Chiranjit 'Ran' Mukherjee, PhD

Excited to share our latest work, UltraSEQ, a novel clinical metagenomics platform that is powered by biology and data science! #Bioinformatics #publication #Battelle

@bielleogy I developed some of these kind of hybrid amplicon protocols back in grad school. For example, you can target V1 as your R1 and V4 as your R2. Read’s won’t overlap, but you can separately analyze them. Otherwise, if you can afford it, long read would be better

@dr_alphalyrae You could always blame the person who’s idea it was to deploy that AI tool :)

my mildly hot take is that AI tools won’t be displacing people anytime soon. Humans inherently like accountability. And when things go wrong we like to pin down a reason. With AI tools there is nobody to layoff, fire or discipline.

A lot has changed, and unfortunately not for the best… #MyTwitterAnniversary

Been out of the #conference circuits since the pandemic, what are some of your favorite events to attend in the #microbiome #Genomics #Bioinformatics Health/Biomedical #DataScience fields? #AcademicChatter #AcademicTwitter

@emily_wissel Congratulations Dr Wissel! 🎉🎈🎊

Passed my PhD defense! Big thank you to all the folks who attended virtually and IRL ❤ and big shout out to the EMERGENT lab group for a fantastic party afterwards!

@nsegata Congratulations! Planning to try it out soon!

More than ten years after the first version, I'm so glad to see the MetaPhlAn concept further developed and improved. Now with SGBs, massive integration of MAGs, higher taxonomic consistency, better coverage of non-human microbiomes. Looking forward to hear users' feedback!

Good, but still not enough. I quit my postdoc at NASA JPL after my 1st year contract ended because I found the $60k salary far below cost of living in Pasadena, Ca. Especially since we we’re starting a family. #postdoc #phdchat

@thekatestewart @AcademicChatter 1. Negotiated a higher salary (programs only set a minimum stipend, not max) 2. Lived in a cheap midwestern city 3. Side jobs (photography, online opps) Privileges: no student loans, partner also had a similarly paying job

Fellow academics: what did you do in your PhD program to make money to pay bills since programs don’t pay a livable wage? @AcademicChatter #AcademicTwitter

@AstrobioMike Curious what database or pipeline you are using for such less studied locations?

Heya #metagenomics folks! It’s pretty standard in my exp for metagenomics data from complex microbial communities (particularly from envs like microbial mats and less-studied locations) to have relatively low proportions be taxonomically classified or functionally annotated (1/2)

@bioinformer Enjoy the food, one of the best in the world.

Traveling to India (Delhi) today. First time. Any advice?

@dgkeyes Whenever I have worked with highly sensitive data, usually its at an institution that has its own enterprise GitHub that’s not open to public. Depending on the institutional data policy and security classification of data, private repos can be used.

If you work with highly sensitive data, how do you work with #rstats and GitHub in a way that keeps that data off of GitHub?

Our recent work on classifying hazardous biological sequences using a function-based fingerprinting approach was just published. This approach can also be used to distinguish between closely related pathogenic & nonpathogenic bacteria. frontiersin.org/articles/10.33…

10 academic writing skills I wish I had learned as a PhD student (with updated links) A thread ⬇️ 🧵 for PhD students and junior scholars:

@dbngsh_mkhrj The power of branding!

Pretty sure every street in Atlanta is named Peachtree Blvd

@devashismukerji I have always believed in being part of a system to change it, but starting to doubt that now…

@dbngsh_mkhrj Oh ya, publishing negative results should be encouraged. But negative result is result too, not expecting “any” result would be a bit worrisome :)

@drcmicro I actually think publishing negative results are important. But it's often easier to write about a positive result, than to find out why something doesn't work and then publish it.

I find the Gita to be an excellent book for an experimentalist. "Do your work, but don't expect any results."

@dbngsh_mkhrj Docker?

Is there a way to export a conda environment exactly (given hardware dependencies)? Often there is a lot of fiddling around to get the env right and an easy way to clone/replicate it will be very useful.

@devashismukerji Will take you to Bob Evans next time you are here, but please, Cici’s and Golden Coral be ready for getting sick after. Add White Castle to the list, maybe.

I have a list called ‘Murica. Striked out are places I have tried. Plan is to get through all by the end of this year. Any other places I missed which should be on here?