Category Archives: Intro Genomics (485)

Material and announcements for the Introduction to Genomics (485) will be posted here

Intro. to Genomics – Spring 2024

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Class time and location
Mon, Wed – 9:30-10:45 (Room: 1st floor, SCI-S-194)
Important dates:
Exam 1: Wednesday 28/2/2024 (10%)
Exam 2: Wednesday 20/3/2024 (10%)
Exam 3: Monday 8/4/2024 (10%)
Exam 4: Wednesday 1/5/2024 (10%)
Report due: Monday 15/4/2024 (10%)
Presentations due: Monday and Wednesday 6-8/5/2024 (10%)
Final Exam: Thursday 23/5/2024 – 11:00-1:00 (40%)

Your report should be typed using Microsoft Word (no lower or upper limit to the report) and be named (YOUR NAME_485). The report should include (to the best of your ability) the following with respect to your organism:

  1. The common and scientific.
  2. The taxonomy.
  3. The closest relatives.
  4. The geographic distribution.
  5. Physical characteristics.
  6. Life cycle.
  7. Any unique information that fascinated you.
 Projects:
  1. Reem Alsayegh (Tuatara, Paper).*/
  2. Saad Almutairi (Asian vine snake, Paper)./
  3. Omar Rashdan (Green anole lizard, Paper).*/
  4. Fatmah Alsahly (Australian dragon lizard, Paper).*/
  5. Dana Altaher (King cobra, Paper)./
  6. Narjes Aleissa (Habu, Paper).*/
  7. Nutaila Almahfudhi (Tiger Rattlesnake, Paper)./
  8. Belqees Almutairi (Anguid lizard, Paper).*/
  9. Duaa Shaher (Leopard gecko, Paper)./
  10. Sara Alwohaib (Guatemalan Beaded Lizard, Paper).*/
  11. Amna Alrashid (Burmese python, Paper)./
  12. (Organism: Common Lizard, Paper)./
 Lecture 1: General Introduction
Lecture 2: History and Review (I)
Lecture 3: History and Review (II)
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 (485_lec6_Sequencing)
Sequencing methods videos:
– Maxam and Gilbert Sequencing
– 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
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:
Make a folder on your desktop named “485 material”.
Do you know what your organism looks like?
Download a high quality photo of your organism.
Visit the wikipedia page of your organism and send a link of the page to your instructor.
14/2/23
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.
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?
16/2/23
Download the pdf of your article into your folder.
Download the supplementary files of your paper into your folder.
Print your article and keep it with you everyday.
DO NOT print your supplementary material.
23/2/2023
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?
30. Can you identify the major components of you scientific paper (Abstract, Intro, M&M, Results, Discussion, and Refs)?
31. In the introduction of your paper, locate the summary paragraph of the study and the detailed objectives (if present).
32. Can you from the introduction of your assigned paper find general information of the organism under investigation?
33. Make a list of the general information regarding your organism that you extracted from the introduction?
34. Are there any information regarding the number of chromosomes and genome architecture of your organism in the introduction?
35. What is the source of DNA used to sequence your organism?
36. What is the sequencing method(s) used in your assigned paper?
37. Make sure that you understand all sequencing methods and specifically the methods in your paper.
38. Send links of YouTube videos of the sequencing methods (your choice) to your instructor.
39. Identify the sequencing strategy used in your paper
40. Send links of YouTube videos of the sequencing strategies to your instructor
41. Identify wether the sequencing single-end or paired-end sequencing was performed in you paper.
42. What is the sequence coverage or sequence depth in your paper
43. What is the total number of reads of your genome?
44. What is the number of contigs in your genome assembly?
45. What is the number of scaffolds in your genome assembly?
46. What is the N50 contig of your genome assembly?
47. What is the N50 scaffold of your genome assembly?
48. What is the size of the largest contig?
49. What is the size of the largest scaffold?
50. Send a draft of your powerpoint presentation to your instructor.
51. What is the number of predicted genes in your organism’s genome? 
52. What is the number of operons in your organism’s genome? (if reported and applicable). 
53. What is the GC content of  your organism’s genome? 
54. What is the average gene size in your organism’s genome? (mention minimum and maximum).
55. What % of your organism’s genome is represented by genes?
56. What is the average number of exons per gene  in your organism’s genome?
57. What is the average number of introns per gene  in your organism’s genome?
58. What is the gene density in your organism’s genome?
59. How many rRNA genes are present in your organism’s genome?
60. How many tRNA genes are present in your organism’s genome?
61. What % of your organism’s genome is represented by repeat elements?
62. What % of your organism’s genome is represented by simple repeats?
63. What % of your organism’s genome is represented by tandem repeat elements?
64. What % of your organism’s genome is represented by psuedo-genes?
65. What % of your organism’s genome is represented by transposable elements?
66. What % of your organism’s genome is represented by LINE elements?
67. What % of your organism’s genome is represented by SINE elements?
68. 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

Intro. to Genomics – Fall 2022

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Class time and location
Sun, Tue, Thur – 12:00-12:50 (Room: SCI-S-119)
 
 
Projects:
Group 1: Felis catus, Presentation:
  1. Bedour Almutairi, Paper, Sup.material.**/
  2. Dalal Almayas, Paper, Sup.material./
  3. Sarah Alresheedy, Paper, Sup.material.*********/
  4. Noor Khanafer, Paper, Sup.material./
Group 2: Canis familiaris, Presentation:
  1. Ghaleya Aldhafeeri, Paper, Sup.material.*****/
  2. Asmaa Alghanem, Paper, Sup.material.*/
  3. Zenab Bahman, Paper, Sup.material.****/
  4. Fatemah Alhusain, Paper, Sup.material./
Group 3: Equus caballus, Presentation:
  1. Maryam Alhajri, Paper, Sup.material.***/
  2. Shahah Alkharafi, Paper, Sup.material.*/
  3. Haya Alshammari, Paper, Sup.material.*/
  4. Rawan Abdulaziz, Paper, Sup.material.*/
Group 4: Bos taurus, Presentation:
  1. Rana Chami, Paper, Sup.material.*/
  2. Shaha Farhan, Paper, Sup.material./
  3. Shouq Alhazaa, Paper, Sup.material.*********/
  4. Belqees Almutairi, Paper, Sup.material.******/
Group 5: Camelus sp., Presentation:
  1. Nazek Haydar, Paper, Sup.material./
  2. Lin Ataya, Paper, Sup.material.*/
  3. Hajer Alshammari, Paper, Sup.material./
  4. Fatmah Abdullah, Paper, Sup.material.*/
 

Intro. to Genomics – Spring 2022

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Class time and location
Mon, Wed – 9:30-10:45 (Room: SCI-S-218)
Important dates:
Exam 1: Monday 4/4/2022
Exam 2: Wednesday 11/5/2022
 All Presentations due: Wednesday 1/6/2022-6pm
Final Exam: Monday 13/6/20222 – 8:00-10:00
* Paper tasks
* General organism info
* Following instructions
* Presentation tasks
@ Did exceptional work
Projects:
  1. Carica papaya (Nusrat Jahan): paper, sup. material, presentation: .***@/
  2. Vitis vinifera (Fatemah Alshaikh): paper, sup. material, presentation: .*/
  3. Citrullus lanatus (Loulwa Alsalali): paper, sup. material, presentation: .*/
  4. Cucumis melo (Shekha Alshemeri): paper, sup. material, presentation: .***/
  5. Hevea brasiliensis (Abdullah Alshamali): paper, sup. material, presentation: .*/
  6. Dalbergia odorifera (Batoul Shakhi): paper, sup. material, presentation: .*/
  7. Durio zibethinus (Amnah Alshammari): paper, sup. material, presentation: .*@/
  8. Prunus mume (Lama Alhajeri): paper, sup. material, presentation: .*/
  9. Prunus persica (Mlehah Almurtaji): paper, sup. material, presentation: .@/
  10. Pyrus bretschneideri (Razan Alsejari): paper, sup. material, presentation: .*@/
  11. Rubus occidentalis (Lulwah Alsenan): paper, sup. material, presentation: .*@/
  12. Eriobotrya japonica (Sheimaa Ali): paper, sup. material, presentation: .*/
  13. Theobroma cacao (Kawthar Akbar): paper, sup. material, presentation: ./
 

Intro to Genomics – Fall 2021

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Projects:
  1. Clonorchis sinensis (Sarah Zakzak): paper, presentation: SaraZaqzaq_485./
  2. Echinococcus multilocularis (Hanan Alshuraian): paper, presentation: HananAlshuraian_485.*/
  3. Schistosoma haematobium (Ali Ahmad): paper, presentation: AliAhmad_485.*/
  4. Schistosoma japonicum (Dalal Alnisof): paper, presentation: DalalAlnisof_485./
  5. Schistosoma mansoni (Arwa Khalil): paper, presentation: ArwaKhaled_485./
  6. Ancylostoma ceylanicum (Kaled Yacob): paper, presentation: KhaledYacob_485.**/
  7. Ascaris suum (Nora Alsaeed): paper, presentation: NoraAlsaeed_485./
  8. Brugia malayi (Hajar Alhajeri): paper, presentation: HajarAlhajiri_485./
  9. Loa loa (Mahdi Ghaedi): paper, presentation: MehdiGhaedi_485./
  10. Necator americanus (Mutlaq Alobayed): paper, presentation: MotluqAlobuied_485.***/
  11. Trichuris trichiura (Abrar Alsharaf): paper, presentation: AbrarAlsharaf_485./
  12. Eisenia fetida (Ahmad Dashti): paper, presentation: AhmadDashti_485.**/

Intro to Genomics Spring 2021

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Projects:
1. Moniliophthora perniciosa (Dalal Alzabi): paper, presentation: Dalal_485./
2. Chinese Auricularia (Shaza Alabdulhadi): paper, presentation: ./
3. Périgord black truffle (Nourah Abuadel): paper, presentation: Nourah_485./
4. Sword-belt Mushroom (Fatmah Muqeem): paper, presentation: Fatmah_485./
5. Shiitake mushroom (Arwa Khalil): paper, presentation: .*/
6. Schizophyllum commune (Mai Almarzooq): paper, presentation: mai_485./

Intro to Genomics – Fall 2020

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* Paper tasks
* Videos
* General organism info
* Presentation tasks
Projects:
1. Moon Jellyfish (Aisha Cender): paper, presentation: aishacender_485.****/
2. Sea Anemone (Bdoor Abouabbas): paper, presentation: None.****/**/
3. Coral (Natalie Dorra): paper, presentation.**
4. Sea Cucumber (Sara Alashqar): paper, presentation: sara alashqar_485.**/
5. Sea Urchin (Shahd Alshuhab): paper, presentation: ShahadAlshehab-485.*****/*/
6. Tunicate (Abdulaziz Shayea): paper, presentation: Abdulaziz_485./
7. Lancelet (Abdulatif Alfulaij): paper, presentation: Abdulatif_485.***/
8. Sea Lamprey (Kafiah Alenezi): paper, presentation.********
9. Whale Shark (Aishah Alfailakawi): paper, presentation: AishaAlfailakawy_485.*/
10. Siamese Fighting Fish (Loulwa Mohammad): paper, presentation: Lulwa_485.***/*/
11. Barred Knifejaw (Aminah Alenezi): paper, presentation: AminaAlenzi-485.*/
12. Cavefish (Raghad Alrefaei): paper, presentation: Raghad-485.*/
13. Tilapia (Noah Mohamed): paper, presentation: Noah_485.*/
14. Coelacanth (Nashmeiah Alshammari): paper, presentation: Nashmeiah_485.**/
15. Northern Pike (Eiman Alsayegh): paper, presentation: EmanAlsayegh_485.***/**/*
16. Icefish (Heyam Qamhiya): paper, presentation.**
17. Snakehead (Hafisa Albadi): paper, presentation: HafsaAlbadi_485./
18. Croaker (Sheimaa Ali): paper, presentation: SHeimaaALali.******/*/
19. Dragonfish (Ayah Alattar): paper, presentation: AyahAlattar_485.***/**/
20. Puffer fish (Fatima Ali): paper, presentation: None.**/
21. Chinook Salmon (Mallak Alrasabiya): paper, presentation: MallakSaleh_485./
22. Black Rockfish (Sara Alsrayea): paper, presentation: SaraAlsrayea_485.*/
23. Channel Catfish (Muneerah Alsabah): paper, presentation: Muneerah.H.AlSabah catfish.*******/**/**
24. Ocean Sunfish (Mohamed Abdellatif): paper, presentation: None.**/**/**
 

Intro to Genomics – Spring 2020

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Projects:
Afnan (Pepper1, Pepper2, AfnanKhaled_485)
Anwar (Lettuce, AnwarAlarbash_485)
Zahraa (Cabbage, ZahraaHasan_485)
Abeer (Tomato1, Tomato2, AbeerAli_485)
Fatima (Carrot, FatimaHaidar_485)
Nehaya (Potato, Nehaia_485)
Amna (Sugar Beet, AmnaAbdullah_485)
Amal (Cucumber1, Cucumber2, AmalAlotaibi_485)
Muneera (Eggplant1, Muneerah_485)
Bader (Pumpkin1, Pumpkin2, Presentation)
Nadine (Asparagus1, Asparagus2, NadineOsama_485)
Nada (Cauliflower, NadaAlhadidi_485) 

Introduction to Genomics (485) – Several classes

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Fall 2019
Group 1: Popular insects
(Nouf: Argentine Ant, Muneera: Bee, Habiba: Butterfly, Baty: Longhorned Beetle, Maryam M: Cockroach)
Presentation: 485_Insects
 
Group 2: Farm birds
(Fajer: Turkey, Maryam: Pigeon1 Pigeon2, Fatima A: Red Junglefowl, Sara: Duck, Shrouq: Ostrich1 Ostrich2)
Presentation: 485_Farmbirds
 
Group 3: Reptiles
(Fatma G: Giant Tortoise, Fatma A: Green Anole Lizard, Zainab: Komodo Dragon, Fatima J: Crocodilian, Hanan: Snake)
Presentation: 485_Reptiles
 
Group 4: Edible fish
(Noor: Salmon, Haneen: Rainbow Trout, Shouq: Tuna, Haya: Sardine, Aisha: Sea bass)
Presentation: 485_EdibleFish
 
Group 5: Exotic mammals
(Hana: Giant Panda, Shaikha: Koala, Bashayer: Platypus, Amna: Kangaroo, Heba: Giraffe)
Presentation: 485_ExoticMammals

Fall 2015:

Rana (E.coli), Albandary (Arabidopsis), Fahad (Zebrafish), Tasneem (C. elegans), Iman (phage), Fatemah (Corn), Shuroq (Mouse), Maliha (Fly), Sakina (Thermus, thermophilus, Oceanithermus profundus, Deinococcus radiodurans), Randa (Yeast), Ali (Human)