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).

• Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage.

  PMID 41779826 · PMC12959883 · eLife · 2026 · 8 claims · 5 setups

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  DeepTX is an interpretable, scalable deep learning inference framework that links mechanistic transcription models to scRNA-seq data to infer genome-wide transcriptional burst kinetics

  synthetic embryonic colorectal computational stochastic scrna-seq deep

• ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

  PMID 16845044 · PMC1538898 · Nucleic acids research · 2006 · 8 claims · 2 setups

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  The ASPIC algorithm, using an optimization procedure that minimizes splice site predictions and transcript isoforms from multiple EST-genome alignments, outperforms other similar AS-prediction tools in sensitivity and selectivity

  hnrpr specified comparative algorithm

• htSNPer1.0: software for haplotype block partition and htSNPs selection.

  PMID 15740612 · PMC1274247 · BMC bioinformatics · 2005 · 6 claims · 1 setups

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  The GBB algorithm finds the globally optimal minimal htSNP set with far less computing time than exhaustive/enumeration search.

  chromosome haplotype

• Evolutionary algorithms for the selection of single nucleotide polymorphisms.

  PMID 12875658 · PMC183839 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  Evolutionary algorithms are well suited to multiobjective optimization problems with large, intractable search spaces such as SNP selection, unlike exact methods (exhaustive enumeration) or single-objective search techniques (tabu search, simulated annealing).

  simulated mhc evolutionary multiobjective

• SNP-RFLPing: restriction enzyme mining for SNPs in genomes.

  PMID 16503968 · PMC1386656 · BMC genomics · 2006 · 8 claims · 2 setups

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  SNP-RFLPing accepts three flexible input types (dbSNP rs#/ss# IDs, HUGO gene name/Entrez gene ID, or free-form SNP-in-sequence including IUPAC or [dNTP1/dNTP2] formats) for human, rat, and mouse genomes

  software existing string-matching feature

• A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

  PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 51

  An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73

  bladder tcga bulk univariate integrative

• DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

  PMID 41055236 · PMC12505516 · RNA biology · 2025 · 8 claims · 5 setups

  Has reproduction · 100

  DeepRNA-Reg, a recurrent neural network-based algorithm, provides a superior prediction set for differential HITS-CLIP analysis compared to dCLIP.

  dgcr8 mir-23 predicted ago2 gene flow

• Proteomics: characterizing the cogs in the machinery of life.

  PMID 14630521 · PMC1241753 · Environmental health perspectives · 2003 · 8 claims · 5 setups

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  Protein expression patterns in blood serum, detected via SELDI-TOF mass spectrometry and analyzed with a genetic algorithm, can distinguish ovarian cancer patients from healthy individuals with very high sensitivity and specificity.

  blood lung hemoglobin proteins seldi-tof proteome tandem

• A third approach to gene prediction suggests thousands of additional human transcribed regions.

  PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

  genome 4.4-mb known nucleotide repeat polyadenylation

• Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

  PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

  non-identical gene3d cath whole-gene domain transmembrane

• Analysis of sequence conservation at nucleotide resolution.

  PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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  SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

  encode population comparative snp functional

• Proteomics as a tool for biomarker discovery.

  PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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  A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

  serum laser ovarian seldi-tof two-dimensional gene

• The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

  PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

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  P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

  sequences orthomcl yeast orthomcl jaccard phylogenetic

• 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

• CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

  PMID 18950538 · PMC2605473 · BMC bioinformatics · 2008 · 7 claims · 4 setups

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  CompMoby identifies cis-regulatory binding sites at both transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factor

  embryonic hela novo genome-wide

• Efficient algorithms for probing the RNA mutation landscape.

  PMID 18688270 · PMC2475669 · PLoS computational biology · 2008 · 8 claims · 4 setups

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  RNAmutants generalizes McCaskill's partition function algorithm to sum over the grand canonical ensemble of all secondary structures of all k-point mutants, simultaneously computing MFE(k) and Z(k) for each k

  element hepatitis hiv utr partition deleterious mutation

• Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

  PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups

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  eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs

  drosophila caenorhabditis xenopus five pairwise evoprint comparison

• Dissecting microregulation of a master regulatory network.

  PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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  143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

  genome mirnas mirna-target predicted p53 mirna cross-referencing

• InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

  PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.

  eukaryotic homo sequence species pairwise algorithm low-complexity

• MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

  PMID 19850495 · PMC2818324 · Journal of the American Society for Mass Spectrometry · 2010 · 7 claims · 4 setups

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  MAZIE is a post-acquisition Perl algorithm that determines precursor ion monoisotopic mass and charge (+1 to +4) from MS1 zoom scan isotopic distributions on a Thermo LTQ-XL

  urine same lc-ms2 ms1 comparative