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Title Rigor and reproducibility in genetics and genomics : peer-reviewed, published, cited / volume editors, Douglas F. Dluzen, Monika H.M. Schmidt
Published London ; San Diego, CA : Academic Press, an imprint of Elsevier, [2024]


Description 1 online resource (xx, 482 pages) : illustrations (chiefly color)
Series Translational and applied genomics series
Translational and applied genomics series.
Contents Introduction. Rigor and reproducibility in genetic research and the effects on scientific reporting and public discourse / Monika H.M. Schmidt and Douglas F. Dluzen -- Unveiling the hidden curriculum : developing rigor and reproducibility values through teaching and mentorship / Marina E. Tourlakis -- Genotyping. Genome-wide association studies (GWAS) : what are they, when to use them? -- GWAS in the learning environment / Amy L. Stark -- Polygenic risk scores and comparative genomics : best practices and statistical considerations / Sally I-Chun Kuo and Fazil Aliev -- Sequence analysis and genomics in the classroom / Rebecca C. Burgess, Rivka Glaser, and Kimberly Pause Tucker -- Classroom to career : implementation considerations for engaging students with meaningful DNA sequencing learning opportunities / Charles Wray -- Next-generation sequencing & gene expression. Review of gene expression using microarray and RNA-seq / Ana B. Villaseñor-Altamirano, Yalbi Itzel Balderas-Martinez, and Alejandra Medina-Rivera -- Guidelines and important considerations for ‘omics-level studies / Francesca Luca and Athma A. Pai -- Rigor and reproducibility of RNA sequencing analysis / Dominik Buschmann, Tom Driedonks, Yiyao Huang, Juan Pablo Tosar, Andrey Turchinovich, and Kenneth W. Witwer -- Validation of gene expression by quantitative PCR / Arundhati Das, Devojyoti Das, and Amaresh C. Panda -- Epigenetic analyses. Best practices for epigenome-wide DNA modification data collection and analysis / Joseph Kochmanski and Alison I. Berntein -- Best practices for the ATAC-seq assay and its data analysis / Haibo Liu, Rui Li, Kai Hu, Jianhong Ou, Magnolia Pak, Michael R. Green, and Lihua Julie Zhu -- Best practice for ChIP-seq and its data analysis / Huayun Hou, Matthew Hudson, and Minggao Liang -- A practical guide for essential analyses of Hi-C data / Yu Liu and Erica M Hildebrand -- Epigenetics in the classroom / Khadijah Makky -- Gene editing technologies. Genome editing technologies / Dana Vera Foss and Alexis Leigh Norris -- Genetic modification of mice using CRISPR-Cas9 : best practices and practical concepts explained / Vishnu Hosur, Benjamin E. Low, and Michael V. Wiles -- CRISPR classroom activities and case studies / TyAnna L. Lovato and Richard M. Cripps
Summary "Rigor and Reproducibility in Genetics and Genomics: Peer-reviewed, Published, Cited provides a full methodological and statistical overview for researchers, clinicians, students, and post-doctoral fellows conducting genetic and genomic research. Here, active geneticists, clinicians, and bioinformaticists offer practical solutions for a variety of challenges associated with several modern approaches in genetics and genomics, including genotyping, gene expression analysis, epigenetic analysis, GWAS, EWAS, genomic sequencing, and gene editing. Emphasis is placed on rigor and reproducibility throughout, with each section containing laboratory case-studies and classroom activities covering step-by-step protocols, best practices, and common pitfalls. Specific genetic and genomic technologies discussed include microarray analysis, DNA-seq, RNA-seq, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis. Training exercises, supporting data, and in-depth discussions of rigor, reproducibility, and ethics in research together deliver a solid foundation in research standards for the next generation of genetic and genomic scientists. Provides practical approaches and step-by-step protocols to strengthen genetic and genomic research conducted in the laboratory or classroom. Presents illustrative case studies and training exercises, discussing common pitfalls and solutions for genotyping, gene expression analysis, epigenetic analysis, GWAS, genomic sequencing, and gene editing, among other genetic and genomic approaches. Examines best practices for microarray analysis, DNA-seq, RNA-seq, gene expression validation, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis. Written to provide trainees and educators with highly applicable tools and strategies to learn or refine a method toward identifying meaningful results with high confidence in their reproducibility."--ProQuest website
Bibliography Includes bibliographical references and index
Notes Douglas F. Dluzen is a geneticist and has previously studied the genetic contributors to aging, drug metabolism, hypertension, and inflammation. Dluzen is particularly interested in how social determinants of health influence gene expression in the immune system. Currently, he is the director of the Professional Development and Career Office at the Johns Hopkins University School of Medicine and has worked previously at the National Institutes of Health and Morgan State University. Monika Schmidt completed her doctoral work in the realm of tandem repeat-associated neuromuscular/neurodegenerative diseases, with a focus upon fragile X syndrome, amyotrophic lateral sclerosis, and DNA metabolism. Monika has a particular interest in wet lab validation of in silico findings, with a penchant for Southern blotting of structurally complex repetitive DNA sequences. Currently, she is a freelance scientific editor, private healthcare liaison, and event organizer
Description based on online resource; title from digital title page (ProQuest Ebook Central, viewed February 26, 2024)
Subject Genetics -- Research -- Methodology
Genomics -- Research -- Methodology
Reproducible research.
Genetics -- Research -- Methodology
Reproducible research
Form Electronic book
Author Dluzen, Douglas F., editor.
Schmidt, Monika H.M., editor
ISBN 9780128172193