Johns Hopkins School of Medicine M.E:800.707
The use of computers has revolutionized biological research. This BCMB core course provides an introduction to bioinformatics, the combined field of biology and informatics (information science and technology). The course focuses on the analysis of proteins, genes, and genomes.
Prerequisites: None. Students may sign up with the Registrar's Office (School of Medicine) to take the course for credit. Auditors (including postdoctoral fellows) are welcome but are requested to register.
Format: West Lecture Hall, Wood Basic Science Building, given 9:00-10:30 a.m. on the dates indicated below. There are seven lectures plus one in-class exam.
Instructor: Jonathan Pevsner
(443-923-2686; pevsner@kennedykrieger.org). My office is 400-D Kennedy Krieger.
Textbook: None is required. I have written a textbook that is based on the lectures given in this course: J. Pevsner, Bioinformatics and Functional Genomics (John Wiley & Sons, 2003). Several copies will be on reserve at Welch Library (reference desk), where you can sign them out for several hours at a time. If you choose, you can order the book through the Matthews Johns Hopkins Medical Book Center (i.e. the bookstore) or at Amazon or Barnes & Noble. Website for textbook: http://www.bioinfbook.org.
Computers: You are encouraged to bring a laptop to class (this is optional). Wireless is available.
Readings: One or two published papers will be assigned for each class. PDFs are posted below.
Grading: 50% of grade is based on problem sets (described below), and 50% is based on an in-class, cumulative final exam given Wednesday, January 18.
Problem sets: For each lecture, there will be a take-home, open-book, unlimited time exercise. There are seven problem sets; we will grade you based on your best five scores (thus counting for 50% of your final grade). The exercises are designed for you to go to a computer and apply what you have learned in each lecture (for example, after the BLAST lecture you will do a BLAST search; after the phylogeny lecture you will make a phylogenetic tree). Each problem set will be given out the day of its lecture, and you will typically have one week to complete it.
Teaching assistants: Hugh Cahill (email), Mayra Garcia (email), Jennifer Turney (email).
Monday | Wednesday | Friday |
December 2 1. Introduction to bioinformatics Lecture powerpoint or pdf Reading: Benson et al. (2005) Reading: Needleman and Wunsch (1970). Exercise 1 (due Dec. 16) |
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December 23 | December 23 | December 9 |
December 23 | December 23 | December 16 |
December 19 3. Gene expression: microarrays Click for powerpoint or pdf. Reading: Barrett et al. (2005) Exercise 3 (due Jan. 6) |
December 21 | December 23 |
December 26 | December 28 | December 30, 2005 |
January 2, 2006 NOTE: Special optional session on Tuesday, January 3, 2-3pm, room 510 KKI |
Wed., January 4, 2006 |
Friday, January 6 |
Monday, January 9 |
January 11 | Friday, January 13 |
January 16 | Wed., January 18 Final exam (in class) |
Your name | Your accession number | Your name | Your accession number | Your name | Your accession number |
Agyeman, Abena | NM_005212 | Hlavin, Erica | NM_000518 | Reynolds, Taylor | NP_002924 |
Allen, Diana | NM_002289 | Horn, Troy | NM_001963 | Richardson, Sarah | NP_000055 |
Ao, Yang | NM_000490 | Howard, Jason | NM_000928 | Robinson, Jon | NP_000509 |
Augustine, Mathew | NM_000476 | Huang, Elizabeth | NP_005203 | Rotty, Jeremy | NP_001954 |
Ballard, Matthew | NM_005143 | Huang, Qing | NP_002280 | Ruch, Travis | NP_000919 |
Bangash, Muhammad | NM_000477 | Hubbi, Maimon | NP_000481 | Saint-Fleur, | NM_000315 |
Beattie, Matthew | NM_000365 | Hughes, Adam | NP_000467 | Sample, Vedangi | NM_000805 |
Beese, Sara | NM_000948 | Jeong, Young | NP_005134 | Santoso, Netty | NM_001033952 |
Berk, Jason | NM_000067 | Jin, Peng | NP_000468 | Shen, Lin | NM_000894 |
Bitok, John | NM_000558 | Johnson, Florence | NP_000356 | Simons, Brian | NM_003381 |
Boto, Agedi | NM_000239 | Johnston, Henry | NP_000939 | Smith, Justin | NM_002933 |
Brown, Allison | NM_005368 | Kalra, Deepak | NP_000058 | Speed, Traci | NM_000064 |
Bruno, Tullia | NM_002506 | Kang, Di | NP_000549 | Spencer, Jeanelle | NM_000518 |
Bullen, John. | NM_001025081 | Keefe, Megan | NP_000230 | Stanley, Erin | NM_001963 |
Byrne, Sean | NM_002854 | Koldobskiy, Michael | NP_005359 | Stine, Zachary | NM_000928 |
Castanares, Mark | NM_002769 | Lan, Zheng | NP_002497 | Szymanski, Megan | NP_005203 |
Chiang, Po-Min | NM_000207 | Lee, Chih-Yung | NP_001020252 | Titov, Denis | NP_002280 |
Cho, Joong | NM_002046 | Lee, Daniel | NP_002845 | Todd Bridget | NP_000481 |
Cranmer, Lisa | NP_005134 | Lee, Ji | NP_002760 | Trow, Jonathan | NP_000467 |
D'Ambola, James | NM_018947 | Lee, Yun-Sil | NP_000198 | Vendetti, Frank | NP_005134 |
Das, Ishita | NM_003279 | Lew. Stefanie | NP_002037 | Vo, Lauren | NP_000468 |
Davidson, Abigail | NM_001885 | Li, Xiaojie | NP_061820 | Wang, Wei | NP_000356 |
Delgoffe, Greg | NM_002054 | Liu, Dan | NP_001634 | Wasserman, David | NP_000939 |
Drummond, Robert | NM_005271 | Liu, Yangfan | NP_003270 | Weber, Genevieve | NP_000058 |
DuFresne, Andrew | NM_003528 | Mandelker, Diana | NP_001876 | Webster, Marie | NP_002497 |
Eyler, Daniel | NM_021009 | McGaughey, David | NP_002045 | Wind, Jennifer | NP_001020252 |
Follstaedt, Susan | NM_000088 | McVey, Emily | NP_005262 | Wind-Rotolo, Megan | NP_002845 |
Gan, Xin | NM_000939 | Mihalas, Anca | NP_003519 | Woodard, Crystal | NP_002760 |
Garay, Joseph | NM_000549 | Moorthy, Anita | NP_066289 | Wu, Zhuhao | NP_000198 |
Garver, Lindsey | NM_005143 | Muend, Sabina | NP_000079 | Xi, Zhiyong | NM_001643 |
Gertz, Barry | NM_000315 | Nicholson, Michael | NP_000930 | Yang, Mei | NP_002037 |
Gisselberg, Jolyn | NM_000805 | Oku, Yuko | NP_000540 | Yarrington, Robert | NP_061820 |
Greenberg, Kathleen | NM_001033952 | Page, Stephen | NP_000306 | Yun, Jihye | NP_003270 |
Greene, Eriko | NM_000894 | Pashos, Evanthia | NP_000796 | Zhang, Yang | NP_001876 |
Haggerty, Christine | NM_003381 | Pradhan, Dennis | NP_001029124 | Zhu, Jianmei | NM_021009 |
Hanigan, Christin | NM_002933 | Prasad, Megana | NP_000885 | Zonies, Seth | NM_000088 |
He, Shan | NM_000064 | Reaves, Erica | NP_003372 |