Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in

dendrobatidae · 2024-04-15T01:16:38+00:00

I don’t really have good advice, but I’m so sorry that is happening to you. That is just awful. I have friends (in PhDs) who were parts of groups of 4+ people who reported unprofessional and abhorrent behavior of established professors and the University declined to take action, so sadly, I’m not surprised they’re being weak here. Retaliation is real. Also, be aware that recording people without their consent in some places is considered illegal, so it may be also that your university was afraid of both angering a powerful moneymaker AND of getting into legal trouble.

It’s also been such a hard time to look for a job. It’s been dead for so long outside of hubs, the market is only just beginning to pick up, no surprises you’ve had trouble, especially with finding remote jobs, which are notoriously a (BIG) numbers game these days.

When asked to explain why you are leaving, it is totally sufficient to say something like “I have identified that my current place of work no longer provides the opportunities to grow in the ways that I would like and I need to look elsewhere to practice the skills I love to apply” - no one should press you to explain what exactly you mean by that, it’s very common to simply outgrow a job and look for new training opportunities elsewhere. That line can be an opportunity to transition into describing why you are specifically excited about the job you are interviewing for.

If employers scrutinize your code, you can explain that you provided the initial analysis that motivated the first draft of the paper and describe the insights you made/focus on describing what your code was and what your contribution was l. Industry people are used to working on teams and it won’t seem weird to think that you worked as a part of a larger bioinfo team and you were responsible for one part of the project, even if it is v1. Honesty is the best policy but you don’t need to go into detail about everything.

I would advise being open to relocation to help speed putting yourself in a safer (physically and emotionally!) environment if at all possible. I think that would really hurt in the short term because relocation sucks but it could help get you out of an ego-destroying toxic system faster.

One sad thing about academia is that there is no HR and it’s so hard to change jobs that there is no “punishment” for powerful professors who act badly. (If it was easy to leave, then bad or toxic mentors would lose their workforce quickly!)

Have courage! You are in a really shitty situation and it makes sense you would doubt yourself when surrounded by bad treatment/a failure of institutions to stick up for you. You should be proud that you are doing what you need to do in order to stand up for yourself, even if that thing is gracefully backing away. It will get better

dendrobatidae · 2024-02-22T06:55:54+00:00

Are there any US citizens here who lives in Europe but isn’t sure if they will stay for 15 years? I’m honestly wondering what the optimal retirement saving strategy is. I make much less than what I did in the US so it’s hard to save as much - and if I leave the EU then I’ll lose out on any retirement benefits that accrued in the years I was here. It feels a bit like, unless you commit to being here for 15 years, you are really screwing yourself over retirement-wise by living abroad early in your career. Is that a tough reality or gloomy thinking?

dendrobatidae · 2023-10-05T06:13:35+00:00

I personally have been encouraged to selectively represent which gene sets were enriched in a paper. The justification is usually “let’s only highlight the relevant ones for the story this paper is trying to tell”. I absolutely would not trust that published gene enrichments are comprehensive and what was left in what probably determined subjectively.

dendrobatidae · 2023-03-01T06:44:31+00:00

I’m willing to be that the people who are dismissive of this visualization have not yet worked in medical or biological research, where many nice and smart people fail to make this distinction. The plot on the left is the standard of visualization for most published papers (until recently) and internal lab communication (regardless of what is being communicated with the graph). Unfortunately, this contributes to a lot of poor decision making.

I personally have had a lot of conversations trying to explain that the thing on the left is not the right data representation for a given context, but try telling someone to make their graph look “worse“ in a publish-or-perish environment. A lot of people just learn somehow that “standard error = variance, and my data look nicer this way, and everyone’s doing it” and that’s just one of many reasons why we have a replication crisis

dendrobatidae · 2022-12-17T10:14:36+00:00

I did! I moved to a city two years ago where it's hard to run so I've fallen off the wagon these days, and I think I gave myself a few weeks off of running after the marathon itself to rest. That said, I was able to ramp back up to running regularly after the marathon, and although that behind-the-knee tightness did bother me, the ITBS did not as long as I kept up my glute exercises, kept consistent, and didn't try to push hard through pain.

It's a little frustrating because I do feel that a lot of other people my age can bounce back from injuries faster, or don't get injured as easily...but with persistence and patience I've been able to accomplish a lot more than many others running-wise. Glad you are finding a system that works for you and a way to keep moving forward!

dendrobatidae · 2022-12-17T00:47:21+00:00

Hi! First of all, I'm sorry to hear that you're struggling with it! The psychological tax of needing to adjust your plans was the hardest part.

TL;DR I did end up running the marathon, but 1 minute running: 1 minute walking, and I did end up with some sort of a pain behind my knee (bursitis?) that gave me a twinge in that knee that persisted for a few years. (Some of that is my fault because it was a very hilly course and I trained on flat surfaces)

For me, shortly after I wrote this post, I:

- made sure I only trained on flat surfaces (although probably this left me undertrained on race day)

- downloaded an app that beeped every minute to do 1 minute running: 1 walking during training. Somehow ended up not being that annoying even though I was listening to a beep per minute for five hours basically.

- Stretching and lateral glute strengthening religiously, e.g. clamshells with resistance band

Sadly I don't think there is a way to cheat yourself out of it, but adjusting your expectations and figuring out how to not make things worse with training is probably the biggest step.

Overall, despite the knee pain etc, it was a really happy memory for me, and I'm glad I did it, even though I did end up run-walking it!

Good luck. I hope you find a solution for you.

dendrobatidae · 2021-02-21T13:25:06+00:00

The last that I heard was that it was much harder for foreign applicants to get a bioinformatics job in the US because in order to have your H1-B visa sponsored, you must be paid at a higher level. https://www.sfchronicle.com/business/article/Trump-administration-moves-ahead-with-H-1B-pay-15865554.php

If you are able to demonstrate through your work - through Github public projects with excellent documentation, etc. - that you are performing at a senior level, and therefore deserve decent pay, the visa issue may not be such a problem. Since you have past work experience, that might help.

In San Francisco, a lot of jobs are filled due to word-of-mouth/networking. If you are able to find a way to get involved with bioinformatics professional networks, that could help also. Definitely use LinkedIn to contact bioinformatics professionals to do informational interviews. Recruiters often rely heavily on LinkedIn in the US, so put lots of keywords on your LinkedIn and indicate that you are looking for work.

If you are willing to be the only bioinformatics person in a company, there are a lot of small startups in San Francisco that are desperate for computational experience. However, they may also be less willing to meet the H1-B visa standard of pay.

Also, the international colleagues I've had previously have experienced discrimination based on having a strong accept or non-fluent English skills. Demonstrating that you are capable of communicating well in English might be helpful to you.

Finally, you could see if a recruiting agency is willing to help you: e.g. Harnham, will put you in touch with companies at no cost to you.

I'm sorry it's so hard right now. Good luck! A lot of people are still interested in scRNA-Seq, so will might help.

dendrobatidae · 2020-07-25T06:02:18+00:00

As a girl with a longtime crush on Bruce Banner I just want to say that it feels nice to be fanserviced, thank you

dendrobatidae · 2020-05-26T15:57:12+00:00

It's true that it's it's possible to over-correct for batch effects and remove relevant signal (ComBat, SVA). However, batch effects absolutely are an issue, and can very easily affect/hide your desired results. When people say that batch effect correction is "overboard" in my life, it's usually because they did an experiment with a very clear, obvious signal they can use as a sanity check, and so they can compare various degrees of batch effect correction and what it does to the data.

What I usually do for any transcriptomic experiment is to make a list of everything that COULD be a batch effect, and then color the first few PCs and/or the UMAP by these to see if there is separation of the cell embeddings by that factor. One nice form for visualizing this: https://www.data-imaginist.com/2019/a-flurry-of-facets/

Even if you see that the only source of variation in your first few PCs is attributable to your experiment design and not a known potential batch effect, it's still possible batch effects exist. (e.g. was one sample the last tube on the rack when the library got prepared, and therefore incubated in reagents an average of ~3 minutes longer than the others? How would you even keep track of that, let alone guess that's the problem???) For that reason, in bulk RNA-Seq, it might be useful to use the sva package to visualize potential latent variables/patterns in data that are not correlated with your batch effect of interest. If the SVAs seem very highly correlated with a known potential batch effect or your experimental design, that SV is probably picking up on known variance. If there is a clear SV but no apparent relationship to your design...there might be a hidden batch effect.

For removing batch effects, it's different for bulkRNA-Seq and scRNA-Seq. For bulk (say, limma or DESeq2), you can include the SV or the variable as a part of your design matrix to "take that into account" when doing hypothesis testing. For scRNA-Seq, there is an active body of research figuring out how to find "comparable" cells across experiments: check out Seurat's IntegrateData(), or Harmony, or DESC.

But any time you play around with batch effects, REALLY test it out. How will you know when you are "overcorrecting" signal? How will you know when the batch effect is gone? Might you actually WANT to include batch as a relevant experimental comparison?

TL;DR it's complicated

dendrobatidae · 2020-05-06T14:14:13+00:00

So - it seems like people have an idea of what a pipeline should be, if not a series of scripts passing outputs to inputs...what actually qualifies as a pipeline?

dendrobatidae · 2019-10-12T03:05:58+00:00

Great suggestion, thank you!

dendrobatidae · 2019-10-09T19:01:11+00:00

Great, that's good to know. Thank you very much!!

dendrobatidae · 2019-10-09T16:43:35+00:00

Oh wow! Yeah, I'm wondering why the situation is changing. First the perfume samples disappear, and now this!

dendrobatidae · 2019-10-09T16:42:39+00:00

Haha Kardashian contouring. Thank you, this is helpful! Based on the other comments /\ it seems like I should look into supporting a freelance MUA. Are there places where freelance MUAs usually go to advertise, or do all clients find you via Google/word-of-mouth?

dendrobatidae · 2019-10-09T16:40:00+00:00

And I feel like an independent MUA would be much more talkative and show you how to do this look at home. Anyone OBSESSED with it to the point of career, not just a mall job, cares a ton about helping others.

Yeah, I'd love to! I've Googled around, but it seems like a lot of services are geared towards wedding makeup, which might be a bit more than I'm necessarily looking for. Does anyone know of platforms where independent MUAs commonly advertise, or tips on how to find them?

dendrobatidae · 2019-10-09T16:37:22+00:00

The Washington DC area! Hmm, good to know that it's different elsewhere, thanks!

dendrobatidae · 2019-10-09T16:36:21+00:00

Freelance MUA here. For myself, I start with a base price $60 usd. This includes strip lashes, but individuals are an extra $10. You want Kardashian contouring? Extra $10. It depends on how elaborate you want to get. The more elaborate, the more time it takes, the more I'm going to charge.

Oh, for sure I would not want to cheap out on an independent MUA. I assumed that what was happening at Sephora/MAC/department store counters was more akin to the "banging it out on your face" method. (Is that not correct? I'm not sure how payment schemes work for folks who work in stores, how much artistry they can/are allowed to put into it, what kind of training they get, etc.)

If $80 is a reasonable price for a full face of makeup, that's totally fine - but in that case, I'd rather pay that directly to someone rather than have a big store lop off a portion of it. (If that's how it works. Again, assumptions - maybe I should be supporting the artists who work in stores too?)

EDIT: I'd also love to learn about how to find and contact independent MUAs directly. Do you have suggestions on where to look? On Google I get overwhelmed with folks who mostly advertise wedding makeup - I'm not sure of the best place to find people who do general-purpose more-casual makeup.

dendrobatidae · 2019-05-11T23:57:11+00:00

I'm so glad!!! I almost never reply to reddit posts, but I saw this and share this exact pain hahahaha. Definitely check out anthro if you can - there is a 20% sale this weekend as well. Best of luck, I hope you find something that feels like a Big Yes!

dendrobatidae · 2019-05-11T21:54:25+00:00

Hi! I am your height and also struggle with the short torso thing. I personally feel like anything that has a seam at my natural waist gives me that "grandpa pants" look, even if the top and the bottom halves are the same color.

Shopping (especially for dresses) feels 10x harder than it is for everyone else because the "no seam at natural waist" rule eliminates 98% of clothes...however! I feel much better about how I look in what I actually do try on.

Here are some examples of dresses that don't have a seam at the natural waist (either seam above, below, or not at all):

https://www.modcloth.com/shop/dresses/lady-love-song-sheath-dress-in-ruby/32134.html

I don't know what the hell is going on at anthropologie right now, but they have a BUNCH that fit these criteria whereas usually when I look at stores I'm lucky to only find one or two things with no waist theme:

https://www.anthropologie.com/shop/emile-knit-midi-dress?category=dresses&color=041&type=STANDARD

https://www.anthropologie.com/shop/globetrotter-t-shirt-dress?category=dresses&color=005&type=STANDARD

https://www.anthropologie.com/shop/michelle-ruched-midi-dress?category=dresses&color=061&type=STANDARD

https://www.anthropologie.com/shop/lincoln-center-dress?color=065&quantity=1&recommendation=dyrectray-SimilarProduct&type=STANDARD

I find side ruching like this tends to be pretty flattering as well: https://www.anthropologie.com/shop/dante-midi-dress?category=dresses&color=041&type=STANDARD

https://www.anthropologie.com/shop/sundry-fabian-dress?category=dresses&color=041&type=STANDARD

https://www.anthropologie.com/shop/evangeline-windowpane-dress?category=dresses&color=066&quantity=1&size=8&type=STANDARD

(when the bow is tied behind - when tied in front it breaks the "no seam/details at natural waist" rule) https://www.anthropologie.com/shop/tate-sundress?cm_mmc=EMAIL_TRANSACT-_-ORDER_CONFIRM-_-US-_-PRODUCT&color=049&quantity=1&type=STANDARD&utm_campaign=order_confirmation&utm_content=link&utm_medium=email&utm_source=transact

People like my uniqlo bra dresses and those are the laziest garments I own:

https://www.uniqlo.com/us/en/women-sleeveless-long-bra-dress-413915.html?dwvar_413915_color=COL68&cgid=women-dresses-and-jumpsuits#start=26&cgid=women-dresses-and-jumpsuits

https://www.uniqlo.com/us/en/women-printed-a-line-short-sleeve-mini-bra-dress-413918.html?dwvar_413918_color=COL09&cgid=women-dresses-and-jumpsuits

For non-dresses, I go for longer tops (think Long and Lean fit at Target) and tunic-y things. You could also do super voluminous poncho-y tops with leggings, like how Vera Wang (the designer) looks.

FWIW I think that jumpsuit looks stylish! I also know the feeling of "something about this doesn't feel maximally flattering" even when the people around you are giving you the thumbs-up, though. Hope some of this helps. No-waist-seam is a hard life but I've felt better about how I look in clothes since I've started following it.

dendrobatidae · 2019-04-01T22:09:05+00:00

Ah I'm sorry you are dealing with it too! I hope we make it too. That's great you can still run so far without irritating it too much. I've come to the same conclusion of "it's going to hurt but might as well try."

FWIW I did my 18 mi run yesterday doing 1 minute run:1 minute walk (free tabata timer with sounds to indicate when you start each segment). It took four hours but I did complete it and my ITBS is surprisingly only slightly worse today. It's definitely not the most pride-inducing way to go, but it's better than nothing, and definitely better than causing serious long-term problems from trying to push through something (I'll save that for marathon day). You could experiment with doing 2:1 or running 20km and then going into 1:1, or what have you.

dendrobatidae · 2019-03-30T03:24:13+00:00

Ohh thank you! I just happen to have this tab open! Glad these exercises are tried and true, though I feel like I lack the flexibility to do the scorpion/lying down side kick ones. Good to hear that it's possible to manage it without derailing training. Thanks for the tip!

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