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).
-
Full-text index only
Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.
PMID 19856998 · PMC2924679 · Journal of proteome research · 2009 · 7 claims · 4 setups
RCL2/CS100-fixed tissues yield peptide and protein identifications by nanoRPLC-MS/MS comparable to matched fresh-frozen tissues, with proteome coverage not obviously compromised by fixation.
-
Full-text index only
A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.
PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups
The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs
-
Full-text index only
An initial characterization of the serum phosphoproteome.
PMID 19824718 · PMC2789176 · Journal of proteome research · 2009 · 8 claims · 8 setups
A TiO2-based phosphopeptide enrichment method coupled with LC-MS/MS (LTQ-Orbitrap CID and LTQ-ETD) was developed and applied to characterize the serum phosphoproteome
-
Full-text index only
Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.
PMID 19803774 · PMC2893889 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 7 claims · 5 setups
Postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate.
-
Full-text index only
Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.
PMID 19794824 · PMC2753780 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 4 setups
141 protein spots are differentially expressed between normal rat sera and MCA-induced lung cancer rat sera (82 overexpressed, 59 underexpressed)
-
Full-text index only
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.
PMID 19758473 · PMC2745591 · BMC bioinformatics · 2009 · 8 claims · 8 setups
None of 39 tested structural properties can be used as a sole classification criterion to separate neutral SNPs from disease mutations.
-
Full-text index only
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.
PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups
2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)
-
Full-text index only
A survey of integral alpha-helical membrane proteins.
PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups
An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.
-
Full-text index only
Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.
PMID 19744353 · PMC2749023 · BMC medical genetics · 2009 · 8 claims · 6 setups
Gross mutations (exon deletions and intragenic insertions) are a frequent, not rare, cause of AOA2
-
Full-text index only
The promise and reality of personal genomics.
PMID 19723346 · PMC2768970 · Genome biology · 2009 · 7 claims · 6 setups
Despite being the most complete and accurate individually sequenced human genome to date, AK1 sequencing still misses a substantial fraction of variants, showing sequencing technology remains far from complete/reliable.
-
Full-text index only
Long-range regulation is a major driving force in maintaining genome integrity.
PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups
Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.
-
Full-text index only
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups
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.
-
Full-text index only
Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.
PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups
Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.
-
Full-text index only
Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.
PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups
The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information
-
Full-text index only
Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.
PMID 19650937 · PMC3224928 · Malaria journal · 2009 · 8 claims · 5 setups
Sequence group 1 (mainly from uncomplicated malaria) is significantly different in distribution from sequence group 3 (mainly from severe malaria)
-
Full-text index only
High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.
PMID 19648524 · PMC4648268 · The European respiratory journal · 2009 · 8 claims · 8 setups
High-throughput -omics technologies have revolutionised understanding of lung cancer biology and hold promise for personalised management of lung cancer
-
Full-text index only
PIK3CA alterations in Middle Eastern ovarian cancers.
PMID 19638206 · PMC2724395 · Molecular cancer · 2009 · 8 claims · 7 setups
PIK3CA gene amplification is frequent in Middle Eastern EOC, found in 54/152 (35.5%) cases
-
Full-text index only
Comparative transcriptome analysis of two pomelo accessions with different parthenocarpic ability provides insight into the molecular mechanisms of parthenocarpy in pomelo (Citrus grandis).
PMID 39135650 · PMC11317442 · Frontiers in plant science · 2024 · 6 claims · 6 setups
G pomelo exhibits significantly higher parthenocarpic ability (ovary growth, cell division, fruit setting) than S pomelo following emasculation
-
Full-text index only
Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.
PMID 41486154 · PMC12828970 · BMC bioinformatics · 2026 · 8 claims · 8 setups
Frag'n'Flow is a Nextflow-based pipeline that encapsulates FragPipe, automating manifest/workflow generation, tool dependency management, and downstream analysis for HPC/cloud/cluster environments.
-
Full-text index only
Alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing.
PMID 41631412 · PMC12885427 · mAbs · 2026 · 8 claims · 8 setups
alpseq is an open-source, end-to-end workflow combining a PCR-free sequencing library prep protocol with a Nextflow pre-processing pipeline and an R-based analysis/reporting module for nanobody NGS data.