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).

• A genomics-based approach to biodefence preparedness.

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

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  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

• With the finished human genome in hand, what next?

  PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

  domestic saccharomyces systemic schistosoma comparative functional genetic

• Characterisation and protein expression profiling of annexins in colorectal cancer.

  PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

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  Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

  dukes colorectal immunised whole-cell gel immunohistochemistry elisa

• Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

  PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups

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  Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.

  blood schizophrenia sjl serum proteomic differential comparative

• Malaria research in the post-genomic era.

  PMID 18843360 · PMC2705782 · Nature · 2008 · 8 claims · 7 setups

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  Genome-dependent methods can partially substitute for forward genetic approaches that are unavailable or limited in malaria parasites.

  falciparum plasmodium malaria hela comparative two-hybrid proteomics

• Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

  PMID 20005973 · PMC2891339 · The international journal of biochemistry & cell biology · 2010 · 8 claims · 5 setups

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  CD45- splenic stem cell-specific proteins are identical to core iPS/ES markers OCT3/4, SOX2, KLF4, c-MYC and NANOG.

  spleen cd45 hox11+ lc-ms rt-pcr immunofluorescence

• The role of proteomics in depression research.

  PMID 19997739 · PMC2940035 · European archives of psychiatry and clinical neuroscience · 2010 · 8 claims · 8 setups

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  Proteomics offers a complementary, functional-endpoint approach that can elucidate MDD pathophysiological mechanisms and biomarkers beyond transcriptomic/targeted studies

  postmortem schizophrenia frontal hypothalamus gel shotgun proteome

• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

  PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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  Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

  gingivalis whole-cell comparative gene

• The secrets of a functional synapse--from a computational and experimental viewpoint.

  PMID 16723009 · PMC1810317 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  Kinesin motor proteins move cargo along axonal microtubules to the synapse, with cargo specificity determined by adaptor/linker proteins rather than lipid recognition

  mammalian kinesin cholinergic dendrites kinesin sequence-based comparative

• From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

  PMID 17983265 · PMC2062474 · PLoS computational biology · 2007 · 8 claims · 7 setups

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  There has been a large turnover of the mitochondrial proteome during evolution: cell envelope synthesis proteins virtually disappeared, and replication, transcription, cell division, transport, regulation, and signal transduction proteins were replaced by eukaryotic proteins

  alpha-proteobacterial reclinomonas reconstructed yeast comparative phylogenomic cog

• Proteomics of the lysosome.

  PMID 18977398 · PMC2684028 · Biochimica et biophysica acta · 2009 · 8 claims · 8 setups

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  The mammalian lysosome has been shown to contain ~60 soluble luminal proteins and ~25 transmembrane proteins

  liver placenta brain conditioned lc-ms n-terminal man6-p

• HUPO Highlights.

  PMID 19862759 · PMC4594800 · Proteomics · 2009 · 8 claims · 8 setups

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  Mass spectrometry analysis of human liver reference samples (French Reference liver + Huh7 hepatoma cells) achieves substantial human genome coverage via PeptideAtlas processing

  liver subcellular models fetal mass antibody-based quantitative

• Proteomics and genomics: perspectives on drug and target discovery.

  PMID 18302945 · PMC2386992 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

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  Protein kinases account for approximately 25% of research and development projects in biotechnology and pharma

  proteins blood carbohydrate medicinal x-ray microarrays glycan

• Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes.

  PMID 36345342 · PMC9636548 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Comparative phosphoproteomics of hyperammonemic myotubes and exercise-model muscle identifies shared enriched pathways: PKA, calcium signaling, MAPK signaling, and protein homeostasis.

  c2c12 hyperammonemic phosphoproteomics immunoblot comparative

• Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

  PMID 18939861 · PMC2669493 · Journal of proteome research · 2008 · 8 claims · 5 setups

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  IEF provides superior reproducibility and resolution of peptide fractionation compared to SCX, for both large (100 µg) and small (10 µg) protein inputs

  rko rectal bovine shotgun comparative ief

• Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

  PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups

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  P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential

  vivax genome comparative microsatellite

• Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

  PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

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  An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

  anopheles gambiae reanocds05 initio full-length rt-pcr

• Predicting FOX gene candidates for oxic nitrogen fixation using multi-omic machine learning and comparative bioinformatics.

  PMID 41764348 · PMC13056922 · Scientific reports · 2026 · 8 claims · 6 setups

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  Random Forest, XGBoost, and logistic regression classifiers can meaningfully differentiate literature-validated FOX genes from conserved non-essential genes, with Random Forest achieving the best ROC-AUC (~0.80)

  anabaena diazotrophic gene-level trained bulk quantitative transcription-start-site-derived

• Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).

  PMID 33793824 · PMC8136920 · The Plant cell · 2021 · 8 claims · 6 setups

  Has reproduction · 100

  Grad-seq resolves complexes with overlapping subunits, such as CpcG1-type versus CpcL-type phycobilisomes or PsaK1 versus PsaK2 photosystem I (pre)complexes, validating the approach.

  synechocystis gradient proteins grad-seq grad-seq denaturing sds-polyacrylamide

• Application of OMICS technologies in occupational and environmental health research; current status and projections.

  PMID 19933307 · PMC2910417 · Occupational and environmental medicine · 2010 · 8 claims · 6 setups

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  Five OMICS technologies are well established: genotyping, transcriptomics, epigenomics, proteomics, and metabolomics

  population genomic blood genome array-based comparative gene