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Dr. Gina Chaput Profile picture
@GinaMChaput
May 10, 2020 • 4 tweets • 3 min read • Read on X
(1/3) Looking for suggestions #sciencetwitter, esp. #Bioinformatics tweeps. We have groups of genes we know are differentially expressed & have identified hub genes within these groups with network analysis. I found this protocol (nature.com/articles/s4159…) which I've been using...
(2/3) But I was hoping to get finer resolution – such as in @jgi IMG/MER you can create KEGG maps from your gene cart highlighting where your genes are. @BioCyc I know does this as well. However both of these don’t either have plant genomes or the one I am working with.
(3/3) I was thinking PathwayTools if you can upload the genome yourself? I don’t think Phytozome has the exact same tools as IMG/MER but I could be wrong (@jgi?) Any suggestions/advice would be greatly appreciated! #AcademicChatter #biology #networkanalysis #RNA #Science #phdchat
I should mention that I really like the protocol above and plan on using it too - this is more of an "addition to" tweet

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More from @GinaMChaput

Dr. Gina Chaput Profile picture
Oct 4, 2020
Good morning #ScienceTwitter! As many know, there was a UNH professor that pretended to be a WOC in STEM with the handle @/piney_the... I don't have a large following so I need some help in getting this around ... a 🧵
(1/n) First, I was one of the many people that was harassed - you may have saw a photo of mine floating around that the account took out of context and tried to get me in trouble by bringing the in the handles of my boss, the university I work at, and OSHA.
(2/n) However, I am just the tip of the iceberg. This person did so much harm to others - much worse than the attempt he made at me. You may have seen screen shots floating around or went to the account prior to it being shut down.
Read 11 tweets
Dr. Gina Chaput Profile picture
Sep 23, 2020
(1/n) W/ morning coffee, my thinking gears are moving a bit faster than usual --> I have a career question: I have a plan in my head of how I eventually want to get to my future research statement plan as a PI (postdoc right now)... But there's a lot of transitions 🧵
(2/n) Undergrad I worked w/ algae/biofuels & interned w/ the EPA looking at coastal eutrophication/eel grass/climate change.... Transitioned during PhD working with anaerobic bacteria/lignin for biofuel/biomaterial applications purposes
(3/n) at the end of my PhD I realized I wanted to eventually shift back to coastal eutrophication/climate change & #eelgrass microbiome ... But I lack the omics skills and my thesis wasn't really ecology... So current postdoc is focusing on what I lacked looking at plant/fungal
Read 6 tweets
Dr. Gina Chaput Profile picture
Aug 14, 2020
(1/) Woke up early for a morning walk, planned my whole day, ready to take on the world... Found the front door had popped open & my eldest indoor cat is no where to be found. Spent morning walking around shaking a treat bag ...
(2/)Eventually we found him. All of a sudden involuntary years came out and my repressed anxiety of what could've happened comes pouring out of me. Walk cancelled and instead have been gripping my tea cup tightly all morning to settle my nerves
(3/) So I can pipette RNA carefully and not screw up my experiments I've worked very hard on. Why am I telling you all of this?
Read 5 tweets
Dr. Gina Chaput Profile picture
Aug 10, 2020
We have two black cats. There's the angel older child and then the younger devil child. Why a devil child you ask? A thread (1/) Image
The little fur ball above is a sweet loving creature ...But... Food insane. We have had to install child locks on ALL our cabinets TWICE because the first kind he figured out how to out smart. We also have a trash lock and hide the plastic lip because he's managed to open it (2/)
Plastic containers can not be left out because he's figured out if you knock them off the counter they split open (3/)
Read 5 tweets

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