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).

• StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

  PMID 24627795 · PMC3938176 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 43

  StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics, backed by an SQL (MySQL) database with Perl and Java APIs.

  fastq mysql perl java fastqc relational programmatic

• Gene Expression Analysis Platform (GEAP): A highly customizable, fast, versatile and ready-to-use microarray analysis platform.

  PMID 34927664 · PMC8754388 · Genetics and molecular biology · 2021 · 8 claims · 2 setups

  Has reproduction · 83

  GEAP is a GUI-based microarray analysis platform combining a C# front-end with an R (RTerm) back-end via the rgeap package, enabling analysis independent of manufacturer/platform.

  sqlite microarray software microarray

• GenePING: secure, scalable management of personal genomic data.

  PMID 16638151 · PMC1524750 · BMC genomics · 2006 · 8 claims · 2 setups

  Full-text index only

  GenePING extends the PING personal health record system to securely store and efficiently share large genome-sized datasets

  geneping threat computational

• Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

  PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups

  Full-text index only

  Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.

  serum aqueous maldi-tof seldi-tof peak

• GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

  PMID 35501696 · PMC9063052 · BMC bioinformatics · 2022 · 6 claims · 3 setups

  Has reproduction · 67

  GEMmaker, an nf-core compliant Nextflow workflow, can quantify gene expression from small to massive RNA-seq datasets while remaining reproducible via versioned containerized software.

  oryza arabidopsis generic rna-seq workflow

• Energy, power, and infrastructure demands from electrifying airport ground support equipment at United States airports.

  PMID 41912553 · PMC13199391 · Nature communications · 2026 · 8 claims · 4 setups

  Has reproduction · 95

  Electrifying major GSE at U.S. airports can significantly increase grid power and energy demand, with peak power at large airports reaching up to 20 MW and annual consumption approaching 51,000 MWh.

  major egse u.s agent-based charging flight

• KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.

  PMID 36430895 · PMC9694301 · International journal of molecular sciences · 2022 · 8 claims · 6 setups

  Has reproduction · 57

  KARAJ automates end-to-end querying and downloading of genomic/transcriptomic sequence data from a list of PMCIDs, URLs, or accession numbers

  fastq gse126379 research sequence download parallel literature

• Compression of structured high-throughput sequencing data.

  PMID 24260313 · PMC3832420 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 43

  Leveraging an explicit data schema (separate field encoding, field modeling, template compression, domain modeling) enables stronger compression of HTS alignment data than general-purpose compression of serialized bytes.

  benchmark ten rna-seq exome genome

• Obesity genes: so close and yet so far..

  PMID 19046411 · PMC2776388 · Journal of biology · 2008 · 8 claims · 7 setups

  Full-text index only

  GWA studies have confirmed only a few obesity-associated loci (INSIG2, FTO, MC4R) so far, each with modest individual effects on BMI

  population drosophila founder genome-wide candidate-region candidate

• Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

  PMID 20031542 · PMC3097376 · Circulation. Cardiovascular genetics · 2008 · 7 claims · 8 setups

  Full-text index only

  Rare Mendelian mutations (e.g., in sarcomere genes, ion channels, FBN1, LMNA) cause specific rare cardiovascular conditions (hypertrophic/dilated cardiomyopathy, long-QT syndrome, thoracic aortic aneurysm, progeria) but explain little of common CVD risk.

  community-based subjects dallas mice exon community-based gene

• 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

  Full-text index only

  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.

  laboratory institutional breast pluripotent ram cpu storage

• TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

  PMID 15608156 · PMC539958 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  TRED is a database collecting both cis-regulatory elements (promoters) and trans-regulatory elements (transcription factor binding/regulation data) with linked access.

  promoter tred-retrieved computational literature relational

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read

• Familial parkinsonism: study of original Sagamihara PARK8 (I2020T) kindred with variable clinicopathologic outcomes.

  PMID 18804399 · PMC2702757 · Parkinsonism & related disorders · 2009 · 6 claims · 4 setups

  Full-text index only

  The same LRRK2 I2020T mutation can produce diverse neuropathologies (pure nigral degeneration, Lewy body pathology, or MSA-P) even when clinical presentation and PET findings are virtually identical across family members.

  living post-mortem pet neuropathologic immunohistochemistry

• Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

  PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

  Full-text index only

  BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

  serum-derived tumour serum ht29 arms sanger topo

• Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

  PMID 19859549 · PMC2762604 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  A comprehensive platelet proteome of 1507 unique proteins was identified from ten independent human platelet samples, the most comprehensive platelet proteome assembled to date

  platelets platelet anti-coagulated lc-ms phospho-proteomic membrane

• LMPD: LIPID MAPS proteome database.

  PMID 16381922 · PMC1347484 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  LMPD is an object-relational database of lipid-associated protein sequences and annotations, publicly available from the LIPID MAPS Consortium website.

  uniprot kegg in-house oracle9i kegg database enzyme

• Integromics: challenges in data integration.

  PMID 12186644 · PMC139396 · Genome biology · 2002 · 8 claims · 7 setups

  Full-text index only

  There is no simple solution to database integration in genomics/bioinformatics

  lines molecular gene monsanto high-throughput cluster-correlation microarray