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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. Identifying and tracking somatic mutations in cell-free DNA (cfDNA) by next-generation sequencing (NGS) has the potential to transform the clinical management of subjects with advanced non-small cell lung canc...

    Authors: John Jiang, Hans-Peter Adams, Maria Lange, Sandra Siemann, Mirjam Feldkamp, Sylvie McNamara, Sebastian Froehler, Stephanie J. Yaung, Lijing Yao, Aarthi Balasubramanyam, Nalin Tikoo, Christine Ju, H. Jost Achenbach, Rainer Krügel and John F. Palma

    Citation: BMC Cancer 2020 20:885

    Content type: Research article

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  2. The treatment of choice for advanced non–small cell lung cancer is selected according to the presence of specific alterations. Patients should undergo molecular testing for relevant modifications and the mutat...

    Authors: Luciene Schluckebier, Rosangela Caetano, Osvaldo Ulises Garay, Giuliana T. Montenegro, Marcelo Custodio, Veronica Aran and Carlos Gil Ferreira

    Citation: BMC Cancer 2020 20:875

    Content type: Research article

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  3. Endometrial cancer (EC) is the most common gynecologic cancer in women, and the incidence of EC has increased by about 1% per year in the U. S over the last 10 years. Although 5-year survival rates for early-s...

    Authors: Daniel G. Piqué, John M. Greally and Jessica C. Mar

    Citation: BMC Cancer 2020 20:857

    Content type: Research article

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  4. Colorectal cancer (CRC) is a multifactorial disease resulting from both genetic predisposition and environmental factors including the gut microbiota (GM), but deciphering the influence of genetic variants, en...

    Authors: Jacob E. Moskowitz, Anthony G. Doran, Zhentian Lei, Susheel B. Busi, Marcia L. Hart, Craig L. Franklin, Lloyd W. Sumner, Thomas M. Keane and James M. Amos-Landgraf

    Citation: BMC Cancer 2020 20:600

    Content type: Research article

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  5. Ex vivo drug screening refers to the out-of-body assessment of drug efficacy in patient derived vital tumor cells. The purpose of these methods is to enable functional testing of patient specific efficacy of a...

    Authors: Rami Mäkelä, Antti Arjonen, Ville Härmä, Nina Rintanen, Lauri Paasonen, Tobias Paprotka, Kerstin Rönsch, Teijo Kuopio, Juha Kononen and Juha K. Rantala

    Citation: BMC Cancer 2020 20:590

    Content type: Research article

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  6. Xenograft mouse tumor models are used to study mechanisms of tumor growth and metastasis formation and to investigate the efficacy of different therapeutic interventions. After injection the engrafted cells fo...

    Authors: Bertin Hoffmann, Tobias Lange, Vera Labitzky, Kristoffer Riecken, Andreas Wree, Udo Schumacher and Gero Wedemann

    Citation: BMC Cancer 2020 20:524

    Content type: Research article

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  7. Urothelial cancer (UC) includes carcinomas of the bladder, ureters, and renal pelvis. New treatments and biomarkers of UC emerged in this decade. To identify the key information in a vast amount of literature ...

    Authors: Hsuan-Jen Lin, Phillip C.-Y. Sheu, Jeffrey J. P. Tsai, Charles C. N. Wang and Che-Yi Chou

    Citation: BMC Cancer 2020 20:462

    Content type: Research article

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  8. Given the differences in embryonic origin, vascular and nervous supplies, microbiotic burden, and main physiological functions of left and right colons, tumor location is increasingly suggested to dictate tumo...

    Authors: Kavitha Mukund, Natalia Syulyukina, Sonia Ramamoorthy and Shankar Subramaniam

    Citation: BMC Cancer 2020 20:317

    Content type: Research article

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  9. Gastric cancer is a considerable burden for worldwide patients. And diffuse gastric cancer is the most insidious subgroup with poor survival. The phenotypic characterization of the diffuse gastric cancer cell ...

    Authors: Seon-Jin Yoon, Jungmin Park, Youngmin Shin, Yuna Choi, Sahng Wook Park, Seok-Gu Kang, Hye Young Son and Yong-Min Huh

    Citation: BMC Cancer 2020 20:314

    Content type: Research article

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  10. Sepsis and cancer are both leading causes of death, and occurrence of any one, increases the likelihood of the other. While cancer patients are susceptible to sepsis, survivors of sepsis are also susceptible t...

    Authors: Himanshu Tripathi, Samanwoy Mukhopadhyay and Saroj Kant Mohapatra

    Citation: BMC Cancer 2020 20:309

    Content type: Research article

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  11. Metabolomics has a great potential in the development of new biomarkers in cancer and it has experiment recent technical advances.

    Authors: Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Elena López-Camacho, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Rocío López-Vacas, Jorge M. Arevalillo, Mariana Díaz-Almirón, Hilario Navarro, Paloma Maín, Enrique Espinosa, Pilar Zamora and Juan Ángel Fresno Vara

    Citation: BMC Cancer 2020 20:307

    Content type: Research article

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  12. The development of tumor cells inside the lymphatics or blood vessels is known as lymphovascular invasion (LVI). The correlation between LVI, lymph node metastasis (LNM), and the diagnosis of superficial esoph...

    Authors: Jinxin Yang, Zhouyi Lu, Lintao Li, Yong Li, Yulong Tan, Dekang Zhang and An Wang

    Citation: BMC Cancer 2020 20:176

    Content type: Research article

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  13. Alteration in gut microbiota has been recently linked with childhood leukemia and the use of chemotherapy. Whether the perturbed microbiota community is restored after disease remission and cessation of cancer...

    Authors: Ling Ling Chua, Reena Rajasuriar, Yvonne Ai Lian Lim, Yin Ling Woo, P’ng Loke and Hany Ariffin

    Citation: BMC Cancer 2020 20:151

    Content type: Research article

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  14. Lung adenocarcinoma (LUAD) is one of the most common cancer types, threatening the human health around the world. However, the high heterogeneity and complexity of LUAD limit the benefits of targeted therapies...

    Authors: Zhenyang Lv and Ting Lei

    Citation: BMC Cancer 2020 20:56

    Content type: Research article

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  15. Combining anti-cancer therapies with orthogonal modes of action, such as direct cytotoxicity and immunostimulatory, hold promise for expanding clinical benefit to patients with metastatic disease. For instance...

    Authors: Qing Wang, Zhijun Wang, Yan Wu and David J. Klinke II

    Citation: BMC Cancer 2020 20:26

    Content type: Research Article

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  16. Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretati...

    Authors: Michal Marczyk, Chunxiao Fu, Rosanna Lau, Lili Du, Alexander J. Trevarton, Bruno V. Sinn, Rebekah E. Gould, Lajos Pusztai, Christos Hatzis and W. Fraser Symmans

    Citation: BMC Cancer 2019 19:1189

    Content type: Research article

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  17. Deciphering the meaning of the human DNA is an outstanding goal which would revolutionize medicine and our way for treating diseases. In recent years, non-coding RNAs have attracted much attention and shown to...

    Authors: Johannes Smolander, Alexey Stupnikov, Galina Glazko, Matthias Dehmer and Frank Emmert-Streib

    Citation: BMC Cancer 2019 19:1176

    Content type: Research Article

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  18. Identification of key regulator/s in ovarian cancer (OC) network is important for potential drug target and prevention from this cancer. This study proposes a method to identify the key regulators of this netw...

    Authors: Md. Zubbair Malik, Keilash Chirom, Shahnawaz Ali, Romana Ishrat, Pallavi Somvanshi and R. K. Brojen Singh

    Citation: BMC Cancer 2019 19:1129

    Content type: Research article

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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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