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Topic Review
Deep Learning for Protein-Protein Interaction
Deep learning is steadily leaving its transformative imprint across multiple disciplines. Within computational biology, it is expediting progress in the understanding of Protein–Protein Interactions (PPIs), key components governing a wide array of biological functionalities.
  • 201
  • 04 Jul 2023
Topic Review
Deep Learning in Predicting Aging-Related Diseases
Aging refers to progressive physiological changes in a cell, an organ, or the whole body of an individual, over time. Aging-related diseases are highly prevalent and could impact an individual’s physical health. Recently, artificial intelligence (AI) methods have been used to predict aging-related diseases and issues, aiding clinical providers in decision-making based on patient’s medical records. Deep learning (DL), as one of the most recent generations of AI technologies, has embraced rapid progress in the early prediction and classification of aging-related issues.
  • 635
  • 29 Nov 2021
Topic Review
Deep Learning in Whole Slide Imaging for Cancer
The significant progress made in the field of cancer prognosis using whole slide images (WSIs) is encouraging, indicating a promising future for cancer diagnosis and management. The ability to accurately predict survival rates and recurrence risk using deep learning methods has significant implications for clinical practice and patient care. As more sophisticated models and techniques are developed, the potential to revolutionize the field of oncology is immense.
  • 204
  • 02 Aug 2023
Topic Review
Directed Cycles Evolve with Junk DNA
Cell responses are usually viewed as transitive events with fixed inputs and outputs that are regulated by feedback loops. In contrast, directed cycles (DCs) have all nodes connected, and the flow is in a single direction. Consequently, DCs can regenerate themselves and implement intransitive logic. DCs are able to couple unrelated chemical reactions to each edge. The output depends upon which node is used as input.
  • 145
  • 22 Nov 2023
Topic Review
Disordered Proteins and Dynamic Interactions
Intrinsically disordered proteins (IDPs) or regions (IDRs), compared to the well-structural proteins, do not have stable tertiary structures under physiological conditions, and even remain dynamic in specific complexes and functional assemblies. It is now recognized that they are highly prevalent and play important roles in biology and human diseases due to the presence of many representative conformational states and potential dynamic interactions, which requires computer simulations for describing disordered protein ensembles and dynamic interactions involved in biological functions, diseases, and therapeutics.
  • 767
  • 27 Oct 2021
Topic Review
Genome by Multidimensional Scaling
The positions of enhancers and promoters on genomic DNA remain poorly understood. Chromosomes cannot be observed during the cell division cycle because the genome forms a chromatin structure and spreads within the nucleus. However, high-throughput chromosome conformation capture (Hi-C) measures the physical interactions of genomes. In previous studies, DNA extrusion loops  were directly derived from Hi-C heat maps. By using Multidimensional Scaling (MDS), we can easily locate enhancers and promoters more precisely.
  • 448
  • 31 Oct 2021
Topic Review
Genome-Scale Metabolic Modelling
Genome-scale metabolic models (GEMs) aim to systematically encode knowledge of the metabolism of an organism. GEMs are composed of different layers of information and are constructed with a combination of automated approaches and manual curation based on the available literature and experimental data. These models not only encode existing knowledge about an organism, but can also generate new knowledge through various analytical methods. The latter are mostly focused on the assessment of reaction fluxes through the metabolic network in different conditions.
  • 422
  • 28 Jan 2023
Topic Review
Global Trends in Cancer Nanotechnology
This study presents a new way to investigate comprehensive trends in cancer nanotechnology research in different countries, institutions, and journals providing critical insights to prevention, diagnosis, and therapy. This paper applies the qualitative method of bibliometric analysis on cancer nanotechnology using the PubMed database during the years 2000-2021. Inspired by hybrid medical models and content-based and bibliometric features for machine learning models, our results show cancer nanotechnology studies have expanded exponentially since 2010. The highest production of articles in cancer nanotechnology is mainly from US institutions, with several countries notably the USA, China, UK, India, and Iran as concentrated focal points as centers of cancer nanotechnology research, especially in the last five years. The analysis shows the greatest overlap between nanotechnology and DNA, RNA, iron oxide or mesoporous silica, breast cancer, and cancer diagnosis and cancer treatment. Moreover, more than 50% of information related to the keywords, authors, institutions, journals, and countries are considerably investigated in the form of publications from the top 100 journals. This study has the potentials to provide past and current lines of research that can unmask comprehensive trends in cancer nanotechnology, key research topics, or pmost productive countries and authors in the field.
  • 374
  • 10 Sep 2021
Topic Review
Hydrotropism
Hydrotropism is the movement or growth of a plant towards water. It is a type of tropism, or directional growth response, that is triggered by water. Plants are able to detect water through various stimuli, including changes in moisture levels and changes in water potential. 
  • 297
  • 23 Feb 2023
Topic Review
Imaging Techniques for Cardiac Function
Cardiac imaging techniques include a variety of distinct applications with which we can visualize cardiac function non-invasively. Through different applications of physical entities such as sound waves, X-rays, magnetic fields, and nuclear energy, along with highly sophisticated computer hardware and software, it is now possible to reconstruct the dynamic aspect of cardiac function in many forms, from static images to high-definition videos and real-time three-dimensional projections.
  • 329
  • 19 Nov 2021
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