Displacement-Optimized Tanglegrams for Trees and Networks Abstract. Phylogenetic trees and networks play a central role in biology, bioinformatics, and mathematical biology, and producing clear, informative visual

Daniel Huson introduces displacement-optimized tanglegrams (DO-tanglegrams), a new approach that applies equally to trees and rooted phylogenetic networks, performing better than cophylo on trees and then NN-tanglegram on networks.

🔗 doi.org/10.1093/molbev/msag066

#evobio #molbio #compbio

piqtree: a python package for seamless phylogenetic inference with IQ-TREE Abstract. piqtree (pronounced pie-cue-tree) is an easy to use, open-source Python package that provides Python script based control of IQ-TREE’s phylogenet

McArthur et al. present piqtree, an easy to use, open-source Python package that provides Python script based control of IQ-TREE’s phylogenetic inference engine.

🔗 doi.org/10.1093/molbev/msag061

#evobio #molbio #compbio

Generalist biological artificial intelligence in modeling the language of life - Nature Biotechnology This Review discusses the promises and pitfalls of biological AI algorithms and presents a vision for generalist biological artificial intelligence, in which models can perform diverse tasks across bi...

Generalist biological artificial intelligence in modeling the language of life www.nature.com/articles/s41... #bioinformatics #compbio

Is it "Data Science" if the most critical step—the generative model—relies on intuition and domain feel? Or are we just high-tech artists painting with numbers? 🖌️

What do you think? Is the "Art" of modeling being overlooked?

#DataScience #Bioinformatics #Bayesian #Modeling #CompBio [5/5]

Will Quantum Computing actually transform #drug discovery? In the age of AI, why are we still betting on Quantum & GPU-accelerated HPC? We’ve just released our whitepaper detailing how the synergy of #QuantumComputing #MachineLearning & #HPC enables quantum-accurate simulations. #compbio #compchem

EvolCompGen presents: Christian Landry on the Evolution of gene duplication, from redundancy to dependency

🧬 EvolCompGen presents: Christian Landry on the Evolution of gene duplication, from redundancy to dependency
@christianlandry.bsky.social

🗓️ Join us on Monday, March 23 at 11:00 AM EDT

📌 Register here: us02web.zoom.us/webinar/regi...

#society #compbio

CCPBioSim Annual Conference

Registration is open for the #CCPBioSim Annual Conference, 6-8 July, Bristol, UK!

See: www.ccpbiosim.ac.uk/bristol2026

Delighted to be hosting the conference @bristoluni.bsky.social, with the theme "Biomolecular simulation across scales, for understanding and design"

#compchem
#compbio
#biodesign

#compchem #machinelearning #quantumcomputing #compbio New preprint: "The Convergence Frontier: Integrating Machine Learning and High Performance Quantum Computing for Next-Generation Drug Discovery".
@qubit-pharma.bsky.social
arxiv.org/abs/2603.17790

OrthoGarden: a pipeline for propagating phylogenetic trees for nonmodel organisms from short reads and de novo genome assemblies Abstract. Phylogenomics pipelines are designed to reconstruct evolutionary relationships among groups of organisms. Existing pipelines are dependent upon r

Turner et al. introduce OrthoGarden, an automated and containerized de novo assembly-based phylogenomics pipeline aimed at recovering accurate and reproducible phylogenies from any combination of short reads and assemblies.

🔗 doi.org/10.1093/molbev/msag053

#evobio #molbio #compbio

HaploThread: a scalable desktop tool for efficient haplotype network inference and interactive visualization Abstract. This note introduces HaploThread, a user-friendly desktop software with a graphical user interface designed for constructing and visualizing hapl

Xu et al. introduce HaploThread, a user-friendly desktop software with a graphical user interface designed for constructing and visualizing haplotype networks.

🔗 doi.org/10.1093/molb...

#evobio #molbio #compbio

The bottom line: Benchmarking—much like success in life—is not a zero-sum game.

It’s about finding the right tool for the right job, not finding the "one tool to rule them all." ⚔️

What’s your "litmus test" for a trustworthy benchmark?

#Bioinformatics #OpenScience #DataScience #CompBio

Promotional graphic showing a section of figure 5 from the white paper of the cysteine-481 sulfur link to Ibrutinib.

Covalent ligand docking is faster, easier, and more accurate in GOLD. ✔️

Find out what's changed and see example results in this new white paper.

Download it here: ccdc-info.com/4re9FCT

#DrugDiscovery #Pharma #CompChemSky #CompBio

Molecular clock dating using complex mixture models: applied to ancient symbionts Abstract. Molecular clocks are a fundamental technique in evolutionary biology for establishing the timing and tempo of organismal divergence. However, cur

@sishuowang.bsky.social & Meade introduce phyloHessian, using complex mixture substitution models in molecular dating. Empirical analysis of ancient symbiont lineages leads to a revised understanding of their host association origins.

🔗 doi.org/10.1093/molbev/msag039

#evobio #molbio #compbio

‘Virtual cell’ captures most-basic process of life: bacterial division Researchers simulated nearly every molecule in a bacterial cell — and then watched the cell grow and reproduce.

#compbio Good read: Virtual cell’ captures most-basic process of life: bacterial division www.nature.com/articles/d41...

Check out recent talk @jsb-ucla.bsky.social gave at Colorado School of Public Health!

#Bioinformatics #FDR #Biostatistics #CompBio #HighThroughputBiology

📢 𝐂𝐚𝐥𝐥 𝐟𝐨𝐫 𝐏𝐚𝐩𝐞𝐫𝐬: 𝐂𝐮𝐫𝐫𝐞𝐧𝐭 𝐁𝐢𝐨𝐢𝐧𝐟𝐨𝐫𝐦𝐚𝐭𝐢𝐜𝐬 🧪

Publish in our Scopus-indexed journal! We offer high visibility and rigorous peer review for the global computational biology community. 🧬

🔗 Submit today: https://bit.ly/4s0XXg1

#Bioinformatics #CompBio #Genomics #DataScience #ScienceSky #AcademicSky

Processing power Meet the LJI scientists changing medical research through artificial intelligence

Forget ChatGPT and Gemini.

“We don’t have that kind of error tolerance."

Here's how LJI scientists are building new AI tools to advance medical research: mag.lji.org/fall2025/pro...

#DataScience #CompBio #AI #ChatGPT

Green graphic with yellow and white text reads, "Vascular Contributions to Cognitive Impairment and Dementia (VCID) | 3 Reasons to attend | April 28 – May 1, 2026 | Washington University in St. Louis."

Green graphic with yellow and white text reads, "#1 Opportunities to present talks or posters and develop grantsmanship through expert guidance and real-time feedback."

Green graphic with yellow and white text reads, "#2 Engaging seminars cover molecular approaches, mouse models of ADRD and computational methods, highlighting current research and future directions."

Green graphic with yellow and white text reads, "#3 Travel awards available for trainees to support skill development and career momentum. Apply during registration!"

⏰ Submit an abstract by April 3 to present a talk or poster!

@jacksonlab.bsky.social's workshop brings together researchers in #VascularBiology and #Neurodegeneration to advance work in #AlzheimersDisease and related dementias.

🔜 Register: www.jax.org/education-an...

#NeuroSkyence #CompBio #ADRD

RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments Abstract. Identifying recurrent changes in biological sequences is important to multiple aspects of biological research—from understanding the molecular ba

Robbins, Liu & Kelly present RECUR, a method for identifying recurrent amino acid substitutions from multiple sequence alignments that is fast, easy to use, and scalable to thousands of sequences.

🔗 doi.org/10.1093/molbev/msag036

#evobio #molbio #compbio

TreeProfiler: large-scale metadata profiling along gene and species trees Abstract. Profiling biological traits along gene or species tree topologies is a well-established approach in comparative genomics, widely employed to infe

@dengziqi1991.bsky.social et al. present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes.

🔗 doi.org/10.1093/molb...

#evobio #molbio #compbio

Normalized compression distance for DNA classification Analyzing the origin and diversity of numerous genomic sequences, such as those sampled from the human microbiome, is an important first step in genomic analysis. The use of normalized compression dis...

#compbio #metagenomics There was a popular-press paper that indicated NCD might be faster than deep neural nets for classification. In metagenomics, w/ lots of comparisons, they're NOT. And they were only better in superkingdom classification - clear kmer patterns. peerj.com/articles/206...

#compbio #bioinformatics

Inference and Visualization of Complex Genotype–Phenotype Maps Abstract. Understanding how biological sequences give rise to observable traits, that is, how genotype maps to phenotype, is a central goal in biology. Yet

Martí-Gómez et al. developed gpmap-tools, integrating models for inference, phenotypic imputation, and error estimation from multiplex assays of variant effect data or natural sequences in the presence of genetic interactions.

🔗 doi.org/10.1093/molbev/msag023

#evobio #molbio #compbio

Call for Papers | Generative AI in Genomics (Gen²) Workshop ICLR Workshop on Generative AI in Genomics (Gen²).

📣 DEADLINE UPDATE: Good news! We’ve extended the Gen² paper submission deadline to:
📅 Feb 8, AoE

We look forward to hearing about your latest research in GenAI in Genomics at @iclr-conf.bsky.social !

🔗 genai-in-genomics.github.io/call_for_pap...

#ICLR2026 #GenAI #CompBio #BioML #Genomics 🧬🧪

Assessing Ancient DNA Sampling Strategies for Natural Selection Inference in Humans Using Allele Frequency Time Series Data Abstract. The increased availability of genomic data from ancient humans allows estimating the strength of natural selection at a given locus using time se

@anchieri.bsky.social @cegamorim.bsky.social et al. benchmark the inference of selection with aDNA-like time series datasets, showing that ApproxWF can estimate selection with datasets of ∼100 individuals when selection is strong.

🔗 doi.org/10.1093/gbe/evaf234

#genome #evolution #compbio

MBE | PharaohFUN: phylogenomic analysis for plant protein history and function elucidation PharaohFUN incorporates a homogeneous representative sampling of key species in Viridiplantae, bridging clades that have traditionally been studied separately, thus establishing a comprehensive evolutionary framework to draw conclusions about sequence evolution and function.

@marcosramos99.bsky.social @franromerocampero.bsky.social et al. present PharaohFUN, a web application designed for evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships.

🔗 doi.org/10.1093/molbev/msag011

#evobio #molbio #compbio

Arc AIxBio Fellows Program for Undergrads | Arc Institute Arc Institute is a independent nonprofit research organization headquartered in Palo Alto, California.

@arcinstitute.org just announced an AI & Bio fellowship for undergrads!

I'm building a team of 2–3 to apply. My interests are in AI for oncology or genomics. Looking for teammates with deep learning/modeling experience.

If you are interested, send me a DM or reply below.

#SciSky #AIxBio #CompBio

2026 Summer Intern (Computational Sciences - Cluster of Excellence) 2026 Summer Intern (Computational Sciences - Cluster of Excellence) The Marioni group in the Computational Sciences (CS) department studies the molecular mechanisms of cell fate decisions in early dev...

🧬 2026 Internship: Marioni Group @genentech.bsky.social Seeking PhD intern for Deep Learning on large-scale genetic screens (Perturb-seq/Optical).
Focus: ML for single-cell + imaging to decode phenotypes.
📍 SSF (On-site) | 12-wk paid
⚠️ Apply via portal only: 🔗 bit.ly/45P7TQB
#CompBio #AI #Genetics

About me.

I am a first-class honors graduate of Biomedical Laboratory Science, from the University of Ibadan. I specialized in Virology.

My interests are in #AI/ML, #Virology, #Bioinformatics, #CompBio, #Proteins, #RNA and #Immunology. I am currently searching for funded MSc or PhD position.

Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base

@proteinmechanic.bsky.social et al. present the web-based Structome-AlignViewer for evaluating structure-aware alignments through spatial mapping of alignment columns to protein structures, and quantitative confidence scoring.

🔗 doi.org/10.1093/gbe/evag004

#genome #evolution #compbio