Article
Biochemistry & Molecular Biology
Yue Yin, Liang-Fei Yao, Yue Hu, Zi-Kai Shao, Xiao-Yue Hong, Paul D. N. Hebert, Xiao-Feng Xue
Summary: This study establishes a DNA barcode reference library for eriophyoid mites, providing coverage for a significant proportion of known species. The barcode analysis reveals clear barcode gaps between species, enabling effective species identification. The study also shows that eriophyoid mites exhibit high host specificity and that the host-mite networks are highly modular. These findings highlight the importance of DNA barcoding in advancing our understanding of eriophyoid mite diversity and their host interactions.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemical Research Methods
Mehrzad Saremi, Maryam Amirmazlaghani
Summary: In this study, an algorithm called GENEREF was developed to accumulate information from multiple datasets in an iterative manner, improving the accuracy of prediction results. The algorithm was extensively tested on multiple datasets and outperformed other algorithms on selected networks, showing competitiveness with existing multi-dataset algorithms.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Ecology
Chun-Wei Chang, Takeshi Miki, Masayuki Ushio, Po-Ju Ke, Hsiao-Pei Lu, Fuh-Kwo Shiah, Chih-hao Hsieh
Summary: A novel approach for reconstructing high-dimensional interaction Jacobian networks without specific model assumptions was proposed in this study, which successfully identified important species and revealed mechanisms governing the dynamical stability of a bacterial community. The method overcame the challenge of high dimensionality in large natural dynamical systems.
Article
Multidisciplinary Sciences
Yipei Guo, Ariel Amir
Summary: Maintaining stable protein concentrations in cells is crucial for proper cellular functioning, with network topology playing a key role in ensuring stability constraints and shaping evolutionary processes.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Guiying Wu, Xiangyu Li, Wenbo Guo, Zheng Wei, Tao Hu, Yiran Shan, Jin Gu
Summary: The inference of gene co-expression associations is a fundamental task in large-scale transcriptomic data analysis. We proposed a method called JEBIN that integrates multiple expression datasets to learn a low-dimensional consensus representation for genes. Simulation experiments confirmed the effectiveness and scalability of JEBIN, and it outperformed commonly used integration methods. JEBIN was also applied to study the gene co-expression patterns of hepatocellular carcinoma (HCC) and identified differentially co-expressed ligand-receptor pairs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Automation & Control Systems
Yuxin Wu, Deyuan Meng, Zheng-Guang Wu
Summary: This paper reviews different disagreement behaviors in signed networks and discusses the convergence and fluctuation behaviors under static and dynamic topologies. For static signed networks, the behaviors with fixed topologies and switching topologies are investigated, and brief introductions on general time-varying signed networks are provided. For dynamic signed networks, the specific descriptions and characteristics are shown, and the disagreement behaviors can be obtained using the derived static signed graphs. Applications to the behavior analysis of static signed networks with high-order dynamics or communication delays are also presented.
IEEE-CAA JOURNAL OF AUTOMATICA SINICA
(2022)
Correction
Multidisciplinary Sciences
Yipei Guo, Ariel Amir
Summary: A correction to the paper has been published.
NATURE COMMUNICATIONS
(2021)
Article
Meteorology & Atmospheric Sciences
Yadi Li, Xichen Li, Juan Feng, Yi Zhou, Wenzhu Wang, Yurong Hou
Summary: El Nino-Southern Oscillation (ENSO) usually intensifies the Hadley Circulation (HC) and restricts its meridional extension, leading to an equatorward movement of the jet system. This study evaluates the capability of eight reanalysis datasets in reproducing the regional HC response to ENSO events using a newly developed three-dimensional HC structure technique. Results show that while these datasets reproduce the spatial structure of HC responses well, they may not capture the amplitudes of the HC responses accurately, especially for ENSO-associated equatorially asymmetric HC anomalies.
ADVANCES IN ATMOSPHERIC SCIENCES
(2023)
Article
Automation & Control Systems
Junyang Jin, Ye Yuan, Jorge Goncalves
Summary: Network inference has been receiving increasing attention in fields such as systems biology and biomedicine. The challenge is to uncover the complex molecular networks behind cells and organisms. This article explores the characteristics of networks, linear network models, and a method based on reversible jump Markov chain Monte Carlo for estimating network topology. Monte Carlo simulations show that this method consistently produces more accurate networks compared to other state-of-the-art methods in various applications.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2021)
Article
Biochemistry & Molecular Biology
Shuibing Liu, Jintao Wu, Wentao Zhang, Hongxia Jiang, Yanan Zhou, Jing Liu, Huirong Mao, Sanfeng Liu, Biao Chen
Summary: This study provides valuable insights into the expression patterns and molecular mechanisms of mRNA-lncRNA-circRNA-miRNA interaction in duck myogenesis, shedding light on the regulation of this critical biological process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Madison Dautle, Shaoqiang Zhang, Yong Chen
Summary: scTIGER is a novel deep-learning-based method that uses the co-differential relationships of gene expression profiles in paired scRNA-seq datasets to infer gene regulatory networks (GRNs). It has been successfully applied to prostate cancer cells and neurons to identify dynamic regulatory networks and demonstrates robustness against dropout noise in scRNA-seq data.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Engineering, Chemical
Okay Altun
Summary: An ore is made up of components/minerals with different physical and chemical properties, which affect the performance of grinding and classification operations. This study compared the air classification performances of pure components and binary feeding states, finding that parameters such as bypass, cut size, and sharpness varied. Powder interactions and material specifications played a role in these variations.
Article
Biotechnology & Applied Microbiology
Pedro G. Nachtigall, Luiz A. Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Summary: Despite the differences in heart development among different vertebrate groups, both conserved and group-specific miRNAs play crucial roles in modulating the core and peripheral genes of heart GRNs. Conserved miRNAs have higher expression levels and more targets, while group-specific miRNAs have lower expression levels and fewer targets.
Article
Plant Sciences
Shu-Yue Wang, Xiao-Chen Sun, Xi-Yu Lv, Jing-Na Li, Bing Han, Kun-Lin Liu, Shuai Wang, Hua-Gang Sheng, Chao Zhang, Fei Guo, Yi-Dong Cui
Summary: In this study, the chemical components of Fructus Tribuli were analyzed and identified, and network pharmacology was used to predict the potential targets for treating vascular endothelial dysfunction. The therapeutic effects of Fructus Tribuli were further confirmed in an animal experiment, which showed that it reduced blood pressure, decreased levels of endothelin-1 and angiotensin II, and increased nitric oxide levels in spontaneously hypertensive rats.
JOURNAL OF ETHNOPHARMACOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Lucas Andre Cavalcanti Brandao, Paola Maura Tricarico, Rossella Gratton, Almerinda Agrelli, Luisa Zupin, Haissam Abou-Saleh, Ronald Moura, Sergio Crovella
Summary: The high volume of information in the omics era has led to a better understanding of pathological processes, but the majority of results are divergent, limiting their applicability. Skin diseases with alterations in the Notch signaling pathway have been extensively studied, yet there are conflicting results.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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)