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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. 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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  2. 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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  3. 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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  4. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  12. 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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  13. 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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  14. 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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  16. 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

  17. 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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  20. 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

    Content type: Research article

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  21. 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

    Content type: Research article

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  22. 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

    Content type: Research article

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  23. 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

    Content type: Research article

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Research article

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  26. While many factors may contribute to the higher prostate cancer incidence and mortality experienced by African-American men compared to their counterparts, the contribution of tumor biology is underexplored du...

    Authors: Jennifer S. Myers, Karin A. Vallega, Jason White, Kaixian Yu, Clayton C. Yates and Qing-Xiang Amy Sang

    Citation: BMC Cancer 2017 17:480

    Content type: Research article

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  27. The study was aimed to quantitatively detect mRNA levels of the catalytic subunit of telomerase (hTERT) in both peripheral blood and circulating tumor cells (CTCs) of patients with nasopharyngeal carcinoma (NP...

    Authors: Xinsa Fu, Congxiang Shen, Huigang Wang, Fang Chen, Guanxue Li and Zhong Wen

    Citation: BMC Cancer 2017 17:479

    Content type: Research article

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  28. miRNAs exert their effect through a negative regulatory mechanism silencing expression upon hybridizing to their target mRNA, and have a prominent position in the control of many cellular processes including c...

    Authors: Blanca Elena Castro-Magdonel, Manuela Orjuela, Javier Camacho, Adda Jeanette García-Chéquer, Lourdes Cabrera-Muñoz, Stanislaw Sadowinski-Pine, Noé Durán-Figueroa, María de Jesús Orozco-Romero, Ana Claudia Velázquez-Wong, Adriana Hernández-Ángeles, Claudia Hernández-Galván, Citlali Lara-Molina and M. Verónica Ponce-Castañeda

    Citation: BMC Cancer 2017 17:458

    Content type: Research article

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  29. During posttreatment surveillance of head and neck cancer patients, imaging is insufficiently accurate for the early detection of relapsing disease. Free circulating tumor DNA (ctDNA) may serve as a novel biom...

    Authors: Joost H. van Ginkel, Manon M. H. Huibers, Robert J. J. van Es, Remco de Bree and Stefan M. Willems

    Citation: BMC Cancer 2017 17:428

    Content type: Research article

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  30. Annual low dose CT (LDCT) screening of individuals at high demographic risk reduces lung cancer mortality by more than 20%. However, subjects selected for screening based on demographic criteria typically have...

    Authors: Jiyoun Yeo, Erin L. Crawford, Xiaolu Zhang, Sadik Khuder, Tian Chen, Albert Levin, Thomas M. Blomquist and James C. Willey

    Citation: BMC Cancer 2017 17:301

    Content type: Research article

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  31. Transforming growth factor-beta (TGF-β) is associated with a higher incidence of distant metastasis and decreased survival. Whether TGF-β can be used as a prognostic indicator of colorectal cancer (CRC) remain...

    Authors: Xin-lin Chen, Zhuo-qun Chen, Shui-lian Zhu, Tian-wen Liu, Yi Wen, Yi-sheng Su, Xu-jie Xi, Yue Hu, Lei Lian and Feng-bin Liu

    Citation: BMC Cancer 2017 17:240

    Content type: Research article

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  32. Ovarian cancer remains the most deadly gynecological cancer with a poor aggregate survival rate; however, the specific rates are highly dependent on the stage of the disease upon diagnosis. Current screening a...

    Authors: Karissa B. Tilbury, Kirby R. Campbell, Kevin W. Eliceiri, Sana M. Salih, Manish Patankar and Paul J. Campagnola

    Citation: BMC Cancer 2017 17:102

    Content type: Research article

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  34. Tumor-infiltrating leukocytes can either limit cancer growth or facilitate its spread. Diagnostic strategies that comprehensively assess the functional complexity of tumor immune infiltrates could have wide-re...

    Authors: Julia Chifman, Ashok Pullikuth, Jeff W. Chou, Davide Bedognetti and Lance D. Miller

    Citation: BMC Cancer 2016 16:911

    Content type: Research Article

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  35. Breast cancer is one of the most common malignancies with increasing incidences every year and a leading cause of death among women. Although early stage breast cancer can be effectively treated, there are lim...

    Authors: Zeynep Kosaloglu, Julia Bitzer, Niels Halama, Zhiqin Huang, Marc Zapatka, Andreas Schneeweiss, Dirk Jäger and Inka Zörnig

    Citation: BMC Cancer 2016 16:901

    Content type: Research article

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  37. Next Generation Sequencing (NGS) has become a valuable tool for molecular landscape characterization of cancer genomes, leading to a better understanding of tumor onset and progression, and opening new avenues...

    Authors: Silvia Bonfiglio, Irene Vanni, Valeria Rossella, Anna Truini, Dejan Lazarevic, Maria Giovanna Dal Bello, Angela Alama, Marco Mora, Erika Rijavec, Carlo Genova, Davide Cittaro, Francesco Grossi and Simona Coco

    Citation: BMC Cancer 2016 16:692

    Content type: Research article

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  38. The progression of colorectal cancer (CRC) involves recurrent amplifications/mutations in the epidermal growth factor receptor (EGFR) and downstream signal transducers of the Ras pathway, KRAS and BRAF. Whethe...

    Authors: Narendra Padhan, Torbjörn E. M. Nordling, Magnus Sundström, Peter Åkerud, Helgi Birgisson, Peter Nygren, Sven Nelander and Lena Claesson-Welsh

    Citation: BMC Cancer 2016 16:683

    Content type: Research article

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  39. Galectin-7 (Gal-7) is negatively regulated in cervical cancer, and appears to be a link between the apoptotic response triggered by cancer and the anti-tumoral activity of the immune system. Our understanding ...

    Authors: Juan Carlos Higareda-Almaraz, Juan S. Ruiz-Moreno, Jana Klimentova, Daniela Barbieri, Raquel Salvador-Gallego, Regina Ly, Ilse A. Valtierra-Gutierrez, Christiane Dinsart, Gabriel A. Rabinovich, Jiri Stulik, Frank Rösl and Bladimiro Rincon-Orozco

    Citation: BMC Cancer 2016 16:680

    Content type: Research article

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  40. Glioblastoma (GBM) tumors exhibit strong phenotypic differences that can be quantified using magnetic resonance imaging (MRI), but the underlying biological drivers of these imaging phenotypes remain largely u...

    Authors: Patrick Grossmann, David A. Gutman, William D. Dunn Jr, Chad A. Holder and Hugo J. W. L. Aerts

    Citation: BMC Cancer 2016 16:611

    Content type: Research article

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  41. Lymph node (LN) status is the most important prognostic variable used to guide ER positive (+) breast cancer treatment. While a positive nodal status is traditionally associated with a poor prognosis, a subset...

    Authors: Jessica G. Cockburn, Robin M. Hallett, Amy E. Gillgrass, Kay N. Dias, T. Whelan, M. N. Levine, John A. Hassell and Anita Bane

    Citation: BMC Cancer 2016 16:555

    Content type: Research article

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  43. The estrogen receptor (ER) inhibitor tamoxifen reduces breast cancer mortality by 31 % and has served as the standard treatment for ER-positive breast cancers for decades. However, 50 % of advanced ER-positive...

    Authors: Sara Kangaspeska, Susanne Hultsch, Alok Jaiswal, Henrik Edgren, John-Patrick Mpindi, Samuli Eldfors, Oscar Brück, Tero Aittokallio and Olli Kallioniemi

    Citation: BMC Cancer 2016 16:378

    Content type: Research article

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  44. Gastric cancer is the fourth most common cancer and the second most deadly cancer worldwide. Study on molecular mechanisms of carcinogenesis will play a significant role in diagnosing and treating gastric canc...

    Authors: Huijuan Wang, Hailong Zhang, Pengchi Deng, Chunqi Liu, Dandan Li, Hui Jie, Hu Zhang, Zongguang Zhou and Ying-Lan Zhao

    Citation: BMC Cancer 2016 16:371

    Content type: Research article

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  45. TFEB (transcription factor EB) regulates metabolic homeostasis through its activation of lysosomal biogenesis following its nuclear translocation. TFEB activity is inhibited by mTOR phosphorylation, which sign...

    Authors: Paula Andrea Marin Zapata, Carsten Jörn Beese, Anja Jünger, Giovanni Dalmasso, Nathan Ryan Brady and Anne Hamacher-Brady

    Citation: BMC Cancer 2016 16:355

    Content type: Research article

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  46. Perturbed genotypes in cancer can now be identified by whole genome sequencing of large number of diverse tumor samples, and observed gene mutations can be used for prognosis and classification of cancer subty...

    Authors: Sarah Daakour, Leon Juvenal Hajingabo, Despoina Kerselidou, Aurelie Devresse, Richard Kettmann, Nicolas Simonis, Franck Dequiedt and Jean-Claude Twizere

    Citation: BMC Cancer 2016 16:335

    Content type: Research article

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  47. We have previously demonstrated that the hydroxylated biphenyl compound D6 (3E,3′E)-4,4′-(5,5′,6,6′-tetramethoxy-[1,1′-biphenyl]-3,3′-diyl)bis(but-3-en-2-one), a structural analogue of curcumin, exerts a stron...

    Authors: Marina Pisano, Antonio Palomba, Alessandro Tanca, Daniela Pagnozzi, Sergio Uzzau, Maria Filippa Addis, Maria Antonietta Dettori, Davide Fabbri, Giuseppe Palmieri and Carla Rozzo

    Citation: BMC Cancer 2016 16:317

    Content type: Research article

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  49. Epithelial-to-mesenchymal transition (EMT) has been associated with the acquisition of metastatic potential and the resistance of cancer cells to therapeutic treatments. MCF-7 breast cancer cells engineered to co...

    Authors: Roman Mezencev, Lilya V. Matyunina, Neda Jabbari and John F. McDonald

    Citation: BMC Cancer 2016 16:236

    Content type: Research article

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  50. Genome-wide association studies (GWASs) have identified several single-nucleotide polymorphisms (SNPs) influencing the risk of thyroid cancer (TC). Most cancer predisposition genes identified through GWASs fun...

    Authors: Hauke Thomsen, Bowang Chen, Gisella Figlioli, Rossella Elisei, Cristina Romei, Monica Cipollini, Alfonso Cristaudo, Franco Bambi, Per Hoffmann, Stefan Herms, Stefano Landi, Kari Hemminki, Federica Gemignani and Asta Försti

    Citation: BMC Cancer 2016 16:227

    Content type: Research article

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