Introduction to Genomics Fall 2025

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Class time and location
Mon, Wed – 9:30-10:45 (Room: 1st floor, SCI-S-123)
Important dates:
Attendance and activity (5%)
Exam 1: Monday 6/10/2025 (15%)
Exam 2: Monday 27/10/2025 (15%)
Exam 3: Wednesday 19/11/2025 (15%)
Exam 4: Wednesday 10/12/2025 (15%)
Four exams and each is worth (15%). The lowest will be dropped. Therefore, the best three exams will count to your final grades (45%)
Report due: Saturday 20/12/2025 (10%) – send pdf by university email.
Presentation due: 15,17,22/12/2025 (10%)
Final exam: Monday 5/1/2026 12-2 (40%)

Download the following file and use it as your report (File). Your report should be typed using Microsoft Word and updated every week. You should send a copy of your file EVERY Saturday before 6pm. The report should include (to the best of your ability) the following with respect to your organism:

  1. Your paper’s title, journal, and year published.
  2. The objective(s) of your paper.
  3. The common and scientific name of your organism. Try to include the meaning of the scientific name.
  4. The number of species under the genus of your organism.
  5. The taxonomy of your organism.
  6. A high-quality photo of your organism.
  7. The life cycle of your organism.
  8. The geographic distribution of your organism.
  9. Unique (if any) physical, physiological, or biochemical characteristics your organism.
  10. The biological sample used to sequence the genome.
  11. The number of chromosomes (2n) of your organism.
  12. A clipart picture (if available) of your organism. Visit (https://www.phylopic.org/) to obtain one.
  13. The sequencing strategy.
  14. The sequencing method(s).
  15. The number of sequence reads.
  16. The total amount of sequence (in Mb or GB) obtained.
  17. The size of the genome (in Mb or Gb).
  18. The sequence coverage (depth).
  19. The number of contigs.
  20. The number of scaffolds.
  21. The average contig length.
  22. The average scaffold length.
  23. The N50 contig size.
  24. The N50 scaffold size.
  25. The size of the largest contig.
  26. The size of the largest scaffold.
  27. The GC content of  your organism’s genome.
  28. The number of predicted genes. 
  29. The % of the genome that is represented by genes.
  30. The number of protein-coding genes. 
  31. The number of rRNA genes.
  32. The number of tRNA genes.
 Projects:
  1. SHAYMAA ALKANDARI (Locusta migratoria, paper)./
  2. BELQEES ALMUTAIRI (Cydia pomonella, paper)./
  3. ABRAR ALHAJRI (Bombyx mori, paper).*******/
  4. JOURI ALMUTAIRI (Danaus plexippus, paper).****/
  5. AHMAD ALADEL (Rhodnius prolixus, paper).***/
  6. MANAYER ALKHATEM (Acyrthosiphon pisum, paper).***/
  7. REEMIAH ALHULAILI (Pogonomyrmex barbatus, paper).***/
  8. FARAH ALHBIARH (Anopheles gambiae, paper).*****/
  9. SHAIMAA ALAJMI (Aldrichina grahami, paper)./
  10. NADIAH ALOTAIBI (Photinus pyralis, paper)./
  11. BASHAIR ALHAJRI (Trypoxylus dichotomus, paper).*/
  12. ALTHURAYA ALASKAR (Apis mellifera, paper)./
  13. ALYAA ALAJMI (Tribolium castaneum, paper).**/
  14. AMEL AL-SHAYEA (Sarcophaga bullata, paper).***/
  15. BATOUL JAMAL (Tenodera sinensis, paper)./
  16. MUNEERAH ALDAITHAN (Gryllus bimaculatus, paper)./
  17. MANAL AWALEH (Drosophila melanogaster, paper).*/
  18. HAYA ALHINDI (Heliconius melpomene, paper).*/
  19. Nourah Alrashidi (Solenopsis invicta, paper).*/
Lecture 1: General Introduction
Lecture 1.5: Academic Communication
Lecture 2: History and Review (I)
Lecture 3: History and Review (II)
Video: Thomas Morgan & Fruit flies – Thanks to Reemiah Alhulaili
Lecture 4: The genome: the word and beyond
Lecture 5: Exploring the genome: workable pieces
Lecture 5.1: 485_lec5.1_DNAExtraction
Lecture 5.2: 485_lec5.2_DNAQualityQuantity
Lecture 6: DNA sequencing: the thing to the information
Sequencing methods videos:
– Maxam and Gilbert Sequencing (Thanks Althuraya Alaskar)
– Sanger Sequencing, V2
– Pyrosequencing, V2
– Illumina Sequencing, V2
– SOLiD Sequencing
– Ion Torrent Sequencing, V2 
– Oxford Nanopore Sequencing, V2
– PacBio Sequencing, V2
Lecture 7: The sequence: Reading the reads
Sequencing strategies videos:
– Hierarchical Sequencing
– Whole-Genome Shotgun Sequencing (WGS)
– The race to the human genome
– Fluorescence In Situ Hybridization (FISH) (Thanks Althuraya Alaskar)
Lecture 8: Stitching the sequences: Genome assembly
– Sequence Alignment (Abdulatif Alfulaij + Hafsa Aziz)
Lecture 9: The meaning: Genome annotation
Lecture 10: Meaningful parts: coding regions
Lecture 11: Functional annotation
RNAi (Abdulatif Alfulaij, Malak Alrasabiya)
CRISPR-Cas9 (Abdulatif Alfulaij), CRISPR-Cas9 (Malak Alrasabiya)
Lecture 12 : Non-coding genomic elements
Lecture 13 : Genetic transfer
Lecture 14: Polymorphisms
Lecture 15: Population Genetics
To Do:
  • Learn the different forms of communication in science.
  • Learn the different forms of printed scientific communication and their levels of scientific details.
  • Learn the process of publishing scientific papers.
  • Learn the difference between scientific journals and news journals.
  • Make a folder on your desktop named “485 material” to save the files related to the course.
  • What is the common name of your organism? Send your instructor the common name of your organism.
  • Do you know what your organism looks like? Download a high quality photo of your organism.
  • Visit the wikipedia page of your organism. Send a link of the page to your instructor.
  • Learn to do a mindful search for genome papers using keywords and search engines.
  • How do I know that a scientific journal is a good journal?
  • Can you search for the genome sequence paper of your organism?
  • Did you find the same article that your instructor assigned to you?
  • Download the pdf of your article into your folder.
  • Print your article and keep it with you everyday.
  • Download the supplementary files of your paper into your folder.
  • DO NOT print your supplementary material.
  • Identify (1) the journal that your paper was published in, (2) the publisher, (3) year published, (4) authors, (5) volume, (6) issue, (7) doi.
  • How many individuals authored your paper?
  • Circle the name of the first author.
  • Circle the name of the last author.
  • Was your paper authored by a consortium?
  • Why genome papers are authored by many authors? 
  • How many words are used in the title?
  • Circle the following words in the title if present: genome, sequence, organism name.
  • What is the common name of your organism?
  • Is the common name of your organism present in the title?
  • What is the scientific name of your organism?
  • Is the scientific name of your organism present in the title?
  • When titles include scientific names and when titles include a common name?
  •  Does the title of your paper reveal the objective of the study?
  • Read the abstract and locate the objective sentence.
  • Does the abstract of your paper contain an introductory sentence?
  • Can you locate the methods sentence(s) in the abstract of your paper?
  • Can you locate the results sentence(s) in the abstract of your paper?
  • Does the abstract of your paper highlight the significance of the study?
  • Can you identify the major components of you scientific paper (Abstract, Intro, M&M, Results, Discussion, and Refs)?
  • In the introduction of your paper, locate the summary paragraph of the study and the detailed objectives (if present).
  • Can you from the introduction of your assigned paper find general information of the organism under investigation?
  • Make a list of the general information regarding your organism that you extracted from the introduction?
  • Are there any information regarding the number of chromosomes and genome architecture of your organism in the introduction?
  • What is the source of DNA used to sequence your organism?
  • What is the sequencing method(s) used in your assigned paper?
  • Make sure that you understand all sequencing methods and specifically the methods in your paper.
  • Send links of YouTube videos of the sequencing methods (your choice) to your instructor.
  • Identify the sequencing strategy used in your paper
  • Send links of YouTube videos of the sequencing strategies to your instructor
  • Identify wether the sequencing single-end or paired-end sequencing was performed in you paper.
  • What is the sequence coverage or sequence depth in your paper
  • What is the total number of reads of your genome?
  • What is the number of contigs in your genome assembly?
  • What is the number of scaffolds in your genome assembly?
  • What is the N50 contig of your genome assembly?
  • What is the N50 scaffold of your genome assembly?
  • What is the size of the largest contig?
  • What is the size of the largest scaffold?
  • Send a draft of your powerpoint presentation to your instructor.
  • What is the number of predicted genes in your organism’s genome? 
  • What is the number of operons in your organism’s genome? (if reported and applicable). 
  • What is the GC content of  your organism’s genome? 
  • What is the average gene size in your organism’s genome? (mention minimum and maximum).
  • What % of your organism’s genome is represented by genes?
  • What is the average number of exons per gene  in your organism’s genome?
  • What is the average number of introns per gene  in your organism’s genome?
  • What is the gene density in your organism’s genome?
  • How many rRNA genes are present in your organism’s genome?
  • How many tRNA genes are present in your organism’s genome?
  • What % of your organism’s genome is represented by repeat elements?
  • What % of your organism’s genome is represented by simple repeats?
  • What % of your organism’s genome is represented by tandem repeat elements?
  • What % of your organism’s genome is represented by psuedo-genes?
  • What % of your organism’s genome is represented by transposable elements?
  • What % of your organism’s genome is represented by LINE elements?
  • What % of your organism’s genome is represented by SINE elements?
  • Send your final summary of data collection Excel file (Fall2020_genomic_data_YourName).
Data collection (YourName_485_data)
Presentation template (PresentationTemplate_485)

Suggested reading material

My Genomics teaching style: Laying a string NOT filling a vessel.
“What is a genome?” by Aaron David Goldman1 and Laura F. Landweber
Evolution of DNA Sequencing by Jonathan Eisen
Figures, photos, and graphs in my lectures are collected using google searches.  I do not claim to have personally produced the material (except for some). I do cite only articles or books used. I thank all owners of the visual aid that I use and apologize for not citing each individual item.  If anybody finds the inclusion of their material in my lectures a violation of their copy rights, please contact me via email.

hhalhaddad@gmail.com