Pablo Cárdenas R.

277 Followers
240 Following
244 Posts

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

Websitehttps://pablo-cardenas.com
Blueskyhttps://bsky.app/profile/pcr-guy.bsky.social
Twitterhttps://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

SMB Epi-PDEE 2023

Website of SMB Epi-PDEE Mini-Conference 2023

Real cool stuff from the group of @robjohnnoble :

"Warlock: an automated computational workflow for simulating spatially structured #tumour #evolution"

https://arxiv.org/abs/2301.07808

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.

arXiv.org

⚠️ 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. 🖥️ → 📈 + 🧬 → 🦠

#ComputationalEpidemiology

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

- https://nejm.org/doi/full/10.1056/NEJMoa2034031

- https://www.nejm.org/doi/full/10.1056/NEJMoa2203067

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.

#malaria #epidemiology

Up on @PLOS Pathogens: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010993

Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis

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.

This particular offering, supposedly (possibly? I shudder) at my current home at MIT Engineering and in my general domain of science, advertises a project along the lines of cryo-EM image classification of proteins using CNNs (autotranslated). 7/🧵
https://www-raytech-group.translate.goog/NewsDetail.aspx?ID=92&_x_tr_sl=auto&_x_tr_tl=en&_x_tr_hl=en&_x_tr_pto=wapp&_x_tr_sch=http
基于深度神经网络的蛋白质智能显微分类系统-The RayTech Group inc,

锐科教育是一个致力于提升学生终身教育竞 争力的教育集团,为赋予学生全球性眼光而 不断努力。我们为学员提供专业的线上学科 辅导、科研指导、留学申请与实习求职辅导 咨询内推服务,通过私人定制化的服务与产 品,提高学员的个人综合实力,最终实现斩 获名校offer与顶级公司实习全职的就业机会。

Clients are offered a full menu of research opportunities at elite schools on topics ranging from finance to behavioral econ to machine learning to structural biology. This could just be false advertising from the company, but if they offer a service, I bet they provide. 6/🧵
https://www-raytech-group.translate.goog/xzdy.aspx?ClassID=21&_x_tr_sl=auto&_x_tr_tl=en&_x_tr_hl=en&_x_tr_pto=wapp&_x_tr_sch=http
Careers-The RayTech Group inc,

锐科教育是一个致力于提升学生终身教育竞 争力的教育集团,为赋予学生全球性眼光而 不断努力。我们为学员提供专业的线上学科 辅导、科研指导、留学申请与实习求职辅导 咨询内推服务,通过私人定制化的服务与产 品,提高学员的个人综合实力,最终实现斩 获名校offer与顶级公司实习全职的就业机会。

The company seems to operate through a variety of schemes, presumably including phony rec letters and application materials. However, a more insidious scheme is paying research supervisors to work with student clients on short-term research projects: 3/🧵
https://www-raytech-group.translate.goog/xzdy.aspx?ClassID=21&_x_tr_sl=auto&_x_tr_tl=en&_x_tr_hl=en&_x_tr_pto=wapp&_x_tr_sch=http
Careers-The RayTech Group inc,

锐科教育是一个致力于提升学生终身教育竞 争力的教育集团,为赋予学生全球性眼光而 不断努力。我们为学员提供专业的线上学科 辅导、科研指导、留学申请与实习求职辅导 咨询内推服务,通过私人定制化的服务与产 品,提高学员的个人综合实力,最终实现斩 获名校offer与顶级公司实习全职的就业机会。

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

Científico Latino

Científico Latino aims to help STEM undergraduate, graduate, and professional students by providing mentorship, open-access resources on scholarships, fellowships and blog posts on professional development.

Científico Latino