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).

• High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

  PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

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  High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

  tuberculosis sanger spectra lc-ms sds-page signal

• Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

  PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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  The IAB algorithm (integration of ANN and BLAST) identifies genome-wide specific oligos much faster than pure BLAST search while maintaining comparable success rate and cross homology

  tigr xanthomonas xcc ann wu-blast whole-genome

• Bases and spaces: resources on the web for accessing the draft human genome.

  PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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  By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

  bac whole-genome draft submitted bac radiation initio

• SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

  PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

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  Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

  genomic cdna known sequence homology transcript

• Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

  PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

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  3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

  arabidopsis phylogenetic tblastn subcellular

• Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

  PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

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  An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

  anopheles gambiae reanocds05 initio full-length rt-pcr

• Characterization of 954 bovine full-CDS cDNA sequences.

  PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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  954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

  bovine translated bflic sequence est primer-walking blastp

• ARED 3.0: the large and diverse AU-rich transcriptome.

  PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

  records est est-derived combined computational est sequence

• Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle.

  PMID 17362520 · PMC1839098 · BMC genomics · 2007 · 8 claims · 8 setups

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  The bovine BPI-like locus spans 470 kbp and contains 14 contiguous genes (13 intact + 1 pseudogene); 9 are orthologous to human/mouse BPI-like genes and 4 (named BSP30A, BSP30B, BSP30C, BSP30D) arose through cattle-specific duplication of the PSP gene

  bovine panel agresearch intact random gene northern