Article
Biology
Arwa Raies, Ewa Tulodziecka, James Stainer, Lawrence Middleton, Ryan S. Dhindsa, Pamela Hill, Ola Engkvist, Andrew R. Harper, Slave Petrovski, Dimitrios Vitsios
Summary: In this study, a stochastic semi-supervised ML framework called DrugnomeAI was developed to estimate the druggability likelihood for every protein-coding gene in the human exome. The tool generates exome-wide predictions based on known drug targets and provides specialized models stratified by disease type or drug therapeutic modality. The results show enrichment of genes previously selected for clinical development programs, as well as genome-wide significance in phenome-wide association studies.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Youlin Zhan, Jiahan Liu, Min Wu, Chris Soon Heng Tan, Xiaoli Li, Le Ou-Yang
Summary: Detecting protein complexes is crucial for studying cellular organizations and functions. Existing computational methods for identifying protein complexes from protein-protein interaction (PPI) networks often ignore the signs of PPIs and do not consider joint clustering of multiple PPI networks. In this study, we propose a novel partially shared signed network clustering (PS-SNC) model that takes into account the signs of PPIs and can identify protein complexes from multiple state-specific signed PPI networks jointly.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemical Research Methods
Xiaodi Yang, Xianyi Lian, Chen Fu, Stefan Wuchty, Shiping Yang, Ziding Zhang
Summary: The study introduces a database called HVIDB that provides comprehensive annotated data on human-virus protein-protein interactions and integrates online PPI prediction tools. Users can easily access reliable information on various human virus PPIs and conduct in-depth analysis through this database.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Lindsey A. Ebke, Satyabrata Sinha, Gayle J. T. Pauer, Stephanie A. Hagstrom
Summary: The study revealed that Tulp1 has two distinct interactomes in photoreceptor cells, binding to compartment-specific proteins in the inner segment and synaptic terminal, and playing a significant role in protein trafficking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Mathematical & Computational Biology
Yekai Zhou, Hongjun Chen, Sida Li, Ming Chen
Summary: The study focuses on databases with structural information of protein-protein interactions, developing a database extension called mPPI for PPI structural visualization. Compared to existing databases, mPPI can display target proteins and their multiple interactors simultaneously, aiding in multi-target drug discovery and protein macro-complex structure prediction.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Biochemical Research Methods
Zaynab Mousavian, Mehran Khodabandeh, Ali Sharifi-Zarchi, Alireza Nadafian, Alireza Mahmoudi
Summary: StrongestPath is a tool that can analyze protein interaction networks, identify interactions with the highest confidence scores, and expand networks. This application is capable of finding proteins that may play important roles in multiple signaling pathways.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Guy Karlebach, Leigh Carmody, Jagadish Chandrabose Sundaramurthi, Elena Casiraghi, Peter Hansen, Justin Reese, Christopher J. Mungall, Giorgio Valentini, Peter N. Robinson
Summary: This article proposes a method called isoform interpretation to infer isoform-specific functions using expectation-maximization. It predicts specific functional annotations for 85,617 isoforms of 17,900 protein-coding genes and outperforms other methods in comparison to manually annotated results.
Article
Multidisciplinary Sciences
Simon Gosset, Annie Glatigny, Melina Gallopin, Zhou Yi, Marion Sale, Marie-Helene Mucchielli-Giorgi
Summary: Protein-protein interactions are crucial for cell processes and analyzing PPI networks can provide insights into protein functions. APPINetwork is a user-friendly open-source package for building and analyzing PPI networks from any species.
Article
Chemistry, Medicinal
Kai-Yang Zhong, Meng-Liang Wen, Fan-Fang Meng, Xin Li, Bei Jiang, Xin Zeng, Yi Li
Summary: In this study, a multimodal deep model called MMDTA was proposed to enhance the prediction of drug-target affinity by integrating heterogeneous information from various modalities of drugs and targets using a hybrid fusion strategy. Experimental results demonstrated that MMDTA outperformed competitive deep learning models, particularly in terms of the key evaluation metric RMSE. Furthermore, MMDTA exhibited excellent generalization and practical application performance on multiple different data sets.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Mohamed Helmy, Miles Mee, Aniket Ranjan, Tong Hao, Marc Vidal, Michael A. Calderwood, Katja Luck, Gary D. Bader
Summary: Understanding protein-protein interactions is crucial for studying biological processes and diseases. The development of a freely-available protein interaction platform allows for standardized storage, visualization, analysis, and dissemination of experimental data.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Genetics & Heredity
Zixuan Meng, Linai Kuang, Zhiping Chen, Zhen Zhang, Yihong Tan, Xueyong Li, Lei Wang
Summary: A prediction model called WPDINM is proposed in this study to detect key proteins based on a novel weighted protein-domain interaction network. Experimental results show that WPDINM achieves significantly higher predictive accuracy for key protein identification compared to traditional competing measures.
FRONTIERS IN GENETICS
(2021)
Article
Cell Biology
Himadri Biswas, Shu-Jun Zhao, Yetunde Makinwa, James S. Bassett, Phillip R. Musich, Jing-Yuan Liu, Yue Zou
Summary: ATR is a PI3K-like kinase protein that plays different roles in the nucleus and mitochondria through isomerization-induced structural changes. This structural alteration defines the subcellular location and compartment-specific functions of ATR, and is essential for promoting cell survival and DNA damage responses.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Microbiology
Gabriel Valiente
Summary: This article provides a systematic review of available virus-host protein-protein interaction database resources, evaluating their specificity, the number of interactions included, and functionality. It also analyzes the overlap of the databases and the structure of the interaction network across viruses and hosts.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nilubon Kurubanjerdjit, Ka-Lok Ng
Summary: This study investigates the role of the oncogenic FoxM1 pathway in controlling the cell cycle process in lung cancer. The findings suggest that a combination of various phytochemicals is effective in the treatment of lung cancer. A web-based system displaying the results of this study has been established for researchers to query.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Christopher D. Go, James D. R. Knight, Archita Rajasekharan, Bhavisha Rathod, Geoffrey G. Hesketh, Kento T. Abe, Ji-Young Youn, Payman Samavarchi-Tehrani, Hui Zhang, Lucie Y. Zhu, Evelyn Popiel, Jean-Philippe Lambert, Etienne Coyaud, Sally W. T. Cheung, Dushyandi Rajendran, Cassandra J. Wong, Hana Antonicka, Laurence Pelletier, Alexander F. Palazzo, Eric A. Shoubridge, Brian Raught, Anne-Claude Gingras
Summary: The study utilized BioID technology to construct a map of subcellular compartments in human cells, identifying the intracellular locations of numerous unique proteins and demonstrating the superior predictive ability of this technique compared to previous methods.
Article
Microbiology
Marton Olbei, Balazs Bohar, David Fazekas, Matthew Madgwick, Padhmanand Sudhakar, Isabelle Hautefort, Aline Metris, Jozsef Baranyi, Robert A. Kingsley, Tamas Korcsmaros
Summary: This study presents SalmoNet2, a major update to the Salmonella strain resource, which includes protein-protein, transcriptional regulatory, and enzyme-enzyme interactions. The update expands the coverage of the database and enhances interoperability with other computational resources.
Article
Multidisciplinary Sciences
Polychronis Pavlidis, Anastasia Tsakmaki, Eirini Pantazi, Katherine Li, Domenico Cozzetto, Jonathan Digby-Bell, Feifei Yang, Jonathan W. Lo, Elena Alberts, Ana Caroline Costa Sa, Umar Niazi, Joshua Friedman, Anna K. Long, Yuchun Ding, Christopher D. Carey, Christopher Lamb, Mansoor Saqi, Matthew Madgwick, Leila Gul, Agatha Treveil, Tamas Korcsmaros, Thomas T. Macdonald, Graham M. Lord, Gavin Bewick, Nick Powell
Summary: This study investigates the mechanisms underlying the non-response to ustekinumab in patients with ulcerative colitis (UC). The authors find that the transcriptional program regulated by IL-22, a cytokine responsive to IL-23, is enriched in non-responders to ustekinumab therapy and is associated with higher colon neutrophil recruitment. They also show that IL-22 plays a role in regulating pro-inflammatory pathways, including neutrophil chemotaxis, in UC. The findings provide insights into the biology of IL-22 in UC and its impact on patient trajectories and responsiveness to treatment.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, General & Internal
James L. Alexander, Benjamin H. Mullish, Nathan P. Danckert, Zhigang Liu, Marton L. Olbei, Aamir Saifuddin, Melissa Torkizadeh, Hajir Ibraheim, Jesus Miguens Blanco, Lauren A. Roberts, Claire M. Bewshea, Rachel Nice, Simeng Lin, Hemanth Prabhudev, Caroline Sands, Verena Horneffer-van der Sluis, Matthew Lewis, Shaji Sebastian, Charlie W. Lees, Julian P. Teare, Ailsa Hart, James R. Goodhand, Nicholas A. Kennedy, Tamas Korcsmaros, Julian R. Marchesi, Tariq Ahmad, Nick Powell
Summary: Gut microbiota and metabolome variation may explain variable serological response to vaccination against SARS-CoV-2 in immunosuppressed IBD patients. Lower gut microbiota diversity was associated with poorer response, while certain microbial taxa and metabolites were associated with better or poorer response. This study suggests a potential role for gut microbiota and metabolites in modulating the immune response.
Article
Biochemistry & Molecular Biology
Bence Hajdu, Luca Csabai, Margita Marton, Marianna Holczer, Tamas Korcsmaros, Orsolya Kapuy
Summary: This study explores the regulatory network of autophagy and identifies 16 potential regulators that could be targeted for anti-cancer and anti-aging therapies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Letter
Biotechnology & Applied Microbiology
Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar, Vincent J. Carey, Pornpimol Charoentong, Katharina Danhauser, Tunca Dogan, Johann Dreo, Ian Dunham, Elias Farr, Adria Fernandez-Torras, Benjamin M. Gyori, Michael Hartung, Charles Tapley Hoyt, Christoph Klein, Tamas Korcsmaros, Andreas Maier, Matthias Mann, David Ochoa, Elena Pareja-Lorente, Ferdinand Popp, Martin Preusse, Niklas Probul, Benno Schwikowski, Buenyamin Sen, Maximilian T. Strauss, Denes Turei, Erva Ulusoy, Dagmar Waltemath, Judith A. H. Wodke, Julio Saez-Rodriguez
NATURE BIOTECHNOLOGY
(2023)
Article
Biology
Navin Ray, Seung Jun Park, Hoyung Jung, Juil Kim, Tamas Korcsmaros, Yuseok Moon
Summary: Stress-responsive Growth Differentiation Factor 15 (Gdf15) contributes to controlling acute renointestinal distress by reorganizing cell-protective autophagic signalling and muco-regulatory microbiota, facilitating mucin production and cellular protection. Clinical transcriptome analysis showed a positive association between PKR and Gdf15 expression in patients with renal injury, and the genetic ablation of Gdf15 worsened chemical-induced lesions in renal tissues and the gut barrier. Additionally, Gdf15 was found to be associated with the abundance of mucin metabolism-linked bacteria and their enzymes. Overall, the activation of Gdf15 counteracts pathological processes by reprogramming the autophagic network and microbial community, providing potential biomarkers and interventions for renointestinal distress.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jonathan W. Lo, Domenico Cozzetto, James L. Alexander, Nathan P. Danckert, Matthew Madgwick, Naomi Knox, Jillian Yong Xin Sieh, Marton Olbei, Zhigang Liu, Hajir Ibraheim, Jesus Miguens Blanco, Hiromi Kudo, Rocio Castro Seoane, Lucia A. Possamai, Robert Goldin, Julian Marchesi, Tamas Korcsmaros, Graham M. Lord, Nick Powell
Summary: Immune checkpoint inhibitors (CPIs) are a new cancer treatment that can potentially cure previously untreatable diseases. However, they can also cause off-target immune-mediated tissue injury. Researchers found that CPI-colitis in mice depends on the composition of the intestinal microbiota and the expression of certain immune molecules. Targeting these factors may hold the key to reversing CPI-colitis.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Federico Bernuzzi, Andre Maertens, Shikha Saha, Perla Troncoso-Rey, Tobias Ludwig, Karsten Hiller, Richard F. Mithen, Tamas Korcsmaros, Maria H. Traka
Summary: Sulforaphane regulates glucose metabolism and ameliorates glucose overload and oxidative stress in human hepatoma cells by activating NRF2, and its effects are mediated through NRF2.
Article
Multidisciplinary Sciences
Manuel Corpas, Carmen de Mendoza, Victor Moreno-Torres, Ilduara Pintos, Pedro Seoane, James R. Perkins, Juan A. G. Ranea, Segun Fatumo, Tamas Korcsmaros, Jose Manuel Martin-Villa, Pablo Barreiro, Octavio Corral, Vicente Soriano
Summary: Characterization of host genetic factors contributing to COVID-19 severity reveals a possible role of T cell response dysfunction, as indicated by the identification of variants in the T cell receptor beta locus associated with severe COVID-19.
Meeting Abstract
Gastroenterology & Hepatology
D. Modos, M. Poletti, J. Brooks-Warburton, B. Bohar, M. Madgwick, B. Verstockt, S. Vermeire, S. Carding, T. Korcsmaros
JOURNAL OF CROHNS & COLITIS
(2023)
Meeting Abstract
Gastroenterology & Hepatology
M. Olbei, D. Modos, D. Cozzetto, N. Powell, T. Korcsmaros
JOURNAL OF CROHNS & COLITIS
(2023)
Meeting Abstract
Gastroenterology & Hepatology
A. Saifuddin, M. Madgwick, D. Cozzetto, P. Pavlidis, B. Verstockt, A. Hart, T. Korcsmaros, N. Powell
JOURNAL OF CROHNS & COLITIS
(2023)
Meeting Abstract
Gastroenterology & Hepatology
D. Modos, L. Gul, J. Lo, M. Madgwick, D. Cozzetto, G. Lord, T. Korcsmaros, N. Powell
JOURNAL OF CROHNS & COLITIS
(2022)
Meeting Abstract
Gastroenterology & Hepatology
M. Olbei, J. Thomas, I. Hautefort, A. Treveil, B. Bohar, M. Madgwick, L. Gul, L. Csabai, D. Modos, T. Korcsmaros
JOURNAL OF CROHNS & COLITIS
(2022)
Meeting Abstract
Gastroenterology & Hepatology
L. Potari-gul, D. Modos, S. Fonseca, M. Madgwick, J. P. Thomas, P. Sudhakar, C. Booth, R. Stentz, S. R. Carding, T. Korcsmaros
JOURNAL OF CROHNS & COLITIS
(2022)