My PhD Journey in the U.S.

Sausalito – (San Rafael) – Petaluma

Sunday, June 29

168.2 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (6/6) | ★★★★☆

I overslept today and didn’t wake up until 11 a.m. The upside is that I finally slept through the night without a coughing episode, proof that the new medication is working. After I got up, I had brunch and devoted the rest of the day to revising the manuscript. During our last meeting, Professor and co-author post-doc, and I decided to post the work quickly on bioRxiv because research on comparative models is advancing so fast. We also agreed that the study might not be substantial enough to be a stand-alone, peer-reviewed paper, so we’ll likely fold the data into future projects while we keep searching for the right journal. My job now is to incorporate all the comments they left on the draft, which is what I focused on today.

I did take a break to hit the gym. The weather was so gorgeous that I didn’t even need a jacket. Just a T-shirt was enough. I squeezed in a good workout, knocked out a load of laundry, and cleaned up the apartment. All in all, it was a relaxed yet productive Sunday.

Monday, June 30

168.8 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (1/6) | ★★★★

I’ve been thinking about my thesis project and realized it may be inappropriate to share details online at this early stage, so I’ll keep future updates brief.

Today Shokat lab held a group meeting. Bill and Kevan noted that attending every meeting in both labs might be difficult, but since I’m still in the learning phase, I’ll join whenever I can. These sessions let me see the exciting work in both groups and observe how top researchers tackle problems.

In the afternoon, I attended DeGrado lab’s computation subgroup meeting, which clarified the methods currently in use. No one is doing exactly what I plan, but there’s plenty of overlap I can exploit. Right after, I met quickly with Bill to confirm my understanding of the state-of-the-art competing methods. I spent the rest of the day researching for my thesis proposal, squeezing in a workout, and doing meal prep.

Tuesday, July 1

168.8 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (2/6) | ★★★★

I finished reading two papers closely related to my potential thesis project. As you know, diving into a new research area always takes extra time, but it’s definitely rewarding. After an afternoon meeting with Chai, I organized my thesis ideas into two possible directions and sent them to my PIs. I’m hoping for constructive feedback soon. I wrapped up the day with my usual workout. Nothing special after that.

Wednesday, July 2

168.8 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Rest (2/6) | ★★★★

I attended the DeGrado lab group meeting this morning. The topic was highly relevant to my future research direction and helped me understand which (experimental) design factors I need to consider. The work had just been submitted last week, so the presenter wanted solid feedback, which I think is a smart way to tap the collective expertise of a large lab.

In the afternoon, I had a meeting with Bill for our regular check-in and shared my current ideas and concerns about potential obstacles. He’s remarkably sharp… just by looking at a PyMOL session of the protein and its interactome, he was able to pinpoint residues that could be exploited in my project. That level of insight clearly comes from years of training and experience. I’m grateful that my PIs take the time to guide and review my progress so often; choosing the right project is hard, and no new graduate student can do it alone.

Thursday, July 3

167.6 lbs (from 162.6 lbs on Dec 28) | 🏃🏻 Done (3/6) | ★★★★

I had a great meeting with the post-doc who presented at the recent Degrado group meeting. He’s also interested in my project and recommended several new papers, while also pointing out a few caveats. One of those caveats was urgent in my opinion, so I spent the entire day searching for a workaround. I think I’ve found a compensatory approach that lets me pursue my original research without relying on the problematic method. In short, my thesis will require a fluorescent dye, but the one we first wanted is so difficult to obtain, so I’ve identified a suitable substitute.

Later, I discussed the plan with a post-doc who has been helping me. He has worked on small-molecule binder design, so he has taught me a lot about computational methods that I can utilize for my projects. After work, I got in a workout and went to bed early for a trip tomorrow!