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 29

System / cell line: chromosome ✕ Assay: classification ✕ Clear

Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups

Has reproduction · 91

A chromosome-level genome assembly of G. vermiculophylla was generated by combining DNBSeq short reads, Nanopore long reads, and Hi-C data.

gracilaria whole-genome nanopore hi-c
Recent segmental and gene duplications in the mouse genome.

PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

genome gene ensembl-annotated chromosome pairwise gene blat
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

pre-mirnas test conserved-hairpin cross-species secondary svm cross-species
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

chromosome dog macaque genomic comparative segmental
Genomic screen for loci associated with tobacco usage in Mission Indians.

PMID 16472381 · PMC1386651 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Regular tobacco use (h2=0.37±0.11) and persistent tobacco use (h2=0.34±0.12) are moderately heritable in this Mission Indian sample

mission pedigrees same participants genotyping multipoint heritability
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

PMID 17553836 · PMC1933124 · Nucleic acids research · 2007 · 8 claims · 8 setups

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A hybrid feature combining local contiguous triplet structure-sequence composition, MFE of the secondary structure, and P-value of a randomization test improves classification of real vs pseudo pre-miRNAs

real combined pre-mirna training random independent repeated
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
A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.

PMID 36028584 · PMC9418232 · Communications biology · 2022 · 8 claims · 8 setups

Has reproduction · 80

A high-quality chromosome-level genome assembly of C. oryzae was generated using PacBio, Illumina, and Hi-C sequencing

oryzae whole-genome genome orthology
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
Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.

PMID 18700039 · PMC2529317 · BMC genomics · 2008 · 8 claims · 6 setups

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Complete genome of P. zucineum HLK1T consists of a 3,996,255 bp circular chromosome and a 382,976 bp circular plasmid encoding 3,861 proteins, 42 tRNAs, and one 16S-23S-5S rRNA operon

phenylobacterium zucineum bacteria genome cog comparative
Vertebrate gene finding from multiple-species alignments using a two-level strategy.

PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

genomic encode entire chromosome multi-species hmm-based classifier
Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

PMID 18559093 · PMC2440550 · Molecular cancer · 2008 · 7 claims · 6 setups

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Gain of chromosome 5p is the most frequent genomic alteration in invasive cervical cancer

cervical tumors pap tumor snp fluorescence fish
Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

PMID 18551166 · PMC2396484 · PLoS computational biology · 2008 · 8 claims · 5 setups

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Y-STR allelic variability is partitioned more by differences among haplogroups than by differences among populations, suggesting Y-STRs carry haplogroup information

globally same computational publicly y-str snp supervised
Supervised learning-based tagSNP selection for genome-wide disease classifications.

PMID 18366619 · PMC2386071 · BMC genomics · 2008 · 7 claims · 2 setups

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SRFA (Supervised Recursive Feature Addition) is a novel feature selection method combining supervised learning and statistical redundancy measures for SNP selection

micc narac snp
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

genome chimpanzee sult1a3 est blast-like comparative pairwise
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
Ab initio identification of human microRNAs based on structure motifs.

PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

genome mirna hairpins chromosome secondary linear five-fold
Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies.

PMID 16899448 · PMC1557808 · Nucleic acids research · 2006 · 7 claims · 4 setups

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3D VizStruct (DFT-based radial mapping + KLD as z-axis) can identify SNPs/polymorphic markers that are predictive of underlying biological class distinctions across diverse datasets

lpl y-chromosome coral simulated snp aflp numerical
Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

PMID 18929582 · PMC2599865 · Mutation research · 2008 · 8 claims · 5 setups

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Overall MSY1 mutation frequencies in sperm (2.68%) and blood (1.88%) are not significantly different

sperm donor hgr1b3 single-molecule fluorescent radioactive
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

Experiments

Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

Recent segmental and gene duplications in the mouse genome.

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

Genomic screen for loci associated with tobacco usage in Mission Indians.

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

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

A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.

The DNA sequence and analysis of human chromosome 13.

Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562.

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

Supervised learning-based tagSNP selection for genome-wide disease classifications.

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

Ab initio identification of human microRNAs based on structure motifs.

Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies.

Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

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