• Discussed Wnt signaling pathway
• Wnt is ligand, binds to receptor (Frizzled, 7-pass), activates cascading pathway
• One part near the end of this are TCF family of DNA binding proteins, have C-terminal domain that binds beta-catenin (activator) as well as HMG-NLS domain
• Beta-catenin accumulation → constitutively active TCFs → abberant regulation
• Regulate (by activation at least) cell cycle proteins, what else?
• Particular member of the family (TCF1) has extra DNA binding domain (other than HMG group that all in the family share) in E-tail (called C-clamp)
• Does having C-clamp allow it to bind to other targets, or more strongly to some known targets?
• For some reason, mutations show up first (often) in intestines/colon
• Microarray performed by Waterman lab (unpublished) shows genes differentially expressed in cancer cells with different forms of TCF expressed (one normal, one missing beta-catenin domain), both with C-clamp
• Look at expression difference, expect constitutively active version w/o B-cat domain to have genes increased in activity

• Went over phastcons scoring method
• One state models phylogenetic tree of conserved regions (with different states for codon position)
• One state models non-conserved regions (multiple types of background

• Discussion of modeling txn reaction, metabolic, etc. networks
• Using machine learning (SVM, kernels) to get edges in the matrices
• ODES governing these systems

• Updated graph image generation in R of stats about motifs, genes
• Downloaded PhastCons scores and RP scores for the new motif Nate described (more flexibility in 3′ end - instead of RCCG)
• Generated stats images for original motifs

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More Hoosier goodness - the 24th ranked Indiana Hoosiers just beat Illinois today! Go IU! I got to see the end of the game after #2 UCLA lost to the Mountaineers. Anyways, thats enough for now!

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I also went skiing for the first time over Winter Break, that was an experience! Thanks Melissa for trying to teach me, and staying somewhat patient. I can at least get down the mountain in one piece!

Not much else going on, hoping to find some time to go ski again, but need to get some winter clothes first!

Research is going, although it has been stalled over break. Going to start in earnest now!

Edit: Why is it warmer in Indiana than in SoCal right now?!?! WTF, mate…

I work in the lab of Pierre Baldi, a prominent computer scientist working on bioinformatics and chemical informatics projects. I am working with a sub group of this lab on the system called ChemDB, which is a database of ~4 milliion chemical structures. Right now, I am working on comparing different similarity measures of molecules - if you have two molecules, how do you determine how similar they are? This project is well underway, and I have some results. The project I have lined up next is to examine some data structures to support fast searching of the database.

My advisor has ~15 students working under him (that’s a lot!) Some of them that I work/hang out with frequently are Ramzi (from Lebanon) and Chayan (from Albuquerque). Ramzi’s girlfriend Kristina (from Sweden) is also around a lot. Some other people I’ve met work in machine learning such as Lars (from Deutschland), Dave, and Todd.

I just finished my 5-week surfing class yesterday! I’ve learned how to maneuver on the board, and can stand up and go straight on my own waves. Surfing is a lot of fun, but it will have to take the backseat for a while, because I don’t have a board or a wetsuit, and its getting a little cold for going without. I met a lot of great people through the class, we all went out to a bar last night after the class. Two of the instructors are brothers about my age who have been teaching surfing for 10 years. Two of the students (Rupert and Joe) are from the London area, and they brought with them some other British friends to the bar. There is a girl from Spain (Maria), and one other girl (Alexandra) that I know. The other people in the class didn’t really stick around to party! Hopefully we will get together again to surf (or drink!)

I am still doing Tae Kwon Do, right now through a class through the Rec Center at UCI. It is going well, although unfortunately more geared toward sparring than I would like. I am really enjoying learning the sport aspect of TKD, but I miss the traditional part that I know from IUTKD (the people aren’t as cool either, but they are awesome too!) I did start learning the Tae Guk forms though, so I will have something to teach you IUTKD’ers when I come back! One of the girls in the class is also supposed to teach me Hap Ki Do forms (from Jin Pal Hap Ki Do) There are about 15 people in the class, with 1/2 being black belts. However, about 1/2 of the black belts haven’t trained for over 5 years and are just coming back. The other half are really good and have been training for an average of 10 years. I am also involved (partly) in getting a TKD sparring club up and running. I’ll probably end up as the webmaster! Go figure. Our goal is to join the Pac West Tae Kwon Do Conference and have a competitive team. So, we are trying to recruit (there have to be people with a 70% Asian population on campus!) and find a coach.

I have also started training in Iaido, the Japanese art of simultaneously drawing and cutting with the samurai sword. Check out a video here. This is much different than the physically strenous activity of TKD, and is much more internal. A short explanation is this art is like Wild West dueling: two people with swords, whoever draws and cuts faster walks away, and the other person is dead. The stresses in this art are focus and concentration, etiquette (lapses of this are the main reason for getting into a duel in the first place!), posture, and body control. The instructor is David Otaguro, who has been practicing for about 15 years. The style of Iaido we do is Suio-ryu Iaido, one of the oldest schools of Iaido in existence, and one of the Japanese martial arts known as Koryu, or ancient arts. This means there are written, verified records of the art over a period of at least 500 (Thanks David!) lot of years. The art of Suio-ryu Iaido was developed in the early 17th century. According to our instructor, there are only about 700 people in the world practicing this art, and UCI has the largest group in the United States. The head of the art is Katsuse Yoshimitsu Kagehiro, who has come to UCI to teach as well as groups of students going to Japan to learn from him.

So I think this is enough of an update for now!

http://www.youtube.com/watch?v=P-_CgWugraA

Otherwise, things are good, getting situated just fine. I got a bunch of furniture for my room, check out the pictues page. I’ll be getting my computer monitor (19″ flat widescreen) sometime today. Super excited, I haven’t had a desktop monitor in over a year!

I’ve been working out too, at the beach. Early mornings are nice, the beach opens at 6 am, and I can drive and park about a 5 minute walk from the beach. Since I’m old and go to sleep really early, I can get up around then to go! Practicing forms on the beach is very serene and peaceful, and a good workout on the legs and balance as well. I need to start working out the upper body though if I want to be able to surf!

Next week I start “working”. I’ll only be taking two classes (Research Seminar in Informatics, and Machine Learning), but these don’t start until September 22. Most of my time will be focused on research. I’m going to start my reading list of papers, books, etc. to start narrowing down a research topic, and meet with my professor (Pierre Baldi) to discuss.

I’ll also be in a Tae Kwon Do class, which meets just as IUTKD Club is finishing up (4:00-5:20 PST). So it will feel like I’m there, just a little late. Check out the class and the video about it and the instructor (he’s pretty awesome). Hopefully I’ll also be able to take the Surfing class!

Anyways, I’m going to watch a little more US Open tennis then run some errands on campus.