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).

• KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

  PMID 36195962 · PMC9531401 · Genome biology · 2022 · 7 claims · 7 setups

  Has reproduction · 42

  KAGE combines population-based kmer count modeling with single-variant prior adjustment into an alignment-free genotyper that matches the accuracy of the best existing alignment-free genotypers while being an order of magnitude faster.

  small snps individual hg002 alignment-free kmer-based genotyping

• In silico analysis of missense substitutions using sequence-alignment based methods.

  PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

  Full-text index only

  Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

  clinically sequence curated deep blosum62 sift align-gvgd

• Bayesian coestimation of phylogeny and sequence alignment.

  PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.

  globin same four-sequence bayesian mcmc comparison

• Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

  PMID 17567995 · PMC1891336 · Genome research · 2007 · 7 claims · 3 setups

  Full-text index only

  Four different alignment methods show large-scale consistency but substantial differences in small-scale rearrangements, sensitivity, and specificity.

  mammalian aligned constrained sequence evolutionary comparative

• Benchmarking tools for the alignment of functional noncoding DNA.

  PMID 14736341 · PMC344529 · BMC bioinformatics · 2004 · 8 claims · 4 setups

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  Global alignment tools (Avid, ClustalW, Lagan, Needle, DiAlign-G) typically have higher sensitivity over entire noncoding sequences and within constrained blocks than local tools

  simulated melanogaster sapiens sequence pairwise genome

• A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

  PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

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  PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

  pax6 brain yeast sequence yeast semi-quantitative

• Towards alignment independent quantitative assessment of homology detection.

  PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

  Full-text index only

  The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

  curated homologene swiss-prot fruit signalp homologene-based fhom

• MutDB: update on development of tools for the biochemical analysis of genetic variation.

  PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

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  MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

  proteins mutdb nonsynonymous genes sequence web functional

• Simple models of genomic variation in human SNP density.

  PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

  Full-text index only

  Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

  genome observed simulated genome hierarchical coalescent

• The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.

  PMID 18796526 · PMC2566872 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  Some common scoring schemes tend to overextend alignments, generating spurious alignment flanks up to hundreds of bp/amino acids in length

  pseudo-random mitochondrial numts human-fugu monte blast smith-waterman

• Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

  PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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  Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

  genome poly est cdna est blast cdna

• DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

  PMID 17980028 · PMC2186358 · BMC bioinformatics · 2007 · 7 claims · 3 setups

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  The DAVID Gene Concept, a single-linkage algorithm, merges gene clusters from Entrez Gene, UniRef100, and PIR-NREF100 that share protein IDs and species into unified DAVID gene clusters, improving cross-referencing between NCBI and UniProt systems

  members entire usp8 sequence annotation

• Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.

  PMID 18974170 · PMC2638935 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 3 setups

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  Slider aligns reads using all bases above a probability threshold (baseMinPrb) from prb files, generating all possible read sequences above a read probability threshold (read_0_MinPrb), rather than only the most probable sequence

  illumina uniquely genome sequence snp reference

• Using multiple alignments to improve seeded local alignment algorithms.

  PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups

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  Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone

  alignment query leave-one-species-out seeded

• The UCSC Proteome Browser.

  PMID 15608236 · PMC540054 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  The UCSC Proteome Browser is tightly integrated with the UCSC Genome Browser, giving users simultaneous access to genome and proteome data.

  swiss-prot sequence domain isoelectric

• NCBI Reference Sequences: current status, policy and new initiatives.

  PMID 18927115 · PMC2686572 · Nucleic acids research · 2009 · 7 claims · 5 setups

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  RefSeq is a curated, non-redundant, explicitly linked database of nucleotide and protein sequences spanning genomes, transcripts and proteins across prokaryotes, eukaryotes and viruses

  microbial bacterial prokaryotic refseq spliced structural functional

• BIPASS: BioInformatics Pipeline Alternative Splicing Services.

  PMID 17584795 · PMC1933140 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  BIPASS offers two complementary services for alternative splicing (AS) research: BIPAS-SpliceDB, a queryable pre-computed AS data warehouse, and BIPAS-Align&Splice, an online pipeline for user-submitted sequences.

  transcript aligned pre-computed user-submitted sequence alternative database

• Assessing Bos taurus introgression in the UOA Bos indicus assembly.

  PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups

  Has reproduction · 86

  Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.

  cattle breed-pooled indian merged whole-genome snv template

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 8 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign is the first RNA sequence/structure pairwise alignment algorithm based on incremental ensemble mountain distance, running in O(n^3) time and O(n^2) space for two sequences of length n.

  sequences sequence trna target pairwise global single

• SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.

  PMID 33932985 · PMC8088074 · BMC bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 65

  SPEAQeasy is a portable, easy-to-install, Nextflow-powered RNA-seq processing pipeline that lowers the computational entry barrier for biologists/clinicians

  provided amygdala rna-seq differentially pipeline bulk rna-based