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).

• Critical care: applying genomics to inflammation outcomes.

  PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

  Full-text index only

  Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

  leukocytes whole-blood healthy peripheral genomewide whole-genome microarray

• The lords of the genomes.

  PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups

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  Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them

  drosophila cdna-derived saccharomyces acid reporter-gene enhancer chromatin

• Bioavailable Nutrients (N and P) and Precipitation Patterns Drive Cyanobacterial Blooms in Missisquoi Bay, Lake Champlain.

  PMID 34683418 · PMC8537112 · Microorganisms · 2021 · 8 claims · 8 setups

  Has reproduction · 67

  High concentrations of N and P were typically measured in April and May, before blooms occurred.

  water filtered lugol's-iodine-preserved 16s 16s nutrient situ

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

  mammary surgically normal single-cell whole-mount integration

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

  PMID 17217514 · PMC1780116 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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  A novel method combining 8-species comparative genomics with de novo motif discovery identifies human TF DNA-binding motifs overrepresented and conserved in upstream regions of co-regulated genes

  muscle-specific novo comparative

• Predictive genomics of cardioembolic stroke.

  PMID 19064790 · PMC2752697 · Stroke · 2009 · 8 claims · 4 setups

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  A Bayesian network multivariate model achieves 86% predictive accuracy (AUC) for cardioembolic stroke on fitted values

  blood-derived gasros same custom bayesian roc

• In silico promoters: modelling of cis-regulatory context facilitates target predictio.

  PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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  An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

  serca2 rantes genes podocyte-associated literature-based promoter cross-referenced

• Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.

  PMID 41813906 · PMC13022341 · Communications biology · 2026 · 8 claims · 7 setups

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  No evidence for recent HGT-mediated dissemination of ARGs across depth layers was detected, despite genetic compatibility among co-occurring bacteria.

  stratified freshwater predicted arg-carrying depth-resolved horizontal arg

• Genomic data sampling and its effect on classification performance assessment.

  PMID 12553886 · PMC149349 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  Cross-validation, leave-one-out, and bootstrap are designed to reduce bias and variance in accuracy estimation from small samples.

  leukemia srbct splice-junction supervised

• X-linked severe combined immunodeficiency syndrome: the first Korean case with gamma c chain gene mutation and subsequent genetic counseling.

  PMID 14966353 · PMC2822247 · Journal of Korean medical science · 2004 · 8 claims · 7 setups

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  The patient's X-SCID is caused by a C690T point mutation in exon 5 of the γc chain gene, producing an R226C amino acid substitution.

  pbmcs mother serum fetal flow direct pcr-rflp

• Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

  PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

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  The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

  dbsnp best-hit omicia hgmd genome-wide correlation disease

• PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.

  PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 7 claims · 6 setups

  Has reproduction · 75

  The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival

  pbmcs sorted expanded cancer multiparameter receptor targeted

• TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

  PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 60

  TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.

  mmetsp query putative ciliate taxonomic similarity non-coding

• The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

  PMID 19912342 · PMC2868947 · FEMS immunology and medical microbiology · 2010 · 7 claims · 5 setups

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  The types of vaginal bacterial communities found in Japanese women closely resemble those previously found in White and Black North American women.

  vaginal japanese t-rflp clone cluster

• The application of genomics to emerging zoonotic viral diseases.

  PMID 19855817 · PMC2734983 · PLoS pathogens · 2009 · 8 claims · 8 setups

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  High-throughput sequencing, mRNA expression profiling, and SNP microarray analysis enable rapid identification and genomic characterization of emerging zoonotic pathogens and host responses to them.

  siv-infected plasmacytoid migratory influenza transcriptional tlr fecal

• Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer.

  PMID 33729159 · PMC8012062 · eLife · 2021 · 8 claims · 7 setups

  Has reproduction · 94

  The SCLC regulatory network is multistable and its steady states map onto four experimentally observed phenotypes (ASCL1high/NEUROD1low, ASCL1low/NEUROD1high, ASCL1high/NEUROD1high, ASCL1low/NEUROD1low)

  sclc randomized ccle gse73160 boolean racipe network

• From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.

  PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 88

  Flower bud developmental stages (organogenesis, paradormancy, endodormancy, dormancy release, ecodormancy) are defined by distinct, stage-specific gene expression programs

  flower sweet sequencing differential principal