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 56

System / cell line: contig ✕ Assay: assembly ✕ Clear

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
A chromosome-level genome assembly of Plantago ovata.

PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 99

A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.

plantago ovata pacbio hi-c k-mer
A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups

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The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs

carp randomly zebrafish reciprocal sequence microarray
Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups

Has reproduction · 90

Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.

cephalopholis analysis next-generation pacbio ont
Comparative genomic analysis of three Leishmania species that cause diverse human disease.

PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

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L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species

infantum major braziliensis leishmania whole-genome comparative pcr
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
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

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Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

five cichlid pairwise lake low-coverage blastx multi-species
Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

PMID 9989976 · PMC2192941 · The Journal of experimental medicine · 1999 · 8 claims · 8 setups

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The Lps locus was fine-mapped to a 0.9-cM interval spanning a 1.7-Mb genomic contig on mouse chromosome 4.

c3h genomic bac multiple-tissue genetic yac direct
The DNA sequence and analysis of human chromosome 13.

PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

chromosome rpci-11 genomic comparative fluorescence
CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.

PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups

Has reproduction · 97

CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly

simulated wgs reference same novo blast-based k-mer
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

monocytogenes additional food j774 whole-genome comparative pcr
A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

pad phylogenetic est est-based
VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.

PMID 37129547 · PMC10191607 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 1 setups

Has reproduction · 83

VirPipe is a new bioinformatics pipeline for detecting viral genomes from Nanopore or Illumina sequencing input with streamlined installation and customization.

lung nanopore
DNA sequence and analysis of human chromosome 9.

PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

bac chromosome fibres chimpanzee clone-based restriction computational
Characterization of 954 bovine full-CDS cDNA sequences.

PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

bovine translated bflic sequence est primer-walking blastp
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr
The DNA sequence of the human X chromosome.

PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

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The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

pac selected chromosome clone-based shotgun comparative
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups

Has reproduction · 91

175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data

camellia sinensis small genome mirna
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

PMID 27832824 · PMC5105290 · Genome biology · 2016 · 7 claims · 7 setups

Has reproduction · 84

The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade the main plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

anoplophora glabripennis insect whole-genome genome orthology

Experiments

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

A chromosome-level genome assembly of Plantago ovata.

A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

Comparative genomic analysis of three Leishmania species that cause diverse human disease.

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

Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

The DNA sequence and analysis of human chromosome 13.

CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.

DNA sequence and analysis of human chromosome 9.

Characterization of 954 bovine full-CDS cDNA sequences.

Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

The DNA sequence of the human X chromosome.

Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.