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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

    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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. Content type: Research article

    Tyrosine phosphorylation (pTyr) is an important cancer relevant posttranslational modification since it regulates protein activity and cellular localization. By controlling cell growth and differentiation it p...

    Authors: Lioudmila Elfineh, Christina Classon, Anna Asplund, Ulf Pettersson, Masood Kamali-Moghaddam and Sara Bergström Lind

    Citation: BMC Cancer 2014 14:435

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  20. Content type: Research article

    This study aimed at the identification of prognostic gene expression markers in early primary colorectal carcinomas without metastasis at the time point of surgery by analyzing genome-wide gene expression prof...

    Authors: Marion Fehlker, Matthew R Huska, Thomas Jöns, Miguel A Andrade-Navarro and Wolfgang Kemmner

    Citation: BMC Cancer 2014 14:64

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  21. Content type: Research article

    Membrane vesicles released by neoplastic cells into extracellular medium contain potential of carrying arrays of oncogenic molecules including proteins and microRNAs (miRNA). Extracellular (exosome-like) vesic...

    Authors: Stefan Kruger, Zakaria Y Abd Elmageed, David H Hawke, Philipp M Wörner, David A Jansen, Asim B Abdel-Mageed, Eckhard U Alt and Reza Izadpanah

    Citation: BMC Cancer 2014 14:44

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  22. Content type: Research article

    Resistance to platinum-based chemotherapy remains a major impediment in the treatment of serous epithelial ovarian cancer. The objective of this study was to use gene expression profiling to delineate major de...

    Authors: Madhuri Koti, Robert J Gooding, Paulo Nuin, Alexandria Haslehurst, Colleen Crane, Johanne Weberpals, Timothy Childs, Peter Bryson, Moyez Dharsee, Kenneth Evans, Harriet E Feilotter, Paul C Park and Jeremy A Squire

    Citation: BMC Cancer 2013 13:549

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  23. Content type: Research article

    Triple Negative subset of (TN) Breast Cancers (BC), a close associate of the basal-like subtype (with limited discordance) is an aggressive form of the disease which convey unpredictable, and poor prognosis du...

    Authors: Nandini Dey, Benjamin G Barwick, Carlos S Moreno, Maja Ordanic-Kodani, Zhengjia Chen, Gabriella Oprea-Ilies, Weining Tang, Charles Catzavelos, Kimberly F Kerstann, George W Sledge Jr., Mark Abramovitz, Mark Bouzyk, Pradip De and Brian R Leyland-Jones

    Citation: BMC Cancer 2013 13:537

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  24. Content type: Research article

    Gastric cancer (GC) is a threat to human health with increasing incidence and mortality worldwide. Down-regulation or absence of RAF kinase inhibitor protein (RKIP) was associated with the occurrence, differen...

    Authors: Huan Gu, Xianquan Zhan, Guiying Zhang, Lu Yan, William CS Cho, Maoyu Li, Ting Liu and Zhuchu Chen

    Citation: BMC Cancer 2013 13:536

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  25. Content type: Research article

    The circadian clock and cell cycle are two global regulatory systems that have pervasive behavioral and physiological effects on eukaryotic cells, and both play a role in cancer development. Recent studies hav...

    Authors: Yingying Mao, Alan Fu, Derek Leaderer, Tongzhang Zheng, Kun Chen and Yong Zhu

    Citation: BMC Cancer 2013 13:498

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  26. Content type: Research article

    The prognosis of pancreatic cancer (PC) is one of the poorest among all cancers, due largely to the lack of methods for screening and early detection. New biomarkers for identifying high-risk or early-stage su...

    Authors: Shawn A Ritchie, Hirofumi Akita, Ichiro Takemasa, Hidetoshi Eguchi, Elodie Pastural, Hiroaki Nagano, Morito Monden, Yuichiro Doki, Masaki Mori, Wei Jin, Tolulope T Sajobi, Dushmanthi Jayasinghe, Bassirou Chitou, Yasuyo Yamazaki, Thayer White and Dayan B Goodenowe

    Citation: BMC Cancer 2013 13:416

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  27. Content type: Technical advance

    Epidermal growth factor receptor (EGFR) gene mutations identify patients withnon-small cell lung cancer (NSCLC) who have a high likelihood of benefitingfrom treatment with anti-EGFR tyrosine kinase inhibitors....

    Authors: Patrick O’Donnell, Jane Ferguson, Johnny Shyu, Robert Current, Taraneh Rehage, Julie Tsai, Mari Christensen, Ha Bich Tran, Sean Shih-Chang Chien, Felice Shieh, Wen Wei, H Jeffrey Lawrence, Lin Wu, Robert Schilling, Kenneth Bloom, Warren Maltzman…

    Citation: BMC Cancer 2013 13:210

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  28. Content type: Research article

    Ovarian carcinoma is a common, and often deadly, gynecological cancer. Mutations in BRCA1 and BRCA2 genes are present in at least a fifth of patients. Uncovering other genes that become mutated subsequent to BRCA...

    Authors: Jian Zhang, Yuhao Shi, Emilie Lalonde, Lili Li, Luca Cavallone, Alex Ferenczy, Walter H Gotlieb, William D Foulkes and Jacek Majewski

    Citation: BMC Cancer 2013 13:146

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  29. Content type: Research article

    The development of resistance to chemotherapies represents a significant barrier to successful cancer treatment. Resistance mechanisms are complex, can involve diverse and often unexpected cellular processes, ...

    Authors: Li Chen, Lynda Stuart, Toshiro K Ohsumi, Shawn Burgess, Gaurav K Varshney, Anahita Dastur, Mark Borowsky, Cyril Benes, Adam Lacy-Hulbert and Emmett V Schmidt

    Citation: BMC Cancer 2013 13:93

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  30. Content type: Research article

    We have recently reported on the changes in plasma free amino acid (PFAA) profiles in lung cancer patients and the efficacy of a PFAA-based, multivariate discrimination index for the early detection of lung ca...

    Authors: Masato Shingyoji, Toshihiko Iizasa, Masahiko Higashiyama, Fumio Imamura, Nobuhiro Saruki, Akira Imaizumi, Hiroshi Yamamoto, Takashi Daimon, Osamu Tochikubo, Toru Mitsushima, Minoru Yamakado and Hideki Kimura

    Citation: BMC Cancer 2013 13:77

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  31. Content type: Research article

    To understand the carcinogenesis caused by accumulated genetic and epigenetic alterations and seek novel biomarkers for various cancers, studying differentially expressed genes between cancerous and normal tis...

    Authors: Mingsong Wu, Tao Tu, Yunchao Huang and Yi Cao

    Citation: BMC Cancer 2013 13:44

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  32. Content type: Research article

    We determined the differently expressed protein profiles and their functions in bladder cancer tissues with the aim of identifying possible target proteins and underlying molecular mechanisms for taking part i...

    Authors: Hong Chung, Bokyung Kim, Seung-Hyo Jung, Kyung-Jong Won, Xiaowen Jiang, Chang-Kwon Lee, So Dug Lim, Sang-Kuk Yang, Ki Hak Song and Hong Sup Kim

    Citation: BMC Cancer 2013 13:45

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  33. Content type: Research article

    The malignant transformation of precancerous colorectal lesions involves progressive alterations at both the molecular and morphologic levels, the latter consisting of increases in size and in the degree of ce...

    Authors: Rosalia Maglietta, Vania Cosma Liuzzi, Elisa Cattaneo, Endre Laczko, Ada Piepoli, Anna Panza, Massimo Carella, Orazio Palumbo, Teresa Staiano, Federico Buffoli, Angelo Andriulli, Giancarlo Marra and Nicola Ancona

    Citation: BMC Cancer 2012 12:608

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  34. Content type: Research article

    Inhibitors targeting the cell cycle-regulated aurora kinase A (AURKA) are currently being developed. Here, we examine the prognostic impact of AURKA in node-negative breast cancer patients without adjuvant sys...

    Authors: Wulf Siggelkow, Daniel Boehm, Susanne Gebhard, Marco Battista, Isabel Sicking, Antje Lebrecht, Christine Solbach, Birte Hellwig, Jörg Rahnenführer, Heinz Koelbl, Mathias Gehrmann, Rosemarie Marchan, Cristina Cadenas, Jan G Hengstler and Marcus Schmidt

    Citation: BMC Cancer 2012 12:562

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  35. Content type: Research article

    Single Base Substitutions (SBS) that alter transcripts expressed in cancer originate from somatic mutations. However, recent studies report SBS in transcripts that are not supported by the genomic DNA of tumor...

    Authors: Laurent Bianchetti, David Kieffer, Rémi Féderkeil and Olivier Poch

    Citation: BMC Cancer 2012 12:509

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  36. Content type: Research article

    We previously observed that a radiotherapy-induced biochemical response in plasma was associated with favourable outcome in head and neck squamous carcinoma cancer (HNSCC) patients. The aim of the present stud...

    Authors: Siv K Bøhn, Kjell M Russnes, Amrit K Sakhi, Magne Thoresen, Marit Holden, JanØ Moskaug, Mari C Myhrstad, Ole K Olstad, Sigbjørn Smeland and Rune Blomhoff

    Citation: BMC Cancer 2012 12:426

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  37. Content type: Research article

    A subset of KIT/PDGFRA wild-type gastrointestinal stromal tumors (WT GIST) have been associated with alteration of the succinate dehydrogenase (SDH) complex II function. A recent report identified four non-syn...

    Authors: Antoine Italiano, Chun-Liang Chen, Yun-Shao Sung, Samuel Singer, Ronald P DeMatteo, Michael P LaQuaglia, Peter Besmer, Nicholas Socci and Cristina R Antonescu

    Citation: BMC Cancer 2012 12:408

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  38. Content type: Research article

    Ovarian cancer is a heterogeneous disease and prognosis for apparently similar cases of ovarian cancer varies. Recurrence of the disease in early stage (FIGO-stages I-II) serous ovarian cancer results in survi...

    Authors: Ingiridur Skirnisdottir, Markus Mayrhofer, Maria Rydåker, Helena Åkerud and Anders Isaksson

    Citation: BMC Cancer 2012 12:407

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  39. Content type: Research article

    BRCA1 (breast cancer 1, early onset) missense mutations have been detected in familial breast and ovarian cancers, but the role of these variants in cancer predisposition is often difficult to ascertain. In th...

    Authors: Caterina Iofrida, Erika Melissari, Veronica Mariotti, Chiara Guglielmi, Lucia Guidugli, Maria Adelaide Caligo and Silvia Pellegrini

    Citation: BMC Cancer 2012 12:207

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  40. Content type: Research article

    The presence of somatic mitochondrial DNA (mtDNA) mutations in cancer cells has been interpreted in controversial ways, ranging from random neutral accumulation of mutations, to positive selection for high pat...

    Authors: Luísa Pereira, Pedro Soares, Valdemar Máximo and David C Samuels

    Citation: BMC Cancer 2012 12:53

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  41. Content type: Research article

    Today's clinical diagnostic tools are insufficient for giving accurate prognosis to breast cancer patients. The aim of our study was to examine the tumor metabolic changes in patients with locally advanced bre...

    Authors: Maria D Cao, Guro F Giskeødegård, Tone F Bathen, Beathe Sitter, Anna Bofin, Per E Lønning, Steinar Lundgren and Ingrid S Gribbestad

    Citation: BMC Cancer 2012 12:39

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  42. Content type: Research article

    The heat shock protein 90 (Hsp90) is required for the stability of many signalling kinases. As a target for cancer therapy it allows the simultaneous inhibition of several signalling pathways. However, its inh...

    Authors: Armin Haupt, Gerard Joberty, Marcus Bantscheff, Holger Fröhlich, Henning Stehr, Michal R Schweiger, Axel Fischer, Martin Kerick, Stefan T Boerno, Andreas Dahl, Michael Lappe, Hans Lehrach, Cayetano Gonzalez, Gerard Drewes and Bodo MH Lange

    Citation: BMC Cancer 2012 12:38

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