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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. Circulating extracelluar vesicles (EVs) in epithelial ovarian cancer (EOC) patients emanate from multiple cells. These EVs are emerging as a new type of biomarker as they can be obtained by non-invasive approa...

    Authors: Wei Zhang, Peng Peng, Xiaoxuan Ou, Keng Shen and Xiaohua Wu

    Citation: BMC Cancer 2019 19:1095

    Content type: Research article

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  2. The evasion of apoptosis is a hallmark of cancer. Understanding this process holistically and overcoming apoptosis resistance is a goal of many research teams in order to develop better treatment options for c...

    Authors: Manuela Salvucci, Zaitun Zakaria, Steven Carberry, Amanda Tivnan, Volker Seifert, Donat Kögel, Brona M. Murphy and Jochen H. M. Prehn

    Citation: BMC Cancer 2019 19:1092

    Content type: Review

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  3. Genetics-based basket trials have emerged to test targeted therapeutics across multiple cancer types. However, while vemurafenib is FDA-approved for BRAF-V600E melanomas, the non-melanoma basket trial was unsucce...

    Authors: Molly J. Carroll, Carl R. Parent, David Page and Pamela K. Kreeger

    Citation: BMC Cancer 2019 19:1025

    Content type: Research article

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  4. In biomedical research, network inference algorithms are typically used to infer complex association patterns between biological entities, such as between genes or proteins, using data from a population. This ...

    Authors: Marieke L Kuijjer, Ping-Han Hsieh, John Quackenbush and Kimberly Glass

    Citation: BMC Cancer 2019 19:1003

    Content type: Software

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  5. Microsatellite instability (MSI), resulting from a defective mismatch repair system, occurs in approximately 15% of sporadic colorectal cancers (CRC). Since MSI is associated with a poor response to 5-fluorour...

    Authors: Amanda Frydendahl Boll Johansen, Christine Gaasdal Kassentoft, Michael Knudsen, Maria Bach Laursen, Anders Husted Madsen, Lene Hjerrild Iversen, Kåre Gotschalck Sunesen, Mads Heilskov Rasmussen and Claus Lindbjerg Andersen

    Citation: BMC Cancer 2019 19:971

    Content type: Research article

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  6. Genomic initiatives such as The Cancer Genome Atlas (TCGA) contain data from -omics profiling of thousands of tumor samples, which may be used to decipher cancer signaling, and related alterations. Managing an...

    Authors: Marta Lucchetta, Isabelle da Piedade, Mohamed Mounir, Marina Vabistsevits, Thilde Terkelsen and Elena Papaleo

    Citation: BMC Cancer 2019 19:824

    Content type: Research article

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  7. Differentiated cells that arise from stem cells in early development contain DNA methylation features that provide a memory trace of their fetal cell origin (FCO). The FCO signature was developed to estimate t...

    Authors: Ze Zhang, John K. Wiencke, Devin C. Koestler, Lucas A. Salas, Brock C. Christensen and Karl T. Kelsey

    Citation: BMC Cancer 2019 19:711

    Content type: Research article

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  8. 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

    Content type: Research article

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  9. 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

    Content type: Research article

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  10. 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

    Content type: Research article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Research article

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Research article

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  17. 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

    Content type: Technical Advance

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Research article

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  20. 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

    Content type: Case report

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  21. 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

    Content type: Research article

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  22. 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

    Content type: Database

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  23. 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

    Content type: Research article

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Research article

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Database

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Debate

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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

  42. 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

    Content type: Research article

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