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).
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Genome informatics: taming the avalanche of genomic data.
PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups
Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown
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Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.
PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups
GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.
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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
PMID 15608248 · PMC539979 · Nucleic acids research · 2005 · 7 claims · 5 setups
RefSeq provides a curated, non-redundant, explicitly linked collection of genomic, transcript and protein sequences spanning prokaryotes, eukaryotes and viruses.
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The truth about mouse, human, worms and yeast.
PMID 15601543 · PMC3525071 · Human genomics · 2004 · 8 claims · 8 setups
Comparing genomes in pairs or larger sets (mouse-human, C. elegans-C. briggsae, multiple Saccharomyces, human-pufferfish, etc.) reveals unsuspected genes and helps eliminate false-positive gene predictions
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Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.
PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups
eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs
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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
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.
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Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.
PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups
Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.
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Developments in CORG: a gene-centric comparative genomics resource.
PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups
CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.
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Dcode.org anthology of comparative genomic tools.
PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups
The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.
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Multiple whole genome alignments and novel biomedical applications at the VISTA portal.
PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups
A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome
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Web-based resources for comparative genomics.
PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups
Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics
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The DNA sequence and analysis of human chromosome 13.
PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups
95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.
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Sequence variation in the human transcription factor gene POU5F1.
PMID 18254969 · PMC2275747 · BMC genetics · 2008 · 7 claims · 5 setups
POU5F1 is highly polymorphic, with a higher polymorphism density than most genes
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Of rats and men.
PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups
The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)
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Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.
PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups
Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR
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PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.
PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups
PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences
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The UCSC Genome Browser Database: update 2006.
PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups
The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.