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Medical bioinformatics

Section edited by Gajendra Raghava

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.

  1. Content type: Methodology

    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

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  2. Content type: Research

    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

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  3. Content type: Research

    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

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  4. Content type: Research

    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

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  5. Content type: Research

    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

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  6. Content type: Research

    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

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  7. Content type: Research

    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

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  8. Content type: Research

    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

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  9. Content type: Research

    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

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  10. Content type: Methodology

    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

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  11. Content type: Research

    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

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  12. Content type: Research

    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

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  13. Content type: Research

    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

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  14. Content type: Research

    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

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  15. Content type: Research

    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

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  16. Content type: Research

    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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  17. Content type: Research

    HIV-1-infected long-term nonprogressors (LTNPs) are characterized by infection with HIV-1 more than 7–10 years, but keeping high CD4+ T cell counts and low viral load in the absence of antiretroviral treatment, w...

    Authors: Qibin Liao, Jin Wang, Zenglin Pei, Jianqing Xu and Xiaoyan Zhang

    Citation: Journal of Translational Medicine 2017 15:41

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  18. Content type: Research

    The gastrointestinal motility is affected by gut microbiota and the relationship between them has become a hot topic. However, mechanisms of microbiota in regulating motility have not been well defined. We thu...

    Authors: Xiaolong Ge, Chao Ding, Wei Zhao, Lizhi Xu, Hongliang Tian, Jianfeng Gong, Minsheng Zhu, Jieshou Li and Ning Li

    Citation: Journal of Translational Medicine 2017 15:13

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  19. Content type: Research

    The current therapy for inflammatory and autoimmune disorders involves the use of nonspecific anti-inflammatory drugs and other immunosuppressant, which are often accompanied with potential side effects. As an...

    Authors: Sudheer Gupta, Ashok K. Sharma, Vibhuti Shastri, Midhun K. Madhu and Vineet K. Sharma

    Citation: Journal of Translational Medicine 2017 15:7

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  20. Content type: Research

    Guizhi-Shaoyao-Zhimu decoction (GSZD) has been extensively used for rheumatoid arthritis (RA) therapy. Marked therapeutic efficacy of GSZD acting on RA has been demonstrated in several long-term clinical trial...

    Authors: Qiuyan Guo, Xia Mao, Yanqiong Zhang, Shuqin Meng, Yue Xi, Yi Ding, Xiaocun Zhang, Yuntao Dai, Xia Liu, Chao Wang, Yuting Li and Na Lin

    Citation: Journal of Translational Medicine 2016 14:165

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  21. Content type: Review

    MicroRNAs (miRs, miRNAs) are small molecules of 18–22 nucleotides that serve as important regulators of gene expression at the post-transcriptional level. One of the mechanisms through which miRNAs regulate ge...

    Authors: Lyudmila F. Gulyaeva and Nicolay E. Kushlinskiy

    Citation: Journal of Translational Medicine 2016 14:143

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  22. Content type: Research

    Previous work found that urea accumulation in urothelial cells caused by urea transporter B knockout led to DNA damage and apoptosis that contributed to the carcinogenesis. The purpose of this study is to expl...

    Authors: Ming Liu, Min Li, Jiangfeng Liu, Hongkai Wang, Dandan Zhong, Hong Zhou and Baoxue Yang

    Citation: Journal of Translational Medicine 2016 14:53

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  23. Content type: Research

    Previous researches has depicted that the performance of the recommended glomerular filtration rate (GFR)-estimating equations in the type 2 diabetic population is inferior to that in the non-diabetic populati...

    Authors: Jinxia Chen, Hua Tang, Hui Huang, Linsheng Lv, Yanni Wang, Xun Liu and Tanqi Lou

    Citation: Journal of Translational Medicine 2015 13:317

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  24. Content type: Research

    Angiogenesis is a hallmark feature in the initiation, progression and growth of tumour. There are various factors for promotion of angiogenesis on one hand and on the other hand, biomolecules have been report...

    Authors: Rashmi K. Ambasta, Saurabh Kumar Jha, Dhiraj Kumar, Renu Sharma, Niraj Kumar Jha and Pravir Kumar

    Citation: Journal of Translational Medicine 2015 13:307

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  25. Content type: Research

    Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. HCC has a poor prognosis associated with tumor recurrence and drug resistance, which has been attributed to the existence of hep...

    Authors: Min Ding, Jiang Li, Yong Yu, Hui Liu, Zi Yan, Jinghan Wang and Qijun Qian

    Citation: Journal of Translational Medicine 2015 13:259

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  26. Content type: Research

    While in the past decades nucleic acid analysis has been predominantly carried out using quantitative low- and high-throughput approaches such as qRT-PCR and microarray technology, next-generation sequencing (...

    Authors: Christina Backes, Jan Haas, Petra Leidinger, Karen Frese, Thomas Großmann, Klemens Ruprecht, Benjamin Meder, Eckart Meese and Andreas Keller

    Citation: Journal of Translational Medicine 2015 13:224

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  27. Content type: Research

    The effectiveness of current therapeutic regimens for Mycobacterium tuberculosis (Mtb) is diminished by the need for prolonged therapy and the rise of drug resistant/tolerant strains. This global health threat, d...

    Authors: Rohit Vashisht, Ashwini G Bhat, Shreeram Kushwaha, Anshu Bhardwaj, OSDD Consortium and Samir K Brahmachari

    Citation: Journal of Translational Medicine 2014 12:263

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  28. Content type: Research

    Drug-induced gene expression dataset (for example Connectivity Map, CMap) represent a valuable resource for drug-repurposing, a class of methods for identifying novel indications for approved drugs. Recently, ...

    Authors: Ling Jin, Jian Tu, Jianwei Jia, Wenbin An, Huanran Tan, Qinghua Cui and Zhixin Li

    Citation: Journal of Translational Medicine 2014 12:153

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  29. Content type: Research

    MicroRNAs (miRNAs) are a class of non-coding regulatory RNAs approximately 22 nucleotides in length that play a role in a wide range of biological processes. Abnormal miRNA function has been implicated in vari...

    Authors: Wenyu Zhang, Jin Zang, Xinhua Jing, Zhandong Sun, Wenying Yan, Dongrong Yang, Feng Guo and Bairong Shen

    Citation: Journal of Translational Medicine 2014 12:66

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  30. Content type: Meeting report

    This is a report on the 4th international conference in ‘Quantitative Biology and Bioinformatics in Modern Medicine’ held in Belfast (UK), 19–20 September 2013. The aim of the conference was to bring together ...

    Authors: Frank Emmert-Streib, Shu-Dong Zhang and Peter Hamilton

    Citation: Journal of Translational Medicine 2014 12:26

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  31. Content type: Research

    While the majority of studies have focused on the association between sex hormones and dementia, emerging evidence supports the role of other hormone signals in increasing dementia risk. However, due to the la...

    Authors: Erfan Younesi and Martin Hofmann-Apitius

    Citation: Journal of Translational Medicine 2013 11:177

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  32. Content type: Research

    Clear cell renal cell carcinoma (ccRCC) represents the most invasive and common adult kidney neoplasm. Mounting evidence suggests that microRNAs (miRNAs) are important regulators of gene expression. But their ...

    Authors: Jiajia Chen, Daqing Zhang, Wenyu Zhang, Yifei Tang, Wenying Yan, Lingchuan Guo and Bairong Shen

    Citation: Journal of Translational Medicine 2013 11:169

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  33. Content type: Methodology

    Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical...

    Authors: Imad Abugessaisa, David Gomez-Cabrero, Omri Snir, Staffan Lindblad, Lars Klareskog, Vivianne Malmström and Jesper Tegnér

    Citation: Journal of Translational Medicine 2013 11:85

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  34. Content type: Research

    Cell penetrating peptides have gained much recognition as a versatile transport vehicle for the intracellular delivery of wide range of cargoes (i.e. oligonucelotides, small molecules, proteins, etc.), that other...

    Authors: Ankur Gautam, Kumardeep Chaudhary, Rahul Kumar, Arun Sharma, Pallavi Kapoor, Atul Tyagi and Gajendra P S Raghava

    Citation: Journal of Translational Medicine 2013 11:74

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  35. Content type: Research

    The disorders in metabolism of energy substances are usually related to some diseases, such as obesity, diabetes and cancer, etc. However, the genetic background for these disorders has not been well understood. ...

    Authors: Cheng Xue, Xiaoming Liu, Yun Gong, Yuhai Zhao and Yun-Xin Fu

    Citation: Journal of Translational Medicine 2013 11:67

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