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).

• The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

  PMID 18778482 · PMC2563025 · Retrovirology · 2008 · 8 claims · 7 setups

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  Intra-host nucleotide diversity of the HIV-2 C2V3C3 region increases over the course of chronic infection in most patients

  pbmcs clonal env deduced nested maximum-likelihood positive

• Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

  PMID 26618080 · PMC4655093 · PeerJ · 2015 · 6 claims · 6 setups

  Has reproduction · 68

  Phylogenetic analyses of full mitochondrial gene sets recover siphonophores as the first diverging clade within Hydroidolina, a well-supported Leptothecata–Filifera III–IV clade, and a second clade of Aplanulata–Capitata s.s.–Filifera I–II.

  hydrozoan nanomia liriope concatenated long-range rna-seq dna-seq

• 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

• Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

  PMID 16254605 · PMC1270012 · PLoS genetics · 2005 · 8 claims · 6 setups

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  Comparative net alignment of human and chimpanzee genome assemblies identifies 1,576 putative inverted regions covering more than 154 Mb of DNA

  build chimpanzee unrelated ceph comparative three-color pcr

• Analysis of chimpanzee history based on genome sequence alignments.

  PMID 18421364 · PMC2278377 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Bonobos and common chimpanzees separated approximately 1.29 million years ago

  bonobo bonobos chimpanzee simulated shotgun sequenom principal

• Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

  PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

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  Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

  paired lung tissue-pair pooled hiv-1 maximum statistical

• Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

  PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

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  Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

  encode genome cdna-to-genome novo comparative

• PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

  PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups

  Has reproduction · 90

  PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.

  heart genome rna-seq rt-pcr

• TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

  PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 69

  TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.

  ppm1d-transgenic genome genome read touchdown-pcr

• 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

• EGASP: the human ENCODE Genome Annotation Assessment Project.

  PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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  Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

  encode computational manual rt-pcr

• Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

  PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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  The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

  chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr

• Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

  PMID 16460646 · PMC3525152 · Human genomics · 2006 · 8 claims · 8 setups

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  GJB2 (connexin 26) mutations account for hearing loss in only 17 of 156 families (11%), a smaller fraction than reported in other populations.

  palestinian genomic probands lymphoblasts targeted sanger pcr

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

  PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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  Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

  cynomolgus 3-year-old macaque est full-insert oligonucleotide

• Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

  PMID 19880432 · PMC2780955 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 8 claims · 5 setups

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  Identified 23,241 human genes transcribed into protein-coding mRNAs using full-length cDNA and 5'-EST sequence data

  tissues genome full-length genes full-length genome orf

• Comparative genomics search for losses of long-established genes on the human lineage.

  PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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  A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

  dog genome chimp gorilla comparative overlap visual