ArticleGenome biology2021
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 46 citations in OpenAlex.
- A machine learning framework combining cfDNA fragmentomics and serum biomarkers for early ovarian cancer detection.Cell communication and signaling : CCS · 2026Article
- Factors Associated with Stage at Diagnosis in Pancreatic Cancer: Implications for Precision Screening and Early Detection.Biomedicines · 2026Review
- DREAM-Stellar: parallel and space efficient exact local alignment.BMC bioinformatics · 2026Article
- Zimin patterns in genomes.PLoS computational biology · 2026Article
- neomerDB: a comprehensive database of neomer biomarkers in cancer.Database : the journal of biological databases and curation · 2026Article
- Taxonomic quasi-primes: peptides charting lineage-specific adaptations and disease-relevant loci.Protein science : a publication of the Protein Society · 2025Article
- Leveraging sequences missing from the human genome to diagnose cancer.Communications medicine · 2025Article
- Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.Nature communications · 2025Article
- MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.BMC bioinformatics · 2025Article
- Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA.Bioinformatics (Oxford, England) · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Cellular Activity of CQWW Nullomer-Derived Peptides.ACS omega · 2025Article
- Identification of the shortest species-specific oligonucleotide sequences.Genome research · 2025Article
- Unraveling diversity by isolating peptide sequences specific to distinct taxonomic groups.bioRxiv : the preprint server for biology · 2025Article
- The topography of nullomer-emerging mutations and their relevance to human disease.Computational and structural biotechnology journal · 2025Article
- Investigating DNA words and their distributions across the tree of life.Computational and structural biotechnology journal · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.Computational and structural biotechnology journal · 2024Article
- Predicting Disease Progression in Inoperable Localized NSCLC Patients Using ctDNA Machine Learning Model.Cancer medicine · 2024Observational
- The fitness cost of spurious phosphorylation.The EMBO journal · 2024Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
Nullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be their having a detrimental impact on an organism.
resultsHere, we identify all possible nullomers and nullpeptides in the genomes and proteomes of thirty eukaryotes and demonstrate that a significant proportion of these sequences are under negative selection. We also identify nullomers that are unique to specific functional categories: coding sequences, exons, introns, 5'UTR, 3'UTR, promoters, and show that coding sequence and promoter nullomers are most likely to be selected against. By analyzing all protein sequences across the tree of life, we further identify 36,081 peptides up to six amino acids in length that do not exist in any known organism, termed primes. We next characterize all possible single base pair mutations that can lead to the appearance of a nullomer in the human genome, observing a significantly higher number of mutations than expected by chance for specific nullomer sequences in transposable elements, likely due to their suppression. We also annotate nullomers that appear due to naturally occurring variants and show that a subset of them can be used to distinguish between different human populations. Analysis of nullomers and nullpeptides across vertebrate evolution shows they can also be used as phylogenetic classifiers.
conclusionsWe provide a catalog of nullomers and nullpeptides in distinct functional categories, develop methods to systematically study them, and highlight the use of variability in these sequences in other analyses.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.