Genomics

Authors and titles for July 2021

[1] arXiv:2107.00388 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: A Multi-task Deep Feature Selection Method for Brain Imaging Genetics Show Chinese title

Title: 一种多任务深度特征选择方法用于脑成像遗传学

Chenglin Yu, Dingnan Cui, Muheng Shang, Shu Zhang, Lei Guo, Junwei Han, Lei Du, Alzheimer's Disease Neuroimaging Initiative

Subjects: Genomics (q-bio.GN)

[2] arXiv:2107.02935 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Sramm: short read alignment mapping metrics Show Chinese title

Title: Sramm：短读取比对映射指标

Alvin Chon, Xiaoqiu Huang

Comments: 7 pages, 2 figures

Journal-ref: Vol. 11, No.1/2, June 2021

Subjects: Genomics (q-bio.GN)

[3] arXiv:2107.03383 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions Show Chinese title

Title: 在明确的因果假设下，评估从现实世界基因分型数据预测抗菌药物耐药性中的潜在偏差

Mattia Prosperi, Simone Marini, Christina Boucher, Jiang Bian

Comments: In DSHealth '21] Joint KDD 2021 Health Day and 2021 KDD Workshop on Applied Data Science for Healthcare, Aug 14--18, 2021, Virtual, 5 pages

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

[4] arXiv:2107.03611 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Stool Studies Don't Pass the Sniff Test: A Systematic Review of Human Gut Microbiome Research Suggests Widespread Misuse of Machine Learning Show Chinese title

Title: 粪便研究经不起嗅觉测试：一项关于人体肠道微生物组研究的系统综述表明机器学习被广泛误用

Thomas P. Quinn

Subjects: Genomics (q-bio.GN)

[5] arXiv:2107.05397 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Enabling microbiome research on personal devices Show Chinese title

Title: 在个人设备上进行微生物组研究

Igor Sfiligoi, Daniel McDonald, Rob Knight

Comments: 2 pages, 4 figures, to be published in proceedings of eScience 2021

Journal-ref: 2021 IEEE 17th International Conference on eScience (eScience), 2021, pp. 229-230

Subjects: Genomics (q-bio.GN) ; Performance (cs.PF) ; Quantitative Methods (q-bio.QM)

[6] arXiv:2107.10115 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Variant-driven multi-wave pattern of COVID-19 via a Machine Learning analysis of spike protein mutations Show Chinese title

Title: 基于机器学习分析刺突蛋白突变的新冠病毒变异驱动多波次模式

Adele de Hoffer, Shahram Vatani, Corentin Cot, Giacomo Cacciapaglia, Maria Luisa Chiusano, Andrea Cimarelli, Francesco Conventi, Antonio Giannini, Stefan Hohenegger, Francesco Sannino

Comments: 16 pages, 6 figures, supplementary material in a separate file. Analysis extended with early warning performance and spike protein diversification

Subjects: Genomics (q-bio.GN)

[7] arXiv:2107.10901 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: A reinforcement learning approach to resource allocation in genomic selection Show Chinese title

Title: 基于强化学习的基因组选择中的资源分配方法

Saba Moeinizade, Guiping Hu, Lizhi Wang

Comments: 18 pages,5 figures

Subjects: Genomics (q-bio.GN) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG) ; Optimization and Control (math.OC)

[8] arXiv:2107.11192 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Optimal transport-based machine learning to match specific patterns: application to the detection of molecular regulation patterns in omics data Show Chinese title

Title: 基于最优传输的机器学习以匹配特定模式：应用于组学数据中分子调控模式的检测

Thi Thanh Yen Nguyen (MAP5 - UMR 8145), Warith Harchaoui (MAP5 - UMR 8145, <a href="http://DERAISON.ai" rel="external noopener nofollow" class="link-external link-http">this http URL</a>), Lucile Mégret (Brain-C), Cloe Mendoza (B2A), Olivier Bouaziz (MAP5 - UMR 8145), Christian Neri (B2A), Antoine Chambaz (MAP5 - UMR 8145)

Subjects: Genomics (q-bio.GN) ; Statistics Theory (math.ST)

[9] arXiv:2107.11381 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: TargetNet: Functional microRNA Target Prediction with Deep Neural Networks Show Chinese title

Title: TargetNet：使用深度神经网络的功能性微RNA靶点预测

Seonwoo Min, Byunghan Lee, Sungroh Yoon

Comments: This article has been accepted for publication in Bioinformatics published by Oxford University Press

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

[10] arXiv:2107.11458 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Variant interpretation using population databases: lessons from gnomAD Show Chinese title

Title: 使用种群数据库进行变异解释：来自gnomAD的教训

Sanna Gudmundsson, Moriel Singer-Berk, Nicholas A. Watts, William Phu, Julia K. Goodrich, Matthew Solomonson, Genome Aggregation Database Consortium, Heidi L. Rehm, Daniel G. MacArthur, Anne ODonnell-Luria

Comments: Version 3: Includes updates to mirror the latest features and layouts available on the gnomAD browser and general improvements to text and figures (clarifications, typos, additional references etc.) as well as the addition of Table S1, S2, Figure S1, S2 and S5

Subjects: Genomics (q-bio.GN)

[11] arXiv:2107.11856 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Graph Representation Learning on Tissue-Specific Multi-Omics Show Chinese title

Title: 组织特异性多组学图表示学习

Amine Amor (1), Pietro Lio' (1), Vikash Singh (1), Ramon Viñas Torné (1), Helena Andres Terre (1)

Comments: This paper was accepted at the 2021 ICML Workshop on Computational Biology

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

[12] arXiv:2107.12817 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Bam-readcount -- rapid generation of basepair-resolution sequence metrics Show Chinese title

Title: Bam-readcount -- 快速生成碱基对分辨率的序列指标

Ajay Khanna, David E. Larson, Sridhar Nonavinkere Srivatsan, Matthew Mosior, Travis E. Abbott, Susanna Kiwala, Timothy J. Ley, Eric J. Duncavage, Matthew J. Walter, Jason R. Walker, Obi L. Griffith, Malachi Griffith, Christopher A. Miller

Subjects: Genomics (q-bio.GN)

[13] arXiv:2107.13247 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: OncoEnrichR: cancer-dedicated gene set interpretation Show Chinese title

Title: OncoEnrichR：癌症专用基因集解释

Sigve Nakken (1 and 2 and 3), Sveinung Gundersen (3), Fabian L. M. Bernal (4), Dimitris Polychronopoulos (5), Eivind Hovig (1 and 3), Jørgen Wesche (1 and 2) ((1) Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Norway, (2) Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway, (3) Centre for Bioinformatics, Department of Informatics, University of Oslo, Norway, (4) University Center for Information Technology, University of Oslo, Norway, (5) Early Data Science and Computational Oncology, Research and Early Development, Oncology R&amp;D, Cambridge, UK)

Subjects: Genomics (q-bio.GN)

[14] arXiv:2107.13537 (cross-list from q-bio.GN) [cn-pdf, pdf, other]

Title: Abordagem probabilística para análise de confiabilidade de dados gerados em sequenciamentos multiplex na plataforma ABI SOLiD Show Chinese title

Title: 基于概率的方法用于分析在ABI SOLiD平台上生成的多重测序数据的可靠性

Fabio M. F. Lobato, Carlos D. N. Damasceno, Péricles L. Machado, Nandamudi L. Vijaykumar, André R. dos Santos, Sylvain H. Darnet, André N. A. Gonçalves, Dayse O. de Alencar, Ádamo L. de Santana

Comments: 8 pages, 4 figures, 2 tables, Published in Portuguese in the Anais of the XLIII Simp\'osio Brasileiro de Pesquisa Operacional (SBPO 2011), 2011. URL: http://www.din.uem.br/sbpo/sbpo2011/pdf/87903.pdf

Subjects: Genomics (q-bio.GN) ; Computational Engineering, Finance, and Science (cs.CE)

[15] arXiv:2107.00648 (cross-list from cs.CV) [cn-pdf, pdf, other]

Title: Deep Orthogonal Fusion: Multimodal Prognostic Biomarker Discovery Integrating Radiology, Pathology, Genomic, and Clinical Data Show Chinese title

Title: 深度正交融合：整合影像学、病理学、基因组学和临床数据的多模态预后生物标志物发现

Nathaniel Braman, Jacob W. H. Gordon, Emery T. Goossens, Caleb Willis, Martin C. Stumpe, Jagadish Venkataraman

Comments: Accepted for presentation at MICCAI 2021

Subjects: Computer Vision and Pattern Recognition (cs.CV) ; Machine Learning (cs.LG) ; Multimedia (cs.MM) ; Genomics (q-bio.GN) ; Quantitative Methods (q-bio.QM)

[16] arXiv:2107.08010 (cross-list from q-bio.PE) [cn-pdf, pdf, other]

Title: Strong, recent selective sweeps reshape genetic diversity in freshwater bivalve Megalonaias nervosa Show Chinese title

Title: 强而近期的定向选择扫荡重塑了淡水双壳类Megalonaias nervosa的遗传多样性

Rebekah L. Rogers, Stephanie L. Grizzard, Jeffrey T. Garner

Comments: 7 figures, 6 supplementary tables, 21 supplementary figures. 60 pages total

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

[17] arXiv:2107.09883 (cross-list from cs.LG) [cn-pdf, pdf, other]

Title: MG-NET: Leveraging Pseudo-Imaging for Multi-Modal Metagenome Analysis Show Chinese title

Title: MG-NET：利用伪成像进行多模态宏基因组分析

Sathyanarayanan N. Aakur, Sai Narayanan, Vineela Indla, Arunkumar Bagavathi, Vishalini Laguduva Ramnath, Akhilesh Ramachandran

Comments: To appear in MICCAI 2021

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