Georgios Pappas Jr
@gpappas.bsky.social
Professor University of Brasilia - Brazil
Computational Genomics and bioinformatics group
Computational Genomics and bioinformatics group
Source: Nature
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Genetic elements promote retention of extrachromosomal DNA in cancer cells - Nature
A combination of genome-wide functional screening, imaging and chromatin profiling identifies a new class of highly prevalent genomic elements that help retain extrachromosomal DNA copies in dividing ...
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November 21, 2025 at 3:36 AM
Source: Nature
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Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes | Nature Genetics share.google/JtM3g872aQID...
Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes - Nature Genetics
Ctyper is a genotyping method for copy number variation and complex genes that produces sequence-resolved genotypes by directly comparing sequencing reads to pangenome haplotypes, achieving increased ...
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October 19, 2025 at 2:08 AM
Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes | Nature Genetics share.google/JtM3g872aQID...
I’ve released a new Quarto extension to help create class schedules and syllabi. The extension makes it simple to distribute a list of topics over a date range using straightforward syntax.
github.com/gpappasunb/c...
#quarto #Education #Syllabi #Teachers
github.com/gpappasunb/c...
#quarto #Education #Syllabi #Teachers
GitHub - gpappasunb/class-schedule: Quarto extension to create a PDF document that renders a specially formatted list of topics, along a pre-defined span of days, allowing you to select the recurring ...
Quarto extension to create a PDF document that renders a specially formatted list of topics, along a pre-defined span of days, allowing you to select the recurring days of the week for the topics. ...
github.com
July 22, 2025 at 7:35 PM
I’ve released a new Quarto extension to help create class schedules and syllabi. The extension makes it simple to distribute a list of topics over a date range using straightforward syntax.
github.com/gpappasunb/c...
#quarto #Education #Syllabi #Teachers
github.com/gpappasunb/c...
#quarto #Education #Syllabi #Teachers
Reposted by Georgios Pappas Jr
ICYMI: New online! Antimicrobial peptides: structure, functions and translational applications
Antimicrobial peptides: structure, functions and translational applications
Nature Reviews Microbiology, Published online: 11 July 2025; doi:10.1038/s41579-025-01200-yIn this Review, Franco and colleagues explore the structural and functional diversity of antimicrobial peptides (AMPs), their mechanism of action, recent advances in AMP design and optimization, and their potential to address antimicrobial resistance.
www.nature.com
July 18, 2025 at 11:01 AM
ICYMI: New online! Antimicrobial peptides: structure, functions and translational applications
Reposted by Georgios Pappas Jr
Protein homologs in large databases are rapidly identified with an alignment-free pipeline go.nature.com/3YWwP6j
rdcu.be/euayR
rdcu.be/euayR
Fast, sensitive detection of protein homologs using deep dense retrieval - Nature Biotechnology
Protein homologs in large databases are rapidly identified with an alignment-free pipeline.
go.nature.com
July 2, 2025 at 2:25 AM
Protein homologs in large databases are rapidly identified with an alignment-free pipeline go.nature.com/3YWwP6j
rdcu.be/euayR
rdcu.be/euayR
A genomic perspective on fungal diversity and evolution | Nature Reviews Microbiology share.google/lPZ2DLtx7ISv...
A genomic perspective on fungal diversity and evolution - Nature Reviews Microbiology
In this Review, Mondo and Grigoriev explore the central role of omics approaches to investigate the biology and evolution of fungi and understand phylogeny and how traits evolved over time within the ...
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July 1, 2025 at 8:48 PM
A genomic perspective on fungal diversity and evolution | Nature Reviews Microbiology share.google/lPZ2DLtx7ISv...
Reposted by Georgios Pappas Jr
A Tutorial in Nature Protocols provides guidelines for the use of machine learning models to mine genomes and proteomes for the discovery of antimicrobial peptides. 🔒
Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery - Nature Protocols
In this Tutorial, we provide guidelines for the use of ML models to mine genomes and proteomes for the discovery of antimicrobial peptides, discussing the various stages of the ML workflow, recent advances in ML models and how to experimentally validate the computational predictions.
go.nature.com
June 11, 2025 at 10:34 PM
A Tutorial in Nature Protocols provides guidelines for the use of machine learning models to mine genomes and proteomes for the discovery of antimicrobial peptides. 🔒
Reposted by Georgios Pappas Jr
The microbiome for clinicians. #Microbiome #ClinicalMedicine @cellpress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
June 6, 2025 at 2:31 PM
The microbiome for clinicians. #Microbiome #ClinicalMedicine @cellpress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Georgios Pappas Jr
ICYMI: New online! Metagenomics distilled: new k-mer-based methods
Metagenomics distilled: new k-mer-based methods
Nature Reviews Microbiology, Published online: 23 May 2025; doi:10.1038/s41579-025-01192-9This Genome Watch highlights the advantages and limitations of k-mer approaches versus standard alignment-based methods for analysing metagenomic data, assisting microbial species identification, microbial abundance estimation and their application in pathogen genomic epidemiology.
www.nature.com
May 30, 2025 at 4:37 PM
ICYMI: New online! Metagenomics distilled: new k-mer-based methods
Reposted by Georgios Pappas Jr
RAxML-NG v2.0 beta is here
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
Release RAxML-NG v2.0-beta2 · amkozlov/raxml-ng
Main new features
Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024)
Multiple fast branch support measures
Integrated model testing
Full Changelog: 1.2.2...2.0-beta2
github.com
May 15, 2025 at 5:35 AM
RAxML-NG v2.0 beta is here
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
Reposted by Georgios Pappas Jr
typst: A new markup-based typesetting system that is powerful and easy to learn. ★40466 https://github.com/typst/typst
typst / typst
A new markup-based typesetting system that is powerful and easy to learn.
github.com
May 16, 2025 at 4:58 PM
typst: A new markup-based typesetting system that is powerful and easy to learn. ★40466 https://github.com/typst/typst
Admixture’s impact on Brazilian population evolution and health | Science www.science.org/doi/10.1126/...
Admixture’s impact on Brazilian population evolution and health
Brazil, the largest Latin American country, is underrepresented in genomic research despite boasting the world’s largest recently admixed population. In this study, we generated 2723 high-coverage who...
www.science.org
May 16, 2025 at 3:05 PM
Admixture’s impact on Brazilian population evolution and health | Science www.science.org/doi/10.1126/...
Reposted by Georgios Pappas Jr
Nature asked computer scientists and bioinformaticians what advice they would give to researchers who recognize the need to pick up some coding skills but don’t know where to start. Here are four key questions to help you decide. #Academicsky #Compsky 🧪
Which programming language should I use? A guide for early-career researchers
Computer scientists and bioinformaticians address four key questions to help rookie coders to make the right choice.
go.nature.com
April 26, 2025 at 1:28 PM
Nature asked computer scientists and bioinformaticians what advice they would give to researchers who recognize the need to pick up some coding skills but don’t know where to start. Here are four key questions to help you decide. #Academicsky #Compsky 🧪
