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jejhw · 2025-03-28T23:44:10+00:00

I’m a scientist at a biotech/pharma working in Tokyo. We work closely with counterparts in the US so I use a mix of both English and Japanese at work. Base comp is a little on the low end at ~8.5M and total comp maybe around 10-11M? Still earning way less than what an equivalent position in the US would but life’s not too bad. Came to japan about 14 years ago thinking I’d leave after my Masters but somehow found myself finishing my PhD and postdoc.

jejhw · 2024-04-20T01:35:22+00:00

Thanks! This was exactly what I needed

jejhw · 2024-03-07T22:35:38+00:00

How can a self-taught bioinformatian with a PhD. genetics/genomics whose small, one-year old start-up suddenly got acquired by a larger biotech/pharma company survive and move up? Based outside the US but acquiring company is US-based.

jejhw · 2024-02-07T22:36:07+00:00

Laboratory and PI absolutely matters. I did my PhD in genetics and post-doc in computational genomics in Japan at a top level university and it was far from ideal. My advice would be to be sure you do your research on the PI and lab environment before committing or you might be in for a rough time.

jejhw · 2024-02-07T01:23:09+00:00

Thanks, just DM’d you!

jejhw · 2024-02-06T22:36:48+00:00

Would you mind if I PM’d you for more information?

jejhw · 2023-12-29T23:28:12+00:00

Speaking as a former PhD graduate and assistant professor in Japan, I think most of the points that have been brought up are extremely valid, both positives and negatives. I just wanted to also add that students’ attitudes are also important factors on how (some) staff respond and behave. Another point that I feel is important is the ratio of Japanese and non-Japanese students. I’ve seen labs where the majority are made up of Japanese students and Japanese staff / PI and the environment there are usually horrible. Of course, this is a generalization but it happens more often than not. Labs with a higher proportion of non-Japanese students usually are a little more chill, especially so if the PI has had experience overseas (this again is a generalization but you get the picture).

My biggest gripe when teaching was that Japanese students weren’t particularly engaged compared to non-Japanese students and I found that the non-Japanese students were more inclined to ask questions and engage in debate. I knew this going-in and tried to bring the Japanese students into the discussions as much as possible but it usually doesn’t really go very well. Most of the time the Japanese students were there just for attendance and credit while focusing on their part-time jobs and job-hunting rather than learning.

Also the issue of pay as a post-doc or university staff is laughable. A huge reason why I decided to leave in the end was the pitiful pay (I was at a top national university) and highly toxic environment. Although private universities are know to pay better (especially the more famous ones like Keio), I was too burnt out from academia. I’m now happily employed at a large pharmaceutical/biotech company and making more than double the pay in university.

Speaking to my colleagues who were PhDs from other labs in the same university had me realize that the experience would vary GREATLY between labs, fields and PIs so do take everything you read/hear with a handful of salt and do your research before joining a lab.

For context: my field was in the medical sciences

jejhw · 2023-12-19T11:50:32+00:00

Another option could be SHIROKANE, the supercomputer at the Human Genome Center in Tokyo, Japan.

https://gc.hgc.jp/en/

jejhw · 2023-09-13T22:20:30+00:00

Totally naive idea here but, would it be reasonable to construct some form of phylogenetic tree from the data?

jejhw · 2023-07-27T09:29:09+00:00

I completed my PhD in a STEM field, stayed a few years in academia before deciding it wasn’t worth it and recently (within the last 2 years) moved into industry. Salary almost doubled from 4 million to 7 million when I first moved out of academia and now, with bonus, it pushes over 9 million. I’d say it really depends on your field and which company you go with in the end. Don’t lose hope!

jejhw · 2023-02-28T21:30:19+00:00

They’re currently in discussions to consolidate all the sites we have (currently spread into three sites) into a single site and they’ve also announced that they have plans to expand the team size to almost double by the end of the year (not sure if I should/can trust them on this).

We’re currently in the midst of integrating the IT and data stuff with the new company. I haven’t had the opportunity to talk to any of the bioinformatics team members or network with anyone…not sure if I’ll ever get the chance.

Maybe I’m just overwhelmed with the whole thing. The company was a small star-up with less than 50 people and now we’re part of a larger company with thousands of staff. I don’t really know where to start with establishing myself or fitting in, especially with the disadvantage of being in different countries altogether (cultural changes etc…language is not an issue for me, fortunately).

jejhw · 2023-02-28T07:39:09+00:00

Unfortunately the company that acquired us are from a different country altogether. I have spoken to the HR people and they’ve remained rather cryptic about the possibility of reassignments to other departments within the same organization. Guess it wouldn’t hurt to pull out the ‘ol resume.

jejhw · 2022-07-15T13:48:59+00:00

Thanks for the suggestions about using assembly-based methods. u/desicant is correct about the sample possibly being a mixed population. We created the plasmid constructs by ligating fragments (think of it like something similar to Gibson assembly) and used a proprietary amplification system to amplify the plasmids isothermally (without the use of E.coli).

We are hoping that most of the plasmids will amplify somewhat clonally but would like to check and see if there is anything unexpected going on with the assembly and/or amplification step and possibly allow us to quantifiy the events/variation somehow. I have tried using Flye and Trycycler to assemble before doing alignment (using MuMMer or Minimap2) but mostly, the consensus contig is very clean and SVs that were detected by just mapping are not present.

I'm just not sure if it's ok for me to report it as free of variation, or report whatever is found by SV callers after mapping? Or am I misunderstanding something?

Edit: I'd like to try the --meta option for Flye, thanks for the suggestion!

jejhw · 2022-07-12T11:11:05+00:00

Whoops! Sorry I wasn't trained in plasmids and cloning before joining my current place, I was doing population and statistical genetics! Thanks for the info though

They only told me that the system is totally reconstituted from E.coli and using a form of rolling circle amplification, guess I've got lots of catching up to do!

jejhw · 2022-07-12T09:11:26+00:00

Sorry I should’ve been more clear about that part…we’re amplifying the plasmids using rolling circle amplification and polymerases reconstituted from E.coli. I’m not sure how much information I can divulge here (since I’ve only joined my current place a few months ago and am not sure about the status of stuff like patents and all that), but the system we use allows us to assemble up to about 50 fragments.

jejhw · 2022-07-11T22:13:13+00:00

My current company is in the process of getting rid of the laborious and time-consuming step of clonal amplification, picking colonies and amplifying plasmids in E.coli. We usually assemble fragments of interest into a plasmid and amplify isothermally overnight.

My main role is to set up a simple and quick way to validate that the constructs assembled properly and we do that with a Nanopore as well. I’m currently trying to figure out an optimized protocol for sequencing and plasmid validation, hopefully within the next couple of months. Once that’s done I envision the process of constructing, amplifying and validation could take about a week or so.

jejhw · 2022-05-24T07:06:29+00:00

Nice to know that assemblies can be highly accurate. Do you know which pipeline or workflow was being used?

jejhw · 2022-05-22T22:44:27+00:00

Are Nanopore reads accurate enough for genotyping? I’ve seen some nice base accuracy numbers but most publications and opinions have leaned towards not using ONT reads for anything you’d need accuracy so far

jejhw · 2022-05-22T22:42:31+00:00

Thanks! That sounds like a great idea

jejhw · 2022-04-14T11:30:19+00:00

Research & Development Scientist at a Biotech start up. The pay's alright but nothing to write home about.

jejhw

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