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Martini L, Baek SH, Lo I, Raby BA, Silverman E, Weiss S, Glass K, Halu A. Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions. Nucleic Acids Res 2024; 52:e5. [PMID: 37953325 PMCID: PMC10783515 DOI: 10.1093/nar/gkad1035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 06/27/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
The versatility of cellular response arises from the communication, or crosstalk, of signaling pathways in a complex network of signaling and transcriptional regulatory interactions. Understanding the various mechanisms underlying crosstalk on a global scale requires untargeted computational approaches. We present a network-based statistical approach, MuXTalk, that uses high-dimensional edges called multilinks to model the unique ways in which signaling and regulatory interactions can interface. We demonstrate that the signaling-regulatory interface is located primarily in the intermediary region between signaling pathways where crosstalk occurs, and that multilinks can differentiate between distinct signaling-transcriptional mechanisms. Using statistically over-represented multilinks as proxies of crosstalk, we infer crosstalk among 60 signaling pathways, expanding currently available crosstalk databases by more than five-fold. MuXTalk surpasses existing methods in terms of model performance metrics, identifies additions to manual curation efforts, and pinpoints potential mediators of crosstalk. Moreover, it accommodates the inherent context-dependence of crosstalk, allowing future applications to cell type- and disease-specific crosstalk.
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Affiliation(s)
- Leonardo Martini
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Computer, Control, and Management Engineering, Sapienza University of Rome, Rome, 00185, Italy
| | - Seung Han Baek
- Division of Pulmonary Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ian Lo
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Benjamin A Raby
- Division of Pulmonary Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Arda Halu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
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Fu B, Zhang X, Wang L, Ren Y, Thanh DNH. Double enhanced residual network for biological image denoising. Gene Expr Patterns 2022; 45:119270. [PMID: 36028213 DOI: 10.1016/j.gep.2022.119270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022]
Abstract
With the achievements of deep learning, applications of deep convolutional neural networks for the image denoising problem have been widely studied. However, these methods are typically limited by GPU in terms of network layers and other aspects. This paper proposes a multi-level network that can efficiently utilize GPU memory, named Double Enhanced Residual Network (DERNet), for biological-image denoising. The network consists of two sub-networks, and U-Net inspires the basic structure. For each sub-network, the encoder-decoder hierarchical structure is used for down-scaling and up-scaling feature maps so that GPU can yield large receptive fields. In the encoder process, the convolution layers are used for down-sampling to obtain image information, and residual blocks are superimposed for preliminary feature extraction. In the operation of the decoder, transposed convolution layers have the capability to up-sampling and combine with the Residual Dense Instance Normalization (RDIN) block that we propose, extract deep features and restore image details. Finally, both qualitative experiments and visual effects demonstrate the effectiveness of our proposed algorithm.
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Affiliation(s)
- Bo Fu
- School of Computer and Information Technology, Liaoning Normal University, 116081, China
| | - Xiangyi Zhang
- School of Computer and Information Technology, Liaoning Normal University, 116081, China
| | - Liyan Wang
- School of Computer and Information Technology, Liaoning Normal University, 116081, China
| | - Yonggong Ren
- School of Computer and Information Technology, Liaoning Normal University, 116081, China.
| | - Dang N H Thanh
- Department of Information Technology, College of Technology and Design, University of Economics Ho Chi Minh City, Ho Chi Minh City, Viet Nam.
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Stolz BJ, Kaeppler J, Markelc B, Braun F, Lipsmeier F, Muschel RJ, Byrne HM, Harrington HA. Multiscale topology characterizes dynamic tumor vascular networks. SCIENCE ADVANCES 2022. [PMID: 35687679 DOI: 10.48550/arxiv.2008.08667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Advances in imaging techniques enable high-resolution three-dimensional (3D) visualization of vascular networks over time and reveal abnormal structural features such as twists and loops, and their quantification is an active area of research. Here, we showcase how topological data analysis, the mathematical field that studies the "shape" of data, can characterize the geometric, spatial, and temporal organization of vascular networks. We propose two topological lenses to study vasculature, which capture inherent multiscale features and vessel connectivity, and surpass the single-scale analysis of existing methods. We analyze images collected using intravital and ultramicroscopy modalities and quantify spatiotemporal variation of twists, loops, and avascular regions (voids) in 3D vascular networks. This topological approach validates and quantifies known qualitative trends such as dynamic changes in tortuosity and loops in response to antibodies that modulate vessel sprouting; furthermore, it quantifies the effect of radiotherapy on vessel architecture.
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Affiliation(s)
| | - Jakob Kaeppler
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Bostjan Markelc
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Franziska Braun
- Data Science, pRED Informatics, Pharma Research & Early Development, Roche Innovation Center Munich, Munich, Germany
| | - Florian Lipsmeier
- Digital Biomarkers, pRED Informatics, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Ruth J Muschel
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Helen M Byrne
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Heather A Harrington
- Mathematical Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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Stolz BJ, Kaeppler J, Markelc B, Braun F, Lipsmeier F, Muschel RJ, Byrne HM, Harrington HA. Multiscale topology characterizes dynamic tumor vascular networks. SCIENCE ADVANCES 2022; 8:eabm2456. [PMID: 35687679 PMCID: PMC9187234 DOI: 10.1126/sciadv.abm2456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Advances in imaging techniques enable high-resolution three-dimensional (3D) visualization of vascular networks over time and reveal abnormal structural features such as twists and loops, and their quantification is an active area of research. Here, we showcase how topological data analysis, the mathematical field that studies the "shape" of data, can characterize the geometric, spatial, and temporal organization of vascular networks. We propose two topological lenses to study vasculature, which capture inherent multiscale features and vessel connectivity, and surpass the single-scale analysis of existing methods. We analyze images collected using intravital and ultramicroscopy modalities and quantify spatiotemporal variation of twists, loops, and avascular regions (voids) in 3D vascular networks. This topological approach validates and quantifies known qualitative trends such as dynamic changes in tortuosity and loops in response to antibodies that modulate vessel sprouting; furthermore, it quantifies the effect of radiotherapy on vessel architecture.
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Affiliation(s)
| | - Jakob Kaeppler
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Bostjan Markelc
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Franziska Braun
- Data Science, pRED Informatics, Pharma Research & Early Development, Roche Innovation Center Munich, Munich, Germany
| | - Florian Lipsmeier
- Digital Biomarkers, pRED Informatics, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Ruth J. Muschel
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Helen M. Byrne
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Heather A. Harrington
- Mathematical Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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