Genomics

Authors and titles for May 2025

[1] arXiv:2505.00572 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: A Bioinformatic Study of Genetics Involved in Determining Mild Traumatic Brain Injury Severity and Recovery Show Chinese title

Title: 生物信息学研究参与轻度创伤性脑损伤严重程度和恢复的遗传因素

Mahnaz Tajik, Michael D Noseworthy

Comments: This paper consists of 43 pages, including references. It contains seven figures and four tables. Details regarding coding and analysis are available upon request

Subjects: Genomics (q-bio.GN) ; Neurons and Cognition (q-bio.NC)

[2] arXiv:2505.01696 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking Show Chinese title

Title: 基于图的可解释模型在多模态生物医学数据整合中的应用：技术综述与基准测试

Alireza Sadeghi, Farshid Hajati, Ahmadreza Argha, Nigel H Lovell, Min Yang, Hamid Alinejad-Rokny

Comments: 41 pages

Subjects: Genomics (q-bio.GN) ; Artificial Intelligence (cs.AI)

[3] arXiv:2505.03377 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: Gene finding revisited: improved robustness through structured decoding from learned embeddings Show Chinese title

Title: 基因识别再访：通过从学习到的嵌入结构解码提高鲁棒性

Frederikke I. Marin, Dennis Pultz, Wouter Boomsma

Comments: 8 pages, 3 figures, 2 tables

Subjects: Genomics (q-bio.GN)

[4] arXiv:2505.06127 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: FastDup: a scalable duplicate marking tool using speculation-and-test mechanism Show Chinese title

Title: FastDup：一种使用推测与测试机制的可扩展重复标记工具

Zhonghai Zhang, Yewen Li, Ke Meng, Chunming Zhang, Guangming Tan

Comments: 4 pages, 1 figure

Subjects: Genomics (q-bio.GN)

[5] arXiv:2505.07740 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Pan-genome Analysis of Plastomes from Lamiales using PGR-TK Show Chinese title

Title: 使用PGR-TK分析唇形目叶绿体基因组的泛基因组分析

Aadhavan Veerendra, Manoj Samanta

Subjects: Genomics (q-bio.GN) ; Populations and Evolution (q-bio.PE)

[6] arXiv:2505.07896 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: Bridging Large Language Models and Single-Cell Transcriptomics in Dissecting Selective Motor Neuron Vulnerability Show Chinese title

Title: 大型语言模型与单细胞转录组学在解析选择性运动神经元脆弱性的结合

Douglas Jiang, Zilin Dai, Luxuan Zhang, Qiyi Yu, Haoqi Sun, Feng Tian

Subjects: Genomics (q-bio.GN) ; Artificial Intelligence (cs.AI)

[7] arXiv:2505.07919 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: Revolutionising Bacterial Genomics: Graph-Based Strategies for Improved Variant Identification Show Chinese title

Title: 革新细菌基因组学：改进变异识别的图基策略

Fathima Nuzla Ismail, Abira Sengupta

Subjects: Genomics (q-bio.GN)

[8] arXiv:2505.08764 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: The Environment-Dependent Regulatory Landscape of the E. coli Genome Show Chinese title

Title: 大肠杆菌基因组的环境依赖性调控图谱

Tom Röschinger, Heun Jin Lee, Rosalind Wenshan Pan, Grace Solini, Kian Faizi, Baiyi Quan, Tsui Fen Chou, Madhav Mani, Stephen Quake, Rob Phillips

Subjects: Genomics (q-bio.GN) ; Molecular Networks (q-bio.MN)

[9] arXiv:2505.08844 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: CellTypeAgent: Trustworthy cell type annotation with Large Language Models Show Chinese title

Title: CellTypeAgent：使用大语言模型的可信细胞类型注释

Jiawen Chen, Jianghao Zhang, Huaxiu Yao, Yun Li

Subjects: Genomics (q-bio.GN) ; Artificial Intelligence (cs.AI)

[10] arXiv:2505.08918 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: When repeats drive the vocabulary: a Byte-Pair Encoding analysis of T2T primate genomes Show Chinese title

Title: 当重复驱动词汇时：基于Byte-Pair Encoding的T2T灵长类基因组分析

Marina Popova, Iaroslav Chelombitko, Aleksey Komissarov

Comments: ICLR 2025 Workshop on Machine Learning for Genomics Explorations

Subjects: Genomics (q-bio.GN) ; Artificial Intelligence (cs.AI)

[11] arXiv:2505.09873 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: Deep Learning and Explainable AI: New Pathways to Genetic Insights Show Chinese title

Title: 深度学习与可解释人工智能：通往遗传学新见解的新路径

Chenyu Wang, Chaoying Zuo, Zihan Su, Yuhang Xing, Lu Li, Maojun Wang, Zeyu Zhang

Subjects: Genomics (q-bio.GN)

[12] arXiv:2505.09883 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: DeepPlantCRE: A Transformer-CNN Hybrid Framework for Plant Gene Expression Modeling and Cross-Species Generalization Show Chinese title

Title: DeepPlantCRE：一种用于植物基因表达建模和跨物种泛化的Transformer-CNN混合框架

Yingjun Wu, Jingyun Huang, Liang Ming, Pengcheng Deng, Maojun Wang, Zeyu Zhang

Subjects: Genomics (q-bio.GN)

[13] arXiv:2505.11041 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: In silico tool for identification of colorectal cancer from cell-free DNA biomarkers Show Chinese title

Title: 用于识别结直肠癌的细胞游离DNA生物标志物的计算机模拟工具

Kartavya Mathur (1 and 2), Shipra Jain (1), Nisha Bajiya (1), Nishant Kumar (1), Gajendra P. S. Raghava (1) ((1) Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, (2) School of Biotechnology, Gautam Buddha University, Uttar Pradesh)

Subjects: Genomics (q-bio.GN)

[14] arXiv:2505.11385 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: Compendium Manager: a tool for coordination of workflow management instances for bulk data processing in Python Show Chinese title

Title: Compendium Manager：用于Python中批量数据处理工作流管理实例协调的工具

Richard J. Abdill, Ran Blekhman

Subjects: Genomics (q-bio.GN) ; Software Engineering (cs.SE)

[15] arXiv:2505.12626 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data Show Chinese title

Title: scSiameseClu：一种用于解释单细胞RNA测序数据的孪生聚类框架

Ping Xu, Zhiyuan Ning, Pengjiang Li, Wenhao Liu, Pengyang Wang, Jiaxu Cui, Yuanchun Zhou, Pengfei Wang

Subjects: Genomics (q-bio.GN) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)

[16] arXiv:2505.12638 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data Show Chinese title

Title: ChromFound：面向单细胞染色质可及性数据的通用基础模型

Yifeng Jiao, Yuchen Liu, Yu Zhang, Xin Guo, Yushuai Wu, Chen Jiang, Jiyang Li, Hongwei Zhang, Limei Han, Xin Gao, Yuan Qi, Yuan Cheng

Subjects: Genomics (q-bio.GN) ; Artificial Intelligence (cs.AI) ; Computational Engineering, Finance, and Science (cs.CE) ; Machine Learning (cs.LG)

[17] arXiv:2505.14402 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: OmniGenBench: A Modular Platform for Reproducible Genomic Foundation Models Benchmarking Show Chinese title

Title: OmniGenBench：可重复生成基础模型基准测试的模块化平台

Heng Yang, Jack Cole, Yuan Li, Renzhi Chen, Geyong Min, Ke Li

Subjects: Genomics (q-bio.GN) ; Computation and Language (cs.CL)

[18] arXiv:2505.14725 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: HR-VILAGE-3K3M: A Human Respiratory Viral Immunization Longitudinal Gene Expression Dataset for Systems Immunity Show Chinese title

Title: HR-VILAGE-3K3M：一项人类呼吸系统病毒免疫纵向基因表达数据集用于系统免疫研究

Xuejun Sun, Yiran Song, Xiaochen Zhou, Ruilie Cai, Yu Zhang, Xinyi Li, Rui Peng, Jialiu Xie, Yuanyuan Yan, Muyao Tang, Prem Lakshmanane, Baiming Zou, James S. Hagood, Raymond J. Pickles, Didong Li, Fei Zou, Xiaojing Zheng

Subjects: Genomics (q-bio.GN) ; Machine Learning (cs.LG) ; Applications (stat.AP)

[19] arXiv:2505.15866 (cross-list from q-bio.GN) [cn-pdf, pdf, html, other]

Title: Multi-omic Causal Discovery using Genotypes and Gene Expression Show Chinese title

Title: 多组学因果发现使用基因型和基因表达

Stephen Asiedu, David Watson

Subjects: Genomics (q-bio.GN) ; Machine Learning (cs.LG)

[20] arXiv:2505.20344 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Genetic Influences on Brain Aging: Analyzing Sex Differences in the UK Biobank using Structural MRI Show Chinese title

Title: 遗传因素对大脑老化的影响：利用结构磁共振成像分析UK Biobank中的性别差异

Karen Ardila, Aashka Mohite, Abdoljalil Addeh, Amanda V. Tyndall, Cindy K. Barha, Quan Long, M. Ethan MacDonald

Comments: 7 pages, 5 figures, conference

Journal-ref: International Society for Magnetic Resonance in Medicine, ISMRM Annual Meeting, May 2025

Subjects: Genomics (q-bio.GN) ; Machine Learning (cs.LG)

[21] arXiv:2505.00650 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: OmicsCL: Unsupervised Contrastive Learning for Cancer Subtype Discovery and Survival Stratification Show Chinese title

Title: OmicsCL：无监督对比学习在癌症亚型发现和生存分层中的应用

Atahan Karagoz

Comments: Code available at: https://github.com/Atahanka/OmicsCL

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Genomics (q-bio.GN) ; Quantitative Methods (q-bio.QM)

[22] arXiv:2505.00934 (cross-list from stat.ME) [cn-pdf, pdf, html, other]

Title: Bayesian Forensic DNA Mixture Deconvolution Using a Novel String Similarity Measure Show Chinese title

Title: 贝叶斯法在使用新型字符串相似性度量的DNA混合物解卷积中的法医学应用

Taylor Petty, Jan Hannig, Hari Iyer

Subjects: Methodology (stat.ME) ; Genomics (q-bio.GN) ; Computation (stat.CO)

[23] arXiv:2505.02033 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Quantum-Enhanced Classification of Brain Tumors Using DNA Microarray Gene Expression Profiles Show Chinese title

Title: 基于DNA微阵列表达谱的量子增强脑肿瘤分类

Emine Akpinar, Batuhan Hangun, Murat Oduncuoglu, Oguz Altun, Onder Eyecioglu, Zeynel Yalcin

Subjects: Machine Learning (cs.LG) ; Genomics (q-bio.GN) ; Molecular Networks (q-bio.MN)

[24] arXiv:2505.03853 (cross-list from q-bio.QM) [cn-pdf, pdf, html, other]

Title: GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype Show Chinese title

Title: GRAPE: 遗传扰动的异构图表示学习针对编码和非编码生物类型的遗传扰动

Changxi Chi, Jun Xia, Jingbo Zhou, Jiabei Cheng, Chang Yu, Stan Z. Li

Subjects: Quantitative Methods (q-bio.QM) ; Artificial Intelligence (cs.AI)

[25] arXiv:2505.04431 (cross-list from cs.DC) [cn-pdf, pdf, html, other]

Title: An Asynchronous Distributed-Memory Parallel Algorithm for k-mer Counting Show Chinese title

Title: 一种异步分布式存储器并行算法用于 k-mer 计数

Souvadra Hati, Akihiro Hayashi, Richard Vuduc

Comments: Accepted at IEEE IPDPS 2025 Conference

Subjects: Distributed, Parallel, and Cluster Computing (cs.DC) ; Genomics (q-bio.GN)

[26] arXiv:2505.08071 (cross-list from cs.AR) [cn-pdf, pdf, html, other]

Title: NMP-PaK: Near-Memory Processing Acceleration of Scalable De Novo Genome Assembly Show Chinese title

Title: NMP-PaK：可扩展从头基因组组装的近内存处理加速

Heewoo Kim, Sanjay Sri Vallabh Singapuram, Haojie Ye, Joseph Izraelevitz, Trevor Mudge, Ronald Dreslinski, Nishil Talati

Comments: To be published in ISCA 2025

Subjects: Hardware Architecture (cs.AR) ; Distributed, Parallel, and Cluster Computing (cs.DC) ; Genomics (q-bio.GN)

[27] arXiv:2505.08341 (cross-list from cs.AI) [cn-pdf, pdf, other]

Title: Benchmarking AI scientists in omics data-driven biological research Show Chinese title

Title: 基准测试在组学数据驱动的生物研究中的AI科学家

Erpai Luo, Jinmeng Jia, Yifan Xiong, Xiangyu Li, Xiaobo Guo, Baoqi Yu, Lei Wei, Xuegong Zhang

Subjects: Artificial Intelligence (cs.AI) ; Multiagent Systems (cs.MA) ; Genomics (q-bio.GN)

[28] arXiv:2505.11610 (cross-list from cs.AI) [cn-pdf, pdf, html, other]

Title: Foundation Models for AI-Enabled Biological Design Show Chinese title

Title: 人工智能驱动的生物设计基础模型

Asher Moldwin, Amarda Shehu

Comments: Published as part of the workshop proceedings at AAAI 2025 in the workshop "Foundation Models for Biological Discoveries"

Subjects: Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG) ; Biomolecules (q-bio.BM) ; Genomics (q-bio.GN)

[29] arXiv:2505.13503 (cross-list from stat.ME) [cn-pdf, pdf, other]

Title: Ancestry-Adjusted Polygenic Risk Scores for Predicting Obesity Risk in the Indonesian Population Show Chinese title

Title: 基于祖先调整的多基因风险评分预测印度尼西亚人群肥胖风险

Jocelyn Verna Siswanto, Belinda Mutiara, Felicia Austin, Jonathan Susanto, Cathelyn Theophila Tan, Restu Unggul Kresnadi, Kezia Irene

Comments: 7 pages, 8 figures

Subjects: Methodology (stat.ME) ; Genomics (q-bio.GN)

[30] arXiv:2505.16680 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Learning Genomic Structure from $k$-mers Show Chinese title

Title: 从$k$-mers学习基因组结构

Filip Thor, Carl Nettelblad

Subjects: Machine Learning (cs.LG) ; Genomics (q-bio.GN) ; Quantitative Methods (q-bio.QM)

[31] arXiv:2505.17257 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model Show Chinese title

Title: JanusDNA：一种强大的双向混合DNA基础模型

Qihao Duan, Bingding Huang, Zhenqiao Song, Irina Lehmann, Lei Gu, Roland Eils, Benjamin Wild

Subjects: Machine Learning (cs.LG) ; Genomics (q-bio.GN)

[32] arXiv:2505.19461 (cross-list from cond-mat.soft) [cn-pdf, pdf, other]

Title: Fluctuations in DNA Packing Density Drive the Spatial Segregation between Euchromatin and Heterochromatin Show Chinese title

Title: DNA包装密度的波动驱动常染色质和异染色质的空间分离

Luming Meng, Boping Liu, Qiong Luo

Subjects: Soft Condensed Matter (cond-mat.soft) ; Genomics (q-bio.GN)

[33] arXiv:2505.20578 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: Ctrl-DNA: Controllable Cell-Type-Specific Regulatory DNA Design via Constrained RL Show Chinese title

Title: Ctrl-DNA：基于约束强化学习的可控细胞类型特异性调控DNA设计

Xingyu Chen, Shihao Ma, Runsheng Lin, Jiecong Lin, Bo Wang

Comments: 9 pages, 3 figures

Subjects: Machine Learning (cs.LG) ; Artificial Intelligence (cs.AI) ; Genomics (q-bio.GN)

[34] arXiv:2505.20836 (cross-list from cs.LG) [cn-pdf, pdf, html, other]

Title: HAD: Hybrid Architecture Distillation Outperforms Teacher in Genomic Sequence Modeling Show Chinese title

Title: HAD：在基因组序列建模中混合架构蒸馏在教师模型之上表现更优

Hexiong Yang, Mingrui Chen, Huaibo Huang, Junxian Duan, Jie Cao, Zhen Zhou, Ran He

Subjects: Machine Learning (cs.LG) ; Genomics (q-bio.GN)

[35] arXiv:2505.23289 (cross-list from quant-ph) [cn-pdf, pdf, html, other]

Title: Intermediate State Formation of Topologically Associated Chromatin Domains using Quantum Annealing Show Chinese title

Title: 使用量子退火的拓扑关联染色质结构域的中间态形成

Tobias Kempe, S.M. Ali Tabei, Mohammad H. Ansari

Subjects: Quantum Physics (quant-ph) ; Soft Condensed Matter (cond-mat.soft) ; Biological Physics (physics.bio-ph) ; Genomics (q-bio.GN)

[36] arXiv:2505.23839 (cross-list from cs.CR) [cn-pdf, pdf, html, other]

Title: GeneBreaker: Jailbreak Attacks against DNA Language Models with Pathogenicity Guidance Show Chinese title

Title: GeneBreaker：基于致病性指导的DNA语言模型越狱攻击

Zaixi Zhang, Zhenghong Zhou, Ruofan Jin, Le Cong, Mengdi Wang

Subjects: Cryptography and Security (cs.CR) ; Genomics (q-bio.GN)

[37] arXiv:2505.24394 (cross-list from q-bio.BM) [cn-pdf, pdf, other]

Title: Refining Platelet Purification Methods: Enhancing Proteomics for Clinical Applications Show Chinese title

Title: 优化血小板纯化方法：提升临床应用的蛋白质组学研究

Vibecke Markhus, Katarina Fritz-Wallace, Olav Mjaavatten, Einar K. Kristoffersen, Dorota Goplen, Frode Selheim

Subjects: Biomolecules (q-bio.BM) ; Genomics (q-bio.GN)