Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology

The complex processes driving cancer have so far impeded the discovery of dichotomous biomarkers associated with its initiation and progression. Reductionist approaches utilizing ‘omics’ technologies have met some success in identifying molecular alterations associated with carcinogenesis. Systems biology is an emerging science that combines high-throughput investigation techniques to define the dynamic interplay between regulatory biological systems in response to internal and external cues. Vibrational spectroscopy has the potential to play an integral role within systems biology research approaches. It is capable of examining global models of carcinogenesis by scrutinizing chemical bond alterations within molecules. The application of infrared or Raman spectroscopic approaches coupled with computational analysis under the systems biology umbrella can assist the transition of biomarker research from the molecular level to the system level. The comprehensive representation of carcinogenesis as a multilevel biological process will inevitably revolutionize cancer-related healthcare by personalizing risk prediction and prevention.

[1]  A. Feinberg,et al.  The epigenetic progenitor origin of human cancer , 2006, Nature Reviews Genetics.

[2]  A. Boligon,et al.  Identification of the Plant Steroid α-Spinasterol as a Novel Transient Receptor Potential Vanilloid 1 Antagonist with Antinociceptive Properties , 2012, Journal of Pharmacology and Experimental Therapeutics.

[3]  Paul Dumas,et al.  Chemical imaging of biological tissue with synchrotron infrared light. , 2006, Biochimica et biophysica acta.

[4]  Tao-Tao Liu,et al.  Metabolomic profiling of human urine in hepatocellular carcinoma patients using gas chromatography/mass spectrometry. , 2009, Analytica chimica acta.

[5]  Qiong Gao,et al.  Resources for integrative systems biology: from data through databases to networks and dynamic system models , 2006, Briefings Bioinform..

[6]  W P Dillon,et al.  Preoperative proton MR spectroscopic imaging of brain tumors: correlation with histopathologic analysis of resection specimens. , 2001, AJNR. American journal of neuroradiology.

[7]  J. M. Wilson,et al.  [Principles and practice of mass screening for disease]. , 1968, Boletin de la Oficina Sanitaria Panamericana. Pan American Sanitary Bureau.

[8]  M. Esteller Aberrant DNA methylation as a cancer-inducing mechanism. , 2005, Annual review of pharmacology and toxicology.

[9]  Pedro Larrañaga,et al.  A review of feature selection techniques in bioinformatics , 2007, Bioinform..

[10]  R. Wilson,et al.  The Next-Generation Sequencing Revolution and Its Impact on Genomics , 2013, Cell.

[11]  I. Weinstein,et al.  The origins of human cancer: molecular mechanisms of carcinogenesis and their implications for cancer prevention and treatment--twenty-seventh G.H.A. Clowes memorial award lecture. , 1988, Cancer research.

[12]  D. Mount Bioinformatics: Sequence and Genome Analysis , 2001 .

[13]  D. Fishman,et al.  Soluble Epidermal Growth Factor Receptor (SEG-FR) and Cancer Antigen 125 (CA125) as Screening and Diagnostic Tests for Epithelial Ovarian Cancer , 2005, Cancer Epidemiology Biomarkers & Prevention.

[14]  D. Chan,et al.  Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. , 2005, Clinical chemistry.

[15]  Xi Chen,et al.  A five-microRNA signature identified from genome-wide serum microRNA expression profiling serves as a fingerprint for gastric cancer diagnosis. , 2011, European journal of cancer.

[16]  T. R. Hebbes,et al.  A "minimal epitope" anti-protein antibody that recognises a single modified amino acid. , 1989, Molecular immunology.

[17]  Rohit Bhargava,et al.  Using Fourier transform IR spectroscopy to analyze biological materials , 2014, Nature Protocols.

[18]  W. Schubert,et al.  Analyzing proteome topology and function by automated multidimensional fluorescence microscopy , 2006, Nature Biotechnology.

[19]  L. Mueller,et al.  Metabolomic analysis using optimized NMR and statistical methods. , 2006, Analytical biochemistry.

[20]  O. Gires,et al.  EpCAM (CD326) finding its role in cancer , 2007, British Journal of Cancer.

[21]  E. Petricoin,et al.  Use of proteomic patterns in serum to identify ovarian cancer , 2002, The Lancet.

[22]  M S Pepe,et al.  Phases of biomarker development for early detection of cancer. , 2001, Journal of the National Cancer Institute.

[23]  G. Getz,et al.  Coupled two-way clustering analysis of gene microarray data. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Christian Stephan,et al.  Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in murine hippocampus , 2008, Proteomics.

[25]  K. Scholich,et al.  Toponomics: studying protein-protein interactions and protein networks in intact tissue. , 2010, Molecular bioSystems.

[26]  R. Preston Epigenetic processes and cancer risk assessment. , 2007, Mutation research.

[27]  Sergei G. Kazarian,et al.  ATR-FTIR spectroscopic imaging: recent advances and applications to biological systems. , 2013, The Analyst.

[28]  Ronald J. Moore,et al.  Toward a Human Blood Serum Proteome , 2002, Molecular & Cellular Proteomics.

[29]  M. Diem,et al.  A decade of vibrational micro-spectroscopy of human cells and tissue (1994-2004). , 2004, The Analyst.

[30]  Vitor Sousa,et al.  Metabolic signatures of lung cancer in biofluids: NMR-based metabonomics of urine. , 2011, Journal of proteome research.

[31]  P. Dalbon,et al.  Differential diagnosis of prostate cancer and benign prostate hyperplasia using two‐dimensional electrophoresis , 2001, Electrophoresis.

[32]  S. Wijmenga,et al.  NMR and pattern recognition methods in metabolomics: from data acquisition to biomarker discovery: a review. , 2012, Analytica chimica acta.

[33]  F. Martin,et al.  Identification of benzo[a]pyrene-induced cell cycle-associated alterations in MCF-7 cells using infrared spectroscopy with computational analysis. , 2012, Toxicology.

[34]  H. Kuerer,et al.  Identification of distinct protein expression patterns in bilateral matched pair breast ductal fluid specimens from women with unilateral invasive breast carcinoma , 2002, Cancer.

[35]  Thomas E. Royce,et al.  Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification , 2007, Nucleic acids research.

[36]  R. Cramer,et al.  MALDI mass spectrometry in prostate cancer biomarker discovery. , 2014, Biochimica et biophysica acta.

[37]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.

[38]  Paul Dumas,et al.  Adding synchrotron radiation to infrared microspectroscopy: what's new in biomedical applications? , 2007, Trends in biotechnology.

[39]  Michael L. Wach,et al.  In vivo determination of the molecular composition of artery wall by intravascular Raman spectroscopy. , 2000, Analytical chemistry.

[40]  Nuzhat Ahmed,et al.  Proteomic tracking of serum protein isoforms as screening biomarkers of ovarian cancer , 2005, Proteomics.

[41]  M. Ebert,et al.  Advances in clinical cancer proteomics: SELDI-ToF-mass spectrometry and biomarker discovery. , 2005, Briefings in functional genomics & proteomics.

[42]  Philip Heraud,et al.  The emergence of biospectroscopy in stem cell research. , 2009, Stem cell research.

[43]  W. Willett,et al.  Multiple loci identified in a genome-wide association study of prostate cancer , 2008, Nature Genetics.

[44]  Walter Schubert,et al.  Topological proteomics, toponomics, MELK-technology. , 2003, Advances in biochemical engineering/biotechnology.

[45]  W. Lam,et al.  Methylation analysis by DNA immunoprecipitation , 2009, Journal of cellular physiology.

[46]  U. P. S. T. Force Genetic Risk Assessment and BRCA Mutation Testing for Breast and Ovarian Cancer Susceptibility: Recommendation Statement , 2005, Annals of Internal Medicine.

[47]  S. Hirohashi,et al.  Multiple genetic alterations in human carcinogenesis. , 1992, Environmental health perspectives.

[48]  Sze Chuen Cesar Wong,et al.  Advanced proteomic technologies for cancer biomarker discovery , 2009, Expert review of proteomics.

[49]  S. P. Fodor,et al.  High density synthetic oligonucleotide arrays , 1999, Nature Genetics.

[50]  C. Sander,et al.  Genomic medicine and the future of health care. , 2000, Science.

[51]  P. Rothberg,et al.  Oncogenes and cancer. , 1983, Cancer investigation.

[52]  A. Godwin,et al.  DNA array‐based method for detection of large rearrangements in the BRCA1 gene , 2002, Genes, chromosomes & cancer.

[53]  Francis L Martin,et al.  Distinguishing cell types or populations based on the computational analysis of their infrared spectra , 2010, Nature Protocols.

[54]  N. Serkova,et al.  Therapeutic targets and biomarkers identified in cancer choline phospholipid metabolism. , 2006, Pharmacogenomics.

[55]  Alan Hutson,et al.  Detection of epithelial ovarian cancer using 1H‐NMR‐based metabonomics , 2005, International journal of cancer.

[56]  A. Villar-Garea,et al.  Analysis of Histone Modifications by Mass Spectrometry , 2008, Current protocols in protein science.

[57]  F. Hamdy,et al.  EZH2 promotes proliferation and invasiveness of prostate cancer cells , 2007, The Prostate.

[58]  Francisco Azuaje,et al.  Bioinformatics as a driver, not a passenger, of translational biomedical research: Perspectives from the 6th Benelux bioinformatics conference , 2012, Journal of Clinical Bioinformatics.

[59]  Tao,et al.  Low-frequency Raman-scattering study of the liquid-glass transition in aqueous lithium chloride solutions. , 1991, Physical review. A, Atomic, molecular, and optical physics.

[60]  W. Hahn,et al.  Modelling the molecular circuitry of cancer , 2002, Nature Reviews Cancer.

[61]  Tony Pawson,et al.  Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases , 2009, Science Signaling.

[62]  M. Caligiuri,et al.  Aberrant CpG-island methylation has non-random and tumour-type–specific patterns , 2000, Nature Genetics.

[63]  F. Martin Epigenetic Influences in the Aetiology of Cancers Arising from Breast and Prostate: A Hypothesised Transgenerational Evolution in Chromatin Accessibility , 2013, ISRN oncology.

[64]  O. Fiehn Metabolomics – the link between genotypes and phenotypes , 2004, Plant Molecular Biology.

[65]  Oliver Fiehn,et al.  Pathway analysis of kidney cancer using proteomics and metabolic profiling , 2006, Molecular Cancer.

[66]  Jian Yang,et al.  Metabolomics spectral formatting, alignment and conversion tools (MSFACTs) , 2003, Bioinform..

[67]  R. Aebersold,et al.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats , 2005, Molecular systems biology.

[68]  Taylor Jensen,et al.  Epigenetic inactivation of the HOXA gene cluster in breast cancer. , 2006, Cancer research.

[69]  T. Bathen,et al.  Comparison of HR MAS MR spectroscopic profiles of breast cancer tissue with clinical parameters , 2006, NMR in biomedicine.

[70]  Y. Liu,et al.  MicroRNA expression signature in atrial fibrillation with mitral stenosis. , 2011, Physiological genomics.

[71]  Julian L. Griffin,et al.  Metabolic profiles of cancer cells , 2004, Nature Reviews Cancer.

[72]  Michael P. Snyder,et al.  RNA‐Seq: A Method for Comprehensive Transcriptome Analysis , 2010, Current protocols in molecular biology.

[73]  N Stone,et al.  Assessment of fiberoptic near-infrared raman spectroscopy for diagnosis of bladder and prostate cancer. , 2005, Urology.

[74]  R. Berkowitz,et al.  Proteomic-Based Discovery and Characterization of Glycosylated Eosinophil-Derived Neurotoxin and COOH-Terminal Osteopontin Fragments for Ovarian Cancer in Urine , 2006, Clinical Cancer Research.

[75]  I. Wilson,et al.  Understanding 'Global' Systems Biology: Metabonomics and the Continuum of Metabolism , 2003, Nature Reviews Drug Discovery.

[76]  M. Manfait,et al.  Diagnosis of hepatocellular carcinoma in cirrhotic patients: a proof-of-concept study using serum micro-Raman spectroscopy. , 2013, The Analyst.

[77]  B. Zhivotovsky,et al.  Carcinogenesis and apoptosis: paradigms and paradoxes. , 2006, Carcinogenesis.

[78]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[79]  S. Eckhardt,et al.  Clinical Applications of Metabolomics in Oncology: A Review , 2009, Clinical Cancer Research.

[80]  P. Prenzler,et al.  Recent and potential developments in the analysis of urine: a review. , 2011, Analytica chimica acta.

[81]  Rachel Cavill,et al.  Metabolic profiling of human colorectal cancer using high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy and gas chromatography mass spectrometry (GC/MS). , 2009, Journal of proteome research.

[82]  Vladimir Shulaev,et al.  Metabolomics technology and bioinformatics , 2006, Briefings Bioinform..

[83]  C. Paweletz,et al.  New approaches to proteomic analysis of breast cancer , 2001, Proteomics.

[84]  A. Chinnaiyan,et al.  The emergence of lncRNAs in cancer biology. , 2011, Cancer discovery.

[85]  M. Vidal,et al.  Integrating 'omic' information: a bridge between genomics and systems biology. , 2003, Trends in genetics : TIG.

[86]  J. van der Greef,et al.  The art and practice of systems biology in medicine: mapping patterns of relationships. , 2007, Journal of proteome research.

[87]  K. Bambery,et al.  Synchrotron Fourier transform infrared (FTIR) analysis of single living cells progressing through the cell cycle. , 2013, The Analyst.

[88]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[89]  N Stone,et al.  The use of Raman spectroscopy to identify and grade prostatic adenocarcinoma in vitro , 2003, British Journal of Cancer.

[90]  Michel Manfait,et al.  Spectroscopy of Biological Molecules , 1985 .

[91]  David S. Wishart,et al.  HMDB 3.0—The Human Metabolome Database in 2013 , 2012, Nucleic Acids Res..

[92]  K. Scholich,et al.  Toponomics Analysis of Functional Interactions of the Ubiquitin Ligase PAM (Protein Associated with Myc) during Spinal Nociceptive Processing*S , 2008, Molecular & Cellular Proteomics.

[93]  B. W. Wright,et al.  High-speed peak matching algorithm for retention time alignment of gas chromatographic data for chemometric analysis. , 2003, Journal of chromatography. A.

[94]  A. Vlahou,et al.  Proteomic approaches to biomarker discovery in prostate and bladder cancers , 2001, Proteomics.

[95]  B. Hudson,et al.  Resonance Raman spectra of mononucleotides obtained with 266 and 213 nm ultraviolet radiation , 1984, Biopolymers.

[96]  Fionn Murtagh,et al.  Interpreting the Kohonen self-organizing feature map using contiguity-constrained clustering , 1995, Pattern Recognit. Lett..

[97]  D. Bluemke,et al.  Proton magnetic resonance spectroscopic imaging of human breast cancer: A preliminary study , 2004, Journal of magnetic resonance imaging : JMRI.

[98]  Robert C. Thompson,et al.  Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis * , 2002, The European journal of neuroscience.

[99]  P. Malfertheiner,et al.  Reduced PTEN expression in gastric cancer and in the gastric mucosa of gastric cancer relatives , 2002, European journal of gastroenterology & hepatology.

[100]  Jean Susini,et al.  Fourier Transform Infrared Microspectroscopy Identifies Symmetric PO2− Modifications as a Marker of the Putative Stem Cell Region of Human Intestinal Crypts , 2008, Stem cells.

[101]  Hui Sun,et al.  Recent and potential developments of biofluid analyses in metabolomics. , 2012, Journal of proteomics.

[102]  B. Haab,et al.  Advances in protein microarray technology for protein expression and interaction profiling. , 2001, Current opinion in drug discovery & development.

[103]  W. Blackstock,et al.  Proteomics: quantitative and physical mapping of cellular proteins. , 1999, Trends in biotechnology.

[104]  지창도 Identification of genes epigenetically silenced by CpG methylation in human gastric carcinoma , 2008 .

[105]  L. F. Waanders,et al.  Top-down Protein Sequencing and MS3 on a Hybrid Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer*S , 2006, Molecular & Cellular Proteomics.

[106]  B. Sitter,et al.  Metabolite composition in breast tumors examined by proton nuclear magnetic resonance spectroscopy. , 1999, Anticancer research.

[107]  O. Fiehn,et al.  Mass spectrometry-based metabolic profiling reveals different metabolite patterns in invasive ovarian carcinomas and ovarian borderline tumors. , 2006, Cancer research.

[108]  Ines Latka,et al.  Diagnosis and screening of cancer tissues by fiber-optic probe Raman spectroscopy , 2012 .

[109]  Ricky A. Sharma,et al.  Oxidative stress and cyclooxygenase activity in prostate carcinogenesis: targets for chemopreventive strategies. , 2005, European journal of cancer.

[110]  Xingming Zhao,et al.  Computational Systems Biology , 2013, TheScientificWorldJournal.

[111]  A. Toland,et al.  Epigenetic alterations in the breast: Implications for breast cancer detection, prognosis and treatment. , 2009, Seminars in cancer biology.

[112]  Walter Schubert,et al.  Next-generation biomarkers based on 100-parameter functional super-resolution microscopy TIS. , 2012, New biotechnology.

[113]  Imran I. Patel,et al.  Surface-Enhanced Raman Spectroscopy of the Endothelial Cell Membrane , 2014, PloS one.

[114]  Pamela K. Kreeger,et al.  Cancer systems biology: a network modeling perspective , 2009, Carcinogenesis.

[115]  C. Auffray,et al.  The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics. , 1999, Genome research.

[116]  John R Yates,et al.  Large-scale protein identification using mass spectrometry. , 2003, Biochimica et biophysica acta.

[117]  E. Sauter,et al.  Proteomic analysis of nipple aspirate fluid to detect biologic markers of breast cancer , 2002, British Journal of Cancer.

[118]  Jemma G. Kelly,et al.  Combining immunolabeling and surface-enhanced Raman spectroscopy on cell membranes. , 2011, ACS nano.

[119]  M. Oka,et al.  Screening for serological biomarkers of pancreatic cancer by two-dimensional electrophoresis and liquid chromatography-tandem mass spectrometry. , 2011, Oncology reports.

[120]  F. Bruggeman,et al.  Cancer: a Systems Biology disease. , 2006, Bio Systems.

[121]  Tatjana Crnogorac-Jurcevic,et al.  Palladin Mutation Causes Familial Pancreatic Cancer and Suggests a New Cancer Mechanism , 2006, PLoS medicine.

[122]  E. Ng,et al.  Differential expression of microRNAs in plasma of patients with colorectal cancer: a potential marker for colorectal cancer screening , 2009, Gut.

[123]  S Gail Eckhardt,et al.  NMR-based metabolomics: translational application and treatment of cancer. , 2007, Current opinion in molecular therapeutics.

[124]  C. Croce,et al.  MicroRNA signatures in human cancers , 2006, Nature Reviews Cancer.

[125]  Thomas Bocklitz,et al.  Toward improving fine needle aspiration cytology by applying Raman microspectroscopy , 2013, Journal of biomedical optics.

[126]  Ji Huang,et al.  [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.

[127]  Petros Karakitsos,et al.  Histology Verification Demonstrates That Biospectroscopy Analysis of Cervical Cytology Identifies Underlying Disease More Accurately than Conventional Screening: Removing the Confounder of Discordance , 2014, PloS one.

[128]  R. Holliday,et al.  A new theory of carcinogenesis , 1979, British Journal of Cancer.

[129]  C. Roberts,et al.  Epigenetics and Cancer: Altered Chromatin Remodeling via Snf5 Loss Leads to Aberrant Cell Cycle Regulation , 2006, Cell cycle.

[130]  Dan Grandér,et al.  How do mutated oncogenes and tumor suppressor genes cause cancer? , 1998, Medical oncology.

[131]  B. Lendl,et al.  A rapid method for the differentiation of yeast cells grown under carbon and nitrogen-limited conditions by means of partial least squares discriminant analysis employing infrared micro-spectroscopic data of entire yeast cells , 2012, Talanta.

[132]  P. Laird Cancer epigenetics. , 2005, Human molecular genetics.

[133]  Michèl Schummer,et al.  The HE4 (WFDC2) protein is a biomarker for ovarian carcinoma. , 2003, Cancer research.

[134]  L. Loeb,et al.  Errors in DNA replication as a basis of malignant changes. , 1974, Cancer research.

[135]  R. Dasari,et al.  Prospects for in vivo Raman spectroscopy , 2000 .

[136]  Andreas Wilke,et al.  BRIGEP—the BRIDGE-based genome–transcriptome–proteome browser , 2005, Nucleic Acids Res..

[137]  Walter Schubert,et al.  Toponome mapping in prostate cancer: detection of 2000 cell surface protein clusters in a single tissue section and cell type specific annotation by using a three symbol code. , 2009, Journal of proteome research.

[138]  J. Gibbs Mechanism-based target identification and drug discovery in cancer research. , 2000, Science.

[139]  Abigail S Haka,et al.  Model‐based biological Raman spectral imaging , 2002, Journal of cellular biochemistry. Supplement.

[140]  David B. A. Epstein,et al.  Toponome imaging system: in situ protein network mapping in normal and cancerous colon from the same patient reveals more than five-thousand cancer specific protein clusters and their subcellular annotation by using a three symbol code. , 2010, Journal of proteome research.

[141]  Thomas P Conrads,et al.  The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. , 2002, Biochemical and biophysical research communications.

[142]  Francis L Martin,et al.  Biospectroscopy to metabolically profile biomolecular structure: a multistage approach linking computational analysis with biomarkers. , 2011, Journal of proteome research.

[143]  A. Sarasin,et al.  An overview of the mechanisms of mutagenesis and carcinogenesis. , 2003, Mutation research.

[144]  P. Nelson,et al.  From genomics to proteomics: techniques and applications in cancer research. , 2001, Trends in cell biology.

[145]  Jian-xin Gao Stem Cells Review Series: Cancer stem cells: the lessons from precancerous stem cells , 2008 .

[146]  司履生 Cancer epigenetics , 2006 .

[147]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[148]  S. Williams,et al.  Cell type-specific fingerprinting of meningioma and meningeal cells by proton nuclear magnetic resonance spectroscopy. , 1995, Cancer research.

[149]  J. C. Martínez-Espinosa,et al.  Cervical cancer detection based on serum sample Raman spectroscopy , 2014, Lasers in Medical Science.

[150]  A. Talari,et al.  Raman Spectroscopy of Biological Tissues , 2007 .

[151]  B. Kramer,et al.  Trends in biomarker research for cancer detection. , 2001, The Lancet. Oncology.

[152]  R. Prayson,et al.  Mutational Heterogeneity in Human Cancers : Origin and Consequences , 2010 .

[153]  H. Barr,et al.  Raman spectroscopy for identification of epithelial cancers. , 2004, Faraday discussions.

[154]  Peter A. Jones,et al.  The fundamental role of epigenetic events in cancer , 2002, Nature Reviews Genetics.

[155]  J. Herman,et al.  Novel Methylation Biomarker Panel for the Early Detection of Pancreatic Cancer , 2013, Clinical Cancer Research.

[156]  Erik K. Malm,et al.  A Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics* , 2005, Molecular & Cellular Proteomics.

[157]  Jeffrey T. Chang,et al.  A Field Guide to Genomics Research , 2014, PLoS biology.

[158]  Anna Gambin,et al.  On consensus biomarker selection , 2007, BMC Bioinformatics.

[159]  Plamen P. Angelov,et al.  IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis , 2013, Bioinform..

[160]  Paolo Vineis,et al.  Models of carcinogenesis: an overview. , 2010, Carcinogenesis.

[161]  Colin C. Collins,et al.  Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors , 2002, Nature Genetics.

[162]  John M Chalmers,et al.  Infrared microscopy of epithelial cancer cells in whole tissues and in tissue culture, using synchrotron radiation. , 2004, Faraday discussions.

[163]  X. Guan,et al.  Prognostic significance of c‐myc and AIB1 amplification in hepatocellular carcinoma , 2002, Cancer.

[164]  N. Serkova,et al.  Pattern recognition and biomarker validation using quantitative 1H-NMR-based metabolomics , 2006, Expert review of molecular diagnostics.

[165]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[166]  P. Vos,et al.  Transcriptomic molecular markers for screening human colon cancer in stool and tissue. , 2007, Cancer genomics & proteomics.

[167]  Ricard Boqué,et al.  Rapid characterization of transgenic and non-transgenic soybean oils by chemometric methods using NIR spectroscopy. , 2013, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[168]  F. Acquati,et al.  The human genome project and the discovery of genetic determinants of cancer susceptibility. , 2004, European journal of cancer.

[169]  Hamid Bolouri,et al.  A data integration methodology for systems biology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[170]  Timothy J Wilt,et al.  Prevention and early detection of prostate cancer. , 2014, The Lancet. Oncology.

[171]  R. Durbin,et al.  A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis , 2008, Nature Biotechnology.

[172]  Dirk Schübeler,et al.  Methylated DNA immunoprecipitation (MeDIP). , 2009, Methods in molecular biology.

[173]  J. Lindon,et al.  Spectroscopic and statistical techniques for information recovery in metabonomics and metabolomics. , 2008, Annual review of analytical chemistry.

[174]  S. Satomura,et al.  AFP-L3: a new generation of tumor marker for hepatocellular carcinoma. , 2001, Clinica chimica acta; international journal of clinical chemistry.

[175]  David B. A. Epstein,et al.  Toponome imaging system: multiplex biomarkers in oncology. , 2012, Trends in molecular medicine.

[176]  E. Miska,et al.  MicroRNA—implications for cancer , 2007, Virchows Archiv.

[177]  S. Ranade,et al.  Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.

[178]  L. Bonetta Epigenomics: Detailed analysis , 2008, Nature.

[179]  M. Esteller,et al.  Genome-Wide and Gene-Specific Epigenomic Platforms for Hepatocellular Carcinoma Biomarker Development Trials , 2014, Gastroenterology research and practice.

[180]  H. Hansen,et al.  Carcinoembryonic antigen (CEA) assay. A laboratory adjunct in the diagnosis and management of cancer. , 1974, Human pathology.

[181]  H. Mantsch The road to medical vibrational spectroscopy--a history. , 2013, The Analyst.

[182]  C. Kendall,et al.  Vibrational spectroscopy: a clinical tool for cancer diagnostics. , 2009, The Analyst.

[183]  Z. Herceg,et al.  Epigenetic interplay between histone modifications and DNA methylation in gene silencing. , 2008, Mutation research.

[184]  H. Kitano Systems Biology: A Brief Overview , 2002, Science.

[185]  Thomas Udelhoven,et al.  Development of a Hierarchical Classification System with Artificial Neural Networks and FT-IR Spectra for the Identification of Bacteria , 2000 .

[186]  Vlad I. Morariu,et al.  Expression , 2015, Principles of Molecular Virology.

[187]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[188]  Thomas D. Wang,et al.  Use of an endoscope-compatible probe to detect colonic dysplasia with Fourier transform infrared spectroscopy. , 2009, Journal of biomedical optics.

[189]  A. Lund,et al.  Chromatin‐modifying proteins in cancer , 2007, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[190]  Daniel Raftery,et al.  Comparing and combining NMR spectroscopy and mass spectrometry in metabolomics , 2007, Analytical and bioanalytical chemistry.

[191]  Daehee Hwang,et al.  From proteomics toward systems biology: integration of different types of proteomics data into network models. , 2008, BMB reports.

[192]  E. Ren,et al.  Two‐dimensional electrophoresis map of the human hepatocellular carcinoma cell line, HCC‐M, and identification of the separated proteins by mass spectrometry , 2000, Electrophoresis.

[193]  M. Rubin,et al.  Profiling and verification of gene expression patterns in normal and malignant human prostate tissues by cDNA microarray analysis. , 2001, Neoplasia.

[194]  Steven R. Emory,et al.  Probing Single Molecules and Single Nanoparticles by Surface-Enhanced Raman Scattering , 1997, Science.

[195]  Joel G. Pounds,et al.  Proteomic Characterization of Nipple Aspirate Fluid: Identification of Potential Biomarkers of Breast Cancer , 2003, Breast Cancer Research and Treatment.

[196]  Andre Terzic,et al.  18O-assisted dynamic metabolomics for individualized diagnostics and treatment of human diseases , 2012, Croatian medical journal.

[197]  T. Pawson,et al.  Network medicine , 2008, FEBS letters.

[198]  H. Moch,et al.  Tissue microarrays for rapid linking of molecular changes to clinical endpoints. , 2001, The American journal of pathology.

[199]  N. Anderson,et al.  The Human Plasma Proteome: History, Character, and Diagnostic Prospects , 2003, Molecular & Cellular Proteomics.

[200]  S. Clark,et al.  High sensitivity mapping of methylated cytosines. , 1994, Nucleic acids research.

[201]  R. Berkowitz,et al.  Prostasin, a potential serum marker for ovarian cancer: identification through microarray technology. , 2001, Journal of the National Cancer Institute.

[202]  Michael E Phelps,et al.  Systems Biology and New Technologies Enable Predictive and Preventative Medicine , 2004, Science.

[203]  R. Bischoff,et al.  Methodological advances in the discovery of protein and peptide disease markers. , 2004, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[204]  W. McKinney,et al.  Synchrotron-Based FTIR Spectromicroscopy: Cytotoxicity and Heating Considerations , 2003, Journal of biological physics.

[205]  Wilson Jm,et al.  Principles and practice of mass screening for disease , 1968 .

[206]  P Boffetta,et al.  Chromosomal aberrations and SCEs as biomarkers of cancer risk. , 2006, Mutation research.

[207]  Gerd Geisslinger,et al.  Proteomics in Neuropathic Pain Research , 2008, Anesthesiology.

[208]  Reinhard Laubenbacher,et al.  Bioinformatics tools for cancer metabolomics , 2011, Metabolomics.

[209]  Nabil Belacel,et al.  NMR metabolic analysis of samples using fuzzy K‐means clustering , 2009, Magnetic resonance in chemistry : MRC.

[210]  L. Liotta,et al.  Proteomic Patterns of Nipple Aspirate Fluids Obtained by SELDI-TOF: Potential for New Biomarkers to Aid in the Diagnosis of Breast Cancer , 2002, Disease markers.

[211]  K. Rodland Proteomics and cancer diagnosis: the potential of mass spectrometry. , 2004, Clinical biochemistry.

[212]  Jason H. Moore,et al.  Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. , 2007, Cancer research.

[213]  R. Richards-Kortum,et al.  Fiber optic probes for biomedical optical spectroscopy. , 2003, Journal of biomedical optics.

[214]  Francis L Martin,et al.  Fourier-transform infrared spectroscopy coupled with a classification machine for the analysis of blood plasma or serum: a novel diagnostic approach for ovarian cancer. , 2013, The Analyst.

[215]  Paolo Vineis,et al.  Third version: response to reviewers , 2010 .

[216]  A. Goesmann,et al.  Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. , 2003, Journal of biotechnology.

[217]  Romà Tauler,et al.  Detection of Olive Oil Adulteration Using FT-IR Spectroscopy and PLS with Variable Importance of Projection (VIP) Scores , 2012 .

[218]  T. R. Hebbes,et al.  A direct link between core histone acetylation and transcriptionally active chromatin. , 1988, The EMBO journal.

[219]  I. Simon,et al.  Evidence for an instructive mechanism of de novo methylation in cancer cells , 2006, Nature Genetics.

[220]  Josep Tabernero,et al.  EGFR and KRAS in colorectal cancer. , 2010, Advances in clinical chemistry.

[221]  Peter K. Sorger,et al.  Logic-Based Models for the Analysis of Cell Signaling Networks† , 2010, Biochemistry.

[222]  T. Bathen,et al.  MR-determined metabolic phenotype of breast cancer in prediction of lymphatic spread, grade, and hormone status , 2007, Breast Cancer Research and Treatment.

[223]  Noureddine Zahid,et al.  Fuzzy clustering based on K-nearest-neighbours rule , 2001, Fuzzy Sets Syst..

[224]  L. Cazares,et al.  MALDI/SELDI protein profiling of serum for the identification of cancer biomarkers. , 2008, Methods in molecular biology.

[225]  Douglas Hanahan,et al.  Accessories to the Crime: Functions of Cells Recruited to the Tumor Microenvironment Prospects and Obstacles for Therapeutic Targeting of Function-enabling Stromal Cell Types , 2022 .

[226]  D. Fishman,et al.  Soluble epidermal growth factor receptor (sEGFR) [corrected] and cancer antigen 125 (CA125) as screening and diagnostic tests for epithelial ovarian cancer. , 2005, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[227]  S. Kazarian,et al.  Applications of ATR-FTIR spectroscopic imaging to biomedical samples. , 2006, Biochimica et biophysica acta.

[228]  Charles Auffray,et al.  From functional genomics to systems biology: concepts and practices. , 2003, Comptes rendus biologies.

[229]  F. Martin,et al.  Vibrational spectroscopy of biofluids for disease screening or diagnosis: translation from the laboratory to a clinical setting , 2014, Journal of biophotonics.

[230]  H. Su,et al.  An epigenetic marker panel for screening and prognostic prediction of ovarian cancer , 2009, International journal of cancer.

[231]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[232]  Daniel W Chan,et al.  Modern Tumor Marker Discovery in Urology: Surface Enhanced Laser Desorption and Ionization (SELDI). , 2003, Reviews in urology.

[233]  Thomas P Conrads,et al.  SELDI-TOF MS for diagnostic proteomics. , 2003, Analytical chemistry.

[234]  Walter Schubert,et al.  Fluorescence detection of protein clusters in individual cells and tissue sections by using toponome imaging system: sample preparation and measuring procedures , 2007, Nature Protocols.

[235]  L. Sillerud,et al.  Citrate concentrations in human seminal fluid and expressed prostatic fluid determined via 1H nuclear magnetic resonance spectroscopy outperform prostate specific antigen in prostate cancer detection. , 2006, The Journal of urology.

[236]  M. Skipper Genomics: Users' guide to the human genome , 2012, Nature Reviews Genetics.

[237]  Francis L Martin,et al.  Diagnostic segregation of human brain tumours using Fourier-transform infrared and/or Raman spectroscopy coupled with discriminant analysis. , 2013, Analytical methods : advancing methods and applications.

[238]  Arul M Chinnaiyan,et al.  RNA-Seq unleashed , 2011, Nature Biotechnology.

[239]  Francis L Martin,et al.  Measuring similarity and improving stability in biomarker identification methods applied to Fourier‐transform infrared (FTIR) spectroscopy , 2014, Journal of biophotonics.

[240]  Dobb's journal staff Of interest , 2001, Administration in mental health.

[241]  D. Phillips,et al.  MGMT promoter hypermethylation and K-RAS, PTEN and TP53 mutations in tamoxifen-exposed and non-exposed endometrial cancer cases , 2014, British Journal of Cancer.

[242]  H. Mantsch,et al.  Infrared spectroscopy: a new frontier in medicine. , 1997, Biophysical chemistry.

[243]  T. Pawson,et al.  Oncogenic re-wiring of cellular signaling pathways , 2007, Oncogene.

[244]  S. Rehman,et al.  Fourier Transform Infrared (FTIR) Spectroscopy of Biological Tissues , 2008 .

[245]  R. Murphy,et al.  Objective Clustering of Proteins Based on Subcellular Location Patterns , 2005, Journal of biomedicine & biotechnology.

[246]  W. Martinez-Lopez,et al.  Chromatin-remodelling mechanisms in cancer. , 2008, Mutation research.

[247]  C. Allis,et al.  Translating the Histone Code , 2001, Science.