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).

• MEROPS: the peptidase database.

  PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

  archaean holotype c-x-c proteins comparative domain substrate

• Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.

  PMID 19063745 · PMC2613935 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  Gene Prospector is a Web-based application that selects and prioritizes potential disease-related genes using a curated, updated literature database of genetic association studies

  huge pdgene snps3d dbsnp curated comparative snp

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

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  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

  PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.

  complete genome escherichia environmental comparative pathway local

• EGASP: Introduction.

  PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups

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  Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.

  genome computational manual rt-pcr

• The dystrobrevin-binding protein 1 gene: features and networks.

  PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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  DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

  vertebrate dtnbp1 comparative cross-species molecular

• AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.

  PMID 17135205 · PMC1781224 · Nucleic acids research · 2007 · 7 claims · 3 setups

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  AnimalQTLdb houses publicly available QTL data for multiple livestock species (pig, cattle, chicken) in one comparable database.

  pig cattle blast comparative database

• Integrating alternative splicing detection into gene prediction.

  PMID 15705189 · PMC550657 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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  An integrative intrinsic/extrinsic method was implemented in the gene finder EuGÈNE (as EuGÈNE-M) to detect AS evidence from aligned transcripts and generate alternative optimal gene predictions consistent with each detected AS event.

  arabidopsis araset thaliana transcript-to-genome initio comparative

• The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

  PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

  genome drosophila transfac b99 profile sequence case-study

• How many human genes can be defined as housekeeping with current expression data?

  PMID 18416810 · PMC2396180 · BMC genomics · 2008 · 8 claims · 4 setups

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  Current EST and microarray transcriptome sampling is far from saturated, limiting gene detectability and understanding of tissue-specific expression

  tissues genes est microarray comparative

• Undergraduate research. Genomics Education Partnership.

  PMID 18974335 · PMC2953277 · Science (New York, N.Y.) · 2008 · 6 claims · 4 setups

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  A course-embedded, multi-institution undergraduate research model (the Genomics Education Partnership) can deliver authentic research experiences during the academic year rather than only in summer programs.

  drosophila dot undergraduate genomic gene comparative

• A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

  PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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  Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

  unigene shuffled real genomes genome-wide alignment gene

• Ensembl 2007.

  PMID 17148474 · PMC1761443 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Ensembl added 18 new chordate genomes this year, increasing total genomes available from 15 to 33, the largest yearly increase to date.

  low-coverage cow chicken genome genome standard customized