#PLOSCompBiol
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dynamicdip.bsky.social
Thrilled that our work is on the cover of the October 2026 issue of PLOS Comp Bio! 🎉 Huge thanks to first author Suman Saha and all collaborators. @plosbiology.org
📖 Paper: lnkd.in/gS8jifwH
🖼️ Cover: lnkd.in/ga5w5dFg
#PLOSCompBiol #CompNeuro #fMRI
November 8, 2026 at 4:32 AM
gokhalecs.bsky.social
Published? indeed journals.plos.org/ploscompbiol...
Ten Simple Rules for Curating and Facilitating Small Workshops
journals.plos.org
November 4, 2026 at 3:33 PM
bffo.bsky.social
From @plos.org #Computational #Biology | Ten simple rules for a department chair | I like all of the rules, but particularly like Rule 2: Build a team, not a collection of superstars | #Education #PLOSCBTSR #OpenScience #Leadership | 🧪🔓🇸🇰
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journals.plos.org/ploscompbiol...
Ten simple rules for a department chair
Department chairs occupy a pivotal position in the university. Teaching, research, graduate education, and much of the academic community's professional and administrative activity are organized at th...
journals.plos.org
November 8, 2026 at 6:36 PM
milosbielcik.bsky.social
journals.plos.org/ploscompbiol...
Coexistence rules for small, antagonistically interacting microbial communities
Author summary Antibiotics have revolutionised our society by their property of killing or attenuating bacteria. However, despite being widespread, antibiotics have a gentler influence in shaping micr...
journals.plos.org
November 9, 2026 at 1:08 PM
elizabethhobson.bsky.social
New research from the lab led by @annemariemarel.bsky.social! We found that captive parakeet groups could shift between different dominance patterns & these shifts were associated with the ranks of birds in our social perturbations journals.plos.org/ploscompbiol...
Graphic showing the title of the journal (PLOS Computational Biology), two parakeets fighting, the title of the paper (Social manipulations trigger shifts in group-level dominance patterns), photos of all the co-authors (Annemarie van der Marel, Xavier Francis, Claire L. O’Connell, Cesar O. Estien, Chelsea Carminito, V. Darby Moore, Elizabeth A. Hobson) and three of the major plots in the paper (one showing pre/post social network change, one showing transitions between dominance patterns, and one showing change over time in which dominance pattern the group used)
November 6, 2026 at 11:17 PM
bffo.bsky.social
From @plos.org #Computational #Biology | Ten simple rules for a successful global health roundtable | #Education #PLOSCBTSR #GlobalHealth #OpenScience | 🧪🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for a successful global health roundtable
Qualitative approaches play a critical role in global health research by capturing the social, political, and contextual dimensions that shape health outcomes. While interviews and focus groups are wi...
journals.plos.org
November 6, 2026 at 6:04 PM
elliot-murphy.bsky.social
Interpretable embeddings of speech explain and enhance the brain encoding performance of audio models

journals.plos.org/ploscompbiol...
Interpretable embeddings of speech explain and enhance the brain encoding performance of audio models
Author summary Modern AI systems trained on large amounts of speech, known as speech foundation models, are remarkably good at predicting how the human brain responds when people listen to spoken lang...
journals.plos.org
November 3, 2026 at 6:59 PM
ppaxisa.bsky.social
Can’t be said enough. Also good to read @lpachter.bsky.social ‘s elephant: journals.plos.org/ploscompbiol... and a good reason to use @erikvannimwegen.bsky.social bonsai tree method doi.org/10.1038/s415...
October 31, 2026 at 1:37 PM
david-p-reichert.bsky.social
Which, fun side note, might the cause of certain forms of hallucinations...

journals.plos.org/ploscompbiol...
Charles Bonnet Syndrome: Evidence for a Generative Model in the Cortex?
Author Summary The cerebral cortex is central to many aspects of cognition and intelligence in humans and other mammals, but our scientific understanding of the computational principles underlying cor...
journals.plos.org
November 1, 2026 at 10:13 PM
netscience.bsky.social
The influence of ensemble size and composition on the performance of combined real-time COVID-19 forecasts journals.plos.org/ploscompbiol...
The influence of ensemble size and composition on the performance of combined real-time COVID-19 forecasts
Author summary Infectious disease outbreaks such as the recent COVID-19 pandemic present uncertain situations for governments, health agencies and the general public. Short-term forecasts of key indic...
journals.plos.org
November 4, 2026 at 8:53 AM
mathcancer.bsky.social
We built phenomenal collaborations to create a thriving international community focused around understanding multiscale cancer-immune interactions.

journals.plos.org/ploscompbiol...

I got to explore academic leadership while working as Associate Dean of Undergraduate Education (ADUE).

4/10
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
Author summary This paper introduces PhysiCell: an open source, agent-based modeling framework for 3-D multicellular simulations. It includes a standard library of sub-models for cell fluid and solid ...
journals.plos.org
November 1, 2026 at 5:06 PM
bffo.bsky.social
From @plos.org #Computational #Biology | Ten simple rules for teaching practical AI to health data teams | #Education #Bioinformatics #PLOSCBTSR #OpenScience #AI #LLM #Research #HealthData | 🧬🖥️🧪🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for teaching practical AI to health data teams
Artificial intelligence (AI) has rapidly entered the healthcare discourse, often framed through the lens of frontier models, generative systems, and transformative potential. Yet for many healthcare d...
journals.plos.org
October 31, 2026 at 2:18 PM
sagitaninta.bsky.social
"You want to go where a question takes you, not where your training left you"

This hits hard journals.plos.org/ploscompbiol...
“Antedisciplinary” Science
journals.plos.org
October 31, 2026 at 8:42 PM
open-hax.bsky.social
The 'prompt-to-genome' shift in generative biology is a jump in agency. This constraint-first framework—moving from fluency to biological feasibility—ensures AI designs are functional, not just plausible. 🧬🛡️

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014865
November 1, 2026 at 2:59 AM
estelle.eurosky.social
Institutions deceive. Here is a call for adventure:

"The first molecular biologists were a motley crew of misfits and revolutionaries with no particularly relevant training, many of them ex-physicists. […] They burned their bridges."

journals.plos.org/ploscompbiol...
computer scientists. It would be silly to argue against large interdisciplinary teams where a mammoth technical goal can be clearly defined. But when I think of new fields in science that have been opened, I don't think of interdisciplinary teams combining existing skills to solve a defined problem—I think of single interdisciplinary people inventing new ways to look at the world. Focusing on interdisciplinary teams instead of interdisciplinary people reinforces standard disciplinary boundaries rather than breaking them down. An interdisciplinary team is a committee in which members identify themselves as an expert in something else besides the actual scientific problem at hand, and abdicate responsibility for the majority of the work because it's not their field. Expecting a team of disciplinary scientists to develop a new field is like sending a team of monolingual diplomats to the United Nations. Progress is driven by new scientific questions, which demand new ways of thinking. You want to go where a question takes you, not where your training left you. We may not have a single clarion call to arms like Schrödinger's What is Life? driving physicists into biology right now, as in the beginnings of molecular biology. But we do have powerful new technologies to harness (computational biology), newly revitalized approaches to old problems (systems biology), and new areas altogether (synthetic biology). New disciplines eventually self-organize around new problems and approaches, creating a new shared culture. This shared culture coalesces into the next essential training regimen for the next generation of scientists, and with luck, some of these people will overcome their training to open up more new fields of inquiry. Interdisciplinary science is just the embryonic stage of a new discipline. To value interdisciplinary science for its own sake is to value history over progress—that is, to value people's past training more than their current work.
November 1, 2026 at 10:05 AM
bffo.bsky.social
From @plos.org #Computational #Biology | Ten simple rules for designing your career pivot | I like all of the rules, but I particularly like RULE 1: Honor your emotions | #Education #PLOSCBTSR #OpenScience | 🧪🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for designing your career pivot
journals.plos.org
October 28, 2026 at 5:56 PM
bffo.bsky.social
From our @reactome.org friends in @plos.org #Computational #Biology | Eight quick tips for using the Reactome knowledgebase | I particularly like Tip 8: Re-use our material | #Bioinformatics #Education #PLOSCBQT
#Proteomics #Pathways #OpenScience | 🧬🖥️🧪🔓
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journals.plos.org/ploscompbiol...
Eight quick tips for using the reactome knowledgebase
journals.plos.org
October 28, 2026 at 5:39 PM
bffo.bsky.social
From @lpc-nl.bsky.social & Oscar Meruvia-Pastor in @plos.org #Computational #Biology |Ten simple rules for preparing a job application for an academic position | I like them all, but particularly Rule 10: Be authentic | #Education #PLOSCBTSR #OpenScience |🧪🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for preparing a job application for an academic position
journals.plos.org
October 28, 2026 at 5:49 PM
bffo.bsky.social
From @gbouras13.bsky.social & colleagues in @plos.org #Computational #Biology | Thirteen quick tips for bacteriophage genome annotation | I like all Tips, but particularly TIP | #Bioinformatics #Education #PLOSCBQT #Virus #Genomics #Biocuration | 🧬🖥️🧪🔓🦠 🇦🇺🇨🇦 🇪🇬🇺🇸
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journals.plos.org/ploscompbiol...
Thirteen quick tips for bacteriophage genome annotation
journals.plos.org
October 27, 2026 at 11:55 AM
lpc-nl.bsky.social
Ten simple rules for preparing a job application for an academic position. PLoS Comput Biol 22(10): e1014889. @plos.org
journals.plos.org/ploscompbiol...
Ten simple rules for preparing a job application for an academic position
journals.plos.org
October 27, 2026 at 9:51 PM
bffo.bsky.social
From @plos.org #Computational #Biology | Ten simple rules for responsible use of AI and LLMs in computational biology | #Education #Bioinformatics #PLOSCBTSR #AI #LLM | 🧬🖥️🧪🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for responsible use of AI and LLMs in computational biology
journals.plos.org
October 24, 2026 at 12:24 PM
joshuasweitz.bsky.social
Here are just a few papers for those who want to explore:

Bacterial escape from phage
www.science.org/doi/10.1126/...

Lysis time variability in plaque expansion
journals.plos.org/ploscompbiol...

Irregular fronts & phage lysis of motile bacteria
www.nature.com/articles/s42...
October 22, 2026 at 12:50 PM
arcane-project.bsky.social
Konrad Sakowski presented Modelling and targeted control of healthcare-associated infections in regional healthcare networks

Link to the recommended a paper
journals.plos.org/ploscompbiol...

#ARCANE2026
October 21, 2026 at 7:32 AM
joshcashaback.bsky.social
journals.plos.org/ploscompbiol...
Mechanical power output during stretch–shortening cycles of rat medial gastrocnemius muscle: Influence of various muscle length trajectories
Author summary The average mechanical power output (AMPO) of cyclic contractions, in which a muscle shortens and lengthens, is a key determinant of performance in tasks like sprint cycling and rowing....
journals.plos.org
October 19, 2026 at 11:57 PM
lacerbi.bsky.social
4/ IBS for model fitting comes from our paper with Bas van Opheusden and Wei Ji Ma (PLOS Comp Biol 2020).
Thanks to Julia Maria Perathoner for the first Python port, and to Claude Code for the heavy lifting on 1.5.

journals.plos.org/ploscompbiol...
Unbiased and efficient log-likelihood estimation with inverse binomial sampling
Author summary Researchers often validate scientific hypotheses by comparing data with the predictions of a mathematical or computational model. This comparison can be quantified by the ‘log-likelihoo...
journals.plos.org
October 19, 2026 at 7:06 PM