Tootfinder

Gene therapy can restore hearing in adults, first-of-its-kind trial shows https://www.sciencealert.com/gene-therapy-can-restore-hearing-in-adults-first-of-its-kind-trial-shows Surprisingly, younger was not always better in…

Gene Therapy Can Restore Hearing in Adults, First-of-Its-Kind Trial Shows
Up to three in every 1,000 newborns has hearing loss in one or both ears.

genetic_multiplex: Multiplex genetic interactions (2014)
Multiplex networks representing different types of genetic interactions, for different organisms. Layers represent (i) physical, (ii) association, (iii) co-localization, (iv) direct, and (v) suppressive, (vi) additive or synthetic genetic interaction. Edge direction (i,j) indicates gene i interacting with gene j.
This network has 6570 nodes and 282755 edges.
Tags: Biological, Gene regulation, Protein interactions, Unw…

Abbott sues to remove Texas House Democratic Caucus Chair Gene Wu from seat (Tara Suter/The Hill)
https://thehill.com/regulation/court-battles/5437860-abbott-sues-remove-texas-house-democratic-caucus-chair-gene-wu/
http://www.memeorandum.com/250805/p134#a250805p134

New Gene Therapy Repairs Deafness Gene, Restores Hearing In Landmark Clinical Trial;
Researchers successfully restored hearing in 10 deaf participants aged 18 months to 24 years
https://studyfinds.org/landmark-trial-gene-therapy-repairs-deafness…

New Gene Therapy Repairs Deafness Gene, Restores Hearing In Landmark Clinical Trial
A new gene therapy trial safely restores hearing in deaf children and adults, offering hope for those with DFNB9 deafness once thought untreatable.

Knowledge-guided Contextual Gene Set Analysis Using Large Language Models
Zhizheng Wang, Chi-Ping Day, Chih-Hsuan Wei, Qiao Jin, Robert Leaman, Yifan Yang, Shubo Tian, Aodong Qiu, Yin Fang, Qingqing Zhu, Xinghua Lu, Zhiyong Lu
https://arxiv.org/abs/2506.04303

Knowledge-guided Contextual Gene Set Analysis Using Large Language Models
Gene set analysis (GSA) is a foundational approach for interpreting genomic data of diseases by linking genes to biological processes. However, conventional GSA methods overlook clinical context of the analyses, often generating long lists of enriched pathways with redundant, nonspecific, or irrelevant results. Interpreting these requires extensive, ad-hoc manual effort, reducing both reliability and reproducibility. To address this limitation, we introduce cGSA, a novel AI-driven framework tha…

The Nevada Legislature rejects a proposal to create a $95M annual tax credit for the Sony- and WBD-backed Summerlin Studios project in Las Vegas (Gene Maddaus/Variety)
https://variety.com/2025/tv/news/las-vegas-studio-prosposal-dies-1236417137/

Las Vegas Studio Proposal Dies in Nevada Legislature
A plan to build a $400 million studio in Las Vegas died in the state legislature on Monday night, after lawmakers balked at subsidies.

On the Spherical Dirichlet Distribution: Corrections and Results
Jose H Guardiola
https://arxiv.org/abs/2506.04441 https://arxiv.org/…

On the Spherical Dirichlet Distribution: Corrections and Results
This note corrects a technical error in Guardiola (2020, Journal of Statistical Distributions and Applications), presents updated derivations, and offers an extended discussion of the properties of the spherical Dirichlet distribution. Today, data mining and gene expressions are at the forefront of modern data analysis. Here we introduce a novel probability distribution that is applicable in these fields. This paper develops the proposed Spherical-Dirichlet Distribution designed to fit vectors …

🌼 Flowers unfold with surprising precision, despite unruly genes
#flowers

Flowers unfold with surprising precision, despite unruly genes
Flowers grow stems, leaves and petals in a perfect pattern again and again. A new Cornell study shows that even in this precise, patterned formation in plants, gene activity inside individual cells is far more chaotic than it appears from the outside.

Modelling transcriptional silencing and its coupling to 3D genome organisation
Massimiliano Semeraro, Giuseppe Negro, Davide Marenduzzo, Giada Forte
https://arxiv.org/abs/2507.02150

Modelling transcriptional silencing and its coupling to 3D genome organisation
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially by modelling. This study employs 3D simulations to study the biophysics of a chromatin fibre where active transcription factors compete with repressors for binding to transcription units along the fibre, and investigates how different silencing mechanisms af…

The High Level Trigger and Express Data Production at STAR
Wayne Betts, Jinhui Chen, Yuri Fisyak, Hongwei Ke, Ivan Kisel, Pavel Kisel, Grigory Kozlov, Jeffery Landgraf, Jerome Lauret, Tonko Ljubicic, Yugang Ma, Spyridon Margetis, Hao Qiu, Diyu Shen, Qiye Shou, Xiangming Sun, Aihong Tang, Gene Van Buren, Iouri Vassiliev, Baoshan Xi, Zhenyu Ye, Zhengqiao Zhang, Maksym Zyzak

The High Level Trigger and Express Data Production at STAR
The STAR experiment at the Relativistic Heavy Ion Collider (RHIC) has developed and deployed a high-performance High Level Trigger (HLT) and Express Data Production system to enable real-time event processing during the Beam Energy Scan phase-II (BES-II) program. Designed to meet the demands of high event rates and complex final states, the HLT performs online tracking, event reconstruction, and physics object selection using parallelized algorithms including the Cellular Automaton Track Finder…

This https://arxiv.org/abs/2411.16699 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_nli…

Bistability and chaos in the discrete two-gene Andrecut-Kauffman model
We conduct numerical analysis of the 2-dimensional discrete-time gene expression model originally introduced by Andrecut and Kauffman (Phys. Lett. A 367: 281-287, 2007). In contrast to the previous studies, we analyze the dynamics with different reaction rates $α_1$ and $α_2$ for each of the two genes under consideration. We explore bifurcation diagrams for the model with $α_1$ varying in a wide range and $α_2$ fixed. We detect chaotic dynamics by means of the positive maximum Lyapunov expo…

Gene editing technology could be used to save species on the brink of extinction
https://phys.org/news/2025-07-gene-technology-species-brink-extinction.html#google_vignette

Marker Gene Method : Identifying Stable Solutions in a Dynamic Environment
Hao Shi, Xi Li, Fangfang Xie
https://arxiv.org/abs/2506.23734 https://

Marker Gene Method : Identifying Stable Solutions in a Dynamic Environment
Competitive Co-evolutionary Algorithms (CCEAs) are often hampered by complex dynamics like intransitivity and the Red Queen effect, leading to unstable convergence. To counter these challenges, this paper introduces the Marker Gene Method (MGM), a framework that establishes stability by using a 'marker gene' as a dynamic benchmark and an adaptive weighting mechanism to balance exploration and exploitation. We provide rigorous mathematical proofs demonstrating that MGM creates strong attractors …

Vinay Prasad,
a critic of broadly administering coronavirus shots
who became the Food and Drug Administration’s top vaccine and gene therapy regulator in May,
was ousted Tuesday,
according to two people familiar with the situation.

Prasad had recently come under fire from some Republicans and conservative activists,
including far-right activist Laura Loomer,
over his approach to drug approvals and his previous support for Democratic politicians.

Vocal FDA critic who became top agency vaccine regulator abruptly departs
Vinay Prasad, who became prominent as a critic of coronavirus vaccine policy, briefly served as the FDA’s top regulator of vaccines, gene therapies and the blood supply.

Russell Simmons sues HBO and the directors of On the Record for $20M, alleging they defamed him in their documentary on sexual assault allegations against him (Gene Maddaus/Variety)
https://variety.com/2025/music/news/russell-s…

Russell Simmons Sues HBO for $20 Million Over 'On the Record' Doc
Russell Simmons filed a $20 million lawsuit against HBO over the 'On the Record' documentary, which debuted five years ago on HBO Max.

Predicting EGFR Mutation in LUAD from Histopathological Whole-Slide Images Using Pretrained Foundation Model and Transfer Learning: An Indian Cohort Study
Sagar Singh Gwal, Rajan, Suyash Devgan, Shraddhanjali Satapathy, Abhishek Goyal, Nuruddin Mohammad Iqbal, Vivaan Jain, Prabhat Singh Mallik, Deepali Jain, Ishaan Gupta
https://arxiv.org…

Predicting EGFR Mutation in LUAD from Histopathological Whole-Slide Images Using Pretrained Foundation Model and Transfer Learning: An Indian Cohort Study
Lung adenocarcinoma (LUAD) is a subtype of non-small cell lung cancer (NSCLC). LUAD with mutation in the EGFR gene accounts for approximately 46% of LUAD cases. Patients carrying EGFR mutations can be treated with specific tyrosine kinase inhibitors (TKIs). Hence, predicting EGFR mutation status can help in clinical decision making. H&E-stained whole slide imaging (WSI) is a routinely performed screening procedure for cancer staging and subtyping, especially affecting the Southeast Asian popula…

A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics
Rushin H. Gindra, Giovanni Palla, Mathias Nguyen, Sophia J. Wagner, Manuel Tran, Fabian J Theis, Dieter Saur, Lorin Crawford, Tingying Peng
https://arxiv.org/abs/2508.01490

A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics
Spatial transcriptomics enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for evaluating multimodal learning methods that leverage both histology images and gene expression data. Here, we present HESCAPE, a large-scale benchmark for cross-modal contrastive pretraining in spatial transcriptomics, built on a curated pan-organ dataset spannin…

This https://arxiv.org/abs/2402.19388 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

A minimal model of pan-immunity maintenance by horizontal gene transfer in the ecological dynamics of bacteria and phages
Bacteria and phages have been in an ongoing arms race for billions of years. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still overcome by counter-defense mechanisms of specific phages. These defense/counter-defense systems are a major element of microbial genetic diversity and have been demonstrated to propagate between strains by Horizontal Gene Transfer (HGT). It has been proposed that the totality of defense systems found in microbial communities …

genetic_multiplex: Multiplex genetic interactions (2014)
Multiplex networks representing different types of genetic interactions, for different organisms. Layers represent (i) physical, (ii) association, (iii) co-localization, (iv) direct, and (v) suppressive, (vi) additive or synthetic genetic interaction. Edge direction (i,j) indicates gene i interacting with gene j.
This network has 155 nodes and 188 edges.
Tags: Biological, Gene regulation, Protein interactions, Unweigh…

Genesis AI, which generates its own synthetic data for training an AI model for robots, emerges from stealth with a $105M seed co-led by Eclipse and Khosla (Marina Temkin/TechCrunch)
https://techcrunch.com/2025/07/01/gene

Genesis AI launches with $105M seed funding from Eclipse, Khosla to build AI models for robots | TechCrunch
Genesis AI, which aims to build a foundational model for powering all kinds of robots, has emerged from stealth with $105M in seed funding.

💉 Research identifies genetic predictor of weight loss with GLP-1RAs
#medicine

Research identifies genetic predictor of weight loss with GLP-1RAs
A new study published by Cleveland Clinic researchers in Diabetes, Obesity and Metabolism investigating the genetic underpinnings of weight loss response has identified a gene, neurobeachin (NBEA), as a predictor of how individuals respond to GLP-1RAs, the class of medications behind popular treatments like liraglutide and semaglutide.

"The RDBMS field is so young, we can actually see it grow through the pages of computer magazines of the 1980s. BYTE Magazine had its first issue dedicated to databases in November 1981, and then another one in October 1984. Dr. Dobb’s Journal did not feature an article about databases until 1984 and did not have many more throughout the decade; actually most of them were authored by Gene Head, and talk about dBASE."

Agnostic Reinforcement Learning: Foundations and Algorithms
Gene Li
https://arxiv.org/abs/2506.01884 https://arxiv.org/pdf/2506.01884…

Agnostic Reinforcement Learning: Foundations and Algorithms
Reinforcement Learning (RL) has demonstrated tremendous empirical success across numerous challenging domains. However, we lack a strong theoretical understanding of the statistical complexity of RL in environments with large state spaces, where function approximation is required for sample-efficient learning. This thesis addresses this gap by rigorously examining the statistical complexity of RL with function approximation from a learning theoretic perspective. Departing from a long history of…

"Why Antidepressants Work Better for Some"
Key Facts:
Immune Pathways: Toll-like receptor and NF-κB pathways were consistently altered between responders and non-responders.
Neural Mechanisms: Signal transduction and GABAergic synapse pathways showed consistent changes with fluoxetine treatment.
Heterogeneity Noted: Patterns of gene expression varied across tissues, models, and individuals, emphasizing the need for larger, more targeted studies.
Paper: Sou…

Gene expression signatures of response to fluoxetine treatment: systematic review and meta-analyses - Molecular Psychiatry
Genomic (and other ‘omic) data have provided valuable insights on the pharmacological signatures of antidepressant response, but results from individual studies are largely heterogeneous. In this work, we synthesized gene expression data for fluoxetine treatment in both human patients and rodent models, to better understand biological pathways affected by treatment, as well as those that may distinguish clinical or behavioral response. Following the PRISMA guidelines, we searched the Gene Exp…

Characterization of reduced-order turbulence models in the L-mode pedestal-forming region in JET
G. Snoep, C. Bourdelle, J. Citrin, A. Ho, M. J. Pueschel, P. Vincenzi, E. R. Solano, M. Sertoli, E. Delabie, Jet Contributors
https://arxiv.org/abs/2506.03459

Characterization of reduced-order turbulence models in the L-mode pedestal-forming region in JET
Linear instability characterization of seven JET discharges just prior to the L-H transition is performed at $ρ_{\text{tor}} \in [0.85,0.9,0.95]$ with the gyrokinetic GENE code. The discharges cover both the low- and high-density branches of the L-H transition at two different triangularities. Sensitivities to driving gradients, normalized electron collisonality $ν_e^*$, hydrogen isotope mass, magnetic geometry and finite-$β$ effects are all characterized. At $ρ_{\text{tor}}=0.85$ and $0.9$…

Spatial Coordinates as a Cell Language: A Multi-Sentence Framework for Imaging Mass Cytometry Analysis
Chi-Jane Chen, Yuhang Chen, Sukwon Yun, Natalie Stanley, Tianlong Chen
https://arxiv.org/abs/2506.01918

Spatial Coordinates as a Cell Language: A Multi-Sentence Framework for Imaging Mass Cytometry Analysis
Image mass cytometry (IMC) enables high-dimensional spatial profiling by combining mass cytometry's analytical power with spatial distributions of cell phenotypes. Recent studies leverage large language models (LLMs) to extract cell states by translating gene or protein expression into biological context. However, existing single-cell LLMs face two major challenges: (1) Integration of spatial information: they struggle to generalize spatial coordinates and effectively encode spatial context as …

Boolean-network simplification and rule fitting to unravel chemotherapy resistance in non-small cell lung cancer
Alonso Espinoza, Eric Goles, Marco Montalva-Medel
https://arxiv.org/abs/2506.02525

Boolean-network simplification and rule fitting to unravel chemotherapy resistance in non-small cell lung cancer
Boolean networks are powerful frameworks for capturing the logic of gene-regulatory circuits, yet their combinatorial explosion hampers exhaustive analyses. Here, we present a systematic reduction of a 31-node Boolean model that describes cisplatin- and pemetrexed-resistance in non-small-cell lung cancer to a compact 9-node core that exactly reproduces the original attractor landscape. The streamlined network shrinks the state space by four orders of magnitude, enabling rapid exploration of cri…

Just finished "Lunar New Year Love Story" written by Gene Luen Yang and illustrated by LeUyen Pham. Despite having just written a big thread about what media get wrong about love and finding a share of those same issues here, I enjoyed it a lot. I've been reading a lot of romance these days and it's got above-average advice, plus lovely illustrations and a mix of interesting Asian-American cultures.
#AmReading

"Ndebele, who is from Zimbabwe, noted that most of the people opposed to the elimination of the mosquitoes “are not based in Africa.” "
https://www.washingtonp…

We finally may be able to rid the world of mosquitoes. But should we?
Gene editing holds the potential of suppressing mosquito species that carry deadly diseases — and raises ethical questions.

Yes, I'm #ActuallyAutistic!
Did you know that mutations in the SETD5 gene are associated with a rare neurodevelopmental disorder? This condition often includes features like intellectual disability, autism spectrum disorder (ASD), and facial dysmorphism.
There are only about 250 people worldwide with this specific genetic change, and I’m one of them! I’m here, I’m th…

🪴 New 'gene gun' design boosts efficiency of plant genetic modification
#plants

New 'gene gun' design boosts efficiency of plant genetic modification
Plant scientists have used a standard "gene gun" since 1988 to genetically modify crops for better yield, nutrition, pest resistance and other valuable traits.

Replaced article(s) found for q-bio.PE. https://arxiv.org/list/q-bio.PE/new
[1/1]:
- A minimal model of pan-immunity maintenance by horizontal gene transfer in the ecological dynamic...
Wenping Cui, Jemma M. Fendley, Sriram Srikant, Boris Shraiman

🇺🇦 #NowPlaying on BBCRadio3's #ClassicalMixtape
Florence Price, Er-Gene Kahng, Janščkova filharmonie Ostrava & Ryan Cockerham:
🎵 Violin Concerto No 1 in D Major: II Andante
#FlorencePrice #ErGeneKahng #RyanCockerham
#Spotify

Bevan M. French (1937-2025) :: Meteoritical Society
Bevan worked on impact science "at a time when impacts on the Earth were not considered mainstream – or even possible." #geology
https://meteo…

Bevan M. French (1937-2025)
Bevan French is most widely known for his pioneering work in planetary science and the field of impact cratering. He was one of the early workers on terrestrial impact materials along with Gene Shoemaker, Nick Short, Richard Grieve, Dieter Stöffler, Ed Chao, and others, at a time when impacts on the Earth were not considered mainstream – or even possible. Throughout his career Bevan was a champion for impact science, particularly centered on petrography, and geologic observations at terrestr…

Characterizing control between interacting subsystems with deep Jacobian estimation
Adam J. Eisen, Mitchell Ostrow, Sarthak Chandra, Leo Kozachkov, Earl K. Miller, Ila R. Fiete
https://arxiv.org/abs/2507.01946

Characterizing control between interacting subsystems with deep Jacobian estimation
Biological function arises through the dynamical interactions of multiple subsystems, including those between brain areas, within gene regulatory networks, and more. A common approach to understanding these systems is to model the dynamics of each subsystem and characterize communication between them. An alternative approach is through the lens of control theory: how the subsystems control one another. This approach involves inferring the directionality, strength, and contextual modulation of c…

Kolmogorov-Arnold Network for Gene Regulatory Network Inference
Tsz Pan Tong, Aoran Wang, George Panagopoulos, Jun Pang
https://arxiv.org/abs/2506.13740 ht…

Kolmogorov-Arnold Network for Gene Regulatory Network Inference
Gene regulation is central to understanding cellular processes and development, potentially leading to the discovery of new treatments for diseases and personalized medicine. Inferring gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data presents significant challenges due to its high dimensionality and complexity. Existing tree-based models, such as GENIE3 and GRNBOOST2, demonstrated scalability and explainability in GRN inference, but they cannot distinguish regula…

Unrolling Nonconvex Graph Total Variation for Image Denoising
Songlin Wei, Gene Cheung, Fei Chen, Ivan Selesnick
https://arxiv.org/abs/2506.02381 https://

Unrolling Nonconvex Graph Total Variation for Image Denoising
Conventional model-based image denoising optimizations employ convex regularization terms, such as total variation (TV) that convexifies the $\ell_0$-norm to promote sparse signal representation. Instead, we propose a new non-convex total variation term in a graph setting (NC-GTV), such that when combined with an $\ell_2$-norm fidelity term for denoising, leads to a convex objective with no extraneous local minima. We define NC-GTV using a new graph variant of the Huber function, interpretable …

Efficient Learning of Balanced Signed Graphs via Sparse Linear Programming
Haruki Yokota, Hiroshi Higashi, Yuichi Tanaka, Gene Cheung
https://arxiv.org/abs/2506.01826

Efficient Learning of Balanced Signed Graphs via Sparse Linear Programming
Signed graphs are equipped with both positive and negative edge weights, encoding pairwise correlations as well as anti-correlations in data. A balanced signed graph is a signed graph with no cycles containing an odd number of negative edges. Laplacian of a balanced signed graph has eigenvectors that map via a simple linear transform to ones in a corresponding positive graph Laplacian, thus enabling reuse of spectral filtering tools designed for positive graphs. We propose an efficient method t…

Gene Wilder's bizarre comedic genius no longer graces Earth, but he was born today (June 11) in 1933.

Consumer Beware! Exploring Data Brokers' CCPA Compliance
Elina van Kempen, Isita Bagayatkar, Pavel Frolikov, Chloe Georgiou, Gene Tsudik
https://arxiv.org/abs/2506.21914

Consumer Beware! Exploring Data Brokers' CCPA Compliance
Data brokers collect and sell the personal information of millions of individuals, often without their knowledge or consent. The California Consumer Privacy Act (CCPA) grants consumers the legal right to request access to, or deletion of, their data. To facilitate these requests, California maintains an official registry of data brokers. However, the extent to which these entities comply with the law is unclear. This paper presents the first large-scale, systematic study of CCPA compliance of…

genetic_multiplex: Multiplex genetic interactions (2014)
Multiplex networks representing different types of genetic interactions, for different organisms. Layers represent (i) physical, (ii) association, (iii) co-localization, (iv) direct, and (v) suppressive, (vi) additive or synthetic genetic interaction. Edge direction (i,j) indicates gene i interacting with gene j.
This network has 325 nodes and 322 edges.
Tags: Biological, Gene regulation, Protein interactions, Unweigh…

KINDLE: Knowledge-Guided Distillation for Prior-Free Gene Regulatory Network Inference
Rui Peng, Yuchen Lu, Qichen Sun, Yuxing Lu, Chi Zhang, Ziru Liu, Jinzhuo Wang
https://arxiv.org/abs/2505.09664

KINDLE: Knowledge-Guided Distillation for Prior-Free Gene Regulatory Network Inference
Gene regulatory network (GRN) inference serves as a cornerstone for deciphering cellular decision-making processes. Early approaches rely exclusively on gene expression data, thus their predictive power remain fundamentally constrained by the vast combinatorial space of potential gene-gene interactions. Subsequent methods integrate prior knowledge to mitigate this challenge by restricting the solution space to biologically plausible interactions. However, we argue that the effectiveness of thes…

Efficient inference of dynamic gene regulatory networks using discrete penalty
Visweswaran Ravikumar, Aaresh Bhathena, Wajd N Al-Holou, Salar Fattahi, Arvind Rao
https://arxiv.org/abs/2507.23106

Efficient inference of dynamic gene regulatory networks using discrete penalty
Gene regulatory networks (GRNs) orchestrate cellular decision making and survival strategies. Inferring the structure of these networks from high-dimensional transcriptomics data is a central challenge in systems biology. Traditional approaches to GRN inference, such as the graphical lasso and its joint extensions, rely on $\ell_1$ penalty to induce sparsity but can bias network recovery and require extensive hyperparameter tuning. Here, we present a scalable framework for the joint inference o…

A Novel cVAE-Augmented Deep Learning Framework for Pan-Cancer RNA-Seq Classification
Vinil Polepalli
https://arxiv.org/abs/2508.02743 https://arxiv.org/pdf…

A Novel cVAE-Augmented Deep Learning Framework for Pan-Cancer RNA-Seq Classification
Pan-cancer classification using transcriptomic (RNA-Seq) data can inform tumor subtyping and therapy selection, but is challenging due to extremely high dimensionality and limited sample sizes. In this study, we propose a novel deep learning framework that uses a class-conditional variational autoencoder (cVAE) to augment training data for pan-cancer gene expression classification. Using 801 tumor RNA-Seq samples spanning 5 cancer types from The Cancer Genome Atlas (TCGA), we first perform feat…

Day 1: Gene starts thread asking why his Thunderbird looks weird.
https://lists.debian.org/msgid-search/acb28fa6-4521-4848-ae20-7fc5b5b72a76@shentel.net
Day 3, 32 mails in: Gene works out which desktop environment he is using.

Classifying Hotspots Mutations for Biosimulation with Quantum Neural Networks and Variational Quantum Eigensolver
Don Roosan, Rubayat Khan, Saif Nirzhor, Tiffany Khou, Fahmida Hai
https://arxiv.org/abs/2507.00072

Classifying Hotspots Mutations for Biosimulation with Quantum Neural Networks and Variational Quantum Eigensolver
The rapid expansion of biomolecular datasets presents significant challenges for computational biology. Quantum computing emerges as a promising solution to address these complexities. This study introduces a novel quantum framework for analyzing TART-T and TART-C gene data by integrating genomic and structural information. Leveraging a Quantum Neural Network (QNN), we classify hotspot mutations, utilizing quantum superposition to uncover intricate relationships within the data. Additionally, a…

UTA and Michael Kassan reach a settlement with undisclosed terms, after a year of legal battles stemming from Kassan's departure from the agency (Gene Maddaus/Variety)
https://variety.com/2025/biz/news/michael-kassan-uta-settlement-1236475716/
…

Michael Kassan and UTA Settle Differences After Explosive Breakup
Michael Kassan and UTA have settled their litigation, a year after Kassan's departure from the company ignited a firestorm.

If Gene Simmons and Jon Hamm were trapped in an elevator, I wonder if they would compare.

Improving statistical learning methods via features selection without replacement sampling and random projection
Sulaiman khan, Muhammad Ahmad, Fida Ullah, Carlos Aguilar Iba\~nez, Jos\'e Eduardo Valdez Rodriguez
https://arxiv.org/abs/2506.00053

Improving statistical learning methods via features selection without replacement sampling and random projection
Cancer is fundamentally a genetic disease characterized by genetic and epigenetic alterations that disrupt normal gene expression, leading to uncontrolled cell growth and metastasis. High-dimensional microarray datasets pose challenges for classification models due to the "small n, large p" problem, resulting in overfitting. This study makes three different key contributions: 1) we propose a machine learning-based approach integrating the Feature Selection Without Re-placement (FSWOR) technique…

Gerade die erste Folge "For all Mankind" gesehen. Wenn man ein paar NASA-Biografien gelesen hat, z.B. von Gene Kranz und Michael Collins, kommen einem ein paar Stellen ziemlich vertraut vor. 😀

genetic_multiplex: Multiplex genetic interactions (2014)
Multiplex networks representing different types of genetic interactions, for different organisms. Layers represent (i) physical, (ii) association, (iii) co-localization, (iv) direct, and (v) suppressive, (vi) additive or synthetic genetic interaction. Edge direction (i,j) indicates gene i interacting with gene j.
This network has 18222 nodes and 170899 edges.
Tags: Biological, Gene regulation, Protein interactions, Un…

What’s rare about that cub is that it lives near a highway in BC, which isn’t exactly covered with roads.
(The blonde fur gives them an edge in salmon fishing so a recessive gene has a solid foothold in coastal BC.) https://flipboard.com/@cbcnews/techn…

Rare spirit bear cub living near B.C. highway stirs excitement, concern, as word of its existence spreads
Shelley Lindaas has long dreamed of seeing a Kermode bear cub in person. An amateur wildlife photographer based in Terrace, near B.C.'s north coast, …

Been making noise in Reason, and animating in Blender and After Effects.
Just an artifact of my ongoing growth and progress - about a minute long.
I didn't intend it to sound like the B-52's, but ended up sounding something like they would sound if Gene Belcher (Son of Bob) joined the band.
#noAI #reason

More Efficient Real-Valued Gray-Box Optimization through Incremental Distribution Estimation in RV-GOMEA
Renzo J. Scholman, Tanja Alderliesten, Peter A. N. Bosman
https://arxiv.org/abs/2506.23738

More Efficient Real-Valued Gray-Box Optimization through Incremental Distribution Estimation in RV-GOMEA
The Gene-pool Optimal Mixing EA (GOMEA) family of EAs offers a specific means to exploit problem-specific knowledge through linkage learning, i.e., inter-variable dependency detection, expressed using subsets of variables, that should undergo joint variation. Such knowledge can be exploited if faster fitness evaluations are possible when only a few variables are changed in a solution, enabling large speed-ups. The recent-most version of Real-Valued GOMEA (RV-GOMEA) can learn a conditional linka…

A Topology-Based Machine Learning Model Decisively Outperforms Flux Balance Analysis in Predicting Metabolic Gene Essentiality
Justin Boone
https://arxiv.org/abs/2507.20406 http…

A Topology-Based Machine Learning Model Decisively Outperforms Flux Balance Analysis in Predicting Metabolic Gene Essentiality
Background: The rational identification of essential genes is a cornerstone of drug discov- ery, yet standard computational methods like Flux Balance Analysis (FBA) often struggle to produce accurate predictions in complex, redundant metabolic networks. Hypothesis: We hypothesized that the topological structure of a metabolic network con- tains a more robust predictive signal for essentiality than functional simulations alone. Methodology: To test this hypothesis, we developed a machine learnin…

GenDMR: A dynamic multimodal role-swapping network for identifying risk gene phenotypes
Lina Qin, Cheng Zhu, Chuqi Zhou, Yukun Huang, Jiayi Zhu, Ping Liang, Jinju Wang, Yixing Huang, Cheng Luo, Dezhong Yao, Ying Tan
https://arxiv.org/abs/2506.01456

GenDMR: A dynamic multimodal role-swapping network for identifying risk gene phenotypes
Recent studies have shown that integrating multimodal data fusion techniques for imaging and genetic features is beneficial for the etiological analysis and predictive diagnosis of Alzheimer's disease (AD). However, there are several critical flaws in current deep learning methods. Firstly, there has been insufficient discussion and exploration regarding the selection and encoding of genetic information. Secondly, due to the significantly superior classification value of AD imaging features com…

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.

Optimizing information transmission in the canonical Wnt pathway
Olivier Witteveen, Samuel J. Rosen, Ryan S. Lach, Maxwell Z. Wilson, Marianne Bauer
https://arxiv.org/abs/2506.22633

Optimizing information transmission in the canonical Wnt pathway
Populations of cells regulate gene expression in response to external signals, but their ability to make reliable collective decisions is limited by both intrinsic noise in molecular signaling and variability between individual cells. In this work, we use optogenetic control of the canonical Wnt pathway as an example to study how reliably information about an external signal is transmitted to a population of cells, and determine an optimal encoding strategy to maximize information transmission …

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 423 nodes and 578 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

California legislature approves increasing the annual film and TV production tax credit cap from $330M to $750M, following months of lobbying from Hollywood (Gene Maddaus/Variety)
https://variety.com/2025/film/news/california-750-mill…

California Legislators Approve $750 Million Film Tax Credit
California lawmakers passed an dramatic expansion of the film tax credit from $330 million to $750 million.

Harnessing Diet and Gene Expression Insights through a Centralized Nutrigenomics Database to Improve Public Health
Fahmida Hai, Shriya Samudrala, Ijeoma Ezengwa, Rubayat Khan, Saif Nirzhor, Don Roosan
https://arxiv.org/abs/2506.19093

Harnessing Diet and Gene Expression Insights through a Centralized Nutrigenomics Database to Improve Public Health
Nutrigenomics is an emerging field that explores the intricate interaction between genes and diet. This study aimed to develop a comprehensive database to help clinicians and patients understand the connections between genetic disorders, associated genes, and tailored nutritional recommendations.

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 423 nodes and 578 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

Nullstrap-DE: A General Framework for Calibrating FDR and Preserving Power in DE Methods, with Applications to DESeq2 and edgeR
Chenxin Jiang, Changhu Wang, Jingyi Jessica Li
https://arxiv.org/abs/2507.20598

Nullstrap-DE: A General Framework for Calibrating FDR and Preserving Power in DE Methods, with Applications to DESeq2 and edgeR
Differential expression (DE) analysis is a key task in RNA-seq studies, aiming to identify genes with expression differences across conditions. A central challenge is balancing false discovery rate (FDR) control with statistical power. Parametric methods such as DESeq2 and edgeR achieve high power by modeling gene-level counts using negative binomial distributions and applying empirical Bayes shrinkage. However, these methods may suffer from FDR inflation when model assumptions are mildly viola…

I guess Gene Simmons is an old lecher now.

Five-Gene Expression Formula Accurately Detects Hepatocellular Carcinoma Tumors
Aram Ansary Ogholbake, Qiang Cheng
https://arxiv.org/abs/2507.00154 https:/…

Five-Gene Expression Formula Accurately Detects Hepatocellular Carcinoma Tumors
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Several diagnostic methods, such as imaging modalities and Serum Alpha-Fetoprotein (AFP) testing, have been used for HCC detection; however, their effectiveness is limited to later stages of the disease. In contrast, transcriptomic analysis of biposy samples has shown promise for early detection. While machine learning techniques have been applied to transcriptomic data for cancer detection, their cl…

ST-DAI: Single-shot 2.5D Spatial Transcriptomics with Intra-Sample Domain Adaptive Imputation for Cost-efficient 3D Reconstruction
Jiahe Qian, Yaoyu Fang, Xinkun Wang, Lee A. Cooper, Bo Zhou
https://arxiv.org/abs/2507.21516

ST-DAI: Single-shot 2.5D Spatial Transcriptomics with Intra-Sample Domain Adaptive Imputation for Cost-efficient 3D Reconstruction
For 3D spatial transcriptomics (ST), the high per-section acquisition cost of fully sampling every tissue section remains a significant challenge. Although recent approaches predict gene expression from histology images, these methods require large external datasets, which leads to high-cost and suffers from substantial domain discrepancies that lead to poor generalization on new samples. In this work, we introduce ST-DAI, a single-shot framework for 3D ST that couples a cost-efficient 2.5D sam…

On the interplay between plasma triangularity and micro-tearing turbulence
Alessandro Balestri, Justin Ball, Stefano Coda
https://arxiv.org/abs/2507.20244 https://

On the interplay between plasma triangularity and micro-tearing turbulence
In this work, we study the interplay between triangularity and micro-tearing turbulence using linear and nonlinear flux tube GENE simulations. We consider scenarios with negative and positive triangularity plasma shaping taken from existing tokamaks (TCV, DIII-D, MAST-U and SMART) and EU-DEMO. The study of all these tokamaks reveals a coherent picture. Negative triangularity geometry is more susceptible to micro-tearing modes (MTM), which, when present, make transport much worse than in positiv…

🇺🇦 #NowPlaying on BBCRadio3's #Unclassified
“Blue” Gene Tyranny:
🎵 Music for David White's "33 Yoyo Tricks" Simultaneously with...
#“Blue”GeneTyranny
https://open.spotify.com/track/7uIgg7wpmnFqwXESOLYT1x

genetic_multiplex: Multiplex genetic interactions (2014)
Multiplex networks representing different types of genetic interactions, for different organisms. Layers represent (i) physical, (ii) association, (iii) co-localization, (iv) direct, and (v) suppressive, (vi) additive or synthetic genetic interaction. Edge direction (i,j) indicates gene i interacting with gene j.
This network has 461 nodes and 620 edges.
Tags: Biological, Gene regulation, Protein interactions, Unweigh…

On Saturday I met Freddie greyhound, Mandy greyhound's nephew¹. Mandy passed away in 2021.
Coincidentally both homed by WGW and Freddie now lives a few miles from where Mandy lived her pet life. His human knows Mandy's humans well.
Considering the rather small greyhound gene pool this is not unusual. Mandy's sire has had over 5,000 offspring so far.
#Greyhounds

This https://arxiv.org/abs/2410.21295 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

TRENDY: Gene Regulatory Network Inference Enhanced by Transformer
Gene regulatory networks (GRNs) play a crucial role in the control of cellular functions. Numerous methods have been developed to infer GRNs from gene expression data, including mechanism-based approaches, information-based approaches, and more recent deep learning techniques, the last of which often overlook the underlying gene expression mechanisms. In this work, we introduce TRENDY, a novel GRN inference method that integrates transformer models to enhance the mechanism-based WENDY approach.…

The Pitfalls and Potentials of Adding Gene-invariance to Optimal Mixing
Anton Bouter, Dirk Thierens, Peter A. N. Bosman
https://arxiv.org/abs/2506.15222 ht…

The Pitfalls and Potentials of Adding Gene-invariance to Optimal Mixing
Optimal Mixing (OM) is a variation operator that integrates local search with genetic recombination. EAs with OM are capable of state-of-the-art optimization in discrete spaces, offering significant advantages over classic recombination-based EAs. This success is partly due to high selection pressure that drives rapid convergence. However, this can also negatively impact population diversity, complicating the solving of hierarchical problems, which feature multiple layers of complexity. While t…

California lawmakers approve Gov. Gavin Newsom's plan to increase funding for the state's film and TV tax incentive program from $330M to $750M per year (Gene Maddaus/Variety)
https://variety.com/2025/film/news/california-750-million-fi…

California Lawmakers Agree on $750 Million for Film and TV Credit
California legislative leaders have accepted Gov. Gavin Newsom's proposal to more than double the film and TV credit, in a win for the industry.

Replaced article(s) found for q-bio.PE. https://arxiv.org/list/q-bio.PE/new
[1/1]:
- The gene's eye-view of quantitative genetics
Philibert Courau, Amaury Lambert, Emmanuel Schertzer

genetic_multiplex: Multiplex genetic interactions (2014)
Multiplex networks representing different types of genetic interactions, for different organisms. Layers represent (i) physical, (ii) association, (iii) co-localization, (iv) direct, and (v) suppressive, (vi) additive or synthetic genetic interaction. Edge direction (i,j) indicates gene i interacting with gene j.
This network has 461 nodes and 620 edges.
Tags: Biological, Gene regulation, Protein interactions, Unweigh…

This https://arxiv.org/abs/2503.09605 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

QWENDY: Gene Regulatory Network Inference Enhanced by Large Language Model and Transformer
Knowing gene regulatory networks (GRNs) is important for understanding various biological mechanisms. In this paper, we present a method, QWENDY, that uses single-cell gene expression data measured at four time points to infer GRNs. Based on a linear gene expression model, it solves the transformation for the covariance matrices. Unlike its predecessor WENDY, QWENDY avoids solving a non-convex optimization problem and produces a unique solution. Then we enhance QWENDY by the transformer neural …

🇺🇦 #NowPlaying on BBCRadio3's #Unclassified
“Blue” Gene Tyranny:
🎵 Background Orchestra for a Performance of Back in Texas Again
#“Blue”GeneTyranny
https://open.spotify.com/track/5YUv61oWrYj233iG0XO3CA

Optimizing Particle Transport for Enhanced Confinement in Quasi-Isodynamic Stellarators
A. Ba\~n\'on Navarro, A. Di Siena, F. Jenko, A. Merlo, E. Laude
https://arxiv.org/abs/2507.21003

Optimizing Particle Transport for Enhanced Confinement in Quasi-Isodynamic Stellarators
Despite significant advances in reducing turbulent heat losses, modern quasi-isodynamic (QI) stellarators -- such as Stellaris -- continue to suffer from poor particle confinement, which fundamentally limits their overall performance. Using gyrokinetic simulations within the GENE--Tango framework, we identify suppressed inward thermodiffusion, caused by unfavorable magnetic geometry, as the primary cause. To overcome this limitation, we design a new configuration with a reduced mirror ratio, wh…

genetic_multiplex: Multiplex genetic interactions (2014)
Multiplex networks representing different types of genetic interactions, for different organisms. Layers represent (i) physical, (ii) association, (iii) co-localization, (iv) direct, and (v) suppressive, (vi) additive or synthetic genetic interaction. Edge direction (i,j) indicates gene i interacting with gene j.
This network has 8215 nodes and 43367 edges.
Tags: Biological, Gene regulation, Protein interactions, Unwe…

On Saturday I met Freddie greyhound, Mandy greyhound's nephew¹. Mandy passed away in 2021.
Coincidentally both homed by WGW and Freddie now lives a few miles from where Mandy lived her pet life. His human knows Mandy's humans well.
Considering the rather small greyhound gene pool this is not unusual. Mandy's sire has had over 5,000 offspring so far.
#Greyhounds

This https://arxiv.org/abs/2404.19158 has been replaced.
initial toot: https://mastoxiv.page/@arX…

Protein-DNA Co-condensation is Prewetting to a Collapsed Polymer
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with particular sequences of DNA. At unphysiological concentrations many of these nuclear proteins can phase-separate in the absence of DNA, and it has been hypothesized that, in vivo, the thermodynamic forces driving these phases help determine chromosomal organizati…

Multi-omic Causal Discovery using Genotypes and Gene Expression
Stephen Asiedu, David Watson
https://arxiv.org/abs/2505.15866 https://

Multi-omic Causal Discovery using Genotypes and Gene Expression
Causal discovery in multi-omic datasets is crucial for understanding the bigger picture of gene regulatory mechanisms, but remains challenging due to high dimensionality, differentiation of direct from indirect relationships, and hidden confounders. We introduce GENESIS (GEne Network inference from Expression SIgnals and SNPs), a constraint-based algorithm that leverages the natural causal precedence of genotypes to infer ancestral relationships in transcriptomic data. Unlike traditional causal…

SPATIA: Multimodal Model for Prediction and Generation of Spatial Cell Phenotypes
Zhenglun Kong, Mufan Qiu, John Boesen, Xiang Lin, Sukwon Yun, Tianlong Chen, Manolis Kellis, Marinka Zitnik
https://arxiv.org/abs/2507.04704

SPATIA: Multimodal Model for Prediction and Generation of Spatial Cell Phenotypes
Understanding how cellular morphology, gene expression, and spatial organization jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell images and gene expression profiles, but machine learning methods typically analyze these modalities in isolation or at limited resolution. We address the problem of learning unified, spatially aware representations that integrate cell morphology, gene ex…

ComiXology veterans David Steinberger and Chip Mosher unveil Neon Ichiban, a digital comic book store to rival Amazon, launching next month after raising $7M (George Gene Gustines/New York Times)
https://www.nytimes.com/2025/06/19/business/…

New Digital Comics Store Takes Aim at Amazon
Two veterans of Comixology, a site that the e-commerce colossus bought in 2014, are now starting a rival to compete with it.

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 424 nodes and 577 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

🇺🇦 #NowPlaying on BBCRadio3's #RoundMidnight
Gene Ammons:
🎵 Blue Ammons
#GeneAmmons
https://open.spotify.com/track/1RdxYYiobKTRUQ8xS26PE7

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 424 nodes and 577 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

Localizing synergies of hidden factors across complex systems: resting brain networks and HeLa gene expression profile as case studies
Marlis Ontivero-Ortega, Gorana Mijatovic, Luca Faes, Daniele Marinazzo, Sebastiano Stramaglia
https://arxiv.org/abs/2506.09053

Localizing synergies of hidden factors across complex systems: resting brain networks and HeLa gene expression profile as case studies
Factor analysis is a well-known statistical method to describe the variability of observed variables in terms of a smaller number of unobserved latent variables called factors. Even though latent factors are conceptually independent of each other, their influence on the observed variables is often joint and synergistic. We propose to quantify the synergy of the joint influence of factors on the observed variables using the O-information, a recently introduced metrics to assess high order depend…

The US Senate votes narrowly early Thursday morning to strip $1.1B in funding from the CPB, in a severe blow to 1,500 local TV and radio stations, PBS, and NPR (Gene Maddaus/Variety)
https://variety.com/2025/politics/news/senate-strips-billion-pub…

Senate Strips $1.1 Billion From Public Broadcasting
The Senate voted early Thursday to strip $1.1 billion in funding from the Corporation for Public Broadcasting, in a severe blow to NPR and PBS.

Brain-wide interpolation and conditioning of gene expression in the human brain using Implicit Neural Representations
Xizheng Yu, Justin Torok, Sneha Pandya, Sourav Pal, Vikas Singh, Ashish Raj
https://arxiv.org/abs/2506.11158

Brain-wide interpolation and conditioning of gene expression in the human brain using Implicit Neural Representations
In this paper, we study the efficacy and utility of recent advances in non-local, non-linear image interpolation and extrapolation algorithms, specifically, ideas based on Implicit Neural Representations (INR), as a tool for analysis of spatial transcriptomics data. We seek to utilize the microarray gene expression data sparsely sampled in the healthy human brain, and produce fully resolved spatial maps of any given gene across the whole brain at a voxel-level resolution. To do so, we first obt…

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 424 nodes and 577 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 424 nodes and 577 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

Replaced article(s) found for q-bio.GN. https://arxiv.org/list/q-bio.GN/new
[1/1]:
- GenoMAS: A Multi-Agent Framework for Scientific Discovery via Code-Driven Gene Expression Analysis
Haoyang Liu, Yijiang Li, Haohan Wang

A US federal judge dismisses Justin Baldoni's $400M defamation claim against Blake Lively, finding Lively's sexual harassment claims were legally protected (Gene Maddaus/Variety)
https://variety.com/2025/film/news/jud

Judge Tosses Justin Baldoni's $400 Million Suit Against Blake Lively
A judge on Monday threw out the $400 million defamation suit filed by Justin Baldoni against Blake Lively.

Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN
Mohammad Saleh Refahi, Gavin Hearne, Harrison Muller, Kieran Lynch, Bahrad A. Sokhansanj, James R. Brown, Gail Rosen
https://arxiv.org/abs/2507.16978

Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN
The exponential growth of DNA sequencing data has outpaced traditional heuristic-based methods, which struggle to scale effectively. Efficient computational approaches are urgently needed to support large-scale similarity search, a foundational task in bioinformatics for detecting homology, functional similarity, and novelty among genomic and proteomic sequences. Although tools like BLAST have been widely used and remain effective in many scenarios, they suffer from limitations such as high com…

yeast_transcription: Yeast transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the yeast Saccharomyces cerevisiae.
This network has 916 nodes and 1094 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.sk…

DeepPlantCRE: A Transformer-CNN Hybrid Framework for Plant Gene Expression Modeling and Cross-Species Generalization
Yingjun Wu, Jingyun Huang, Liang Ming, Pengcheng Deng, Maojun Wang, Zeyu Zhang
https://arxiv.org/abs/2505.09883

DeepPlantCRE: A Transformer-CNN Hybrid Framework for Plant Gene Expression Modeling and Cross-Species Generalization
The investigation of plant transcriptional regulation constitutes a fundamental basis for crop breeding, where cis-regulatory elements (CREs), as the key factor determining gene expression, have become the focus of crop genetic improvement research. Deep learning techniques, leveraging their exceptional capacity for high-dimensional feature extraction and nonlinear regulatory relationship modeling, have been extensively employed in this field. However, current methodologies present notable limi…

yeast_transcription: Yeast transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the yeast Saccharomyces cerevisiae.
This network has 916 nodes and 1094 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.sk…

Modeling Gene Expression Distributional Shifts for Unseen Genetic Perturbations
Kalyan Ramakrishnan, Jonathan G. Hedley, Sisi Qu, Puneet K. Dokania, Philip H. S. Torr, Cesar A. Prada-Medina, Julien Fauqueur, Kaspar Martens
https://arxiv.org/abs/2507.02980

Modeling Gene Expression Distributional Shifts for Unseen Genetic Perturbations
We train a neural network to predict distributional responses in gene expression following genetic perturbations. This is an essential task in early-stage drug discovery, where such responses can offer insights into gene function and inform target identification. Existing methods only predict changes in the mean expression, overlooking stochasticity inherent in single-cell data. In contrast, we offer a more realistic view of cellular responses by modeling expression distributions. Our model pre…

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 423 nodes and 578 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…