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).

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

  PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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  Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

  simulated same mcmc-based direct original

• Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

  PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

  non-identical gene3d cath whole-gene domain transmembrane

• ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.

  PMID 17710137 · PMC1940324 · PloS one · 2007 · 8 claims · 4 setups

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  ADaCGH implements eight CNA detection methods, including the best-performing ones from recent reviews (CBS, GLAD, CGHseg, HMM)

  30-node web-based cluster simulated computational web comparison

• Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.

  PMID 17349043 · PMC1829165 · BMC bioinformatics · 2007 · 8 claims · 6 setups

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  A combined target-selection approach — pursuing both structurally uncharacterised domain families and additional targets from large structurally characterised superfamilies — is essential for comprehensive structural coverage of the genomes.

  sp-trembl hmm-based domain computational

• Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

  PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

  predicted non-masked genome interpro hmm tblastn inter-species

• Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

  PMID 17090320 · PMC1654190 · BMC evolutionary biology · 2006 · 8 claims · 5 setups

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  HHpred (HMM-HMM comparison) detects remote homologs in the human proteome with higher sensitivity than hmmpfam (HMMER), giving 10% more functional domain coverage and 20% higher residue coverage against Pfam-A families.

  proteome homo domains hmm-hmm hmm subtractive

• A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

  PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.

  hapmap bladder prostate simulated affymetrix simulation

• A computational screen for type I polyketide synthases in metagenomics shotgun data.

  PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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  Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

  predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds

• The protein-phosphatome of the human malaria parasite Plasmodium falciparum.

  PMID 18793411 · PMC2559854 · BMC genomics · 2008 · 8 claims · 8 setups

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  P. falciparum possesses 27 putative protein phosphatase sequences across the four major PP families (PPP, PPM, PTP, NIF), plus 7 additional sequences predicted to dephosphorylate non-protein substrates, totaling 34.

  sapiens ppp-domain metallophosphatase pf14_0142 hmm sequence neighbour-net

• Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

  PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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  High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

  genomic normalized simulated tiling-resolution snp oligonucleotide

• The EH1 motif in metazoan transcription factors.

  PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

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  There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

  homeobox-containing forkhead-containing complete combined meme hmm logistic

• Vertebrate gene finding from multiple-species alignments using a two-level strategy.

  PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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  DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

  genomic encode entire chromosome multi-species hmm-based classifier

• Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

  PMID 41738778 · PMC12962854 · Genome biology and evolution · 2026 · 8 claims · 8 setups

  Has reproduction · 89

  Eight sericin genes were identified in the Actias luna genome, including two clusters of closely related paralogs.

  actias genomes translated luna genome hmm manual

• A model-based approach to selection of tag SNPs.

  PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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  The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

  hapmap encode enr112 tag cross-validated entropy tagged

• 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

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• A comparative study on recombination activity in cattle.

  PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups

  Has reproduction · 93

  Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)

  six paternal alphasimr-simulated brown snp recombination simulation

• L1Base: from functional annotation to prediction of active LINE-1 elements.

  PMID 15608246 · PMC539998 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  L1Base is a database of putatively active LINE-1 insertions in human, mouse and rat genomes, containing FLI-L1s (intact in both ORFs), ORF2-L1s (intact ORF2, disrupted ORF1), and FLnI-L1s (full-length, >6000 bp, non-intact)

  sapiens orf1 orf fli-l1s genomic repeatmasker hmm-profile

• Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

  PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

  quintessentialset-88 hth same newly lcs svm traditional