Janssen M. Kotah, PhD 🇵🇭

Pinoy neuroscientist who will share my love of the brain with anyone willing to listen. Postdoc at the @EggenBart lab. UPD Psych/Neurasmus/UvA alum.

[Janssen M. Kotah, PhD 🇵🇭 @jmkotah]

Looking to connect with other scientists on the other platform! https://t.co/YEyPfM6c1G

[Immunity @ImmunityCP]

Online now: Microglial lipid phosphatase SHIP1 limits complement-mediated synaptic pruning in the healthy developing hippocampus https://t.co/4tF9xzkXJX

[evo-devo @Xiaojie_Qiu]

We are thrilled to share that our first paper from my new lab, Spateo (https://t.co/a0BC0Cf3Ec) for spatiotemporal modeling of molecular holograms, is now online in Cell: https://t.co/UUZkyXYJtG. Spateo is a comprehensive analytical framework for 3D whole-embryo spatiotemporal modeling. Its advanced features include:
• 3D alignment and reconstruction at the whole-mouse-embryo scale (see the animation).
• 3D spatial domain digitization and cell-cell communication analysis to understand spatial gene expression gradients and both inter- and intracellular communication.
• 3D morphometric and volumetric analyses along with 3D morphogenesis vector field modeling to quantify dynamics such as surface area, volume, and cell density across organs, and to dissect the interplay between morphogenesis factors and cell migration.
• A “Google Earth”-like browser, Spateo-viewer (https://t.co/s33SS7jvYL and https://t.co/BbY6bIJtS0), for interactive and intuitive exploration of 3D spatial data.
• Additional features, such as RNA signal-based single-cell segmentation.

We are also honored that Nature “News and Views” has highlighted this work as well: https://t.co/8F4s6GJeBY.

This is really an amazing outcome after two years' heroic revision process that rewrite the entire paper using a new data (https://t.co/xbahWSeGgx) for whole mouse embryos.

[Nature Neuroscience @NatureNeuro]

A pair of papers uses single-cell and spatial transcriptomics to gain insight into multiple sclerosis (#MS) lesions:

Assessing white matter (WM) and grey matter (GM) MS reveals progression trajectories

@EggenBart @KooistraSusanne @jmkotah

https://t.co/zJvXUfPjAA

[kellie 🌻👩‍🔬 @kellie_horan_]

Two fantastic papers were published today in @NatureNeuro highlighting some major advances in understanding MS using spatial transcriptomics 🧬

I feel very lucky to have the chance to write a News & Views article about them! ⭐️ https://t.co/1XF0BHjKpC

[Janssen M. Kotah, PhD 🇵🇭 @jmkotah]

Super proud and grateful to have been a part of this cool project!!

[Vini Tiwari, PhD @vinitiwari1]

Excited to share a preview of our latest article by🧪🔬@jmkotah @EggenBart @ImmunityCP --offering a fascinating perspective on turning back the clock 🕰️on aging associated myelin impairments with BCG !

[Joachim Goedhart @joachimgoedhart]

Happy to announce our preprint "EzReverse - a Web Application for Background Adjustment of Color Images" that reports a web app generated by @s_xinwei
https://t.co/2TE8md2NqL

[Mayank Chugh (he/him) @mayank_mchugh]

📢'The World Is Your Oyster' is for those who are born in global north countries--don't experience visa bureaucracy & emotional burden that non-white global south scholars do. Citizenship is a privilege that we need to recognize in the academe. 1/n

https://t.co/0PyvvH7fGM

[Lior Pachter @lpachter]

The difference in @10xGenomics' Cell Ranger's default between version 6 and 7 is discussed in this thread, but it's such a big deal that it's worth its own thread.

tl;dr: in v7 Cell Ranger changed how it produces the gene count matrix leading to a huge difference in results. 1/

[Eduard Porta @eportacangen]

Sometimes an image is really worth a thousand words

Same sample, consecutive sections, VISIUM CytAssist vs Xenium

Very nice @SergiCervilla!

[Janssen M. Kotah, PhD 🇵🇭 @jmkotah]

This was one of the last major projects I led during my PhD @KorosiAniko's lab, and closes a chapter I will look back on fondly. Thanks to all our collaborators who contributed to this work, and to the reviewers and editors who helped improve the paper.

[Janssen M. Kotah, PhD 🇵🇭 @jmkotah]

Happy to share that our project on proteomic changes in hippocampal synaptosomes after early-life stress in wildtype and APP/PS1 mice is now published! This was a collaboration between the @KorosiAniko and Mark Verheijen labs, co-led by Mandy Kater. https://t.co/ELG8ei33nd

[Janssen M. Kotah, PhD 🇵🇭 @jmkotah]

One of things I am proudest of is this Shiny app I built where our data can be accessed, and hopefully contribute to other studies: https://t.co/iDMieFT02j.

This has been a challenge to learn, but I luckily had help from several people @SILS_UvA, especially @joachimgoedhart.

[Keerthana Gopalakrishnan @keerthanpg]

The hardest part about being an immigrant is not the immigration system but having to choose between pursuing a world class career and seeing your parents grow old