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).

• Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer.

  PMID 40145684 · PMC11948951 · Current protocols · 2025 · 6 claims · 5 setups

  Has reproduction · 90

  Streaming minimap2 alignment output directly into HLAminer via Unix pipe (-a stream mode) enables HLA class I and II allele prediction without storing bulky SAM alignment files on disk

  wgs

• Sequencing of human genomes with nanopore technology.

  PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups

  Has reproduction · 75

  A novel reference panel-free, read-based phasing algorithm substantially improves SNV calling accuracy over standard filtering in ONT data.

  na12878 ataxia-pancytopenia simulated whole-genome snv read-based

• Enhanced protein isoform characterization through long-read proteogenomics.

  PMID 35241129 · PMC8892804 · Genome biology · 2022 · 6 claims · 4 setups

  Has reproduction · 79

  A long-read proteogenomics pipeline integrating PacBio long-read RNA-seq with MS-based proteomics enhances isoform-resolved protein characterization

  jurkat jurkat-derived long-read transcript orf

• Telomere-to-telomere assembly of a complete human X chromosome.

  PMID 32663838 · PMC7484160 · Nature · 2020 · 8 claims · 8 setups

  Full-text index only

  Produced the first gapless, telomere-to-telomere assembly of a human chromosome (the X chromosome) using the CHM13 cell line

  chm13htert chm13 ultra-long-read pacbio linked-read

• Determination of complete chromosomal haplotypes by bulk DNA sequencing.

  PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups

  Has reproduction · 97

  A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts

  rpe-1 na12878 aneuploid linked-read hi-c bulk

• Nimbus: a design-driven analyses suite for amplicon-based NGS data.

  PMID 29538618 · PMC6084620 · Bioinformatics (Oxford, England) · 2018 · 7 claims · 5 setups

  Has reproduction · 64

  Nimbus tracks the source amplicon of reads throughout alignment and SNP/InDel calling

  blood na15510 twin haloplex haloplex spiked-in humanexome-12

• Cell fixation and preservation for droplet-based single-cell transcriptomics.

  PMID 28526029 · PMC5438562 · BMC biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  Methanol fixation stabilizes and preserves dissociated cells for weeks without compromising single-cell RNA-seq data quality

  hek293 dissociated facs-sorted hek drop-seq bulk trizol

• Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.

  PMID 29221171 · PMC5707065 · Oncotarget · 2017 · 8 claims · 6 setups

  Has reproduction · 73

  A customised SAAV peptide database built from RNA-seq/WGS variant calls can be used to search proteomics data and detect single amino acid variant (SAAV)-containing peptides at the protein level

  jurkat rna-seq genome proteomics

• Statistical framework for calling allelic imbalance in high-throughput sequencing data.

  PMID 39966391 · PMC11836314 · Nature communications · 2025 · 8 claims · 6 setups

  Has reproduction · 89

  MIXALIME is a versatile computational framework for calling allele-specific variants (ASVs) from diverse high-throughput omics data

  wa01 left heart chip-seq rna-seq cage-seq

• Landscape of allele-specific transcription factor binding in the human genome.

  PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 82

  A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.

  gtrd k562 mcf7 types chip-seq variant bayesian

• Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

  PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

  lncap lncap-derived r1881-treated massively blast blat

• GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.

  PMID 36321867 · PMC9805576 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

  Has reproduction · 67

  GAVISUNK is an open-source pipeline that validates phased diploid HiFi assemblies by assessing concordance of inter-SUNK distances against orthogonal Oxford Nanopore (ONT) reads.

  chm13 chm1 hg02723 genome sunk haplotype

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.

  PMID 37444556 · PMC10340377 · Cancers · 2023 · 8 claims · 6 setups

  Has reproduction · 90

  EV extraction methods vary in reproducibility for isolating small RNAs, with effects on small RNA composition

  evs matched plasma cell-line small differential adapter

• Calibration-free NGS quantitation of mutations below 0.01% VAF.

  PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 96

  QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation

  h37rv repository healthy same single-plex 10-plex 22-plex

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Bayesian transcriptome assembly.

  PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.

  k562 embryonic dendritic rna-seq simulated paired-end long-read

• Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.

  PMID 34103501 · PMC8187371 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 99

  Existing Nanopore methylation detection tools present a tradeoff between false positives and false negatives and show high dispersion relative to expected methylation frequency values.

  coli individual lymphoblastoid na12878 nanopore per-read consensus

• MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

  PMID 29901703 · PMC6025204 · GigaScience · 2018 · 8 claims · 7 setups

  Has reproduction · 95

  The MetaMap pipeline recapitulates known infection agents in bona fide dual RNA-seq validation studies (Salmonella, HPV, HSV, rhinovirus)

  hela tumor lymphoblast rna-seq dual blastn-based