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).

• Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

  PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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  Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

  pooled computational identified additional label-free lspad pathway-associated

• Target SNP selection in complex disease association studies.

  PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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  A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

  genes pooled primer computational maldi-tof blast

• Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.

  PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups

  Has reproduction · 64

  A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs

  peripheral genome blood bulk illumina ion

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• Non-EST based prediction of exon skipping and intron retention events using Pfam information.

  PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

  refseq dbest genome pfam initio est comparative

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

  PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

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  SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

  independent ceph same unrelated snp individual simulated

• Translating genome sequences into biological understanding.

  PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups

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  Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.

  embryonic transfectable drosophila computational gene-trap pooled cross-species

• PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

  PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

  individually reference equimolar independently snp reference pooled

• Identification of serum biomarkers for colon cancer by proteomic analysis.

  PMID 16755300 · PMC2361335 · British journal of cancer · 2006 · 8 claims · 8 setups

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  Complement C3a des-arg, α1-antitrypsin and transferrin were identified as serum proteins with diagnostic potential for CRC.

  serum pooled seldi seldi-tof seldi artificial

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

  PMID 19936259 · PMC2775948 · PloS one · 2009 · 8 claims · 8 setups

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  Integrated proteomic analysis of a cancer mouse model and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  k-ras ovarian lists tumor quantitative pathway immunoblot

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• Science review: searching for gene candidates in acute lung injury.

  PMID 15566614 · PMC1065043 · Critical care (London, England) · 2004 · 8 claims · 8 setups

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  The candidate gene approach combined with an ortholog gene database and gene ontology analysis identifies ALI candidate genes, with blood coagulation and inflammation ontologies most highly represented

  lung canine pulmonary alveolar microarray gene immunoassay

• A DNA microarray survey of gene expression in normal human tissues.

  PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

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  Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

  normal common computational each two-color comparative unsupervised

• Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays.

  PMID 17430969 · PMC1888820 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Developed an LPE-based error-pooling and weighted ANOVA modeling approach for statistical analysis of high-density tiling array data

  cell-cycle-synchronized hela computational differentially tiling cdna statistical

• Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

  PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

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  DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

  standard dsic-labeled immunodepleted serum labeling quantitative in-solution

• A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

  PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups

  Has reproduction · 69

  Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.

  mus chuniphyes hormiphora pleuromamma rna-seq homology

• Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

  PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

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  42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

  genomic metaphase computational array-cgh fish real-time