Sadik Muzemil
@sadikmz.bsky.social
📤 30
📥 86
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Computational biologist
reposted by
Sadik Muzemil
PlantEvolution 🌱🌾
10 months ago
Awesome new work from
@labschneeberger.bsky.social
(with a small contribution from the Weigel lab). Experimentally observed mutational patterns in centromeres underpin a model that recapitulates intra-specific centromere divergence!
www.biorxiv.org/content/10.1...
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Sadik Muzemil
bioRxiv Bioinfo
10 months ago
Pangenome-aware DeepVariant
https://www.biorxiv.org/content/10.1101/2025.06.05.657102v1
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Sadik Muzemil
Stephen Turner
11 months ago
Lossless Pangenome Indexing Using Tag Arrays
www.biorxiv.org/content/10.1...
🧬🖥️🧪
github.com/parsaeskanda...
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Sadik Muzemil
Nature Reviews Genetics
11 months ago
New online! Predicting gene expression from DNA sequence using deep learning models
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Predicting gene expression from DNA sequence using deep learning models
Nature Reviews Genetics, Published online: 13 May 2025; doi:10.1038/s41576-025-00841-2Barbadilla-Martínez et al. review recent progress in deep-learning-based sequence-to-expression models, which predict gene expression levels solely from DNA sequence. These models are providing new insights into the complex combinatorial logic underlying cis-regulatory control of gene expression.
https://www.nature.com/articles/s41576-025-00841-2?utm_source=dlvr.it&utm_medium=bluesky
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reposted by
Sadik Muzemil
Stephen Turner
12 months ago
Parsing GTF and FASTA files using the eccLib Library
www.biorxiv.org/content/10.1...
🧬🖥️🧪
gitlab.platinum.edu.pl/eccdna/eccLib
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Parsing GTF and FASTA files using the eccLib Library
Summary: Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic contexts. To the best of the authors' knowledge, it…
https://www.biorxiv.org/content/10.1101/2025.04.24.650481v1
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Sadik Muzemil
Charikleia Karageorgiou (Clio)
12 months ago
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Sex chromosome evolution in haploid plants: Microchromosomes, disappearing chromosomes, and giant chromosomes | PNAS
As in many diploid organisms with genetic sex determination, haploid-dominant organisms have also evolved sex chromosomes or extensive genomic regi...
https://www.pnas.org/doi/abs/10.1073/pnas.2425050122
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reposted by
Sadik Muzemil
Stephen Turner
12 months ago
Vizitig: context-rich exploration of sequencing datasets
www.biorxiv.org/content/10.1...
🧬🖥️🧪
gitlab.inria.fr/vizisoft/viz...
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Sadik Muzemil
Stephen Turner
12 months ago
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals
www.nature.com/articles/s41...
🧬🖥️🧪
#Rstats
bioconductor.org/packages/Syn...
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reposted by
Sadik Muzemil
Stephen Turner
12 months ago
Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling
academic.oup.com/bioinformati...
🧬🖥️🧪
github.com/PacificBiosc...
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Sadik Muzemil
Nature Reviews Genetics
about 1 year ago
ICYMI: New online! Computational analysis of DNA methylation from long-read sequencing
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Computational analysis of DNA methylation from long-read sequencing
Nature Reviews Genetics, Published online: 28 March 2025; doi:10.1038/s41576-025-00822-5Long-read sequencing technologies can directly profile methylation modifications across the genome. In this Review, Fu et al. overview the long-read computational tools to identify and compare methylation signals, as well as tools that use these methylation signals to analyse cell-type diversity and gain additional genomic insights.
https://www.nature.com/articles/s41576-025-00822-5?utm_source=dlvr.it&utm_medium=bluesky
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
The minda tool helps with SV benchmarking and merging by decomposing SVs into start and end records, supporting other types of SVs beyond primarily germine indels processed by truvari, SVanalyzer, SURVIVOR, Jasmine, etc.
github.com/KolmogorovLa...
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences
arxiv.org/abs/2503.20766
🧬🖥️🧪
github.com/yana-safonov...
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reposted by
Sadik Muzemil
Nature Reviews Genetics
about 1 year ago
New online! Transcriptomics in the era of long-read sequencing
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Transcriptomics in the era of long-read sequencing
Nature Reviews Genetics, Published online: 28 March 2025; doi:10.1038/s41576-025-00828-zAdvances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read RNA sequencing, including experimental and computational tools, current applications, challenges and opportunities.
https://www.nature.com/articles/s41576-025-00828-z?utm_source=dlvr.it&utm_medium=bluesky
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
Generating multiple alignments on a pangenomic scale
academic.oup.com/bioinformati...
🧬🖥️🧪
gitlab.com/qwerzuiop/pa...
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model
academic.oup.com/bib/article/...
🧬🖥️🧪
github.com/xiaoyan-wang...
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
CarpeDeam: A De Novo Metagenome Assembler for Heavily Damaged Ancient Datasets
www.biorxiv.org/content/10.1...
🧬🖥️🧪
github.com/LouisPwr/Car...
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reposted by
Sadik Muzemil
Will Ratcliff
about 1 year ago
1/35 New paper out! @jamesTstroud and I dive into why long-term studies are crucial for understanding evolution. They reveal processes impossible to detect in short timescales and capture rare events that transform our understanding of evolutionary dynamics.
www.nature.com/articles/s41...
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
Learning the language of protein-protein interactions
www.biorxiv.org/content/10.1...
🧬🖥️🧪
github.com/VarunUllanat...
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
geneviewer - Gene Cluster Visualizations in R. Imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps.
github.com/nvelden/gene...
#Rstats
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reposted by
Sadik Muzemil
Albert Vilella, PhD.
about 1 year ago
The long, unsteady path to ecosystem recovery
phys.org/news/2025-03...
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Plants struggled for millions of years after the world's worst climate catastrophe, scientists reveal
A team of scientists from University College Cork (UCC), the University of Connecticut, and the Natural History Museum of Vienna have uncovered how plants responded to catastrophic climate changes 250...
https://phys.org/news/2025-03-struggled-millions-years-world-worst.html
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reposted by
Sadik Muzemil
PlantEvolution 🌱🌾
about 1 year ago
This looks quite cool, latest paper from Frank Johannes on somatic mutations in trees: Branching architecture limits the rate of somatic mutation accumulation in trees
doi.org/10.1101/2025...
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reposted by
Sadik Muzemil
David Lowry
about 1 year ago
We have a new paper out today, where, among other things, we find evidence that a locally adaptive chromosomal inversion likely trapped an even older inversion along its path to becoming the supergene it is today.
onlinelibrary.wiley.com/doi/10.1111/...
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The Evolution of Locally Adaptive Chromosome Inversions in Mimulus guttatus
Chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a significant role in the evolution of adaptations in those species. Inversions are thought to op...
https://onlinelibrary.wiley.com/doi/10.1111/mec.17708
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
Simulating 500 million years of evolution with a language model
www.science.org/doi/10.1126/...
🧬🖥️🧪
github.com/evolutionary...
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reposted by
Sadik Muzemil
Jean-Marc Aury
about 1 year ago
For those working with Hi-C data and the Arima workflow, we have rewritten the Arima tools using htslib to speed up the process. Any feedback is welcome:
github.com/Genoscope-LB...
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping
https://www.biorxiv.org/content/10.1101/2025.02.11.637720v1
🧬🖥️🧪
https://github.com/SchriderLab/TEforest
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reposted by
Sadik Muzemil
Stephen Turner
about 1 year ago
Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants
https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1
🧬🖥️🧪
https://github.com/harvardinformatics/scrub-jay-genomics
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Review: Foundation models in bioinformatics
doi.org/10.1093/nsr/...
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Foundation models in bioinformatics
This review presents recent advancements in bioinformatics Foundation Models (FMs) that employed in a variety of downstream tasks, including genomics, tran
https://doi.org/10.1093/nsr/nwaf028
about 1 year ago
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