Article
Computer Science, Artificial Intelligence
Nisar Wani, Khalid Raza
Summary: The study introduces a gene regulatory network inference method based on multiple kernel learning, which can run on multi-processor machines and learn large-scale GRNs from multiple heterogeneous datasets. This approach demonstrates superior classification accuracy and enhanced speedup potential compared to other state-of-the-art methods.
PEERJ COMPUTER SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Xiusheng Zhu, Qitong Huang, Jing Luo, Dashuai Kong, Yubo Zhang
Summary: Gene regulatory networks are critical in precision biology, offering insights into how genes and regulatory elements interact to control gene expression. The interactions involve various elements such as promoters, enhancers, transcription factors, silencers, insulators, and long-range regulatory elements, occurring within the nucleus. Understanding three-dimensional chromatin conformation and structural biology is essential for interpreting biological effects and gene regulatory networks. This review summarizes the latest advancements in three-dimensional chromatin conformation, microscopic imaging, and bioinformatics, and provides an outlook on future directions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Beatriz Andrea Otalora-Otalora, Cristian Gonzalez Prieto, Lucia Guerrero, Camila Bernal-Forigua, Martin Montecino, Alejandra Canas, Liliana Lopez-Kleine, Adriana Rojas
Summary: The use of a new bioinformatics pipeline identified deregulated transcription factors in lung cancer, with RUNX2 potentially playing a key role in the gene regulatory network. Experimental validation of RUNX2's regulatory function could lead to its use as a biomarker for diagnostic tools and specific treatments against lung tumoral diseases.
Article
Computer Science, Information Systems
Qingtao Pan, Jun Tang, Meng Wu, Xiaomin Zhu, Yutong Yuan, Ji OuYang, Hao Li, Songyang Lao
Summary: Compared with a single robot, a multirobot system exhibits better performance when dealing with complex tasks. This study innovatively proposes an adaptive cooperative gene regulatory network (AC-GRN) optimized by an elastic deformation algorithm for multirobot hunting. The AC-GRN model integrates various situational information of the task environment using the protein concentration diffusion mechanism, and adaptively measures the weight of information from different sources to complete the hunting task more efficiently, accurately, and robustly. Simulation experiments and practical testing using Kilobot robots validate the feasibility, efficiency, and practicality of the proposed AC-GRN model.
IEEE SYSTEMS JOURNAL
(2023)
Article
Immunology
Leilane Oliveira Goncalves, Andres F. Vallejo Pulido, Fernando Augusto Siqueira Mathias, Alexandre Estevao Silverio Enes, Maria Gabriela Reis Carvalho, Daniela de Melo Resende, Marta E. Polak, Jeronimo C. Ruiz
Summary: In this study, the role of inducing factors of the Th17 pathway in Leishmania-macrophage infection was investigated through computational modeling. The results showed an increase in Th17 induction in the early stages of infection, followed by a decrease in the later stages. The generated gene regulatory network model provided an integrative and dynamic view of the Leishmania-macrophage interaction.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Developmental Biology
Ran Gu, Shuwen Zhang, Subbroto Kumar Saha, Yu Ji, Kurt Reynolds, Moira McMahon, Bo Sun, Mohammad Islam, Paul A. Trainor, Yiping Chen, Ying Xu, Yang Chai, Diana Burkart-Waco, Chengji J. Zhou
Summary: This study used mouse genetic and genomic approaches to uncover the mechanisms underlying normal and defective midfacial morphogenesis, revealing that Wls plays a critical role in midfacial development.
Review
Engineering, Chemical
Seong Beom Cho
Summary: This review introduces various methods for inferring gene regulatory networks in cancer research, including pair-wise measures, multivariate measures, and supervised integrative approaches. Most methods are not specifically designed for cancer transcriptome data, indicating the need for a better understanding of cancer pathophysiology and the development of more systematic validation methods in the context of cancer biology.
Article
Environmental Sciences
Aifeng Zhai, Guohua Fan, Xiaowen Ding, Guohe Huang
Summary: Efficient and accurate hydrological forecasting model is crucial for water management and flood control. This study applied the ensemble model to predict daily discharge and proved its suitability using survey data. Compared with multiple linear regression and artificial neural network models, the ensemble model showed better performance in discharge simulation and prediction.
Article
Biochemical Research Methods
Aimin Chen, Tianshou Zhou, Tianhai Tian
Summary: This article introduces effective methods for the inference of gene regulatory networks and advocates the development of ensemble methods that combine multiple approaches.
CURRENT BIOINFORMATICS
(2022)
Article
Engineering, Multidisciplinary
Wanie M. Ridwan, Michelle Sapitang, Awatif Aziz, Khairul Faizal Kushiar, Ali Najah Ahmed, Ahmed El-Shafie
Summary: In this study, various Machine Learning models and methods were used to predict rainfall data in Tasik Kenyir, Terengganu, Malaysia. The results showed that ML models had higher accuracy compared to M2 in different time horizons, with the BDTR model performing the best.
AIN SHAMS ENGINEERING JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Young Koung Lee, Sunita Kumari, Andrew Olson, Felix Hauser, Doreen Ware
Summary: Zinc finger homeodomain (ZF-HD) transcription factors have important roles in the growth, development, and architecture regulation of plants. In Arabidopsis, ZF-HD TFs negatively regulate miR157 and positively regulate SPL10, creating a feed-forward loop that constitutes a miRNA regulatory module.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Developmental Biology
Nicolas Lonfat, Su Wang, ChangHee Lee, Mauricio Garcia, Jiho Choi, Peter J. Park, Connie Cepko
Summary: The study identified the important role of transcription factors Otx2 and Oc1 in coordinating cone development and function, and discovered many new cis-regulatory modules (CRMs) that could potentially be used as useful reagents for gene therapy of cone diseases.
Article
Developmental Biology
Jacobo Solorzano, Enrique Carrillo-de Santa Pau, Teresa Laguna, Ana Busturia
Summary: By analyzing gene regulatory circuits between Polycomb/trithorax (PcG/trxG) proteins and microRNAs in the genome of Drosophila melanogaster, we have identified three classes of miRNA-PcG/trxG crosstalk interactions that define potential regulatory circuits, revealing a novel mechanism for the control of PcG/trxG and miRNA levels of expression in fruit flies.
DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pengyu Wang, Jingxin Wang, Xiaomeng Sun, Xue Yang, Shilin Sun, Xue Han, Dandan Li, Yucheng Wang
Summary: By constructing a three-layered gene regulatory network, the regulatory mechanism of Shanxin poplar in response to drought stress was investigated. The network contained 1869 regulatory relationships, including 11 and 19 transcription factors (TFs) in the first and second layers, respectively, and 158 structural genes involved in eight enriched biological processes. Validation experiments confirmed the reliability of the network, and important biological processes related to drought tolerance were identified. This study provides insights into the adaptation mechanism of Shanxin poplar under drought stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Ruiqing Zheng, Min Li, Xiang Chen, Siyu Zhao, Fang-Xiang Wu, Yi Pan, Jianxin Wang
Summary: Gene regulatory networks play a crucial role in biological processes and exhibit diversity under different biological conditions. Reconstructing these networks from gene expression data has been a significant challenge in the past decades. The proposed PBMarsNet method shows superior performance and generalization compared to other state-of-the-art methods in inferring directed GRNs from multifactorial gene expression data.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Computer Science, Information Systems
Wajdi Dhifli, Nour El Islem Karabadji, Mohamed Elati
INFORMATION SCIENCES
(2020)
Article
Oncology
Jerome Raffenne, Remy Nicolle, Francesco Puleo, Delphine Le Corre, Camille Boyez, Raphael Marechal, Jean Francois Emile, Peter Demetter, Armelle Bardier, Pierre Laurent-Puig, Louis de Mestier, Valerie Paradis, Anne Couvelard, Jean Luc VanLathem, John R. MacKey, Jean-Baptiste Bachet, Magali Svrcek, Jerome Cros
Article
Biochemistry & Molecular Biology
Natalia Juiz, Abdessamad Elkaoutari, Martin Bigonnet, Odile Gayet, Julie Roques, Remy Nicolle, Juan Iovanna, Nelson Dusetti
Article
Medicine, General & Internal
Remy Nicolle, Yuna Blum, Pauline Duconseil, Charles Vanbrugghe, Nicolas Brandone, Flora Poizat, Julie Roques, Martin Bigonnet, Odile Gayet, Marion Rubis, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Aurelien de Reynies, Marc Giovannini, Philippe Grandval, Stephane Garcia, Cindy Canivet, Jerome Cros, Barbara Bournet, Louis Buscail, Vincent Moutardier, Marine Gilabert, Juan Iovanna, Nelson Dusetti
Review
Oncology
Marc Hilmi, Remy Nicolle, Corinne Bousquet, Cindy Neuzillet
Article
Oncology
Jerome Raffenne, Fernando A. Martin, Remy Nicolle, Marina Konta, Yuna Blum, Jerome Torrisani, Francesco Puleo, Jean Baptiste Bachet, Magali Svrcek, Armel Bardier-Dupas, Jean Francois Emile, Peter Demetter, Miroslav Radman, Jean Luc Van Laethem, Pascal Hammel, Vinciane Rebours, Valerie Paradis, Anne Couvelard, Jerome Cros
Summary: Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed in the 7th decade, but around 10% of patients are diagnosed before the age of 55. Molecular features of early-onset tumors (<= 55 y.o.) were found to be similar to late-onset tumors (>= 70 y.o.), indicating that younger patients can serve as a good molecular surrogate model for the general older population with PDAC. The study also highlighted the impact of ageing on DNA methylation and proteome integrity, as well as the association of oxidative stress responses with PDAC.
Review
Oncology
Tatjana Arsenijevic, Remy Nicolle, Christelle Bouchart, Nicky D'Haene, Pieter Demetter, Francesco Puleo, Jean-Luc Van Laethem
Summary: Microbiota on oral, gut, and intratumoral regions have significant impacts on the development, progression, and chemoresistance of pancreatic ductal adenocarcinoma, potentially serving as diagnostic, prognostic, and predictive biomarkers for this aggressive cancer.
Article
Oncology
Owen Hoare, Nicolas Fraunhoffer, Abdessamad Elkaoutari, Odile Gayet, Martin Bigonnet, Julie Roques, Remy Nicolle, Colin McGuckin, Nico Forraz, Emilie Sohier, Laurie Tonon, Pauline Wajda, Sandrine Boyault, Valery Attignon, Severine Tabone-Eglinger, Sandrine Barbier, Caroline Mignard, Olivier Duchamp, Juan Iovanna, Nelson J. Dusetti
Summary: The study compares three preclinical models directly derived from PDAC patients, showing their unique basal-like/classical transcriptomic phenotype significantly influences global chemosensitivity. Each model is imperfect but complementary, suggesting a more representative clinical approach could be achieved by combining them.
Article
Health Care Sciences & Services
Quentin Miagoux, Vidisha Singh, Dereck de Mezquita, Valerie Chaudru, Mohamed Elati, Elisabeth Petit-Teixeira, Anna Niarakis
Summary: Rheumatoid arthritis is a complex autoimmune disease with various genetic and environmental factors. By using systems biology approaches and machine learning, researchers aim to uncover mechanisms regulating key transcription factors and derive patient-specific models. Integrating multiple data types can help analyze disease heterogeneity and treatment response in a more comprehensive manner.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Pathology
Thomas Depoilly, Raffaele Leroux, Dafne Andrade, Remy Nicolle, Marco Dioguardi Burgio, Ilaria Marinoni, Safi Dokmak, Philippe Ruszniewski, Olivia Hentic, Valerie Paradis, Louis De Mestier, Aurel Perren, Anne Couvelard, Jerome Cros
Summary: Serotonin producing pancreatic neuroendocrine tumors (SP-PanNET) are a distinct and specific subtype of pancreatic neuroendocrine tumors with atypical serotonin secretion and abundant dense stroma deposition. They have a unique genomic profile and activation of the TGF-beta pathway, leading to the characteristic fibrotic aspect. The cell of origin within the pancreas is still unclear.
Article
Oncology
Nicolas A. Fraunhoffer, Analia Meilerman Abuelafia, Martin Bigonnet, Odile Gayet, Julie Roques, Remy Nicolle, Gwen Lomberk, Raul Urrutia, Nelson Dusetti, Juan Iovanna
Summary: This study developed a Master Regulators (MR)-Gradient model based on transcriptomic profiles derived from both PDAC epithelial and microenvironment cells to reveal the transcriptional networks, epigenomic states, and metabolic pathways underlying PDAC heterogeneity. Integration of methylome and metabolome datasets, along with experimental measurements, showed a close association between PDAC prognosis, tumor epithelial cell phenotype, and immunological component. Metabolic analysis indicated a positive correlation between favorable PDAC phenotype and enzymes involved in complex lipid biosynthesis, while an unfavorable phenotype exhibited an OXPHOS independent metabolism centered on the Warburg effect and glutaminolysis. The study also identified key deregulated pathways in PDAC related to epigenetics.
NPJ PRECISION ONCOLOGY
(2022)
Article
Oncology
Cindy Neuzillet, Remy Nicolle, Jerome Raffenne, Annemilai Tijeras-Raballand, Alexia Brunel, Lucile Astorgues-Xerri, Sophie Vacher, Floriane Arbateraz, Marjorie Fanjul, Marc Hilmi, Remi Samain, Christophe Klein, Aurelie Perraud, Vinciane Rebours, Muriel Mathonnet, Ivan Bieche, Hemant Kocher, Jerome Cros, Corinne Bousquet
Summary: This study refined the subtypes of cancer-associated fibroblasts (CAFs) in pancreatic ductal adenocarcinoma (PDAC) using RNAseq and immunostaining, and found associations between different CAF subtypes and tumor characteristics as well as patient survival. Periostin-positive CAFs were linked to aggressive tumors, while podoplanin-positive CAFs were associated with immune-related phenotypes.
JOURNAL OF PATHOLOGY
(2022)
Article
Oncology
Matteo Ponzo, Anais Debesset, Melissande Cossutta, Mounira Chalabi-Dchar, Claire Houppe, Caroline Pilon, Alba Nicolas-Boluda, Sylvain Meunier, Fabio Raineri, Allan Thiolat, Remy Nicolle, Federica Maione, Serena Brundu, Carina Florina Cojocaru, Philippe Bouvet, Corinne Bousquet, Florence Gazeau, Christophe Tournigand, Jose Courty, Enrico Giraudo, Jose L. Cohen, Ilaria Cascone
Summary: This study explores the effects of a selective inhibitor of nucleolin (NCL) on the immune microenvironment of pancreatic ductal adenocarcinoma (PDAC), and highlights a new therapeutic strategy to restrain immunosuppressive cells, promote T-cell recruitment and activation, and re-program the tumor stroma of PDAC.
Article
Biochemistry & Molecular Biology
Marc Hilmi, Lucile Armenoult, Mira Ayadi, Remy Nicolle
Summary: RNA sequencing (RNA-Seq) is a powerful tool with significant clinical potential, especially in oncology. This study compared five FFPE-compatible kits for RNA-Seq and found that the Smarter Pico V3 ribodepletion approach was the most reliable and reproducible technique, with comparable performance to Nanostring and Truseq. In addition, the 3' Lexogen kit showed an interesting quality-price ratio for samples with limited quantities.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Urology & Nephrology
Zohra El Ati, Hanene Machfar, Hamza Boussafa, Nidhal Ati, Olfa Ben Omrane Sioud, Baha Zantour, Hassen Bouzidi, Mohamed Elati
SAUDI JOURNAL OF KIDNEY DISEASES AND TRANSPLANTATION
(2020)