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).

Publications 1.3k Datasets 392.5k Experiments 345

System / cell line: genome ✕ Assay: alignment ✕ Clear

Simple models of genomic variation in human SNP density.

PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

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Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

genome observed simulated genome hierarchical coalescent
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

genome h-invdb gene sets genome transcript-to-genome coding
Sequence context affects the rate of short insertions and deletions in flies and primates.

PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

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The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

chimpanzee simulans chimp primate comparative direct nucleotide
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

genome chimpanzee sult1a3 est blast-like comparative pairwise
Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

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Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

encode genome cdna-to-genome novo comparative
A macaque's-eye view of human insertions and deletions: differences in mechanisms.

PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups

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Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms

chimpanzee non-overlapping 1-mb 100-kb comparative regression kruskal-wallis
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

PMID 19043541 · PMC2580819 · PLoS computational biology · 2008 · 8 claims · 5 setups

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A general model-free methodological framework is proposed for reconstructing Contiguous Ancestral Regions (CARs) from conserved syntenies, generalizing prior computational and cytogenetic approaches

genome boreoeutherian ferungulate marker-presence whole-genome ancestral combinatorial
Designating eukaryotic orthology via processed transcription units.

PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

ortholog blat exon-intron blast-based
Searching for SNPs with cloud computing.

PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

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Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

han local short simulated whole-genome cloud
Long-range regulation is a major driving force in maintaining genome integrity.

PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups

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Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.

opossum genome comparative identification statistical
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
In silico meets in vivo.

PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups

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About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.

genome lines prokaryotic genomes genome genome-wide gene
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

PMID 16179648 · PMC1236720 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Deeply conserved human-zebrafish non-coding elements are enriched for in vivo cis-acting transcriptional regulatory activity.

ncbi genes zebrafish comparative annotation gfp
Systematic identification of pseudogenes through whole genome expression evidence profiling.

PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

genome ensembl vega celera spliced protein-to-genome pseudogene
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

genome vertebrate multi-species whole-genome conservation non-synonymous
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

genome full-length ~3x10^7 isoform whole-genome full-length polysome
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

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ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

genome animal aligned est genome-wide comparative est
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups

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PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences

sequences poly cdna trace pssm-based

Experiments

Simple models of genomic variation in human SNP density.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Sequence context affects the rate of short insertions and deletions in flies and primates.

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

Designating eukaryotic orthology via processed transcription units.

Searching for SNPs with cloud computing.

Long-range regulation is a major driving force in maintaining genome integrity.

Ensembl 2007.

In silico meets in vivo.

Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

Systematic identification of pseudogenes through whole genome expression evidence profiling.

Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.