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).

• Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection.

  PMID 35072628 · PMC8887901 · eLife · 2022 · 8 claims · 3 setups

  Has reproduction · 57

  mRNA vaccination induces antibody binding to additional Spike epitopes (NTD and CTD in S1) beyond those seen after mild infection (FP and SH-H in S2)

  serum combined phage-dms principal

• Proteomics technologies and challenges.

  PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

  serum myeloid formalin-fixed general maldi-tof phage maldi

• Autoantibody profiling for the study and treatment of autoimmune disease.

  PMID 12223102 · PMC128938 · Arthritis research · 2002 · 8 claims · 8 setups

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  Custom-fabricated antigen microarrays (spotted on poly-L-lysine-coated glass slides) enable multiplex profiling of autoantibody responses in autoimmune disease sera.

  serum antigen-antibody antigens fetal spotted elisa microarray

• CD155/PVR plays a key role in cell motility during tumor cell invasion and migration.

  PMID 15471548 · PMC524493 · BMC cancer · 2004 · 8 claims · 8 setups

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  A FALI-coupled scFv antibody library screen identifies CD155 (poliovirus receptor) as a mediator of tumor cell invasion

  ht1080 u87mg normal 96-well transwell immunoblot

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

  PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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  A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

  pooled genome est novel tandem whole-genome est

• Molecular cloning and characterisation of the RESA gene, a marker of genetic diversity of Plasmodium falciparum.

  PMID 19816792 · PMC2900597 · Molecular biology reports · 2010 · 8 claims · 8 setups

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  RESA was cloned from a P. falciparum Dd2 expression library screened with human immune sera, yielding a 1,336 bp insert with a 936 bp ORF encoding a 317-aa protein.

  falciparum falciparum-infected coli sera cdna sequencing pcr

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read

• Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

  PMID 16840528 · PMC1524903 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  MS-PET, which dimerizes PETs prior to 454 multiplex sequencing, achieves an approximate 100-fold efficiency increase over standard Sanger-based PET analysis

  mcf7 hct116 flcdna gis-pet chip-pet quantitative

• Systematic elucidation of genetic mechanisms underlying cholesterol uptake.

  PMID 37228746 · PMC10203276 · Cell genomics · 2023 · 8 claims · 8 setups

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  Genome-scale CRISPR-Cas9 knockout screening in HepG2 cells identifies 490 genes whose disruption alters LDL-C uptake

  hepg2 depmap flow genome-scale individual

• 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

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

  lncap lncap-derived r1881-treated massively blast blat

• 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

• The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

  PMID 19855822 · PMC2752168 · PLoS genetics · 2009 · 8 claims · 8 setups

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  Reverse vaccinology (in silico genome screening for surface/secreted proteins) can identify vaccine candidates far faster than conventional approaches, as demonstrated by the MenB project.

  neisseria streptococcus coli vibrio reverse pan-genomic comparative

• Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

  PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

  rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact