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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. Diffuse hemispheric glioma H3 G34-mutant (G34-DHG) is a new type of pediatric-type diffuse high-grade glioma in the fifth edition of the WHO Classification of Tumors of the Central Nervous System. The current ...

    Authors: Wanming Hu, Hao Duan, Sheng Zhong, Jing Zeng and Yonggao Mou
    Citation: Journal of Translational Medicine 2022 20:64
  2. Identification of novel biomarker is important for development of molecular-targeted therapy agents for patients with hepatocellular carcinoma (HCC). This study aims to identify potential prognostic biomarkers...

    Authors: Zengwei Tang, Yuan Yang, Wen Chen, Enliang Li and Tingbo Liang
    Citation: Journal of Translational Medicine 2022 20:49

    The Correction to this article has been published in Journal of Translational Medicine 2022 20:594

  3. The identification of pathogenic variant in patients with thoracic aortic aneurysms and dissections (TAAD) was previously found to be a significant indicator pointing to earlier need for surgical intervention....

    Authors: Joanna Kinga Ponińska, Zofia Teresa Bilińska, Grażyna Truszkowska, Ewa Michalak, Anna Podgórska, Małgorzata Stępień-Wojno, Przemysław Chmielewski, Anna Lutyńska and Rafał Płoski
    Citation: Journal of Translational Medicine 2022 20:42
  4. Ovarian cancer was one of the leading causes of female deaths. Patients with OC were essentially incurable and portends a poor prognosis, presumably because of profound genetic heterogeneity limiting reproduci...

    Authors: Hongyu Zhao, Yu Teng, Wende Hao, Jie Li, Zhefeng Li, Qi Chen, Chenghong Yin and Wentao Yue
    Citation: Journal of Translational Medicine 2021 19:454
  5. Ovarian cancer, a highly metastatic malignancy, has benefited tremendously from advances in modern human genomics. However, the genomic variations related to the metastasis remains unclear.

    Authors: Mengyao Xu, Shan Huang, Jiahui Chen, Wanxue Xu, Rong Xiang, Yongjun Piao and Shuangtao Zhao
    Citation: Journal of Translational Medicine 2021 19:447
  6. High-grade glioma has a poor prognosis, and GSCs can have pivotal roles in glioma pathology. This study investigated GSC exosome-containing circRNA mechanisms affecting the malignant progression of glioma.

    Authors: Guowei Li and Qing Lan
    Citation: Journal of Translational Medicine 2021 19:444
  7. Epidermal growth factor receptor (EGFR) and lanthionine synthetase C-like 2 (LanCL2) genes locate in the same amplicon, and co-amplification of EGFR and LANCL2 is frequent in glioblastoma. However, the prognostic...

    Authors: Hua-fu Zhao, Xiu-ming Zhou, Jing Wang, Fan-fan Chen, Chang-peng Wu, Peng-yu Diao, Lin-rong Cai, Lei Chen, Yan-wen Xu, Jing Liu, Zong-yang Li, Wen-lan Liu, Zhong-ping Chen, Guo-dong Huang and Wei-ping Li
    Citation: Journal of Translational Medicine 2021 19:372
  8. Luminal breast cancer (BC) is the most frequent subtype accounting for more than 70% of BC. LncRNAs, a class of non-coding RNAs with more than 200 nucleotides, are involved in a variety of cellular processes a...

    Authors: Sepideh Mehrpour Layeghi, Maedeh Arabpour, Abbas Shakoori, Mohammad Mehdi Naghizadeh, Yaser Mansoori, Javad Tavakkoly Bazzaz and Rezvan Esmaeili
    Citation: Journal of Translational Medicine 2021 19:364
  9. The exploration of genomic alterations in Chinese colorectal liver metastasis (CRLM) is limited, and corresponding genetic biomarkers for patient’s perioperative management are still lacking. This study aims t...

    Authors: Hong-Wei Wang, Xiao-Luan Yan, Li-Jun Wang, Meng-Huan Zhang, Chun-He Yang, Wei-Liu, Ke-Min Jin, Quan Bao, Juan Li, Kun Wang and Bao-Cai Xing
    Citation: Journal of Translational Medicine 2021 19:313
  10. Surgical resection is the only potentially curative treatment for pancreatic ductal adenocarcinoma (PDAC) and the survival of patients after radical resection is closely related to relapse. We aimed to develop...

    Authors: Xiawei Li, Litao Yang, Zheping Yuan, Jianyao Lou, Yiqun Fan, Aiguang Shi, Junjie Huang, Mingchen Zhao and Yulian Wu
    Citation: Journal of Translational Medicine 2021 19:281
  11. The identification of novel functional biomarkers is essential for recognizing high-risk patients, predicting recurrence, and searching for appropriate treatment. However, no prognostic biomarker has been appl...

    Authors: Wei Zhang, Liewen Lin, Ligang Xia, Wanxia Cai, Weier Dai, Chang Zou, Lianghong Yin, Donge Tang, Yong Xu and Yong Dai
    Citation: Journal of Translational Medicine 2021 19:273
  12. In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analy...

    Authors: Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow and Lisa M. McShane
    Citation: Journal of Translational Medicine 2021 19:269
  13. Circular RNAs (circRNAs) are a new class of noncoding RNAs that have gained increased attention in human tumor research. However, the identification and function of circRNAs are largely unknown in the context ...

    Authors: Zhijie Dong, Zhaoyu Liu, Min Liang, Jinhui Pan, Mingzhen Lin, Hai Lin, Yuanwei Luo, Xinke Zhou and Wenxia Yao
    Citation: Journal of Translational Medicine 2021 19:226
  14. Glioma is an extremely aggressive malignant neoplasm of the central nervous system. MicroRNA (miRNA) are known to bind to specific target mRNA to regulate post-transcriptional gene expression and are, therefor...

    Authors: Lei Wang, Yan Liu, Zhengtao Yu, Jianwu Gong, Zhiyong Deng, Nianjun Ren, Zhe Zhong, Hao Cai, Zhi Tang, Haofeng Cheng, Shuai Chen and Zhengwen He
    Citation: Journal of Translational Medicine 2021 19:213
  15. Clinically relevant glioma subtypes, such as the glioma-CpG island methylator phenotype (G-CIMP), have been defined by epigenetics. In this study, the role of long non-coding RNAs in association with the poor-...

    Authors: Indrani Datta, Houtan Noushmehr, Chaya Brodie and Laila M. Poisson
    Citation: Journal of Translational Medicine 2021 19:182
  16. Posterior fossa ependymoma (EPN-PF) can be classified into Group A posterior fossa ependymoma (EPN-PFA) and Group B posterior fossa ependymoma (EPN-PFB) according to DNA CpG island methylation profile status a...

    Authors: Guanyi Wang, Yibin Jia, Yuqin Ye, Enming Kang, Huijun Chen, Jiayou Wang and Xiaosheng He
    Citation: Journal of Translational Medicine 2021 19:174
  17. The epigenetic abnormality of tumor-associated genes contributes to the pathogenesis of colorectal carcinoma (CRC). However, methylation in colorectal cancer is still poorly characterized.

    Authors: Hui Zhang, Chenxin Xu, Chen Shi, Junying Zhang, Ting Qian, Zhuo Wang, Rong Ma, Jianzhong Wu, Feng Jiang and Jifeng Feng
    Citation: Journal of Translational Medicine 2021 19:98
  18. Microbes are closely related to human health and diseases. Identification of disease-related microbes is of great significance for revealing the pathological mechanism of human diseases and understanding the i...

    Authors: Da Xu, Hanxiao Xu, Yusen Zhang, Mingyi Wang, Wei Chen and Rui Gao
    Citation: Journal of Translational Medicine 2021 19:66
  19. Copy number variation (CNV) suggests genetic changes in malignant tumors. Abnormal expressions of long non-coding RNAs (lncRNAs) resulted from genomic and epigenetic abnormalities play a driving role in tumori...

    Authors: Qihang Zhong, Minzhen Lu, Wanqiong Yuan, Yueyi Cui, Hanqiang Ouyang, Yong Fan, Zhaohui Wang, Congying Wu, Jie Qiao and Jing Hang
    Citation: Journal of Translational Medicine 2021 19:58
  20. Genome-wide association studies have identified genetic variants associated with the risk of brain-related diseases, such as neurological and psychiatric disorders, while the causal variants and the specific v...

    Authors: Jinting Guan, Yiping Lin, Yang Wang, Junchao Gao and Guoli Ji
    Citation: Journal of Translational Medicine 2021 19:20
  21. Hysteroscopy is a commonly used technique for diagnosing endometrial lesions. It is essential to develop an objective model to aid clinicians in lesion diagnosis, as each type of lesion has a distinct treatmen...

    Authors: YunZheng Zhang, ZiHao Wang, Jin Zhang, CuiCui Wang, YuShan Wang, Hao Chen, LuHe Shan, JiaNing Huo, JiaHui Gu and Xiaoxin Ma
    Citation: Journal of Translational Medicine 2021 19:10
  22. Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, ...

    Authors: Xinlu Yuan, Jianjun Diao, Anqing Du, Song Wen, Ligang Zhou and Yangbin Pan
    Citation: Journal of Translational Medicine 2020 18:476
  23. Alternative splicing (AS) plays critical roles in generating protein diversity and complexity. Dysregulation of AS underlies the initiation and progression of tumors. Machine learning approaches have emerged a...

    Authors: Qidong Cai, Boxue He, Pengfei Zhang, Zhenyu Zhao, Xiong Peng, Yuqian Zhang, Hui Xie and Xiang Wang
    Citation: Journal of Translational Medicine 2020 18:463
  24. Drug repositioning, the strategy of unveiling novel targets of existing drugs could reduce costs and accelerate the pace of drug development. To elucidate the novel molecular mechanism of known drugs, consider...

    Authors: Yihan Zhao, Kai Zheng, Baoyi Guan, Mengmeng Guo, Lei Song, Jie Gao, Hua Qu, Yuhui Wang, Dazhuo Shi and Ying Zhang
    Citation: Journal of Translational Medicine 2020 18:434
  25. Most often, the patients with pancreatic diseases are presented with a mass in pancreatic head region and existing methods of diagnosis fail to confirm whether the head mass is malignant or benign. As subseque...

    Authors: Bishnupriya Chhatriya, Moumita Mukherjee, Sukanta Ray, Barsha Saha, Somdatta Lahiri, Sandip Halder, Indranil Ghosh, Sujan Khamrui, Kshaunish Das, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra and Srikanta Goswami
    Citation: Journal of Translational Medicine 2020 18:420
  26. The incidence of stage I and stage II lung adenocarcinoma (LUAD) is likely to increase with the introduction of annual screening programs for high-risk individuals. We aimed to identify a reliable prognostic s...

    Authors: Pancheng Wu, Yi Zheng, Yanyu Wang, Yadong Wang and Naixin Liang
    Citation: Journal of Translational Medicine 2020 18:380
  27. Spectrin repeat containing nuclear envelope family member 3 (SYNE3) encodes an essential component of the linker of the cytoskeleton and nucleoskeleton (LINC) complex, namely nesprin-3. In a tumor, invasivenes...

    Authors: Liwei Liao, Longshan Zhang, Mi Yang, Xiaoqing Wang, Weiqiang Huang, Xixi Wu, Hua Pan, Lu Yuan, Wenqi Huang, Yuting Wu and Jian Guan
    Citation: Journal of Translational Medicine 2020 18:355
  28. Previous findings have indicated that the tumor, nodes, and metastases (TNM) staging system is not sufficient to accurately predict survival outcomes in patients with non-small lung carcinoma (NSCLC). Thus, th...

    Authors: Rui-Qi Wang, Xiao-Ran Long, Chun-Lei Ge, Mei-Yin Zhang, Long Huang, Ning-Ning Zhou, Yi Hu, Rui-Lei Li, Zhen Li, Dong-Ni Chen, Lan-Jun Zhang, Zhe-Sheng Wen, Shi-Juan Mai and Hui-Yun Wang
    Citation: Journal of Translational Medicine 2020 18:320
  29. Lung cancer is one of the most common carcinomas in the world, and lung adenocarcinoma (LUAD) is the most lethal and most common subtype of lung cancer. Cigarette smoking is the most leading risk factor of lun...

    Authors: Jin Wang, Tao Chen, Xiaofan Yu, Nan OUYang, Lirong Tan, Beibei Jia, Jian Tong and Jianxiang Li
    Citation: Journal of Translational Medicine 2020 18:313
  30. Measuring the DNA methylome may offer the opportunity to identify novel disease biomarkers and insights into disease mechanisms. Although aberrant DNA methylation has been investigated in many human cancers an...

    Authors: Runhua Lin, Chenxi Li, Zhaohui Liu, Ruinuan Wu and Jianghong Lu
    Citation: Journal of Translational Medicine 2020 18:292
  31. Covid-19 morbidity and mortality are associated with a dysregulated immune response. Tools are needed to enhance existing immune profiling capabilities in affected patients. Here we aimed to develop an approac...

    Authors: Darawan Rinchai, Basirudeen Syed Ahamed Kabeer, Mohammed Toufiq, Zohreh Tatari-Calderone, Sara Deola, Tobias Brummaier, Mathieu Garand, Ricardo Branco, Nicole Baldwin, Mohamed Alfaki, Matthew C. Altman, Alberto Ballestrero, Matteo Bassetti, Gabriele Zoppoli, Andrea De Maria, Benjamin Tang…
    Citation: Journal of Translational Medicine 2020 18:291
  32. Triple-negative breast cancer (TNBC) is widely concerning because of high malignancy and poor prognosis. There is increasing evidence that alternative splicing (AS) plays an important role in the development o...

    Authors: Shanshan Yu, Chuan Hu, Lixiao Liu, Luya Cai, Xuedan Du, Qiongjie Yu, Fan Lin, Jinduo Zhao, Ye Zhao, Cheng Zhang, Xuan Liu and Wenfeng Li
    Citation: Journal of Translational Medicine 2020 18:286
  33. The task of identifying a representative and yet manageable target gene list for assessing the pathogenesis of complicated and multifaceted diseases is challenging. Using Inflammatory Bowel Disease (IBD) as an...

    Authors: Mathieu Garand, Manoj Kumar, Susie Shih Yin Huang and Souhaila Al Khodor
    Citation: Journal of Translational Medicine 2020 18:279
  34. Survival outcomes of patients with resected SCLC differ widely. The aim of our study was to build a model for individualized risk assessment and accurate prediction of overall survival (OS) in resectable SCLC ...

    Authors: Yu Wang, Zhaofei Pang, Xiaowei Chen, Tao Yan, Jichang Liu and Jiajun Du
    Citation: Journal of Translational Medicine 2020 18:237
  35. Cervical cancer (CC) represents the fourth most frequently diagnosed malignancy affecting women all over the world. However, effective prognostic biomarkers are still limited for accurately identifying high-ri...

    Authors: Yimin Li, Shun Lu, Mei Lan, Xinhao Peng, Zijian Zhang and Jinyi Lang
    Citation: Journal of Translational Medicine 2020 18:223
  36. Sepsis is a fatal disease referring to the presence of a known or strongly suspected infection coupled with systemic and uncontrolled immune activation causing multiple organ failure. However, current knowledg...

    Authors: Lixin Cheng, Chuanchuan Nan, Lin Kang, Ning Zhang, Sheng Liu, Huaisheng Chen, Chengying Hong, Youlian Chen, Zhen Liang and Xueyan Liu
    Citation: Journal of Translational Medicine 2020 18:217
  37. With the recent emergence of immune checkpoint inhibitors, microsatellite instability (MSI) status has become an important biomarker for immune checkpoint blockade therapy. There are growing technical demands ...

    Authors: Kai Zheng, Hua Wan, Jie Zhang, Guangyu Shan, Ningning Chai, Dongdong Li, Nan Fang, Lina Liu, Jingbo Zhang, Rong Du, Qixi Wu, Xichuan Li and Chunze Zhang
    Citation: Journal of Translational Medicine 2020 18:215
  38. Recent studies have shown that selenium-binding protein 1 (SELENBP1) is significantly down-regulated in a variety of solid tumors. Nevertheless, the clinical relevance of SELENBP1 in human bladder cancer has n...

    Authors: Yulei Wang, Wenzhen Zhu, Xiaoqing Chen, Guangnan Wei, Guosong Jiang and Guochun Zhang
    Citation: Journal of Translational Medicine 2020 18:17
  39. This study aimed to establish and validate a nomogram for predicting brain metastasis in patients with bladder cancer (BCa) and assess various treatment modalities using a primary cohort comprising 234 patient...

    Authors: Zhixian Yao, Zhong Zheng, Wu Ke, Renjie Wang, Xingyu Mu, Feng Sun, Xiang Wang, Shivank Garg, Wenyin Shi, Yinyan He and Zhihong Liu
    Citation: Journal of Translational Medicine 2019 17:411
  40. Tumor surrounding the internal carotid artery or invading to the cavernous sinus is an important characteristic of invasive pituitary adenoma, and a pivotal factor of tumor residue and regrowth. Without specif...

    Authors: Sen Cheng, Weiyan Xie, Yazhou Miao, Jing Guo, Jichao Wang, Chuzhong Li and Yazhuo Zhang
    Citation: Journal of Translational Medicine 2019 17:407
  41. Cervical cancer is a common malignant carcinoma of the gynecological tract with high morbidity and mortality. Therefore, it is crucial to elucidate the pathogenesis, prevention, diagnosis and prognosis of cerv...

    Authors: Yue-Xin Hu, Ming-Jun Zheng, Wen-Chao Zhang, Xiao Li, Rui Gou, Xin Nie, Qing Liu, Ying-Ying Hao, Juan-Juan Liu and Bei Lin
    Citation: Journal of Translational Medicine 2019 17:379
  42. Oxidative stress has a determinantal effect on human dental pulp stromal cells (hDPSCs), including affecting their longevity and functionality. Circular RNAs (circRNAs) play an essential role in stromal cell b...

    Authors: Jingying Zhang, Dan Li, Dan Wang, Kenny Man and Xuebin Yang
    Citation: Journal of Translational Medicine 2019 17:327
  43. Recently, numerous biological experiments have indicated that microRNAs (miRNAs) play critical roles in exploring the pathogenesis of various human diseases. Since traditional experimental methods for miRNA-di...

    Authors: Guobo Xie, Zhiliang Fan, Yuping Sun, Cuiming Wu and Lei Ma
    Citation: Journal of Translational Medicine 2019 17:322
  44. Prostate cancer (PCa) remains the second leading cause of deaths due to cancer in the United States in men. The aim of this study was to perform an integrative epigenetic analysis of prostate adenocarcinoma to...

    Authors: Ning Xu, Yu-Peng Wu, Zhi-Bin Ke, Ying-Chun Liang, Hai Cai, Wen-Ting Su, Xuan Tao, Shao-Hao Chen, Qing-Shui Zheng, Yong Wei and Xue-Yi Xue
    Citation: Journal of Translational Medicine 2019 17:311
  45. Surgery, adjuvant chemotherapy, and radiotherapy are the primary treatment options for soft tissue sarcomas (STSs). However, identifying ways to improve the prognosis of patients with STS remains a considerabl...

    Authors: Xia Yang, Wen-ting Huang, Rong-quan He, Jie Ma, Peng Lin, Zu-cheng Xie, Fu-chao Ma and Gang Chen
    Citation: Journal of Translational Medicine 2019 17:283
  46. Diabetic nephropathy (DN) affects about 40% of diabetes mellitus (DM) patients and is the leading cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD) all over the world, especially in high...

    Authors: Gang Wang, Jian Ouyang, Shen Li, Hui Wang, Baofeng Lian, Zhihong Liu and Lu Xie
    Citation: Journal of Translational Medicine 2019 17:264
  47. Individualized drug response prediction is vital for achieving personalized treatment of cancer and moving precision medicine forward. Large-scale multi-omics profiles provide unprecedented opportunities for p...

    Authors: Yanjun Xu, Qun Dong, Feng Li, Yingqi Xu, Congxue Hu, Jingwen Wang, Desi Shang, Xuan Zheng, Haixiu Yang, Chunlong Zhang, Mengting Shao, Mohan Meng, Zhiying Xiong, Xia Li and Yunpeng Zhang
    Citation: Journal of Translational Medicine 2019 17:255
  48. Gastric cancer (GC) is a leading cause of cancer deaths, and an increased number of GC patients adopt to next-generation sequencing (NGS) to identify tumor genomic alterations for precision medicine.

    Authors: Hui Cai, Changqing Jing, Xusheng Chang, Dan Ding, Ting Han, Junchi Yang, Zhengmao Lu, Xuguang Hu, Zhaorui Liu, Jinshen Wang, Liang Shang, Shouxin Wu, Peng Meng, Ling Lin, Jiangman Zhao, Mingming Nie…
    Citation: Journal of Translational Medicine 2019 17:189
  49. Glioma accounts for a large proportion of cancer, and an effective treatment for this disease is still lacking because of the absence of specific driver molecules. Current challenges in the treatment of glioma...

    Authors: Xiaonan Xi, Yahui Chu, Ning Liu, Qianqian Wang, Zheng Yin, Yaxin Lu and Yue Chen
    Citation: Journal of Translational Medicine 2019 17:129

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