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Medical bioinformatics

Section edited by Michele Ceccarelli

The 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. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. Angiogenesis inhibition research is a cutting edge area in angiogenesis-dependent disease therapy, especially in cancer therapy. Recently, studies on anti-angiogenic peptides have provided promising results in...

    Authors: Javad Zahiri, Babak Khorsand, Ali Akbar Yousefi, Mohammadjavad Kargar, Ramin Shirali Hossein Zade and Ghasem Mahdevar
    Citation: Journal of Translational Medicine 2019 17:71
  22. Lung cancer has become the most common cancer type and caused the most cancer deaths. Lung adenocarcinoma (LUAD) is one of the major type of lung cancer. This study aimed to establish a signature based on immu...

    Authors: Qian Song, Jun Shang, Zuyi Yang, Lanlin Zhang, Chufan Zhang, Jianing Chen and Xianghua Wu
    Citation: Journal of Translational Medicine 2019 17:70
  23. Progesterone resistance is a problem in endometrial carcinoma, and its underlying molecular mechanisms remain poorly understood. The aim of this study was to elucidate the molecular mechanisms of progesterone ...

    Authors: Wenzhi Li, Shufen Wang, Chunping Qiu, Zhiming Liu, Qing Zhou, Deshui Kong, Xiaohong Ma and Jie Jiang
    Citation: Journal of Translational Medicine 2019 17:58
  24. Atrial fibrillation (AF) is one of the most prevalent sustained arrhythmias, however, epidemiological data may understate its actual prevalence. Meanwhile, AF is considered to be a major cause of ischemic stro...

    Authors: Rongjun Zou, Dingwen Zhang, Lei Lv, Wanting Shi, Zijiao Song, Bin Yi, Bingjia Lai, Qian Chen, Songran Yang and Ping Hua
    Citation: Journal of Translational Medicine 2019 17:45
  25. One of the key reasons for the high failure rate of new agents and low therapeutic benefit of approved treatments is the lack of preclinical models that mirror the biology of human tumors. At present, the opti...

    Authors: Quanxue Li, Wentao Dai, Jixiang Liu, Yi-Xue Li and Yuan-Yuan Li
    Citation: Journal of Translational Medicine 2019 17:39
  26. Despite that most HIV-infected individuals experience progressive CD4+ T cell loss and develop AIDS, a minority of HIV-infected individuals remain asymptomatic and maintain high level CD4+ T cell counts severa...

    Authors: Jiwei Ding, Ling Ma, Jianyuan Zhao, Yongli Xie, Jinming Zhou, Xiaoyu Li and Shan Cen
    Citation: Journal of Translational Medicine 2019 17:35
  27. The common treatment for pediatric cataracts is to replace the cloudy lens with an artificial one. However, patients may suffer complications (severe lens proliferation into the visual axis and abnormal high i...

    Authors: Kai Zhang, Xiyang Liu, Jiewei Jiang, Wangting Li, Shuai Wang, Lin Liu, Xiaojing Zhou and Liming Wang
    Citation: Journal of Translational Medicine 2019 17:2
  28. Multiple myeloma (MM) is the plasma cell tumor, which is characterized by clonal proliferation of tumor cells, with high risk of progression to renal impairment, bone damage and amyloidosis. Although the survi...

    Authors: Weilong Zhang, Yuansheng Lin, Xiaoni Liu, Xue He, Ye Zhang, Wei Fu, Zuozhen Yang, Ping Yang, Jing Wang, Kai Hu, Xiuru Zhang, Weiyou Liu, Xiaoliang Yuan and Hongmei Jing
    Citation: Journal of Translational Medicine 2018 16:363
  29. Identification of miRNA-disease associations has attracted much attention recently due to the functional roles of miRNAs implicated in various biological and pathological processes. Great efforts have been mad...

    Authors: Cheng Liang, Shengpeng Yu, Ka-Chun Wong and Jiawei Luo
    Citation: Journal of Translational Medicine 2018 16:357
  30. Research on microRNAs (miRNAs) has attracted increasingly worldwide attention over recent years as growing experimental results have made clear that miRNA correlates with masses of critical biological processe...

    Authors: Xing Chen, De-Hong Zhang and Zhu-Hong You
    Citation: Journal of Translational Medicine 2018 16:348
  31. The events in early HIV infection (EHI) are important determinants of disease severity and progression rate to AIDS, but the mechanisms of pathogenesis in EHI have not been fully understood. Circular RNAs (cir...

    Authors: Yue Zhang, Hui Zhang, Minghui An, Bin Zhao, Haibo Ding, Zining Zhang, Youwen He, Hong Shang and Xiaoxu Han
    Citation: Journal of Translational Medicine 2018 16:332
  32. The aim of the study is described the regulatory mechanisms and prognostic values of differentially expressed RNAs in prostate cancer and construct an mRNA signature that predicts survival.

    Authors: Ning Xu, Yu-Peng Wu, Hu-Bin Yin, Xue-Yi Xue and Xin Gou
    Citation: Journal of Translational Medicine 2018 16:274
  33. Hepatocellular carcinoma (HCC) is one of the most lethal cancer, mainly attributing to its high tendency to metastasis. Vascular invasion provides a direct path for solid tumor metastasis. Mounting evidence ha...

    Authors: Weiyang Lou, Jing Chen, Bisha Ding, Danni Chen, Huilin Zheng, Donghai Jiang, Liang Xu, Chang Bao, Guoqiang Cao and Weimin Fan
    Citation: Journal of Translational Medicine 2018 16:266
  34. The use of medical data for research purposes requires an informed consent of the patient that is compliant with the EU General Data Protection Regulation. In the context of multi-centre research initiatives a...

    Authors: Martin Bialke, Thomas Bahls, Lars Geidel, Henriette Rau, Arne Blumentritt, Sandra Pasewald, Robert Wolff, Jonas Steinmann, Tobias Bronsch, Björn Bergh, Galina Tremper, Martin Lablans, Frank Ückert, Stefan Lang, Tarik Idris and Wolfgang Hoffmann
    Citation: Journal of Translational Medicine 2018 16:256
  35. Major differences exist between men and women in both physiology and pathophysiology. Dissecting the underlying processes and contributing mechanisms of sex differences in health and disease represents a cruci...

    Authors: Changting Cui, Chuanbo Huang, Kejia Liu, Guoheng Xu, Jichun Yang, Yong Zhou, Yingmei Feng, Georgios Kararigas, Bin Geng and Qinghua Cui
    Citation: Journal of Translational Medicine 2018 16:236
  36. Hepatitis B virus (HBV) infection is strongly associated with hepatocellular carcinoma due to the main pathogenic X protein of HBV (HBx). Whether HBV infection and the HBx protein could result in macular degen...

    Authors: Ruey-Hwang Chou, Chang-Yin Lee, Lee-Won Chong, Kuang-Hsi Chang, Cheng-Li Lin, Ke-Sin Yan, Chingfu Tsou and Yi-Chao Hsu
    Citation: Journal of Translational Medicine 2018 16:221
  37. The purpose of this study was to achieve early and accurate diagnosis of lung cancer and long-term monitoring of the therapeutic response.

    Authors: Zhirui Fan, Wenhua Xue, Lifeng Li, Chaoqi Zhang, Jingli Lu, Yunkai Zhai, Zhenhe Suo and Jie Zhao
    Citation: Journal of Translational Medicine 2018 16:205
  38. Acute renal allograft rejection is a common complication after renal transplantation that often leads to chronic rejection and ultimate graft loss. While renal allograft biopsy remains the gold standard for di...

    Authors: Long Zheng, Jina Wang, Wenjun Gao, Chao Hu, Shuo Wang, Ruiming Rong, Yinlong Guo, Tongyu Zhu and Dong Zhu
    Citation: Journal of Translational Medicine 2018 16:202
  39. Evidences in literature strongly advocate the potential of immunomodulatory peptides for use as vaccine adjuvants. All the mechanisms of vaccine adjuvants ensuing immunostimulatory effects directly or indirect...

    Authors: Gandharva Nagpal, Kumardeep Chaudhary, Piyush Agrawal and Gajendra P. S. Raghava
    Citation: Journal of Translational Medicine 2018 16:181
  40. Bipolar disorder (BD), a type of psychiatric mood disorder, is manifested by chronic and recurrent mood fluctuations. This study aims to determine whether hepatitis B virus (HBV) or hepatitis C virus (HCV) inf...

    Authors: Lee-Won Chong, Chih-Chao Hsu, Chang-Yin Lee, Ruey-Hwang Chou, Cheng-Li Lin, Kuang-Hsi Chang and Yi-Chao Hsu
    Citation: Journal of Translational Medicine 2018 16:173
  41. Despite great development in genome and proteome high-throughput methods, treatment failure is a critical point in the management of most solid cancers, including breast cancer (BC). Multiple alternative mecha...

    Authors: Claudia Cava, Gloria Bertoli and Isabella Castiglioni
    Citation: Journal of Translational Medicine 2018 16:154
  42. Chronic obstructive pulmonary disease (COPD) patients often show skeletal muscle dysfunction that has a prominent negative impact on prognosis. The study aims to further explore underlying mechanisms of skelet...

    Authors: Ákos Tényi, Isaac Cano, Francesco Marabita, Narsis Kiani, Susana G. Kalko, Esther Barreiro, Pedro de Atauri, Marta Cascante, David Gomez-Cabrero and Josep Roca
    Citation: Journal of Translational Medicine 2018 16:34
  43. In most research projects budget, staff and IT infrastructures are limiting resources. Especially for small-scale registries and cohort studies professional IT support and commercial electronic data capture sy...

    Authors: Martin Bialke, Henriette Rau, Oliver C. Thamm, Ronny Schuldt, Peter Penndorf, Arne Blumentritt, Robert Gött, Jens Piegsa, Thomas Bahls and Wolfgang Hoffmann
    Citation: Journal of Translational Medicine 2018 16:16
  44. Asthma is a complex, heterogeneous disorder with similar presenting symptoms but with varying underlying pathologies. Exhaled breath condensate (EBC) is a relatively unexplored matrix which reflects the signat...

    Authors: Anirban Sinha, Koundinya Desiraju, Kunal Aggarwal, Rintu Kutum, Siddhartha Roy, Rakesh Lodha, S. K. Kabra, Balaram Ghosh, Tavpritesh Sethi and Anurag Agrawal
    Citation: Journal of Translational Medicine 2017 15:262
  45. The problem of drug resistance and bacterial persistence in tuberculosis is a cause of global alarm. Although, the UN’s Sustainable Development Goals for 2030 has targeted a Tb free world, the treatment gap ex...

    Authors: Divneet Kaur, Shalu Mathew, Chinchu G. S. Nair, Azitha Begum, Ashwin K. Jainanarayan, Mukta Sharma and Samir K. Brahmachari
    Citation: Journal of Translational Medicine 2017 15:261
  46. Recently, as the research of microRNA (miRNA) continues, there are plenty of experimental evidences indicating that miRNA could be associated with various human complex diseases development and progression. He...

    Authors: Xing Chen, Ya-Wei Niu, Guang-Hui Wang and Gui-Ying Yan
    Citation: Journal of Translational Medicine 2017 15:251
  47. The progression of complex diseases, such as diabetes and cancer, is generally a nonlinear process with three stages, i.e., normal state, pre-disease state, and disease state, where the pre-disease state is a ...

    Authors: Pei Chen, Yongjun Li, Xiaoping Liu, Rui Liu and Luonan Chen
    Citation: Journal of Translational Medicine 2017 15:217
  48. The Connectivity Map (CMAP) database, an important public data source for drug repositioning, archives gene expression profiles from cancer cell lines treated with and without bioactive small molecules. Howeve...

    Authors: Jun He, Haidan Yan, Hao Cai, Xiangyu Li, Qingzhou Guan, Weicheng Zheng, Rou Chen, Huaping Liu, Kai Song, Zheng Guo and Xianlong Wang
    Citation: Journal of Translational Medicine 2017 15:198
  49. Only a handful of long noncoding RNAs have been functionally characterized. They are known to modulate regulation through interacting with other biomolecules in the cell: DNA, RNA and protein. Though there hav...

    Authors: Saakshi Jalali, Amrita Singh, Souvik Maiti and Vinod Scaria
    Citation: Journal of Translational Medicine 2017 15:186

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