Glori

genome evolution,
phylogenomics

[Savage Lab @SavageCatsOnly]

Can CRISPR edits enable precise tuning of plant gene expression? We think: yes.

In our newest manuscript, we measured the effects of >30,000 CRISPR-like promoter mutations in sorghum protoplasts.

[Jayen Thakker @JayenThakker]

How to Choose the Right Statistical Test

[GAMA Miguel Angel 🐦‍⬛🔑 @miangoar]

🧵one of my favorite tools: Foldseek (1/7)

We have traced the evo of species by comparing their proteins. We use models that assign a %similarity between seqs and confidently infer that 2 proteins are homologous if share ≥25% SeqSim. But what happens when it’s less than this?

[Glori @ztisbest]

@miangoar Oh man, this is pure gold, thanks so much!

[Glori @ztisbest]

@heisinvwu 人中右偏

[Glori @ztisbest]

Evolution of S-RNase genes and their syntenic relationships in angiosperms, findings on the lineage-specific transpositions and the implications of the gamma triplication event are particularly intriguing

[bioRxiv Evobio @biorxiv_evobio]

S-RNase Evolution in Self-Incompatibility: Phylogenomic Insights into Synteny with S-Like Genes https://t.co/TsTCo8awRv #biorxiv_evobio

[Glori @ztisbest]

Evolution of S-RNase genes and their syntenic relationships in angiosperms, lineage-specific transpositions and the implications of the gamma triplication event are particularly intriguing..

[bioRxiv Evobio @biorxiv_evobio]

S-RNase Evolution in Self-Incompatibility: Phylogenomic Insights into Synteny with S-Like Genes https://t.co/TsTCo8awRv #biorxiv_evobio

[antisense. @razoralign]

Fast-scBatch: Batch Effect Correction Using Neural Network-Driven Distance Matrix Adjustment https://t.co/0HiRTeN78G

[Mile Sikic @msikic]

Ready for >Q30 ONT reads? Herro error correction now supports both R9.4.1 and R10.4.1. simplex reads w/ @domstanojevic @DehuiLin (CHM13 -R9.4.1) #nanopore #longreads

[antisense. @razoralign]

GNNome: Geometric deep learning framework for de novo genome assembly https://t.co/OkzGU5jx2T

[Nature Biotechnology @NatureBiotech]

AlphaFold2 and RoseTTAFold are limited to predicting the 3D structure of proteins. A new all-atom method models complete biomolecular assemblies, including proteins, nucleic acids, small molecules, metals, and covalent modifications. #NBThighlight https://t.co/a9relIlKLC

[Moritz K. Nowack @moritznowack.bsky.social @MoritzNowack]

The endosperm's life span as a crucial but transient seed tissue is controlled by programmed cell death processes.
If you want to know more about how, when and why the endosperm bites the dust - see our latest review by
@NicolasMDoll
hot off the press
https://t.co/eYNRNnI49F

[Stephen Turner 🦋 @stephenturner.us @strnr]

Multi-genome synteny detection using minimizer graph mappings https://t.co/VntPSXMtQU 🧬🖥️ https://t.co/S17ccih0C9

[bioRxiv Bioinfo @biorxiv_bioinfo]

Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs https://t.co/1363lmS6Br #biorxiv_bioinfo

[bioRxiv Bioinfo @biorxiv_bioinfo]

ChemGLaM: Chemical-Genomics Language Models for Compound-Protein Interaction Prediction https://t.co/JETQHJ5COZ #biorxiv_bioinfo

[antisense. @razoralign]

Puzzle Hi-C: an accurate scaffolding software https://t.co/8AwUg4AICU

[Nature Reviews Genetics @NatureRevGenet]

This Review discusses the latest computational approaches, including machine-learning-based methods and integrative structure-modelling frameworks, for studying 3D genome organization

[Chenxin Li, PhD (@chenxinli2.bsky.social) @ChenxinLi2]

Friends don't let friends forget to reorder stacked bar plots. Stacked bar plots are commonly used in research (e.g., to visualize admixture analysis). It can get messy! After reordering the bars, wow, it really made a difference, don't you think?

Link: https://t.co/AogVczy0Ee

[New papers in Network Science @networkspapers]

Chaos: Dynamics of cascades in spatial interdependent networks
https://t.co/5YK7qTZDyE

[Martin Rosvall @m_rosvall]

New preprint: Community Detection with the Map Equation and Infomap: Theory and Applications https://t.co/zCk0pajzYp

Explore the map equation's theoretical framework and learn to apply Infomap to diverse research problems. @antoneri @daniel_edler @chrisbloecker