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).

• Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.

  PMID 17517773 · PMC1920257 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  An endonuclease-independent pathway (NCLI) for L1 insertion has been active in recent human genome evolution

  genome chimpanzee genomic pcr computational triple pcr

• Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

  PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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  Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

  genes autosomes dog genome comparative blat sliding-window

• Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

  PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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  Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

  genome poly est cdna est blast cdna

• COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.

  PMID 19958500 · PMC2788389 · BMC genomics · 2009 · 8 claims · 6 setups

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  COMUS is a bioinformatics system for detecting and depositing new mutations from patient DNA with a clinician-friendly interface

  ab1 fasta mutation hemophilia base-calling sequence known-variant

• Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

  PMID 11870543 · PMC2375272 · British journal of cancer · 2002 · 8 claims · 5 setups

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  DFFA is localized within the 1p36.2-3 smallest region of overlap (SRO) of deletions defined in Scandinavian neuroblastoma tumours, distal to marker D1S244

  scandinavian chromosome unfinished neuroblastoma pcr bac-library in-silico

• GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

  PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

  transcriptome genome spliced transcripts est genomic splice-orientation

• The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS.

  PMID 18522722 · PMC2447851 · BMC genomics · 2008 · 8 claims · 4 setups

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  A consensus Reference Human NumtS compilation (RHNumtS) was produced by comparing Blastn, MegaBlast and BLAT results with previously published compilations.

  genome genomic blastn megablast blat

• Recent segmental and gene duplications in the mouse genome.

  PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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  33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

  genome gene ensembl-annotated chromosome pairwise gene blat

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

  PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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  High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

  lncap lncap-derived r1881-treated massively blast blat

• Genomic characterization of five deletions in the LDL receptor gene in Danish Familial Hypercholesterolemic subjects.

  PMID 16796766 · PMC1523332 · BMC medical genetics · 2006 · 7 claims · 5 setups

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  All five LDLR deletions are flanked by Alu elements, supporting unequal homologous recombination between Alu repeats as the causative mechanism

  genomic pcr-amplified ldlr blood long-range cycle diagnostic

• GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

  PMID 16698959 · PMC3303178 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  GREM enables genome-wide isolation and quantitative analysis of transcriptionally active (promoter-active) repetitive elements while excluding read-through transcript background

  testicular genomic coli grem rt-pcr race

• MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

  PMID 16381984 · PMC1347458 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  MPromDb is a novel database integrating experimentally supported gene promoters, TSS annotation, cis-regulatory elements, CpG islands, and ChIP-chip data with an integrated visualization interface.

  chip-chip sequence genbank

• CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.

  PMID 17981843 · PMC2238977 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  CTCF is the only identified trans-acting factor in vertebrates that confers enhancer-blocking insulator activity

  ohlsson ren zhao tissues chip-chip massive motif

• Widely variable endogenous retroviral methylation levels in human placenta.

  PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups

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  Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters

  term placenta genome bisulfite rt-pcr genome-wide

• hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

  PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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  hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

  mgc cloned orfs genome gateway orf blat

• 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

• An empirical study of choosing efficient discriminative seeds for oligonucleotide design.

  PMID 19958494 · PMC2788383 · BMC genomics · 2009 · 8 claims · 3 setups

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  The spaced seed is the most efficient discriminative seed for oligonucleotide design among the five algorithms tested.

  simulated pmoa nirs seed

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat

• NEIBank: genomics and bioinformatics resources for vision research.

  PMID 18648525 · PMC2480482 · Molecular vision · 2008 · 8 claims · 7 setups

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  NEIBank is an integrated genomics and bioinformatics resource for vision research, combining EST/cDNA clone data, SAGE expression data, and eye disease gene databases.

  dissected eye retina cdna est serial sequence