Fengjun(FJ) Zhang, PhD

🚀Meet the 𝐀𝐭𝐥𝐚𝐬 𝐨𝐟 𝐍𝐞𝐮𝐭𝐫𝐨𝐩𝐡𝐢𝐥 𝐁𝐢𝐨𝐥𝐨𝐠𝐲 & its companion app 𝑁𝑒𝑢𝑡𝑟𝑜𝑝ℎ𝑖𝑙 𝐶𝑎𝑛𝑣𝑎𝑠. — a hub for exploring #neutrophils with #scRNAseq. Discover, compare & interact with #singlecell neutrophil across studies. #Bioinformatics #DataViz #OpenScience

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Arguably most of the biology GitHub repository is poorly maintained anyway But after some workshops and training for RSE, I’m really trying to do things more consciously

Just a reminder that the article provides performance metrics only in the training dataset, with some "cellular aging clocks" showing there correlations with chronological age of r<0.3 x.com/MariosGeorgaki…

From what I read this week in a coding book published 2004 My developer friends in the industry always laugh about research community Cuz we are so behind our fellows Maintaining a readable repository takes time and efforts Which is so opposed to those single cell paper factories

Funny such project always *claims* to be transparent on their code while their README.md file is just 10 lines of text without any meaningful explanation. thanks to Claude I just prompt to skip all those confusing terms and simply get out a list of ranked genes

It really is overwhelming to follow big scRNAseq papers in the top journals I feel like their goals are actually to trap your mindset into their internally complex technical world so you get lost and forget why you're here So that preventing you from picky picky on their results

A hot fix after the Kubernetes clusters update Now my Atlas App is back online

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As the whole Chinese Netizens were debating on how to improve our scientific practice in Chinese academia I myself also learned a key lesson from this fabrication report as peer reviewer in general * The whole investigation was conducted by an influencer called “Classmate Geng”

Paper 4 This one I checked myself additional to the informant’s report Supplementary figures are titled in Mandarin Chinese, not English And you clearly see strange pixel combinations in the Western blot pictures doi.org/10.1038/s43587…

Recently academic fabrication was a huge news headlines on Chinese internet Several Chinese authors were accused of making up figures and numbers in their Nature papers Here’re 4 of the papers: - 1 Nat Aging - 2 Nat commun - 1 Nat Cell Biology

@GorinGennady @ClarkPolner @arjunrajlab Yes I do. We have one of the best HPCs in the region. I poured every published dataset with exactly the same pipeline to keep the consistency.

@fengjun_zhang @ClarkPolner @arjunrajlab Sure. I am familiar. Fair enough, Arc doesn't reannotate. Are you requantifying?

Can someone start a journal called “Cell Atlases” so that the rest of the journals can go back to publishing interesting things?

@GorinGennady @ClarkPolner @arjunrajlab I focus on “cell” atlases, which has very unique data structure and its deep meaning in cell biology The app is my first trial on aligning diverse studies onto one community’s interpretation We just got approved for another round of funding and I am building much more than an app

@fengjun_zhang @ClarkPolner @arjunrajlab Isn't that just the Arc's database?

@ClarkPolner @arjunrajlab I tried to curate every public single cell using the exact same pipeline so that they can be merged afterwards But I’m still experimenting to integrate different techniques Next week I’m going research software day Berlin to see if any open source infrastructure suits my project

@ClarkPolner @arjunrajlab Very true. I started to have this idea cuz I worked in a consortium specialized in one type of cell I worked closely with them to understand what were their focus I built a small app for them to play with public data and annotated samples based on their needs

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Was asked why I bought this coding book from pre-AI era For better vibe coding of course 😅😅 Hope I can extract most of it and maybe teach my fellow biologist colleagues in the near future ❤️❤️