Dealing with noise and biases in omics: statistical methods, deep learning and workflows

Authors: Jin Wu, Suzanne

Thesis Advisors: Notredame, Cedric

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Transcriptomic analysis, Noise and biases, Normalization, Deep learning, Differential abundance, Gene-gene correlation, Compositional bias, Bioinformatics, Pipelines

File Description: application/pdf

Access URL: https://hdl.handle.net/10803/696721

Endothelial dysfunction in chronic thromboembolic pulmonary hypertension: a comprehensive study of molecular, functional, and metabolic alterations

Authors: Peracaula Domínguez, Míriam

Contributors: University/Department: Universitat de Girona. Departament de Ciències Mèdiques

Thesis Advisors: Tura-Ceide, Olga, Vert Company, Anna, Ramos Blanes, Rafel

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Hipertensió pulmonar tromboembòlica crònica, Hipertensión pulmonar tromboembólica crónica, Chronic thromboembolic pulmonary hypertension, Disfunció endotelial, Disfunción endotelial, Endothelial dysfunction, Cèl·lules endotelials, Células endoteliales, Endothelial cells, Alteració sistèmica, Alteración sistémica, Systemic alteration, Remodelatge del citoesquelet, Remodelaje del citoesqueleto, Cytoskeleton remodeling, Perfil transcriptòmic, Perfil transcriptómico, Transcriptomic profiling, Perfil metabòlic, Perfil metabólico, Metabolic profiling

Time: 616.2

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/696456

Structural-Genomic Prioritization of Autism Risk Genes: Bridging Genomic Architecture and Transcriptional Vulnerability

Authors: Sharma, Ashisha, Naskar, Annesha, Joshi, Anshul, I, Priya Stella Mary, K, Vinay, R, Stephen

Source: 2026 3rd International Conference on Integrated Intelligence and Communication Systems (ICIICS) Integrated Intelligence and Communication Systems (ICIICS), 2026 3rd International Conference on. :1-5 Jun, 2026

Relation: 2026 3rd International Conference on Integrated Intelligence and Communication Systems (ICIICS)

Polyethylenimine-Coated MXene Quantum Dots Integrate Anti-Oomycete Activity with Host Immunity Activation for Plant Oomycete Control

Authors: Wu, Rui-Xin^aff1, Zhai, Xin-Yu^aff1, Jin, Jing-Hao^aff1, Zhang, Li-Hang^aff1, Dai, Ting-Ting^aff2, Wu, Hong-Hong^aff3, Srivastava, Vaibhav^aff4, Chen, Xiao-Ren^aff1

Source: Journal of Agricultural and Food Chemistry. 74(35):27402-27415

Availability: https://pubs.acs.org/doi/10.1021/acs.jafc.6c05093

Developmental Toxicity and Mechanistic Insights into the Novel Fungicide Fluindapyr in Zebrafish Embryos

Authors: Qian, Le^{aff1, aff2}, Zhang, Mengge^{aff1, aff2}, Jiang, Jia^{aff1, aff2}, He, Kai^{aff1, aff2}, Zhang, Yikai^{aff1, aff2}, Huang, Xiaobo^{aff1, aff2}, Che, Zhiping^{aff1, aff2}, Chen, Genqiang^{aff1, aff2}, Liu, Shengming^{aff1, aff2}

Source: Journal of Agricultural and Food Chemistry. 74(32):24974-24988

Availability: https://pubs.acs.org/doi/10.1021/acs.jafc.6c02355

Exploring Neural Mechanisms of Visual Working Memory for Real-World Stimuli Categories: Insights From the Fusiform Gyrus

Authors: Xiong, R., Wei, X., Zhang, J., Jin, Z., Li, L.

Source: IEEE Journal of Biomedical and Health Informatics IEEE J. Biomed. Health Inform. Biomedical and Health Informatics, IEEE Journal of. 30(7):5794-5805 Jul, 2026

Robust Algorithm With Contrastive Learning for Identifying Spatial Domains From Noised Spatial Transcriptomics Data

Authors: Ma, Y., Kang, K., Zhang, M., Liang, P., Ma, X.

Source: IEEE Transactions on Computational Biology and Bioinformatics IEEE Trans. Comput. Biol. Bioinform. Computational Biology and Bioinformatics, IEEE Transactions on. 23(3):1451-1462 Jun, 2026

Integrative Machine Learning Framework for Effector Gene Prediction in Magnaporthe Oryzae

Authors: Lakshmi, Adluri Vijaya, Bhukya, Raju

Source: 2026 International Conference on Emerging Systems and Intelligent Computing (ESIC) Emerging Systems and Intelligent Computing (ESIC), 2026 International Conference on. :834-840 Feb, 2026

Relation: 2026 International Conference on Emerging Systems and Intelligent Computing (ESIC)

Transcriptomic Insights into the Life-History and Population Responses of Brachionus plicatilis to Artificial Light at Night

Authors: Yu, Qingqing^aff1, Xu, Tianyang^aff1, Shen, Yiru^aff1, Tao, Siying^aff1, Wang, Gongyuan^aff1, Lee, Jae-Seong^aff2, Yang, Zhou^aff1, Sun, Yunfei^aff1

Source: Environmental Science & Technology. 60(31):21927-21937

Availability: https://pubs.acs.org/doi/10.1021/acs.est.6c05454

Mechanism-Based Multitarget Modeling for Pathway-Level Prediction of PI3K/Akt Signaling Perturbation Induced by Liquid Crystal Monomers

Authors: Cheng, Jiawei^aff1, He, Yuhe^aff2, Yuan, Yawen^aff1, Mu, Yunsong^aff1, Zhao, Xiaoli^aff3, Wu, Fengchang^aff3, Sayes, Christie M.^aff4, Giesy, John P.^{aff4, aff5, aff6}

Source: Environmental Science & Technology. 60(25):17666-17678

Availability: https://pubs.acs.org/doi/10.1021/acs.est.6c00371

Transcriptomic and Metabolomic Analyses Reveal Color Variation and Taste Formation of Different Radish Sprouts

Authors: Shen, Yanxi, Qin, Han, Wei, Yingying, Chen, Yi, Shao, Xingfeng, Xu, Feng, Chen, Jiahui

Source: Journal of Agricultural and Food Chemistry. 74(22):17592-17605

Availability: https://pubs.acs.org/doi/10.1021/acs.jafc.5c13912

Multiomics Reveals the Mechanisms of Rhizosphere Symbiotic Fungi in Mitigating Micro(nano)plastics Transfer and Toxicity in Food Chains

Authors: Li, Xinru^{aff1, aff2}, Wang, Fanfan^aff1, Shi, Feng^aff3, Wei, Yuan^aff1, Zhou, Min^aff1, Wu, Fengchang^aff1, Su, Hailei^aff1, Liu, Xuesong^aff1

Source: Environmental Science & Technology. 60(22):16099-16110

Availability: https://pubs.acs.org/doi/10.1021/acs.est.5c16131

Elevated CO2 Modulates Hormonal Signaling and Galactose Metabolism to Improve Photosynthetic Performance and Water Use Efficiency in Peanut (Arachis hypogaea L.)

Authors: Zhang, Chunyu^aff1, Jin, Jian^{aff1, aff2}, Li, Yansheng^aff1, Han, Qingqing^aff3, Liu, Changkai^aff1, Zhang, Jinyuan^aff1, Hu, Xiaojing^aff1, Wang, Guanghua^aff1, Liu, Xiaobing^aff1, Yu, Zhenhua^aff1

Source: Journal of Agricultural and Food Chemistry. 74(21):16087-16099

Availability: https://pubs.acs.org/doi/10.1021/acs.jafc.5c12792

Zero-Shot Grounding of Histological Images Using Single-Cell Transcriptomic Profiles

Authors: Wu, Chaochen, Zuo, Meiyun, Xie, Lei

Source: 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2025 IEEE International Conference on. :1338-1343 Dec, 2025

Relation: 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Synergnn: A Synergistic Graph Neural Network Fusing Database Knowledge and Cohort-Specific Patterns for Cross-Cohort Survival Analysis

Authors: Sun, Tianze, Guo, Jilong, Song, Aoxiang, Xie, Linhai

Source: 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2025 IEEE International Conference on. :1825-1830 Dec, 2025

Relation: 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Development of Personalized Cancer Drug Strategies Using Omics Data and Machine Learning

Authors: Gayathri, S., Hemamalini, S., Midasala, Vasujadevi, Surendran, R, Balamurugan, K S.

Source: 2025 5th International Conference on Advancement in Electronics & Communication Engineering (AECE) Advancement in Electronics & Communication Engineering (AECE), 2025 5th International Conference on. :1112-1116 Nov, 2025

Relation: 2025 5th International Conference on Advancement in Electronics & Communication Engineering (AECE)

Spheroid cultures reveal cancer stem cell enrichment and distinct chemotherapeutic response in triple-negative breast cancer

Authors: Sarathchandra, Sithumini, 1994, Author, Fittipaldi, Chiara, 0, Author, Alamukii, Nanfizat Abiket, 1987, Author, Kovács, Anikó, 1961, Author, Parris, Toshima, 1978, Author

Contributors: Sarathchandra, Sithumini, 1994, Author, Fittipaldi, Chiara, 0, Author, Alamukii, Nanfizat Abiket, 1987, Author, Kovács, Anikó, 1961, Author, Parris, Toshima, 1978, Author

Source: BMC Cancer. 26(1)

Subject Terms: Cancer and Oncology, Cancer och onkologi, 2D monolayers, 3D spheroids, Breast cancer stem cells, RNA sequencing, Therapeutic vulnerability, Transcriptomic profiling

Access URL: https://gup.ub.gu.se/publication/366093

Exploring survival-associated transcriptomic subtypes in ovarian cancer using RNAseq from FFPE tissues in a clinical trial cohort

Authors: Kjeldsen, Maj K., Author, Bagger, Frederik Otzen, Author, Roed, Henrik, Author, Nyvang, Gitte-Bettina, Author, Haslund, Charlotte Aaquist, Author, Knudsen, Anja Oer, Author, Motavaf, Anne Krejbjerg, Author, Malander, Susanne, Author, Anttila, Maarit, Author, Lindahl, Gabriel, Author, Maenpaa, Johanna, Author, Dimoula, Maria, Author, Werner, Theresa, Author, Iversen, Trine Zeeberg, Author, Hietanen, Sakari, Author, Fokdal, Lars, Author, Dahlstrand, Hanna, Author, Bjorge, Line, Author, Birrer, Michael, Author, Mirza, Mansoor Raza, Author, Rossing, Maria, Author

Contributors: Kjeldsen, Maj K., Author, Bagger, Frederik Otzen, Author, Roed, Henrik, Author, Nyvang, Gitte-Bettina, Author, Haslund, Charlotte Aaquist, Author, Knudsen, Anja Oer, Author, Motavaf, Anne Krejbjerg, Author, Malander, Susanne, Author, Anttila, Maarit, Author, Lindahl, Gabriel, Author, Maenpaa, Johanna, Author, Dimoula, Maria, Author, Werner, Theresa, Author, Iversen, Trine Zeeberg, Author, Hietanen, Sakari, Author, Fokdal, Lars, Author, Dahlstrand, Hanna, Author, Bjorge, Line, Author, Birrer, Michael, Author, Mirza, Mansoor Raza, Author, Rossing, Maria, Author

Source: Translational Oncology. 67

Subject Terms: Epithelial Ovarian Cancer (EOC), RNA sequencing (RNAseq), Overall Survival (OS), Transcriptomic subtypes, Differentially Expressed Genes (DEGs)

File Description: electronic

Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-222386
https://doi.org/10.1016/j.tranon.2026.102740

Integrative Epigenomic and Transcriptomic Profiling Define Malignancy- and Cluster-Specific Signatures in Pheochromocytomas and Paragangliomas

Authors: Tababi, Mouna, Author, Lysiak, Malgorzata, Author, Gimm, Oliver, Author, Söderkvist, Peter, Author

Contributors: Tababi, Mouna, Author, Lysiak, Malgorzata, Author, Gimm, Oliver, Author, Söderkvist, Peter, Author

Source: Cells. 15(2)

Subject Terms: pheochromocytoma/paraganglioma, methylation, transcriptomic, TCGA

File Description: electronic

Access URL: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-220947
https://doi.org/10.3390/cells15020198

Integrated Transcriptomic and Metabolomic Analysis Reveals the Antibacterial Mechanisms of the Novel Peptide FxCy2 against Helicobacter pylori

Authors: Bi, Bo^aff1, Ye, Zhuming^aff1, Yang, Zhijie^aff1, He, Zeqi^aff1, Tan, Jiaojiao^aff1, Xie, Wenxi^aff1, Chen, Yunjiao^aff1, Song, Mingyue^aff1, Bao, Anru^aff1, Ho, Chi-Tang^aff3, Li, Xiaoqing^aff2, Cao, Yong^aff1

Source: Journal of Agricultural and Food Chemistry. 74(16):12906-12917

Availability: https://pubs.acs.org/doi/10.1021/acs.jafc.5c17294