Our new preprint on quantifying microbial sample diversity/complexity in a way that accounts for both metagenome architecture and taxonomic composition is now live on bioRxiv: www.biorxiv.org/content/10.6... #metagenomics #bioinformatics #dataanalysis #graphdata

Our new preprint on the inconsistency of the combined gene tree parsimony costs is now live on bioRxiv: www.biorxiv.org/content/10.6...

Check out our new preprint on improving gene regulatory network inference by incorporating a prior from plain-text gene descriptions. It's a simple idea, but we show that it proves to be quite powerful and adaptable. [1/4] www.biorxiv.org/content/10.1...

GRNITE: Gene Regulatory Network Inference with Text Embeddings

Gene regulatory networks (GRNs) capture complex regulatory relationships that govern gene expression in cells. Inference of GRNs from single-cell RNA-seq (scRNA-seq) data has been an active topic of r...

biorxiv.org

Nicolae Sapoval @nsapoval.bsky.social presented "Theoretical and empirical performance of pseudo-likelihood- based Bayesian inference of species trees under the multispecies coalescent" A fantastic theory talk, offering intuitive insights! Paper: doi.org/10.1101/2025.01.28.635282

Our preprint on using pseudo-likelihood for Bayesian inference of species trees from gene tree data under the multispecies coalescent is now online: doi.org/10.1101/2025... [1/n]

Theoretical and Empirical Performance of Pseudo-likelihood-based Bayesian Inference of Species Trees under the Multispecies Coalescent

Likelihood-based inference under the multispecies coalescent provides accurate estimates of species trees. However, maximum likelihood and Bayesian inference are both computationally very demanding. P...

doi.org

It’s that time of the year when I get some writing done. Here are some notes on how I work with academic literature: plume-lifeboat-00b.notion.site/How-I-find-o...

How I find, organize, and read papers | Notion

Introduction

plume-lifeboat-00b.notion.site

I just completed "Ceres Search" - Day 4 - Advent of Code 2024 #AdventOfCode adventofcode.com/2024/day/4 (A little bit behind the schedule this year, but gotta keep it going)

I was waiting for a great topic for my first Bluesky post, and I cannot thing of a better one: I’m thrilled to be hosting @aphillippy.bsky.social at Rice University today and looking forward to his talk at 4pm! events.rice.edu/event/345896...

Distinguished Lecture: Dr. Adam Phillippy

A Ken Kennedy Institute Distinguished Lecture by Dr. Adam Phillippy, Senior Investigator at National Human Genome Research Institute, National Inst...

events.rice.edu