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Medical Bioinformatics

Section edited by Michele Ceccarelli

© metamorworks / Getty Images / iStockThe explosion of genome sequencing data along with genotype to phenotype correlation studies has created data deluge in the area of biomedical sciences. The aim of the Medical bioinformatics section is to aid the development and maturation of the field by providing a platform for the translation of these datasets into useful clinical applications. The increase in computing capabilities and availability of different data from advanced technologies will allow researchers to build System Biology models of various diseases in order to efficiently develop new therapeutic interventions and reduce the current prohibitively large costs of drug discovery.


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  1. Machine learning (ML) represents a powerful tool to capture relationships between molecular alterations and cancer types and to extract biological information. Here, we developed a plain ML model aimed at dist...

    Authors: Veronica Zelli, Andrea Manno, Chiara Compagnoni, Rasheed Oyewole Ibraheem, Francesca Zazzeroni, Edoardo Alesse, Fabrizio Rossi, Claudio Arbib and Alessandra Tessitore
    Citation: Journal of Translational Medicine 2023 21:836
  2. The morbidity of cancer keeps growing worldwide, and among that, the colorectal cancer (CRC) has jumped to third. Existing early screening tests for CRC are limited. The aim of this study was to develop a diag...

    Authors: Yang Yang, Zhipeng Wang, Xinxing Li, Jianfeng Lv, Renqian Zhong, Shouhong Gao, Feng Zhang and Wansheng Chen
    Citation: Journal of Translational Medicine 2023 21:824
  3. Epitranscriptomic abnormalities, which are highly prevalent in primary central nervous system malignancies, have been identified as crucial contributors to the development and progression of gliomas. RNA epitr...

    Authors: Shengrong Long, Yu Yan, Hongyu Xu, Lesheng Wang, Jiazhi Jiang, Ziyue Xu, Runming Liu, Qiangqiang Zhou, Xiaopeng Huang, Jincao Chen, Zhiqiang Li, Wei Wei and Xiang Li
    Citation: Journal of Translational Medicine 2023 21:810
  4. In recent decades, using circulating tumor cell (CTC), circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), exosomes and etc. as liquid biomarkers has received enormous attention in various tumors, in...

    Authors: You Shuai, Zhonghua Ma, Jie Ju, Tong Wei, Songlin Gao, Yikun Kang, Zixuan Yang, Xue Wang, Jian Yue and Peng Yuan
    Citation: Journal of Translational Medicine 2023 21:809
  5. Ulcerative colitis (UC) is a chronic inflammatory disease of the intestine characterized by a compromised intestinal epithelial barrier. Mucin glycans are crucial in preserving barrier function during bacteria...

    Authors: Juan Wei, Chunyan Chen, Jing Feng, Shuping Zhou, Xiaoyue Feng, Zhao Yang, Heng Lu, Hui Tao, Liuying Li, Huabing Xv, Ji Xuan and Fangyu Wang
    Citation: Journal of Translational Medicine 2023 21:793
  6. The precise prediction of epidermal growth factor receptor (EGFR) mutation status and gross tumor volume (GTV) segmentation are crucial goals in computer-aided lung adenocarcinoma brain metastasis diagnosis. H...

    Authors: Zichun Zhou, Min Wang, Rubin Zhao, Yan Shao, Ligang Xing, Qingtao Qiu and Yong Yin
    Citation: Journal of Translational Medicine 2023 21:788
  7. Prior research has shown that the deconvolution of cell-free RNA can uncover the tissue origin. The conventional deconvolution approaches rely on constructing a reference tissue-specific gene panel, which cann...

    Authors: Fengyao Yan, Limin Jiang, Fei Ye, Jie Ping, Tetiana Y. Bowley, Scott A. Ness, Chung-I Li, Dario Marchetti, Jijun Tang and Yan Guo
    Citation: Journal of Translational Medicine 2023 21:783
  8. Prostate cancer (PCa), a globally prevalent malignancy, displays intricate heterogeneity within its epithelial cells, closely linked with disease progression and immune modulation. However, the clinical signif...

    Authors: Weian Zhu, Hengda Zeng, Jiongduan Huang, Jianjie Wu, Yu Wang, Ziqiao Wang, Hua Wang, Yun Luo and Wenjie Lai
    Citation: Journal of Translational Medicine 2023 21:782
  9. Analyzing meningioma of distinct pathological types at the single-cell level can provide new and valuable insights into the specific biological mechanisms of each cellular subpopulation, as well as their vital...

    Authors: Hailang Fan, Lairong Song, Jian Fan, Junpeng Ma, Xiaojie Li, Junting Zhang, Jian Hu, Zhen Wu, Dake Zhang and Liang Wang
    Citation: Journal of Translational Medicine 2023 21:751
  10. Feature selection is a critical step for translating advances afforded by systems-scale molecular profiling into actionable clinical insights. While data-driven methods are commonly utilized for selecting cand...

    Authors: Mohammed Toufiq, Darawan Rinchai, Eleonore Bettacchioli, Basirudeen Syed Ahamed Kabeer, Taushif Khan, Bishesh Subba, Olivia White, Marina Yurieva, Joshy George, Noemie Jourde-Chiche, Laurent Chiche, Karolina Palucka and Damien Chaussabel
    Citation: Journal of Translational Medicine 2023 21:728
  11. Currently, there are no accurate markers for predicting potentially lethal prostate cancer (PC) before biopsy. This study aimed to develop urine tests to predict clinically significant PC (sPC) in men at risk.

    Authors: Hsiang-Po Huang, Chung-Hsin Chen, Kai-Hsiung Chang, Ming-Shyue Lee, Cheng-Fan Lee, Yen-Hsiang Chao, Shih-Yu Lu, Tzu-Fan Wu, Sung-Tzu Liang, Chih-Yu Lin, Yuan Chi Lin, Shih-Ping Liu, Yu-Chuan Lu, Chia-Tung Shun, William J. Huang, Tzu-Ping Lin…
    Citation: Journal of Translational Medicine 2023 21:714
  12. Low serum selenium and altered tumour RNA expression of certain selenoproteins are associated with a poor breast cancer prognosis. Selenoprotein expression stringently depends on selenium availability, hence c...

    Authors: Kamil Demircan, Ylva Bengtsson, Thilo Samson Chillon, Johan Vallon-Christersson, Qian Sun, Christer Larsson, Martin Malmberg, Lao H. Saal, Lisa Rydén, Åke Borg, Jonas Manjer and Lutz Schomburg
    Citation: Journal of Translational Medicine 2023 21:658
  13. The early differential diagnosis between bacterial meningitis (BM) and tuberculous meningitis (TBM) or cryptococcal meningitis (CM) remains a significant clinical challenge. Neutrophil Gelatinase-Associated Li...

    Authors: Qi Wang, Qingwen Lin, Haiyan Wang, Minjie Tang, Kengna Fan, Zeqin Zhang, Er Huang, Weiqing Zhang, Fengqing Wang, Qishui Ou and Xiaofeng Liu
    Citation: Journal of Translational Medicine 2023 21:603
  14. Accurately predicting the outcome of isocitrate dehydrogenase (IDH) wild-type glioblastoma (GBM) remains hitherto challenging. This study aims to Construct and Validate a Robust Prognostic Model for IDH wild-type...

    Authors: Hang Ji, Fang Wang, Zhihui Liu, Yue Li, Haogeng Sun, Anqi Xiao, Huanxin Zhang, Chao You, Shaoshan Hu and Yi Liu
    Citation: Journal of Translational Medicine 2023 21:533
  15. Transcriptional programs are often dysregulated in cancers. A comprehensive investigation of potential regulons is critical to the understanding of tumorigeneses. We first constructed the regulatory networks f...

    Authors: Yi Xiong, Yihao Zhang, Na Liu, Yueshuo Li, Hongwei Liu, Qi Yang, Yu Chen, Zhizhi Xia, Xin Chen, Siyi Wanggou and Xuejun Li
    Citation: Journal of Translational Medicine 2023 21:499
  16. We aimed to evaluate whether extracellular vesicles (EV)-derived microRNAs (miRNAs) can be used as biomarkers for advanced adenoma (AA) and colorectal cancer (CRC).

    Authors: Yun-Jie Shi, Yu-Xiang Fang, Tong-Guan Tian, Wei-Ping Chen, Qiang Sun, Fang-Qi Guo, Pi-Qing Gong, Chun-Mei Li, Hao Wang, Zhi-Qian Hu and Xin-Xing Li
    Citation: Journal of Translational Medicine 2023 21:421
  17. Computational drug repurposing is crucial for identifying candidate therapeutic medications to address the urgent need for developing treatments for newly emerging infectious diseases. The recent COVID-19 pand...

    Authors: Yonghyun Nam, Anastasia Lucas, Jae-Seung Yun, Seung Mi Lee, Ji Won Park, Ziqi Chen, Brian Lee, Xia Ning, Li Shen, Anurag Verma and Dokyoon Kim
    Citation: Journal of Translational Medicine 2023 21:415
  18. Cognitive dysfunction is the most common non-motor symptom in Parkinson’s disease (PD), and timely detection of a slight cognitive decline is crucial for early treatment and prevention of dementia. This study ...

    Authors: Boyu Chen, Ming Xu, Hongmei Yu, Jiachuan He, Yingmei Li, Dandan Song and Guo Guang Fan
    Citation: Journal of Translational Medicine 2023 21:310
  19. Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classifie...

    Authors: Romy Walker, Khalid Mahmood, Jihoon E. Joo, Mark Clendenning, Peter Georgeson, Julia Como, Sharelle Joseland, Susan G. Preston, Yoland Antill, Rachel Austin, Alex Boussioutas, Michelle Bowman, Jo Burke, Ainsley Campbell, Simin Daneshvar, Emma Edwards…
    Citation: Journal of Translational Medicine 2023 21:282
  20. Remote ischemic preconditioning (RIPC) refers to a brief episode of exposure to potential adverse stimulation and prevents injury during subsequent exposure. RIPC has been shown to increase tolerance to ischem...

    Authors: Yang Du, Rui Qiu, Lei Chen, Yuewen Chen, Zhifeng Zhong, Peng Li, Fangcheng Fan and Yong Cheng
    Citation: Journal of Translational Medicine 2023 21:241
  21. This study aimed to characterize the genetic profile of patients with glioma and discuss the impact of next-generation sequencing in glioma diagnosis and treatment.

    Authors: Veronica Villani, Beatrice Casini, Antonio Tanzilli, Mario Lecce, Fabrizio Rasile, Stefano Telera, Andrea Pace, Francesca Piludu, Irene Terrenato, Francesca Rollo, Francesca De Nicola, Maurizio Fanciulli, Matteo Pallocca, Gennaro Ciliberto and Mariantonia Carosi
    Citation: Journal of Translational Medicine 2023 21:215
  22. Papillary thyroid microcarcinoma (PTMC) incidence has significantly increased, and some cases still exhibit invasive traits. The entire molecular landscape of PTMC, which can offer hints for the etiology of ca...

    Authors: Qiang Li, Tienan Feng, Tengteng Zhu, Weituo Zhang, Ying Qian, Huan Zhang, Xiangqian Zheng, Dapeng Li, Xinwei Yun, Jingzhu Zhao, Yangyang Li, Herbert Yu, Ming Gao and Biyun Qian
    Citation: Journal of Translational Medicine 2023 21:206
  23. In the repair of maxillofacial bone defects, autogenous craniofacial bone can often provide superior clinical results over long bone grafts. Most current studies have focused on the osteogenic differences betw...

    Authors: Lanxin Gu, Zhongyuan Wang, Hong Gu, Hua Wang, Luwei Liu and Wei-Bing Zhang
    Citation: Journal of Translational Medicine 2023 21:193
  24. Sepsis is a frequent complication in critically ill patients, is highly heterogeneous and is associated with high morbidity and mortality rates, especially in the elderly population. Utilizing RNA sequencing (...

    Authors: I-Chieh Chen, Hsin-Hua Chen, Yu-Han Jiang, Tzu-Hung Hsiao, Tai-Ming Ko and Wen-Cheng Chao
    Citation: Journal of Translational Medicine 2023 21:141
  25. Osteosarcoma (OS) is the most frequent and aggressive primary malignant sarcoma among adolescents and chemotherapy has not substantially progressed for decades. New insights into OS development and therapeutic...

    Authors: Yifeng Sun, Chunming Zhang, Qiongxuan Fang, Wenqiang Zhang and Wei Liu
    Citation: Journal of Translational Medicine 2023 21:99
  26. Colorectal cancer (CRC) is one of the most prevalent cancers, with over one million new cases per year. Overall, prognosis of CRC largely depends on the disease stage and metastatic status. As precision oncolo...

    Authors: Friederike Praus, Axel Künstner, Thorben Sauer, Michael Kohl, Katharina Kern, Steffen Deichmann, Ákos Végvári, Tobias Keck, Hauke Busch, Jens K. Habermann and Timo Gemoll
    Citation: Journal of Translational Medicine 2023 21:41
  27. The pathogenicity of pneumococcus with high morbidity, mortality, and multi-drug resistance patterns has been increasing. The limited coverage of the licensed polysaccharide-based vaccines and the replacement ...

    Authors: Elnaz Afshari, Reza Ahangari Cohan, Fattah Sotoodehnejadnematalahi and Seyed Fazlollah Mousavi
    Citation: Journal of Translational Medicine 2023 21:13
  28. Chagas disease is a neglected tropical disease in Latin America and an imported emerging disease worldwide. Chronic Chagas disease cardiomyopathy (CCC) is the most prominent clinical form and can lead to heart...

    Authors: Gregório Guilherme Almeida, Inga Rimkute, Isabela Natália Pascoal Campos do Vale, Thomas Liechti, Priscilla Miranda Henriques, Ester Roffe, Fernanda Fortes de Araújo, Manoel Otávio da Costa Rocha, Silvana Maria Elói Santos, Olindo Assis Martins-Filho, Dragana Jankovic, Alan Sher, Andrea Teixeira-Carvalho, Mario Roederer and Lis Ribeiro do Valle Antonelli
    Citation: Journal of Translational Medicine 2022 20:551
  29. The genetic architecture underlying Familial Hypercholesterolemia (FH) in Middle Eastern Arabs is yet to be fully described, and approaches to assess this from population-wide biobanks are important for public...

    Authors: Geethanjali Devadoss Gandhi, Waleed Aamer, Navaneethakrishnan Krishnamoorthy, Najeeb Syed, Elbay Aliyev, Aljazi Al-Maraghi, Muhammad Kohailan, Jamil Alenbawi, Mohammed Elanbari, Borbala Mifsud, Younes Mokrab, Charbel Abi Khalil and Khalid A. Fakhro
    Citation: Journal of Translational Medicine 2022 20:502
  30. RNA methylation modifications, especially m6A mRNA modification, are known to be extensively involved in tumor development. However, the relationship between N3-methylcytidine (m3C) related genes and tumorigen...

    Authors: Shuai Wang, Huiting Li, Jiheng Liu, Qianqian Zhang, Wei Xu, Juanjuan Xiang, Li Fang, Ping Xu and Zheng Li
    Citation: Journal of Translational Medicine 2022 20:476
  31. As a key process in transcriptional regulatory mechanisms, alternative splicing (AS) plays a crucial role in maintaining the diversity of RNA and protein expression, and mediates the immune response in infecti...

    Authors: Yaxin Chen, Gang Wang, Jingyi Li, Lei Xia, Lin Zhu, Wenxing Li, Qiang Luo, Yinlu Liao, Yao Lin, Liyun Bi, Hubin Chen, Jiemei Chu, Yueqi Li, Jinming Su, Li Ye, Jun-jun Jiang…
    Citation: Journal of Translational Medicine 2022 20:473
  32. According to the Global Cancer Statistics in 2020, the incidence and mortality of colorectal cancer (CRC) rank third and second among all tumors. The disturbance of ubiquitination plays an important role in th...

    Authors: Wei Zhang, Yan Yang, Liewen Lin, Jingquan He, Jingjing Dong, Bin Yan, Wanxia Cai, Yumei Chen, Lianghong Yin, Donge Tang, Fanna Liu and Yong Dai
    Citation: Journal of Translational Medicine 2022 20:445
  33. Detecting trans-ethnic common associated genetic loci can offer important insights into shared genetic components underlying complex diseases/traits across diverse continental populations. However, effective s...

    Authors: Jiahao Qiao, Zhonghe Shao, Yuxuan Wu, Ping Zeng and Ting Wang
    Citation: Journal of Translational Medicine 2022 20:424
  34. Streptococcus pneumoniae is the leading reason for invasive diseases including pneumonia and meningitis, and also secondary infections following viral respiratory diseases such as flu and COVID-19. Currently, ser...

    Authors: Zohreh Bahadori, Mona Shafaghi, Hamid Madanchi, Mohammad Mehdi Ranjbar, Ali Akbar Shabani and Seyed Fazlollah Mousavi
    Citation: Journal of Translational Medicine 2022 20:389
  35. Hepatocellular carcinoma (HCC) is one of the most malignant tumors to threaten human life, and the survival rate remains low due to delayed diagnosis. Meanwhile, lncRNAs have great potential for application in...

    Authors: Xia-Hui Lin, Dan-Ying Zhang, Zhi-Yong Liu, Wen-qing Tang, Rong-Xin Chen, Dong-ping Li, Shuqiang Weng and Ling Dong
    Citation: Journal of Translational Medicine 2022 20:379
  36. Genomic studies of colorectal cancer have revealed the complex genomic heterogeneity of the tumor. The acquisition and selection of genomic alterations may be critical to understanding the initiation and progr...

    Authors: Jian Shi, Li Wang, Xiangzhe Yin, Lixia Wang, Lin Bo, Kailai Liu, Ke Feng, Shihua Lin, Yanjun Xu, Shangwei Ning and Hongying Zhao
    Citation: Journal of Translational Medicine 2022 20:362
  37. Kidney transplantation is a lifesaving option for patients with end-stage kidney disease. In Taiwan, urothelial carcinoma (UC) is the most common de novo cancer after kidney transplantation (KT). UC has a grea...

    Authors: Lee-Moay Lim, Wen-Yu Chung, Daw-Yang Hwang, Chih-Chuan Yu, Hung-Lung Ke, Peir-In Liang, Ting-Wei Lin, Siao Muk Cheng, A-Mei Huang and Hung-Tien Kuo
    Citation: Journal of Translational Medicine 2022 20:324
  38. Glioma is the most common malignant tumors in the brain. Previous studies have revealed that, as the innate immune cells in nervous system, microglia cells were involved in glioma pathology. And, the resident ...

    Authors: Chunlong Zhang, Jiaxin Zhao, Wanqi Mi, Yuxi Zhang, Xiaoling Zhong, Guiyuan Tan, Feng Li, Xia Li, Yanjun Xu and Yunpeng Zhang
    Citation: Journal of Translational Medicine 2022 20:277
  39. Ampullary adenocarcinoma (AAC) arises from the ampulla of Vater where the pancreatic duct and bile duct join and empty into the duodenum. It can be classified into intestinal and pancreatobiliary types based o...

    Authors: Jun Cheng, Yize Mao, Wenhui Hong, Wanming Hu, Peng Shu, Kun Huang, Jingjing Yu, Maofen Jiang, Liqin Li, Wei Wang, Dong Ni and Shengping Li
    Citation: Journal of Translational Medicine 2022 20:272
  40. There are sudden deterioration phenomena during the progression of many complex diseases, including most cancers; that is, the biological system may go through a critical transition from one stable state (the ...

    Authors: Juntan Liu, Dandan Ding, Jiayuan Zhong and Rui Liu
    Citation: Journal of Translational Medicine 2022 20:254
  41. The correlations between circulating tumour DNA (ctDNA)-derived genomic markers and treatment response and survival outcome in Chinese patients with advanced breast cancer (ABC) have not been extensively chara...

    Authors: Hao Liao, Jiayang Zhang, Tiantian Zheng, Xiaoran Liu, Jianxin Zhong, Bin Shao, Xiaoxi Dong, Xiaohong Wang, Pan Du, Bonnie L. King, Shidong Jia, Jianjun Yu and Huiping Li
    Citation: Journal of Translational Medicine 2022 20:211
  42. We develop a new risk score to predict patients with stroke-associated pneumonia (SAP) who have an acute intracranial hemorrhage (ICH).

    Authors: Jing Yan, Weiqi Zhai, Zhaoxia Li, LingLing Ding, Jia You, Jiayi Zeng, Xin Yang, Chunjuan Wang, Xia Meng, Yong Jiang, Xiaodi Huang, Shouyan Wang, Yilong Wang, Zixiao Li, Shanfeng Zhu, Yongjun Wang…
    Citation: Journal of Translational Medicine 2022 20:193
  43. Recent studies exploring the roles of invasion-metastasis associated miRNAs in gallbladder cancer (GBC) are limited. In the study, we aimed to identify the invasion-metastasis associated miRNAs in GBC by bioin...

    Authors: Jiasheng Cao, Huijiang Shao, Jiahao Hu, Renan Jin, Anyun Feng, Bin Zhang, Shijie Li, Tianen Chen, Sarun Jeungpanich, Win Topatana, Yitong Tian, Ziyi Lu, Xiujun Cai and Mingyu Chen
    Citation: Journal of Translational Medicine 2022 20:188
  44. Genome-wide association studies (GWAS) have revealed numerous loci associated with stroke. However, the underlying mechanisms at these loci in the pathogenesis of stroke and effective stroke drug targets are e...

    Authors: Bang-Sheng Wu, Shu-Fen Chen, Shu-Yi Huang, Ya-Nan Ou, Yue-Ting Deng, Shi-Dong Chen, Qiang Dong and Jin-Tai Yu
    Citation: Journal of Translational Medicine 2022 20:181
  45. For a long time, breast cancer has been a leading cancer diagnosed in women worldwide, and approximately 90% of cancer-related deaths are caused by metastasis. For this reason, finding new biomarkers related t...

    Authors: Qingqing Li, Hui Yang, Peipei Wang, Xiaocen Liu, Kun Lv and Mingquan Ye
    Citation: Journal of Translational Medicine 2022 20:177
  46. Determining the tissue of origin (TOO) is essential for managing cancer of unknown primary (CUP). In this study, we evaluated the concordance between genome profiling and DNA methylation analysis in determinin...

    Authors: Kaiyan Chen, Fanrong Zhang, Xiaoqing Yu, Zhiyu Huang, Lei Gong, Yanjun Xu, Hui Li, Sizhe Yu and Yun Fan
    Citation: Journal of Translational Medicine 2022 20:158
  47. Once malignancy tumors were diagnosed, the determination of tissue origin and tumor type is critical for clinical management. Although the significant advance in imaging techniques and histopathological approa...

    Authors: Wei Sun, Wei Wu, Qifeng Wang, Qian Yao, Qin Feng, Yue Wang, Yu Sun, Yunying Liu, Qian Lai, Gu Zhang, Peng Qi, Yifeng Sun, Chenhui Qian, Wanli Ren, Zhengzhi Luo, Jinying Chen…
    Citation: Journal of Translational Medicine 2022 20:114
  48. Revealing the impacts of endogenous and exogenous mutagenesis processes is essential for understanding the etiology of somatic genomic alterations and designing precise prognostication and treatment strategies...

    Authors: Amir Farmanbar, Sanaz Firouzi, Robert Kneller and Hossein Khiabanian
    Citation: Journal of Translational Medicine 2022 20:65

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