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).

• Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

  PMID 41597744 · PMC12843639 · Microorganisms · 2026 · 7 claims · 8 setups

  Has reproduction · 95

  The complete 832,614 bp circular chromosome of the H. obsoletus-transmissible 'Ca. P. solani' 16SrXII-A strain POT was assembled and functionally reconstructed.

  catharanthus pacbio smrt pot experimental endpoint smrt

• Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

  PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

  genome functional registered omim comparative kendall's homology

• Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

  PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

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  Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

  coli cerevisiae comparative machine single-gene

• Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

  PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

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  Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

  bifidobacterium longum xbai-digested whole-genome base codon

• Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

  PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

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  MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

  genome tissues novo pairwise rt-pcr

• Comparing whole genomes using DNA microarrays.

  PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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  DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.

  genome saccharomyces mitochondrial sars array comparative resequencing

• Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

  PMID 19997482 · PMC2776985 · PLoS computational biology · 2009 · 7 claims · 4 setups

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  An ILP formulation of the Boolean pathway optimization problem fits phosphoproteomic data faster and more efficiently than the previously used genetic algorithm (GA) approach.

  hepg2 computational same bead-based integer comparative

• Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

  PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

  genome genomic kinase psi-blast comparative genscan

• A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

  PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

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  149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

  zebrafish sequence comparative cross-validation

• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

  PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

  genome random cd4+ six average mutual chip-seq

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• 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

• Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

  PMID 16204454 · PMC1243798 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  Cis-encoded natural antisense RNAs show striking preferential complementarity to 3′-UTRs of their target genes in human and mouse genomes

  human-mouse model genome-wide comparative computational

• EGASP: the human ENCODE Genome Annotation Assessment Project.

  PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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  Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

  encode computational manual rt-pcr

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.

  PMID 19073697 · PMC2632920 · Nucleic acids research · 2009 · 8 claims · 5 setups

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  Combining high protein-interaction network scores with significant PID-related GO terms identifies novel PID candidate genes

  immunome known protein-interaction gene comparative

• Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

  PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

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  A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

  macrophage hela vaccinia bacillus gene protein-protein comparative

• The flexible pocketome engine for structural chemogenomics.

  PMID 19727619 · PMC2975493 · Methods in molecular biology (Clifton, N.J.) · 2009 · 8 claims · 8 setups

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  A comprehensive structural Pocketome combined with ensemble docking enables de novo, structure-based prediction of ligand binding poses and activities for new proteins and new chemical scaffolds.

  pdb bacteriorhodopsin enr asn automated virtual energy-based

• Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.

  PMID 34576004 · PMC8466565 · International journal of molecular sciences · 2021 · 8 claims · 7 setups

  Has reproduction · 76

  Multiple partially or fully intron-spliced intermediates co-exist within an organelle, and both cis- and trans-splicing introns are spliced randomly (no fixed order), generating diverse intermediates.

  nymphaea liriodendron pacbio illumina strand-specific