Suggested Reading for Msc Precision Medicine
Suggested Reading for MSc Precision Medicine
General programme reading
A wellness study of 108 individuals using personal, dense, dynamic data clouds. Nathan D Price, Andrew T Magis, John C Earls, Gustavo Glusman, Roie Levy, Christopher Lausted, Daniel T McDonald, Ulrike Kusebauch, Christopher L Moss, Yong Zhou, Shizhen Qin, Robert L Moritz, Kristin Brogaard, Gilbert S Omenn , Jennifer C Lovejoy , Leroy Hood. Nat Biotechnol. 2017;35(8):747-756.
Integrative omics for health and disease. Karczewski, K., Snyder, M. Nat Rev Genet 19, 299–310 (2018).
Pharmaco-Geno-Proteo-Metabolomics and Translational Research in Cancer. Fernández-Figueroa EA, Lino- Silva S, Peña-Velasco JE, Rangel-Escareño C.Adv Exp Med Biol. 2019;1168:1-7.
Clinical potential of mass spectrometry-based proteogenomics. Zhang B, Whiteaker JR, Hoofnagle AN, Baird GS, Rodland KD, Paulovich AG.Nat Rev Clin Oncol. 2019 Apr;16(4):256-268.
Genetics and Genomics unit
Websites National Human Genome Research Institute (NHGRI), Education pages http://www.genome.gov/10001772 All about the Human Genome Project Fact sheets Webinars
University of Manchester MOOC Clinical Bioinformatics: Unlocking Genomics in Healthcare Free online course. 5 weeks, 2 hrs per week; next start tbc. Learn about the role of clinical bioinformaticians in healthcare and how their work is helping to realise the genomics revolution. https://www.futurelearn.com/courses/bioinformatics
Journal Articles (some restricted access) Essentials of Genomic and Personalized Medicine, 2010 Edited by: Geoffrey S. Ginsburg, M.D., Ph.D., and Huntington F. Willard, Ph.D. ISBN: 978-0-12-374934-5
Nature Reviews Genetics ‘Collections’ – some examples https://www.nature.com/nrg/collections Clinical applications of Next Generation Sequencing Translational Genetics Disease Mechanisms Overcoming Challenges in Rare Diseases
Nature. 2011 (470):187-97 | doi:10.1038/nature09792. Initial impact of the sequencing of the human genome.
Sci Transl Med. 2012; (4) 54ra135 | DOI: 10.1126/scitranslmed.3004041 Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units
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Books Genetics and Genomics in Medicine Author(s):Tom Strachan, Judith Goodship, Patrick Chinnery ISBN: 9780815344803 Date: June 01, 2014, 1st edition
Book Chapters: Lewin's Genes X, J.E. Krebs, E.S. Goldstein & S.T. Kilpatrick Chapter 5 The Content of the Genome Chapter 6 Genome Sequences and Gene Numbers Chapter 20 Eukaryotic Transcription Chapter 21 RNA Splicing and Processing Chapter 28 Eukaryotic Transcription Regulation Chapter 29 Epigenetic Effects Are Inherited Chapter 30 Regulatory RNA
Proteomics and Metabolomics unit
Beebe K (2014). Metabolomics: Completing the Picture in Systems Biology. https://www.youtube.com/watch?v=4lKD65lCDnA
Journal Articles (some restricted access) Shen et al. (2020) Proteomic and Metabolomic Characterization of COVID-19 Patient Sera. Cell, in press. https://www.sciencedirect.com/science/article/pii/S0092867420306279
The Functions of Proteins Are Determined by Their Three-Dimensional Structures. Nature. Primer ( http://www.nature.com/scitable/ebooks/essentials-of-cell-biology- 14749010/122996920#bookContentViewAreaDivID ).
Proteins Are Responsible for a Diverse Range of Structural and Catalytic Functions in Cells. Nature. Primer (http://www.nature.com/scitable/ebooks/essentials-of-cell-biology- 14749010/122996980#bookContentViewAreaDivID ).
Aebersold R, Mann M. Mass-spectrometric exploration of proteome structure and function. Nature. 2016 537(7620):347-55.
Gahoi N, Ray S, Srivastava S. Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics. 2015 ;15(2-3):218-31. doi: 10.1002/pmic.201400261.
Rogowska-Wrzesinska A, Le Bihan MC, Thaysen-Andersen M, Roepstorff P. 2D gels still have a niche in proteomics. J Proteomics. 2013;88:4-13. Chait BT. Mass spectrometry: bottom-up or top-down? Science. 2006;314(5796):65-6.
Marcotte EM. How do shotgun proteomics algorithms identify proteins? Nat Biotechnol. 2007;25(7):755-7.
Domon B, Aebersold R. Mass spectrometry and protein analysis. Science. 2006 Apr 14;312(5771):212-7. Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics. 2015 (18):3193-208.
Wishart DS (2016). Emerging applications of metabolomics in drug discovery and precision medicine. Nature Rev. Drug. Discov. doi: 10.1038/nrd.2016.32.
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Holmes et al. (2008). Metabolic phenotyping in health and disease. Cell 134:714-717.
Kell DB (2004). Metabolomics and systems biology: Making sense of the soup. Current Opinion in Microbiology 7(3):296-307.
Chen et al. (2012). Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148:1293- 1307.
Gika et al. (2014). Current practice of liquid chromatography-mass spectrometry in metabolomics and metabonomics. Journal of Pharmaceutical and Biomedical Analysis 87:12-25
Latosinska A, Vougas K, Makridakis M, Klein J, Mullen W, Abbas M, Stravodimos K, Katafigiotis I, Merseburger AS, Zoidakis J, Mischak H, Vlahou A, Jankowski V. Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PLoS One. 2015;10(9):e0137048. doi: 10.1371/journal.pone.0137048. Erratum in: PLoS One. 2015;10(10):e0139268. Floegel et al. (2014). Identification of serum metabolites associated with risk of type 2 diabetes using a targeted metabolomic approach. Diabetes 62(2):639-648.
Goodacre, R. Vaidyanathan, S., Dunn, W.B., Harrigan, G.G. & Kell, D.B. (2004) Metabolomics by numbers - acquiring and understanding global metabolite data. Trends in Biotechnology 22, 245-252 Goodacre, R. (2007) Metabolomics of a superorganism. Journal of Nutrition 137, 259S-266S Trivedi, D. et al (2017) Metabolomics for the masses: the future of metabolomics in a personalised world. New Horizons In Translational Metabolomics 3(6):294-305 Mamas, M., Dunn, W.B., Neyses, L. & Goodacre, R. (2011) The role of metabolites and metabolomics in clinically- applicable biomarkers of disease. Archives of Toxicology 85, 5-17.
Ludwig, C., Gillet, L., Rosenberger, G., Amon, S., Collins, B. C., Aebersold, R. (2018) Data-independent acquisition- based SWATH-MS for quantitative proteomics: a tutorial. Molecular Systems Biology 14: e8126. Tate, S., Hunter, C. (2011) MS/MSALL with SWATH Acquisition. AB SCIEX technical notes, link: https://sciex.com/Documents/Downloads/Literature/Tech-Note-MSMSall-SWATH-Acquisition.pdf Geary, B., Walker, M.J., Snow, J.T., Lee, D.C.H., Pernemalm, M., Maleki-Dizaji, S., Azadbakht, N., Apostolidou, S., Barnes, J., Krysiak, P., Shah, R., Booton, R., Dive, C., Crosbie, P.A., Whetton, A.D. Identification of a Biomarker Panel for Early Detection of Lung Cancer Patients. J Proteome Res. 2019 Aug 21. doi: 10.1021/acs.jproteome.9b00287. Anjo, S.I., Santa, C., Manadas, B. SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications. Proteomics. 2017 Feb;17 (3-4). doi: 10.1002/pmic.201600278. Zhou et al. J Proteome Res. 2012 Apr 6; 11(4): 2103–2113. Geyer et al. Mol Syst Biol. 2017 Sep; 13(9): 942. Blankley et al Mol Cell Proteomics. 2013 Nov; 12(11): 3148–3159. Lawal O, Ahmed WM, Nijsen TME, Goodacre R, Fowler SJ. Exhaled breath analysis: a review of ‘breath-taking’ methods for off-line analysis. Metabolomics 2017;13:110. doi:10.1007/s11306-017-1241-8 Bos LD, Sterk PJ, Fowler SJ. Breathomics in the setting of asthma and chronic obstructive pulmonary disease. J Allergy Clin Immunol 2016;138:970-6
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Laboratory Skills unit
Helgason CD and Miller CL (eds) (2012) Basic cell culture protocols. Humana Press.ISBN1-62703-127-8. N.B. 2004 edition available via JRULM electronic resources http://link.springer.com/book/10.1385/1592598382/page/1
JP Mather, PE Roberts (eds) (1998) Introduction to cell and tissue culture: theory and technique. Plenum Press, London, ISBN: 0306458594, 9780306458590 (Blue 2: 571.538/MAT)
Cabibbo A, Grant RP, Helmer-Citterich M (eds) (2004) Internet for the Cell and Molecular Biologist (2nd Edition) Horizon Scientific Press, Wymondham, ISBN: 1-898-48632-8 (Blue 2: 570.285/CAB)
McPherson MJ, Møller SG (2006) PCR: The Basics (2nd Edition) BIOS, Oxford, ISBN: 0-415-35547-8 (Blue 2: 572.808/MCP). Available via JRULM electronic resources http://www.netLibrary.com/urlapi.asp?action=summary&v=1&bookid=53951
Schrijver I (ed) (2011) Diagnostic Molecular Pathology in Practice: A Case-Based Approach. Springer Berlin Heidelberg. ISBN9783642196775. Available via JRULM electronic resources http://link.springer.com/book/10.1007%2F978-3-642-19677-5
T Brown (ed) (2000, 2001) Essential Molecular Biology Vols 1&2: A Practical Approach: v. 2. OUP Oxford. ISBN-13: 978-0199636426, 978-0199636440
Rosenberg, Ian M (2006) Protein Analysis and Purification: Benchtop Techniques (2nd Edition) Birkhäuser Boston MA. ISBN: 9780817644123, 9780817643409. Available via JRULM electronic resources: Springer e-books http://www.springerlink.com/content/k3183r/#section=500456&page=1
Nature “Statistics for Biologists” web collection for Research Methods Unit and Research Projects: http://www.nature.com/collections/qghhqm
The Biomedical & Life Sciences Collection. The Collection contains over 2,700 lectures, covering the fundamentals as well as the latest advancements in the fields of Life Sciences, Medicine and Pharmacology. All talks were specially commissioned by leading world experts, including a number of Nobel laureates.
The University of Manchester has full and unlimited access to all the lectures via www.hstalks.com/access.
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