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).

• Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

  PMID 19823676 · PMC2757908 · PloS one · 2009 · 8 claims · 4 setups

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  Cross-reactivity of antibodies against C-terminal sequences of ribosomal P proteins from several animals, plants and protozoa with heart tissue may mediate EMF similarly to how T. cruzi C-termini mediate Chaga's disease

  tcp0 tcp2β blast-p phylogenetic structure

• A survey of integral alpha-helical membrane proteins.

  PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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  An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.

  pfam-a organisms 34-genome integral transmembrane comparative sequence

• 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

• Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

  PMID 16204447 · PMC1243803 · Nucleic acids research · 2005 · 8 claims · 3 setups

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  A Bayesian model incorporating experimental covariates (array, pen, probe, dye, scanning) can estimate absolute transcript concentrations from spotted microarray intensities without needing calibration of each sample or gene individually

  cervix same spotted quantitative

• Updated three-stage model for the peopling of the Americas.

  PMID 18797500 · PMC2527656 · PloS one · 2008 · 8 claims · 3 setups

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  Removing nine non-Native American mtDNA sequences eliminates the previously reported early (~40 kya) expansion signal for the proto-Amerind population

  native mitochondrial new bayesian mtdna molecular

• Identifying the important HIV-1 recombination breakpoints.

  PMID 18787691 · PMC2522274 · PLoS computational biology · 2008 · 8 claims · 3 setups

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  Local sequence identity between co-packaged parental RNAs strongly influences the probability of strand-transfer/breakpoint location, with fewer breakpoints occurring near mismatches

  inter-subtype parental copy-choice probabilistic comparative

• SNAP predicts effect of mutations on protein function.

  PMID 18757876 · PMC2562009 · Bioinformatics (Oxford, England) · 2008 · 8 claims · 3 setups

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  SNAP is a publicly available web-server implementation predicting functional effects (neutral/non-neutral) of single amino acid substitutions.

  mutant insulin neural alanine mutation

• An empirical study of choosing efficient discriminative seeds for oligonucleotide design.

  PMID 19958494 · PMC2788383 · BMC genomics · 2009 · 8 claims · 3 setups

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  The spaced seed is the most efficient discriminative seed for oligonucleotide design among the five algorithms tested.

  simulated pmoa nirs seed

• BLASTO: a tool for searching orthologous groups.

  PMID 17483516 · PMC1933156 · Nucleic acids research · 2007 · 7 claims · 2 setups

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  BLASTO treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences

  randomly sequences blast blasto

• The functional importance of disease-associated mutation.

  PMID 12220483 · PMC128831 · BMC bioinformatics · 2002 · 6 claims · 1 setups

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  Disease-associated mutations occur in conserved regions of genes and can be used to identify likely disease-causing mutations

  disease-associated sequence

• IMGT, the international ImMunoGeneTics information system.

  PMID 15608269 · PMC540019 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  IMGT is a high-quality integrated knowledge resource for immunoglobulins (IG), T cell receptors (TR), MHC, and related proteins of the immune system (RPI) across vertebrate species

  igh mhc pairs automated junction structure

• Database resources of the National Center for Biotechnology Information.

  PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

  genbank genomic eukaryotic completely sequence rapid est

• SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

  PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

  user-submitted query genomes proteins domain profile-profile comparative

• CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping.

  PMID 16686952 · PMC1471797 · BMC genetics · 2006 · 7 claims · 1 setups

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  CapsID identifies snip-SNPs (SNPs that alter restriction endonuclease recognition sites) within reference sequence alignments and designs PCR primers around them

  sequence restriction

• Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

  PMID 12734010 · PMC156586 · Genome biology · 2003 · 8 claims · 6 setups

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  L1 elements with transduction-derived 3' sequence (L1-TDs) can be computationally identified using RepeatMasker/TSDfinder and grouped into families sharing a common progenitor via BLAST comparison of downstream sequences.

  genome database l1-td ncbi genome-wide blast pairwise

• Pegasys: software for executing and integrating analyses of biological sequences.

  PMID 15096276 · PMC406494 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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  Pegasys is a flexible, modular, customizable software system for executing and integrating heterogeneous biological sequence analysis tools

  eukaryotic formatted genomic input initio sequence gene

• A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm.

  PMID 16002787 · PMC1174901 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  An evolution-mimicking algorithm (EMA) that shuffles and mutates loop sequences while keeping the G-quartet intact can screen DNA aptamers based on inhibitory activity rather than binding affinity.

  plasma bovine clot-inhibition binding

• Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

  PMID 17217514 · PMC1780116 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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  A novel method combining 8-species comparative genomics with de novo motif discovery identifies human TF DNA-binding motifs overrepresented and conserved in upstream regions of co-regulated genes

  muscle-specific novo comparative

• Use of modified U1 snRNAs to inhibit HIV-1 replication.

  PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

  hiv-1 293t hela bioinformatic western reporter

• Diversity of tRNA genes in eukaryotes.

  PMID 17088292 · PMC1693877 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  The number of tRNA genes having the same anticodon but different sequences elsewhere (isodecoder genes) varies significantly (10–246) across 11 eukaryotes despite isoacceptor numbers being similar (41–55)

  eukaryotic bacterial genome synthetic genome-wide sequence manual