Review
Biochemistry & Molecular Biology
Elettra Barberis, Shahzaib Khoso, Antonio Sica, Marco Falasca, Alessandra Gennari, Francesco Dondero, Antreas Afantitis, Marcello Manfredi
Summary: This review discusses the application of recent technological innovations in mass spectrometry to metabolomics analysis, with a focus on the use of artificial intelligence (AI) strategies. The article also explores the challenges and limitations of implementing metabolomics-AI systems, as well as recent tools and studies in disease classification and biomarker identification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Aydin Demircioglu
Summary: In radiomic studies, the features selected by different models can vary greatly, even among statistically similar models. It is misleading to consider features selected by a single model, making it difficult to determine if these features are candidate biomarkers.
INSIGHTS INTO IMAGING
(2022)
Article
Biochemical Research Methods
Pengfei Liang, Hao Wang, Yuchao Liang, Jian Zhou, Haicheng Li, Yongchun Zuo
Summary: Feature-scML is an effective toolkit for analyzing single-cell RNA omics datasets, automating the machine learning process, and customizing visual analysis of the results.
CURRENT BIOINFORMATICS
(2022)
Article
Computer Science, Information Systems
Bing Li, Xiaoli Zheng, Wei Guo, Yunhan Wang, Ronghu Mao, Xiuyan Cheng, Chengcheng Fan, Ting Wang, Zhaoyang Lou, Hongchang Lei, Lingguang Meng, Yuanpeng Zhang, Hong Ge
Summary: In this study, a novel machine learning-based pipeline was developed for predicting radiation pneumonitis in non-small cell lung cancer patients. The study considered the stability and discrimination ability of features in the feature selection phase and developed a decision criterion for selecting appropriate feature selection methods. In the modeling phase, a non-sparse multi-kernel learning method with manifold regularization was used to fuse multi-omics data and reduce overfitting.
HUMAN-CENTRIC COMPUTING AND INFORMATION SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Linnea Hases, Ahmed Ibrahim, Xinsong Chen, Yanghong Liu, Johan Hartman, Cecilia Williams
Summary: The study reveals sex differences in the transcriptome of normal colon and CRC tissue, with some biomarkers showing sex-specific prognostic value. 20 sex-specific CRC prognostic biomarkers, including ESM1, GUCA2A, and VWA2 for males and CLDN1 and FUT1 for females, are proposed, which can help improve CRC survival rates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Virgile Raufaste-Cazavieille, Raoul Santiago, Arnaud Droit
Summary: The use of omics approaches, such as genomics and transcriptomics, has revolutionized cancer research, revealing the complexity and diversity within tumors and offering new opportunities for precision medicine. In this review, the authors provide an overview of the latest innovations in multi-omics integration in oncology, highlighting the importance of combining clinical and multi-omics data for personalized therapy. The review also explores the advances in understanding the tumor immune environment and host-tumor interaction through immunomics and microbiomics.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemical Research Methods
Kai Shi, Wei Lin, Xing-Ming Zhao
Summary: Molecular biomarkers are specific molecules that can aid in diagnosing or predicting diseases. Advances in high-throughput technologies have allowed for the accumulation of large omics data for screening biomarkers. Research involves various machine learning approaches to identify biomarkers and address potential challenges in biomedical data for future biomarker identification.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Fabio Valenti, Italia Falcone, Sara Ungania, Flora Desiderio, Patrizio Giacomini, Chiara Bazzichetto, Fabiana Conciatori, Enzo Gallo, Francesco Cognetti, Gennaro Ciliberto, Aldo Morrone, Antonino Guerrisi
Summary: Treatment and management of metastatic melanoma have evolved significantly in the era of personalized medicine, benefiting from immunotherapy and advancements in multi-omics analyses. While improving clinical management, precision medicine plays a crucial role in guiding treatment decisions for individual patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Rheumatology
Lee Jin Lim, Ashley J. W. Lim, Brandon N. S. Ooi, Justina Wei Lynn Tan, Ee Tzun Koh, Ttsh Rheumatoid Arthritis Study Group, Samuel S. Chong, Chiea Chuen Khor, Lisa Tucker-Kellogg, Caroline G. Lee, Khai Pang Leong
Summary: This study identified sensitive and specific predictors of MTX response in RA patients through a novel strategy combining biologically meaningful genetic feature selection and machine learning. These predictors may facilitate better treatment decision-making in RA management.
Article
Medicine, General & Internal
Niamh Errington, James Iremonger, Josephine A. Pickworth, Sokratis Kariotis, Christopher J. Rhodes, Alexander Mk Rothman, Robin Condliffe, Charles A. Elliot, David G. Kiely, Luke S. Howard, John Wharton, A. A. Roger Thompson, Nicholas W. Morrell, Martin R. Wilkins, Dennis Wang, Allan Lawrie
Summary: This study identified two microRNAs using consensus machine learning approaches to distinguish PAH from both disease and healthy controls. These circulating microRNAs and their target genes may offer insights into PAH pathogenesis and reveal potential drug targets.
Article
Mathematical & Computational Biology
Xin Niu, Jiangtao Gou, Hansoo Chang, Michael Lowe, Fengqing (Zoe) Zhang
Summary: This article discusses the importance of using machine learning in brain imaging studies and proposes a new metric to evaluate the reproducibility of neuroimaging feature selection. The results show that the proposed model is effective in distinguishing informative features from noise features and reducing coefficient estimation errors.
STATISTICS IN MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Ziyi Yang, Dandan Zhou, Jun Huang
Summary: This study developed models using artificial intelligence and single-cell analysis for early detection of ovarian cancer and extraction of important characteristic genes as diagnostic biomarkers. The expression of characteristic genes was associated with cancer-associated fibroblast infiltration and patient survival rates. Additionally, a novel fibroblast subset signature was explored to evaluate immune checkpoint inhibitor response and tumor protein P53 mutation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Filippo Lococo, Luca Boldrini, Charles-Davies Diepriye, Jessica Evangelista, Camilla Nero, Sara Flamini, Angelo Minucci, Elisa De Paolis, Emanuele Vita, Alfredo Cesario, Salvatore Annunziata, Maria Lucia Calcagni, Marco Chiappetta, Alessandra Cancellieri, Anna Rita Larici, Giuseppe Cicchetti, Esther G. C. Troost, Adany Roza, Nuria Farre, Ece Ozturk, Dominique Van Doorne, Fausto Leoncini, Andrea Urbani, Rocco Trisolini, Emilio Bria, Alessandro Giordano, Guido Rindi, Evis Sala, Giampaolo Tortora, Vincenzo Valentini, Stefania Boccia, Stefano Margaritora, Giovanni Scambia
Summary: The LANTERN project aims to develop predictive models based on the integration of multi-omics data for early detection, improved tumor diagnosis, and personalized treatment protocols.
Article
Biotechnology & Applied Microbiology
Abhibhav Sharma, Pinki Dey
Summary: A machine learning approach was used to explore genetic risk factors of Alzheimer's disease, revealing novel and highly predictive biomarkers.
Article
Microbiology
Jose Linares-Blanco, Carlos Fernandez-Lozano, Jose A. Seoane, Guillermo Lopez-Campos
Summary: This study generated a metagenomic signature with predictive capacity to identify inflammatory bowel disease (IBD) from fecal samples. Different machine learning models were trained and the identified signature showed high performance in both subtypes of IBD. The study also identified different genera that play an important and common role in the development of these two subtypes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Reproductive Biology
Maira Bianchi Rodrigues Alves, Laura Girardet, Celine Augiere, Kyeong Hye Moon, Camille Lavoie-Ouellet, Agathe Bernet, Denis Soulet, Ezequiel Calvo, Maria E. Teves, Charles Joly Beauparlant, Arnaud Droit, Alexandre Bastien, Claude Robert, Jinwoong Bok, Barry T. Hinton, Clemence Belleannee
Summary: Primary cilia are crucial for embryonic patterning and organogenesis through the Hedgehog signaling pathway. This study investigated the role of Hedgehog signaling and primary cilia in the development of male reproductive ductules, such as the epididymis. The findings suggest that primary cilia-dependent Hedgehog signaling acts as a master regulator of genes involved in Wolffian duct development, providing new insights into sexual differentiation and male infertility issues. Modulating primary ciliogenesis and downstream Hedgehog signaling may control the development of the Wolffian duct.
BIOLOGY OF REPRODUCTION
(2023)
Article
Food Science & Technology
Atena Mahdavi, Mickael Leclercq, Antoine Bodein, Clarisse Gotti, Karine Greffard, Jean-Francois Bilodeau, Arnaud Droit, Michel Lebel, Iwona Rudkowska
Summary: This study aims to investigate the relationship between high α-tocopherol levels and serum protein profiles during intake of adequate or high dairy products. The results show that α-tocopherol levels are positively correlated with proteins involved in lipid metabolism. However, this correlation changes after high dairy product intake.
JOURNAL OF FUNCTIONAL FOODS
(2023)
Article
Andrology
Donovan Chan, Lundi Ly, Edgar Martinez Duncker Rebolledo, Josee Martel, Mylene Landry, Marie-Pier Scott-Boyer, Arnaud Droit, Jacquetta M. Trasler
Summary: This study investigated the effects of lifetime exposure to diets with low or high levels of folic acid on DNA methylation in germ cells. The results suggest that folate levels are associated with DNA methylation in germ cells, particularly during the prenatal period.
Article
Biotechnology & Applied Microbiology
William Poisson, Julien Prunier, Alexandra Carrier, Isabelle Gilbert, Gabriela Mastromonaco, Vicky Albert, Joelle Taillon, Vincent Bourret, Arnaud Droit, Steeve D. Cote, Claude Robert
Summary: This study used Oligopaint FISH technology to design specific probes and successfully upgraded the published caribou chromosome-level genomes. By combining physical mapping and comparative genomics, the chromosomal evolution among Cervidae and closely related bovids was revealed. These results provide validation for the current chromosome-level genome assembly and resources for chromosome banding studies in caribou.
Article
Plant Sciences
Christine C. Chiu, Gervais Pelletier, Juliana Stival Sena, Florence Roux-Dalvai, Julien Prunier, Arnaud Droit, Armand Seguin
Summary: The emerald ash borer, an Asian insect species, has invaded North America for 20 years and caused the death of millions of American ash trees. Studying the natural defenses of susceptible American ash trees can help breed resistant varieties.
Article
Biochemistry & Molecular Biology
Sarah Lafleur, Antoine Bodein, Joanna Mbuya Malaika Mutombo, Alban Mathieu, Charles Joly Beauparlant, Xavier Minne, Fatiha Chandad, Arnaud Droit, Vanessa P. Houde
Summary: This study investigates the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis. It reveals the key variables, including genes, bacteria, and inflammatory cytokines, that contribute to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. The findings shed light on the complex interrelationships involved in the regulation of periodontal inflammation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Benjamin Muselius, Florence Roux-Dalvai, Arnaud Droit, Jennifer Geddes-McAlister
Summary: Fungal pathogens are becoming a growing concern for global health due to climate change and increased distribution. Accurate detection and diagnosis of fungal infections are crucial for effective treatment options. Protein biomarkers show promise for improved diagnostics, but prior knowledge of infection characteristics is necessary for this approach.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Zainab Fakih, Melodie B. Plourde, Charlene Eugenie Tomi Nkouankou, Victor Fourcassie, Sylvie Bourassa, Arnaud Droit, Hugo Germain
Summary: Plants have developed strategies to cope with various stresses, and ribosomes can adapt to different stress conditions. By analyzing immunopurified ribosomes from Arabidopsis leaves treated with an inducer of plant innate immunity, potential ribosome-associated proteins involved in innate immunity were identified.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Cell Biology
Frederic Ebstein, Sebastien Kuery, Victoria Most, Cory Rosenfelt, Marie-Pier Scott-Boyer, Geeske M. van Woerden, Thomas Besrard, Jonas Johannes Papendorf, Maja Studencka-Turski, Tianyun Wang, Tzung-Chien Hsieh, Richard Golnik, Dustin Baldridge, Cara Forster, Charlotte de Konink, Selina M. W. Teurlings, Virginie Vignard, Richard H. van Jaarsveld, Lesley Ades, Benjamin Cogne, Cyril Mignot, Wallid Deb, Marjolijn C. J. Jongmans, F. Sessions Cole, Marie-Jose H. van den Boogaard, Jennifer A. Wambach, Daniel J. Wegner, Sandra Yang, Vickie Hannig, Jennifer Ann Brault, Neda Zadeh, Bruce Bennetts, Boris Keren, Anne-Claire Gelineau, Zoee Powis, Meghan Towne, Kristine Bachman, Andrea Seeley, Anita E. Beck, Jennifer Morrison, Rachel Westman, Kelly Averill, Theresa Brunet, Judith Haasters, Melissa T. Carter, Matthew Osmond, Patricia G. Wheeler, Francesca Forzano, Shehla Mohammed, Yannis Trakadis, Andrea Accogli, Rachel Harrison, Yiran Guo, Hakon Hakonarson, Sophie Rondeau, Genevieve Baujat, Giulia Barcia, Rene Guenther Feichtinger, Johannes Adalbert Mayr, Martin Preisel, Frederic Laumonnier, Tilmann Kallinich, Alexej Knaus, Bertrand Isidor, Peter Krawitz, Uwe Voelker, Elke Hammer, Arnaud Droit, Evan E. Eichler, Ype Elgersma, Peter W. Hildebrand, Francois Bolduc, Elke Krueger, Stephane Bezieau
Summary: This study identified mutations in the PSMC3 gene that are associated with protein homeostasis dysfunction, leading to neurodevelopmental delay and intellectual disability. The mutations affected dendrite development in neurons and impaired learning capabilities in fruit flies, potentially through disruption of protein translocation and induction of proteotoxic stress. The findings suggest a potential link between protein homeostasis dysfunction and neurodevelopmental disorders, opening up new avenues for further research.
SCIENCE TRANSLATIONAL MEDICINE
(2023)
Article
Nutrition & Dietetics
Farzad Mohammadi, Miranda Green, Emma Tolsdorf, Karine Greffard, Mickael Leclercq, Jean-Francois Bilodeau, Arnaud Droit, Jane Foster, Nicolas Bertrand, Iwona Rudkowska
Summary: This study compared the effects of consuming 2-3% industrially originated trans-fatty acids (I-tFAs) and ruminant trans-fatty acids (R-tFAs) on gut microbiome and fecal metabolite profiles in mice. Results showed that TPA intake decreased the abundance of Staphylococcus sp55 but increased Staphylococcus sp119. EA intake also increased the abundance of Staphylococcus sp119 but decreased Ruminococcaceae UCG-014, Lachnospiraceae, and Clostridium sensu stricto 1. Fecal short-chain fatty acids were increased after TPA while decreased after EA after 7 and 28 days. This study highlights the distinct effects of TPA and EA on specific microbial taxa and fecal metabolite profiles.
Article
Genetics & Heredity
Gabriel Lamothe, Julie Carbonneau, Charles Joly Beauparlant, Thierry Vincent, Patrik Quessy, Anthony Guedon, Gary Kobinger, Jean-Francois Lemay, Guy Boivin, Arnaud Droit, Nathalie Turgeon, Jacques P. Tremblay
Summary: In this study, the THRASOS pipeline was developed to discover lineage-specific mutation signatures and guide the development of CRISPR-based diagnostic tests. Additionally, a strategy to modify loop-mediated isothermal amplification amplicons for use with Cas12 and Cas13 was optimized for future multiplexing. The BA.1 and BA.2 variants of SARS-CoV-2 (Omicron), which share close ancestry, were chosen as candidates for the first test using this workflow. The created test is ideal for settings such as mobile clinics lacking equipment and personnel for Next-Generation Sequencers or Sanger Sequencers.
Article
Chemistry, Analytical
Khawla Seddiki, Frederic Precioso, Melissa Sanabria, Michel Salzet, Isabelle Fournier, Arnaud Droit
Summary: Liquid chromatography-mass spectrometry (LC-MS) is a powerful method for cell profiling in cancer research. However, the presence of noise, peak shifts, and high dimensionality of the data make early cancer diagnosis challenging. This study proposes an end-to-end deep learning methodology that addresses these challenges and preserves the potential of LC-MS data.
ANALYTICAL CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Julien A. Clain, Henintsoa Rabezanahary, Gina Racine, Steven Boutrais, Calaiselvy Soundaramourty, Charles Joly Beauparlant, Mohammad -Ali Jenabian, Arnaud Droit, Petronela Ancuta, Ouafa Zghidi-Abouzid, Jerome Estaquier
Summary: Identifying immune cells and anatomical tissues that contribute to viral reservoirs is crucial in HIV-1 cure research. This study using SIVmac251-infected rhesus macaques found that the liver and lungs showed higher levels of inflammation, pyroptosis, and chemokine genes, as well as ISG transcripts, in the absence of ART. Early ART drastically reduced viral seeding and inflammatory reactions.
Article
Plant Sciences
Clement Plessis, Thomas Jeanne, Antoine Dionne, Julien Vivancos, Arnaud Droit, Richard Hogue
Summary: The taxonomic assignment of sequences obtained through high throughput amplicon sequencing is limited for various applications. To address this issue, a new tool called ASVmaker has been developed to create custom databases and improve the accuracy of specific identifications.