Max Planck Research Group Leader at MPI for Molecular Genetics, Berlin. Passionate about RNA, transposons & evolution
Past: Postdoc
@mpi_ie
and PhD
@embl
Proudly presenting our new findings on how
#RNA
binding proteins (RBPs) may increase the tolerance of genomes to transposable element (TE) insertions. If you want to know more read this thread or our story
@Nature
Today marks 15 years since I moved to Germany to start my PhD at
@embl
. I'm glad that my scientific vision has been continuously supported. Special thanks to
@maxplanckpress
for the last ~10 years. Here is a photo of a young and excited PhD student ๐
Itโs my great pleasure to announce the first paper from our group. Itโs a true team effort. If you are interested in biomolecular condensates, splicing and RNA biology read the thread๐. Especially if you have worked with SRSF2 or nuclear speckles. (1/9)
A pretty image from today's microscopy (done by the postdoc). In orange you see the Nuclear Speckles, stained for SON & SRRM2. We are getting close to commercial style images ๐
Cell line credit
@MMalszycki
Honored to be listed in
@Tagesspiegel
"The 100 most important minds in Berlin science 2023" together with Aydan
@bulutkarslioglu
The full list is here (with Aydan on the cover):
Mass spec results just arrived and the RNA we used in this pull down seems to be an hnRNP heaven. It was only a preliminary experiment but now I can go through the list and start dreaming things ๐ญ
Good news, right before the end of the week! Our manuscript is accepted
@eLife
We're extremely happy with the revision process. Many thanks to eLife editors&reviewers, especially in these times.
SON and SRRM2 are essential for nuclear speckle formation
Our state-of-the-art review on
#NuclearSpeckles
is out now
@FEBSJournal
. Many thanks to the editors and the reviewers! Reviewers were very helpful and they had great suggestions. Enjoy reading:
Proud PI moment: First MSc student, Theresa successfully defended the thesis today๐ We also took the opportunity to get a quick lab photo while the sun was momentarily shining (directly on to Theresa ๐ )
We are 5 years young!
A shout out to former & current team members๐ I am still enjoying this journey and looking forward to celebrating many more lab anniversaries.
We are looking for a PhD student (see details of the project below). Apply at before 3rd of January, 2021 if you're interested.
Max Planck Institute for Molecular Genetics - PhD project in the Aktas lab
A western blot result I've been waiting since 6 months comes as we countdown to the closing of the institute. Last result needed to write the paper comes on the last day of work. Perfect timing ๐
My first PhD student gave an institute seminar today and it went all well. I felt strangely nervous, which is something I no longer have when I'm the one giving talks. I know one day they will fly the nest, but until then I'm protecting them.
We are looking for a bioinformatics postdoc who has previous experience with analysis of CLIP-like datasets. Please spread the news.
Max Planck Institute for Molecular Genetics - Postdoctoral Associate (f/m/d) | Computational Biology
I never trash reagents. These membranes are probably 20 years old, left in one of our lab rooms, and today, we used them to test some RNA probes for Northern blots. It just works, I guess I can continue being a hoarder ๐
1st anniversary of Quantitative RNA Biology Lab. Last year had been amazing for me, and I am looking forward to having many more years like this with these talented team members.
More speckles for the new year! My students gave me one of the most creative Christmas presents I've ever seen. I don't think we'd get tired of looking at nuclear speckles.
3 years after starting my lab, I temporarily stopped doing bench work to finish some writing business. And now I realize; writing is so easy if I'm not doing experiments in parallel! Still not fun but at least I found out that I'm not as slow in writing as I once thought ๐
Sometimes as we make the libraries we have an indication that particular RNA binding protein is a good RNA-binder, as seen by the clumping beads ๐ (The one on the right is a negative control)
Our new intern รmer
@omrysrq
started working with us today. The original plan was for the summer of 2020 (I guess I don't need to explain what happened in 2020), but I'm glad that it eventually worked out. I wish รmer lots of luck and success ๐ค
An extremely well conducted study on a rare disease identifies a non coding RNA which regulates a developmental gene. Congratulations
@lila_allou
and
@StefanMundlos
! interested should also see the thread by Lila๐
Most important thing I learned from Asifa: "I donโt dwell on disappointments. Instead, I look forward to the new challenge ahead. You have to seize the moment. There are many times when I had setbacks, but I get up, try to see where my strengths are and move forward with those"๐
โWe need a cultural change to remain competitiveโ: interview with the utterly brilliant Asifa Akhtar, Vice President
@maxplanckpress
, about her engagement in a cultural change towards more diversity & inclusion @ Max Planck Society๐ค
#DiversityDay
@mpi_ie
I am extremely excited to announce our 2023 "Metabolism & Life Symposium" with a terrific line up of speakers. Supported & organized by
@sabriulkerctr
&
@SU_foundation
the meeting will be on the waters of the Bosphorus. Mark your calendars for this scientific and cultural feast.
A crazy afternoon! The MSc student said she has homozygous clones. Not one but 4. Now the postdoc says sequencing data are here for an experiment I've been impatient to see. The other postdoc tells me the mutants don't bind RNA. What's next? I'm becoming addicted to good news ๐งฟ
Lab of
@EddaGSchulz
identified a novel Xist-enhancing regulatory transcript; Xert!
@RutgerGjaltema
presented at our RNA Salon Berlin, I was fascinated by the quality of the work but also surprised to hear there are still so many unknowns of XCI. Read๐
Thank you
@RNASociety
for supporting our RNA salon application. Together with Marina
@chekulae
we continue bringing RNA enthusiasts in Berlin together.
#RNAclubBerlin
A perfect reminder for why I like my job. I love helping younger generation of scientists and I am very lucky to be surrounded by so many of the good ones. A beautiful surprise from Liza today๐บ
๐โโ๏ธEsra รz ile Bilim Sohbetleri devam ediyor
๐งฌMax Planck Enstitรผsรผโnden Dr. Tuฤรงe Aktaล, zฤฑplayan genlerin neden olduฤu genetik parmak eksikliฤi ve Alu transpozonlarฤฑnฤฑn neden olduฤu hรผcre รถlรผmlerinin รถnรผne geรงen รงalฤฑลmalarฤฑnฤฑ anlattฤฑ.
@_taktas_
๐
The first one of our joined efforts with
@AlexandraBergf1
from Markus Wahl's lab at
@FUBiochemistry
is officially out. Our star๐; Alexandra is now a postdoc at Yale and I hope we will have the chance to work together in the future again.
Thanks to the German system which makes us keep record of every genetically modified organism (FormblattZ), I know exactly how many cell lines we have generated in 1.5 years. We are almost at 100! I think we should celebrate the 100th cell line ๐ฅณ
Almost ready for vacation starting in 2 days after preparing all the cell lines with treatments etc. to be sequenced while we're gone. The postdoc (also my significant other) consumed all his energy to turn these into 48 libraries. We'll have a drink to celebrate tonight ๐ฅ
This Thursday, together with
@TazebayUygar
we will be talking about transposable elements live on YouTube (unfortunately only in Turkish).
Bu perลembe gรผnรผ รงekirdek konuลmalarฤฑna konuk oluyorum. Transpozonlar ve genom evrimi รผzerine gerรงekleลtireceฤimiz sohbete hepinizi beklerim.
In Freiburg to teach a course tomorrow and had a reunion with
@Iovino_Lab
. It was a wonderful fun dinner with Nicola, but just too short. Next time we meet in Berlin๐
I can't believe I'm saying this, but after spending the whole January writing and submitting a manuscript and a grant, committee meetings start to sound interesting.
A beautiful present from
@OlgaJasnovidova
before she leaves our lab to start a new adventure at her home country. The
#octopus
represents someone who can do many things (has 8 hands working in parallel). I am trying my best but I don't think I am an octopus yet๐
Almost a year later, the reunion with
@Iovino_Lab
in Berlin this time. Very excited to host him for a seminar and hear about the latest adventures of team Iovino.
Here comes the second one from
@AlexandraBergf1
. This time also including the great support from Marco (
@pre_mRCO
) from the lab of Florian Heyd
@FUBiochemistry
. Happy to be part of this work ๐ฅณ
The applications for our PhD program (IMPRS-BAC) are now open. We are recruiting in this round as well. Please forward to the interested and RT.
Max Planck Institute for Molecular Genetics - PhD project proposals 2023
I don't know if anyone did this already. For me the most obvious thing to type was "transposable elements" and this is how it looks: like gaps in genome assembly
Trying to purify a protein we accidentally made hydrogels. At least it shows our hypothesis was correct ๐ image recognition thinks it's a freshwater snail. ๐
First time I saw TLS I couldn't believe how real they look. Finally the story is out. Congratulations
@jvveenvliet
@adrianobolondi
@helenekretzmer
Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites
๐State-of-the-Art Review๐
Nuclear speckles: dynamic hubs of gene expression regulation
โ๏ธBy ฤฐbrahim Avลar Ilฤฑk and Tuฤรงe Aktaล from
@MPI_MolGen
๐
Part of our Special Issue on Organelle Homeostasis!
I get frustrated when people tell me that I'm "lucky" to have this and that... Especially for things that I worked hard, planned and organized each step. My father told me when I was younger: You create your own luck!
Welcome to our new lab member
@OlgaJasnovidova
. Olga will be working on revealing hidden potential of RNA binding proteins by introducing a few selected ones from various species into human cells.
My colleague and good friend, Aydan
@bulutkarslioglu
summarized my feelings quite well. I believe it was a rare occasion to have two candidates from the same institute. We gave them a glimpse into the groundbreaking research done at
@MPI_MolGen
Day trip to Frankfurt for the Paul Ehrlich Prize symposium. Regardless of the outcome had a great day. Together with
@_taktas_
strong showcase for
@MPI_MolGen
. Tomorrow off to the
@MPI_MolGen
retreat. Together with ERC preps, may I say I am TIRED
Happy to announce the continuation of the Berlin RNA club in 2022, co-organized with
@SamanthaMendon4
,
@ILoedige
, and
@_taktas_
. We will meet every 2d Wednesday of the month at 5 pm. If you would like to join the club or present, let us know!
Nowadays, I often find myself discussing with my colleagues about things to change (or revolutionize) in academia. I believe the unexpected developments we experienced over the last year changed our mindsets dramatically. I hope we use these new ideas to change for the better.
It was a lot of fun to meet and interact with IMPRS for GS students. We mostly talked about career planning, (personal) definition of success and adaptive management styles. Smart students here โจ๏ธ
I'm preparing for that time of the year when I get asked if all the documents (Formblatt-Z) are up to date. This way I realize that we have more than 400 glycerol stocks and ~120 cell lines frozen. Not bad ๐
๐ Save the date! Donโt miss the 3rd Symposium on Medical Epigenetics by CRC992 MEDEP.
18-20 March 2024 in
#Freiburg
(Germany)
Registration is already open:
Even though it was all virtual, I had a great day full of science in Dresden
@CRTDpress
. Thank you
@MareikeAlbert
for being a fantastic host! And also everyone else who spared their time to talk with me๐
@CytoLabKoc
Years ago we got a similar reviewer comment and did nothing about it (because there was nothing to correct) but thanked the reviewer and said we now got the language checked in our response letter. The reviewer thanked and said the text was improved ๐
Why haven't you heard of multipartite viruses : ย โTheyโre everywhere, but because theyโre mainly on plants, no one cares.โ
I think we should care about these very interesting new findings
The Metabolism and Life Symposium returns on May 9-10, 2023 and brings together expert scientists from around the world!
#Sabri
รlkerFoundation
#MetabolismandLifeSymposium
My first animal handling was Parhyale hawaiensis at M.Gerberding's group at MPI in Tรผbingen in 2005 as a summer intern. So happy to see this paper which looks into Parhyale development in detail.
The first preprint from my thesis work in the Patel Lab
@Parflyale
is out!
We generated new functional genomic resources for our favorite emerging model crustacean, Parhyale hawaiensis, using a timecourse of Omni-ATAC-Seq and RNA-Seq.
Thread below๐
1/n
What is better than seeing other scientists following up your work? DHX9 levels seem to be the best correlating (99%) with circRNA levels and serves as an example!
Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals
Great start to Day2 of
#IBCRetreat2023
@ETH_en
with super-fascinating talk from
@_taktas_
@MPI_MolGen
Condensates and IDPs make most sense in the light of evolution โจ๏ธ a lot of food for thought ๐ค Looking forward to discussions following for next 1.5 days.
@BioCondensates
I'm sometimes very impatient. I connected to our gel doc system from home to check the results of a western blot my student finished yesterday. Since she hasn't told me anything I thought the results were no good. It turns out she had 2 hom. out of 3 clones :) It's a good Sunday.
We are very happy to be part of this amazing work spearheaded by
@RahaWeigert
. See Raha's thread if you want to know more about the regulation of placental DNA & histone methylation.
Ever wondered how the peculiar placental epigenome is regulated? We discovered a dynamic DNMT3B/Polycomb-antagonism that maintains it! Beyond thrilled to share my PhD work together with
@hetzel_s
published
@NatureCellBiology
.
@MPI_MolGen
#MeissnerLab
(1/9)
To be honest (tbh), navigating the career path in
#academia
& beyond is often based on informal knowledge, on watercooler conversations, or lucky coincidences. The
#tbhconference
is the place where such conversations take center-stage.โก๏ธ Register here:
โA biologist from Pakistan thought Germany would be a stopover in her career. Twenty years later, sheโs one of the most prominent researchers from abroad.โ
@maxplanckpress
Vice President and
@mpi_ie
director
@AsifaAkhtar1
in an interview with
@zeitcampus
Every scientist I know complains about things which are obviously not ideal and they also have some ideas on how to improve. But we all somehow fail to join forces to implement these changes. Talking about the problem is a good start but we also need to take actions.
It was a fantastic seminar by our guest
@MariekeOudelaar
today, including new methodoligies to functionally address genome architecture and in vitro re-constitutions. Co-hosting together with
@EddaGSchulz
as participants of
@spp2202_dfg
My name (Tuฤรงe) is difficult to type on an EN keyboard and predatory journals don't put so much effort into this (or is this even on purpose to get our attention๐ค). I have mostly seen versions with missing fonts (first photo) but this is new (second)๐
Role of Dhx9 in SMA. When I proposed a research of Dhx9 in disease I was told I'm "walking on thin ice", so nice to see my hunch was correct.
Human Survival Motor Neuron genes generate a vast repertoire of circular RNAs
We are looking for a bioinformatics postdoc who has previous experience with analysis of CLIP-like datasets. Please spread the news.
Max Planck Institute for Molecular Genetics - Postdoctoral Associate (f/m/d) | Computational Biology
I hope the re-evaluation of past research brings a positive outcome. Perhaps we will be able to understand things which didnโt make sense before or it will even lead to new discoveries. Such as ours: we identified the core of nuclear speckles
Evolution in action! Alternative paths lead to the same destination. A great story on the evolution of fly dosage compensation.
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling