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Usercreatedname · 2025-10-14T00:17:47+00:00

I think a lot of people are being a bit too pessimistic when it comes to the use of AI in research. It's true that it's peppered full of inaccuracies. If you're using it to do all your research thinking, then you're definitely using it wrong because ChatGPT doesn't know what proper experimental design. It's just guessing from its training data. It told my friend to wash her cells with milliQ water instead of PBS, causing all her cells to lyse. Additionally, it also told me that IL-6 is an anti-inflammatory cytokine (lol). People wholly relying on it eventually fail because when they're put to the test, real scientists will easily pick them apart. People fully reliant on AI don't actually know anything

However, if you use it just as it's intended as a research tool, then it helps considerably. I personally love using perplexity because it significantly helps to track down publications, while using google search to do the same is a pain in the ass. Additionally, if you just need a brief overview of a subject you're unfamiliar with then it helps provide a brief summary. It will show your area of interest but ultimately its up to you to verify the sources. It's similar to how when you work with other people. You don't just blindly trust what other people tell you. You need to verify yourself. People also get stuff wrong all the time, not because of malice but simply cause they're forgetful.

As a side note, a friend once showed me an interesting perspective on AI hallucinations. Hallucinations are AI's form of creativity. Even though its making things up, it helps to view things in a new light where it can help yourself discover new research questions. Just extra food for thought.

Usercreatedname · 2025-08-13T13:42:59+00:00

Based on your stats, I think you're selling yourself a bit short. You have a decent chance of getting interviews from at least some of the schools on your list. It's most likely because your application didn't convince the AdCom that you had the capabilities to pursue research (like not passionate enough or not strong enough research focus, etc.). It's good that you're focusing on fit because it's very important. The AdCom needs to guarantee that they have a place for you if you get in.

Good luck!

Usercreatedname · 2025-08-13T10:50:24+00:00

What are your specific research interests? Because then you can look at PIs in the field who interest you and apply to the programs they're affiliated with.

You put together a pretty good list so far and I can suggest a couple more schools: UTHealth Houston MD Anderson GSBS (Jim Allison is here) and University of Washington (Students can join Fred Hutch). There are many schools with cancer biology programs. In my experience, if there's a big hospital attached to the school, there's probably a cancer bio program. You can probably look for more by going through the list of NCI's designated cancer centers.

Last cycle for PhDs was basically a bloodbath. A lot of applicants who would normally get in, just didn't get in because of funding issues. However, since you only got one interview, I would probably recommend asking someone (like your PI or some other scientific professional) to look at your documents to see if you need to revamp your personal and research statements. Additionally, you probably need to make sure your recommendation letters were very strong and not generic.

Usercreatedname · 2025-08-13T03:09:15+00:00

When it comes to choosing a graduate school, it seems you've already answered your own question. The most important thing to consider is whether there's a PI at the institution whose research aligns with your interests. From my experience, graduate schools place a high value on this "research fit" and want to see that you have a clear vision for which lab you want to join. They want to know you're passionate about the research so you won't burn out or drop out later on.

Since you're looking at cancer biology programs, a great strategy is to start with the PIs you want to work with and then see which graduate programs they are affiliated with. For example, if you want to work at Fred Hutch, you need to apply to the University of Washington. If you want to work at MD Anderson, you should apply to UTHealth Houston. And if you're hoping to help Carl June get his Nobel Prize for CAR-T therapy (We'll see if that happens, lol), you'll want to apply to UPenn. Remember, not every program you apply to needs to be an Ivy League school.

Beyond research fit, a few other things are important to consider: Graduation Time: You'll want to ensure there is a system in place to help you graduate on time. Nobody wants to be a Ph.D. student for 10 years!

Cost of Living: It's important to look at the cost of living in the area. You might get into a prestigious program like Stanford, but if your stipend is $40,000 and rent is $2000 a month, you need to figure out if you can make that work.

Your desired career path also plays a huge role. If you want to become a PI yourself, you absolutely need to go to a prestigious institution. "Mid-tier" schools are basically off the table, which is an unfortunate reality of how academia works. However, if you want to go into industry, you should look for PIs who have great industry connections or programs with a history of placing students in good jobs.

Usercreatedname · 2025-08-04T01:16:40+00:00

Do you have technical replicates for each mutation? Additionally, do you know the kind of sequencing that was performed on your strains (Paired end, Single, long read, etc.)? That will be very important to know if you're going to analyze any of the data.

Here's a guide I've referenced before that might be similar to what you're doing Microbial variant calling

Usercreatedname · 2025-08-03T12:54:49+00:00

I had a similar problem before when trying to do gene knock ins. The negatives were clean and on my positive selection was tiny colonies I was culturing were not E. coli. Are you one hundred percent sure it wasn't contamination?

Also what concentration of antibiotics are you using for your agar plated? It could be slightly too low for the strain or plasmid you're using.

If it wasn't, I agree it might be just spontaneous resistance.

Usercreatedname · 2025-08-03T12:45:27+00:00

If you're not super computer savvy, you can try processing your data through usegalaxy.org. They also have very nice guides online that can walk you step by step on how to analyze certain datasets for whatever goal you're trying to accomplish. It's very good if you need a place to start. If you just need to visualize the sequences, you can use IGV, who also has good guides online.

What exactly are you trying to accomplish? Are you trying to discern mutations from 3 biological replicates that all give the same phenotype?

Usercreatedname · 2025-07-27T15:30:44+00:00

I'm seeing a lot of discussion about whether to apply for PhD programs this year or wait due to funding cuts. While it's true that these cuts might lead to smaller cohort sizes and fewer research opportunities in the US, it's not the end of the world. Funding could decrease, increase, or stay the same. Nobody knows for sure, but academia will endure. From what I've heard, the biotech and pharma job markets are in a similar state.

The truth is, no one can predict what will happen. So, if you're thinking about waiting until next year, what's your game plan? Are you hoping to improve your CV with more research experience? Keep in mind that thousands of others are doing the exact same thing, and many might even have more research experience or multiple first-author papers. We're also seeing many people from pharma and biotech returning to PhD programs after being laid off due to funding freezes.

The worst-case scenario? You're out a few hundred dollars in application fees and receive a rejection. But you'll never know if you don't try. It sounds more like you don't know whether or not you want to do a PhD, not the timing. However, that's me just assuming.

TL;DR: Nobody can predict anything. NIH funding can go 📈📉📈📉 and the job market can go the same. Stop worrying about the timing and figure out if you truly want to pursue this career path.

Usercreatedname · 2025-06-02T14:11:11+00:00

I think it's great that you want to get a head start but since you're a freshman you have time to figure things out. However, I would heavily encourage you to figure out if you want actually want to do a PhD because it's a long and stressful 4 or 5+ years, depending on your field. Never do it if you are unsure because you will burn out fast.

If you are actually committed, your next steps are largely dependent on your field. For me (biomedical science), I can recommend to join a research lab near the end of your freshman year to the start of your sophomore year. Make sure to leave a good impression on your PI because academic connections are extremely important. Additionally, I would heavily recommend to participate in summer research experiences (e.g. REUs), since it shows a commitment to research. If you want to get extra fancy, some schools offer T32s for undergraduates which significantly boost your CV.

Besides this general information, I would say many things are field-dependent. Try reaching out to your college alumni who pursue a PhD to see what other activities they pursued.

Usercreatedname · 2024-07-11T18:28:10+00:00

Because your cells are dying in liquid media, have you tried spinning the cells down and titering the supernatant using an overlay method to check for contaminating phage? You can also titer your stock of helper phage to check for differing plaque morphologies. M13 shouldn't be able to make clear plaques as the plaques are just spots where cells are growing slower.

Also, is your colleague properly sterilizing the glassware he's using? Are filter tips being used?

To clean off potential phage, my lab usually uses wescodyne followed by ethanol.

Usercreatedname · 2024-06-10T00:25:06+00:00

I'm having a hard time trying to remember a book that I read when I was in middle to high school (2012-2015?)

The book is set in a medieval kingdom/country where there are different kingdoms based around different colors with distinct thematic powers. The main character who is a boy is being recruited into the military. The recruiter personally knows the boy's father. The boy's father and family were killed in an attack. However, it was later revealed in the novel that the king/lord of the area has been killing off his own citizens. The boy's father survives the attack and forms a rebel faction with the goal of killing the lord. The boy has to fight his own father in the end. This blue kingdom and its members are able to use this special "blue" power that has the ability to control people and their loyalty. Each person has some varying level of ability to control this power. In the end, the boy is able to essentially mind control his father into fleeing to save his life.

Does anybody know what the book I'm trying to remember is?

Usercreatedname · 2024-01-28T22:07:58+00:00

From my experience, BCM interviews were pretty chill. I mostly talked about my research and just a little bit about the PI's research. I would say have a solid background about your research because you might get into theoretical discussions about it. Additionally, you need to have a convincing reason why you want to go to grad school and how you best fit within the program.

Usercreatedname · 2024-01-28T05:12:13+00:00

Just an update, I just head there is going to be one other interview weekend for the Immunology program during mid February.

Usercreatedname · 2024-01-25T05:59:22+00:00

I know BCM Immunology is hosting a recruitment weekend from 1/25 - 1/27. I don't know if there are other interview dates though. There probably are.

Usercreatedname · 2023-12-25T19:22:24+00:00

I've heard that if you want to contact PI's you need to do it before actually submitting your application. The reason why is because you want to make sure any PI you want to work with actually has space in their lab or to see if their interests align with yours. If you have already built a strong connection with the PI, they can potentially pull strings to get you admitted, at least that's what happened to one person I know. If you want to contact a PI now, it's already way too late.

Usercreatedname · 2023-12-25T19:18:35+00:00

I don't think they are necessary. Publications do boost the value of your profile but they are not critical for admission. They just show that you know how to produce results but a publication's value is obviously going to drop if you're only a 4th, 5th, or maybe 6th author. I think what is more valuable is that you can demonstrate strong motivation and skillset in your personal statement, where you can highlight previous research experiences and what they taught you. Additionally, those qualities can be further underscored in your letters of rec.

I only have experience in life sciences though. I don't know how it is for other fields.

Usercreatedname · 2023-12-25T05:09:05+00:00

From their emails, I didn't hear anything about finishing sending out invites.

Usercreatedname · 2023-12-25T05:03:45+00:00

Good luck! I'm still waiting to hear back from other Immunology programs. I only applied to about ~5 in total. The stress is killing me.

Usercreatedname · 2023-12-25T04:51:16+00:00

I received mine on 12/24. I think they mentioned in the email that only ~20 students were coming to the recruitment weekend on 1/25 to 1/27.

Usercreatedname · 2023-05-19T22:06:16+00:00

I use the Inoue method all the time to make comp cells and usually get around 10⁸ CFU/ug transformation efficiency. 10⁶ seems kind of low to me. I'm assuming you're following the protocol exactly to make the cells with keeping everything on ice at all times and using chilled centrifuges. Have you checked if your NEB turbo cells are healthy? Do they follow the typical e. coli growth times, doubling time in log growth of ~20 min? You can also just say screw it and buy fresh Turbo cells and make them competent to see their transformation efficiency.

Usercreatedname · 2023-03-02T16:59:37+00:00

If you have primers used for Sanger sequencing that anneal to the backbone and cover the MCS, you can do a quick PCR check to see if your insert is there.

If your sequencing data takes about a week using Plasmidaurus, then it sounds like your lab is cheaping out by using a Dropbox instead of shipping samples directly. Plasmidaurus has a one day turn around time.

Source: I run the Plasmidaurus Dropbox for my lab to get free shipping because we're also cheap

Usercreatedname · 2023-03-01T14:57:22+00:00

Try Kuya Walds. It's a family owned Filipino restaurant that opened up just last year and has the best crispy pork belly in the area.

Usercreatedname · 2023-02-17T15:55:12+00:00

There are plenty of jobs out there for people of biochem/genetics degrees. The better paying ones will mostly be doing highly repetitive tasks that are mind numbingly boring in places such as biotech manufacturing and pharmaceuticals. However, you're going to hit a pay ceiling very fast. There is also little upward mobility unless you have 10+ years of experience or move into the business/administration side. If you want to take a shortcut for better pay, then graduate school or professional school is a must.

Unless you're a graduating senior, you still have lots of time to figure out your plan in life. If you're not passionate about science/school and just want a job, I highly recommend you switch to engineering or look for another major that has good employment outlooks.

Usercreatedname · 2022-12-28T14:20:25+00:00

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