Ali Altıntaş

Assistant Professor @Metabolcenter, University of Copenhagen 🇩🇰 | #Bioinformatician | #Molecular #Biologist | Forged in 🇹🇷

[Ali Altıntaş @_AliAltintas_]

@BiologistHairy Thank you, John! 🤗

[Ali Altıntaş @_AliAltintas_]

The fruits of a fantastic collaboration is now out! 🎉

[Luke McIlvenna @LukeMcIlvenna]

Dissociation Between Metabolic Improvements and Mitochondrial Transcriptional Changes Following Exercise Training in Women with Polycystic Ovary Syndrome
https://t.co/gEbrO8K94s @albut_ @_AliAltintas_

[Babraham Bioinf @babraham_bioinf]

New name. New place. Same great training opportunities from Babraham Bioinformatics at The Babraham Institute @BabrahamUK - virtually around the UK and rest of the world.
Come and find us! https://t.co/zCI28o6gHI
and on Blue Sky, Facebook and LinkedIn!

[Ali Altıntaş @_AliAltintas_]

🚨 Deadline: Jan 11, Sunday

📢 Don’t miss your chance to join the PhD course “#Bioinformatics Analysis of #Gene #Expression Data from Bulk #RNAseq” at University of Copenhagen!

📅 26 Jan – 12 Feb 2026

👉 Apply here: https://t.co/n9lYPD6tuc

[Ali Altıntaş @_AliAltintas_]

🔔 Excited to teach the PhD course “Bioinformatics Analysis of Gene Expression Data from Bulk RNA-seq” at University of Copenhagen!

📅 26 Jan – 12 Feb 2026

👍 Bring your own data (or use a public one) and learn the full RNA-seq pipeline:

👉 Apply: https://t.co/n9lYPD6tuc

[Ming "Tommy" Tang @tangming2005]

solid foundation in statistics is even more important in the age of AI.
This interactive app explaining statistic concepts is great
https://t.co/dO0YSMF9hf

[Ali Altıntaş @_AliAltintas_]

It is time to find out who "The Reviewer 2" is 😈

[Oded Rechavi @OdedRechavi]

😱OMG: "A subtle bug in OpenReview’s API briefly exposed one of the most sensitive parts of the research process, REVIEWER ANONYMITY. Researchers discovered they could query the identities of their reviewers"
https://t.co/eTMGPOxDNz

[Ali Altıntaş @_AliAltintas_]

You will learn:
✔ QC & alignment
✔ Differential expression
✔ Pathway enrichment
✔ Hands-on with Galaxy, UCloud & R

✅ Free for Danish PhD students

🧑‍🏫 Together with Stefan E. Seemann, Nadezhda T. Doncheva & Jan Gorodkin.

#Bioinformatics #RNAseq #PhDCourses #DataAnalysis

[Ali Altıntaş @_AliAltintas_]

🔔 Excited to teach the PhD course “Bioinformatics Analysis of Gene Expression Data from Bulk RNA-seq” at University of Copenhagen!

📅 26 Jan – 12 Feb 2026

👍 Bring your own data (or use a public one) and learn the full RNA-seq pipeline:

👉 Apply: https://t.co/n9lYPD6tuc

[Christoph Bock Lab @ CeMM & MedUni Vienna @BockLab]

🗨️ Just published in @NatureBiotech: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper link and annotated walkthrough in the thread below (1/11)

[Ali Altıntaş @_AliAltintas_]

And finally, huge congrats, @bahti_yil! 👏 Thanks for the opportunity and for leading such an impressive piece of work. Proud to be part of this global effort with you! 🌍🧬

[Ali Altıntaş @_AliAltintas_]

🌍 Excited to be part of this global effort! 🦠

Microbial and metabolic diversity was mapped across 51 vivaria & 12 wild colonies, revealing striking functional convergence despite taxonomic divergence.

🔗 https://t.co/8E8iBShkMk

[Ali Altıntaş @_AliAltintas_]

🔍 Want to explore the data yourself? Check out the interactive resources:

🔗 https://t.co/etkZvqPJbD
🔗 https://t.co/ESMSYAha2c

[Bahtiyar Yilmaz @bahti_yil]

🚨 New paper out in Cell Host & Microbe!
We built the first global atlas of mouse microbiome diversity across 51 vivaria and 12 wild colonies 🌍🐭
https://t.co/onoPv2OZsd

[Ali Altıntaş @_AliAltintas_]

📖 https://t.co/lLzMYOnCSJ

[Ali Altıntaş @_AliAltintas_]

🚨 Dealing with sparse, noisy single-cell DNA methylation data (scBS-seq)? Check out #scDMV.

It uses a zero-one inflated beta mixture model to tackle the excess of 0s/1s and low coverage, boosting accuracy in identifying differentially methylated regions (DMRs).

[Nature Medicine @NatureMedicine]

Genotype-phenotype data from over 450,000 individuals was analysed to discover 205 genomic loci where an allele associated with increased adiposity was associated with a lower cardiometabolic disease risk to an individual https://t.co/IRvwKQtrwE

[Ali Altıntaş @_AliAltintas_]

On the art of great article titles: this one’s dedicated to all the Reviewer 2s out there.

🔗 https://t.co/M6sX6Pd1YZ

[Ali Altıntaş @_AliAltintas_]

What a fantastic event! So great catching up with so many amazing colleagues ✨

[Juleen R. Zierath @JuleenRZierath]

The Zierath/Krook/Wallberg lab celebrated our current & former fellows and students at Nobel Forum sept 1 with a fantastic symposium on insulin action & metabolism. Grateful for all the trainees who traveled far & near to be with us to focus on science, inclusion, and innovation!

[Ali Altıntaş @_AliAltintas_]

All you need is:
1) Transcriptome (equivalent of transcriptome #FASTA file)
2) Gene annotations (equivalent of #GTF/#GFF file)
3) RNAseq reads (your #FASTQ file)

#BgeeCall will handle the rest and will let you know if a gene is present or absent!

[Ali Altıntaş @_AliAltintas_]

❓ How do you know if a gene is expressed or not in a certain tissue/organ?

👉 If you are interested in animals, #Bgee database is the first place to go. 52 species, several tissues/organs...

https://t.co/N4EpziKllp

[Ali Altıntaş @_AliAltintas_]

❓ And what if your species is not present in this database? What do you do then?
❓ Isn't it enough to decide on an arbitrary cutoff (e.g. TPM < 1) for expression?

👉 Actually, you can do better than that. How? #BgeeCall #R package:

https://t.co/A0RUrPPmL2