Tootfinder

This is long, but hits on something that has been bothering me about Star Trek: Strange New Worlds, too.
https://reactormag.com/bioessentialism-in-star-trek-strange-new-worlds/

In Star Trek: Strange New Worlds, Is Biology Destiny? - Reactor
Vulcans are logic machines, Gorn are monsters... or so Strange New Worlds might have us believe.

i stumbled across a fragment of my online dating profile from two decades ago
I'm into Monk, chaos theory, Björk, Vermeer, Frosted Mini-Wheats, Wallace Stevens, Saint-Saëns, Tim O'Brien, Miro, evolutionary biology, Ravel, Gregory Corso, fresh berries, UFOs, Ellington, Bible comics, computational complexity, Nespresso, The Kinks, Diane DiPrima, fresh-squeezed OJ, Köln's Kompakt music label, Giacometti, Mingus, that sort of thing. I'm very curious and never bored.
s…

Thickness Dependence and Fundamental Limitations for Ion Permeation in Nanoscale Films
Jay Prakash Singh, Konstantin I. Morozov, Viatcheslav Freger
https://arxiv.org/abs/2509.14725

Thickness Dependence and Fundamental Limitations for Ion Permeation in Nanoscale Films
Nanoscale films play a central role in biology and osmotic separations. Their water/salt selectivity is often regarded as intrinsic property, favoring thinner membranes for faster permeation. Here we highlight and quantify a fundamental limitation arising from the dependence of ion self-energy on film thickness, governed by its ratio to Bjerrum length. The resulting relation factors out this dependence from intrinsic ion permeability, which agrees well with available data and enables evaluation…

🧠 Brain organoids reveal potential neural basis of schizophrenia and bipolar disorder
https://medicalxpress.com/news/2025-09-brain-organoids-reveal-potential-neural.html

Brain organoids reveal potential neural basis of schizophrenia and bipolar disorder
Pea-sized brains grown in a lab have for the first time revealed the unique way neurons might misfire due to schizophrenia and bipolar disorder, psychiatric ailments that affect millions of people worldwide but are difficult to diagnose because of the lack of understanding of their molecular basis.

Branching Flows: Discrete, Continuous, and Manifold Flow Matching with Splits and Deletions
Hedwig Nora Nordlinder (Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet), Lukas Billera (Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet), Jack Collier Ryder (Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet), Anton Oresten (Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet), Aron St{\aa}lmarck (…

Microsoft researchers say AI models can be used to design toxins that evade biosecurity systems used to screen DNA orders for potential biothreats (Antonio Regalado/MIT Technology Review)
https://www.technologyreview.com/2025/10/0…

Microsoft says AI can create “zero day” threats in biology
Artificial intelligence can design toxins that evade security controls.

My department at California State University Northridge is hiring! We're looking for a new colleague studying microbiology or molecular/cellular biology. I'm not on the search committee, but happy to answer questions about the department and campus, and life in LA

[2025-09-19 Fri (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
toXiv_bot_toot

Biology-driven assessment of deep learning super-resolution imaging of the porosity network in dentin
Lauren Anderson, Lucas Chatelain, Nicolas Tremblay, Kathryn Grandfield, David Rousseau, Aur\'elien Gourrier
https://arxiv.org/abs/2510.08407

Biology-driven assessment of deep learning super-resolution imaging of the porosity network in dentin
The mechanosensory system of teeth is currently believed to partly rely on Odontoblast cells stimulation by fluid flow through a porosity network extending through dentin. Visualizing the smallest sub-microscopic porosity vessels therefore requires the highest achievable resolution from confocal fluorescence microscopy, the current gold standard. This considerably limits the extent of the field of view to very small sample regions. To overcome this limitation, we tested different deep learning …

My next bedtime book, is a big biology book; heck it's not light reading; it's 3kg!
(I got the older 5th edition for about ~£10 - the current edition is a fortune)
I suspect it'll take me a couple of years.
https://en.wikipedia.org/wiki/Molecula

Molecular Biology of the Cell (book) - Wikipedia

from my link log —
Quantitative metaphors for sizes in biology.
https://press.asimov.com/articles/metaphors-size
saved 2025-11-05 https://

Metaphors for Biology: Sizes
A series of quantitative metaphors on the sizes and shapes of biomolecules and organisms.

🔦 Engineered protein switches may lead to safer, smarter medicines
#biology

Engineered protein switches may lead to safer, smarter medicines
A new way to potentially control when drugs are active or inactive in the body is introduced in a study reported Sept. 24 in Nature. The research showed that, instead of controlling how tightly proteins bind to partner molecules, scientists can now directly control how long they stay bound. This advance has broad implications for developing safer medicines.

Neurons in auditory cortex integrate information within a constrained and context-invariant temporal window (in ferret auditory cortex) https://www.cell.com/current-biology/fulltext/S0960-9822(25)01479-4 integration windows in human auditory cortex "range from a…

SemCSE-Multi: Multifaceted and Decodable Embeddings for Aspect-Specific and Interpretable Scientific Domain Mapping
Marc Brinner, Sina Zarrie{\ss}
https://arxiv.org/abs/2510.11599

SemCSE-Multi: Multifaceted and Decodable Embeddings for Aspect-Specific and Interpretable Scientific Domain Mapping
We propose SemCSE-Multi, a novel unsupervised framework for generating multifaceted embeddings of scientific abstracts, evaluated in the domains of invasion biology and medicine. These embeddings capture distinct, individually specifiable aspects in isolation, thus enabling fine-grained and controllable similarity assessments as well as adaptive, user-driven visualizations of scientific domains. Our approach relies on an unsupervised procedure that produces aspect-specific summarizing sentences…

Inhomogeneous continuous-time Markov chains to infer flexible time-varying evolutionary rates
Pratyusa Datta, Philippe Lemey, Marc A. Suchard
https://arxiv.org/abs/2510.11982 ht…

Inhomogeneous continuous-time Markov chains to infer flexible time-varying evolutionary rates
Reconstructing evolutionary histories and estimating the rate of evolution from molecular sequence data is of central importance in evolutionary biology and infectious disease research. We introduce a flexible Bayesian phylogenetic inference framework that accommodates changing evolutionary rates over time by modeling sequence character substitution processes as inhomogeneous continuous-time Markov chains (ICTMCs) acting along the unknown phylogeny, where the rate remains as an unknown, positiv…

a beautifully weird mckenna-ish mystery: chinese mushrooms that reliably bring the little people, but don't seem to contain any psychoactive elements (& yet obviously do) https://nhmu.utah.edu/articles/experts-explore-new-mushroom-which-cau…

Experts Explore New Mushroom Which Causes Fairytale-Like Hallucinations
Between traditional folklore and modern biology, the wild forest floor and the sterile scientific laboratory, lies the story of the lilliputian mushroom.

🦎 City lizards turn out to be surprisingly social
#lizards

City lizards turn out to be surprisingly social
Streets, walls, concrete—cities may seem like a harsh environment. Yet some animals adapt remarkably well. A new study published in Biology Letters from Bielefeld University shows that common wall lizards (Podarcis muralis) behave far more socially in urban areas than in the countryside.

TopoSPAM: Topology grounded Simulation Platform for morphogenesis and biological Active Matter
Abhinav Singh (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany, Center for Systems Biology Dresden, Dresden, Germany, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA), Abhijeet Krishna (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany, Center for Systems Biology Dresden, Dresden, Germany), Aboutaleb …

TopoSPAM: Topology grounded Simulation Platform for morphogenesis and biological Active Matter
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications across the biomedical sciences. Addressing these problems will require flexible, cross-scale models of tissue shape, development, and dysfunction that can be tuned to understand, model, and predict relevant individual cases. Current approaches to simulating anato…

Effectiveness of Quota Policies Across STEM, Biological, and Humanities Programs
Ricardo D. Matheus, Elmer M. Gennaro, Marcelo T. Yamashita
https://arxiv.org/abs/2510.08261 http…

Effectiveness of Quota Policies Across STEM, Biological, and Humanities Programs
We examine more than a decade of quota policy at Unesp, analyzing Physics, Biology, and Pedagogy as representative programs of distinct assessment styles. Quotas show little impact in Physics, where the admission barrier is low, and in Pedagogy, where high pass rates make it difficult to differentiate students, but they reveal systematic differences in Biology. Focusing the analysis on Calculus I - an introductory course in Physics and other Science, Technology, Engineering, and Mathematics (ST…

Attosecond-level synchronisation of chip-integrated oscillators
Alexander E. Ulanov, Bastian Ruhnke, Thibault Wildi, Tobias Herr
https://arxiv.org/abs/2510.11630 https://…

Attosecond-level synchronisation of chip-integrated oscillators
Attosecond science provides a window to the fastest processes in chemistry, materials science, and biology. Accessing this time scale requires precisely synchronised oscillators. In free-electron X-ray lasers, which also provide sub-atomic resolution, synchronisation must be achieved across hundreds of meters. Current approaches to synchronisation based on mode-locked lasers deliver this level of performance but complexity, cost and size hinder their deployment in facility-wide multi-node netwo…

"Specialist" and "generalist" are surprisingly slippery categories— biology abhors a binary— but quantifying the shared evolutionary history of plants eaten by insects introduced to North America let these authors predict their plant-damaging impacts https://doi.org/10.1111/ele.70083

Global weak martingale solutions to a stochastic two-sidedly degenerate aggregation-diffusion equation issued from biology
Mostafa Bendahmane, Mohamed Mehdaoui, Mouhcine Tilioua
https://arxiv.org/abs/2510.03947

Global weak martingale solutions to a stochastic two-sidedly degenerate aggregation-diffusion equation issued from biology
The purpose of this paper is to establish the well-posedness of martingale (probabilistic weak) solutions to stochastic degenerate aggregation--diffusion equations arising in biological and public health contexts. The studied equation is of a stochastic degenerate parabolic type, featuring a nonlinear two-sidedly degenerate diffusion term accounting for repulsion, a locally Lipschitz reaction term representing competitive interactions, and a stochastic perturbation term capturing environmental …

I was taught in biology class in school that being able to roll your tongue is a genetic trait and an example of Mendelian inheritance.
This is false. It‘s a myth that science has long debunked.
https://www.pbs.org/newshour/science/genetic-myth-textbook…

Debunking the biggest genetic myth of the human tongue
You didn’t inherit your tongue rolling ability from your parents.

I'm gonna dip the Christmas tree in ranch dressing and eat it as a snack

Towards Label-Free Biological Reasoning Synthetic Dataset Creation via Uncertainty Filtering
Josefa Lia Stoisser, Lawrence Phillips, Aditya Misra, Tom A. Lamb, Philip Torr, Marc Boubnovski Martell, Julien Fauqueur, Kaspar M\"artens
https://arxiv.org/abs/2510.05871

Towards Label-Free Biological Reasoning Synthetic Dataset Creation via Uncertainty Filtering
Synthetic chain-of-thought (CoT) traces are widely used to train large reasoning models (LRMs), improving generalization by providing step-level supervision. Yet most approaches require ground-truth labels to seed or filter these traces - an expensive bottleneck in domains like biology where wet-lab data are scarce. We propose a label-free alternative: uncertainty-based filtering, which uses a model's own confidence - quantified through established uncertainty metrics like self-consistency and …

An optimal-control framework for reaction diffusion systems with application to synthetic developmental biology
Mohamed Amine Ouchdiri, Hamza Faquir, Saad Benjelloun, Mohamed Adlene Maghenem, Irene Otero-Muras, Adnane Saoud
https://arxiv.org/abs/2509.15889

An optimal-control framework for reaction diffusion systems with application to synthetic developmental biology
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of optimal control for a class of coupled reaction-diffusion systems. The couplings are justified by the shared regulatory mechanisms encountered in synthetic biology. Furthermore, we introduce inputs and polynomial input-gain functions to guarantee well-posedness o…

The Grammar of FAIR: A Granular Architecture of Semantic Units for FAIR Semantics, Inspired by Biology and Linguistics
Lars Vogt, Barend Mons
https://arxiv.org/abs/2509.26434 ht…

The Grammar of FAIR: A Granular Architecture of Semantic Units for FAIR Semantics, Inspired by Biology and Linguistics
The FAIR Principles aim to make data and knowledge Findable, Accessible, Interoperable, and Reusable, yet current digital infrastructures often lack a unifying semantic framework that bridges human cognition and machine-actionability. In this paper, we introduce the Grammar of FAIR: a granular and modular architecture for FAIR semantics built on the concept of semantic units. Semantic units, comprising atomic statement units and composite compound units, implement the principle of semantic modu…

Toward a Robust Biomimetic Hybrid Battery: Bridging Biology, Electrochemistry and Data-Driven Control
Raheel Ali, Rayid Ali
https://arxiv.org/abs/2509.23837 https://

Toward a Robust Biomimetic Hybrid Battery: Bridging Biology, Electrochemistry and Data-Driven Control
Electric vehicles and renewable energy systems need batteries that charge quickly, last many years and still store a lot of energy, but current chemistries struggle to deliver all three. Inspired by electric fish that deliver bursts of current and birds that sleep with half their brains, we propose a hybrid battery concept called SwiftPulse. It combines sodium-ion cells that provide energy with niobium-oxide cells that accept high-power pulses. A pulse-based charger and a battery-management str…

🔥 Novel way to 'rev up' brown fat burns calories, limits obesity in mice
#biology

Novel way to 'rev up' brown fat burns calories, limits obesity in mice
Researchers at Washington University School of Medicine in St. Louis have identified a novel way brown fat—an energy-burning form of fat—can rev the body's metabolic engine, consuming cellular fuel and producing heat in a way that improves metabolic health. The study, in mice, reveals new avenues to exploit brown fat to treat metabolic diseases, such as insulin resistance and obesity.

Dry ice baths as liquid nitrogen substitutes for physics demonstrations
David Marasco, Paolo Marasco
https://arxiv.org/abs/2510.09971 https://arxiv.org/pdf…

Probing Phase Diagrams of Ordered Two-Dimensional Ice
Bingzheng Wu, Jianming Wu, Sai Duan, Xin Xu
https://arxiv.org/abs/2510.07717 https://arxiv.org/pdf/25…

Probing Phase Diagrams of Ordered Two-Dimensional Ice
Water, a ubiquitous and fundamental substance, plays a critical role across a wide range of disciplines from physics and chemistry to biology and engineering. Despite theoretical predictions of several phases of two-dimensional (2D) ice confined between idealized hydrophobic walls, experimental validation has been limited to the square phase, whose structural origin remains controversial. Here, we propose a realistic nanoconfinement setup using wide-bandgap hexagonal boron nitride (h-BN) as the…

Julia Platt was a brilliant scientist. #Science She made experimental breakthroughs in developmental biology from the late 1800s to the 1920s. She worked in universities in the U.S. and Europe. Her non-standard ideas and techniques were eventually accepted and shown to be correct by male scientists, after she died.
Here's a portrait of her after she was mayor of Pacific Grove, California. She h…

Replaced article(s) found for q-bio.QM. https://arxiv.org/list/q-bio.QM/new
[1/1]:
- BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology
Mitchener, Laurent, Andonian, Tenmann, Narayanan, Wellawatte, White, Sani, Rodriques

Information and the living tree of life: A theory of measurement grounded in biology
Kevin Hudnall
https://arxiv.org/abs/2510.00155 https://arxiv.org/pdf/2…

Information and the living tree of life: A theory of measurement grounded in biology
We extend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall \& D'Souza, 2025). That work showed that time itself is multifractal -- not a universal background dimension, but an observer-dependent geometry. Here we develop the corresponding theory of measurement: showing that a multifractal conception of time not only permits measurement, but grounds it more rigorously in the structure of biology. The tree of life is modeled as the ou…

"Celebrating 50 Years of Single-Channel Recording with the Patch Clamp". Nice review by Catacuzzeno & Franciolini, though some of the history is a bit dodgy, and misunderstands the fitting of models to data.
https://link.springer.com/article/10.1007/s00232-025-00362…

Celebrating 50 Years of Single-Channel Recording with the Patch Clamp - The Journal of Membrane Biology
Fifty years ago, Erwin Neher and Bert Sakmann published a Nature paper on their recording of discrete, step-like currents of a few picoamps passing through individual acetylcholine receptor channels of frog muscle fibers. This observation, the first on native channels, immediately ended the decade-long dispute about the presence of ion channels on cell membranes by convincing even the most reluctant scientists that this was indeed the case. More importantly, however, the ability to record singl…

A path towards AI-scale, interoperable biological data
Brian Aevermann, Andrea Califano, Chi-Li Chiu, Nathan Clack, William M. Clemons Jr., Jonah Cool Florence D. D'Orazi, Joseph L. DeRisi, Joshua E. Elias, Elizabeth Fahsbender, Scott E. Fraser, Carlos G. Gonzalez, Matthias Haury, Theofanis Karaletsos, Shana O. Kelley, Aly A. Khan, Alan R. Lowe, Emma Lundberg, Ryan A. McClure, Stephani Otte, Evan O. Paull, Lo\"ic A. Royer, Dana Sadgat, Sandra L. Schmid, Samantha Scovanner, Cat…

A path towards AI-scale, interoperable biological data
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing AI to accelerate basic research, drug discovery, personalized medicine, and synthetic biology. However, despite these opportunities, scientific data have proven a bottleneck, and progress has been slow and fragmented. Unless the scientific community takes a t…

GEM: 3D Gaussian Splatting for Efficient and Accurate Cryo-EM Reconstruction
Huaizhi Qu, Xiao Wang, Gengwei Zhang, Jie Peng, Tianlong Chen
https://arxiv.org/abs/2509.25075 https…

GEM: 3D Gaussian Splatting for Efficient and Accurate Cryo-EM Reconstruction
Cryo-electron microscopy (cryo-EM) has become a central tool for high-resolution structural biology, yet the massive scale of datasets (often exceeding 100k particle images) renders 3D reconstruction both computationally expensive and memory intensive. Traditional Fourier-space methods are efficient but lose fidelity due to repeated transforms, while recent real-space approaches based on neural radiance fields (NeRFs) improve accuracy but incur cubic memory and computation overhead. Therefore, …

@… at least, some proof of your existence.
"In a twist, the findings lend credence to the Australian folk hoax of the “drop bear,” a ferocious, carnivorous variety of koala said to fall upon its victims from the canopy. Paleontologists think Thylacoleo was an adept climber and ambush predator that could dive upon its prey from tree branches or roc…

"Experts urge canceling fossil fuel contracts to meet Paris climate goals"
#FossilFuels #Cliamte #ClimateChange

Experts urge canceling fossil fuel contracts to meet Paris climate goals
The countries participating in the UN Climate Change Conference (COP30), currently taking place in Brazil, must cancel fossil fuel concessions in order to keep the Paris Agreement alive. This is the main message of a paper published in the journal Nature and signed by experts Martí Orta, Gorka Muñoa and Marcel Llavero, from the Faculty of Biology and the Biodiversity Research Institute (IRBio) of the University of Barcelona, and Guillem Rius, from the Barcelona Institute for Global Health (IS…

Experts urge canceling fossil fuel contracts to meet Paris climate goals #climate

Experts urge canceling fossil fuel contracts to meet Paris climate goals
The countries participating in the UN Climate Change Conference (COP30), currently taking place in Brazil, must cancel fossil fuel concessions in order to keep the Paris Agreement alive. This is the main message of a paper published in the journal Nature and signed by experts Martí Orta, Gorka Muñoa and Marcel Llavero, from the Faculty of Biology and the Biodiversity Research Institute (IRBio) of the University of Barcelona, and Guillem Rius, from the Barcelona Institute for Global Health (IS…

Efficient Learning-based Graph Simulation for Temporal Graphs
Sheng Xiang, Chenhao Xu, Dawei Cheng, Xiaoyang Wang, Ying Zhang
https://arxiv.org/abs/2510.05569 https://

Efficient Learning-based Graph Simulation for Temporal Graphs
Graph simulation has recently received a surge of attention in graph processing and analytics. In real-life applications, e.g. social science, biology, and chemistry, many graphs are composed of a series of evolving graphs (i.e., temporal graphs). While most of the existing graph generators focus on static graphs, the temporal information of the graphs is ignored. In this paper, we focus on simulating temporal graphs, which aim to reproduce the structural and temporal properties of the observed…

“If our world survives, the next great challenge to watch out for will come — you heard it here first — when the curves of research and development in artificial intelligence, molecular biology and robotics all converge.”
– Thomas Pynchon [writing in 1984]

Weekend #Plankton Factoid 🦠🦐
Tintinnids ("tinkling bells") are ciliates found in fresh and saltwater known for their characteristic vase-shaped shell called a lorica. These are formed of tough proteins, incorporating minerals from the water and vary considerably by species. The shell offers protection and optimizes feeding on phytoplankton, bacteria and flagellates. These small pro…

Analyzing Computational Approaches for Differential Equations: A Study of MATLAB, Mathematica, and Maple
Arhonefe Joseph Ogethakpo, Ignatius Nkonyeasua Njoseh
https://arxiv.org/abs/2510.02346

Analyzing Computational Approaches for Differential Equations: A Study of MATLAB, Mathematica, and Maple
Differential equations are fundamental to modeling dynamic systems in physics, engineering, biology, and economics. While analytical solutions are ideal, most real-world problems necessitate numerical approaches. This study conducts a detailed comparative analysis of three leading computational software packages: MATLAB, Mathematica, and Maple in solving various differential equations, including ordinary differential equations (ODEs), partial differential equations (PDEs), and systems of differ…

I've been reading biology related books and by sheer hubris and ADHD delusion I thought about switching careers*! Figuring out life's systems feels more fascinating than figuring out how IT systems should be working together.
Then I found out that Alan Turing has touched both fields. I did not know about that! So here I stand with interests between Turing machines and Turing patterns! Always pretty cool to find out about these connections between fields!
* I won’t!
…

Turing pattern - Wikipedia

Two-Stage Trigonometric Regression for Modeling Circadian Rhythms
Michael T. Gorczyca, Jenna D. Li, Charissa M. Newkirk, Arjun S. Srivatsa, Hugo F. M. Milan
https://arxiv.org/abs/2510.08309

Two-Stage Trigonometric Regression for Modeling Circadian Rhythms
Gene expression levels, hormone secretion, and internal body temperature each oscillate over an approximately 24-hour cycle, or display circadian rhythms. Many circadian biology studies have investigated how these rhythms vary across cohorts, uncovering associations between atypical rhythms and diseases such as cancer, metabolic syndrome, and sleep disorders. A challenge in analyzing circadian biology data is that the oscillation peak and trough times for a phenomenon differ across individuals.…

Single-cell sequencing of trophoblasts in preeclampsia and chemical hypoxia in BeWo b30 cells reveals EBI3, COL17A1, miR-27a-5p, and miR-193b-5p as hypoxia-response markers
Evgeny Knyazev (Faculty of Biology and Biotechnology, HSE University, Moscow, Russia, Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia), Timur Kulagin (Faculty of Biology and Biotechnology, HSE Universi…

Single-cell sequencing of trophoblasts in preeclampsia and chemical hypoxia in BeWo b30 cells reveals EBI3, COL17A1, miR-27a-5p, and miR-193b-5p as hypoxia-response markers
Background. Preeclampsia (PE) complicates 2-8% of pregnancies and is marked by placental hypoxia and HIF-pathway activation, especially in early-onset PE (eoPE). Integrating patient tissue analyses with experimental models may reveal common molecular markers of trophoblast hypoxia. Methods. We analyzed scRNA-seq data from 10 eoPE, 7 late-onset PE (loPE), and corresponding control placentas, identifying villous cytotrophoblast (VCT), syncytiotrophoblast (SCT), and extravillous trophoblast (EVT…

BioBO: Biology-informed Bayesian Optimization for Perturbation Design
Yanke Li, Tianyu Cui, Tommaso Mansi, Mangal Prakash, Rui Liao
https://arxiv.org/abs/2509.19988 https://

BioBO: Biology-informed Bayesian Optimization for Perturbation Design
Efficient design of genomic perturbation experiments is crucial for accelerating drug discovery and therapeutic target identification, yet exhaustive perturbation of the human genome remains infeasible due to the vast search space of potential genetic interactions and experimental constraints. Bayesian optimization (BO) has emerged as a powerful framework for selecting informative interventions, but existing approaches often fail to exploit domain-specific biological prior knowledge. We propose…

Interleaving Distance as an Edit distance
Woojin Kim, Won Seong
https://arxiv.org/abs/2509.24233 https://arxiv.org/pdf/2509.24233

Interleaving Distance as an Edit distance
The concept of edit distance, which dates back to the 1960s in the context of comparing word strings, has since found numerous applications with various adaptations in computer science, computational biology, and applied topology. By contrast, the interleaving distance, introduced in the 2000s within the study of persistent homology, has become a foundational metric in topological data analysis. In this work, we show that the interleaving distance on finitely presented single- and multi-paramet…

Efficient Quantum Protein Structure Prediction with Problem-Agnostic Ansatzes
Hanna Linn, Rui-Hao Li, Alexander Holden, Abdullah Ash Saki, Frank DiFilippo, Tomas Radivoyevitch, Daniel Blankenberg, Laura Garc\'ia-\'Alvarez, G\"oran Johansson
https://arxiv.org/abs/2509.18263

Was talking to an acquaintance at church yesterday and she mentioned that things are not good with her job. She’s a secondary school biology teacher. She said more by what she didn’t say. She just clammed up and looked lost. Next time I see her, I want to tell her that it doesn’t have to be that way. That she has transferable skills and can find work that pays the bills without destroying her soul. That there are other places that will value and support her.

Replaced article(s) found for cond-mat.stat-mech. https://arxiv.org/list/cond-mat.stat-mech/new
[1/2]:
- Information theory for data-driven model reduction in physics and biology
Schmitt, Koch-Janusz, Fruchart, Seara, Rust, Vitelli

Profluent, which wants to use AI for protein design in drug discovery, raised $106M led by Bezos Expeditions and Altimeter, bringing its total funding to $150M (Amy Feldman/Forbes)
http://www.forbes.com/sites/amyfeldman/20

Jeff Bezos Is Backing An AI Startup Aiming To Make Proteins Programmable
Profluent has raised $106 million to scale up use of its AI models for biology in drug development and agriculture.

my link log mostly works as an external memory, provided i can remember the keywords in the headline
i edit headlines to stuff in extra keywords that make them easier to retrieve: implicit tags without the hash
but sometimes it can be a little frustrating
just now i was trying to remember something to do with numerical? analogies? sizes? units?
took me about 10 minutes to remember the other key word was “bio”
after which i was reminded the key words i had not-qu…

Metaphors for Biology: Sizes
A series of quantitative metaphors on the sizes and shapes of biomolecules and organisms.

Replaced article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
- Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences (Octob...
Gavin Farrell, et al.

Sample-based Quantum Diagonalization Methods for Modeling the Photochemistry of Diazirine and Diazo Compounds
Saurabh Shivpuje, Tanvi P. Gujarati, Richard Van, Frank C. Pickard IV, Triet Friedhoff, Ieva Liepuoniute, Wade Davis, Gavin O. Jones, Alexey Galda
https://arxiv.org/abs/2510.00484

Sample-based Quantum Diagonalization Methods for Modeling the Photochemistry of Diazirine and Diazo Compounds
Diazirines and diazo compounds are widely employed as photoreactive precursors for generating carbenes, key intermediates in chemical biology and materials science. However, computationally modeling their reaction pathways remains challenging due to a need for large active spaces and the requirement to accurately capture excited-state surfaces along with transition states and conical intersections. In this work, we utilize a hybrid quantum-classical workflow for investigating carbene formation …

Wafer-Level Prototyping Tools for CMOS Bioelectronic Sensors
Advait Madhavan, Ruohong Shi, Alokik Kanwal, Glenn Holland, Jacob M. Majikes, Paul N. Patrone, Anthony J. Kearsley, Arvind Balijepalli
https://arxiv.org/abs/2509.24075

Wafer-Level Prototyping Tools for CMOS Bioelectronic Sensors
Integrating biology with complementary metal-oxide-semiconductor (CMOS) sensors can enable highly parallel measurements with minimal parasitic effects, significantly enhancing sensitivity. However, realizing this potential often requires overcoming substantial barriers related to design, fabrication, and heterogeneous integration. In this context, we present a comprehensive suite of tools and methods designed for wafer-scale biosensor prototyping that is sensitive, highly parallelizable, and ma…

🥁 Blink to the beat: Scientists discover that when we listen to music, we unconsciously blink our eyes
https://medicalxpress.com/news/2025-11-scientists-music-unconsciously-eyes.html

Blink to the beat: Scientists discover that when we listen to music, we unconsciously blink our eyes
Yi Du and colleagues from the Chinese Academy of Sciences published an article in the open access journal PLOS Biology detailing their findings about a new way our bodies naturally respond to music. Given a steady beat, our eyes blink in synchrony.

A fluorescence microscopy platform for time-resolved studies of spin-correlated radical pairs in biological systems
Noboru Ikeya, Jonathan R. Woodward
https://arxiv.org/abs/2510.05600

A fluorescence microscopy platform for time-resolved studies of spin-correlated radical pairs in biological systems
The importance of spin-correlated radical pairs in biology is increasingly recognized, with roles in biological effects of weak magnetic fields and emerging quantum spin-based biomedical applications. Fluorescence microscopy offers sufficient sensitivity to study magnetic field effects on radical pair reactions in living cells, but conventional techniques cannot directly resolve their dynamics because most biologically relevant radical pairs are non-emissive. To overcome this challenge, we intr…

A general optimization framework for mapping local transition-state networks
Qichen Xu, Anna Delin
https://arxiv.org/abs/2509.26269 https://arxiv.org/pdf/2…

A general optimization framework for mapping local transition-state networks
Understanding how complex systems transition between states requires mapping the energy landscape that governs these changes. Local transition-state networks reveal the barrier architecture that explains observed behaviour and enables mechanism-based prediction across computational chemistry, biology, and physics, yet current practice either prescribes endpoints or randomly samples only a few saddles around an initial guess. We present a general optimization framework that systematically expand…

Quantum-like representation of neuronal networks' activity: modeling "mental entanglement"
Andrei Khrennikov, Makiko Yamada
https://arxiv.org/abs/2509.16253 https:…

Quantum-like representation of neuronal networks' activity: modeling "mental entanglement"
Quantum-like modeling (QLM) - quantum theory applications outside of physics - are intensively developed with applications in biology, cognition, psychology, and decision-making. For cognition, QLM should be distinguished from quantum reductionist models in the spirit of Hameroff and Penrose and well as Umezawa and Vitiello. QLM is not concerned with just quantum physical processes in the brain but also QL information processing by macroscopic neuronal structures. Although QLM of cognition and …

Hierarchical self-assembly of Brownian particle-like pulses in a modelocked laser
Aladin \c{S}ura, F. \"Omer Ilday
https://arxiv.org/abs/2510.05344 https://

Hierarchical self-assembly of Brownian particle-like pulses in a modelocked laser
Passive modelocking involves self-locking of thousands of frequency modes to form ultrashort pulses. In fundamental modelocking, a single intracavity pulse provides high stability and reproducibility, but limits the repetition rate. Harmonic modelocking can overcome this by supporting multiple pulses, but suffers from instabilities and poor reproducibility, with specific states achievable only sporadically. Biology exploits hierarchy to organise complexity, which has inspired hierarchical self-…

Nonlocal modeling of spatial fractional diffusion with truncated interaction domains and truncated kernel function singularity
Shiping Zhou, Yanzhi Zhang, Max Gunzburger
https://arxiv.org/abs/2509.16315

Nonlocal modeling of spatial fractional diffusion with truncated interaction domains and truncated kernel function singularity
Parabolic partial differential equations (PDEs) are in ubiquitous, very effective use to model diffusion processes. However, there are many applications (e.g., such as in hydrology, animal foraging, biology, and light diffusion just do name a few) for which results obtained through the use of parabolic PDEs do not agree with observations. In many situations the use of fractional diffusion models has been found to be more faithful to that which is observed. Specifically, we replace the Laplacian…

Empirical partially Bayes two sample testing
Wanyi Ling, Wufang Hong, Nikolaos Ignatiadis
https://arxiv.org/abs/2510.00432 https://arxiv.org/pdf/2510.00432…

Empirical partially Bayes two sample testing
A common task in high-throughput biology is to test for differences in means between two samples across thousands of features (e.g., genes or proteins), often with only a handful of replicates per sample. Moderated t-tests handle this problem by assuming normality and equal variances, and by applying the empirical partially Bayes principle: a prior is posited and estimated for the nuisance parameters (variances) but not for the primary parameters (means). This approach has been highly successfu…

♨️ Underwater thermal vents may have given rise to the first molecular precursors of life
https://phys.org/news/2025-10-underwater-thermal-vents-molecular-precursors.html

Underwater thermal vents may have given rise to the first molecular precursors of life
A study published in the Journal of the American Chemical Society has recreated in the laboratory chemical reactions that may have occurred on Earth about four billion years ago, producing the first molecular precursors for the emergence of life.

Replaced article(s) found for q-bio.BM. https://arxiv.org/list/q-bio.BM/new
[1/1]:
- Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability o...
He, Ren, Tang, Xu, Li, Yang, Zhang, Yuan, Chen, Zhang, Li, Dong, Ouyang, Zhou, Ye

Nephrobase Cell : Multimodal Single-Cell Foundation Model for Decoding Kidney Biology
Chenyu Li, Elias Ziyadeh, Yash Sharma, Bernhard Dumoulin, Jonathan Levinsohn, Eunji Ha, Siyu Pan, Vishwanatha Rao, Madhav Subramaniyam, Mario Szegedy, Nancy Zhang, Katalin Susztak
https://arxiv.org/abs/2509.26223 …

Nephrobase Cell+: Multimodal Single-Cell Foundation Model for Decoding Kidney Biology
Background: Large foundation models have revolutionized single-cell analysis, yet no kidney-specific model currently exists, and it remains unclear whether organ-focused models can outperform generalized models. The kidney's complex cellular architecture further complicate integration of large-scale omics data, where current frameworks trained on limited datasets struggle to correct batch effects, capture cross-modality variation, and generalize across species. Methods: We developed Nephrobase …

Replaced article(s) found for q-bio.MN. https://arxiv.org/list/q-bio.MN/new
[1/1]:
- When algebra twinks system biology: a conjecture on the structure of Gr\"obner bases in complex c...
Paola Ferrari, Sara Sommariva, Michele Piana, Federico Benvenuto, Matteo Varbaro

Cell2Text: Multimodal LLM for Generating Single-Cell Descriptions from RNA-Seq Data
Oussama Kharouiche, Aris Markogiannakis, Xiao Fei, Michail Chatzianastasis, Michalis Vazirgiannis
https://arxiv.org/abs/2509.24840

Cell2Text: Multimodal LLM for Generating Single-Cell Descriptions from RNA-Seq Data
Single-cell RNA sequencing has transformed biology by enabling the measurement of gene expression at cellular resolution, providing information for cell types, states, and disease contexts. Recently, single-cell foundation models have emerged as powerful tools for learning transferable representations directly from expression profiles, improving performance on classification and clustering tasks. However, these models are limited to discrete prediction heads, which collapse cellular complexity …

Behavioural Classification in C. elegans: a Spatio-Temporal Analysis of Locomotion
Nemanja Antonic, Monika Scholz, Aymeric Vellinger, Euphrasie Ramahefarivo, Elio Tuci
https://arxiv.org/abs/2510.00086 …

Behavioural Classification in C. elegans: a Spatio-Temporal Analysis of Locomotion
The 1mm roundworm C. elegans is a model organism used in many sub-areas of biology to investigate different types of biological processes. In order to complement the n-vivo analysis with computer-based investigations, several methods have been proposed to simulate the worm behaviour. These methods extract discrete behavioural units from the flow of the worm movements using different types of tracking techniques. Nevertheless, these techniques require a clear view of the entire worm body, which …

[2025-10-15 Wed (UTC), 1 new article found for q-bio.OT Other Quantitative Biology]
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Great RadioLab interview with Ella al-Shamahi, about her journey from religious anti-evolutionism into evolutionary biology. New perspective but also familiar if you (like me) grew up among Christian creationists; really moving on what faith, even "denialist" faith, means to people
#science #evolution

🪸 Tree rings of the sea: How environmental conditions influence microalgae and coral communities
https://phys.org/news/2025-11-tree-sea-environmental-conditions-microalgae.html

Tree rings of the sea: How environmental conditions influence microalgae and coral communities
An international research team led by marine biologist Prof. Dr. Maren Ziegler from Justus Liebig University Giessen (JU) has developed an innovative method for reconstructing the past of corals and their symbiosis with algae by drilling into coral skeletons. The results, published in Global Change Biology, offer new insights into changes in symbiotic single-celled algae species that are crucial to the survival of coral reefs.

Brilliant source of 19.2 attosecond soft X-ray pulses below the atomic unit of time
Fernando Ardana-Lamas, Seth L. Cousin, Juliette Lignieres, Jens Biegert
https://arxiv.org/abs/2510.04086

Brilliant source of 19.2 attosecond soft X-ray pulses below the atomic unit of time
Electronic correlations occur on attosecond timescales, dictating how chemical bonds form, energy flows, and materials respond to light. Capturing such many-body processes requires light pulses of similar duration. The soft X-ray water window is vital because it encompasses the principle absorption edges of carbon, nitrogen, and oxygen that underpin chemistry, biology, and materials science. However, generating and characterising isolated attosecond pulses that reach into the soft X-ray water w…

Dispersion Formation Control: from Geometry to Distribution
Jin Chen, Jesus Bautista Villar, Bayu Jayawardhana, Hector Garcia de Marina
https://arxiv.org/abs/2509.19784 https://…

Dispersion Formation Control: from Geometry to Distribution
We introduce and develop the concept of dispersion formation control, bridging a gap between shape-assembly studies in physics and biology and formation control theory. In current formation control studies, the control objectives typically focus on achieving desired local geometric properties, such as inter-agent distances, bearings, or relative positions. In contrast, our dispersion formation control approach enables agents to directly regulate the dispersion of their spatial distribution, a g…

Mapping gene expression dynamics to developmental phenotypes with information entropy analysis
Ben Ansbacher, Malachy Guzman, Jordi Garcia-Ojalvo, Arjendu K Pattanayak
https://arxiv.org/abs/2510.04101 …

Mapping gene expression dynamics to developmental phenotypes with information entropy analysis
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions of cells. A statistical mechanics of developmental processes would help to understand how microscopic genotypes map onto macroscopic phenotypes, a general goal across biology. Here we follow this approach, hypothesizing that development should be understood as…

Nonlinear Response Relations and Fluctuation-Response Inequalities for Nonequilibrium Stochastic Systems
Jiming Zheng, Zhiyue Lu
https://arxiv.org/abs/2509.19606 https://…

Nonlinear Response Relations and Fluctuation-Response Inequalities for Nonequilibrium Stochastic Systems
Predicting how systems respond to external perturbations far from equilibrium remains a fundamental challenge across physics, chemistry, and biology. We present a unified response framework for stochastic Markov dynamics that integrates linear and nonlinear perturbations. Our formalism expresses nonlinear responses of observables in terms of the covariance between the observable and a nonlinear conjugate variable. The nonlinear conjugate variable is subject to the complete Bell polynomial form …

A scaling law for large-deformation contact in soft materials
Tong Mu, Shizhuo Weng, Changhong Linghu, Ruozhang Li, Jingyi Yu, Zhonghao Xu, Yingjie Fu, Lin Yang, Domenico Campolo, Yanju Liu, Jinsong Leng, K. Jimmy Hsia, Huajian Gao
https://arxiv.org/abs/2509.18581

A scaling law for large-deformation contact in soft materials
Compression of soft bodies is central to biology, materials science, and robotics, yet existing contact theories break down at large deformations. Here, we develop a general framework for soft-body compression by extending the method of dimensionality reduction into the nonlinear regime. Analytical solutions for contact force and radius are derived and validated against finite element simulations and experiments on canonical geometries (cone, hemisphere, cylinder), achieving high accuracy up to…

🪸 Scientists reveal the mechanism behind sea urchin twinning
#biology

Scientists reveal the mechanism behind sea urchin twinning
Researchers at University of Tsukuba examined how twin organisms can emerge from a single fertilized egg by studying sea urchin embryos. Their findings revealed that when an early-stage embryo is split in half, each portion is able to regenerate its own developmental plan. The team uncovered the dynamic cellular processes and genetic programs that allow each fragment to reorganize and grow into a complete individual.

[2025-10-14 Tue (UTC), 4 new articles found for q-bio.OT Other Quantitative Biology]
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Modeling discrete lattice data using the Potts and tapered Potts models
Maria Paula Duenas-Herrera, Stephen Berg, Murali Haran
https://arxiv.org/abs/2509.21478 https://

Modeling discrete lattice data using the Potts and tapered Potts models
The Ising and Potts models, among the most important models in statistical physics, have been used for modeling binary and multinomial data on lattices in a wide variety of disciplines such as psychology, image analysis, biology, and forestry. However, these models have several well known shortcomings: (i) they can result in poorly fitting models, that is, simulations from fitted models often do not produce realizations that look like the observed data; (ii) phase transitions and the presence o…

13CFLUX - Third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis
Anton Stratmann, Martin Bey{\ss}, Johann F. Jadebeck, Wolfgang Wiechert, Katharina N\"oh
https://arxiv.org/abs/2509.23847

13CFLUX - Third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis
13C-based metabolic flux analysis (13C-MFA) is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a third-generation simulation platform that combines a high-performance C++ engine with a convenient Python interface. The software delivers substantial performance gains across isotopically stationary and nonstationary analysis workflows, while remaining flexible to acco…

Equilibrium flow: From Snapshots to Dynamics
Yanbo Zhang, Michael Levin
https://arxiv.org/abs/2509.17990 https://arxiv.org/pdf/2509.17990

Equilibrium flow: From Snapshots to Dynamics
Scientific data, from cellular snapshots in biology to celestial distributions in cosmology, often consists of static patterns from underlying dynamical systems. These snapshots, while lacking temporal ordering, implicitly encode the processes that preserve them. This work investigates how strongly such a distribution constrains its underlying dynamics and how to recover them. We introduce the Equilibrium flow method, a framework that learns continuous dynamics that preserve a given pattern dis…

Predicting cell-specific gene expression profile and knockout impact through deep learning
Yongjian He, Vered Klein, Orr Levy, Xu-Wen Wang
https://arxiv.org/abs/2510.03359 https…

Predicting cell-specific gene expression profile and knockout impact through deep learning
Gene expression data is essential for understanding how genes are regulated and interact within biological systems, providing insights into disease pathways and potential therapeutic targets. Gene knockout has proven to be a fundamental technique in molecular biology, allowing the investigation of the function of specific genes in an organism, as well as in specific cell types. However, gene expression patterns are quite heterogeneous in single-cell transcriptional data from a uniform environme…

[2025-10-13 Mon (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
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Replaced article(s) found for physics.bio-ph. https://arxiv.org/list/physics.bio-ph/new
[1/1]:
- Information theory for data-driven model reduction in physics and biology
Schmitt, Koch-Janusz, Fruchart, Seara, Rust, Vitelli

Replaced article(s) found for q-bio.QM. https://arxiv.org/list/q-bio.QM/new
[1/1]:
- Discrete vs. continuous dynamics in biology: When do they align and when do they diverge?
Shuyun Jiao, David Waxman

🐠 3D-printed helix shelters increase baby coral survival rates
#coral

3D-printed helix shelters increase baby coral survival rates
To dramatically increase coral survival rates, scientists at the University of Hawaiʻi at Mānoa Hawaiʻi Institute of Marine Biology (HIMB) have developed innovative 3D-printed ceramic structures that provide crucial protection for baby corals. These new designs offer a low-cost and scalable solution to enhance reef recovery worldwide.

Meso-chiral optical properties of plasmonic nanoparticles: uncovering hidden chirality
Yuanyang Xie, Alexey V. Krasavin, Anatoly V. Zayats
https://arxiv.org/abs/2509.20178 https…

Meso-chiral optical properties of plasmonic nanoparticles: uncovering hidden chirality
Molecular chirality plays an important role in chemistry and biology, allows control of biological interactions, affects drugs efficacy and safety, and promotes synthesis of new materials. In general, chirality manifests itself in optical activity (circular dichroism or circular birefringence). Chiral plasmonic nanoparticles have been recently developed for molecular enantiomer separation, chiral sensing and chiral photocatalysis. Here, we show that optical chirality of plasmonic nanoparticles …

Replaced article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
- Charting dissipation across the microbial world
Tommaso Cossetto, Jonathan Rodenfels, Pablo Sartori

🔦 Scientists develop faster technique to uncover hidden gene switches
#biology

Scientists develop faster technique to uncover hidden gene switches
Researchers at the Max Delbrück Center have developed a new method to discover how DNA controls genes. Their technique, published in Cell Genomics, can reveal the genetic "switches" that regulate important genes more quickly than existing methods.

Crosslisted article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
- The Software Observatory: aggregating and analysing software metadata for trend computation and F...
Eva Mart\'in del Pico, Josep Llu\'is Gelp\'i, Salvador Capella-Guti\'errez

[2025-10-10 Fri (UTC), 1 new article found for q-bio.OT Other Quantitative Biology]
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[2025-10-09 Thu (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
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[2025-10-08 Wed (UTC), 1 new article found for q-bio.OT Other Quantitative Biology]
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[2025-10-07 Tue (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
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Crosslisted article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
- Automated Genomic Interpretation via Concept Bottleneck Models for Medical Robotics
Zijun Li, Jinchang Zhang, Ming Zhang, Guoyu Lu

[2025-10-06 Mon (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
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