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).

Publications 1.3k Datasets 392.5k Experiments 268

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Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

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A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

sakazakii cronobacter sequenced multilocus biotyping phylogenetic
Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

PMID 19851457 · PMC2760143 · PLoS pathogens · 2009 · 8 claims · 4 setups

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Genetically distinct RV clades of the same G/P-type (G3P[8]) can co-circulate within a single epidemic season and cause disease

g3p[8] rv-positive concatenated deduced rt-pcr pcr-elisa phylogenetic
Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

PMID 19825160 · PMC2767350 · BMC medical genetics · 2009 · 8 claims · 6 setups

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A novel 16 bp deletion variant (g.-6_+10del) was identified in the DJ-1 5'-UTR, spanning the transcription start site, 93 bp downstream of a known Sp1 site.

genomic hek293 m17 south sscp dual-luciferase pcr-rflp
Reconstructing Indian population history.

PMID 19779445 · PMC2842210 · Nature · 2009 · 8 claims · 8 setups

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Most Indian populations descend from a mixture of two ancient, genetically divergent populations: ANI (close to Middle Easterners, Central Asians, Europeans) and ASI (as distinct from ANI and East Asians as those are from each other).

indian pairs gujarati genome-wide principal fst-based
Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

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Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

hiv-1 longitudinal 0-month single pseudovirus single site-directed
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
Ontological Discovery Environment: a system for integrating gene-phenotype associations.

PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups

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ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems

strains integrated bipartite phish gene differential pairwise
Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

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A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

novel hpv gene h5n1 whole-genome intrinsic statistical
A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

PMID 37247570 · PMC10878300 · Ticks and tick-borne diseases · 2023 · 7 claims · 3 setups

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The MPAS pipeline is a portable, reproducible Nextflow-based bioinformatics pipeline that identifies and summarizes amplicon sequences produced by the MPAS assay.

host-seeking mpas same targeted mpas clc
Comparative genomics of vertebrate Fox cluster loci.

PMID 17062144 · PMC1634998 · BMC genomics · 2006 · 8 claims · 3 setups

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Two additional human paralogous Fox cluster regions exist, on chromosomes 14 and 20, beyond the previously known chromosome 6 and 16 loci

chimp sequences genomic blast molecular comparative
FGF: a web tool for Fishing Gene Family in a whole genome database.

PMID 17584790 · PMC1933194 · Nucleic acids research · 2007 · 6 claims · 3 setups

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FGF efficiently searches and identifies gene families in whole-genome databases and outputs visual phylogenetic trees annotated with gene structure, chromosome position, duplication fate, and selective pressure (Ka/Ks)

genome rice gene large-scale
Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates.

PMID 18541024 · PMC2446394 · BMC evolutionary biology · 2008 · 8 claims · 3 setups

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Extant bony vertebrates (osteichthyans) retain only Lbx1- and Lbx2-type genes; no distinct Lbx3/Lbx4 proteins exist.

osteichthyan aligned genome blast maximum comparative
Vibrio cholerae pathogenic clones.

PMID 16318732 · PMC3367346 · Emerging infectious diseases · 2005 · 8 claims · 1 setups

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The US Gulf clone, the Australian clone, and 3 prepandemic El Tor strains are related to the seventh pandemic clone.

vibrio multilocus
Ensembl 2013.

PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

Has reproduction · 85

Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

genome species supported variants evidence-based rna-seq chip-seq
From microarrays to genome duplications.

PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

tumor cancer plated saccharomyces comparative nonsense-mediated cell-based
Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

PMID 19797407 · PMC2778335 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 7 setups

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ProSeq3 is a program with a graphic user interface that simplifies preparation and basic population genetic analysis of multigenic DNA polymorphism datasets

software authors sequence polymorphism phylogenetic
A2TEA: Identifying trait-specific evolutionary adaptations.

PMID 37224329 · PMC10186066 · F1000Research · 2022 · 8 claims · 7 setups

Has reproduction · 90

A2TEA integrates gene family expansion analysis with differential expression data across species to identify genes that were targets of evolutionary adaptation to a given stress/treatment

user-provided multi-species genes sequences rna-seq orthologous phylogenetic
DFAST and DAGA: web-based integrated genome annotation tools and resources.

PMID 27867804 · PMC5107635 · Bioscience of microbiota, food and health · 2016 · 8 claims · 7 setups

Has reproduction · 89

DFAST is a web-based genome annotation pipeline with integrated quality assessment (CheckM) and taxonomic assessment (ANI) that produces DDBJ submission-ready files

lactobacillus representative lab genomes genome average novo
Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

PMID 33967968 · PMC8100199 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

Has reproduction · 73

An undergraduate CURE combining field sampling, wet-lab microbiology, and genomic bioinformatics can be used to isolate and characterize environmental S. enterica strains.

putative enterica selected assembled endpoint genome long-read
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 · 8 claims · 8 setups

Has reproduction · 68

Siphonophorae is the first diverging clade within Hydroidolina.

hydroidolinan nanomia liriope assembled long-range rna-seq dna-seq

Experiments

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

Reconstructing Indian population history.

Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

Ontological Discovery Environment: a system for integrating gene-phenotype associations.

Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

Comparative genomics of vertebrate Fox cluster loci.

FGF: a web tool for Fishing Gene Family in a whole genome database.

Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates.

Vibrio cholerae pathogenic clones.

Ensembl 2013.

From microarrays to genome duplications.

Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

A2TEA: Identifying trait-specific evolutionary adaptations.

DFAST and DAGA: web-based integrated genome annotation tools and resources.

Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

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