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 14

System / cell line: high ✕ Assay: blast ✕ Clear

Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

Has reproduction · 81

A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

lung sequencing assembled deer high-throughput metagenomic reference
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

sus pig concatenated three-species whole-genome repeat comparative
Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

embryonic high-quality unique m15e est sequence comparative
Having a BLAST with bioinformatics (and avoiding BLASTphemy).

PMID 11597340 · PMC138974 · Genome biology · 2001 · 8 claims · 4 setups

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BLAST is the most widely used tool for searching biological sequences for regions of local similarity

superfamilies blocks query pairwise phylogenetic sequence heuristic
Identification and characterization of insect-specific proteins by genome data analysis.

PMID 17407609 · PMC1852559 · BMC genomics · 2007 · 8 claims · 7 setups

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Comparative genome analysis across five holometabolous insects and three non-insect eukaryotes (opisthokonts) identifies 154 insect-specific orthologous groups (refined to 51 proteins) and 466 eukaryote/opisthokont-core orthologous groups

drosophila insect-core locusta insect-specific comparative est functional
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
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
Molecular archeology of L1 insertions in the human genome.

PMID 12372140 · PMC134481 · Genome biology · 2002 · 8 claims · 4 setups

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TSDfinder, a new algorithm, refines RepeatMasker-identified L1 boundaries by locating poly(A) tails, TSDs, and inversion breakpoints

genome tsd 50-nt full-length repeat sequence repeat-content
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

pcr candidate embl clinical snp manual homology
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

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PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

sequences query swiss-prot naive-bayes blast feature
GenBank.

PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

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GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

sapiens organisms genbank large-scale genome expressed blast
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

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An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

genomic gonystylus subset restriction-digested custom self-self blast
The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

PMID 16859552 · PMC1538596 · BMC genomics · 2006 · 7 claims · 7 setups

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Numts co-amplified with mtDNA during PCR generate false heteroplasmic signals at specific nucleotide positions.

143b ffpe blood cloned southern pcr rt-pcr
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race

Experiments

Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

Having a BLAST with bioinformatics (and avoiding BLASTphemy).

Identification and characterization of insect-specific proteins by genome data analysis.

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

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Molecular archeology of L1 insertions in the human genome.

Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

GenBank.

Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.