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Dr. John Killian O'Brien

 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