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Systems biology, post-genomic analysis and emerging technologies

This section will consider studies on all aspects of the function of biological systems at the molecular and cellular level, in particular those addressing network modeling, quantitative analyses and the integration of different levels of information. Topics of interest include, but are not limited to, deep sequencing-based technologies, computational biology and machine learning in relation to cancer biology.

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  1. Content type: Research article

    Longitudinal studies of tumor volume have used certain named mathematical growth models. The Bertalanffy-Pütter differential equation unifies them: It uses five parameters, amongst them two exponents related t...

    Authors: Manfred Kühleitner, Norbert Brunner, Werner-Georg Nowak, Katharina Renner-Martin and Klaus Scheicher

    Citation: BMC Cancer 2019 19:683

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  2. Content type: Research article

    Muscle-invasive bladder tumors are associated with a high risk of relapse and metastasis even after neoadjuvant chemotherapy and radical cystectomy. Therefore, further therapeutic options are needed and molecu...

    Authors: Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Jorge M. Arevalillo, María Ferrer-Gómez, Hilario Navarro, Paloma Maín, Enrique Espinosa, Álvaro Pinto and Juan Ángel Fresno Vara

    Citation: BMC Cancer 2019 19:636

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  3. Content type: Research article

    The NTRK2 genetic locus encodes neurotrophin membrane receptors that play an important role in normal neural tissue plasticity, growth, and survival. One NTRK2-encoded protein is TrkB-FL, which can regulate mu...

    Authors: Yalu Zhou, Saurabh Sinha, Joel L. Schwartz and Guy R. Adami

    Citation: BMC Cancer 2019 19:607

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  4. Content type: Research article

    Circulating tumor cells (CTC) and plasma cell-free RNA (cfRNA) can serve as biomarkers for prognosis and treatment response in lung cancer. One barrier to the selected or routine use of CTCs and plasma cfRNA i...

    Authors: Tim N. Beck, Yanis A. Boumber, Charu Aggarwal, Jianming Pei, Catherine Thrash-Bingham, Patricia Fittipaldi, Ramillya Vlasenkova, Chandra Rao, Hossein Borghaei, Massimo Cristofanilli, Ranee Mehra, Ilya Serebriiskii and R. Katherine Alpaugh

    Citation: BMC Cancer 2019 19:603

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  5. Content type: Research article

    Receptor tyrosine kinase (RTK) inhibitors are frequently used to treat cancers and the results have been mixed, some of these small molecule drugs are highly successful while others show a more modest response...

    Authors: Jian Li, Kathrin Halfter, Mengying Zhang, Christian Saad, Kai Xu, Bernhard Bauer, Yijiang Huang, Lei Shi and Ulrich R. Mansmann

    Citation: BMC Cancer 2019 19:600

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  6. Content type: Research article

    Cancer patients with advanced disease routinely exhaust available clinical regimens and lack actionable genomic medicine results, leaving a large patient population without effective treatments options when th...

    Authors: Noah E. Berlow, Rishi Rikhi, Mathew Geltzeiler, Jinu Abraham, Matthew N. Svalina, Lara E. Davis, Erin Wise, Maria Mancini, Jonathan Noujaim, Atiya Mansoor, Michael J. Quist, Kevin L. Matlock, Martin W. Goros, Brian S. Hernandez, Yee C. Doung, Khin Thway…

    Citation: BMC Cancer 2019 19:593

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  7. Content type: Research article

    Alterations in protein glycosylation patterns have potentially been targeted for biomarker discovery in a wide range of diseases including cancer. Although there have been improvements in patient diagnosis and...

    Authors: Abrha G. Gebrehiwot, Daniel Seifu Melka, Yimenashu Mamo Kassaye, Tufa Gemechu, Wajana Lako, Hiroshi Hinou and Shin-Ichiro Nishimura

    Citation: BMC Cancer 2019 19:588

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  8. Content type: Research article

    To evaluate the value of a three dimension (3D)visualization operative planning system in ultrasound-guided percutaneous microwave ablation (US-PMWA) for large hepatic hemangiomas (LHHs).

    Authors: Xin Li, Chao An, Fangyi Liu, Zhigang Cheng, Zhiyu Han, Xiaoling Yu, Linan Dong, Jie Yu and Ping Liang

    Citation: BMC Cancer 2019 19:550

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  9. Content type: Research article

    Obesity is an important cause of multiple cancer types, amongst which endometrial cancer (EC). The relation between obesity and cancer is complicated and involves alterations in insulin metabolism, response to...

    Authors: Willem Jan van Weelden, Kristine Eldevik Fasmer, Ingvild L. Tangen, Joanna IntHout, Karin Abbink, Antionius E. van Herwaarden, Camilla Krakstad, Leon F. A. G. Massuger, Ingfrid S. Haldorsen and Johanna M. A. Pijnenborg

    Citation: BMC Cancer 2019 19:547

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  10. Content type: Technical advance

    Most methods that integrate network and mutation data to study cancer focus on the effects of genes/proteins, quantifying the effect of mutations or differential expression of a gene and its neighbors, or iden...

    Authors: Matthew Ruffalo and Ziv Bar-Joseph

    Citation: BMC Cancer 2019 19:370

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  11. Content type: Research article

    Worldwide, breast cancer is the main cause of cancer mortality in women. Most cases originate in mammary ductal cells that produce the nipple aspirate fluid (NAF). In cancer patients, this secretome contains p...

    Authors: Giselle Villa Flor Brunoro, Paulo Costa Carvalho, Valmir C. Barbosa, Dante Pagnoncelli, Claudia Vitória De Moura Gallo, Jonas Perales, René Peiman Zahedi, Richard Hemmi Valente and Ana Gisele da Costa Neves-Ferreira

    Citation: BMC Cancer 2019 19:365

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  12. Content type: Research article

    Though the management of malignancies has improved vastly in recent years, many treatment options lack the desired efficacy and fail to adequately augment patient morbidity and mortality. It is increasingly cl...

    Authors: Andrew Riley, Victoria Green, Ramsah Cheah, Gordon McKenzie, Laszlo Karsai, James England and John Greenman

    Citation: BMC Cancer 2019 19:259

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  13. Content type: Case report

    Central nervous system lymphomas (CNSL) is a devastating disease. Currently, a confirmatory biopsy is required prior to treatment.

    Authors: Anne-Katrin Hickmann, Maximilian Frick, Dirk Hadaschik, Florian Battke, Markus Bittl, Oliver Ganslandt, Saskia Biskup and Dennis Döcker

    Citation: BMC Cancer 2019 19:192

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  14. Content type: Research article

    The nucleic acid mutation status in intracranial metastasis is markedly significant clinically. The goal of the current study was to explore whether the tumor-associated mutations can be detected by different ...

    Authors: Mengxi Ge, Qiong Zhan, Zhenzhen Zhang, Xiaoyu Ji, Xinli Zhou, Ruofan Huang and Xiaohua Liang

    Citation: BMC Cancer 2019 19:143

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  15. Content type: Database

    microRNAs (miRNAs) are crucially important in the development of cancer. Their dysregulation, commonly observed in various types of cancer, is largely cancer-dependent. Thus, to understand the tumor biology an...

    Authors: Aaron L. Sarver, Anne E. Sarver, Ce Yuan and Subbaya Subramanian

    Citation: BMC Cancer 2018 18:1223

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  16. Content type: Research article

    Cervical cancer is the most common genital malignant tumor in women worldwide. However, the reliability of different detection methods may vary according to populations and epidemics. This study analyzed facto...

    Authors: Sulaiya Husaiyin, Lili Han, Lin Wang, Chunhua Ma, Zumurelaiti Ainiwaer, Nuermanguli Rouzi, Mireguli Akemujiang, Hatiguli Simayil, Zumulaiti Aniwa, Rouzi Nurimanguli and Mayinuer Niyazi

    Citation: BMC Cancer 2018 18:1162

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  17. Content type: Research article

    Earlier diagnosis is beneficial for the prognosis of hepatocellular carcinoma (HCC). Alpha fetoprotein (AFP) is the most widely used biomarker for HCC, but its sensitivity and specificity are only 60 and 90%, ...

    Authors: Chenghua Zhang, Ran Xia, Bo Zhang and Haibo Wang

    Citation: BMC Cancer 2018 18:1110

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  18. Content type: Research article

    Systemic inflammation has been implicated in cancer development and progression. This study examined the best cutoff value of erythrocyte sedimentation rate (ESR) in diffuse large B-cell lymphoma (DLBCL) patie...

    Authors: Shuang Wu, Ye Zhou, Hai-Ying Hua, Yan Zhang, Wen-Yan Zhu, Zhi-Qing Wang, Jin Li, Hua-Qiang Gao, Xiao-Hong Wu, Ting-Xun Lu and Dong Hua

    Citation: BMC Cancer 2018 18:997

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  19. Content type: Research article

    Pulmonary imaging often identifies suspicious abnormalities resulting in supplementary diagnostic procedures. This study aims to investigate whether the metabolic fingerprint of plasma allows to discriminate b...

    Authors: K. Vanhove, P. Giesen, O. E. Owokotomo, L. Mesotten, E. Louis, Z. Shkedy, M. Thomeer and P. Adriaensens

    Citation: BMC Cancer 2018 18:868

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  20. Content type: Research article

    Metastatic melanoma is an aggressive form of skin cancer that evades various anti-cancer treatments including surgery, radio-,immuno- and chemo-therapy. TRAIL-induced apoptosis is a desirable method to treat m...

    Authors: Radhika S. Saraf, Aniruddha Datta, Chao Sima, Jianping Hua, Rosana Lopes and Michael Bittner

    Citation: BMC Cancer 2018 18:855

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  21. Content type: Research article

    An increase in naturally-occurring porphyrins has been described in the blood of subjects bearing different kinds of tumors, including colorectal, and this is probably related to a systemic alteration of heme ...

    Authors: Manuela Lualdi, Adalberto Cavalleri, Luigi Battaglia, Ambrogio Colombo, Giulia Garrone, Daniele Morelli, Emanuele Pignoli, Elisa Sottotetti and Ermanno Leo

    Citation: BMC Cancer 2018 18:841

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  22. Content type: Research article

    Aberrant AKT activation is prevalent across human cancer lineages, providing an important therapeutic target. AKT comprises three isoforms that mediate critical non-redundant, even opposing functions in cancer...

    Authors: Jue Wang, Wei Zhao, Huifang Guo, Yong Fang, Sarah Elizabeth Stockman, Shanshan Bai, Patrick Kwok-Shing Ng, Yang Li, Qinghua Yu, Yiling Lu, Kang Jin Jeong, Xiaohua Chen, Meng Gao, Jiyong Liang, Wentao Li, Xingsong Tian…

    Citation: BMC Cancer 2018 18:742

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  23. Content type: Research article

    Synovial Sarcomas (SS) are rare tumors occurring predominantly in adolescent and young adults with a dismal prognosis in advanced phases. We report a first-in-human phase I of monoclonal antibody (OTSA-101) ta...

    Authors: Anne-Laure Giraudet, Philippe Alexandre Cassier, Chicaco Iwao-Fukukawa, Gwenaelle Garin, Jean-Noël Badel, David Kryza, Sylvie Chabaud, Laurence Gilles-Afchain, Gilles Clapisson, Claude Desuzinges, David Sarrut, Adrien Halty, Antoine Italiano, Masaharu Mori, Takuya Tsunoda, Toyomasa Katagiri…

    Citation: BMC Cancer 2018 18:646

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  24. Content type: Research article

    Melanoma is the deadliest type of skin cancer with highest mortality rate. However, the annihilation in its early stage implies a high survival rate therefore, it demands early diagnosis. The accustomed diagno...

    Authors: M. Attique Khan, Tallha Akram, Muhammad Sharif, Aamir Shahzad, Khursheed Aurangzeb, Musaed Alhussein, Syed Irtaza Haider and Abdualziz Altamrah

    Citation: BMC Cancer 2018 18:638

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  25. Content type: Research article

    Gene-expression companion diagnostic tests, such as the Oncotype DX test, assess the risk of early stage Estrogen receptor (ER) positive (+) breast cancers, and guide clinicians in the decision of whether or n...

    Authors: Jon Whitney, German Corredor, Andrew Janowczyk, Shridar Ganesan, Scott Doyle, John Tomaszewski, Michael Feldman, Hannah Gilmore and Anant Madabhushi

    Citation: BMC Cancer 2018 18:610

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  26. Content type: Research article

    Efforts have been made to classify Hepatocellular Carcinoma (HCC) at surgically curable stages because molecular classification, which is prognostically informative, can accurately identify patients in need of...

    Authors: Sung-Min Ahn, Farhan Haq, Inkeun Park, Jean-Charles Nault, Jessica Zucman-Rossi and Eunsil Yu

    Citation: BMC Cancer 2018 18:571

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  27. Content type: Research article

    The smoothened (SMO) receptor is an essential component of the Sonic hedgehog (SHH) signalling, which is associated with the development of skin basal cell carcinoma (BCC). SMO inhibitors are indicated for BCC...

    Authors: Antoine Buetti-Dinh, Rebecca Jensen and Ran Friedman

    Citation: BMC Cancer 2018 18:569

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  28. Content type: Research article

    Single Nucleotide Polymorphisms (SNPs) can influence patient outcome such as drug response and toxicity after drug intervention. The purpose of this study is to develop a systematic pathway approach to accurat...

    Authors: Vachiranee Limviphuvadh, Chee Seng Tan, Fumikazu Konishi, Piroon Jenjaroenpun, Joy Shengnan Xiang, Yuliya Kremenska, Yar Soe Mu, Nicholas Syn, Soo Chin Lee, Ross A. Soo, Frank Eisenhaber, Sebastian Maurer-Stroh and Wei Peng Yong

    Citation: BMC Cancer 2018 18:555

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  29. Content type: Database

    Liver cancer is the second leading cause of cancer-related deaths and characterized by heterogeneity and drug resistance. Patient-derived xenograft (PDX) models have been widely used in cancer research because...

    Authors: Sheng He, Bo Hu, Chao Li, Ping Lin, Wei-Guo Tang, Yun-Fan Sun, Fang-You-Min Feng, Wei Guo, Jia Li, Yang Xu, Qian-Lan Yao, Xin Zhang, Shuang-Jian Qiu, Jian Zhou, Jia Fan, Yi-Xue Li…

    Citation: BMC Cancer 2018 18:550

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  30. Content type: Research article

    In the last decade many studies showed that the exhaled breath of subjects suffering from several pathological conditions has a peculiar volatile organic compound (VOC) profile. The objective of the present wo...

    Authors: Andrea Princivalle, Lorenzo Monasta, Giovanni Butturini, Claudio Bassi and Luigi Perbellini

    Citation: BMC Cancer 2018 18:529

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  31. Content type: Research article

    Gene therapy is a potent method to increase the therapeutic efficacy against cancer. However, a gene that is specifically expressed in the tumor area has not been identified. In addition, nonspecific expressio...

    Authors: Shu-Yi Ho, Bo-Hau Chang, Chen-Han Chung, Yu-Ling Lin, Cheng-Hsun Chuang, Pei-Jung Hsieh, Wei-Chih Huang, Nu-Man Tsai, Sheng-Chieh Huang, Yen-Ku Liu, Yu-Chih Lo and Kuang-Wen Liao

    Citation: BMC Cancer 2018 18:480

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  32. Content type: Debate

    Improving our understanding of cancer and other complex diseases requires integrating diverse data sets and algorithms. Intertwining in vivo and in vitro data and in silico models are paramount to overcome intrin...

    Authors: Claire Jean-Quartier, Fleur Jeanquartier, Igor Jurisica and Andreas Holzinger

    Citation: BMC Cancer 2018 18:408

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  33. Content type: Research article

    Carcinoembryonic antigen (CEA) and carbohydrate antigen (CA)19–9 are used in clinical practice as tumor markers to diagnose or monitor colorectal cancer (CRC) patients, However, their specificities and sensiti...

    Authors: Eiji Shinozaki, Kazuhiro Tanabe, Takashi Akiyoshi, Tomohiro Tsuchida, Yuko Miyazaki, Nozomi Kojima, Masahiro Igarashi, Masashi Ueno, Mitsukuni Suenaga, Nobuyuki Mizunuma, Kensei Yamaguchi, Konosuke Nakayama, Sadayo Iijima and Toshiharu Yamaguchi

    Citation: BMC Cancer 2018 18:406

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  34. Content type: Research article

    Programmed Death Ligand 1 (PD-L1) is a co-stimulatory and immune checkpoint protein. PD-L1 expression in non-small cell lung cancers (NSCLC) is a hallmark of adaptive resistance and its expression is often use...

    Authors: Kim A. Brogden, Deepak Parashar, Andrea R. Hallier, Terry Braun, Fang Qian, Naiyer A. Rizvi, Aaron D. Bossler, Mohammed M. Milhem, Timothy A. Chan, Taher Abbasi and Shireen Vali

    Citation: BMC Cancer 2018 18:225

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    The Correction to this article has been published in BMC Cancer 2018 18:413

  35. Content type: Research article

    NRF2 is the key regulator of oxidative stress in normal cells and aberrant expression of the NRF2 pathway due to genetic alterations in the KEAP1 (Kelch-like ECH-associated protein 1)-NRF2 (nuclear factor eryt...

    Authors: Akhileshwar Namani, Md. Matiur Rahaman, Ming Chen and Xiuwen Tang

    Citation: BMC Cancer 2018 18:46

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  36. Content type: Research article

    The clinical benefit of adjuvant chemotherapy for stage II colorectal cancer (CRC) is controversial. This study aimed to explore novel gene signature to predict outcome benefit of postoperative 5-Fu-based ther...

    Authors: Bangrong Cao, Liping Luo, Lin Feng, Shiqi Ma, Tingqing Chen, Yuan Ren, Xiao Zha, Shujun Cheng, Kaitai Zhang and Changmin Chen

    Citation: BMC Cancer 2017 17:844

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  37. Content type: Research article

    The epithelial to mesenchymal transition (EMT) plays a key role in lung cancer progression and drug resistance. The dynamics and stability of gene expression patterns as cancer cells transition from E to M at ...

    Authors: Daifeng Wang, John D. Haley and Patricia Thompson

    Citation: BMC Cancer 2017 17:830

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  38. Content type: Research article

    The differentiation of pancreatic ductal adenocarcinoma (PDAC) could be associated with prognosis and may influence the choices of clinical management. No applicable methods could reliably predict the tumor di...

    Authors: Shi Wen, Bohan Zhan, Jianghua Feng, Weize Hu, Xianchao Lin, Jianxi Bai and Heguang Huang

    Citation: BMC Cancer 2017 17:708

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  39. Content type: Research article

    Triple-negative breast cancer (TN) is more aggressive than other subtypes of breast cancer and has a lower survival rate. Furthermore, detailed biological information about the disease is lacking. This study i...

    Authors: Yuji Yamashita, Shin Nishiumi, Seishi Kono, Shintaro Takao, Takeshi Azuma and Masaru Yoshida

    Citation: BMC Cancer 2017 17:589

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  40. Content type: Research article

    Hotspot mutations of the oncogenes BRAF and NRAS are the most common genetic alterations in cutaneous melanoma. Specific inhibitors of BRAF and MEK have shown significant survival benefits in large phase III t...

    Authors: Markus V. Heppt, Timo Siepmann, Jutta Engel, Gabriele Schubert-Fritschle, Renate Eckel, Laura Mirlach, Thomas Kirchner, Andreas Jung, Anja Gesierich, Thomas Ruzicka, Michael J. Flaig and Carola Berking

    Citation: BMC Cancer 2017 17:536

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  41. Content type: Research article

    Human cancer cell lines are used in research to study the biology of cancer and to test cancer treatments. Recently there are already some large panels of several hundred human cancer cell lines which are char...

    Authors: Lin Wang, Xiaozhong Li, Louxin Zhang and Qiang Gao

    Citation: BMC Cancer 2017 17:513

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