Article
Biochemical Research Methods
Lanlan Wu, Fei Liu, Hongmin Cai
Summary: IOAT is an interactive desktop tool developed to assist non-technical users in safely and conveniently analyzing private multi-omics data while combining clinical information. Users can conduct data preprocessing, feature selection, risk assessment, clustering, and survival analysis through this tool to find a suitable model for their data.
BMC BIOINFORMATICS
(2021)
Article
Plant Sciences
Hua Cheng, Hua Zhang, Jing Song, Jiafu Jiang, Sumei Chen, Fadi Chen, Likai Wang
Summary: Horticultural plants greatly contribute to human's life quality. However, the current resources for cross-species data mining in this field are not satisfactory. GERDH, a database platform based on uniformly processed publicly available omics libraries, allows for interactive cross-species analysis and identification of key genes, such as those related to postharvest storage.
Article
Biochemistry & Molecular Biology
Swapnil Potdar, Filipp Ianevski, Aleksandr Ianevski, Ziaurrehman Tanoli, Krister Wennerberg, Brinton Seashore-Ludlow, Olli Kallioniemi, Paeivi Ostling, Tero Aittokallio, Jani Saarela
Summary: Functional precision medicine (fPM) simplifies the search for appropriate applications of existing molecules and enhances therapeutic potential. The latest version of Breeze (release 2.0) provides advanced data exploration capabilities and interactive visualization options for accurate interpretation of drug sensitivity and resistance data. It allows integration and cross-comparison of user-uploaded data with publicly available drug response datasets.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Shichao Ma, Xiunan Fang, Yu Yao, Jianfu Li, Daniel C. Morgan, Yongyan Xia, Crystal S. M. Kwok, Michelle C. K. Lo, Dickson M. D. Siu, Kevin K. Tsia, Andrian Yang, Joshua W. K. Ho
Summary: StarmapVis is a convenient web application that provides an interactive downstream analysis of single-cell expression or spatial transcriptomic data. It offers visualization tools from multiple angles to display clustering information and connectivity networks among coordinates. The tool also has a unique feature of automated animation of camera view and provides a useful animated transition between two-dimensional spatial omic data and three-dimensional single cell coordinates.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Muhammad Arif, Cheng Zhang, Xiangyu Li, Cem Gungor, Bugra Cakmak, Metin Arslanturk, Abdellah Tebani, Berkay Ozcan, Oguzhan Subas, Wenyu Zhou, Brian Piening, Hasan Turkez, Linn Fagerberg, Nathan Price, Leroy Hood, Michael Snyder, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu
Summary: iNetModels is an interactive database and visualization platform that showcases the associations between various omics data, allowing users to explore human wellness and disease research with ease.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Pharmacology & Pharmacy
Yijun Liu, Fuhu Song, Zhi Li, Liang Chen, Ying Xu, Huiyan Sun, Yi Chang
Summary: Precision medicine in cancer treatment is important to provide specific treatment based on patients' genetic characteristics. However, most current research only focuses on drug effects on cell lines and integrating data for patient treatment requires significant effort. Furthermore, the adverse effects of drugs on patients are often neglected. We developed DBPOM, a web server that considers both efficacy and toxicity of drugs, providing a valuable resource for drug development and mechanism studies.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Biochemical Research Methods
Benbo Gao, Jing Zhu, Soumya Negi, Xinmin Zhang, Stefka Gyoneva, Fergal Casey, Ru Wei, Baohong Zhang
Summary: Quickomics is a feature-rich tool powered by R Shiny that allows biologists to explore complex omics statistical analysis results and perform advanced analysis in an easy-to-use interactive interface. It covers a broad range of secondary and tertiary analytical tasks, with customizable options for each functional module and the generation of both interactive and publication-ready plots to uncover biological insights from data. Its modular design makes the tool easily extensible.
Article
Biochemical Research Methods
Elise Maigne, Celine Noirot, Julien Henry, Yaa Adu Kesewaah, Ludovic Badin, Sebastien Dejean, Camille Guilmineau, Arielle Krebs, Fanny Mathevet, Audrey Segalini, Laurent Thomassin, David Colongo, Christine Gaspin, Laurence Liaubet, Nathalie Vialaneix
Summary: ASTERICS is a publicly available web interface designed for the analyses of omics datasets, providing both standard and complex exploratory and integration analysis workflows. It offers high quality interactive plots and comprehensive documentation. Its modular organization allows easy incorporation of new workflows and analyses, making it a user-friendly platform for omics data exploration and integration.
BMC BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Thomas Naake, Wolfgang Huber
Summary: MatrixQCvis is an interactive data quality metric visualization tool implemented using R's shiny framework. It provides efficient and standardized ways to analyze the quality of quantitative omics data, ensuring high-quality datasets and inference for biological questions.
Article
Biochemistry & Molecular Biology
Fergal Casey, Soumya Negi, Jing Zhu, Yu H. Sun, Maria Zavodszky, Derrick Cheng, Dongdong Lin, Sally John, Michelle A. Penny, David Sexton, Baohong Zhang
Summary: With advancements in NGS technologies, there is a growing need for bench scientists to access and analyze the petabytes of transcriptional profiling data deposited in public repositories. OmicsView is an open source analytics and visualization platform that allows users to easily explore and mine expression data across various disease areas. The platform comes preloaded with thousands of samples from the GTEx database, providing researchers with the capability to uncover disease pathology and identify robust biomarkers.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Rosa Hernansaiz-Ballesteros, Christian H. Holland, Aurelien Dugourd, Julio Saez-Rodriguez
Summary: The FUNKI tool provides a user-friendly interface for analyzing various types of omics data, allowing for visualization and post-analysis. It also offers a scripted version written in R.
Article
Biochemical Research Methods
Joe Wandy, Ronan Daly
Summary: GraphOmics is a user-friendly platform for exploring and integrating multiple omics datasets, allowing for horizontal data integration by mapping biological entities to common reactions and pathways. Demonstrations show that interactive exploration with GraphOmics can rapidly reveal interesting insights and biological hypotheses.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Aman Chandra Kaushik, Mengyang Li, Aamir Mehmood, Xiaofeng Dai, Dong-Qing Wei
Summary: The development of the anti-cancer Scanner (ACPS) tool aims to quickly and accurately identify anti-cancer targets with over 95% accuracy, providing crucial support for current bioinformatics research.
CHEMICAL BIOLOGY & DRUG DESIGN
(2021)
Article
Biochemical Research Methods
Xiaobo Yang, Bei Zhang, Siqi Wang, Ye Lu, Kaixian Chen, Cheng Luo, Aihua Sun, Hao Zhang
Summary: Omics and Text driven Translational Medicine (OTTM) is a classification tool that can accelerate the discovery of effective drugs and targets from omics data.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
Brian B. Nadel, David Lopez, Dennis J. Montoya, Feiyang Ma, Hannah Waddel, Misha M. Khan, Serghei Mangul, Matteo Pellegrini
Summary: The Gene Expression Deconvolution Interactive Tool (GEDIT) is a flexible tool that accurately predicts cell type abundances using gene expression data. Extensive evaluations using simulated and experimental data show that GEDIT performs robustly under a wide variety of conditions, including different platforms, tissue types, and species.
Article
Biochemistry & Molecular Biology
Raffaele Iennaco, Giulio Formenti, Camilla Trovesi, Riccardo Lorenzo Rossi, Chiara Zuccato, Tiziana Lischetti, Vittoria Dickinson Bocchi, Andrea Scolz, Cristina Martinez-Labarga, Olga Rickards, Michela Pacifico, Angelica Crottini, Anders Pape Moller, Richard Zhenghuan Chen, Thomas Francis Vogt, Giulio Pavesi, David Stephen Horner, Nicola Saino, Elena Cattaneo
Summary: This study investigated the function and evolution of the CAG repeat sequence in the Huntingtin gene. It found that the CAG-encoded polyQ sequence is under natural selection and small variations in its length can influence neuronal function. These findings highlight the importance of CAG repeat sequences in evolutionary adaptation.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Multidisciplinary Sciences
Elisabetta Cameroni, John E. Bowen, Laura E. Rosen, Christian Saliba, Samantha K. Zepeda, Katja Culap, Dora Pinto, Laura A. VanBlargan, Anna De Marco, Julia di Iulio, Fabrizia Zatta, Hannah Kaiser, Julia Noack, Nisar Farhat, Nadine Czudnochowski, Colin Havenar-Daughton, Kaitlin R. Sprouse, Josh R. Dillen, Abigail E. Powell, Alex Chen, Cyrus Maher, Li Yin, David Sun, Leah Soriaga, Jessica Bassi, Chiara Silacci-Fregni, Claes Gustafsson, Nicholas M. Franko, Jenni Logue, Najeeha Talat Iqbal, Ignacio Mazzitelli, Jorge Geffner, Renata Grifantini, Helen Chu, Andrea Gori, Agostino Riva, Olivier Giannini, Alessandro Ceschi, Paolo Ferrari, Pietro E. Cippa, Alessandra Franzetti-Pellanda, Christian Garzoni, Peter J. Halfmann, Yoshihiro Kawaoka, Christy Hebner, Lisa A. Purcell, Luca Piccoli, Matteo Samuele Pizzuto, Alexandra C. Walls, Michael S. Diamond, Amalio Telenti, Herbert W. Virgin, Antonio Lanzavecchia, Gyorgy Snell, David Veesler, Davide Corti
Summary: The Omicron variant of SARS-CoV-2 has raised concerns due to its 37 amino acid substitutions in the spike protein, particularly in the receptor-binding domain (RBD), leading to increased binding affinity with human ACE2. Neutralizing activity against Omicron was greatly reduced in convalescent and vaccinated individuals compared to the ancestral virus, but this decrease was less significant after a third vaccine dose. Broadly neutralizing monoclonal antibodies recognizing conserved RBD epitopes may be crucial in combating the Omicron variant and future zoonotic transmissions.
Article
Genetics & Heredity
Federica Marasca, Shruti Sinha, Rebecca Vadala, Benedetto Polimeni, Valeria Ranzani, Elvezia Maria Paraboschi, Filippo Vittorio Burattin, Marco Ghilotti, Mariacristina Crosti, Maria Luce Negri, Susanna Campagnoli, Samuele Notarbartolo, Andrea Sartore-Bianchi, Salvatore Siena, Daniele Prati, Giovanni Montini, Giuseppe Viale, Olga Torre, Sergio Harari, Renata Grifantini, Giulia Solda, Stefano Biffo, Sergio Abrignani, Beatrice Bodega
Summary: This study reveals how non-canonical splicing variant LINE1 maintains T cell quiescence and interferes with gene expression, thus affecting cell function.
Article
Immunology
Ganesh E. Phad, Dora Pinto, Mathilde Foglierini, Murodzhon Akhmedov, Riccardo L. Rossi, Emilia Malvicini, Antonino Cassotta, Chiara Silacci Fregni, Ludovica Bruno, Federica Sallusto, Antonio Lanzavecchia
Summary: This study provides a systematic description of the structure, stability, and dynamics of the human memory B cell pool, and suggests that memory B cells play a crucial role in the generation of plasma cells.
Review
Immunology
Samuele Notarbartolo, Sergio Abrignani
Summary: CD4(+) and CD8(+) T-RM cells play a crucial role in the adaptive immune response against tumors. However, tumors can evade the surveillance of T-RM cells, leading to clinical manifestation. The generation and maintenance of T-RM cells, as well as their role in antitumor immunity and immunotherapy, are still areas of ongoing research.
SEMINARS IN IMMUNOPATHOLOGY
(2022)
Article
Medicine, General & Internal
Annarita Miluzio, Alessandro Cuomo, Chiara Cordiglieri, Lorena Donnici, Elisa Pesce, Mauro Bombaci, Matteo Conti, Alessandra Fasciani, Luigi Terracciano, Lara Manganaro, Mirco Toccafondi, Alessandra Scagliola, Stefania Oliveto, Sara Ricciardi, Renata Grifantini, Raffaele De Francesco, Sergio Abrignani, Nicola Manfrini, Stefano Biffo
Summary: The study found that the binding of the SARS-CoV-2 virus to hACE2 receptors is the first step in infection, but the abundance of receptors is influenced by various factors. Further research revealed SLC1A5 as a factor involved in receptor localization and viral entry, and co-expression with hACE2 improved the prediction of SARS-CoV-2 binding and entry. The Omicron variant showed higher efficiency in binding to hACE2 sites, but was equally sensitive to SLC1A5 downregulation.
Article
Biochemistry & Molecular Biology
Lisa Pagani, Clizia Chinello, Giulia Risca, Giulia Capitoli, Lucrezia Criscuolo, Andrea Lombardi, Riccardo Ungaro, Davide Mangioni, Isabella Piga, Antonio Muscatello, Francesco Blasi, Andrea Favalli, Martina Martinovic, Andrea Gori, Alessandra Bandera, Renata Grifantini, Fulvio Magni
Summary: By studying the plasma proteome of 43 COVID-19 patients, differentially expressed proteins related to the severity of infection were identified. Three proteins were found to be able to accurately distinguish different stages of infection. These proteins may be associated with the severity of the disease and the immune response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pharmacology & Pharmacy
Giulia Birolini, Marta Valenza, Ilaria Ottonelli, Francesca Talpo, Lucia Minoli, Andrea Cappelleri, Mauro Bombaci, Claudio Caccia, Caterina Canevari, Arianna Trucco, Valerio Leoni, Alice Passoni, Monica Favagrossa, Maria Rosaria Nucera, Laura Colombo, Saverio Paltrinieri, Renzo Bagnati, Jason Thomas Duskey, Riccardo Caraffi, Maria Angela Vandelli, Franco Taroni, Mario Salmona, Eugenio Scanziani, Gerardo Biella, Barbara Ruozi, Giovanni Tosi, Elena Cattaneo
Summary: The study demonstrates that delivering cholesterol to the brain using nanoparticles can effectively reverse cognitive decline and neuropathological signs in Huntington's disease (HD). The administration of hybrid-g7-NPs-chol in both early and late stages of HD shows long-term therapeutic effects without adverse reactions. The findings highlight the therapeutic potential of cholesterol-based strategies in HD patients.
PHARMACOLOGICAL RESEARCH
(2023)
Article
Immunology
Elisa Pesce, Chiara Cordiglieri, Mauro Bombaci, Serenella Eppenberger-Castori, Stefania Oliveto, Cristina Manara, Mariacristina Crosti, Caner Ercan, Mairene Coto, Andrea Gobbini, Susanna Campagnoli, Tiziano Donnarumma, Manuele Martinelli, Valeria Bevilacqua, Elisa De Camilli, Paola Gruarin, Maria L. Sarnicola, Elisa Cassinotti, Ludovica Baldari, Giuseppe Viale, Stefano Biffo, Sergio Abrignani, Luigi M. Terracciano, Renata Grifantini
Summary: Colorectal cancer (CRC) is a major cause of cancer-related death. The interplay between effector immune cells and cancer cells in the tumor site plays a key role in determining tumor elimination or outgrowth. TMEM123 protein is over-expressed in infiltrating CD4 and CD8 T lymphocytes and contributes to their effector phenotype. TMEM123 plays a role in lymphocyte migration and cytoskeleton organization, and its presence is associated with improved survival in CRC patients.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Ylenia Silvestri, Francesca Clemente, Giorgia Moschetti, Sara Maioli, Elena Carelli, Alejandro Espadas de Arias, Rosanna Torelli, Elena Longhi, Tullia De Feo, MariaCristina Crosti, Maria Lucia Sarnicola, Mario Salvi, Giovanna Mantovani, Maura Arosio, Mauro Bombaci, Elisa Pesce, Renata Grifantini, Sergio Abrignani, Jens Geginat, Ilaria Muller
Summary: SARS-CoV-2 infection can lead to thyroid disorders like subacute thyroiditis (SAT). This study aimed to investigate the role of T-cells in SAT following severe COVID disease (COV-A-SAT). T-cells from COV-A-SAT patients were analyzed and compared to controls. The results showed that COV-A-SAT was associated with specific HLA haplotypes and activated T-cell responses. Tissue-resident memory cells were present in the thyroid, suggesting a prolonged immune response in the target tissue.
CLINICAL IMMUNOLOGY
(2023)
Correction
Immunology
Elisa Pesce, Chiara Cordiglieri, Mauro Bombaci, Serenella Eppenberger-Castori, Stefania Oliveto, Cristina Manara, Mariacristina Crosti, Caner Ercan, Mairene Coto, Andrea Gobbini, Susanna Campagnoli, Tiziano Donnarumma, Manuele Martinelli, Valeria Bevilacqua, Elisa De Camilli, Paola Gruarin, Maria L. Sarnicola, Elisa Cassinotti, Ludovica Baldari, Giuseppe Viale, Stefano Biffo, Sergio Abrignani, Luigi M. Terracciano, Renata Grifantini
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Health Care Sciences & Services
Andrea Lombardi, Giacomo M. Butta, Lorena Donnici, Giorgio Bozzi, Massimo Oggioni, Patrizia Bono, Malvina Matera, Dario Consonni, Serena Ludovisi, Antonio Muscatello, Ferruccio Ceriotti, Matteo Conti, Susanna Scaglioni, Greta Gallo, Edoardo Scarpa, Michael Letko, Sergio Abrignani, Renata Grifantini, Raffaele De Francesco, Andrea Gori, Lara Manganaro, Alessandra Bandera
Summary: This study assessed the immunogenicity of the mRNA-1273 vaccine in people living with HIV (PLWHIV). The results showed that in PLWHIV with well-controlled ART, viral suppression, and CD4+ T cell count, inoculation with the mRNA-1273 vaccine produced detectable antibody response, similar to individuals without HIV infection.
LANCET REGIONAL HEALTH-EUROPE
(2022)