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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. 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
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  2. 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
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  3. 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
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  4. 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
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  5. 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
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  6. 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
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  7. 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
    Content type: Research Published on:

  8. 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
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  9. 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
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  10. 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
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  11. 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
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  12. 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
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  13. 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
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  14. 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
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  15. 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
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  16. 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
    Content type: Research Published on:

  17. 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
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  18. 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
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  19. 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
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  20. 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
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  21. 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
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  22. 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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  23. 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
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  24. 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
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    The Correction to this article has been published in Journal of Translational Medicine 2022 20:594

  25. 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
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  27. 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
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  28. 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
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  29. 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
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  30. 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
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  31. 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
    Content type: Research Published on:

  32. 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
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  33. 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
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  34. 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
    Content type: Research Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Published on:

  37. 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
    Content type: Research Published on:

  38. 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
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  39. 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
    Content type: Research Published on:

  40. 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
    Content type: Research Published on:

  41. 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
    Content type: Research Published on:

  42. 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
    Content type: Research Published on:

  43. 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
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  44. 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
    Content type: Research Published on:

  45. 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
    Content type: Research Published on:

  46. 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
    Content type: Research Published on:

  47. 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
    Content type: Research Published on:

  48. 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
    Content type: Research Published on:

  49. 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
    Content type: Research Published on:

  50. 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
    Content type: Research Published on:
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