Tootfinder

🧬 Need a new 3D material? Build it with DNA
#dna

Need a new 3D material? Build it with DNA
When the Empire State Building was constructed, its 102 stories rose above midtown one piece at a time, with each individual element combining to become, for 40 years, the world's tallest building. Uptown at Columbia, Oleg Gang and his chemical engineering lab aren't building Art Deco architecture; their landmarks are incredibly small devices built from nanoscopic building blocks that arrange themselves.

Mehr Präzision bei DNA-Manipulation: KI half bei der Entwicklung
Ein neues Verfahren soll präzise Manipulationen an großen DNA-Abschnitten erlauben. Zum Beweis stellten die Forscher herbizidresistenten Reis her.

DNA Probe Computing System for Solving NP-Complete Problems
Jin Xu, XiaoLong Shi, Xin Chen, Fang Wang, Sirui Li, Pali Ye, Boliang Zhang, Di Deng, Zheng Kou, Xiaoli Qiang
https://arxiv.org/abs/2507.12470

DNA Probe Computing System for Solving NP-Complete Problems
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the Turing machine's one-dimensional data processing and sequential operations, struggle to address these issues effectively. To overcome this bottleneck, computational models must adopt multidimensional data structures and parallel information processing mechanisms. …

"Researchers call this mummy the Younger Lady. DNA analysis indicates that she is King Tut’s mother and a sister of Akhenaten, but her name is unknown."

Um link para deixar cheganos a espumar da boca.
tl;dr - nunca existiu nenhuma espécie de "sangue português". Sempre foi uma gigantesca misturada, com imigrantes vindos de tudo quanto é sítio a contribuir para a caldeirada.
https://link.springer.com/article/10.118…

The genetic history of Portugal over the past 5,000 years - Genome Biology
Background Recent ancient DNA studies uncovering large-scale demographic events in Iberia have presented very limited data for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we present the most comprehensive collection of Portuguese ancient genome-wide data, from 67 individuals spanning 5000 years of human history, from the Neolithic to the nineteenth century. Results We identify early admixture between local hunter-gatherers and Anatolian-related farmers in N…

Property-Isometric Variational Autoencoders for Sequence Modeling and Design
Elham Sadeghi, Xianqi Deng, I-Hsin Lin, Stacy M. Copp, Petko Bogdanov
https://arxiv.org/abs/2509.14287

Property-Isometric Variational Autoencoders for Sequence Modeling and Design
Biological sequence design (DNA, RNA, or peptides) with desired functional properties has applications in discovering novel nanomaterials, biosensors, antimicrobial drugs, and beyond. One common challenge is the ability to optimize complex high-dimensional properties such as target emission spectra of DNA-mediated fluorescent nanoparticles, photo and chemical stability, and antimicrobial activity of peptides across target microbes. Existing models rely on simple binary labels (e.g., binding/non…

🇺🇦 #NowPlaying on KEXP's #AfternoonShow
DNA feat. Suzanne Vega:
🎵 Tom’s Diner
#DNA #SuzanneVega
https://jottanavarroakacooldeeper.bandcamp.com/album/dna-feat-suzanne-vega-toms-diner-jotta-navarro-urban-edit

Oxford University Press stops publishing a journal sponsored by China's Ministry of Justice after years of concerns it did not meet standards on DNA collection (Amy Hawkins/The Guardian)
https://www.theguardian.com/scie…

OK, this one is weird. She died in 1991. Her skull was found in 1992. But she was supposed to have been cremated. #ColdCase #forensics #DNA
"Skull found in Wisconsin woods belonged to Stillwater …

Ancient DNA reveals 37,000 years of hidden human infections - Earth.com
https://www.earth.com/news/ancient-dna-reveals-37000-years-of-hidden-human-infections/

Baby’s met DNA van drie ouders: baanbrekende techniek verlost kinderen van erfelijke ziekten | de Volkskrant
https://archive.ph/ph4pn

Globalisierung, 7. Jh. https://www.science.org/content/article/youths-buried-anglo-saxon-cemeteries-carried-west-african-dna

Knotted DNA Configurations in Bacteriophage Capsids: A Liquid Crystal Theory Approach
Pei Liu, Zhijie Wang, Tamara Christiani, Mariel Vazquez, M. Carme Calderer, Javier Arsuaga
https://arxiv.org/abs/2509.10410

Knotted DNA Configurations in Bacteriophage Capsids: A Liquid Crystal Theory Approach
Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement of DNA that corresponds to a hexagonal chromonic liquid-crystalline phase, and increase the topological complexity of the genome in the form of knots. A mathematical model that implements a chromonic liquid-crystalline phase and that captures the changes in t…

Aggregating Epigenetic Clocks to Study Human Capital Formation
Giorgia Menta, Pietro Biroli, Divya Mehta, Conchita D'Ambrosio, Deborah Cobb-Clark
https://arxiv.org/abs/2509.14422

Aggregating Epigenetic Clocks to Study Human Capital Formation
Epigenetics is the study of how people's behavior and environments influence the way their genes are expressed, even though their DNA sequence is itself unchanged. By aggregating age-related epigenetic markers, epigenetic 'clocks' have become the leading tool for studying biological aging. We make an important contribution by developing a novel, integrated measure of epigenetic aging--the Multi EpiGenetic Age (MEGA) clock--which combines several existing epigenetic clocks to reduce measurement …

MITs DNA-Sensor erkennt HPV oder HIV für weniger als ein Dollar
Das MIT hat einen DNA-Sensor entwickelt, der durch Spannungsänderungen HPV- und HIV-Infektionen erkennen kann. Der Sensor ist haltbar und preisgünstig.

The AI Shadow War: SaaS vs. Edge Computing Architectures
Rhea Pritham Marpu, Kevin J McNamara, Preeti Gupta
https://arxiv.org/abs/2507.11545 https://

The AI Shadow War: SaaS vs. Edge Computing Architectures
The very DNA of AI architecture presents conflicting paths: centralized cloud-based models (Software-as-a-Service) versus decentralized edge AI (local processing on consumer devices). This paper analyzes the competitive battleground across computational capability, energy efficiency, and data privacy. Recent breakthroughs show edge AI challenging cloud systems on performance, leveraging innovations like test-time training and mixture-of-experts architectures. Crucially, edge AI boasts a 10,000x…

Achievable Rates of Nanopore-based DNA Storage
Brendon McBain, Emanuele Viterbo
https://arxiv.org/abs/2508.08567 https://arxiv.org/pdf/2508.08567

Achievable Rates of Nanopore-based DNA Storage
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the Scrappie pore model generates average output levels via i.i.d. geometric sample duplications corrupted by i.i.d. Gaussian noise (NNC-Scrappie). Simplified message passing algorithms are derived for efficient soft decoding of nanopore signals using NNC-Scrappie. Pr…

Conversational DNA: A New Visual Language for Understanding Dialogue Structure in Human and AI
Baihan Lin
https://arxiv.org/abs/2508.07520 https://arxiv.or…

Conversational DNA: A New Visual Language for Understanding Dialogue Structure in Human and AI
What if the patterns hidden within dialogue reveal more about communication than the words themselves? We introduce Conversational DNA, a novel visual language that treats any dialogue -- whether between humans, between human and AI, or among groups -- as a living system with interpretable structure that can be visualized, compared, and understood. Unlike traditional conversation analysis that reduces rich interaction to statistical summaries, our approach reveals the temporal architecture of d…

tree-of-life: Protein interactomes across the tree of life (2019)
Protein-protein iteraction networks ("interactome") for 1,840 species. An interactome captures all physical protein-protein interactions within one species, from direct biophysical protein-protein interactions to regulatory protein-DNA and metabolic interactions. .
This network has 1178 nodes and 7623 edges.
Tags: Biological, Protein interactions

About three-quarters of fungi are “dark taxa” – species known only by their DNA sequence, as physical specimens have not been found.
https://www.theguardian.com/environment/2025/aug/15/biology-mycorrhizal-fungi-map-restoring-world-fore…

Non-equilibrium lifetimes of DNA under electronic current in a molecular junction
Julian A. Lawn, Nicholas S. Davis, Daniel S. Kosov
https://arxiv.org/abs/2509.08307 https://

Non-equilibrium lifetimes of DNA under electronic current in a molecular junction
We investigate the non-equilibrium mechanical motion of double-stranded DNA in a molecular junction under electronic current using Keldysh-Langevin molecular dynamics. Non-equilibrium electronic force reshapes the effective potential energy surface, and along with electronic viscosity force and stochastic force, governs voltage-dependent dynamics of DNA's collective mechanical coordinate. We compute mean first-passage times to quantify the non-equilibrium lifetime of the DNA junction. At low vo…

Computing and Bounding Equilibrium Concentrations in Athermic Chemical Systems
Hamidreza Akef, Minki Hhan, David Soloveichik
https://arxiv.org/abs/2507.12699

Computing and Bounding Equilibrium Concentrations in Athermic Chemical Systems
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form complexes (polymers). Rather than employing free-energy parameters for each polymer, we focus on the athermic setting where all interactions preserve enthalpy. This setting aligns with the strongly bonded (domain-based) regime in DNA nanotechnology when stran…

What would compel someone, with everything happening right now, to trust a tech company to host & protect your personal DNA or health data?
Ignorance? Sloth? Apathy? All 3?
From: @…
htt…

American biotech company Regeneron Pharmaceuticals announced today that it's buying 23andMe,
the bankrupt consumer-genomics company that sold take-home DNA kits.
Regeneron is to pay $256 million in cash to acquire "substantially all" of 23andMe's assets,
including its massive biobank of around 15 million customer genetic samples and data.
Put simply, the genetic information of millions is now in the hands of a drugmaker seeking to mine it to make n…

Bankrupt 23andMe Just Sold Off All Your DNA Data
The consumer-genomics company 23andMe just sold its biobank of customer genetic data to drugmaker Regeneron for $256 million.

Olin yhteydessä DNA:n chattiin. Onneksi tarjosi mahdollisuuden keskustella ihmisen kanssa koska botti ei ollenkaan ymmärtänyt kysymystä. Mutta ei sekään pihan mennyt kuin Strömsöössä.
#asiakaspalvelu

Monitoring Single DNA Docking Site Activity With Sequential Modes of an Optoplasmonic Whispering-Gallery Mode Biosensor
Narima Eerqing, Ekaterina Zossimova, Sivaraman Subramanian, Hsin-Yu Wu, Frank Vollmer
https://arxiv.org/abs/2507.08591

Monitoring Single DNA Docking Site Activity With Sequential Modes of an Optoplasmonic Whispering-Gallery Mode Biosensor
In recent years, there has been rapid advancement in single-molecule techniques, driven by their unparalleled precision in studying molecules whose sizes are beyond the diffraction limit. Among these techniques, optoplasmonic whispering gallery mode sensing has demonstrated great potential in label-free single-molecule characterization. It combines the principles of localized surface plasmon resonance (LSPR) and whispering gallery mode (WGM) sensing, offering exceptional sensing capabilities, e…

“On June 27, 2025, the U.S. Bankruptcy Court for the Eastern District of Missouri approved the proposed purchase of all of the assets of 23andMe by TTAM Research Institute (“TTAM”) … TTAM is a nonprofit medical research organization founded by Anne Wojcicki (Co-Founder and former CEO of 23andMe).”
– 23andMe bankruptcy notice
Well this all sounds above board…
#DNA

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects
Hongyang Li, Sanjoy Dey, Bum Chul Kwon, Michael Danziger, Michal Rosen-Tzvi, Jianying Hu, James Kozloski, Ching-Huei Tsou, Bharath Dandala, Pablo Meyer
https://arxiv.org/abs/2507.05265

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects
Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-…

Alphagenome: Deepmind KI analysiert Auswirkungen von DNA-Veränderungen
Deepminds neue KI Alphagenome analysiert DNA-Veränderungen, um Auswirkungen auf unsere Gesundheit zu entschlüsseln.
ht…

🪙 Polymer-protected DNA sensors enable two-month storage for 50-cent disease diagnostics
#dna…

Polymer-protected DNA sensors enable two-month storage for 50-cent disease diagnostics
Using an inexpensive electrode coated with DNA, MIT researchers have designed disposable diagnostics that could be adapted to detect a variety of diseases, including cancer or infectious diseases such as influenza and HIV.

Multivariate regression with missing response data for modelling regional DNA methylation QTLs
Shomoita Alam, Yixiao Zeng, Sasha Bernatsky, Marie Hudson, In\'es Colmegna, David A. Stephens, Celia M. T. Greenwood, Archer Y. Yang
https://arxiv.org/abs/2507.05990

Multivariate regression with missing response data for modelling regional DNA methylation QTLs
Identifying genetic regulators of DNA methylation (mQTLs) with multivariate models enhances statistical power, but is challenged by missing data from bisulfite sequencing. Standard imputation-based methods can introduce bias, limiting reliable inference. We propose \texttt{missoNet}, a novel convex estimation framework that jointly estimates regression coefficients and the precision matrix from data with missing responses. By using unbiased surrogate estimators, our three-stage procedure avoids…

#ecosystems #agriculture #insectapocalypse
Even in "remote" areas
"They found that 79% of Fiji’s endemic ant species were in decline, with impacts beginning at the time of…

#ecosystems #agriculture #insectapocalypse
Even in "remote" areas
"They found that 79% of Fiji’s endemic ant species were in decline, with impacts beginning at the time of…

Next up is #DNA & Molecular #Biology: A 2025 digital view in Andromeda. Livestream here: https://streaming.media.ccc.de/why2025

Nonequilibrium Work Fluctuations in Force-induced Melting of a Short B-DNA
S. Siva Nasarayya Chari, Prabal K. Maiti
https://arxiv.org/abs/2508.07354 https://

Nonequilibrium Work Fluctuations in Force-induced Melting of a Short B-DNA
A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by pulling one end of the DNA while restraining its other end. The finite time pulling process is performed at a constant rate of the applied force until a maximum value of 400 pN. The associated nonequilibrium work done $(W)$ during this process is determined by …

Google DeepMind unveils AlphaGenome, an AI tool to predict the effects of DNA changes on molecular processes, available via an API for non-commercial research (Antonio Regalado/MIT Technology Review)
https://www.technologyreview.com/2025/06/25/1…

Google’s new AI will help researchers understand how our genes work
First came AlphaFold. Now comes AlphaGenome for DNA.

Hybrid Tokenization Strategy for DNA Language Model using Byte Pair Encoding and K-MER Methods
Ganesh Sapkota, Md Hasibur Rahman
https://arxiv.org/abs/2507.18570 https://…

Hybrid Tokenization Strategy for DNA Language Model using Byte Pair Encoding and K-MER Methods
This paper presents a novel hybrid tokenization strategy that enhances the performance of DNA Language Models (DLMs) by combining 6-mer tokenization with Byte Pair Encoding (BPE-600). Traditional k-mer tokenization is effective at capturing local DNA sequence structures but often faces challenges, including uneven token distribution and a limited understanding of global sequence context. To address these limitations, we propose merging unique 6mer tokens with optimally selected BPE tokens gener…

DNA from Prehistoric Proto-City Reveals 'Surprising' Signs of Female-Centered Society https://www.404media.co/dna-from-prehistoric-proto-city-reveals-surprising-signs-of-female-centered-society/

🇺🇦 Auf radioeins läuft...
Suzanne Vega & DNA:
🎵 Tom's Diner
#NowPlaying #SuzanneVega #DNA
https://thebeatvault1.bandcamp.com/track/suzanne-vega-dna-toms-diner

AI, AGI, and learning efficiency
My 4-month-old kid is not DDoSing Wikipedia right now, nor will they ever do so before learning to speak, read, or write. Their entire "training corpus" will not top even 100 million "tokens" before they can speak & understand language, and do so with real intentionally.
Just to emphasize that point: 100 words-per-minute times 60 minutes-per-hour times 12 hours-per-day times 365 days-per-year times 4 years is a mere 105,120,000 words. That's a ludicrously *high* estimate of words-per-minute and hours-per-day, and 4 years old (the age of my other kid) is well after basic speech capabilities are developed in many children, etc. More likely the available "training data" is at least 1 or 2 orders of magnitude less than this.
The point here is that large language models, trained as they are on multiple *billions* of tokens, are not developing their behavioral capabilities in a way that's remotely similar to humans, even if you believe those capabilities are similar (they are by certain very biased ways of measurement; they very much aren't by others). This idea that humans must be naturally good at acquiring language is an old one (see e.g. #AI #LLM #AGI

MOTGNN: Interpretable Graph Neural Networks for Multi-Omics Disease Classification
Tiantian Yang, Zhiqian Chen
https://arxiv.org/abs/2508.07465 https://arx…

MOTGNN: Interpretable Graph Neural Networks for Multi-Omics Disease Classification
Integrating multi-omics data, such as DNA methylation, mRNA expression, and microRNA (miRNA) expression, offers a comprehensive view of the biological mechanisms underlying disease. However, the high dimensionality and complex interactions among omics layers present major challenges for predictive modeling. We propose Multi-Omics integration with Tree-generated Graph Neural Network (MOTGNN), a novel and interpretable framework for binary disease classification. MOTGNN employs eXtreme Gradient B…

TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling
Qirong Yang, Yucheng Guo, Zicheng Liu, Yujie Yang, Qijin Yin, Siyuan Li, Shaomin Ji, Linlin Chao, Xiaoming Zhang, Stan Z. Li
https://arxiv.org/abs/2507.19229

TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we propose TrinityDNA, a novel DNA foundational model designed to address these challenges. The model integrates biologically informed components, including Groove Fusion for capturing DNA's structural features and Gated Reverse Complement (GRC) to handle the inhe…

Crosslisted article(s) found for q-bio.BM. https://arxiv.org/list/q-bio.BM/new
[1/1]:
- Knotted DNA Configurations in Bacteriophage Capsids: A Liquid Crystal Theory Approach
Pei Liu, Zhijie Wang, Tamara Christiani, Mariel Vazquez, M. Carme Calderer, Javier Arsuaga

Ah yes, MIPS Technologies.
https://mips.com/products/hardware/
The famous designer of MIPS (microprocessor without interlocked pipeline stages) architecture processors.
Such a well named company /s

IP Processors - MIPS
Products Forging a New Path for the AI Compute Era Billions of Units Shipped MIPS Sub-Systems – More than a Core A foundation of compute DNA built over decades with billions of units shipped Bring Your Own Accelerators Flexible Integration Coherent Through Coherence Manager Fabric or Connect Direct to CPU RISC-V Core RISC-V Multi-threading Custom […]

Bridging CGR and $k$-mer Frequencies of DNA
Haoze He, Lila Kari, Pablo Millan Arias
https://arxiv.org/abs/2506.22172 https://arxiv.or…

Bridging CGR and $k$-mer Frequencies of DNA
This paper establishes formal mathematical foundations linking Chaos Game Representations (CGR) of DNA sequences to their underlying $k$-mer frequencies. We prove that the Frequency CGR (FCGR) of order $k$ is mathematically equivalent to a discretization of CGR at resolution $2^k \times 2^k$, and its vectorization corresponds to the $k$-mer frequencies of the sequence. Additionally, we characterize how symmetry transformations of CGR images correspond to specific nucleotide permutations in the …

Elon Musk’s Secret Son in Kenya? | Man Demands DNA Test in Viral Twist 😱🧬
https://youtube.com/shorts/ZaQvG0cLtMA?si=AKhbxYNwDcPYEBHA

The DNA of nuclear models: How AI predicts nuclear masses
Kate A. Richardson, Sokratis Trifinopoulos, Mike Williams
https://arxiv.org/abs/2508.08370 https://

The DNA of nuclear models: How AI predicts nuclear masses
Obtaining high-precision predictions of nuclear masses, or equivalently nuclear binding energies, $E_b$, remains an important goal in nuclear-physics research. Recently, many AI-based tools have shown promising results on this task, some achieving precision that surpasses the best physics models. However, the utility of these AI models remains in question given that predictions are only useful where measurements do not exist, which inherently requires extrapolation away from the training (and t…

Somehow I only just found out that Jolly Ranchers were "banned" in the UK a month ago.
(They're not banned as such, but most shops won't sell products when informed they're not compliant with food standards. London's thousand "American candy" shops will still have them if you want the forbidden hydrocarbons.)

Several US Jolly rancher sweets unsafe to eat, FSA says
The FSA says chemical compounds in the sweets can increase the risk of cancer and damage DNA.

3D DNA Origami-Enabled Molecularly Addressable Optical Nanocircuit
Jaewon Lee, Hayun Ahn, Kyung Hun Rho, Shelley F. J. Wickham, William M. Shih, Seungwoo Lee
https://arxiv.org/abs/2508.05440

3D DNA Origami-Enabled Molecularly Addressable Optical Nanocircuit
The optical nanocircuit concept provides a predictive framework analogous to an electric RLC circuit, where induced dipoles in plasmonic nanoparticle (NPs), ohmic losses in NPs, and dielectric gaps serve as inductors (L), capacitors (C), and resistors (R), respectively. This modular theory allows unprecedented design flexibility, expanding the range of achievable optical resonances in plasmonic clusters. However, existing experimental approaches, such as atomic force microscope tip-enabled nano…

#DNA evidence hit finds 18 year old charged with multiple felonies for #rape and sexual assaults made on female victim he stalked late one evening along #ContraCosta

Computational Insight into the Complexation of DNA-Functionalized Gold Nanoparticles
J. Hingies Monisha, V. Vasumathi, Prabal K Maiti
https://arxiv.org/abs/2509.06399 https://…

Computational Insight into the Complexation of DNA-Functionalized Gold Nanoparticles
Ensuring the stability of the AuNP-gene complex until it reaches the target sites is a crucial factor for the success of gene therapy. Though different AuNP sizes and AuNP-to-DNA ratios are investigated for specific therapeutic needs, their role on the stability and packaging of AuNP-DNA complex remains unclear. In this study, we employ all-atom molecular dynamics simulations to investigate the influence of cationic ligand-functionalized AuNP (CAuNP) size and CAuNP-to-DNA ratio on DNA wrapping …

discovery and analysis of centuries-old dna reveals the meline origins of people who type in lowercase

@… how are you with FUSE_DNA forensics?
newer xc7k325t's don't have scraped off QR codes, they have a weird surface texture though

Every newborn baby in England will have their DNA mapped to assess their risk of hundreds of diseases, under NHS plans for the next 10 years.
The scheme, first reported by the Daily Telegraph, is part of a government drive towards predicting and preventing illness, which will also see £650m invested in DNA research for all patients by 2030.
Health Secretary Wes Streeting said gene technology would enable the health service to "leapfrog disease, so we're in front of it ra…

NHS plans to DNA test all babies in England to assess disease risk
Scheme is part of the government's 10-year plan for the NHS in England aimed at easing pressure on services.

The SChISM study: Cell-free DNA size profiles as predictors of progression in advanced carcinoma treated with immune-checkpoint inhibitors
Linh Nguyen Phuong (COMPO), Frederic Fina (COMPO, APHM), Laurent Greillier (COMPO, APHM), Pascale Tomasini (APHM, COMPO), Jean-Laurent Deville (TIMONE), Romain Zakrasjek (COMPO), Lucie Della-Negra (COMPO), Audrey Boutonnet (COMPO), Fr\'ed\'eric Ginot (COMPO), Jean-Charles Garcia (COMPO), S\'ebastien Benzekry (COMPO), S\'ebastien Sala…

The SChISM study: Cell-free DNA size profiles as predictors of progression in advanced carcinoma treated with immune-checkpoint inhibitors
Background: Many advanced cancer patients experience progression under immune-checkpoint inhibitors (ICIs). Circulating cell-free DNA (cfDNA) size profiles offer a promising noninvasive multi-cancer approach to monitor and predict immunotherapy response. Methods: In the SChISM (Size CfDNA Immunotherapy Signature Monitoring) study (NCT05083494), pre-treatment plasmatic cfDNA size profiles from 126 ICI-treated advanced carcinomas were quantified using the BIABooster device. Fragmentomederived var…

#LB Finalmente uma explicação científica de eu ser tão banana rs.
https://noc.social/@todayilearned/115073565538086346

tree-of-life: Protein interactomes across the tree of life (2019)
Protein-protein iteraction networks ("interactome") for 1,840 species. An interactome captures all physical protein-protein interactions within one species, from direct biophysical protein-protein interactions to regulatory protein-DNA and metabolic interactions. .
This network has 1537 nodes and 8028 edges.
Tags: Biological, Protein interactions

Crosslisted article(s) found for cond-mat.mes-hall. https://arxiv.org/list/cond-mat.mes-hall/new
[1/1]:
- Patterning programmable spin arrays on DNA origami for quantum technologies
Zhang, Morrison, Hughes, Wu, Liu, Bluvstein, Yao, Fygenson, Jayich

"‘New hope’: ash trees rapidly evolving resistance to dieback, study reveals"
#UK #UnitedKingdom #Trees

The Random Variables of the DNA Coverage Depth Problem
\c{S}eyma Bodur, Stefano Lia, Hiram H. L\'opez, Rati Ludhani, Alberto Ravagnani, Lisa Seccia
https://arxiv.org/abs/2507.20645

The Random Variables of the DNA Coverage Depth Problem
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on minimizing the expected number of reads needed to recover information strands encoded via a linear code. We compute the asymptotic performance of a recently proposed code construction, establishing and refining a conjecture in the field by giving two independ…

Widespread remote introgression in the grass genomes
Yujie Huang, Shiyu Zhang, Hanyang Lin, Chenxu Liu, Zhefu Li, Kun Yang, Yutong Liu, Linfeng Jin, Chuanlong Lu, Yuan Cheng, Chaoyi Hu, Huifang Zhao, Guoping Zhang, Qian Qian, Longjiang Fan, Dongya Wu
https://arxiv.org/abs/2507.07761

Widespread remote introgression in the grass genomes
Genetic transfers are pervasive across both prokaryotes and eukaryotes, encompassing canonical genomic introgression between species or genera and horizontal gene transfer (HGT) across kingdoms. However, DNA transfer between phylogenetically distant species, here defined as remote introgression (RI), has remained poorly explored in evolutionary genomics. In this study, we present RIFinder, a novel phylogeny-based method for RI event detection, and apply it to a comprehensive dataset of 122 gras…

Oh those poor ICE goons. They are so afraid of getting a nasty e-mail. Oh woe is them.
Yet they beat up, arrest, deport, and terrorize people. True Nazi scum those ICE people.
And they insist they must hide their identities - as in "The Trial" by Kafka.
I, on the other hand, think they should be exposed - totally exposed: name, affiliation, DNA sequence and so forth. They should even be required, like sex offenders, to walk neighborhoods warning of their prese…

Healthy Babies Born in Britain After Scientists Used DNA From Three People to Avoid Genetic Disease - Slashdot
https://science.slashdot.org/story/25/07/20/0328203/healthy-babies-born-in-britain-after-scientists-used-dna-from-three-people-to-avoid-genetic-disease

Finding low-complexity DNA sequences with longdust
Heng Li, Brian Li
https://arxiv.org/abs/2509.07357 https://arxiv.org/pdf/2509.07357

Finding low-complexity DNA sequences with longdust
Motivation: Low-complexity (LC) DNA sequences are compositionally repetitive sequences that are often associated with increased variant density and variant calling artifacts. While algorithms for identifying LC sequences exist, they either lack rigorous mathematical foundation or are inefficient with long context windows. Results: Longdust is a new algorithm that efficiently identifies long LC sequences including centromeric satellite and tandem repeats with moderately long motifs. It defines…

Vitamin C flips your skin’s “youth genes,” reversing age-related thinning #nutrition

Vitamin C flips your skin’s “youth genes,” reversing age-related thinning
Japanese researchers have found that vitamin C can thicken skin by switching on genes that boost skin cell growth, helping reverse age-related thinning. It works by reactivating DNA through a process that lets cells regenerate more effectively—potentially a game-changer for aging skin.

Integrating nano- and micrometer-scale energy deposition models for mechanistic prediction of radiation-induced DNA damage and cell survival
Giulio Bordieri, Marta Missiggia, Gianluca Lattanzi, Carmen Villagrasa, Yann Perrot, Francesco G. Cordoni
https://arxiv.org/abs/2507.00929

Integrating nano- and micrometer-scale energy deposition models for mechanistic prediction of radiation-induced DNA damage and cell survival
We present an integrated modeling framework that combines the Generalized Stochastic Microdosimetric Model (GSM2), used to predict cell survival fractions, with MINAS-TIRITH, a fast and efficient Geant4 DNA-based tool for simulating radiation-induced DNA damage in cell populations. This approach enables the generation of spatially and structurally resolved double-strand break (DSB) distributions, capturing key features such as damage complexity and chromosome specificity. A novel application of…

Ancient #DNA solves #Plague of #Justinian mystery to rewrite #pandemic history.

Ancient DNA solves Plague of Justinian mystery to rewrite pandemic history
For the first time, researchers have uncovered direct genomic evidence of the bacterium behind the Plague of Justinian—the world's first recorded pandemic—in the Eastern Mediterranean, where the outbreak was first described nearly 1,500 years ago.

Replaced article(s) found for cs.OH. https://arxiv.org/list/cs.OH/new
[1/1]:
- Motif Caller: Sequence Reconstruction for Motif-Based DNA Storage
Parv Agarwal, Nimesh Pinnamaneni, Thomas Heinis

Invisible invaders:
unveiling the carcinogenic threat of microplastics and nanoplastics in colorectal cancer
Key findings reveal that MicroPlastics/NanoPlastics,
via ingestion, inhalation, and dermal contact,
translocate across biological barriers to induce DNA damage, oxidative stress, and intestinal barrier disruption by reducing tight junction proteins,
while triggering chronic inflammation through pro-inflammatory cytokines and gut microbiota dysbiosis.

Frontiers | Invisible invaders: unveiling the carcinogenic threat of microplastics and nanoplastics in colorectal cancer-a systematic review
ObjectiveMicroplastics (MPs, 0.1–5000 μm) and nanoplastics (NPs, 0.001–0.1 μm) are ubiquitous environmental pollutants with strong persistence and bioaccumul...

Directed evolution effectively selects for DNA based physical reservoir computing networks capable of multiple tasks
Tanmay Pandey, Petro Feketa, Jan Steink\"uhler
https://arxiv.org/abs/2509.04000

Directed evolution effectively selects for DNA based physical reservoir computing networks capable of multiple tasks
DNA and other biopolymers are being investigated as new computing substrates and alternative to silicon-based digital computers. However, the established top-down design of biomolecular interaction networks remains challenging and does not fully exploit biomolecular self-assembly capabilities. Outside of the field of computation directed evolution has been used as a tool for goal directed optimization of DNA sequences. Here, we propose integrating directed evolution with DNA-based reservoir com…

Investigating DNA words and their distributions across the tree of life
Charalampos Koilakos, Kimonas Provatas, Michail Patsakis, Aris Karatzikos, Ilias Georgakopoulos-Soares
https://arxiv.org/abs/2509.05539

Investigating DNA words and their distributions across the tree of life
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural language, prior studies have attempted to model genomic k-mer usage using Zipf's law, a rank-frequency law originally formulated for words in human language. However, the extent to which this law accurately captures the distribution of k-mers across diverse species remains unclear. Here, we systematically analyze k-mer …

The Coverage Depth Problem in DNA Storage Over Small Alphabets
Matteo Bertuzzo, Alberto Ravagnani, Eitan Yaakobi
https://arxiv.org/abs/2507.20639 https://a…

The Coverage Depth Problem in DNA Storage Over Small Alphabets
The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the base field is not large enough to allow the existence of MDS codes. We investigate the performance for the coverage depth problem of codes defined over a small finite field, providing closed formulas for the expected number of reads for various code families…

Machine Learning Guided Multiscale Design of DNA-functionalized Nanoparticles for Targeted Self-Assembly of the Double Gyroid
Luis Nieves-Rosado (Cornell University), Fernando Escobedo (Cornell University)
https://arxiv.org/abs/2507.03025

Machine Learning Guided Multiscale Design of DNA-functionalized Nanoparticles for Targeted Self-Assembly of the Double Gyroid
In soft matter science, it is often the goal to design new materials with targeted properties. These materials can be used in many applications, each requiring specific features to be optimized for maximum fitness. The use of self-assembly processes, where a target structure is attained from suitably designed building blocks, is a powerful tool for this optimization. However, it is still an open question how to generally design realizable building blocks that lead to the desired phases. In this…

DNA Unzipping Transition
Somendra M. Bhattacharjee
https://arxiv.org/abs/2506.24064 https://arxiv.org/pdf/2506.24064

DNA Unzipping Transition
This review focuses on the force-induced unzipping transition of double-stranded DNA. It begins with a brief history of DNA melting, which emerged alongside the growth of the field of molecular biology, juxtaposed with the advancements in physics during the same post-World War II period. The earlier theories of melting of DNA were based on the Ising model and its modifications, but gradually moved towards polymer-based models. The idea of force-induced unzipping was first introduced in 1999 as …

🌲 A Sequoia Forest Grows in Detroit
#detroit

A Sequoia Forest Grows in Detroit
Using the DNA of the world’s mightiest trees, a tree grower in Michigan aims to replenish old-growth forests, one sapling at a time.

"Donald Trump has Epstein DNA smeared all over him. He tries to hide who he is with concealer pancake make-up. It doesn’t work. We know who he is. He is Jeffrey Epstein’s best friend."
#trump #epstein
From: @…

tree-of-life: Protein interactomes across the tree of life (2019)
Protein-protein iteraction networks ("interactome") for 1,840 species. An interactome captures all physical protein-protein interactions within one species, from direct biophysical protein-protein interactions to regulatory protein-DNA and metabolic interactions. .
This network has 255 nodes and 251 edges.
Tags: Biological, Protein interactions

CodonMoE: DNA Language Models for mRNA Analyses
Shiyi Du, Litian Liang, Jiayi Li, Carl Kingsford
https://arxiv.org/abs/2508.04739 https://arxiv.org/pdf/250…

CodonMoE: DNA Language Models for mRNA Analyses
Genomic language models (gLMs) face a fundamental efficiency challenge: either maintain separate specialized models for each biological modality (DNA and RNA) or develop large multi-modal architectures. Both approaches impose significant computational burdens - modality-specific models require redundant infrastructure despite inherent biological connections, while multi-modal architectures demand massive parameter counts and extensive cross-modality pretraining. To address this limitation, we i…

this is an underrated dees, its composition evokes dali and carrington landscapes in a way none of his other stuff does

Visualizing Poloidal Orientation in DNA Minicircles
Tony Lemos, Harold D. Kim
https://arxiv.org/abs/2508.15091 https://arxiv.org/pdf/2508.15091

Visualizing Poloidal Orientation in DNA Minicircles
A short (<150 bp) double-stranded DNA (dsDNA) molecule ligated end-to-end forms a DNA minicircle. Due to sequence-dependent, nonuniform bending energetics, such a minicircle is predicted to adopt a certain inside-out orientation, known as the poloidal orientation. Despite theoretical and computational predictions, experimental evidence for this phenomenon has been lacking. In this study, we introduce a single-molecule approach to visualize the poloidal orientation of DNA minicircles. We constru…

Stochastic modelling reveals that chromatin folding buffers epigenetic landscapes against sirtuin depletion during DNA damage
Daria Stepanova, Helen M. Byrne, Tom\'as Alarc\'on
https://arxiv.org/abs/2508.16548

Stochastic modelling reveals that chromatin folding buffers epigenetic landscapes against sirtuin depletion during DNA damage
Epigenetic landscapes, represented by patterns of chemical modifications on histone tails, are essential for maintaining cell identity and tissue homeostasis. These landscapes are shaped by multiple factors, including local biochemical signals and the three-dimensional organisation of chromatin. However, their response to genomic stress, such as DNA double-strand breaks (DSBs), remains incompletely understood. Here, we use a stochastic model of histone modification dynamics integrated with chro…

Louisiana Republicans have passed a new law that effectively eviscerates people's ability to claim their innocence and seek relief once they've been convicted.
A massive blow to the rights of people in prison in a state that's full of wrongful convictions:
https://

Louisiana Is Bulldozing the Right of Prisoners to Prove Their Innocence After a Conviction - Bolts
Malcolm Alexander had been incarcerated at Angola prison 14 years already when he learned about DNA testing, the thing that would ultimately free him, while watching television coverage of the... Read More

On reversible and reversible-complementary DNA codes over $\mathbb{F}_{4}$
E. J. Garc\'ia-Claro
https://arxiv.org/abs/2506.19170 https://

On reversible and reversible-complementary DNA codes over $\mathbb{F}_{4}$
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA codes that satisfy the reverse and reverse-complement constraints. By analyzing a module-theoretic structure of these codes, their generating matrices are characterized in terms of their isomorphism type, and explicit formulas for counting them are provided. The…

Role of bubble positioning in force induced melting of DNA
Bidisha Mukherjee, Amit Raj Singh, Garima Mishra
https://arxiv.org/abs/2506.18821 https://

Role of bubble positioning in force induced melting of DNA
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by using DNA molecules with 50% AT - 50% GC base-pair composition which ensures constant enthalpy. Our results reveal that it is not just the sequence itself, but its specific arrangement that influences DNA stability. We examine two types of DNA sequences contain…

tree-of-life: Protein interactomes across the tree of life (2019)
Protein-protein iteraction networks ("interactome") for 1,840 species. An interactome captures all physical protein-protein interactions within one species, from direct biophysical protein-protein interactions to regulatory protein-DNA and metabolic interactions. .
This network has 813 nodes and 2611 edges.
Tags: Biological, Protein interactions

Replaced article(s) found for q-bio.QM. https://arxiv.org/list/q-bio.QM/new
[1/1]:
- KinDEL: DNA-Encoded Library Dataset for Kinase Inhibitors
Benson Chen, et al.

Here are the three primary kinds of community-based events we’ll be sponsoring during 31 Days of Action:

Open/community lab meetings over Zoom or live-streamed lab tours/demos

Teach-ins at local community centers, churches, parks, basically anywhere that’s not a college campus

Stand Up For Science tabling and demos that include “Ask a Scientist” booths,
pond water under a microscope,
strawberry DNA extraction,
egg drop competitions, …

SUFS 31 Days of Action Guidebook
🧬 WHAT IS STAND UP FOR SCIENCE? Stand Up for Science (SUFS) is a 501(c)(4) non-profit organization born from the rallies held in cities throughout the United States and around the world on March 7th, 2025. We believe that science is a public good that benefits everyone, and we’re leading...

Neural Polar Decoders for DNA Data Storage
Ziv Aharoni, Henry D. Pfister
https://arxiv.org/abs/2506.17076 https://arxiv.org/pdf/2506.…

Neural Polar Decoders for DNA Data Storage
Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as insertion-deletion-substitution (IDS) channels, for which designing maximum-likelihood decoders is computationally expensive. In this work, we propose a data-driven approach based on neural polar decoders (NPDs) to design low-complexity decoders for channels with synchronization errors. …

🐍 Where did RNA come from? Origin-of-life scientists help to answer the question
#rna

Where did RNA come from? Origin-of-life scientists help to answer the question
In living organisms today, complex molecules like RNA and DNA are constructed with the help of enzymes. So how did these molecules form before life (and enzymes) existed? Why did some molecules end up as the building blocks of life and not others? A new study by Scripps Research scientists helps answer these longstanding questions.

Single-Trajectory Bayesian Modeling Reveals Multi-State Diffusion of the MSH Sliding Clamp
Seongyu Park, Inho Yang, Jinseob Lee, Sinwoo Kim, Juana Mart\'in-L\'opez, Richard Fishel, Jong-Bong Lee, Jae-Hyung Jeon
https://arxiv.org/abs/2506.21943

Single-Trajectory Bayesian Modeling Reveals Multi-State Diffusion of the MSH Sliding Clamp
DNA mismatch repair (MMR) is the essential mechanism for preserving genomic integrity in various living organisms. In this process, MutS homologs (MSH) play crucial roles in identifying mismatched basepairs and recruiting downstream MMR proteins. The MSH protein exhibits distinct functions and diffusion dynamics before and after the recognition of mismatches while traversing along DNA. An ADP-bound MSH, known as the MSH searching clamp, scans DNA sequences via rotational diffusion along the DNA…

Topological Sequence Analysis of Genomes: Category Approaches
Jian Liu, Li Shen, Mushal Zia, Guo-Wei Wei
https://arxiv.org/abs/2507.08043 https://

Topological Sequence Analysis of Genomes: Category Approaches
Sequence data, such as DNA, RNA, and protein sequences, exhibit intricate, multi-scale structures that pose significant challenges for conventional analysis methods, particularly those relying on alignment or purely statistical representations. In this work, we introduce category-based topological sequence analysis (CTSA ) of genomes. CTSA models a sequence as a resolution category, capturing its hierarchical structure through a categorical construction. Substructure complexes are then derived …

tree-of-life: Protein interactomes across the tree of life (2019)
Protein-protein iteraction networks ("interactome") for 1,840 species. An interactome captures all physical protein-protein interactions within one species, from direct biophysical protein-protein interactions to regulatory protein-DNA and metabolic interactions. .
This network has 1501 nodes and 6848 edges.
Tags: Biological, Protein interactions

When Ashley Robinson and her mother took DNA tests 10 years ago and began meeting long lost cousins,
they stumbled across a surprising family history that changed their lives.
Robinson’s lineage traced back to the 272 West Africans who were enslaved by Jesuits
and sold to plantation owners in the southern US in 1838.
The sale of the enslaved Africans helped fund Georgetown University,
the oldest Jesuit higher education institution in the US,
and served a…

Replaced article(s) found for cs.IT. https://arxiv.org/list/cs.IT/new
[1/1]:
- GC Code: A Systematic Short Blocklength Code for Correcting Random Edit Errors in DNA Storage
Serge Kas Hanna

DNA Dynamics in Dual Nanopore Tug-of-War
Zezhou Liu, Wangwei Dong, Thomas St-Denis, Matheus Azevedo Silva Pess\^oa, Sajad Shiekh, Preethi Ravikumar, Walter Reisner
https://arxiv.org/abs/2508.21144

DNA Dynamics in Dual Nanopore Tug-of-War
Solid state nanopores have emerged as powerful tools for single-molecule sensing, yet the rapid uncontrolled translocation of the molecule through the pore remains a key limitation. We have previously demonstrated that an active dual-nanopore system, consisting of two closely spaced pores operated via feedback controlled biasing, shows promise in achieving controlled, slowed-down translocation. Translocation control is achieved via capturing the DNA in a special tug-of-war configuration, whereb…

⚗️ Secrets of the dark genome could spark new drug discoveries
#drugs

Secrets of the dark genome could spark new drug discoveries
Since the Human Genome Project first produced the genetic instructions for a human being by sequencing DNA 22 years ago, scientists have been focused on roughly 2% of the genome-producing proteins.

tree-of-life: Protein interactomes across the tree of life (2019)
Protein-protein iteraction networks ("interactome") for 1,840 species. An interactome captures all physical protein-protein interactions within one species, from direct biophysical protein-protein interactions to regulatory protein-DNA and metabolic interactions. .
This network has 277 nodes and 291 edges.
Tags: Biological, Protein interactions

Diverse, Distinct, and Densely Packed DNA Droplets
Aria S. Chaderjian, Sam Wilken, Omar A. Saleh
https://arxiv.org/abs/2508.18574 https://arxiv.org/pdf/250…

Diverse, Distinct, and Densely Packed DNA Droplets
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of dense liquid (`condensate') phases. The relationship between sequence design and the diversity of the resultant phases is therefore of interest. Here, we explore this question using the DNA nanostar system which permits the creation of multi-phase condensate …

On the Maximum Size of Codes Under the Damerau-Levenshtein Metric
Zuo Ye, Gennian Ge
https://arxiv.org/abs/2507.04806 https://arxiv.o…

On the Maximum Size of Codes Under the Damerau-Levenshtein Metric
The Damerau-Levenshtein distance between two sequences is the minimum number of operations (deletions, insertions, substitutions, and adjacent transpositions) required to convert one sequence into another. Notwithstanding a long history of this metric, research on error-correcting codes under this distance has remained limited. Recently, motivated by applications in DNA-based storage systems, Gabrys \textit{et al} and Wang \texit{et al} reinvigorated interest in this metric. In their works, som…