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- Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: a joint recommendation of the Association for Molecular Pathology and the College of American Pathologists.J Mol Diagn. 2018; 20: 4-27
- Clinical bioinformatics: a new emerging science.J Clin Bioinforma. 2011; 1: 1
- Long-read sequencing emerging in medical genetics.Front Genet. 2019; 10: 426
- Next-generation sequencing informatics: challenges and strategies for implementation in a clinical environment.Arch Pathol Lab Med. 2016; 140: 958-975
- Efficient storage of high throughput DNA sequencing data using reference-based compression.Genome Res. 2011; 21: 734-740
- Advances in next-generation sequencing bioinformatics for clinical diagnostics: taking precision oncology to the next level.Adv Mol Pathol. 2018; 1: 149-166
- Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches.Cancer Genet. 2013; 206: 432-440
- RNA-based detection of gene fusions in formalin-fixed and paraffin-embedded solid cancer samples.Cancers (Basel). 2019; : 11
- Clinical implications of a targeted RNA-sequencing panel in the detection of gene fusions in solid tumors.J Mol Diagn. 2021; 23: 1749-1760
- Principles and recommendations for standardizing the use of the next-generation sequencing variant file in clinical settings.J Mol Diagn. 2017; 19: 417-426
- Guidelines for validation of next-generation sequencing-based oncology panels: a joint Consensus recommendation of the Association for Molecular Pathology and College of American Pathologists.J Mol Diagn. 2017; 19: 341-365
- A review of bioinformatic pipeline frameworks.Brief Bioinform. 2017; 18: 530-536
- A review of scalable bioinformatics pipelines.Data Sci Eng. 2017; 2: 245-251
- Clinical implementation and validation of automated human genome variation society (HGVS) nomenclature system for next-generation sequencing-based assays for cancer.J Mol Diagn. 2018; 20: 628-634
- A variant by any name: quantifying annotation discordance across tools and clinical databases.Genome Med. 2017; 9: 7
- Genomics in the cloud: using Docker, GATK, and WDL in Terra.1st edition. O’Reilly Media, Sebastopol2020
- VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.Nucleic Acids Res. 2016; 44: e108
- Strelka2: fast and accurate calling of germline and somatic variants.Nat Methods. 2018; 15: 591-594
- VarGrouper: a bioinformatic tool for local haplotyping of deletion-insertion variants from next-generation sequencing data after variant calling.J Mol Diagn. 2019; 21: 384-389
- Containers in bioinformatics: applications, practical considerations, and best practices in molecular pathology.J Mol Diagn. 2022; 24: 442-454
- Platform-agnostic deployment of bioinformatics pipelines for clinical NGS assays using containers, infrastructure orchestration, and workflow manager (Abstract #I031).J Mol Diagn. 2019; 21: 1119-1249
- Singularity: scientific containers for mobility of compute.PLoS One. 2017; 12: e0177459