Article
Biochemical Research Methods
Lakshay Anand, Carlos M. Rodriguez Lopez
Summary: ChromoMap is an R package for the construction of interactive visualizations of chromosomes and feature-associated multi-omics data, providing flexibility and extensive application.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Yuanpeng Zhang, Kaijian Xia, Yizhang Jiang, Pengjiang Qian, Weiwei Cai, Chengyu Qiu, Khin Wee Lai, Dongrui Wu
Summary: With the development of sensors, there is an increasing amount of multimodal data in biomedical and bioinformatics fields. This study proposes a feature-level multimodal fusion model using multi-kernel learning and transfer learning, specifically designed for insufficient training samples. The model achieved better performance compared to baselines in multiple scenarios evaluated using epilepsy EEG data.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Review
Biochemical Research Methods
Abubakar Abdussalam, Guobao Xu
Summary: ECL has advantages like near-zero background response, and ECL luminophores play an essential role in the light generation process. Despite advancements in synthesizing new luminophores, there is a lack of comprehensive summaries on ECL luminophores. This review discusses recent advances in various types of ECL luminophores and their roles.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Idris Salmon, Sergei Grebenyuk, Abdel Rahman Abdel Fattah, Gregorius Rustandi, Thomas Pilkington, Catherine Verfaillie, Adrian Ranga
Summary: The generation of tissue and organs requires close interaction with vasculature. This study presents a 3D printing-based platform that allows pluripotent stem cells to interact with vascular cells in a spatially determined manner, resulting in the formation of organized vascular networks. This method provides a means to vascularize organoids and opens new avenues for understanding and manipulating the co-development of tissue-specific organoids with vasculature.
Article
Biochemical Research Methods
Bo-Wei Zhao, Lun Hu, Zhu-Hong You, Lei Wang, Xiao-Rui Su
Summary: Identifying new indications for drugs is crucial in drug research and development. Computational methods, particularly the HINGRL model proposed in this study, that utilize heterogeneous information networks and graph representation learning techniques have shown promising performance in accurately predicting drug-disease associations. By integrating biological networks and knowledge, HINGRL considers both network topology and biological perspectives, leading to improved accuracy. The results demonstrate HINGRL's superiority over state-of-the-art models and its potential in identifying novel drug-disease associations for new diseases.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemical Research Methods
Jingxin Dong, Mingyi Zhao, Yuansheng Liu, Yansen Su, Xiangxiang Zeng
Summary: This review comprehensively summarizes the development process of retrosynthesis in the context of deep learning, covering aspects such as datasets, models, and tools. Representative models from academia and available platforms in the industry are discussed. The review also addresses the limitations of existing models and provides potential future trends for beginners to understand and participate in retrosynthesis planning.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Xiaoquan Chu, Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai, Jianfeng Pei
Summary: A sequence-based prediction tool for LLPS proteins (PSPredictor) was developed with a machine learning algorithm, achieving an accuracy of 94.71% in tenfold cross-validation and outperforming previously reported PSPs prediction tools. A user-friendly PSPredictor web server was built for predicting potential PSPs.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Song Zhang, Kuerbannisha Amahong, Chenyang Zhang, Fengcheng Li, Jianqing Gao, Yunqing Qiu, Feng Zhu
Summary: This study demonstrates that the genomic RNA of SARS-CoV-2 can absorb host miRNAs that regulate immune-related genes, suggesting that this may be a crucial mechanism for the virus to survive and develop in the host. By analyzing miRNA datasets and identifying enriched immune-related pathways and protein-protein interactions, the study reveals an imbalance in the host immune response caused by the absorption of SARS-CoV-2 to host miRNAs, with implications for infection and pathogenesis. Additionally, the study finds that the absorption of host miRNAs by SARS-CoV-2 may contribute to the increased infectivity and pathogenicity of certain mutant strains.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Farhat Afza, Muhammad Sharif, Mamta Mittal, Muhammad Attique Khan, Jude Hemanth
Summary: A hierarchical framework based on two-dimensional superpixels and deep learning was proposed to improve the accuracy of skin cancer classification. By enhancing original images, segmenting lesions, and applying a deep learning model with optimization algorithms, high accuracies were achieved on three different datasets, showing the potential of this method for skin cancer classification.
Article
Biochemical Research Methods
Yuki Miura, Min-Yin Li, Omer Revah, Se-Jin Yoon, Genta Narazaki, Sergiu P. Pasca
Summary: This article describes a method for generating human brain assembloids and studying neural circuits. By converting human pluripotent stem cells into brain region-specific organoids, which are then fused and integrated to form assembloids, complex cell-cell interactions, circuit formation, and maturation can be studied using self-organization. A series of assays, including viral labeling and retrograde tracing, 3D live imaging, and electrophysiology, are used to model and manipulate neural circuits in the assembloids. These approaches are valuable for understanding human-specific aspects of neural circuit assembly and modeling neurodevelopmental disorders.
Article
Biochemical Research Methods
Anne F. Nielsen, Albrecht Bindereif, Irene Bozzoni, Mor Hanan, Thomas B. Hansen, Manuel Irimia, Sebastian Kadener, Lasse S. Kristensen, Ivano Legnini, Mariangela Morlando, Morten T. Jarlstad Olesen, R. Jeroen Pasterkamp, Stephan Preibisch, Nikolaus Rajewsky, Christin Suenkel, Jorgen Kjems
Summary: There is a growing number of circular RNA (circRNA) papers in recent years, highlighting the urgent need for common experimental standards and best practice principles to advance the field and enhance understanding of this group of RNA molecules.
Article
Biochemical Research Methods
Anqi Lin, Chang Qi, Ting Wei, Mengyao Li, Quan Cheng, Zaoqu Liu, Peng Luo, Jian Zhang
Summary: Immune checkpoint inhibitors (ICIs) and immunotherapy have revolutionized tumor diagnostics and treatment. However, current web tools lack the ability to facilitate data mining and mechanism analyses specifically related to immunotherapy. Therefore, the development of the web-based tool CAMOIP provides a comprehensive analysis of biomarkers for immunotherapy and enables various analyses, promoting the further development of immunotherapy.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Supat Chupradit, Mahyuddin K. M. Nasution, Heshu Sulaiman Rahman, Wanich Suksatan, Abduladheem Turki Jalil, Walid Kamal Abdelbasset, Dmitry Bokov, Alexander Markov, Irina N. Fardeeva, Gunawan Widjaja, Mohammed Nader Shalaby, Marwan Mahmood Saleh, Yasser Fakri Mustafa, A. Surendar, Ramtin Bidares
Summary: Leukemia is a disease caused by dysfunctions in hematopoietic stem cells lineages, and different types of leukemia require different diagnosis and treatment options. Early detection is crucial for effective treatment, and genosensors and electrochemical sensors can help detect cancer cells and leukemia-related genes. The use of nanomaterials can increase the sensitivity of detection.
ANALYTICAL BIOCHEMISTRY
(2022)
Review
Biochemical Research Methods
Shaoqiong Liu, Chau-Sang Lau, Kun Liang, Feng Wen, Swee Hin Teoh
Summary: This article reviews the advances in the design and fabrication of marine collagen-based constructs for medical applications and highlights the potential applications of marine collagen in the regeneration of skin, bone and cartilage.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Michelle S. Frei, Miroslaw Tarnawski, M. Julia Roberti, Birgit Koch, Julien Hiblot, Kai Johnsson
Summary: HaloTag variants offer unique brightness and fluorescence lifetimes compared to HaloTag7 when labeled with rhodamines, enabling multiplexed imaging and creating cell cycle indicators. These variants are powerful tools for fluorescence microscopy and can be used to generate fluorescence lifetime-based biosensors, with the brightest variant showing up to 40% higher brightness in live-cell imaging applications.
Review
Biochemical Research Methods
Ingela Lanekoff, Varun V. Sharma, Catia Marques
Summary: Single-cell metabolomics with mass spectrometry allows for the detection of multiple metabolites from individual cells simultaneously, providing insights into phenotypes at the single-cell level. This field is steadily progressing, with an increasing number of research groups, advancements in cell sampling and ionization techniques, data analysis tools, and applications in various biomedical and environmental studies.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Yongxiang Feng, Zhen Cheng, Huichao Chai, Weihua He, Liang Huang, Wenhui Wang
Summary: The study demonstrates the use of neural network technology to achieve real-time characterization of cellular intrinsic properties and classification based on intrinsic parameters, significantly improving calculation speed. Experimental results show a high accuracy in cell type classification and minimal impact on cell properties from IFC testing.
Article
Biochemical Research Methods
Airlie J. McCoy, Massimo D. Sammito, Randy J. Read
Summary: The results of AlphaFold2 in CASP14 indicate that accurate predictions of protein structure domains are on the horizon, regardless of their similarity to known structures. As highly accurate models are generated using correlated mutations and deep learning, methods of phasing in crystallography, especially molecular-replacement phasing using in silico models, are expected to be impacted.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Review
Biochemical Research Methods
Matteo Chialva, Luisa Lanfranco, Paola Bonfante
Summary: Plants in nature interact closely with microbial communities, which are important for understanding plant responses to microbes and driving microbial community structure and function. Rational engineering of plant microbiota can improve the sustainability of agriculture.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Rong Tang, Zijian Wu, Zeyin Rong, Jin Xu, Wei Wang, Bo Zhang, Xianjun Yu, Si Shi
Summary: This study developed an accurate prognostic model based on the expression patterns of ferroptosis-associated lncRNAs, which can contribute greatly to the evaluation of patient prognosis, molecular characteristics, and treatment modalities in PDAC. The study identified novel ferroptosis-related lncRNAs and validated their role in ferroptosis resistance. There were significant differences between patients with different risk scores and potential drugs for the treatment of low-risk patients were identified.
BRIEFINGS IN BIOINFORMATICS
(2022)
