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 8

System / cell line: filtered ✕ Assay: novo ✕ Clear

LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups

Has reproduction · 86

LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.

zymobiomics assembled assembler-generated novo reference-based contig
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.

PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups

Has reproduction · 91

De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads

whole-body cultripes expression-filtered bulk novo transcriptome
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

Has reproduction · 67

Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

anas duck million random illumina read novo
Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens.

PMID 19906940 · PMC2885759 · The Journal of general virology · 2010 · 8 claims · 5 setups

Full-text index only

Both PCR sequencing and IGA sequencing (via de novo assembly guiding reference-dependent assembly plus PCR finishing) can successfully generate complete HCMV genome sequences from infected cell cultures and clinical specimens

hcmv six pcr illumina reference-dependent
Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle.

PMID 32523568 · PMC7261829 · Frontiers in microbiology · 2020 · 6 claims · 6 setups

Has reproduction · 97

Photosynthesis-related and translational transcripts are upregulated at midday (high light) compared to night/darkness in the pond microeukaryotic community

microeukaryotic phytoplankton pond filtered metatranscriptomics accessory situ
Experimental identification and in silico prediction of bacterivory in green algae.

PMID 33649548 · PMC8245530 · The ISME journal · 2021 · 7 claims · 6 setups

Has reproduction · 93

Five prasinophyte strains (Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, Dolichomastix tenuilepis CCMP3274) ingest live fluorescently labeled bacteria, detected by microscopy and/or flow cytometry

prasinophyte same green pelagibaca flow epifluorescence gene-based
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

Full-text index only

Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

embryonic neural t-cells mm8 chip-seq chip-chip pwm
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

Experiments

LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens.

Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle.

Experimental identification and in silico prediction of bacterivory in green algae.

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

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.