Abstract
Translational bioinformatics plays an indispensable role in transforming psychoneuroimmunology (PNI) into personalized medicine. It provides a powerful method to bridge the gaps between various knowledge domains in PNI and systems biology. Translational bioinformatics methods at various systems levels can facilitate pattern recognition, and expedite and validate the discovery of systemic biomarkers to allow their incorporation into clinical trials and outcome assessments. Analysis of the correlations between genotypes and phenotypes including the behavioral-based profiles will contribute to the transition from the disease-based medicine to human-centered medicine. Translational bioinformatics would also enable the establishment of predictive models for patient responses to diseases, vaccines, and drugs. In PNI research, the development of systems biology models such as those of the neurons would play a critical role. Methods based on data integration, data mining, and knowledge representation are essential elements in building health information systems such as electronic health records and computerized decision support systems. Data integration of genes, pathophysiology, and behaviors are needed for a broad range of PNI studies. Knowledge discovery approaches such as network-based systems biology methods are valuable in studying the cross-talks among pathways in various brain regions involved in disorders such as Alzheimer’s disease.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Mabry PL, Olster DH, Morgan GD et al (2008) Interdisciplinarity and systems science to improve population health: a view from the NIH Office of Behavioral and Social Sciences Research. Am J Prev Med 35(2 suppl):S211–S224
Yan Q (2008) The integration of personalized and systems medicine: bioinformatics support for pharmacogenomics and drug discovery. Methods Mol Biol 448:1–19
Yan Q (2005) Pharmacogenomics and systems biology of membrane transporters. Mol Biotechnol 29:75–88
Madhavan S, Zenklusen JC et al (2009) Rembrandt: helping personalized medicine become a reality through integrative translational research. Mol Cancer Res 7:157–167
Wang X, Liu L, Fackenthal J et al (2009) Translational integrity and continuity: personalized biomedical data integration. J Biomed Inform 42:100–112
Gebicke-Haerter PJ (2008) Systems biology in molecular psychiatry. Pharmacopsychiatry 41(suppl 1):S19–S27
Yan Q (2010) Translational bioinformatics and systems biology approaches for personalized medicine. Methods Mol Biol 662:167–178
Giegling I, Hartmann AM, Genius J, Benninghoff J, Möller H-J, Rujescu D (2008) Systems biology and complex neurobehavioral traits. Pharmacopsychiatry 41(suppl 1):S32–S36
Yan Q (2003) Bioinformatics and data integration in membrane transporter studies. Methods Mol Biol 227:37–60
Huys QJM, Moutoussis M, Williams J (2011) Are computational models of any use to psychiatry? Neural Netw 24:544–551
American Medical Informatics Association (AMIA). Available from http://www.amia.org/applications-informatics/translational-bioinformatics. Accessed Nov 2011
Yan Q (2000) Preventing adverse drug events (ADEs): the role of computer information systems. Drug Inf J 34:1247–1260
Radulovic D, Jelveh S et al (2004) Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 3:984–997
Bloss CS, Schiabor KM, Schork NJ (2010) Human behavioral informatics in genetic studies of neuropsychiatric disease: multivariate profile-based analysis. Brain Res Bull 83:177–188
Tretter F, Albus M (2008) Systems biology and psychiatry—modeling molecular and cellular networks of mental disorders. Pharmacopsychiatry 41(suppl 1):S2–S18
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Sigrist CJA, Cerutti L, de Castro E et al (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 38(Database issue):D161–D166
The UniProt Consortium (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38(Database issue):D142–D148
Rost B, Yachdav G, Liu J (2004) The PredictProtein server. Nucleic Acids Res 32(Web Server issue):W321–W326
Rose PW, Beran B, Bi C et al (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res 39(Database issue):D392–D401
Frazer KA, Ballinger DG, Cox DR et al (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851–861
Manolio TA, Brooks LD, Collins FS (2008) A HapMap harvest of insights into the genetics of common disease. J Clin Invest 118:1590–1605
Sherry ST, Ward MH, Kholodov M et al (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311
Salomonis N, Hanspers K, Zambon AC et al (2007) GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics 8:217
Kanehisa M, Goto S, Hattori M et al (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34(Database issue):D354–D357
Keshava Prasad TS, Goel R, Kandasamy K et al (2009) Human protein reference database—2009 update. Nucleic Acids Res 37(Database issue):D767–D772
Croft D, O’Kelly G, Wu G et al (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39(Database issue):D691–D697
Stark C, Breitkreutz B-J, Chatr-Aryamontri A et al (2011) The BioGRID interaction database: 2011 update. Nucleic Acids Res 39(Database issue):D698–D704
Hamosh A, Scott AF, Amberger JS et al (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33(Database issue):D514–D517
Barrett T, Edgar R (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 411:352–369
Lombard Z, Park C, Makova KD et al (2011) A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis. Biol Direct 6:30
Gormanns P, Mueller NS, Ditzen C et al (2011) Phenome-transcriptome correlation unravels anxiety and depression related pathways. J Psychiatr Res 45:973–979
Wolford G, Rosenberg SD, Rosenberg HJ et al (2008) A clinical trial comparing interviewer and computer-assisted assessment among clients with severe mental illness. Psychiatr Serv 59:769–775
Yan Q (2010) Bioinformatics for transporter pharmacogenomics and systems biology: data integration and modeling with UML. Methods Mol Biol 637:23–45
Daemen A, Gevaert O, Ojeda F et al (2009) A kernel-based integration of genome-wide data for clinical decision support. Genome Med 1:39
Croning MDR, Marshall MC, McLaren P et al (2009) G2Cdb: the genes to cognition database. Nucleic Acids Res 37(Database issue):D846–D851
Sabb FW, Bearden CE, Glahn DC et al (2008) A collaborative knowledge base for cognitive phenomics. Mol Psychiatry 13:350–360
Kim S, Webster MJ (2010) The stanley neuropathology consortium integrative database: a novel, web-based tool for exploring neuropathological markers in psychiatric disorders and the biological processes associated with abnormalities of those markers. Neuropsychopharmacology 35:473–482
Hucka M, Finney A, Bornstein BJ et al (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Syst Biol (Stevenage) 1:41–53
Rassinoux AM (2008) Decision support, knowledge representation and management: structuring knowledge for better access. Findings from the yearbook 2008 section on decision support, knowledge representation and management. Yearb Med Inform 2008:80–82
Peleg M, Tu S (2006) Decision support, knowledge representation and management in medicine. Yearb Med Inform 2006:72–80
Moskovitch R, Martins SB, Behiri E et al (2007) A comparative evaluation of full-text, concept-based, and context-sensitive search. J Am Med Inform Assoc 14:164–174
Thomas PD, Mi H, Swan GE et al (2009) A systems biology network model for genetic association studies of nicotine addiction and treatment. Pharmacogenet Genomics 19:538–551
Roque FS, Jensen PB, Schmock H et al (2011) Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS Comput Biol 7:e1002141
Cohen T, Blatter B, Patel V (2008) Simulating expert clinical comprehension: adapting latent semantic analysis to accurately extract clinical concepts from psychiatric narrative. J Biomed Inform 41:1070–1087
Vodovotz Y, An G (2010) Systems biology and inflammation. Methods Mol Biol 662:181–201
Yan Q (2010) Immunoinformatics and systems biology methods for personalized medicine. Methods Mol Biol 662:203–220
Cohen AM, Hersh WR (2005) A survey of current work in biomedical text mining. Brief Bioinform 6:57–71
Nelson TD, Aylward BS, Rausch JR (2011) Dynamic p-technique for modeling patterns of data: applications to pediatric psychology research. J Pediatr Psychol 36:959–968
Rudan I (2010) New technologies provide insights into genetic basis of psychiatric disorders and explain their co-morbidity. Psychiatr Danub 22:190–192
Tretter F, Gebicke-Haerter PJ, an der Heiden U et al (2011) Affective disorders as complex dynamic diseases—a perspective from systems biology. Pharmacopsychiatry 44(suppl 1):S2–S8
Tretter F (2010) Mental illness, synapses and the brain–behavioral disorders by a system of molecules within a system of neurons? Pharmacopsychiatry 43(suppl 1):S9–S20
Xiao X, Dawson N, Macintyre L et al (2011) Exploring metabolic pathway disruption in the subchronic phencyclidine model of Âschizophrenia with the Generalized Singular Value Decomposition. BMC Syst Biol 5:72
Liu Z-P, Wang Y, Zhang X-S et al (2010) Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer’s disease brains. BMC Syst Biol 4(suppl 2):S11
Schreiber G, Akkermans H, Anjewierden A et al (2000) Knowledge engineering and management: the common KADS methodology. The MIT Press, Cambridge, MA
Spaulding W, Deogun J (2011) A pathway to personalization of integrated treatment: informatics and decision science in psychiatric rehabilitation. Schizophr Bull 37(suppl 2):S129–S137
Haueis P, Greil W, Huber M et al (2011) Evaluation of drug interactions in a large sample of psychiatric inpatients: a data interface for mass analysis with clinical decision support software. Clin Pharmacol Ther 90:588–596
Mane KK, Bizon C, Schmitt C et al (2012) VisualDecisionLinc: a visual analytics approach for comparative effectiveness-based clinical decision support in psychiatry. J Biomed Inform 45(1):101–106
Woltmann EM, Wilkniss SM, Teachout A et al (2011) Trial of an electronic decision support system to facilitate shared decision making in community mental health. Psychiatr Serv 62:54–60
Brunette MF, Ferron JC, McHugo GJ et al (2011) An electronic decision support system to motivate people with severe mental illnesses to quit smoking. Psychiatr Serv 62:360–366
Goldstein LA, Connolly Gibbons MB, Thompson SM et al (2011) Outcome assessment via handheld computer in community mental health: consumer satisfaction and reliability. J Behav Health Serv Res 38:414–423
Freeman JB, Ambady N (2010) MouseTracker: software for studying real-time mental processing using a computer mouse-tracking method. Behav Res Methods 42:226–241
Carroll KM, Rounsaville BJ (2010) Computer-assisted therapy in psychiatry: be brave-it’s a new world. Curr Psychiatry Rep 12:426–432
Marks I, Cavanagh K (2009) Computer-aided psychological treatments: evolving issues. Annu Rev Clin Psychol 5:121–141
Stuhlmiller C, Tolchard B (2009) Computer-assisted CBT for depression & anxiety: increasing accessibility to evidence-based mental health treatment. J Psychosoc Nurs Ment Health Serv 47:32–39
Kiluk BD, Sugarman DE, Nich C et al (2011) A methodological analysis of randomized clinical trials of computer-assisted therapies for psychiatric disorders: toward improved standards for an emerging field. Am J Psychiatry 168:790–799
The eMERGE Network. Available from https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Main_Page. Accessed Oct 2011
National Human Genome Research Institute. Available from http://www.genome.gov/24519851. Accessed Oct 2011
The Health Insurance Portability and Accountability Act (HIPAA). Available from http://www.hhs.gov/ocr/privacy/. Accessed Oct 2011
Hesse BW, Suls JM (2011) Informatics-enabled behavioral medicine in oncology. Cancer J 17:222–230
Marcus DS, Harwell J, Olsen T et al (2011) Informatics and data mining tools and strategies for the human connectome project. Front Neuroinform 5:4
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Yan, Q. (2012). Translational Bioinformatics in Psychoneuroimmunology: Methods and Applications. In: Yan, Q. (eds) Psychoneuroimmunology. Methods in Molecular Biology, vol 934. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-071-7_20
Download citation
DOI: https://doi.org/10.1007/978-1-62703-071-7_20
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-070-0
Online ISBN: 978-1-62703-071-7
eBook Packages: Springer Protocols