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).

• Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

  PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 5 setups

  Has reproduction

  Expression stability in CHO cell lines is controlled at three levels: choice of integration site, transgene integrity/concatemerization pattern, and stress-related cellular processes.

  horizon same cho genome rna-seq targeted

• Biocomputing enters its adolescence.

  PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

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  A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

  bank antibody-antigen yeast genome protein-protein empirical integrative

• Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection.

  PMID 16953805 · PMC1859983 · Cellular microbiology · 2007 · 7 claims · 8 setups

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  Ile-91 is the primary docking residue required for binding of all tested Nm and Hi strains to CEACAM1, despite structural diversity of bacterial ligands

  ceacam1 meningitidis influenzae ha3 homology site-directed receptor

• Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV V2 apex broadly neutralizing antibody development.

  PMID 41686912 · PMC13015429 · Science immunology · 2026 · 8 claims · 8 setups

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  Efficiency of B cell priming, not complexity of Env-guided affinity maturation, is the primary obstacle to V2 apex bNAb elicitation in SHIV-infected macaques.

  shiv-infected plasma igg+ rhesus plasma single-genome next-generation

• The nuclear pore complex.

  PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

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  NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

  xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a

• Evaluating deep learning based structure prediction methods on antibody-antigen complexes.

  PMID 41863324 · PMC13061134 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Increased sampling improves the chance of generating a correct antibody-antigen model in a roughly log-linear manner with sample size

  alphafold2.3 alphafold3 boltz-1 chai-1 complex structural

• The identification and characterization of a novel protein, c19orf10, in the synovium.

  PMID 17362502 · PMC1906808 · Arthritis research & therapy · 2007 · 8 claims · 8 setups

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  c19orf10 is a novel protein produced in significant amounts by fibroblast-like synoviocytes (FLSs), identified via proteomic analysis

  fibroblast-like coli balb chicken two-dimensional recombinant monoclonal

• Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

  PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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  Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

  families genes individuals kidney genome-wide sanger resequencing

• 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

• Endemic Venezuelan equine encephalitis in northern Peru.

  PMID 15200823 · PMC3323213 · Emerging infectious diseases · 2004 · 8 claims · 8 setups

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  Four VEE complex lineages cocirculate in the Peruvian Amazon region: subtype ID (Panama genotype and Colombia/Venezuela genotype), subtype IIIC, and a newly proposed subtype IIID

  veev pe2 subtype cotton sscp pcr phylogenetic

• Influenza A (H3N2) outbreak, Nepal.

  PMID 16102305 · PMC3320503 · Emerging infectious diseases · 2005 · 7 claims · 6 setups

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  Nepal H3N2 outbreak isolates show antigenic drift, with ~40% antigenically distinct from the A/Wyoming/3/03 vaccine strain by hemagglutination inhibition

  influenza throat ha1 amino hemagglutination rt-pcr rapid

• Integrated reiterative pipeline for rapid epitope-based pan-alphavirus vaccines.

  PMID 41811958 · PMC12978219 · Science advances · 2026 · 6 claims · 7 setups

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  An integrated pipeline combining ML-based epitope prediction (netMHCpan, EpiDope, BepiPred), TCRpMHC structural modeling/docking, and JessEV vaccine design can prioritize viral peptides by immunogenicity, allele coverage, solubility, and stability.

  preexposed alphaviral peptide-hla modeled peptide epitope structural

• Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.

  PMID 41674383 · PMC12895067 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  HNRNPU forms extensive protein networks including an association with the mammalian SWI/SNF chromatin-remodeling complex

  ipsc-derived computational neocortical ip-ms formaldehyde alphapulldown expression-weighted

• Assembling a jigsaw puzzle with 20,000 parts.

  PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups

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  Re-routing the intracellular interaction domains of receptor tyrosine kinases can redirect their signaling output, e.g. converting a growth signal into an apoptosis signal.

  yeast caenorhabditis escherichia proteome-wide microarray yeast rnai