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 23

System / cell line: six ✕ Assay: alignment ✕ Clear

Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups

Has reproduction · 92

Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes

six same polished each nanopore illumina novo
Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.

PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups

Has reproduction · 51

Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.

giab hg001 brca1 filtered long-read read bam
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

genome transcriptome gene genes full-length genome cdna
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

pooled genome est novel tandem whole-genome est
Empirical codon substitution matrix.

PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

orthologous million codon same pairwise empirical comparative
Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

genbank hiv-1 protease integrase blastp phylogenetic amino
Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 6 claims · 8 setups

Has reproduction · 82

Genome-based taxonomy (GTDB-Tk and ANI) reclassified the isolate A55848, phenotypically identified as K. oxytoca, as Klebsiella michiganensis

klebsiella isolate a55848 assembled short-read phenotypic genome-based
Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.

PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 7 claims · 7 setups

Has reproduction · 71

A custom ECF pipeline identified 13,401 lncRNAs in the A. crassicauda transcriptome (12,642 novel, 759 known).

androctonus crassicauda paired-end coding homology
Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

nine animals completed fungal combined sequence biochemical
Assessing the gene space in draft genomes.

PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

caenorhabditis toxoplasma homo briggsae cegma blast tblastn
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition

standard thp-1 replicate lc-ms manual cross-instrument
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 78

73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

triticum taiqd wheat promoter genome-wide phylogenetic synteny
Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.

PMID 41826827 · PMC13202766 · BMC microbiology · 2026 · 8 claims · 8 setups

Has reproduction · 71

R. artemisiae harbors six prokaryotic taxa: two plant pathogens ('Ca. P. solani', 'Ca. A. phytopathogenicus') and four insect endosymbionts ('Ca. Vidania', 'Ca. Purcelliella', 'Ca. Karelsulcia', and Wolbachia).

individual long endosymbiont artemisiae pcr-free pcr nucleic
Structural evolution of the protein kinase-like superfamily.

PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

bank representative same kinase comparative manual structure-annotated
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

genome tissues novo pairwise rt-pcr
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

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The human genome encodes at least 71 kelch-repeat proteins

genome yeast kelch-repeat full-length blast blastp cross-referencing
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

Has reproduction · 66

S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

chimpanzee retrofitted primate aspm tar restriction genomic
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 38

A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

gossypium uppermost root reads bulk leaf rt-qpcr
A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.

PMID 19958498 · PMC2788387 · BMC genomics · 2009 · 8 claims · 4 setups

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Comparative homology modeling of wild-type and mutant α-mannosidase across human, cow, cat and guinea pig reveals a significant correlation between genotype severity and phenotype severity in α-mannosidosis

lysosomal full-length pro-peptide bovine homology sequence weblogo

Experiments

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

Empirical codon substitution matrix.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

Assessing the gene space in draft genomes.

IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

Structural evolution of the protein kinase-like superfamily.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.