Embedded Files
Instructor: Prof. INDIKA Rajapakse (indikar@umich.edu)
Teaching Assistant: RAM Prakash (nuvi@umich.edu)
Location: 1200 Chemistry Building, Class Time: Tuesday and Thursday, 8:30 AM - 10:00 AM
Office Hours:
Indika R - Tuesday and Thursday , 4:00 PM - 5:00 PM: https://meet.google.com/dnm-zipr-tsb or in person after class
Ram P - Wednesday 3:00 - 4:00 PM Zoom and Friday 3:00 PM - 4:00 PM in person Room 3370, NCRC B520
James Simons: My Guiding Principles
Links
Canvas, Piazza, and Comments/feedback
MATLAB: 1) MATLAB Tutorial 2) Basic Functions Reference
A service course on linear algebra regularly taught by Gil Strang. Here is the course webpage.
Recommended Reading Material
Dr. Cleve Book: Numerical Computing with MATLAB
Jon Kleinberg's Book: Networks, Crowds, and Markets
Francesco Bullo's Book: Lectures on Network Systems
Albert-László Barabási's Book: Network Science
References of Interest
Great Blogs! I visit these from time to time, and they have many great articles: Cleve Moler's Blog and Bits of DNA
PROBLEM SETS
PROBLEM SETS
PS1: Due September 9, 2025
Computing the Normalized Laplacian Matrix
PS2: Due September 30, 2025
Data: PS2_data.mat
MATLAB Starter Code: PS2_code.mlx
PROBLEM OF THE DAY
PROBLEM OF THE DAY
NOTES, SLIDES, AND PAPERS
NOTES, SLIDES, AND PAPERS
Date: 08-26-2025
Date: 08-26-2025
Introduction: Slides
Papers
Turing, Alan Mathison. "The chemical basis of morphogenesis." Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1666), p.20140218. (Classic!)
Rajapakse I. "Conversation with Dr. Steve Smale and Dr. Lee Hartwell." NOTICES OF THE AMERICAN MATHEMATICAL SOCIETY, 68 (9).
Date: 8-28-2025
Date: 8-28-2025
Quote of the Day
"Optimism is the faith that leads to achievement. Nothing can be done without hope and confidence" ― Helen Keller
Notes
Papers
Small World: Watts, Duncan J., and Steven H. Strogatz. "Collective dynamics of ‘small-world’networks." Nature 393.6684 (1998): 440-442.
Small World: Milgram, Stanley. "The small world problem." Psychology today 2, no. 1 (1967): 60-67.
Scale-free: Barabási, Albert-László, and Réka Albert. "Emergence of scaling in random networks." Science 286, no. 5439 (1999): 509-512.
FUN readings.....
Alon, Uri. "Biological networks: the tinkerer as an engineer." Science 301.5641 (2003): 1866-1867.
Date: 09- 02-2025
Date: 09- 02-2025
Quote of the Day
"If you don’t believe in yourself why is anyone else going to believe in you?" ― Tom Brady
Notes
Singular Value Decomposition (SVD)
Date: 09-04-2024
Date: 09-04-2024
Quote of the Day
"No great discovery was ever made without a bold guess" ― Isaac Newton
Notes
Singular Value Decomposition (SVD)
Papers
Turk, Matthew, and Alex Pentland. "Eigenfaces for recognition." Journal of cognitive neuroscience 3.1 (1991): 71-86. (Classic! just browse)
Sweeney P, Chen C, Rajapakse I, Cone R. "Network Dynamics of Hypothalamic Feeding Neurons." Proceedings of the National Academy of Sciences, 118.14 (2021).
Date: 09-09-2025
Date: 09-09-2025
Quote of the Day
"Things won't go perfect. It's all about how you adapt from those things and learn from mistakes" ― Michael Phelps
Notes
Inverse and Pseudoinverse of a Matrix
Papers
Lieberman-Aiden, Erez, ..., Groudine Mark, ..., Lander Eric. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science 326.5950 (2009): 289-293.
Chen H, Chen J, Muir LA, Ronquist S, Meixner W, Ljungman M, Ried T, Smale S, Rajapakse I. "Functional Organization of the Human 4D Nucleome. " Proceedings of the National Academy of Sciences 112.26 (2015): 8002-8007. Supporting Information
Date: 09-11-2025
Date: 09-11-2025
Quote of the Day
"You never lose a dream, it just incubates as a hobby" ― Larry Page
Notes
Date: 09-16-2025
Date: 09-16-2025
Quote of the Day
"Young man, in mathematics you don't understand things. You just get used to them" ― John von Neumann
Guest Lecture: Dr. Cleve Moler
MathWorks Co-Founder and Chief Mathematician Cleve B. Moler
GENERAL READING
GENERAL READING
I will add to this list throughout the semester
Strogatz SH. "Exploring complex networks." Nature. 2001 Mar;410(6825):268-76.
Rajapakse I. "Conversation with Dr. Steve Smale and Dr. Lee Hartwell." NOTICES OF THE AMERICAN MATHEMATICAL SOCIETY, 68 (9).
Hartwell, Leland H., et al. "From molecular to modular cell biology." Nature 402.6761 (1999): C47-C52.
Strogatz, Steven H. "Love affairs and differential equations." Mathematics Magazine 61, no. 1 (1988): 35-35. (FUN read!)
Stephen Hoge:
https://www.youtube.com/watch?v=Rn9sRkkqGT4
https://www.youtube.com/watch?v=1-kHTzt7EVs
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