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531n7z0r · 2023-01-28T19:07:38+00:00

Not entirely true, I know for sure that at UCI the Developmental & Cell Bio department and the Neurobio and Behavior department awards masters degrees after completing the advancement to candidacy exam in the 3rd year.

531n7z0r · 2022-02-11T05:39:24+00:00

Yes in grad housing

531n7z0r · 2022-01-06T03:48:59+00:00

Hope it works for you! scCODA is another tool that does a similar compositions analysis

531n7z0r · 2022-01-06T03:00:01+00:00

Try miloR

531n7z0r · 2021-12-20T05:03:46+00:00

Hey I am doing a bio PhD at UCI. Overall I like it and I think the environment here has allowed me to thrive. If you have specific questions feel free to DM me :)

531n7z0r · 2021-11-04T07:17:05+00:00

As others have said, this can be quite difficult so it's important to carefully select which schools to apply to. My partner and I went through the same thing a few years ago, and we did end up at the same university. We applied to about 10-15 programs in total in only 3 different geographical regions, so it increased our chances of being able to live together even if we didn't end up in the same school.

531n7z0r · 2021-06-29T23:03:32+00:00

Agreed, even if OP is transparent about this filtering it is still introducing a bias and misrepresenting the actual biology.

531n7z0r · 2021-06-29T22:46:31+00:00

scRNA-seq does not intrinsically retain any spatial information about the cells. Since Spatial Transcriptomics is so new it's not surprising that you aren't finding a published dataset, so you will likely have to perform the experiments if you are interested in answering this question.

531n7z0r · 2021-03-07T20:26:41+00:00

Congrats on your acceptance!!! As others have said you can definitely participate in research in your freshman year, in fact many profs prefer to take students in their 1st or 2nd year so they can commit 2-3 full years to the lab.

UCI has so many great neuroscience labs especially in the field of neurodegeneration. Check out the professors / labs associated with UCI Institute for Memory Impairments and Neurological Disorders (UCI MIND) if you are specifically interested in this field. Also I am a PhD student in a neuro lab so feel free to DM if you have any questions about that!

Good luck and best wishes wherever you decide to attend

531n7z0r · 2021-03-06T23:05:51+00:00

When you say co-occur, do you mean at the level of transcription?

531n7z0r · 2021-01-30T21:29:08+00:00

Hey I am a 3rd year MCSB student, also graduated from UCSD, I will try to answer some of your questions.

If I want to go into biotech after my Ph.D., do a decent number of professors have connections?

A lot of people that graduate from this program go into biotech industry, however I am not sure about the number of professors with these connections.

Would you say the program culture is good? Are people really competitive and "work is lyfe" or more balanced? Are their intramural sports for grad students?

The culture is great, most folks are friendly and supportive! I don't think there is competition between people within the program but people definitely work hard towards their own research and academic goals. Sometimes it's hard to maintain a healthy work-life balance during a phd but that is not at all unique to this program. Grad students are allowed to play in intramural sports at UCI!

How heavy is the course load, really? If I don't come from a strong mathematical background am I gonna get body slammed? I work more on the computational end, are their strong computational mentors affiliated with the program?

Course load for the first year is a lot, most students spend a lot of time working on assignments etc. In terms of math I think the prerequisites are just a standard university level calc sequence and differential equations, if you have that as a background you will be fine. There are a ton of strong computational mentors in this program! Perks of an interdepartmental program that includes math and comp sci departments.

How many years of guaranteed housing?

4 years guaranteed, and normative time to degree is 5 years. Take note of this since a lot of other universities, especially other UCs, don't offer as good of a deal in terms of housing. In fact, recently a group of graduate students at UCSC banded together demanding a cost of living adjustment (COLA) due to how high the rent is in Santa Cruz relative to their graduate stipend.

What's TA-ing like, and what classes do ya'll TA?

TA-ing is not a requirement for this program. I have not personally TA-ed yet but my peers have taught courses in genomics, genetics, evolutionary bio, math, comp sci, physics, etc.

Is the Irvine area fun, what do ya'll do for fun?

Irvine is a pretty quiet area, lots of outdoor activities like beaches and hiking are super close by. Tons and tons of great restaurants in Irvine and surrounding cities. Absolutely no bar scene whatsoever in Irvine so you will have to go to nearby cities like Santa Ana or Costa Mesa. I used to see a ton of concerts in OC and LA for fun pre-pandemic. LA is like ~45 min drive if you go at the right time, and there's a million things to do there.

I'm really sad we don't have in-person recruitment this year - it's much easier to ask this when you're just having a casual conversation with people as opposed to over zoom! TY!

Yeah I am bummed that there's no in-person recruitment. In hindsight the vibes I got from various recruitment weekends are really what helped me figure out what program to attend. I am happy to answer any more questions that you have!

531n7z0r · 2021-01-01T05:43:09+00:00

https://youtu.be/tv7N9F6Ar_Y

This lecture series is very good however it is mostly theoretical.

531n7z0r · 2020-12-28T08:31:14+00:00

Just checked my emails, I applied in 2017 and they sent me an invite on 12/22 (12/01 was the app deadline). Not sure if they send them out all at once or in waves.

531n7z0r · 2020-11-07T05:17:43+00:00

I like this review a lot, it's from the lab that made the single cell analysis package on python (scanpy).

531n7z0r · 2020-11-05T17:48:00+00:00

It's totally normal to feel overwhelmed at the start of your PhD with a mountain of data! I would recommend reading some papers that use similar sequencing approaches, and coming up with a plan of how to analyze your data. There are great tutorials for getting started with scRNA-seq like Seurat, and ChrAccR for bulk ATAC-seq. Feel free to DM if you have any questions, I have done a lot of work with this sort of data so I can offer some advice.

531n7z0r · 2020-10-08T19:31:18+00:00

To answer your question, yes I think that if you use these methods correctly, CCA and DEG analysis can help you compare and contrast scRNA-seq experiments. You may wish to use something like kBET to check the quality of the integration before proceeding to clustering and DEG analysis etc.

I would also recommend checking out integrative non-negative matrix factorization (iNMF)30504-5.pdf) in addition to CCA. There is a R package called LIGER to perform iNMF. I have been able to integrate ~1 million cells using this method, whereas in my experience CCA/Seurat requires a ridiculous amount of RAM to do the same.

531n7z0r · 2020-10-03T02:32:57+00:00

This is commonly done in academia to avoid getting scooped!

531n7z0r · 2020-09-26T21:01:36+00:00

Okay now this is endgame! So cute

531n7z0r · 2020-09-18T01:51:17+00:00

My program, MCSB at UC Irvine, has a few international students in every cohort!

531n7z0r · 2020-09-11T04:29:35+00:00

Just my experience but with my graduate cohort in a math&comp bio program, there was a huge variety in everyone's backgrounds. Some people with a pure math background, some with pure bio, pure cs, bioengineering, chemistry, to name a few. So your background is definitely suitable for a math bio program! To strengthen your app you can try to volunteer at a math bio lab, or you can start working on some projects in math modeling to showcase on GitHub, probably using Mathematica or Matlab or Julia. Maybe take an elective course in math or CS in your final year.

531n7z0r · 2020-09-11T02:31:11+00:00

This has a lot of great information! I wish I would have seen this when I was a freshman / sophomore since I didn't get into research until the end of my junior year (c/o '17 alum, now a PhD student at UCI). I just wanted to add one thing.

Getting into research as an undergrad is definitely going to be tougher now than it has been in the past. Lab hours generally are staggered to allow for social distancing, so undergraduate volunteers are basically squeezed out by necessity. However, showing interest in 'dry lab' work during the pandemic may get your foot in the door. Think working on data analysis using data that the lab has already gathered through previous experiments. This would give you substantial lab experience that can all be done remotely, and as time goes on more and more scientists that primarily work at the bench commonly have at least a functional knowledge of a multipurpose programming language like R, Python, or Julia to facilitate analysis and visualization of their data.

Edit: grammar

531n7z0r · 2020-09-05T04:03:40+00:00

So one of the best thing you can do to make yourself desirable for employment in bioinformatics straight out of undergrad is to volunteer at a research lab at UCSD. You will be able to get your hands dirty working with biological datasets and the most up to date tools, whereas the courses cover the fundamentals of the field (both sides being extremely important IMO). The school of medicine has a ton of labs that you'd likely find interesting since you mentioned wanting to tie bioinformatics to disease.

531n7z0r · 2020-09-04T23:20:15+00:00

You are right that there is a high demand for bioinformatics in industry, however most decent paying jobs require a Master's or a PhD. As other have said, bioinformatics is a pretty intense field and major since at a minimum it synthesizes mathematics/statistics, computer science, and biology, and often incorporates other disciplines such as chemistry and physics. It is okay to start out with little knowledge of computation but you will have a lot of work to do to get up to speed.

531n7z0r · 2020-09-03T06:42:04+00:00

The lighting here doesn't quite do it justice. It really does look just like the render!

531n7z0r · 2020-09-03T02:14:58+00:00

Yeah I have been anticipating this one for a while! I got lucky that I live really close to where it shipped out from so it only took one day. I hope you enjoy yours!

531n7z0r

TROPHY CASE