Research map: Multi-Omics Integration in Clinical Practice for the Identification of Genetic Variants in Rare Diseases

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Papers in this map

  1. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology · Sue M. Richards · 2015 · 33500 citations · Cited by this paper
  2. Associations between Red Blood Cell Transfusions and Health-Related Outcomes in Older Adults with Hip Fractures: A Systematic Review with Meta-Analysis · 2026 · Related
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  5. A cross-platform toolkit for mass spectrometry and proteomics · Matthew Chambers · 2012 · 4464 citations · Cited by this paper
  6. Developmental Origins of Health and Disease: The role of Clostridioides difficile Colonization of Gut Microbiota During Infancy · 2027 · Related
  7. Nextflow enables reproducible computational workflows · Paolo Di Tommaso · 2017 · 4460 citations · Cited by this paper
  8. Molecular Prenatal Diagnosis of Monogenic Diseases, Towards Non-invasive Procedures · 2026 · Related
  9. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses · Christine Vogel · 2012 · 4360 citations · Cited by this paper
  10. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data · Tomáš Pluskal · 2010 · 4033 citations · Cited by this paper
  11. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput · Vadim Petrovich Demichev · 2019 · 3669 citations · Cited by this paper
  12. Metabolomics: beyond biomarkers and towards mechanisms · Caroline Helen Johnson · 2016 · 2910 citations · Cited by this paper
  13. DELLY: structural variant discovery by integrated paired-end and split-read analysis · Tobias Rausch · 2012 · 2813 citations · Cited by this paper
  14. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing · Robert C. Green · 2013 · 2581 citations · Cited by this paper
  15. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications · Xiaoyu Chen · 2015 · 2511 citations · Cited by this paper
  16. Chromatin accessibility and the regulatory epigenome · Sandy L. Klemm · 2019 · 2040 citations · Cited by this paper
  17. A universal SNP and small-indel variant caller using deep neural networks · Ryan E. Poplin · 2018 · 2005 citations · Cited by this paper
  18. Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database · Stéphanie Nguengang Wakap · 2019 · 1877 citations · Cited by this paper
  19. Exploring tissue architecture using spatial transcriptomics · Anjali N. Rao · 2021 · 1836 citations · Cited by this paper
  20. LUMPY: a probabilistic framework for structural variant discovery · Ryan M. Layer · 2014 · 1807 citations · Cited by this paper
  21. Long-read human genome sequencing and its applications · Glennis A. Logsdon · 2020 · 1357 citations · Cited by this paper
  22. Genome sequencing identifies major causes of severe intellectual disability · Christian Gilissen · 2014 · 1175 citations · Cited by this paper
  23. De novo mutations in human genetic disease · Joris A. Veltman · 2012 · 903 citations · Cited by this paper
  24. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing · Beryl B. Cummings · 2017 · 845 citations · Cited by this paper
  25. Genetic diagnosis of Mendelian disorders via RNA sequencing · Laura Sophie Kremer · 2017 · 615 citations · Cited by this paper
  26. Accurate and efficient detection of gene fusions from RNA sequencing data · Sebastian Uhrig · 2021 · 559 citations · Cited by this paper
  27. New insights into the generation and role of de novo mutations in health and disease · Rocío Acuña‐Hidalgo · 2016 · 506 citations · Cited by this paper
  28. The Human Phenotype Ontology in 2024: phenotypes around the world · Michael A. Gargano · 2023 · 420 citations · Cited by this paper
  29. GENCODE 2025: reference gene annotation for human and mouse · Jonathan M. Mudge · 2024 · 410 citations · Cited by this paper
  30. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome · Shruti Marwaha · 2022 · 398 citations · Cited by this paper
  31. Highly accurate long-read HiFi sequencing data for five complex genomes · Ting Hon · 2020 · 373 citations · Cited by this paper
  32. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts · Undiagnosed Diseases Network · 2019 · 367 citations · Cited by this paper
  33. Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data · Qian Liu · 2019 · 365 citations · Cited by this paper
  34. Snakemake—a scalable bioinformatics workflow engine · Johannes Köster · 2018 · 361 citations · Cited by this paper
  35. Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform · Fengchao Yu · 2023 · 316 citations · Cited by this paper
  36. DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning · Peng Ni · 2019 · 278 citations · Cited by this paper
  37. PhenoTips: Patient Phenotyping Software for Clinical and Research Use · Marta Gîrdea · 2013 · 263 citations · Cited by this paper
  38. OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data · Felix Brechtmann · 2018 · 243 citations · Cited by this paper
  39. Diagnostic utility of transcriptome sequencing for rare Mendelian diseases · Hane Lee · 2019 · 237 citations · Cited by this paper

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