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).

• BTW: a web server for Boltzmann time warping of gene expression time series.

  PMID 16845055 · PMC1538860 · Nucleic acids research · 2006 · 5 claims · 4 setups

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  Symmetric time warping distance is more flexible than Euclidean distance or correlation coefficient for identifying genes with similar temporal expression profiles, especially across sequences of different length.

  cerevisiae homologous yeast boltzmann histogram time

• Environmental genome project: a positive sequence of events.

  PMID 11171540 · PMC1242069 · Environmental health perspectives · 2001 · 8 claims · 5 setups

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  Exposure to alkylating agents evokes at least threefold expression changes in about one-third of the yeast genome (~2,000 genes), far beyond DNA repair genes alone

  yeast genes population microarray time-course resequencing

• Evaluation of classification and forecasting methods on time series gene expression data.

  PMID 33156855 · PMC7647064 · PloS one · 2020 · 6 claims · 3 setups

  Has reproduction · 74

  Deep learning based methods generally outperform traditional approaches for time series gene expression classification

  five gene microarray time

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental

• The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

  PMID 17145711 · PMC1751528 · Nucleic acids research · 2007 · 7 claims · 5 setups

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  GermOnline is a cross-species systems browser providing comprehensive curated information on genes and gene products relevant for sexual reproduction across nine model organisms including human.

  saccharomyces mus rodent classical tiling comparative

• Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.

  PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups

  Has reproduction · 68

  Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival.

  cerevisiae colony-forming-unit bulk pooled

• Visualization-based discovery and analysis of genomic aberrations in microarray data.

  PMID 15953389 · PMC1181623 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  ChARMView integrates dynamic visualization with automated statistical analysis (EM-based breakpoint detection, one-sample sign test, permutation mean test) to discover chromosomal aberrations from array CGH and gene expression data

  saccharomyces breast yeast array gene

• Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

  PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

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  RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

  yeast liver eight-node microarray k-means hybrid

• Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis.

  PMID 32762840 · PMC7413667 · eLife · 2020 · 8 claims · 8 setups

  Has reproduction · 81

  mRNA localization to mitochondria is condition-dependent: ATP3 mRNA switches from low (diffuse) association in fermentative conditions to strong mitochondrial association in respiratory conditions, while TIM50 is constitutively localized and TOM22 is diffuse.

  cerevisiae computational live-cell single-molecule single-cell

• Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments.

  PMID 18765474 · PMC2577354 · Nucleic acids research · 2008 · 6 claims · 6 setups

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  Extensive sonication reduces crosslinked chromatin to an average fragment size of ~200 bp (range 75–300 bp) and fragmentation is largely random with respect to genomic region and nucleosome position.

  cerevisiae hela chip-qpcr nucleosome gel

• Estimation of peptide elongation times from ribosome profiling spectra.

  PMID 33885812 · PMC8136808 · Nucleic acids research · 2021 · 8 claims · 3 setups

  Has reproduction · 76

  A maximum-likelihood model that separates context-dependent bias factors from elongation-time factors enables bias-corrected estimation of peptide elongation times at single-codon resolution from Ribo-Seq spectra.

  coli saccharomyces ribosome

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

  PMID 30899024 · PMC6428865 · Nature communications · 2019 · 7 claims · 8 setups

  Has reproduction · 85

  Xrn1 promotes translation of a specific group of mRNAs encoding membrane/secretome proteins, acting at translation initiation.

  cerevisiae yeast xrn1∆ western luciferase polysome

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

• Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

  PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 8 setups

  Has reproduction · 90

  Replacing the mitotic kleisin Scc1 with the meiotic kleisin Rec8 impairs sister chromosome cohesion, advances genome replication timing, and reduces reproductive fitness by 45%.

  cerevisiae parallel evolved rec8-expressing competitive experimental whole-genome

• Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

  PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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  Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

  homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular

• RNA modifications detection by comparative Nanopore direct RNA sequencing.

  PMID 34893601 · PMC8664944 · Nature communications · 2021 · 7 claims · 5 setups

  Has reproduction · 50

  Nanocompore is a model-free comparative method that uses a 2-component Gaussian mixture model (GMM) and univariate statistical tests on signal intensity/dwell time to detect RNA modifications in Nanopore direct RNA sequencing data without needing a training set

  simulated synthetic escherichia saccharomyces nanopore computational

• Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

  PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

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  MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

  kidney mdct tissues xenopus oligonucleotide northern real-time

• Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data.

  PMID 29420797 · PMC5961211 · Nucleic acids research · 2018 · 7 claims · 3 setups

  Has reproduction · 68

  Octopus-toolkit is a stand-alone application that automatically installs required tools and retrieves/processes public epigenomic and transcriptomic NGS data (ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq, RNA-seq) from GEO in a single step.

  mammary saccharomyces chip-seq rna-seq

• Microarray analysis: genome-scale hypothesis scanning.

  PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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  Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

  drosophila yeast diffuse breast microarray integrated gene