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).

• Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

  PMID 16093549 · PMC1184218 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Created the Mammalian Orthologous Intron Database (MOID) containing orthologous introns of human, mouse and rat identified via conserved reading-frame position

  introns ribosomal rrna comparative orthologous pairwise

• Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

  PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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  Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

  muscle-specific bovine refseq cardiac novo est blastn

• The EH1 motif in metazoan transcription factors.

  PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

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  There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

  homeobox-containing forkhead-containing complete combined meme hmm logistic

• In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

  PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

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  In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

  hmlh1 same cos-7 hela ese splice minigene

• A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

  PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

  orthologous randomized high-score promoters pssm-based comparative motif

• Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

  PMID 20008508 · PMC2836564 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Most TEs insert within specific 'hotspots' along the targeted TE rather than uniformly.

  genome sequences unique nested chi-square position-specific

• Computational identification of transcriptional regulatory elements in DNA sequence.

  PMID 16855295 · PMC1524905 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  Weight matrix (PWM/PSSM) models of TF binding sites are grounded in biophysical theory of protein-DNA interactions, with position weights corresponding to log-odds contributions to binding free energy

  saccharomyces generic pwm-based pwm

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk

• Ab initio identification of putative human transcription factor binding sites by comparative genomics.

  PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

  human-mouse conserved gene consensus comparative statistical gene

• NetworKIN: a resource for exploring cellular phosphorylation networks.

  PMID 17981841 · PMC2238868 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  NetworKIN integrates consensus substrate motifs with probabilistic network context modelling to predict cellular kinase-substrate relations.

  phosphoproteome kinome interactome 53bp1 consensus blastp probabilistic

• Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

  PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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  14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

  h3n2 meme sequence entropy

• In silico promoters: modelling of cis-regulatory context facilitates target predictio.

  PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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  An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

  serca2 rantes genes podocyte-associated literature-based promoter cross-referenced

• Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

  PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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  Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

  organisms cide cideb hmmer tblastn sequence

• The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements.

  PMID 18353860 · PMC2377421 · Nucleic acids research · 2008 · 7 claims · 1 setups

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  A large number of upstream PQSSs incorporate the SP1-binding element, establishing a clear link between PQSS occurrence and SP1 elements

  genome genome-wide

• Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

  PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

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  The human genome encodes at least 71 kelch-repeat proteins

  genome yeast kelch-repeat full-length blast blastp cross-referencing

• TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

  PMID 15608156 · PMC539958 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  TRED is a database collecting both cis-regulatory elements (promoters) and trans-regulatory elements (transcription factor binding/regulation data) with linked access.

  promoter tred-retrieved computational literature relational

• PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

  PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC

  homo peroxisomal bona eukaryotic annotation comparative sequence

• CRSD: a comprehensive web server for composite regulatory signature discovery.

  PMID 16845073 · PMC1538777 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  CRSD is a comprehensive web server integrating six large-scale databases (UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway, GO) plus two newly constructed genome-wide databases (MRS and TRS) for composite regulatory signature discovery

  gene 3'-utr promoter user-submitted genome-wide microrna binding

• Automated recognition of retroviral sequences in genomic data--RetroTector.

  PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

  reference genome chimpanzee red motif whole-genome simulated

• Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

  PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

  genome insect yy1-related zinc blast sequence synonymous