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).

• A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

  PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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  Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

  unigene shuffled real genomes genome-wide alignment gene

• MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

  PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups

  Has reproduction · 50

  MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.

  bovine simulated cami trimming decontamination assembly

• Sequence similarity network reveals common ancestry of multidomain proteins.

  PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

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  Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

  curated complete well-studied sequence alignment domain

• Comprehensive benchmarking of large language models for RNA secondary structure prediction.

  PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

  Has reproduction · 88

  Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.

  archiveii bprna large-scale secondary cross-family self-supervised

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines.

  PMID 18005451 · PMC2216041 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Parepro, an SVM-based method integrating three attribute sets (RD, MI, IE) derived from evolutionary and residue-property information, predicts whether an nsSNP is deleterious or neutral.

  sequences target svm benchmark homology

• Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.

  PMID 19758467 · PMC2745585 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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  MutationTagger achieves 87% F-measure for the mutation retrieval task on a benchmark dataset

  pubmed uniprot five mutation gene sequence

• MACSIMS: multiple alignment of complete sequences information management system.

  PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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  MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

  balibase-derived sequences same query automatic database initio

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

  PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

  Has reproduction · 87

  TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

  testseta bprna-new ts-inter individual jaccard pca ensemble

• TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

  PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

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  TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

  scop-derived malt nr-70 scop profile-based dali remote

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 3 setups

  Has reproduction · 67

  PSPred-ALE, a deep learning predictor using a self-adaptive learning embedding algorithm, automatically extracts contextual sequence features and identifies SARS-CoV-2 phosphorylation sites without feature engineering.

  lung peptide same bulk deep traditional

• Macrel: antimicrobial peptide screening in genomes and metagenomes.

  PMID 33384902 · PMC7751412 · PeerJ · 2020 · 8 claims · 8 setups

  Has reproduction · 83

  Macrel is an end-to-end pipeline that predicts high-quality AMP candidates from peptides, contigs, or reads of (meta)genomes

  curated hemopi-1 xiao cd-hit random amp homology-aware

• Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.

  PMID 37243151 · PMC10224212 · Viruses · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  An exhaustive-search workflow can recover intra-host co-existing SARS-CoV-2 strains from the reference-genome read set (SRR11092062) that de Bruijn-graph assemblers discard.

  sars-cov-2 spike predicted california short-read read sequence

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript