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Prof. Carlos
Blanco –
Scientific Advisor
PERSONAL PROFILE
Very skilled in all aspects of data management, from data collection, data cleaning, database design and management, through all kinds of data manipulation, parsing and assembly, to various kinds of analysis, interpretation and report creation. Highly skilled in complex data analysis. Have performed detailed analyses for scientific publications, clinical studies and research projects using both specialized software and code I wrote myself. In most cases this included graphical summaries of data – plots and other diagrams – as well as statistical assessment. Strong IT skills. Have written complex web-based user interfaces to project databases. Built and administered databases. Excellent communication skills. Experienced at collecting user requirements and ongoing interaction with end-users during project development. Have organised and led several training courses, including on the use of R. Writes clear and comprehensive documentation of software, and data dictionaries. Background in molecular biology. Direct experience of data collection from instrument output, building pipelines to parse, quality control, and summarize experimental data. Also experienced in handling human-generated input – questionnaires, health records, etc. Also in designing questionnaires to gather such input.
KEY COMPETENCES
Professional and IT Skills | ||
· Data management | · Bash shell scripting | · Catalyst MVC framework |
· Complex data analysis | · Perl scripts | · Issue tracking systems |
· R statistical environment | · SQL queries | · PostgreSQL |
· SPSS | · Version control software | · MySQL |
· SAS | · System administration | · SQLite |
· Statistical tests (Chi-Square, ANOVA, Regression models) | · Linux (Debian, Kubuntu, Slackware, Redhat) | · Microsoft Access |
EDUCATIONAL RECORD
B.Sc. (Hons.) Biotechnology, Dublin City University 1989
Ph.D., Molecular Biology, Dublin City University 1993
Postgraduate Diploma in Statistics, Trinity College, Dublin 2005
GCP Certificate (2015)
CAREER HISTORY
STATISTICAMEDICA Ltd, biostatistics company in Dublin, Ireland 2014 – Present
Data Science Consultant reporting to CEO
· Statistical support and data-management services to commercial and academic clients, mostly in biomedical fields
· Creating data entry interfaces (eCRFs) and databases, data cleaning and integration
· Study design, statistical analysis of study data (hypothesis tests, linear and logistic regression, survival curves, ROC curves, etc.)
SCHOOL OF PUBLIC HEALTH, UNIVERSITY COLLEGE DUBLIN 2011 – 2014
School Data Manager
· Responsible for all aspects of data management in the School (supervision of data entry, design, implementation and maintenance of databases, using PostgreSQL and SQLite, and the construction of web-interfaces, etc.)
· Involved in study design, data collection, complex SQL queries, data analysis and interpretation
· Full documentation of the databases and all code built around them
WELLCOME TRUST SANGER INSTITUTE, CAMBRIDGE 2008 – 2011
Senior Developer
Achievements
Development and maintenance of a pipeline for the downstream processing, assembly, archival, and evaluation of next-generation DNA sequence data from Illumina DNA sequencers. These machines produce hundreds of Gigabytes of data per day and our team managed the output from 40 such instruments, performing QC, monitoring instruments and runs via a web-interface custom-written for the task, feeding the data into analytic pipelines and archiving the raw data and results. Most of this work was performed using Perl, but it also required web design using HTML, CSS, Javascript and Ajax.
BIOINFORMATICS CONSULTANT 2006 – 2008
· Own business providing data-management and bioinformatics support to a number of clients in project design, data capture and analysis
CENTRE FOR HUMAN PROTEOMICS AT RCSI, DUBLIN 2004 – 2006
· Responsible for all the bioinformatics analysis for the CHP (most of the research based on protein arrays)
· Performed a lot of bespoke analysis such as mapping array results to gene ontologies, or DNA/protein sequence clustering
Achievements
Established a PostgreSQL database to hold the results of CHP experiments, typically ~ 70,000 data points per experiment and hundreds of experiments. As well as this, the database held the clinical data that was relevant to the experiments.
DEPT. OF CLINICAL PHARMACOLOGY, AT RCSI, DUBLIN 2000 – 2004
Achievements
Established a core genotyping group as part of the Institute of Biopharmaceutical Sciences, bringing together clinical research and cutting edge molecular biology techniques.
ABTEILUNG LEHRACH, MAX-PLANCK-INSTITUT FÜR MOLEKULARE GENETIK, BERLIN 1995 – 2000
· Leading a multidisciplinary group comprised of biologists, mathematicians, and programmers, which focused on applying high-throughput automation to the construction and analysis of cDNA libraries, reducing them to smaller non-redundant collections of clones, which were then used in DNA sequencing, and mapping projects. This work involved a great deal of image analysis and data clustering, as well as many molecular biology techniques.
LEHRSTUHL FÜR BIOCHEMIE U. ORGANISCHE CHEMIE
TECHNISCHE UNIVERSITÄT MÜNCHEN 1993 – 1995
· Post-doctoral position, studying the biosynthesis of molybdopterin in Escherichia coli
PUBLICATIONS/DISSERTATIONS
Kelleher C, Viljoen K, Khalil H, Somerville R, O’Brien J, Shrivastava A, and Murrin C.
Longitudinal follow-up of the relationship between dietary intake and growth and development in the Lifeways cross-generation cohort study 2001–2013
Proceedings of the Nutrition Society, 2014 73(1):118-31. PMID: 24300176
Shrivastava A, Murrin C, O’Brien J, Viljoen K, Heavey P, Grant T and Kelleher C.
Grandparental morbidity and mortality patterns are associated with infant birth weight in the Lifeways cross-generation cohort study 2001–2010.
Journal of Developmental Origins of Health and Disease 2012 3(6):458-468. PMID:
Murphy M, O’Connell D, O’Kane S, O’Brien J, O’Toole S, Martin C, Sheils O, O’Leary J and Cahill D.
Epitope presentation is an important determinant of the utility of antigens identified from protein arrays in the development of autoantibody diagnostic assays
Journal of Proteomics 2012 75(15):4668–4675. PMID: 22415278
O’Kane S, O’Brien J, and Cahill D.
Optimized Autoantibody Profiling on Protein Arrays
Protein Microarrays. Methods in Molecular Biology, 2011, Volume 785(3):331-341 PMID: 21901610
O’Connell J, Bauer M, O’Brien J, Johnson W, Divizio C, O’Kane S, Berggård T, Merino A, Åkerfeldt K, Linse S Cahill D, Integrated protein array screening and high throughput validation of 70 novel neural calmodulin binding proteins.
Molecular Cellular Proteomics 2010 Jun, 9(6):1118-32 PMID: 20068228
Gibson D, Banha J, Penque D, Conrads T, Costa L, Cahill D, O’Brien J, Rooney M.
Diagnostic and Prognostic Biomarker Discovery Strategies for Autoimmune Disorders.
Journal of Proteomics 2010 Apr 18; 73(6):1045-60. PMID: 19995622
Moore N, Dicker P, O’Brien JK, Stojanovic M, Conroy RM, Treumann A, O’Brien ET, Fitzgerald D, Shields D, Stanton AV.
Renin gene polymorphisms and haplotypes, blood pressure, and responses to renin-angiotensin system inhibition.
Hypertension. 2007 Aug;50(2):340-7. PMID: 17562974
O’Halloran A, Curtin R, O’Connor F, Dooley M, Fitzgerald A, O’Brien J, Fitzgerald D, Shields
The impact of genetic variation in the region of the GPIIIa gene, on PIA2 expression bias and GPIIb/IIIa receptor density in platelets.
British J Haematol. 2006 Feb;132(4):494-502. PMID: 16412022
Hillmann A, Harmon S, Park S, O’Brien J, Shields D, Moran N, Kenny D.
Comparative RNA expression analyses from small-scale, single donor platelet samples.
J Thromb Haemost. 2006 Feb; 4(2):349-56. PMID: 16420564
Dolan C, Shields D, Stanton A, O’Brien E, Lambert D, O’Brien J, Treacy E.
Polymorphisms of the Flavin Containing monooxygenase 3 (FMO3) gene do not predispose to essential hypertension in Caucasians.
BMC Med Genet. 2005 Dec; 6(1):41 PMID: 16324215
Maree A, Curtin R, Chubb A, Dolan C, Cox D, O’Brien J, Crean P, Shields D, Fitzgerald D.
Cyclooxygenase-1 haplotype modulates platelet response to aspirin.
J Thromb Haemost. 2005 Oct; 3(10):2340-5. PMID: 16150050
Dolan C, O’Halloran A, Bradley D, Croke D, Evans A, O’Brien J, Dicker P, Shields D.
Genetic stratification of pathogen-response-related and other variants within a homogeneous Caucasian Irish population.
Eur J Hum Genet. 2005 Jul; 13(7):798-806. PMID: 15785776
Gutjahr C, Murphy D, Lueking A, Koenig A, Janitz M, O’Brien J, Korn B, Horn S, Lehrach H, Cahill D.
Mouse protein arrays from a TH1 cell cDNA library for antibody screening and serum profiling
Genomics 2005 Mar; 85(3):285-296. PMID: 15718096
Malecová B, Ramser J, O’Brien J, Janitz M, Júdová J, Lehrach H, Šimúth J.
Honeybee (Apis mellifera L.) mrjp gene family: computational analysis of putative promoters and genomic structure of mrjp1, the gene coding for the most abundant protein of larval food.
Gene 2003 Jan 16; 303(1-2):165-75. PMID: 12559578
Herwig R, Schulz B, Weisshaar B, Hennig S, Steinfath S, Drungowski M, Wruck W, O’Brien J, Lehrach H, Radelof U.
Construction of a ‘unigene’ cDNA clone set by oligonucleotide fingerprinting allows access to 25,000 potential sugar beet genes.
The Plant Journal 2002 Dec; 32(5):845-857. PMID: 12472698
Fuchs T, Malecova B, Linhart C, Sharan R, Khen M, Herwig R, Shmulevich D, Elkon R, Steinfath M, O’Brien J, Radelof U, Lehrach H, Lancet D, Shamir R.
DEFOG: A Practical Scheme for Deciphering Families of Genes.
Genomics 2002 Sep; 80(3):295. PMID: 12213199
Wruck W, Griffiths H, Steinfath M, Lehrach H, Radelof U, O’Brien J.
Xdigitise: visualization of hybridization experiments.
Bioinformatics 2002 May; 18(5):757-760. PMID: 12050072
Guerasimova A, Nyarsik L, Girnus I, Steinfath M, Wruck W, Griffiths H, Herwig R, Wierling C, O’Brien J, Eickhoff H, Lehrach H, Radelof U.
New tools for oligonucleotide fingerprinting.
Biotechniques 2001 Sep; 31(3):490-5 PMID: 11570491
Steinfath M, Wruck W, Seidel H, Lehrach H, Radelof U, O’Brien, J.
Automated image analysis for array hybridization experiments.
Bioinformatics 2001 Jul; 17(7):634-41 PMID: 11448881
Hüttenhofer A, Kiefmann M, Meier-Ewert S, O’Brien J, Lehrach H, Bachellerie J, Brosius J.
RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse.
EMBO J 2001 Jun 1; 20(11):2943-53 PMID: 11387227
Lynch D, O’Brien J, Welch T, Clarke P, Ó Cuív P, Crosa J, O’Connell M.
Genetic organization of the region encoding regulation, biosynthesis, and transport of Rhizobactin 1021, a siderophore produced by Sinorhizobium meliloti.
J Bacteriol. 2001 Apr; 183(8):2576-85. PMID: 11274118
Herwig R, Schmitt A, Steinfath M, O’Brien J, Seidel H, Meier-Ewert S, Lehrach H, Radelof U.
Information theoretical probe selection for hybridisation experiments.
Bioinformatics. 2000 Oct; 16(10):890-8. PMID: 11120678
O’Brien J, Cahill D, Radelof U, Lehrach H, Maurer C. (2000).
“High-throughput Technologies and Resources.” pp95-100 in “Molecular Pathogenesis of Pancreatic Cancer” Ed. T.M. Gress. IOS Press, Amsterdam.
Eickhoff H, Schuchhardt J, Ivanov I, Meier-Ewert S, O’Brien J, Malik A, Tandon N, Wolski E-W, Rohlfs E, Nyarsik L, Reinhardt R, Nietfeld W, Lehrach H.
Tissue gene expression analysis using arrayed normalized cDNA libraries.
Genome Res. 2000 Aug; 10(8):1230-40. PMID: 10958641
Bull C, Sobanov Y, Röhrdanz B, O’Brien J, Lehrach H, Hofer E.
The centromeric part of the human NK gene complex: linkage of LOX-1 and LY49L with the CD94/NKG2 region.
Genes Immun. 2000; 1(4):280-7. PMID: 11196705
Cahill DJ, Nordhoff E, O’Brien J, Klose J, Eickhoff H, and Lehrach H. (2000).
“Bridging Genomics and Proteomics.” Chp 1: pp. 1-17 in “Proteomics.” Eds. Pennington, S. and Dunn, M. BIOS Scientific Publishers Ltd.
Herwig R, Poustka A, Muller C, Bull C, Lehrach H, O’Brien J.
Large-scale clustering of cDNA-fingerprinting data.
Genome Res. 1999 Nov; 9(11):1093-105. PMID: 10568749
Hildmann T, Kong X, O’Brien J, Dagand E, Christensen M, Riesselman L, Steiger J, Röhrdanz B, Lehrach H, Yaspo M-L.
A contiguous 3 Megabase sequence-ready map in the Down’s syndrome-associated congenital heart defect region on chromosome 21.
Genome Res. 1999 Apr; 9(4):360-72. PMID: 10207158
Rieder C, Eisenreich W, O’Brien J, Richter G, Götze E, Boyle P, Blanchard S, Bacher A, Simon H.
Rearrangement reactions in the biosynthesis of molybdopterin: An NMR study with multiply 13C/15N labeled precursors.
Eur J Biochem. 1998 Jul 1; 255(1):24-36. PMID: 9692897
Bancroft D, O’Brien J, Guerasimova A, Lehrach H.
Simplified handling of high-density genetic filters using rigid plastic laminates.
Nucleic Acids Res. 1997 Oct 15; 25(20):4160-1. PMID: 9321673