UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE
Study programmes & Course catalogue
for academic year 2023/2024
UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE
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Course: Introduction to Genomics

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Course title Introduction to Genomics
Course code KMB/358
Organizational form of instruction Lecture + Lesson
Level of course Bachelor
Year of study 2
Frequency of the course In each academic year, in the summer semester.
Semester Summer
Number of ECTS credits 3
Language of instruction English
Status of course Compulsory
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Course availability The course is available to visiting students
Lecturer(s)
  • Horák Aleš, Mgr. Ph.D.
  • Bruce Alexander William, prof. Ph.D.
  • Tukur Hammed Abolade
Course content
This course will be split into a traditionally lecture taught component covering theoretical knowledge (x7 ~2h lectures) compromising 35% of the final grade (as assessed by an end of semester multiple choice question exam) and practical hands-on (computer based) series of sessions (x5 ~2 hour each) in which course relevant problem solving exercises will be addressed (and assessed, contributing the final 65% of the course grade). Content of courses: - Introduction to the 'Genome' (definition of the genome/genetic material, types and variety of genome in biology, genome-transcriptome-proteome central dogma, genome structure i.e. concept of genes, regulatory elements and repetitive DNA, genome organisation i.e. chromosomes and histones/ chromatin, DNA replication). - Historical overview of first 'Genomic' methods . Introduction to nucleic acid sequencing from a historical perspective; first organisms - bacteriophages (MS2 PhiX174), bacteria (E. coli), first eukaryotic genomes. Sequencing of human genome. Individual research group led DNA sequencing of specific loci of more complex organisms. Creation of common databases for this information - need to consolidate and coordinate DNA sequencing efforts - Scaled-up DNA sequencing to tackle larger genomes (use of human genome project as a case study). - Historical perspective and public versus private initiatives. Techniques used to perform large scale sequencing, Genome sequencing of model organisms - which, how and why? Creation of synthetic organisms (Craig Venter). - Interpreting the sequenced genome - identifying genes/ transcripts in the sequence and cataloguing them - birth of 'Bioinformatics'. Databases, Development of more sophisticated genome browsers with increasing amounts of annotation. 'Gene cards' and gene specific information features and using BLAST searches to identify experimentally derived sequences against the genome sequence reference. Practical examples of genome search in human genome. - Genome evolution, historical concepts of genome evolution, evolutionary forces that shape the structure and content of the genomes, changes in genomes related to the life-history of organisms - Applying genomics at the bench (development of numerous experimental strategies e.g. originally microarray based now based on novel large scale sequencing technologies) - inclusion of relevant case study examples e.g. the international ENCODE consortium - Depositing, retrieving and interpreting bench-based genomic experiment data/ results - cross referencing with our experimental databases and web resources Content of practicals: Computer based problem solving exercises - accessing on line Genome browsers and Genomics data repositories.

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Work with text (with textbook, with book), Practical training
  • Preparation for credit - 5 hours per semester
  • Preparation for classes - 42 hours per semester
  • Preparation for exam - 20 hours per semester
  • Class attendance - 20 hours per semester
Learning outcomes
To provide participating students (of all levels; Bachelors, Masters and Ph.D. level) with a solid foundation in the basics of genome research that can act as a basis for further lecture series within the Bioinformatics program and beyond.
Students successfully navigating this combined course of theory learning and practical implementation will have received a foundational education as to biological questions can be addressed on the whole genome scale and how to generate such data, curate it and ultimately utilise it. This course will act as a primer for future more in-depth and specialised courses offered (for example in the field of Bioinformatics) as well as providing students with Molecular & Cellular Biology and Genetics interests with additional and relevant perspectives relating to these subject areas.
Prerequisites
Enrolling students should have a pre-existing grounding in basic molecular and cellular biology. For example, as taught in the course KMB758. However, the course relevant parts of the KMB758 will be recapped during the first two lectures. Nevertheless a solid and fundamental understanding of basic molecular and cellular biology is necessary.

Assessment methods and criteria
Written examination, Test

Combined examination with a) multiple choice question component (relating to the theory); 35% and b) computer based practical assessment/ problem solving exercise component; 65%) Combined minimum pass grade of 51%. The "basic pass grade" (3) is 51-59%, grade "good" (2.5) is 60-66%, grade "very good" (2) is 67-74%, grade "excellent minus" (1.5) is 75-82% and the grade "excellent" (1) is 83-100%.
Recommended literature
  • Asgard archaea illuminate the origin of eukaryotic cellular complexity. Zaremba-Nedzwiecka et al. 2017. Nature 541, 353-358.
  • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Bradnam KR et al. 2013 Gigascience. 22;2(1).
  • David P. Clark: Molecular Biology Understanding the Genetic Revolution, Academic Cell.
  • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Nat Genet. 2007 Mar;39(3):311-8. Epub 2007 Feb 4.
  • ENCODE whole-genome data in the UCSC Genome Browser. Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. Epub 2009 Nov 17.
  • Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Allen et al. 2011.Nature 473, 203-207.
  • Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level. Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, Vetrie D. Genome Res. 2009 Jun;19(6):994-1005. Epub 2009 Apr 28.
  • Genome reduction as the dominant mode of evolution. Wolf Y, Koonin EV. 2013. Bioessays 35 (9):829-837.
  • Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Roh TY, Wei G, Farrell CM, Zhao K. Genome Res. 2007 Jan;17(1):74-81. Epub 2006 Nov 29.
  • Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ. Genome Res. 2008 Dec;18(12):1906-17. Epub 2008 Sep 11.
  • Genomic approaches uncover increasing complexities in the regulatory landscape at the human SCL (TAL1) locus. Dhami P, Bruce AW, Jim JH, Dillon SC, Hall A, Cooper JL, Bonhoure N, Chiang K, Ellis PD, Langford C, Andrews RM, Vetrie D. PLoS One. 2010 Feb 5;5(2):e9059.
  • High-resolution profiling of histone methylations in the human genome. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. Cell. 2007 May 18;129(4):823-37.
  • https://genohub.com/next-generation-sequencing-guide/.
  • Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Johnson R, Gamblin RJ, Ooi L, Bruce AW, Donaldson IJ, Westhead DR, Wood IC, Jackson RM, Buckley NJ. Nucleic Acids Res. 2006;34(14):3862-77. Epub 2006 Aug 9.
  • Prediction of regulatory elements in mammalian genomes using chromatin signatures. Won KJ, Chepelev I, Ren B, Wang W. BMC Bioinformatics. 2008 Dec 18;9:547.
  • The landscape of histone modifications across 1% of the human genome in five human cell lines. Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I. Genome Res. 2007 Jun;17(6):691-707.
  • The origin and early evolution of eukaryotes in the light of phylogenomics. Koonin EV. 2010. Genome Biology 11:209.
  • Tracing the peopling of the world through genomics. Nielsen et al. 2017. Nature 541, 302-310.


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Bioinformatics (1) Category: Informatics courses 1 Recommended year of study:1, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Biological Chemistry (1) Category: Chemistry courses 2 Recommended year of study:2, Recommended semester: Summer
UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE, date of update: 25.04.2024 23:50. Data created for academic year 2023/2024