Berger, B., & Yu, Y. W. (2022). Navigating bottlenecks and trade-offs in genomic data analysis. Nature reviews. Genetics, 10.1038/s41576-022-00551-z. Advance online publication. https://doi.org/10.1038/s41576-022-00551-z
Du, F. X., Clutter, A. C., & Lohuis, M. M. (2007). Characterizing linkage disequilibrium in pig populations. International journal of biological sciences, 3(3), 166–178. https://doi.org/10.7150/ijbs.3.166
Fowler, S., Roush, R., & Wise, J. (2017). 6. In Concepts of Biology. essay, OpenStax College, Rice University.
GenScript. (n.d.). Coding sequence - Terminology of Molecular Biology. Retrieved from https://www.genscript.com/biology-glossary/12079/Coding-sequence
Gharesouran, J., Hosseinzadeh, H., Ghafouri-Fard, S., Taheri, M., & Rezazadeh, M. (2021). STRs: Ancient Architectures of the Genome beyond the Sequence. Journal of molecular neuroscience : MN, 71(12), 2441–2455. https://doi.org/10.1007/s12031-021-01850-6
Grindley, N. D., Whiteson, K. L., & Rice, P. A. (2006). Mechanisms of site-specific recombination. Annual review of biochemistry, 75, 567–605. https://doi.org/10.1146/annurev.biochem.73.011303.073908
Hughes D. (2003). Exploiting genomics, genetics and chemistry to combat antibiotic resistance. Nature reviews. Genetics, 4(6), 432–441. https://doi.org/10.1038/nrg1086
Hyduke, D. R., & Palsson, B. Ø. (2010). Towards genome-scale signalling network reconstructions. Nature reviews. Genetics, 11(4), 297–307. https://doi.org/10.1038/nrg2751
Innan, H., & Kondrashov, F. (2010). The evolution of gene duplications: classifying and distinguishing between models. Nature reviews. Genetics, 11(2), 97–108. https://doi.org/10.1038/nrg2697
Isbel, L., Grand, R. S., & Schübeler, D. (2022). Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nature reviews. Genetics, 23(12), 728–740. https://doi.org/10.1038/s41576-022-00512-9
Keren, H., Lev-Maor, G., & Ast, G. (2010). Alternative splicing and evolution: diversification, exon definition and function. Nature reviews. Genetics, 11(5), 345–355. https://doi.org/10.1038/nrg2782
Khalil, A. S., & Collins, J. J. (2010). Synthetic biology: applications come of age. Nature reviews. Genetics, 11(5), 367–379. https://doi.org/10.1038/nrg2777
Kim, T. K., & Eberwine, J. H. (2010). Mammalian cell transfection: the present and the future. Analytical and bioanalytical chemistry, 397(8), 3173–3178. https://doi.org/10.1007/s00216-010-3821-6
Kobayashi, A., & Behringer, R. R. (2003). Developmental genetics of the female reproductive tract in mammals. Nature reviews. Genetics, 4(12), 969–980. https://doi.org/10.1038/nrg1231
Kress, W. J., & Erickson, D. L. (2008). DNA barcodes: genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences of the United States of America, 105(8), 2761–2762. https://doi.org/10.1073/pnas.0800476105
Lahiry, P., Torkamani, A., Schork, N. J., & Hegele, R. A. (2010). Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nature reviews. Genetics, 11(1), 60–74. https://doi.org/10.1038/nrg2711
Laird, P. Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11, 191–203 (2010). https://doi.org/10.1038/nrg2743
Lane, J. M., Qian, J., Mignot, E., Redline, S., Scheer, F. A. J. L., & Saxena, R. (2022). Genetics of circadian rhythms and sleep in human health and disease. Nature reviews. Genetics, 10.1038/s41576-022-00519-z. Advance online publication. https://doi.org/10.1038/s41576-022-00519-z
Lauer, S., & Gresham, D. (2019). An evolving view of copy number variants. Current genetics, 65(6), 1287–1295. https://doi.org/10.1007/s00294-019-00980-0
Law, J. A., & Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature reviews. Genetics, 11(3), 204–220. https://doi.org/10.1038/nrg2728
Liu, L., Parekh-Olmedo, H., & Kmiec, E. B. (2003). The development and regulation of gene repair. Nature reviews. Genetics, 4(9), 679–689. https://doi.org/10.1038/nrg1158
Long, M., Betrán, E., Thornton, K., & Wang, W. (2003). The origin of new genes: glimpses from the young and old. Nature reviews. Genetics, 4(11), 865–875. https://doi.org/10.1038/nrg1219
Luikart, G., England, P. R., Tallmon, D., Jordan, S., & Taberlet, P. (2003). The power and promise of population genomics: from genotyping to genome typing. Nature reviews. Genetics, 4(12), 981–994. https://doi.org/10.1038/nrg1252
MacLean, R. C., Hall, A. R., Perron, G. G., & Buckling, A. (2010). The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nature reviews. Genetics, 11(6), 405–414. https://doi.org/10.1038/nrg2780
Mank J. E. (2022). Sex-specific morphs: the genetics and evolution of intra-sexual variation. Nature reviews. Genetics, 10.1038/s41576-022-00524-2. Advance online publication. https://doi.org/10.1038/s41576-022-00524-9
Marchini, J., & Howie, B. (2010). Genotype imputation for genome-wide association studies. Nature reviews. Genetics, 11(7), 499–511. https://doi.org/10.1038/nrg2798
Margueron, R., & Reinberg, D. (2010). Chromatin structure and the inheritance of epigenetic information. Nature reviews. Genetics, 11(4), 285–296. https://doi.org/10.1038/nrg2758
Marraffini, L. A., & Sontheimer, E. J. (2010). CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature reviews. Genetics, 11(3), 181–190. https://doi.org/10.1038/nrg2758
Matharu, N., & Ahituv, N. (2020). Modulating gene regulation to treat genetic disorders. Nature reviews. Drug discovery, 19(11), 757–775. https://doi.org/10.1038/s41573-020-0083-9
Meftahi, G. H., Bahari, Z., Zarei Mahmoudabadi, A., Iman, M., & Jangravi, Z. (2021). Applications of western blot technique: From bench to bedside. Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology, 49(4), 509–517. https://doi.org/10.1002/bmb.21516
MGI. (n.d.). Glossary: conserved sequence. Retrieved from https://www.informatics.jax.org/glossary/conserved_sequence
Millán-Zambrano, G., Burton, A., Bannister, A. J., & Schneider, R. (2022). Histone post-translational modifications - cause and consequence of genome function. Nature reviews. Genetics, 23(9), 563–580. https://doi.org/10.1038/s41576-022-00468-9
National Human Genome Research Institute. (n.d.). Autosomal Dominant Disorder. Retrieved from https://www.genome.gov/genetics-glossary/Autosomal-Dominant-Disorder
National Human Genome Research Institute. (n.d.). Bacterial Artificial Chromosome. Retrieved from https://www.genome.gov/genetics-glossary/Bacterial-Artificial-Chromosome
National Human Genome Research Institute. (n.d.). Gene Amplification. Retrieved from https://www.genome.gov/genetics-glossary/Gene-Amplification
Nature Publishing Group. (n.d.). Nature news - Definition Codon. Retrieved from https://www.nature.com/scitable/definition/codon-155/
Novakovsky, G., Dexter, N., Libbrecht, M. W., Wasserman, W. W., & Mostafavi, S. (2022). Obtaining genetics insights from deep learning via explainable artificial intelligence. Nature reviews. Genetics, 10.1038/s41576-022-00532-2. Advance online publication. https://doi.org/10.1038/s41576-022-00532-2
Ott, J., Wang, J. & Leal, S. Genetic linkage analysis in the age of whole-genome sequencing. Nat Rev Genet 16, 275–284 (2015). https://doi.org/10.1038/nrg3909
Paigen, K., & Petkov, P. (2010). Mammalian recombination hot spots: properties, control and evolution. Nature reviews. Genetics, 11(3), 221–233. https://doi.org/10.1038/nrg2729
Perissi, V., Jepsen, K., Glass, C. K., & Rosenfeld, M. G. (2010). Deconstructing repression: evolving models of co-repressor action. Nature reviews. Genetics, 11(2), 109–123. https://doi.org/10.1038/nrg2738
Preissl, S., Gaulton, K. J., & Ren, B. (2022). Characterizing cis-regulatory elements using single-cell epigenomics. Nature reviews. Genetics, 10.1038/s41576-022-00509-1. Advance online publication. https://doi.org/10.1038/s41576-022-00509-5
Price, A. L., Zaitlen, N. A., Reich, D., & Patterson, N. (2010). New approaches to population stratification in genome-wide association studies. Nature reviews. Genetics, 11(7), 459–463. https://doi.org/10.1038/nrg2813
Rackham, O., & Filipovska, A. (2022). Organization and expression of the mammalian mitochondrial genome. Nature reviews. Genetics, 23(10), 606–623. https://doi.org/10.1038/s41576-022-00480-x
Rackham, O., & Filipovska, A. (2022). Organization and expression of the mammalian mitochondrial genome. Nature reviews. Genetics, 23(10), 606–623. https://doi.org/10.1038/s41576-022-00480-x
Revy, P., Kannengiesser, C., & Bertuch, A. A. (2022). Genetics of human telomere biology disorders. Nature reviews. Genetics, 10.1038/s41576-022-00527-z. Advance online publication. https://doi.org/10.1038/s41576-022-00527-z
Rhind, S. M., Taylor, J. E., De Sousa, P. A., King, T. J., McGarry, M., & Wilmut, I. (2003). Human cloning: can it be made safe?. Nature reviews. Genetics, 4(11), 855–864. https://doi.org/10.1038/nrg1209
Roderick, G. K., & Navajas, M. (2003). Genes in new environments: genetics and evolution in biological control. Nature reviews. Genetics, 4(11), 889–899. https://doi.org/10.1038/nrg1210
Rosenberg, N. A., Huang, L., Jewett, E. M., Szpiech, Z. A., Jankovic, I., & Boehnke, M. (2010). Genome-wide association studies in diverse populations. Nature reviews. Genetics, 11(5), 356–366. https://doi.org/10.1038/nrg2769
Rutledge, J., Oh, H., & Wyss-Coray, T. (2022). Measuring biological age using omics data. Nature reviews. Genetics, 23(12), 715–727. https://doi.org/10.1038/s41576-022-00511-7
Santaguida S, Amon A. Short- and long-term effects of chromosome mis-segregation and aneuploidy. Nat Rev Mol Cell Biol. 2015 Aug;16(8):473-85. doi: 10.1038/nrm4025. Erratum in: Nat Rev Mol Cell Biol. 2015 Sep;16(9):576. PMID: 26204159.
Schaffer, L. V., Millikin, R. J., Miller, R. M., Anderson, L. C., Fellers, R. T., Ge, Y., Kelleher, N. L., LeDuc, R. D., Liu, X., Payne, S. H., Sun, L., Thomas, P. M., Tucholski, T., Wang, Z., Wu, S., Wu, Z., Yu, D., Shortreed, M. R., & Smith, L. M. (2019). Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics, 19(10), e1800361. https://doi.org/10.1002/pmic.201800361
Schmitt, E., Coureux, P. D., Kazan, R., Bourgeois, G., Lazennec-Schurdevin, C., & Mechulam, Y. (2020). Recent Advances in Archaeal Translation Initiation. Frontiers in microbiology, 11, 584152. https://doi.org/10.3389/fmicb.2020.584152
ScienceDirect. (n.d.). Cosmid - an overview. Retrieved from https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cosmid
Silva, J., Fernandes, R., & Romão, L. (2019). Translational Regulation by Upstream Open Reading Frames and Human Diseases. Advances in experimental medicine and biology, 1157, 99–116. https://doi.org/10.1007/978-3-030-19966-1_5
Southern E. M. (1988). Prospects for a complete molecular map of the human genome. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 319(1194), 299–307. https://doi.org/10.1098/rstb.1988.0051
Spitale, R. C., & Incarnato, D. (2022). Probing the dynamic RNA structurome and its functions. Nature reviews. Genetics, 1–19. Advance online publication. https://doi.org/10.1038/s41576-022-00546-w
Stumpf, M. P., & McVean, G. A. (2003). Estimating recombination rates from population-genetic data. Nature reviews. Genetics, 4(12), 959–968. https://doi.org/10.1038/nrg1245
Teo, Y. Y., Small, K. S., & Kwiatkowski, D. P. (2010). Methodological challenges of genome-wide association analysis in Africa. Nature reviews. Genetics, 11(2), 149–160. https://doi.org/10.1038/nrg2739
Thomas D. (2010). Gene--environment-wide association studies: emerging approaches. Nature reviews. Genetics, 11(4), 259–272. https://doi.org/10.1038/nrg2772
Turner, K. J., Vasu, V., & Griffin, D. K. (2019). Telomere Biology and Human Phenotype. Cells, 8(1), 73. https://doi.org/10.3390/cells8010073
Ureta-Vidal, A., Ettwiller, L., & Birney, E. (2003). Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nature reviews. Genetics, 4(4), 251–262. https://doi.org/10.1038/nrg1055
Wall, J. D., & Pritchard, J. K. (2003). Haplotype blocks and linkage disequilibrium in the human genome. Nature reviews. Genetics, 4(8), 587–597. https://doi.org/10.1038/nrg1129
Wang, G., & Vasquez, K. M. (2022). Dynamic alternative DNA structures in biology and disease. Nature reviews. Genetics, 10.1038/s41576-022-00539-9. Advance online publication. https://doi.org/10.1038/s41576-022-00539-9
Wilkins, J. F., & Haig, D. (2003). What good is genomic imprinting: the function of parent-specific gene expression. Nature reviews. Genetics, 4(5), 359–368. https://doi.org/10.1038/nrg1064
Wood, A. J., Severson, A. F., & Meyer, B. J. (2010). Condensin and cohesin complexity: the expanding repertoire of functions. Nature reviews. Genetics, 11(6), 391–404. https://doi.org/10.1038/nrg2805
Wright, A. F., Chakarova, C. F., Abd El-Aziz, M. M., & Bhattacharya, S. S. (2010). Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait. Nature reviews. Genetics, 11(4), 273–284. https://doi.org/10.1038/nrg2719
Yi, E., Chamorro González, R., Henssen, A. G., & Verhaak, R. G. W. (2022). Extrachromosomal DNA amplifications in cancer. Nature reviews. Genetics, 23(12), 760–771. https://doi.org/10.1038/s41576-022-00521-9
Yook K. Complementation. 2005 Oct 6. In: WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK19726/
Zhdanova N. S. (2002). Radiatsionnoe kartirovanie genomov. Nastoiashchee i budushchee [Genome radiation hybrid mapping: summary and future directions]. Genetika, 38(5), 581–594.
Berger, B., & Yu, Y. W. (2022). Navigating bottlenecks and trade-offs in genomic data analysis. Nature reviews. Genetics, 10.1038/s41576-022-00551-z. Advance online publication. https://doi.org/10.1038/s41576-022-00551-z
Cirulli, E. T., & Goldstein, D. B. (2010). Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nature reviews. Genetics, 11(6), 415–425. https://doi.org/10.1038/nrg2779
Daly A. K. (2010). Genome-wide association studies in pharmacogenomics. Nature reviews. Genetics, 11(4), 241–246. https://doi.org/10.1038/nrg2751
Ensembl East (Ed.). (n.d.). Ensembl genome browser 109. Retrieved from https://useast.ensembl.org/index.html
Genome Research Limited. (n.d.). Samtools. Retrieved April 28, 2023, from http://www.htslib.org/
GNU Operating System. (n.d.). What is Shell? What is bash? (bash reference manual). Retrieved from https://www.gnu.org/software/bash/manual/html_node/What-is-Bash_003f.html
Hyduke, D. R., & Palsson, B. Ø. (2010). Towards genome-scale signalling network reconstructions. Nature reviews. Genetics, 11(4), 297–307. https://doi.org/10.1038/nrg2752
Illumina. (n.d.). Paired-end vs. single-read Sequencing Technology. Retrieved from https://www.illumina.com/science/technology/next-generation-sequencing/plan-experiments/paired-end-vs-single-read.html
Integrative Genomics Viewer. (n.d.). Home | Integrative Genomics Viewer. Retrieved from https://software.broadinstitute.org/software/igv/
Khalil, A. S., & Collins, J. J. (2010). Synthetic biology: applications come of age. Nature reviews. Genetics, 11(5), 367–379. https://doi.org/10.1038/nrg2777
Laird, P. Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11, 191–203 (2010). https://doi.org/10.1038/nrg2737
MacLean, R. C., Hall, A. R., Perron, G. G., & Buckling, A. (2010). The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nature reviews. Genetics, 11(6), 405–414. https://doi.org/10.1038/nrg2778
Marchini, J., & Howie, B. (2010). Genotype imputation for genome-wide association studies. Nature reviews. Genetics, 11(7), 499–511. https://doi.org/10.1038/nrg2800
Paigen, K., & Petkov, P. (2010). Mammalian recombination hot spots: properties, control and evolution. Nature reviews. Genetics, 11(3), 221–233. https://doi.org/10.1038/nrg2713
Price, A. L., Zaitlen, N. A., Reich, D., & Patterson, N. (2010). New approaches to population stratification in genome-wide association studies. Nature reviews. Genetics, 11(7), 459–463. https://doi.org/10.1038/nrg2828
Rosenberg, N. A., Huang, L., Jewett, E. M., Szpiech, Z. A., Jankovic, I., & Boehnke, M. (2010). Genome-wide association studies in diverse populations. Nature reviews. Genetics, 11(5), 356–366. https://doi.org/10.1038/nrg2766
Source Forge. (n.d.). Maq: Mapping and Assembly with Qualities . Retrieved from https://maq.sourceforge.net/maq-man.shtml
Teo, Y. Y., Small, K. S., & Kwiatkowski, D. P. (2010). Methodological challenges of genome-wide association analysis in Africa. Nature reviews. Genetics, 11(2), 149–160. https://doi.org/10.1038/nrg2750
The Caprpentries. (n.d.). Navigating files and directories. Navigating Files and Directories – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/02-the-filesystem/
The Carpentries (Ed.). (n.d.). Working with files and directories. Working with Files and Directories – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/03-working-with-files/
The Carpentries. (n.d.). Assessing read quality. Assessing Read Quality – Data Wrangling and Processing for Genomics. Retrieved from https://datacarpentry.org/wrangling-genomics/02-quality-control/
The carpentries. (n.d.). Data tidiness. Data Tidiness – Project Organization and Management for Genomics. Retrieved from https://datacarpentry.org/organization-genomics/01-tidiness/
The Carpentries. (n.d.). Introducing the Shell. Introducing the Shell – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/01-introduction/
The Carpentries. (n.d.). Planning for NGS Projects – Project Organization and Management for Genomics. Retrieved from https://datacarpentry.org/organization-genomics/02-project-planning/
The Carpentries. (n.d.). Redirection. Redirection – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/04-redirection/
The Carpentries. (n.d.). Trimming and Filtering – Data Wrangling and Processing for Genomics. Retrieved from https://datacarpentry.org/wrangling-genomics/03-trimming/
The Carpentries. (n.d.). Variant calling workflow. Variant Calling Workflow – Data Wrangling and Processing for Genomics. Retrieved from https://datacarpentry.org/wrangling-genomics/04-variant_calling/
The Carpentries. (n.d.). Writing Scripts and Working with Data – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/05-writing-scripts/
Thomas D. (2010). Gene--environment-wide association studies: emerging approaches. Nature reviews. Genetics, 11(4), 259–272. https://doi.org/10.1038/nrg2778
U.S. National Library of Medicine. (n.d.). Home - SRA - NCBI. National Center for Biotechnology Information - SRA. Retrieved from https://www.ncbi.nlm.nih.gov/sra
Berger, B., & Yu, Y. W. (2022). Navigating bottlenecks and trade-offs in genomic data analysis. Nature reviews. Genetics, 10.1038/s41576-022-00551-z. Advance online publication. https://doi.org/10.1038/s41576-022-00551-z
Fowler, S., Roush, R., & Wise, J. (2017). 6. In Concepts of Biology. essay, OpenStax College, Rice University.
Handel, M. A., & Schimenti, J. C. (2010). Genetics of mammalian meiosis: regulation, dynamics and impact on fertility. Nature reviews. Genetics, 11(2), 124–136. https://doi.org/10.1038/nrg2723
Hawkins, R. D., Hon, G. C., & Ren, B. (2010). Next-generation genomics: an integrative approach. Nature reviews. Genetics, 11(7), 476–486. https://doi.org/10.1038/nrg2795
Hawkins, R. D., Hon, G. C., & Ren, B. (2010). Next-generation genomics: an integrative approach. Nature reviews. Genetics, 11(7), 476–486. https://doi.org/10.1038/nrg2796
Keren, H., Lev-Maor, G., & Ast, G. (2010). Alternative splicing and evolution: diversification, exon definition and function. Nature reviews. Genetics, 11(5), 345–355. https://doi.org/10.1038/nrg2779
Khalil, A. S., & Collins, J. J. (2010). Synthetic biology: applications come of age. Nature reviews. Genetics, 11(5), 367–379. https://doi.org/10.1038/nrg2778
Law, J. A., & Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature reviews. Genetics, 11(3), 204–220. https://doi.org/10.1038/nrg2726
Marraffini, L. A., & Sontheimer, E. J. (2010). CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature reviews. Genetics, 11(3), 181–190. https://doi.org/10.1038/nrg2750
Perissi, V., Jepsen, K., Glass, C. K., & Rosenfeld, M. G. (2010). Deconstructing repression: evolving models of co-repressor action. Nature reviews. Genetics, 11(2), 109–123. https://doi.org/10.1038/nrg2737
Weake, V. M., & Workman, J. L. (2010). Inducible gene expression: diverse regulatory mechanisms. Nature reviews. Genetics, 11(6), 426–437. https://doi.org/10.1038/nrg2786
Wood, A. J., Severson, A. F., & Meyer, B. J. (2010). Condensin and cohesin complexity: the expanding repertoire of functions. Nature reviews. Genetics, 11(6), 391–404. https://doi.org/10.1038/nrg2795
Berger, B., & Yu, Y. W. (2022). Navigating bottlenecks and trade-offs in genomic data analysis. Nature reviews. Genetics, 10.1038/s41576-022-00551-z. Advance online publication. https://doi.org/10.1038/s41576-022-00551-z
Cirulli, E. T., & Goldstein, D. B. (2010). Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nature reviews. Genetics, 11(6), 415–425. https://doi.org/10.1038/nrg2779
Daly A. K. (2010). Genome-wide association studies in pharmacogenomics. Nature reviews. Genetics, 11(4), 241–246. https://doi.org/10.1038/nrg2751
Du, F. X., Clutter, A. C., & Lohuis, M. M. (2007). Characterizing linkage disequilibrium in pig populations. International journal of biological sciences, 3(3), 166–178. https://doi.org/10.7150/ijbs.3.166
Ensembl East (Ed.). (n.d.). Ensembl genome browser 109. Retrieved from https://useast.ensembl.org/index.html
Fowler, S., Roush, R., & Wise, J. (2017). 6. In Concepts of Biology. essay, OpenStax College, Rice University.
Genome Research Limited. (n.d.). Samtools. Retrieved April 28, 2023, from http://www.htslib.org/
GenScript. (n.d.). Coding sequence - Terminology of Molecular Biology. Retrieved from https://www.genscript.com/biology-glossary/12079/Coding-sequence
Gharesouran, J., Hosseinzadeh, H., Ghafouri-Fard, S., Taheri, M., & Rezazadeh, M. (2021). STRs: Ancient Architectures of the Genome beyond the Sequence. Journal of molecular neuroscience : MN, 71(12), 2441–2455. https://doi.org/10.1007/s12031-021-01850-6
GNU Operating System. (n.d.). What is Shell? What is bash? (bash reference manual). Retrieved from https://www.gnu.org/software/bash/manual/html_node/What-is-Bash_003f.html
Grindley, N. D., Whiteson, K. L., & Rice, P. A. (2006). Mechanisms of site-specific recombination. Annual review of biochemistry, 75, 567–605. https://doi.org/10.1146/annurev.biochem.73.011303.073908
Handel, M. A., & Schimenti, J. C. (2010). Genetics of mammalian meiosis: regulation, dynamics and impact on fertility. Nature reviews. Genetics, 11(2), 124–136. https://doi.org/10.1038/nrg2723
Hawkins, R. D., Hon, G. C., & Ren, B. (2010). Next-generation genomics: an integrative approach. Nature reviews. Genetics, 11(7), 476–486. https://doi.org/10.1038/nrg2796
Hughes D. (2003). Exploiting genomics, genetics and chemistry to combat antibiotic resistance. Nature reviews. Genetics, 4(6), 432–441. https://doi.org/10.1038/nrg1086
Hyduke, D. R., & Palsson, B. Ø. (2010). Towards genome-scale signalling network reconstructions. Nature reviews. Genetics, 11(4), 297–307. https://doi.org/10.1038/nrg2752
Illumina. (n.d.). Paired-end vs. single-read Sequencing Technology. Retrieved from https://www.illumina.com/science/technology/next-generation-sequencing/plan-experiments/paired-end-vs-single-read.html
Innan, H., & Kondrashov, F. (2010). The evolution of gene duplications: classifying and distinguishing between models. Nature reviews. Genetics, 11(2), 97–108. https://doi.org/10.1038/nrg2697
Integrative Genomics Viewer. (n.d.). Home | Integrative Genomics Viewer. Retrieved from https://software.broadinstitute.org/software/igv/
Isbel, L., Grand, R. S., & Schübeler, D. (2022). Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nature reviews. Genetics, 23(12), 728–740. https://doi.org/10.1038/s41576-022-00512-9
Keren, H., Lev-Maor, G., & Ast, G. (2010). Alternative splicing and evolution: diversification, exon definition and function. Nature reviews. Genetics, 11(5), 345–355. https://doi.org/10.1038/nrg2782
Khalil, A. S., & Collins, J. J. (2010). Synthetic biology: applications come of age. Nature reviews. Genetics, 11(5), 367–379. https://doi.org/10.1038/nrg2777
Kim, T. K., & Eberwine, J. H. (2010). Mammalian cell transfection: the present and the future. Analytical and bioanalytical chemistry, 397(8), 3173–3178. https://doi.org/10.1007/s00216-010-3821-6
Kobayashi, A., & Behringer, R. R. (2003). Developmental genetics of the female reproductive tract in mammals. Nature reviews. Genetics, 4(12), 969–980. https://doi.org/10.1038/nrg1231
Kress, W. J., & Erickson, D. L. (2008). DNA barcodes: genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences of the United States of America, 105(8), 2761–2762. https://doi.org/10.1073/pnas.0800476105
Lahiry, P., Torkamani, A., Schork, N. J., & Hegele, R. A. (2010). Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nature reviews. Genetics, 11(1), 60–74. https://doi.org/10.1038/nrg2711
Laird, P. Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11, 191–203 (2010). https://doi.org/10.1038/nrg2743
Lane, J. M., Qian, J., Mignot, E., Redline, S., Scheer, F. A. J. L., & Saxena, R. (2022). Genetics of circadian rhythms and sleep in human health and disease. Nature reviews. Genetics, 10.1038/s41576-022-00519-z. Advance online publication. https://doi.org/10.1038/s41576-022-00519-z
Lauer, S., & Gresham, D. (2019). An evolving view of copy number variants. Current genetics, 65(6), 1287–1295. https://doi.org/10.1007/s00294-019-00980-0
Law, J. A., & Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature reviews. Genetics, 11(3), 204–220. https://doi.org/10.1038/nrg2728
Liu, L., Parekh-Olmedo, H., & Kmiec, E. B. (2003). The development and regulation of gene repair. Nature reviews. Genetics, 4(9), 679–689. https://doi.org/10.1038/nrg1158
Long, M., Betrán, E., Thornton, K., & Wang, W. (2003). The origin of new genes: glimpses from the young and old. Nature reviews. Genetics, 4(11), 865–875. https://doi.org/10.1038/nrg1219
Luikart, G., England, P. R., Tallmon, D., Jordan, S., & Taberlet, P. (2003). The power and promise of population genomics: from genotyping to genome typing. Nature reviews. Genetics, 4(12), 981–994. https://doi.org/10.1038/nrg1252
MacLean, R. C., Hall, A. R., Perron, G. G., & Buckling, A. (2010). The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nature reviews. Genetics, 11(6), 405–414. https://doi.org/10.1038/nrg2780
Mank J. E. (2022). Sex-specific morphs: the genetics and evolution of intra-sexual variation. Nature reviews. Genetics, 10.1038/s41576-022-00524-2. Advance online publication. https://doi.org/10.1038/s41576-022-00524-9
Marchini, J., & Howie, B. (2010). Genotype imputation for genome-wide association studies. Nature reviews. Genetics, 11(7), 499–511. https://doi.org/10.1038/nrg2800
Margueron, R., & Reinberg, D. (2010). Chromatin structure and the inheritance of epigenetic information. Nature reviews. Genetics, 11(4), 285–296. https://doi.org/10.1038/nrg2758
Marraffini, L. A., & Sontheimer, E. J. (2010). CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature reviews. Genetics, 11(3), 181–190. https://doi.org/10.1038/nrg2758
Matharu, N., & Ahituv, N. (2020). Modulating gene regulation to treat genetic disorders. Nature reviews. Drug discovery, 19(11), 757–775. https://doi.org/10.1038/s41573-020-0083-9
Meftahi, G. H., Bahari, Z., Zarei Mahmoudabadi, A., Iman, M., & Jangravi, Z. (2021). Applications of western blot technique: From bench to bedside. Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology, 49(4), 509–517. https://doi.org/10.1002/bmb.21516
MGI. (n.d.). Glossary: conserved sequence. Retrieved from https://www.informatics.jax.org/glossary/conserved_sequence
Millán-Zambrano, G., Burton, A., Bannister, A. J., & Schneider, R. (2022). Histone post-translational modifications - cause and consequence of genome function. Nature reviews. Genetics, 23(9), 563–580. https://doi.org/10.1038/s41576-022-00468-9
National Human Genome Research Institute. (n.d.). Autosomal Dominant Disorder. Retrieved from https://www.genome.gov/genetics-glossary/Autosomal-Dominant-Disorder
National Human Genome Research Institute. (n.d.). Bacterial Artificial Chromosome. Retrieved from https://www.genome.gov/genetics-glossary/Bacterial-Artificial-Chromosome
National Human Genome Research Institute. (n.d.). Gene Amplification. Retrieved from https://www.genome.gov/genetics-glossary/Gene-Amplification
Nature Publishing Group. (n.d.). Nature news - Definition Codon. Retrieved from https://www.nature.com/scitable/definition/codon-155/
Novakovsky, G., Dexter, N., Libbrecht, M. W., Wasserman, W. W., & Mostafavi, S. (2022). Obtaining genetics insights from deep learning via explainable artificial intelligence. Nature reviews. Genetics, 10.1038/s41576-022-00532-2. Advance online publication. https://doi.org/10.1038/s41576-022-00532-2
Ott, J., Wang, J. & Leal, S. Genetic linkage analysis in the age of whole-genome sequencing. Nat Rev Genet 16, 275–284 (2015). https://doi.org/10.1038/nrg3909
Paigen, K., & Petkov, P. (2010). Mammalian recombination hot spots: properties, control and evolution. Nature reviews. Genetics, 11(3), 221–233. https://doi.org/10.1038/nrg2729
Preissl, S., Gaulton, K. J., & Ren, B. (2022). Characterizing cis-regulatory elements using single-cell epigenomics. Nature reviews. Genetics, 10.1038/s41576-022-00509-1. Advance online publication. https://doi.org/10.1038/s41576-022-00509-5
Price, A. L., Zaitlen, N. A., Reich, D., & Patterson, N. (2010). New approaches to population stratification in genome-wide association studies. Nature reviews. Genetics, 11(7), 459–463. https://doi.org/10.1038/nrg2828
Rackham, O., & Filipovska, A. (2022). Organization and expression of the mammalian mitochondrial genome. Nature reviews. Genetics, 23(10), 606–623. https://doi.org/10.1038/s41576-022-00480-x
Revy, P., Kannengiesser, C., & Bertuch, A. A. (2022). Genetics of human telomere biology disorders. Nature reviews. Genetics, 10.1038/s41576-022-00527-z. Advance online publication. https://doi.org/10.1038/s41576-022-00527-z
Rhind, S. M., Taylor, J. E., De Sousa, P. A., King, T. J., McGarry, M., & Wilmut, I. (2003). Human cloning: can it be made safe?. Nature reviews. Genetics, 4(11), 855–864. https://doi.org/10.1038/nrg1209
Roderick, G. K., & Navajas, M. (2003). Genes in new environments: genetics and evolution in biological control. Nature reviews. Genetics, 4(11), 889–899. https://doi.org/10.1038/nrg1210
Rosenberg, N. A., Huang, L., Jewett, E. M., Szpiech, Z. A., Jankovic, I., & Boehnke, M. (2010). Genome-wide association studies in diverse populations. Nature reviews. Genetics, 11(5), 356–366. https://doi.org/10.1038/nrg2769
Rutledge, J., Oh, H., & Wyss-Coray, T. (2022). Measuring biological age using omics data. Nature reviews. Genetics, 23(12), 715–727. https://doi.org/10.1038/s41576-022-00511-7
Santaguida S, Amon A. Short- and long-term effects of chromosome mis-segregation and aneuploidy. Nat Rev Mol Cell Biol. 2015 Aug;16(8):473-85. doi: 10.1038/nrm4025. Erratum in: Nat Rev Mol Cell Biol. 2015 Sep;16(9):576. PMID: 26204159.
Schaffer, L. V., Millikin, R. J., Miller, R. M., Anderson, L. C., Fellers, R. T., Ge, Y., Kelleher, N. L., LeDuc, R. D., Liu, X., Payne, S. H., Sun, L., Thomas, P. M., Tucholski, T., Wang, Z., Wu, S., Wu, Z., Yu, D., Shortreed, M. R., & Smith, L. M. (2019). Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics, 19(10), e1800361. https://doi.org/10.1002/pmic.201800361
Schmitt, E., Coureux, P. D., Kazan, R., Bourgeois, G., Lazennec-Schurdevin, C., & Mechulam, Y. (2020). Recent Advances in Archaeal Translation Initiation. Frontiers in microbiology, 11, 584152. https://doi.org/10.3389/fmicb.2020.584152
ScienceDirect. (n.d.). Cosmid - an overview. Retrieved from https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cosmid
Silva, J., Fernandes, R., & Romão, L. (2019). Translational Regulation by Upstream Open Reading Frames and Human Diseases. Advances in experimental medicine and biology, 1157, 99–116. https://doi.org/10.1007/978-3-030-19966-1_5
Source Forge. (n.d.). Maq: Mapping and Assembly with Qualities . Retrieved from https://maq.sourceforge.net/maq-man.shtml
Southern E. M. (1988). Prospects for a complete molecular map of the human genome. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 319(1194), 299–307. https://doi.org/10.1098/rstb.1988.0051
Spitale, R. C., & Incarnato, D. (2022). Probing the dynamic RNA structurome and its functions. Nature reviews. Genetics, 1–19. Advance online publication. https://doi.org/10.1038/s41576-022-00546-w
Stumpf, M. P., & McVean, G. A. (2003). Estimating recombination rates from population-genetic data. Nature reviews. Genetics, 4(12), 959–968. https://doi.org/10.1038/nrg1245
Teo, Y. Y., Small, K. S., & Kwiatkowski, D. P. (2010). Methodological challenges of genome-wide association analysis in Africa. Nature reviews. Genetics, 11(2), 149–160. https://doi.org/10.1038/nrg2750
The Caprpentries. (n.d.). Navigating files and directories. Navigating Files and Directories – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/02-the-filesystem/
The Carpentries (Ed.). (n.d.). Working with files and directories. Working with Files and Directories – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/03-working-with-files/
The Carpentries. (n.d.). Assessing read quality. Assessing Read Quality – Data Wrangling and Processing for Genomics. Retrieved from https://datacarpentry.org/wrangling-genomics/02-quality-control/
The carpentries. (n.d.). Data tidiness. Data Tidiness – Project Organization and Management for Genomics. Retrieved from https://datacarpentry.org/organization-genomics/01-tidiness/
The Carpentries. (n.d.). Introducing the Shell. Introducing the Shell – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/01-introduction/
The Carpentries. (n.d.). Planning for NGS Projects – Project Organization and Management for Genomics. Retrieved from https://datacarpentry.org/organization-genomics/02-project-planning/
The Carpentries. (n.d.). Redirection. Redirection – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/04-redirection/
The Carpentries. (n.d.). Trimming and Filtering – Data Wrangling and Processing for Genomics. Retrieved from https://datacarpentry.org/wrangling-genomics/03-trimming/
The Carpentries. (n.d.). Variant calling workflow. Variant Calling Workflow – Data Wrangling and Processing for Genomics. Retrieved from https://datacarpentry.org/wrangling-genomics/04-variant_calling/
The Carpentries. (n.d.). Writing Scripts and Working with Data – Introduction to the Command Line for Genomics. Retrieved from https://datacarpentry.org/shell-genomics/05-writing-scripts/
Thomas D. (2010). Gene--environment-wide association studies: emerging approaches. Nature reviews. Genetics, 11(4), 259–272. https://doi.org/10.1038/nrg2778
Turner, K. J., Vasu, V., & Griffin, D. K. (2019). Telomere Biology and Human Phenotype. Cells, 8(1), 73. https://doi.org/10.3390/cells8010073
U.S. National Library of Medicine. (n.d.). Home - SRA - NCBI. National Center for Biotechnology Information - SRA. Retrieved from https://www.ncbi.nlm.nih.gov/sra
Ureta-Vidal, A., Ettwiller, L., & Birney, E. (2003). Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nature reviews. Genetics, 4(4), 251–262. https://doi.org/10.1038/nrg1055
Wall, J. D., & Pritchard, J. K. (2003). Haplotype blocks and linkage disequilibrium in the human genome. Nature reviews. Genetics, 4(8), 587–597. https://doi.org/10.1038/nrg1129
Wang, G., & Vasquez, K. M. (2022). Dynamic alternative DNA structures in biology and disease. Nature reviews. Genetics, 10.1038/s41576-022-00539-9. Advance online publication. https://doi.org/10.1038/s41576-022-00539-9
Weake, V. M., & Workman, J. L. (2010). Inducible gene expression: diverse regulatory mechanisms. Nature reviews. Genetics, 11(6), 426–437. https://doi.org/10.1038/nrg2786
Wilkins, J. F., & Haig, D. (2003). What good is genomic imprinting: the function of parent-specific gene expression. Nature reviews. Genetics, 4(5), 359–368. https://doi.org/10.1038/nrg1064
Wood, A. J., Severson, A. F., & Meyer, B. J. (2010). Condensin and cohesin complexity: the expanding repertoire of functions. Nature reviews. Genetics, 11(6), 391–404. https://doi.org/10.1038/nrg2805
Wright, A. F., Chakarova, C. F., Abd El-Aziz, M. M., & Bhattacharya, S. S. (2010). Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait. Nature reviews. Genetics, 11(4), 273–284. https://doi.org/10.1038/nrg2719
Yi, E., Chamorro González, R., Henssen, A. G., & Verhaak, R. G. W. (2022). Extrachromosomal DNA amplifications in cancer. Nature reviews. Genetics, 23(12), 760–771. https://doi.org/10.1038/s41576-022-00521-9
Yook K. Complementation. 2005 Oct 6. In: WormBook: The Online Review of C. elegans Biology [Internet]. Pasadena (CA): WormBook; 2005-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK19726/
Zhdanova N. S. (2002). Radiatsionnoe kartirovanie genomov. Nastoiashchee i budushchee [Genome radiation hybrid mapping: summary and future directions]. Genetika, 38(5), 581–594.
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