene partial

• Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

  PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups

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  ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.

  blood baseline-corrected 953-dimensional training seldi-tof wavelet ant

• 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

  Has reproduction · 49

  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.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored