ReviewNature reviews. Genetics2023
Navigating bottlenecks and trade-offs in genomic data analysis.
Review in Nature reviews. Genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Machine Learning Approaches for Microorganism Identification, Virulence Assessment, and Antimicrobial Susceptibility Evaluation Using DNA Sequencing Methods: A Systematic Review.Molecular biotechnology · 2025Pooled it
- PPGLomics: an interactive platform for pheochromocytoma and paraganglioma transcriptomics.Endocrine-related cancer · 2026Article
- Transforming routine solid tumor profiling with automated next-generation sequencing: experience from a reference general hospital.Virchows Archiv : an international journal of pathology · 2026Article
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Specialized Metabolic Reprogramming in Plant Immunity: Biosynthetic Networks, Spatiotemporal Regulation, and Quantitative Defense.Plants (Basel, Switzerland) · 2026Review
- bronko: ultrafast, alignment-free detection of viral genome variation.bioRxiv : the preprint server for biology · 2026Article
- PPGLomics: An Interactive Platform for Pheochromocytoma and Paraganglioma Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- A Novel Paradigm for Targeting Challenging Targets: Advancing Technologies and Future Directions of Molecular Glue Degraders.Molecules (Basel, Switzerland) · 2026Review
- Utilisation of Machine Learning Approaches Improves RNA-Seq Transcriptome Analyses in Alzheimer's Disease Brain.Journal of molecular neuroscience : MN · 2026Article
- ACmix-Swin Deep Learning of 4-Day-OldGenes · 2025Article
- MTBseq-nf: Enabling Scalable Tuberculosis Genomics "Big Data" Analysis Through a User-Friendly Nextflow Wrapper for MTBseq Pipeline.Microorganisms · 2025Article
- SPDEv3.0: A Swiss Army knife for plant genomics and breeding analysis.Plant physiology · 2025Article
- Rapid species-level metagenome profiling and containment estimation with sylph.Nature biotechnology · 2025Article
- Reassessing the promise of NGS in sepsis diagnosis: overcoming scalability barriers.Future microbiology · 2025Article
- Pytrf: a python package for finding tandem repeats from genomic sequences.BMC bioinformatics · 2025Article
- gymnotoa-db: a database and application to optimize functional annotation in gymnosperms.Database : the journal of biological databases and curation · 2025Article
- Advancing neonatal health: the promise and challenges of universal genome sequencing in newborn screening.Pediatric research · 2025Article
- Genomic privacy and security in the era of artificial intelligence and quantum computing.Discover computing · 2025Review
- Rapid whole genome sequencing in newborn screening for metabolic diseases.Frontiers in pediatrics · 2025Review
- A comprehensive comparison of tools for fitting mutational signatures.Nature communications · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Genome sequencing and analysis allow researchers to decode the functional information hidden in DNA sequences as well as to study cell to cell variation within a cell population. Traditionally, the primary bottleneck in genomic analysis pipelines has been the sequencing itself, which has been much more expensive than the computational analyses that follow. However, an important consequence of the continued drive to expand the throughput of sequencing platforms at lower cost is that often the analytical pipelines are struggling to keep up with the sheer amount of raw data produced. Computational cost and efficiency have thus become of ever increasing importance. Recent methodological advances, such as data sketching, accelerators and domain-specific libraries/languages, promise to address these modern computational challenges. However, despite being more efficient, these innovations come with a new set of trade-offs, both expected, such as accuracy versus memory and expense versus time, and more subtle, including the human expertise needed to use non-standard programming interfaces and set up complex infrastructure. In this Review, we discuss how to navigate these new methodological advances and their trade-offs.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.