I’m happy to share that I started a new position as Professor at University Bonn, UKB. We will continue to harness Big Data & Omics to illuminate the Brain and Body.
Proud to share our new method for combined
#MERFISH
Spatial Transcriptomics correlated Electron Microscopy
#STcEM
spearheaded by
@AndrovicPeter
,
@KatrinPAnderson
and Martina Schifferer.
Spatial Transcriptomics-correlated Electron Microscopy
@DaniBeckman
People born spanish influenza times had almost triple risk of getting Parkinson compared to those born before 1888 or after 1924. This hints that having the flu early in life might increase PD risk. We will see how covid-19 plays out....
Our group is moving to the University of Bonn
@UniBonn
and
@DZNE_en
. We are sad to say goodbye to our home for last 5 years
@ISD_Research
. I am filled with gratitude for the fun collaborations and the alps. To those around Bonn region, I’d love to connect!
From today, the majority of foreign university students cannot bring family members to the UK.
In 2024, we’re already delivering for the British people.
Are you interested to join The Gokce lab and the Simons lab to develop new strategies for the prevention of aging and neurodegenerative diseases?
We have Postdoc, Ph.D. student and technician positions available immediately!
Details below.
RTs appreciated!
So happy! Our collaborative publication with Simons lab: white matter aging drives microglial diversity. Here goes first manuscript twitter-thread strom :)
Single-cell profiling of aging mouse white matter reveals a population of interferon (IFN)-responsive
#oligodendrocytes
, which localize in proximity to CD8+ T cells
New from
@ozgungokce
Mikael Simons and colleagues
Our work with Mika Simons Lab, " White matter aging drives microglial diversity" is on the
@NeuroCellPress
cover. The cover is an illustration of the myelin whorls. So much fun to put this cover together with amazing
@garipay
!
Our group is moving to the University of Bonn
@UniBonn
and
@DZNE_en
. We are sad to say goodbye to our home for last 5 years
@ISD_Research
. I am filled with gratitude for the fun collaborations and the alps. To those around Bonn region, I’d love to connect!
Received a gorgeous goodbye gift from
@ISD_Research
. I'm excited about joining
@UniBonn
&
@DZNE_en
and the opportunities it brings, but I'll also miss the amazing friends and colleagues at Munich. I want to thank everyone for their support and collaboration in the past 5 years!
Thank you,
@vizgen_inc
! The final version is just out and exceptionally impressive! Kudos to
@AndrovicPeter
for leading the amazing job, and our electron microscopy guru
@MaSchifferer
. 🔥 Make sure to check out the final version here:
Dr. Simon Besson-Girard stands distinct, the first PhD beacon from Gokce Lab. My gratitude for your artful bioinformatics and genomics alchemy. Your works already echo far and wide!
18-20 Mart 2022 tarihlerinde online olarak gerçekleştireceğimiz
#BIOINFOCONGRESS
II organizasyonumuzun ilk afişini sizlere heyecan ile sunuyoruz.
Katılım ücretsizdir ve kayıt için başvurularımız başlamıştır.
Tüm bilimseverleri davet ediyoruz.
Kayıt için:
Proud to share the second part results of our partnership between Simons and Gokce Labs on brain aging. Imagine, we postpone the effects of brain aging – it’s a possibility. Check out
@tugberkkaya
, Nicola Mattugini, and
@LuLiu_Laura
’s work
#thread
Check out the latest Nature Immunology: Views where
@LabListon
and Lidia Yshii discuss our recent work and highlight the links of a physiological role for interferon during development! Thank you!
News & views:
Article:
Excited to attend
@ChanZuckerberg
's
#NDChallengeNetwork
annual meeting in San Diego! I'll be showcasing our innovative research on how the correlation of Merfish and electron microscopy enhances our understanding of rare immune responses in neurodegeneration.
Utilizing both electron microscopy and MERFISH, we're nearing Feynman's dream of a more efficient EM! Take a look at our research on brain injuries below 🔥 please RT!
Is ultrastructure of the cell mirrored by its transcriptional state? What is the relationship between molecular and structural phenotypes? How do they localize in the tissue and reorganize after brain injury? A thread on our new study…🧵
@TheBcellArtist
Compare to my period 2009, now very few wants to go US for postdoc. One reason is many labs in Europe and China are competitive. a US postdoc is no longer a must. Other is a possible second term of Trump...
Please RT | We are looking for a computational postdoctoral or a Ph.D. student with prior coding experience in Python or R. Project is part of Chan Zuckerberg’s Neurodegeneration Challenge Network.
Please RT 📣 JOB ALERT. We are looking for PhD students to join and decipher mechanistic links between immune cells and brain aging. Contact me if interested via e-mail or DM.
Tonight introducing my group's research
@TazebayUygar
in Turkish (a first for me).
Bu akşam TR saati ile 21:00'de
@TazebayUygar
ile Labimizdaki çalışmalar üzerine konuşacağız.
Perşembe akşamı saat 21:00'de Çekirdek Konuşmaları değerli Özgün Gökçe'yi (Münih, Almanya) konuk ediyor. Sevgili Gökçe ile bağışıklık ve sinir sistemleri arasındaki ilginç hücresel ve moleküler etkileşimleri konuşacağız. Sakın kaçırmayın!
YouTube canlı:
@ozgungokce
Sayın Dr. Özgün Gökçe (
@ozgungokce
) hocamıza davetimizi kabul ederek bilgilendirici konuşması ve bizimle gerçekleştirdiği keyifli etkinlik için teşekkür ederiz.
#bilimlekalal
ım
Honored and excited to join
@ChanZuckerberg
’s Neurodegeneration Challenge Network with Mika Simons to study Role of White Matter and Cerebrovascular Aging in Neurodegeneration
@DZNE
@cziscience
@ISD_Research
We’re welcoming 60 new grantees to
@ChanZuckerberg
’s Neurodegeneration Challenge Network! These researchers are piloting innovative approaches to fighting neurodegenerative diseases like
#Alzheimers
,
#Parkinsons
+
#ALS
Feel very privileged and proud to be part of this network! Thanks
@cziscience
and
#NDChallengeNetwork
for building such a scientific culture created together with patients and trainees!
Thanks to all who joined the
#NDChallengeNetwork
meeting! It was great to connect & hear from
@singletonneuro
+
@nachogenePD
about the Global Parkinson’s Genetics Program & its goal to increase diversity in Parkinson’s disease research.
Imagine you could stain whole adult mice with standard IgG antibodies. What you couldn't do! We present wildDISCO technology for this🤗, creating the first whole body vascular, lymphatic, and nerve atlases. By
@HongchengM
@jieluo692
🧵👇🏼(turn on the sound)
Marking International Day of Women & Girls in Science, I took an implicit bias test: My results showed a slight bias associating men with career & women with family. Let's all strive for improvement starting from ourselves.
#WomenInScience
Always on the lookout for team players eager to navigate at the intersection of wetlab & drylab. Join us in exploring ways to maintain a longer, healthier mind and body!
The
#UniversityofBonn
is among the top 100 universities in the world. This is the result of the internationally renowned
#THEranking
of the UK-based magazine “Times Higher Education”.
➡ Read more:
I am excited to share our collaboration with
@tugberkkaya_
, Nico (twitterless), supervised by
@ozgungokce
, and Mikael Simons. Our study identified age-related interferon-responsive oligodendrocytes induced by CD8+ T cells in white matter.
As Boğaziçi University alumni, I am proud of the students and teachers who peacefully protested for academic freedom and the university’s independence. A key moment for defending the Turkey's future: the appointed rector is removed!
#TurkiyeKazandi
#BogaziciKazandi
Are you interested to join The Gokce lab and the Simons lab to develop new strategies for the prevention of aging and neurodegenerative diseases?
We have Postdoc, Ph.D. student and technician positions available immediately!
Details below.
RTs appreciated!
Emotional to be back at my PhD institute EPFL as a PI to share my group’s work in
#Latsis
Symposium! Many thanks to
@Hlashuel
for invitation and organization!
Program:
……
Zoom Registration
…
Bir
@UniBogazici
mezunu olarak Bonn Üniversitesinde profesörüm. Ama akedemik ünvan insanı insan yapmıyor valla. Pek ciddiye almayın ben surda burda Prof'um diyenleri.
2024'de güney kampusde özgürce tavla atma ümidiyle!
Sevgili
@UniBogazici
li genc ogrenciler
Florida Uni’de profesörüm. Yani, mezun olunca gelmek isteyeceğiniz yerlere siz doğmadan önce geldim
Sizi bu saçma sapan eylemlere yönlendiren ve gaz veren tuhaf tipleri kaale almayin. Kandiriliyorsunuz. Aptal yerine konuyorsunuz
Please RT. We made a surprising finding that CD8 T cells drive brain aging. Now, we are looking for computational colleagues to understand this further:
Single-cell profiling of aging mouse white matter reveals a population of interferon (IFN)-responsive
#oligodendrocytes
, which localize in proximity to CD8+ T cells
New from
@ozgungokce
Mikael Simons and colleagues
Istanbul Mayor and opposition's VP candidate
@ekrem_imamoglu
's campaign bus was attacked with stones during a rally in the eastern province of Erzurum
See how Can Yang, Angela Wu
@thegellybear
and et al. are revolutionizing the field of spatial transcriptomics with SpatialScope. A new approach to integrating scRNA-seq and ST data.
#SpatialScope
#scRNAseq
#STdata
here it is- read about 3D virtual tissue blocks, metastasis-lymph node boundaries and unlocking molecular mechanisms in 3D. biggest congratz to the entire team. Open-ST: High-resolution spatial transcriptomics in 3D | bioRxiv
Finally had the time to compile at least some of the workshop/course materials together:
@RSGTurkey
events - Scientific figure design, Introduction to ggplot2
@bioinforange
event - Introduction to R (in Turkish)
Short lecture - Introduction to tidyverse
Imaging-based spatial transcriptomics methods such as
#MERFISH
are amazing with their ability to detect individual transcripts within the cell. Unfortunately, tissue ultrastructure is destroyed in the process.
The achievements of my lab are done by who have chosen to work in my lab! I'm grateful for your contributions and hope that I've been able to support your success as much as you've supported mine!
Our
@STARProtocols
is now live! This is
@LuLiu_Laura
's first author paper from our group. She optimised almost every step of our
#scRNASeq
preparation and put together a step-by-step protocol for artifact free results. Also, today is her birthday, Happy Birthday
@LuLiu_Laura
!
Our
@STARProtocols
paper is out. If you want to perform droplet or plate-based scRNA-seq experiments with microglia, and all the tips that
@LuLiu_Laura
and GokceLab
@ozgungokce
optimized to prevent dissociation artifacts, please don’t miss our paper.
I'm thrilled to host
@ozgungokce
from
@DZNE_en
for our
#neurogenomics
seminars next Tuesday, 3pm UK time. Join us to hear about his exciting work highlighting the role of T cells in ageing 🧠🧬
@TreutleinLab
’s PANDO in
#HCA2022GM
, a flexible linear model-based framework that incorporates multi-omic data to plot the prettiest global gene regulatory networks describing organoid development
@humancellatlas
Just published
@ScienceMagazine
We've known
#SARSCoV2
unique feature is cleavage of its muring polybasic site, but it's neuropilin (NRP1) binding that is key factor for its infectivity, a new potential target
#BIOINFOCONGRESS
ve
#Bioinforange
’e güzel organizasyon için çok teşekkür ederim. Tek hücre ve alansal genomik yöntemlerle bunama ve yaşlılık üzerine yaptığımız çalışmaları Bioinformatik öğrencileri ile paylaşmaktan çok mutlu oldum.
#BIOINFOCONGRESS
II kapsamında 19 Mart 2022 tarihinde gerçekleştirilen etkinlikte Sayın Dr. Özgün Gökçe (
@ozgungokce
) hocamızın Functional Genomics of Neuroinflammation in Aging and Neurodegeneration konulu konuşmasının videosu paylaşılmıştır.
Link:
@pdhsu
Double Nobel Laureate Frederick Sanger only had 10 PhD students from which Elizabeth Blackburn and Rodney Porter also received Nobel prize. I don't know anyone with 20% of their PhD students end up Nobel Laureate... impressive
So proud! Our rising star🌟Ph.D. student
@KatrinPAnderson
awarded Daiichi Sankyo-Master-Preis for her master thesis in our group! Many exciting findings ahead! 🥳
Finally! In our new
@NeuroCellPress
manuscript, amazing
@TheRealGStanley
developed computational method that distinguished discrete versus continuous heterogeneity in scRNA-seq data. thread
Continuous and Discrete Neuron Types of the Adult Murine Striatum
@BreakingWave411
@DaniBeckman
Brain health is challenged by many illnesses, but what will be COVID's impact on dementia? Is it similar to the flu which is not small, or a deeper threat? How does vaccination change the game? Keeps me awake at night...
Stimulating and fun visit from Bram Heijs
@Imagine_Imaging
! Exciting opportunities in combining MSI-based in situ imaging with spatial and single cell genomics. Thanks for
#Rockon
visit!
Please RT 📣 JOB ALERT. We are looking for PhD students to join and decipher mechanistic links between immune cells and brain aging. Contact me if interested via e-mail or DM.
#STcEM
then allowed us to directly match transcriptional states to the morphological categories defined from EM images, revealing transcriptional signature of foamy microglia and morphology of interferon-microglia.
Nice example why we don't use t-SNE and UMAP as distance preserving tools to interpret data. We use them to give overview of the dataset generated and highlight subpopulations further dive in. Problem is misuse of the tool not the tool.
It's time to stop making t-SNE & UMAP plots. In a new preprint w/ Tara Chari we show that while they display some correlation with the underlying high-dimension data, they don't preserve local or global structure & are misleading. They're also arbitrary.🧵
Fantastic talks at the Sabri Ülker Symposium on Metabolism and Life 2021!
#MetabolismandLife2021
many congrats to
@ghotamis
for organising. My favorite talk from my classmate
@nilyapici
on neural basis of food intake from fly to mice to human! amazing work!
Remind me again why I do this? (Done ~100 in the past 7-8 months with people at all stages from around the world.) Oh yeah, because it turns out that I actually really like helping people :). Anyway, if anyone is still left to take me up on it, the offer still stands…
Sobering view at Athens: The Antikythera Mechanism, the world’s first computer, was made 2200 years ago. Yet, no similar advanced device emerged for the next 2 millennia. History shows we’ve often slid back – hoping we’ve learned Smt…🕊️
#HBD
Xiaowei Zhuang, Breakthrough Prize laureate who has helped create technologies like STORM & MERFISH that push past the diffraction limit of light to reveal images of proteins and other molecular actors in the cell. Learn more:
Photo Brigitte Lacombe
We then used
#MERFISH
data to characterize transcriptional cell states responding to white-matter injury, including lipid-associated
#microglia
and interferon-response microglia.
If you need a solid example for contributions of immigrants please use this one:
#Turkish
#immigrantscientist
couple founded BioNTech, whose value is more than four times of Lufthansa and also developed a
#COVID19Vaccine
!