Bioinformatics

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)
December 23 December 23

December 9
2. Pairwise alignment and BLAST
postponed due to snow...

December 23 December 23

December 16
2. Pairwise alignment and BLAST
Powerpoint: slides on pairwise alignment from December 2
Powerpoint: Dec 9 (now 16th) lecture; pdf.
Reading: Altschul et al. (1990)
Exercise 2 (due Jan. 4)

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
4. Protein analysis and proteomics
Click for powerpoint or pdf.
Reading: none.
Exercise 4: due Jan. 9

Friday, January 6
5. Multiple sequence alignment
Click for powerpoint or pdf.
Reading: Thompson ClustalW
Optional reading: Feng and Doolittle (1987)
Exercise 5: due Jan. 13

Monday, January 9
6. Molecular phylogeny and evolution
Click for powerpoint or pdf.
Reading: Tree-thinking (2005)
Reading: MEGA3 (2004)
Exercise 6: due Jan. 13

January 11

Friday, January 13
7. Genomics: the tree of life
Click for powerpoint or pdf.
Reading: UCSC browser (2003)
Exercise 7: due Jan. 18

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