Article
Biochemical Research Methods
Haotian Teng, Ye Yuan, Ziv Bar-Joseph
Summary: This study developed a new method (FICT) that accurately identifies cell types and sub-types by considering both gene expression and neighborhood information. Compared to methods that solely rely on expression, FICT performs better in clustering spatial transcriptomics data and provides novel hypotheses about the new functions of excitatory and inhibitory neurons.
Article
Biochemical Research Methods
Zhourun Wu, Mingyue Guo, Xiaopeng Jin, Junjie Chen, Bin Liu
Summary: CFAGO is a novel method for protein function prediction that integrates single-species PPI networks and protein biological attributes using a multi-head attention mechanism. Benchmark experiments on human and mouse datasets show that CFAGO outperforms state-of-the-art single-species network-based methods in terms of m-AUPR, M-AUPR, and Fmax, demonstrating the significant improvement in protein function prediction achieved by the cross-fusion using the multi-head attention mechanism.
Article
Immunology
Ali Mahmoudia, Stephen L. Atkin, Tannaz Jamialahmadi, Amirhossein Sahebkar
Summary: This study aimed to investigate the effect of statins on genes/proteins involved in foam cell formation. Analysis of gene expression profiles and protein-protein interactions revealed various critical overexpressed genes, including G6PD, NPC1, ABCA1, ABCG1, PGD, PLIN2, PPAP2B, and TXNRD1. Functional enrichment analysis showed that these genes were involved in cholesterol metabolism and biosynthesis. Molecular docking analysis indicated that lipophilic statins, especially pitavastatin and lovastatin, had a significant effect on foam cell formation, with ABCA1 being the most important protein target.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Su Yon Jung
Summary: The study investigated the molecular processes and key regulatory factors of the IGF-I/IR axis by integrating genomics and multi-omics data. The findings revealed potential genetic targets and mechanisms associated with diseases such as diabetes and cancer.
Article
Biochemical Research Methods
Benjamin M. Good, Kimberly Van Auken, David P. Hill, Huaiyu Mi, Seth Carbon, James P. Balhoff, Laurent-Philippe Albou, Paul D. Thomas, Christopher J. Mungall, Judith A. Blake, Peter D'Eustachio
Summary: GO-CAMs combine individual gene product associations with cellular components, molecular functions, and biological processes into causally linked activity flow models. The software tool Pathways2GO converts the entire set of Reactome pathways into GO-CAMs, providing standard GO annotations and quality control for the bioinformatics community. This conversion ensures a seamless integration between Reactome and GO resources.
Article
Pharmacology & Pharmacy
Balakarthikeyan Janani, Mayakrishnan Vijayakumar, Kannappan Priya, Jin Hee Kim, Ayman Geddawy, Mohammad Shahid, Mahmoud H. H. El-Bidawy, Sameer Al-Ghamdi, Mohammed Alsaidan, Mohammad Hassan Abdelzaher, Abubucker Peer Mohideen, Thiyagarajan Ramesh
Summary: This study investigated the potential regulatory mechanisms of andrographolide in treating colorectal cancer (CRC) using a network pharmacology approach. The results demonstrated that andrographolide can inhibit cellular proliferation, migration, and growth, and induce apoptosis by targeting hub genes involved in CRC migration and invasion.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Nuclear Science & Technology
Wenhuai Li, Peng Ding, Wenqing Xia, Shu Chen, Fengwan Yu, Chengjie Duan, Dawei Cui, Chen Chen
Summary: This paper analyzes the feasibility of reconstructing the core three-dimensional power distribution by using different combinations of detectors, compares the multilayer perceptron (MLP) network and radial basis function (RBF) network, and discusses methods to reduce the influence of detector failure and uncertainty.
NUCLEAR ENGINEERING AND TECHNOLOGY
(2022)
Article
Chemistry, Analytical
Felipe Raposo Passos Mansoldo, Rafael Garrett, Veronica da Silva Cardoso, Marina Amaral Alves, Alane Beatriz Vermelho
Summary: Genetic information and computational tools are used in various fields to analyze and classify data. Recently, the chemical ontology of metabolites has become computationally obtainable, allowing for the application of genetic taxonomy methods in the field of metabolite classification. Community ecology tools, with their mature methods and established statistical tools, are well-suited for this adaptation. The Metabology approach presented in this study transforms metabolites into an ecosystem based on chemical ontology. The applicability of this approach is demonstrated using publicly available data from a metabolomics study of human plasma and an untargeted metabolomics study of a fungal pathogen.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biochemistry & Molecular Biology
Juan Manuel Guzman-Flores, Victoriano Perez-Vazquez, Fernando Martinez-Esquivias, Mario Alberto Isiordia-Espinoza, Juan Manuel Viveros-Paredes
Summary: This study explored the pharmacological mechanism of C. sativa in treating type 2 diabetes (T2D) and found that it exerts anti-diabetic effects through the insulin signaling pathway, with the participation of HIF-1 and FoxO.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Seong Beom Cho
Summary: Endometriosis is a common gynecological disorder in women of reproductive age, characterized by symptoms such as dysmenorrhea, irregular menstruation, and infertility. The pathogenesis of endometriosis remains unclear, but omics experiments have provided valuable insights into the molecular mechanisms involved.
Article
Biochemical Research Methods
Khandakar Tanvir Ahmed, Jiao Sun, Sze Cheng, Jeongsik Yong, Wei Zhang
Summary: This study introduces omicsGAN, a generative adversarial network model that integrates two omics data and their interaction network to generate synthetic data with improved performance in cancer outcome classification and patients' survival prediction compared to original datasets. The integrity of the interaction network is crucial for creating synthetic data with higher predictive quality.
Article
Biochemistry & Molecular Biology
Yue Wu, Lingping Yang, Xianglu Wu, Lidan Wang, Hongbo Qi, Qian Feng, Bin Peng, Yubin Ding, Jing Tang
Summary: Revealing key genes and elucidating pathogenic mechanism of PCOS is crucial for targeted clinical therapy. Integrating PCOS-associated molecules, an integrative PPMI network identified potential PCOS-associated genes and significant differences in PCOS-specific tissue. The novel gene FXR2 was found to be significantly increased in PCOS patients' ovarian granulosa cells.
Article
Remote Sensing
Luis M. Vilches-Blazquez, Jhonny Saavedra
Summary: Efforts around land administration have been made worldwide, but heterogeneity of data and systems remains a challenge. This paper proposes a graph-based approach to integrate multiple and heterogeneous data sources, aiming to prevent data isolation and enable cross-dataset integration. A real case study demonstrates the applicability of the approach.
GEO-SPATIAL INFORMATION SCIENCE
(2022)
Article
Genetics & Heredity
Mohd Murshad Ahmed, Zoya Shafat, Safia Tazyeen, Rafat Ali, Majed N. Almashjary, Rajaa Al-Raddadi, Steve Harakeh, Aftab Alam, Shafiul Haque, Romana Ishrat
Summary: This study aimed to identify diagnostic biomarkers and therapeutic targets for patients with chronic kidney disease (CKD). Through analysis of gene expression profile datasets, 6 overlapping hub genes were identified. These hub genes and their associated miRNAs may serve as potential diagnostic biomarkers and therapeutic targets for CKD.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Imam Cartealy, Li Liao
Summary: This study aimed to improve the accuracy of inferring protein membership in metabolic pathways by integrating ontology and sequential information. Through the use of a neural network model with a tailored architecture, it was found that our deep neural network method outperforms existing methods significantly in the pathway-centric mode and either outperforms or performs comparably in the protein-centric mode.
Article
Biochemical Research Methods
Vladimir Gligorijevic, Noel Malod-Dognin, Natasa Przulj
Review
Biochemical Research Methods
Vladimir Gligorijevic, Noel Malod-Dognin, Natasa Przulj
Editorial Material
Multidisciplinary Sciences
Natasa Przulj, Noel Malod-Dognin
Article
Multidisciplinary Sciences
Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda van Leeuwen, Nydia van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li, Zhijian Li, Mojca Mattiazzi Usaj, Hiroki Okada, Natasha Pascoe, Bryan-Joseph San Luis, Sara Sharifpoor, Emira Shuteriqi, Scott W. Simpkins, Jamie Snider, Harsha Garadi Suresh, Yizhao Tan, Hongwei Zhu, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G. Troyanskaya, Igor Stagljar, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M. Steinmetz, Claire L. Moore, Adam P. Rosebrock, Amy A. Caudy, Chad L. Myers, Brenda Andrews, Charles Boone
Article
Biochemistry & Molecular Biology
Kate Sokolina, Saranya Kittanakom, Jamie Snider, Max Kotlyar, Pascal Maurice, Jorge Gandia, Abla Benleulmi-Chaachoua, Kenjiro Tadagaki, Atsuro Oishi, Victoria Wong, Ramy H. Malty, Viktor Deineko, Hiroyuki Aoki, Shahreen Amin, Zhong Yao, Xavier Morato, David Otasek, Hiroyuki Kobayashi, Javier Menendez, Daniel Auerbach, Stephane Angers, Natasa Przulj, Michel Bouvier, Mohan Babu, Francisco Ciruela, Ralf Jockers, Igor Jurisica, Igor Stagljar
MOLECULAR SYSTEMS BIOLOGY
(2017)
Article
Multidisciplinary Sciences
Anida Sarajlic, Noel Malod-Dognin, Omer Nebil Yaveroglu, Natasa Przulj
SCIENTIFIC REPORTS
(2016)
Article
Multidisciplinary Sciences
Noel Malod-Dognin, Kristina Ban, Natasa Przulj
SCIENTIFIC REPORTS
(2017)
Review
Pharmacology & Pharmacy
Sandra Kraljevic Pavelic, Jasmina Simovi Medica, Darko Gumbarevic, Ana Filosevic, Natasa Przulj, Kresimir Pavelic
FRONTIERS IN PHARMACOLOGY
(2018)
Article
Multidisciplinary Sciences
Noel Malod-Dognin, Julia Petschnigg, Sam F. L. Windels, Janez Povh, Harry Hemmingway, Robin Ketteler, Natasa Przulj
NATURE COMMUNICATIONS
(2019)
Article
Biochemical Research Methods
N. Malod-Dognin, V Pancaldi, A. Valencia, N. Przulj
Article
Biochemical Research Methods
D. A. Salazar, N. Przulj, C. F. Valencia
Summary: This study introduces a novel method capable of integrating multi-omic data from different sources and identifying patient and cell line groups enriched in cancer-associated gene clusters. The method also predicts drug profiles for patients and identifies genetic signatures for tumors resistant and sensitive to specific drugs.
Article
Biochemistry & Molecular Biology
Alexandros Xenos, Noel Malod-Dognin, Carme Zambrana, Natasa Przulj
Summary: To understand COVID-19, researchers used an integrated cell (iCell) concept with three omics networks to study its molecular basis. They compared patient-based and cell line-based iCells and found significant differences, indicating the limitations of using cell lines in studying this disease. By comparing infected and control patient-based iCells, they identified genes whose functioning is altered by the disease. They also predicted drugs for repurposing and confirmed the binding of these drugs to their targets. The study highlights the applicability of the iCell framework for studying human diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Mathematical & Computational Biology
Noel Malod-Dognin, Natasa Przulj
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2017)
Article
Biochemical Research Methods
Omer Nebil Yaveroglu, Noel Malod-Dognin, Tijana Milenkovic, Natasa Przulj
Proceedings Paper
Computer Science, Interdisciplinary Applications
Vladimir Gligorijevic, Noel Malod-Dognin, Natasa Przulj
PACIFIC SYMPOSIUM ON BIOCOMPUTING 2016
(2016)