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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

    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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. Content type: Research article

    The biological mechanisms underlying cancer cell motility and invasiveness remain unclear, although it has been hypothesized that they involve some type of epithelial-mesenchymal transition (EMT).

    Authors: Dimitris Anastassiou, Viktoria Rumjantseva, Weiyi Cheng, Jianzhong Huang, Peter D Canoll, Darrell J Yamashiro and Jessica J Kandel

    Citation: BMC Cancer 2011 11:529

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  26. Content type: Research article

    A universal hallmark of cancer cells is the change in their glycosylation phenotype. One of the most frequent alterations in the normal glycosylation pattern observed during carcinogenesis is the enhancement o...

    Authors: Laura Muinelo-Romay, Susana Villar-Portela, Elisa Cuevas, Emilio Gil-Martín and Almudena Fernández-Briera

    Citation: BMC Cancer 2011 11:508

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  27. Content type: Research article

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) has been demonstrated to be useful for molecular profiling of common solid tumors. Using recently developed MALDI matrices for lipid p...

    Authors: Han Sung Kang, Seok Cheol Lee, Young Seung Park, Young Eun Jeon, Jeong Hwa Lee, So-Youn Jung, In Hae Park, Seok Hoon Jang, Hye Min Park, Chong Woo Yoo, Seok Hee Park, Sang Yun Han, Kwang Pyo Kim, Young Hwan Kim, Jungsil Ro and Hark Kyun Kim

    Citation: BMC Cancer 2011 11:465

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  28. Content type: Research article

    Circulating tumor cells (CTCs) have been associated with prognosis especially in breast cancer and have been proposed as a liquid biopsy for repeated follow up examinations. Molecular characterization of CTCs ...

    Authors: Areti Strati, Athina Markou, Cleo Parisi, Eleni Politaki, Dimitris Mavroudis, Vasilis Georgoulias and Evi Lianidou

    Citation: BMC Cancer 2011 11:422

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  29. Content type: Research article

    Serum protein profiles have been investigated frequently to discover early biomarkers for breast cancer. So far, these studies used biological samples collected at or after diagnosis. This may limit these studies...

    Authors: Annemieke WJ Opstal-van Winden, Esmeralda JM Krop, Monica H Kåredal, Marie-Christine W Gast, Christian H Lindh, Marina C Jeppsson, Bo AG Jönsson, Diederick E Grobbee, Petra HM Peeters, Jos H Beijnen, Carla H van Gils and Roel CH Vermeulen

    Citation: BMC Cancer 2011 11:381

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  30. Content type: Technical advance

    Detection of mutations by DNA sequencing can be facilitated by scanning methods to identify amplicons which may have mutations. Current scanning methods used for the detection of germline sequence variants are...

    Authors: Heather L Hondow, Stephen B Fox, Gillian Mitchell, Rodney J Scott, Victoria Beshay, Stephen Q Wong and Alexander Dobrovic

    Citation: BMC Cancer 2011 11:265

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  31. Content type: Research article

    The ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In cert...

    Authors: Al Muktafi Sadi, Dong-Yu Wang, Bruce J Youngson, Naomi Miller, Scott Boerner, Susan J Done and Wey L Leong

    Citation: BMC Cancer 2011 11:253

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  32. Content type: Research article

    Tissue microarray (TMA) data are commonly used to validate the prognostic accuracy of tumor markers. For example, breast cancer TMA data have led to the identification of several promising prognostic markers o...

    Authors: Angela P Presson, Nam K Yoon, Lora Bagryanova, Vei Mah, Mohammad Alavi, Erin L Maresh, Ayyappan K Rajasekaran, Lee Goodglick, David Chia and Steve Horvath

    Citation: BMC Cancer 2011 11:230

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  33. Content type: Research article

    The Mayo Lung Project (MLP), a randomized controlled clinical trial of lung cancer screening conducted between 1971 and 1986 among male smokers aged 45 or above, demonstrated an increase in lung cancer surviva...

    Authors: Lu Shi, Haijun Tian, William J McCarthy, Barbara Berman, Shinyi Wu and Rob Boer

    Citation: BMC Cancer 2011 11:92

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  34. Content type: Research article

    Epidermal growth factor receptor inhibitor therapy is now approved for treatment of metastatic colorectal carcinomas (CRC) in patients with tumors lacking KRAS mutations. Several procedures to detect KRAS mutatio...

    Authors: Magnus Sundström, Karolina Edlund, Monica Lindell, Bengt Glimelius, Helgi Birgisson, Patrick Micke and Johan Botling

    Citation: BMC Cancer 2010 10:660

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  35. Content type: Research article

    Conflicting data exist regarding the prognostic and predictive impact of survivin (BIRC5) in breast cancer. We previously reported survivin cytoplasmic-to-nuclear ratio (CNR) as an independent prognostic indic...

    Authors: Elton Rexhepaj, Karin Jirstrom, Darran P O'Connor, Sallyann L O'Brien, Goran Landberg, Michael J Duffy, Donal J Brennan and William M Gallagher

    Citation: BMC Cancer 2010 10:639

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  36. Content type: Research article

    Combining gene expression microarrays and high resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) of the same tissue samples enables comparison of the transcriptional and metabolic pr...

    Authors: Eldrid Borgan, Beathe Sitter, Ole Christian Lingjærde, Hilde Johnsen, Steinar Lundgren, Tone F Bathen, Therese Sørlie, Anne-Lise Børresen-Dale and Ingrid S Gribbestad

    Citation: BMC Cancer 2010 10:628

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  37. Content type: Research article

    The simplicity and potential of minimal invasive testing using serum from patients make auto-antibody based biomarkers a very promising tool for use in diagnostics of cancer and auto-immune disease. Although s...

    Authors: René Stempfer, Parvez Syed, Klemens Vierlinger, Rudolf Pichler, Eckart Meese, Petra Leidinger, Nicole Ludwig, Albert Kriegner, Christa Nöhammer and Andreas Weinhäusel

    Citation: BMC Cancer 2010 10:627

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  38. Content type: Research article

    Developing the right drugs for the right patients has become a mantra of drug development. In practice, it is very difficult to identify subsets of patients who will respond to a drug under evaluation. Most of...

    Authors: Erich P Huang, Jane Fridlyand, Nicholas Lewin-Koh, Peng Yue, Xiaoyan Shi, David Dornan and Bart Burington

    Citation: BMC Cancer 2010 10:586

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  39. Content type: Research article

    Most patients with ovarian cancer are diagnosed with advanced stage disease (i.e., stage III-IV), which is associated with a poor prognosis. Differentially expressed genes (DEGs) in stage III serous ovarian carci...

    Authors: Yun-Sook Kim, Jin Hwan Do, Sumi Bae, Dong-Han Bae and Woong Shick Ahn

    Citation: BMC Cancer 2010 10:576

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  40. Content type: Software

    Genome wide gene expression data is a rich source for the identification of gene signatures suitable for clinical purposes and a number of statistical algorithms have been described for both identification and...

    Authors: Martin Lauss, Attila Frigyesi, Tobias Ryden and Mattias Höglund

    Citation: BMC Cancer 2010 10:532

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