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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

    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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  2. 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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  3. 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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  4. Content type: Research article

    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

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  5. Content type: Research article

    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

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  6. Content type: Research article

    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

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  7. Content type: Research article

    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

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  8. Content type: Research article

    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

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  9. Content type: Research article

    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

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  10. Content type: Research article

    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

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  11. Content type: Research Article

    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

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  12. Content type: Research article

    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

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  13. Content type: Research article

    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

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  14. Content type: Research article

    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

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  15. Content type: Research article

    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

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  16. Content type: Research article

    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

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  17. Content type: Research article

    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

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  18. Content type: Research article

    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

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Research article

    “Biomarker-driven targeted therapy,” the practice of tailoring patients’ treatment to the expression/activity levels of disease-specific genes/proteins, remains challenging. For example, while the anti-ERBB2 m...

    Authors: Hae Ryung Chang, Hee Seo Park, Young Zoo Ahn, Seungyoon Nam, Hae Rim Jung, Sungjin Park, Sang Jin Lee, Curt Balch, Garth Powis, Ja-Lok Ku and Yon Hui Kim

    Citation: BMC Cancer 2016 16:200

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  26. Content type: Research article

    In past, numerous quantitative structure-activity relationship (QSAR) based models have been developed for predicting anticancer activity for a specific class of molecules against different cancer drug targets...

    Authors: Harinder Singh, Rahul Kumar, Sandeep Singh, Kumardeep Chaudhary, Ankur Gautam and Gajendra P. S. Raghava

    Citation: BMC Cancer 2016 16:77

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  27. Content type: Research article

    Cell fusion is a fast and highly efficient technique for cells to acquire new properties. The fusion of somatic cells with stem cells can reprogram somatic cells to a pluripotent state. Our research on the fus...

    Authors: Ran Wang, Shuxun Chen, Changxian Li, Kevin Tak Pan Ng, Chi-wing Kong, Jinping Cheng, Shuk Han Cheng, Ronald A. Li, Chung Mau Lo, Kwan Man and Dong Sun

    Citation: BMC Cancer 2016 16:56

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  28. Content type: Research article

    The mixture of volatile organic compounds in the headspace gas of urine may be able to distinguish lung cancer patients from relevant control populations.

    Authors: Peter J. Mazzone, Xiao-Feng Wang, Sung Lim, Humberto Choi, James Jett, Anil Vachani, Qi Zhang, Mary Beukemann, Meredith Seeley, Ray Martino and Paul Rhodes

    Citation: BMC Cancer 2015 15:1001

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  29. Content type: Research article

    EGFR is important in maintaining metabolic homeostasis in healthy cells, but in tumors it activates downstream signaling pathways, causing proliferation, angiogenesis, invasion and metastasis. Consequently, EG...

    Authors: Sidra Younis, Qamar Javed and Miroslav Blumenberg

    Citation: BMC Cancer 2015 15:369

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  30. Content type: Technical advance

    Circulating tumor cells (CTCs) are malignant cells that have migrated from solid cancers into the blood, where they are typically present in rare numbers. There is great interest in using CTCs to monitor respo...

    Authors: Daniel E Campton, Arturo B Ramirez, Joshua J Nordberg, Nick Drovetto, Alisa C Clein, Paulina Varshavskaya, Barry H Friemel, Steve Quarre, Amy Breman, Michael Dorschner, Sibel Blau, C Anthony Blau, Daniel E Sabath, Jackie L Stilwell and Eric P Kaldjian

    Citation: BMC Cancer 2015 15:360

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  31. Content type: Research Article

    Histologically similar tumors even from the same anatomical position may still show high variability at molecular level hindering analysis of genome-wide data. Leveling the analysis to a gene regulatory networ...

    Authors: Chengyu Liu, Riku Louhimo, Marko Laakso, Rainer Lehtonen and Sampsa Hautaniemi

    Citation: BMC Cancer 2015 15:319

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  32. Content type: Research article

    Intrahepatic cholangiocarcinoma (ICC) is a highly aggressive tumor of the bile duct, and a significant public health problem in East Asia, where it is associated with infection by the parasite Opisthorchis viverr...

    Authors: Jordan Plieskatt, Gabriel Rinaldi, Yanjun Feng, Jin Peng, Samantha Easley, Xinying Jia, Jeremy Potriquet, Chawalit Pairojkul, Vajarabhongsa Bhudhisawasdi, Banchob Sripa, Paul J Brindley, Jeffrey Bethony and Jason Mulvenna

    Citation: BMC Cancer 2015 15:309

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  33. Content type: Technical advance

    Mounting evidence demonstrates a causal role for S100 proteins in tumourigenesis and several S100 isoforms have shown utility as biomarkers of several types of cancer. The S100 family is comprised of 21 small ...

    Authors: Juan Martínez-Aguilar, Roderick Clifton-Bligh and Mark P Molloy

    Citation: BMC Cancer 2015 15:199

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  34. Content type: Research article

    Cancers of unknown primary (CUPs) constitute ~5% of all cancers. The tumors have an aggressive biological and clinical behavior. The aim of the present study has been to uncover whether CUPs exhibit distinct m...

    Authors: Jonas Vikeså, Anne Kirstine H Møller, Bogumil Kaczkowski, Rehannah Borup, Ole Winther, Ricardo Henao, Anders Krogh, Katharina Perell, Flemming Jensen, Gedske Daugaard and Finn C Nielsen

    Citation: BMC Cancer 2015 15:151

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  35. Content type: Research article

    Colorectal cancer is one of the major causes of cancer mortality world-wide. Prevention would improve if at-risk subjects could be identified. The aim of this study was to characterise plasma protein biomarker...

    Authors: Michela Bertuzzi, Cristina Marelli, Renzo Bagnati, Alessandro Colombi, Roberto Fanelli, Calogero Saieva, Marco Ceroti, Benedetta Bendinelli, Saverio Caini, Luisa Airoldi and Domenico Palli

    Citation: BMC Cancer 2015 15:56

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  36. Content type: Research article

    The evolution of mutations in the BCR-ABL1 fusion gene transcript renders CML patients resistant to tyrosine kinase inhibitor (TKI) based therapy. Thus screening for BCR-ABL1 mutations is recommended particularly...

    Authors: Lucia Cavelier, Adam Ameur, Susana Häggqvist, Ida Höijer, Nicola Cahill, Ulla Olsson-Strömberg and Monica Hermanson

    Citation: BMC Cancer 2015 15:45

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  37. Content type: Software

    We recently published PROGgene, a tool that can be used to study prognostic implications of genes in various cancers. The first version of the tool had several areas for improvement. In this paper we present s...

    Authors: Chirayu Pankaj Goswami and Harikrishna Nakshatri

    Citation: BMC Cancer 2014 14:970

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  38. Content type: Research article

    Strongly increased uptake of glucose is a hallmark of solid malignant tumors. This phenotype can be triggered by hypoxia-induced gene expression changes or can occur independently of hypoxia as a consequence o...

    Authors: Arnulf Mayer, Marcus Schmidt, Alexander Seeger, André Franke Serras, Peter Vaupel and Heinz Schmidberger

    Citation: BMC Cancer 2014 14:760

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  39. Content type: Research article

    Dysregulation of transcriptional programs leads to cell malfunctioning and can have an impact in cancer development. Our study aims to characterize global differences between transcriptional regulatory program...

    Authors: David Cordero, Xavier Solé, Marta Crous-Bou, Rebeca Sanz-Pamplona, Laia Paré-Brunet, Elisabet Guinó, David Olivares, Antonio Berenguer, Cristina Santos, Ramón Salazar, Sebastiano Biondo and Víctor Moreno

    Citation: BMC Cancer 2014 14:708

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  40. Content type: Research article

    Increasing focus on potentially unnecessary diagnosis and treatment of certain breast cancers prompted our investigation of whether clinical and mammographic features predictive of invasive breast cancer versu...

    Authors: Mehmet US Ayvaci, Oguzhan Alagoz, Jagpreet Chhatwal, Alejandro Munoz del Rio, Edward A Sickles, Houssam Nassif, Karla Kerlikowske and Elizabeth S Burnside

    Citation: BMC Cancer 2014 14:584

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