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).

• Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

  PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

  Full-text index only

  Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

  pediatric same oligonucleotide quantitative

• Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

  PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

  proteins cdc candidate yersinia all-against-all computational cross-species

• Web-based resources for comparative genomics.

  PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

  yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood

• The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

  PMID 20052305 · PMC2801442 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 6 setups

  Full-text index only

  The Mammalian Phenotype (MP) Ontology enables classification and organization of phenotypic data for mouse and other mammalian species in a computationally useful, standardized manner.

  genotypes neural inbred viable phenotype phylogenetic comparative

• Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

  PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

  Full-text index only

  Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

  tumor-derived tumor lash gene cytotoxicity sirna ribozyme

• Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

  PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

  Full-text index only

  Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

  fresh-frozen same banked resected array mutational pcr

• Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

  PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

  Full-text index only

  Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

  liver chimpanzee h-invitational tar genome blastn secondary

• Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

  PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

  Full-text index only

  Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

  yeast familial human-mouse comparative gene mutation

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

  Full-text index only

  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features.

  PMID 18769486 · PMC2518524 · PloS one · 2008 · 8 claims · 4 setups

  Full-text index only

  Unsupervised clustering of expression profiles from 62 medulloblastomas identifies 5 molecular subtypes (A–E)

  relapsed medulloblastoma independent expression array targeted

• Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

  PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

  Full-text index only

  PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

  rt4d6 gst-sox10 microarray comparative real

• Adaptive history of single copy genes highly expressed in the term human placenta.

  PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

  term single same lists microarray comparative site

• Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

  PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

  Full-text index only

  Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

  lms independent soft gene array immunohistochemistry

• High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

  PMID 19648524 · PMC4648268 · The European respiratory journal · 2009 · 8 claims · 8 setups

  Full-text index only

  High-throughput -omics technologies have revolutionised understanding of lung cancer biology and hold promise for personalised management of lung cancer

  tumour serum nsclc comparative snp methylation

• SEMdag: Fast learning of Directed Acyclic Graphs via node or layer ordering.

  PMID 39775401 · PMC11709272 · PloS one · 2025 · 8 claims · 5 setups

  Has reproduction · 81

  SEMdag() is a two-step order-based algorithm for fast learning of high-dimensional linear SEMs, using knowledge-based (KB) or data-driven bottom-up (BU) node/layer ordering followed by penalized (L1) DAG estimation

  amyotrophic breast coronavirus st-elevation rna-seq comparative

• Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.

  PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups

  Has reproduction · 67

  Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies

  frugiperda satellite million contigs comparative homology divergence

• Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.

  PMID 35862823 · PMC9426513 · mSystems · 2022 · 8 claims · 5 setups

  Has reproduction · 56

  The vast majority of recovered gene cluster families (GCFs) in sponge microbiomes show no similarity to any characterized BGC, revealing extreme biosynthetic novelty

  microbiomes sponge shotgun nonpareil 16s

• The post-genomic era for a select few.

  PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

  takifugu physcomitrella coli vibrio comparative genetic dna-microarray

• A genomics-based approach to biodefence preparedness.

  PMID 14708013 · PMC7097618 · Nature reviews. Genetics · 2004 · 7 claims · 8 setups

  Full-text index only

  Genome sequence data are now available for essentially all 25-30 principal human bacterial pathogens, including most CDC category A-C bioterror agents

  bacillus brucella neisseria gastric comparative transcriptome two-dimensional

• Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

  PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

  orthologous diverse tissues gene comparative est microarray