PhD candidate @MIT Dept. of Biological Engineering • 🦟 🦠 🧬 🇨🇴 •
#Pathogens, computational + synthetic #biology (#synbio), #epidemiology, #evolution
Yes my initials are PCR but that hasn't made me better at it
coming from twitter @pcr_guy, trying threads @pcr.guy
| Website | https://pablo-cardenas.com |
| Bluesky | https://bsky.app/profile/pcr-guy.bsky.social |
| https://twitter.com/pcr_guy |
aight folks see ya next week for #evoluncheons in full force; here's a free pic of the balkan countryside, en la buena parceritos
8/8
Want a free online conference? Among many great talks, catch the great Brandon Ogbunugafor on Tuesday (and stick around to hear me afterwards!)
SMB Mathematical #Epidemiology and Population Dynamics, #Ecology, & #Evolution registration is free, sign up here: https://intranet.math.vt.edu/SMBEpiPDEE/registration.html
Real cool stuff from the group of @robjohnnoble :
"Warlock: an automated computational workflow for simulating spatially structured #tumour #evolution"
A primary goal of modern cancer research is to characterize tumour growth and evolution, to improve clinical forecasting and individualized treatment. Agent-based models support this endeavour but existing models either oversimplify spatial structure or are mathematically intractable. Here we present warlock, an open-source automated computational workflow for fast, efficient simulation of intratumour population genetics in any of a diverse set of spatial structures. Warlock encapsulates a deme-based oncology model (demon), designed to bridge the divide between agent-based simulations and analytical population genetics models, such as the spatial Moran process. Model output can be readily compared to multi-region and single-cell sequencing data for model selection or biological parameter inference. An interface for High Performance Computing permits hundreds of simulations to be run in parallel. We discuss prior applications of this workflow to investigating human cancer evolution.
⚠️ Tomorrow! ⚠️
"Genomic epidemiological models with Opqua describe pathogen evolution across fitness valleys"
Join on Zoom to hear how computational simulations can explore the ways infectious disease #epidemiology and #evolution intertwine and shape each other. 🖥️ → 📈 + 🧬 → 🦠
13 Jan, 2 PM Eastern, Zoom ID: 94767206749.
Azza Idris is one of the kindest humans and best mentors I know, and she's starting a research group @ragoninstitute ! If you're interested in #malaria and/or #immunology, I can't think of a more welcoming person to work with and learn from. Her group is #hiring #postdocs, #technicians, and #labmanagers 👀
Some representative articles of the excellent science she has contributed to include:
- https://nature.com/articles/nm.4512
One more step towards understanding the unique ways in which malaria persists and spreads in South American transmission environments. We keep banging our drum—drug resistance emerges and spreads in small populations!
Big ups to Manuela and Angela for leading this work. Very grateful to all the authors for letting me tag along as a clueless undergrad/grad student even though my early spins with the data didn't pan out.
Up on @PLOS Pathogens: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010993
Author summary Malaria caused by Plasmodium falciparum is a leading cause of mortality in young children, primarily in sub-Saharan Africa. Safe and effective antimalarials have spurred decades of declining prevalence, but drug resistance threatens global elimination efforts. In the Americas, P. falciparum transmission and genetic diversity are low. The region accounts for only a small proportion of global infections and mortality, yet it has historically contributed to the emergence and dissemination of P. falciparum antimalarial drug resistance. Genomic surveillance in the region can detect emerging drug resistance, dissect its evolutionary dynamics, and impede its spread to highly endemic regions. In this work, we generated and analyzed whole genome sequence data from samples collected in the Pacific Coast region of Colombia and Ecuador, a hotspot of P. falciparum malaria. This region exhibits a large proportion of single-clone infections as well as long-term clonal persistence. Our study analyzes this inbred population structure using relatedness estimates calculated as identity-by-descent. We describe the spatial and temporal dynamics of clonal transmission and outcrossing, demonstrating that selection is still effective in this small, inbred population. These findings will support future drug resistance surveillance in regions with intense interventions and declining prevalence.
I've done my best to help a couple dozen grad school applicants from all around the world through programs like Científico Latino (https://www.cientificolatino.com)
and MIT BE's BEAAP (https://be.mit.edu/academic-programs/prospective-graduate/beaap).
Realizing some of those bright students may be passed over in favor of shams like this makes my blood boil. 1/🧵
#academia #gradschool #phd