Lmst

#computationalBiology

Want a sneak peek or to try it on your own data? Try EnrichMap https://enrichmap.readthedocs.io/en/latest/
#SpatialTranscriptomics #ComputationalBiology #EnrichMap #spatialomics

New math reveals how hidden symmetries in DNA models could turbocharge genetics, medicine, and evolution research. #computationalbiology #genetics #mathematics

https://geekoo.news/cracking-the-genetic-codes-hidden-symmetries/

🧬 New review out in Drug Discovery Today:

🔗 https://doi.org/10.1016/j.drudis.2025.104382

We take a critical look at how AI — especially AlphaFold(-Multimer/3) — has changed protein complex prediction.

End-to-end models work well for rigid complexes. Flexibility, disorder, and transient interfaces remain unsolved.

AI is shiny. Biology is complicated. We map what’s working, what isn’t, and what’s next.

#ComputationalBiology #Bioinformatics #DrugDiscovery #AlphaFold

🧬 Could the grammar of DNA be unraveled using tools from natural language processing?

🔗 A review on the applications of Transformer-based language models for nucleotide sequence analysis. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.03.024

📚 CSBJ: https://www.csbj.org/

#Bioinformatics #AIinBiology #Transformers #Genomics #NLP #DeepLearning #PrecisionMedicine #TransformerModels #DNABERT #ComputationalBiology

A review on the applications of Transformer-based language models for nucleotide sequence analysis. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.03.024

🤖 How resilient are deep learning models to real-world imperfections in microscopy?

🔗 Practical guidelines for cell segmentation models under optical aberrations in microscopy. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.09.002

📚 CSBJ Quantum Biology and Biophotonics: https://www.csbj.org/qbio

#CellSegmentation #Microscopy #AIinBiology #OpticalAberrations #DeepLearning #BiomedicalAI #Cellpose #ComputationalBiology #PLCM

Practical guidelines for cell segmentation models under optical aberrations in microscopy. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.09.002

🐦🧭 How do migratory birds sense Earth’s magnetic field? Quantum biology might hold the answer.

🔗 Cryptochrome magnetoreception: Time course of photoactivation from non-equilibrium coarse-grained molecular dynamics. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.001

📚 CSBJ Quantum Biology and Biophotonics: https://www.csbj.org/qbio

#Biophysics #QuantumBiology #Magnetoreception #MolecularDynamics #BirdNavigation #ComputationalBiology #Cryptochrome

Cryptochrome magnetoreception: Time course of photoactivation from non-equilibrium coarse-grained molecular dynamics. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.001

🧬 How do AlphaFold2 and ESMFold stack up when it comes to functional annotation?

🔗 AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.01.008

📚 CSBJ: https://www.csbj.org/

#AlphaFold2 #ESMFold #AIinScience #ProteinStructure #Enzymes #Pfam #UniProt #AlphaFold #HumanProteome #FunctionalAnnotation #AIinBiology #ComputationalBiology #FunctionalGenomics

AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.01.008

This isn't just about data—it's about vision, purpose, and turning insight into impact. Clear, bold, and future-focused. 🔬💡 #DataDriven #Bioinformatics, #ComputationalBiology, #Genomics, #MedicalResearch, #PersonalizedMedicine, #DataAnalysis, #ITInnovation, #Innovation, #HighSpeedComputing, #CloudComputing, #TeamWork, #Collaboration, #GlobalHealth, #DigitalArt, #VisualInspiration, #Motivation, #Revolution, #ModernMedicine, #PatientCare, #HealthcareTech, #InnovateNow, #YourVoiceMatters, #FutureForward, #JoinTheRevolution, #BoldSteps
https://medium.com/@sanjay.mohindroo66/transforming-medicine-it-innovations-in-bioinformatics-computational-biology-b8da9b30a34e

👥TALKING HeaDS – May 2025👥

Join us for an exciting health data science seminar with Kresten Lindorff-Larsen, Professor of Computational Protein Biophysics. He will discuss missense variants, protein stability, and machine learning’s role in genetic disease research.

🗓 27 May 2025, 15:00
📍 Faculty Club, Panum

👉 RSVP: https://heads.ku.dk/calendar/2025/talking-heads/talking-heads-may2025/

Thank you to DDSA for the support!

#HealthDataScience #MachineLearning #NetworkingEvent #Genetics #UCPH #Protein #Biophysics #ComputationalBiology

Now published in Peer Community Journal, section Mathematical &
#ComputationalBiology: Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algo
https://peercommunityjournal.org/articles/10.24072/pcjournal.547/

👥TALKING HeaDS – May 2025👥

🗓 27 May 2025, 15:00
📍 Faculty Club, Panum

👉 RSVP: https://heads.ku.dk/calendar/2025/talking-heads/talking-heads-may2025/

Thank you to DDSA for the support!

#HealthDataScience #MachineLearning #NetworkingEvent #Genetics #UCPH #Protein #Biophysics #ComputationalBiology

Job - Alert 💊

✨ Postdoctoral Researcher (f/m/d)

Deadline: Position is open until filled

Location: Germany, Düsseldorf, Nordrhein Westfalen

https://www.academiceurope.com/job/?id=7467

#hiring #DiabetesResearch #Bioinformatics #Postdoc #ObesityResearch #computationalbiology #DDZ

I'm pleased to announce that my article "Computer models explain how histones establish contacts in the cell nucleus and regulate accessibility" has just been published in "Biologie in unserer Zeit" journal as early view. The article provides an easy-to-understand overview of our research work from recent years on modeling chromatin. The text is available exclusively in German language. https://doi.org/10.11576/biuz-7986 #Chromatin #Bioinformatics #ScienceCommunication #ComputationalBiology

🧠 How do prediction models perform in recognizing disordered regions with specific binding functions?

🔗 Evaluation of predictions of disordered binding regions in the CAID2 experiment. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.12.009

📚 CSBJ: https://www.csbj.org/

#Bioinformatics #ProteinDisorder #CAID2 #IntrinsicallyDisorderedProteins #LigandBinding #ComputationalBiology #AIinScience #DeepLearning #MolecularBiology

Evaluation of predictions of disordered binding regions in the CAID2 experiment. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.12.009

"Lindenmayer Systems, Fractals, and Plants" (PRUSINKIEWICZ; HANAN, 1989) https://link.springer.com/book/10.1007/978-1-4757-1428-9

#LSystem #Fractals #Mandelbrot #ComputationalBiology

$Preface L-systems are a mathematical formalism which was proposed by Aristid Lindenmayer in 1968 as a foundation for an axiomatic theory of development. The notion promptly attracted the attention of computer scientists, who investigated L-systems from the viewpoint of formal language theory. This theoretical line of research was pursued very actively in the seventies, resulting in over one thousand publications. A different research direction was taken in 1984 by Alvy Ray Smith, who proposed L-systems as a tool for synthesizing realistic images of plants and pointed out the relationship between L-systems and the concept of fractals introduced by Benoit Mandelbrot. The work by Smith inspired our studies of the application of L-systems to computer graphics. Originally, we were interested in two problems: • Can L-systems be used as a realistic model of plant species found in nature? • Can L-systems be applied to generate images of a wide class of fractals? It turned out that both questions had affirmative answers. Subsequently we found that L-systems could be applied to other areas, such as the generation of tilings, reproduction of a geometric art form from East India, and synthesis of musical scores based on an interpretation of fractals. This book collects our results related to the graphical applications of 1systems. It is a corrected version of the notes which we prepared for the ACM SIGGRAPH '88 course on fractals. [...]$

🤖 What if predicting antibody activity was as simple as reading a protein sequence?

🔗 Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.03.038

📚 CSBJ: https://www.csbj.org/

#AIforBiotech #AntibodyDiscovery #LLM #InfluenzaResearch #ComputationalBiology #PrecisionMedicine #Immunology #Immunoinformatics #Proteomics

Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.03.038

👥TALKING HeaDS – May 2025👥

🗓 27 May 2025, 15:00
📍 Faculty Club, Panum

👉 RSVP: https://heads.ku.dk/calendar/2025/talking-heads/talking-heads-may2025/

Thank you to DDSA for the support!

#HealthDataScience #MachineLearning #NetworkingEvent #Genetics #UCPH #Protein #Biophysics #ComputationalBiology

Job - Alert 💊

🩺 Doktorand*in (m/w/d) Laboratoriumsmedizin

Deadline: 2025-05-09

Location: Germany, Dresden, Sachsen

https://www.academiceurope.com/job/?id=7376

#hiring #PhD #LaboratoryMedicine #medicine #Biochemistry #Bioinformatics #Biotechnology #ComputationalBiochemistry #ComputationalBiology

Now published in Peer Community Journal, section Mathematical & #ComputationalBiology: Proper account of auto-correlations improves decoding performances of state-space (semi) Markov models
https://buff.ly/PpTIzQa