Engineer Assistant

J. ENRIQUE HERRERA-GALEANO

**** ********* *****, ********, ** 21045

Phone: 443-***-**** Email: ***************@*****.***

Citizenship: USA

Objective

To actively contribute to the scientific advancement of the field of Bioinformatics and Computational Genomics. To utilize the tools of Bioinformatics to support the research of collaborators in the biomedical field.

Education

PhD. 2012 George Mason University Bioinformatics and Computational Biology

M.S. 2005 Johns Hopkins University Computer Science

M.S. 2000 University of Antioquia Genetics

B.S. 1994 University of Antioquia Microbiology

Professional Experience

Senior Bioinformatics Programmer Columbia University New York City, NY Jan 2011- Present

I recently joined the Center for Infectious and Immune Diseases at Columbia University where I develop and implement algorithms for the analysis for high throughput data, such as microarray analysis and next-generations sequencing. I have developed applications in PERL to analyze microarray results with non-parametric statistics and I have also worked in extending a RUBY ON RAILS portal for the sharing of the data.

Biomedical Research Engineer Philips Research Briarcliff Manor, NY Feb 2010 – Dec 2010

Knowledge Representation and GUI development

As a biomedical engineer at Philips Research I am in charge of the development and algorithm's implementation for a Biomedical Ontology Management System. I developed a standalone Graphical User Interface and an application for browsing and editing the Philips Biomedical Ontology. The ontology is represented as a Directed Acyclic Graph (DAG) and the system implements all the algorithm's to traverse the graph, display all the slot information and follow different concept relationships. The application is fully developed in JAVA, the application uses swing, AWT and JDBC to connect to an SQLite dbms.

Bioinformatics Analyst/PhD Student NHGRI-NIH Bethesda, MD June 2009 - Sept 2009

Genome Annotation, Phylogenetics and Perl development

At the NHGRI Bioinformatics Core, I participated in the annotation of the Genome of the Mnemiopsis Leidyi, a Next-Generation Sequencing project to 10X coverage. I predicted genes using Genscan and the Unix version of NCBI blast, performed the alignments using Jalview and obtained the phylogenetic relationships using Phylip, MrBayes and other phylogenetics tools. I also worked in analyzing the influence of conserved motifs in phylogenetic distance calculations. All analysis was conducted in linux servers and clusters.

Special Volunteer/PhD Student NHGRI-NIH Baltimore, MD Jan 2007 - June 2009

Genetic Epidemiology, Statistical analysis, R development

During my time at the Inherited Disease Branch of NHGRI, I worked on the comparison of statistical genetics methods, particularly in the lack of correlation among thousands of tests performed with extended pedigrees. Methods such as SAGE-ASSOC, FBAT and R-GEE were compared and a lack of agreement in their distributions was found (Poster at ASHG meeting, 2007). All analysis were conducted under linux.

Faculty Research Associate Johns Hopkins Baltimore, MD Jan 2003 - May 2009

Faculty research, scientific presentation, publications

As part of the faculty at the School of Medicine, my area of research was family based genetic association studies. I performed thousands of statistical tests with pedigree data and genetic markers, this work culminated with the publication of an association between the gene PEAR1 and platelet aggregation measures in response to Aspirin (Herrera-Galeano,et al 2008). I also developed and implemented an algorithm for the selection of SNPs using Monte Carlo Markov Models. In addition, I presented the group's work in several scientific meeting including ASHG and AHA. I was in charge of a 64-CPU Linux Cluster for Genetic and Bioinformatics analysis. All applications developed were fully implemented in JAVA, the SNP’s positions were rendered using JAVA2D, swing, AWT and XML parsers.

Database Curator Johns Hopkins Baltimore, MD Jul 2001 – Jan 2003

I reviewed scientific literature to add new DNA elements to the database, I also wrote PERL scripts to automatically update the database with entries from NCBI, UCSC Genome Bioinformatics and other databases. I administer a Linux server to automate database updating scripts.

Data Analyst Winstar McLean, VA Oct. 1999 - July 2001

I updated and administrated number databases.

Fogarty Research Fellow NIH NCI Frederick, MD Jun 1998 - Jun 1999

At Marry Carrington's lab, I worked in HLA genotyping using labeled nucleotides hybridization, I also found

novel SNPs using single stranded conformational polymorphisms.

Research Assistant/Teaching Assistant University of Antioquia Medellin, Colombia June 1994 - July 1998

Reviewer

Bioinformatics, the Journal

Skills

Programming languages : Java, Perl, Python, C++ .

Statistical languages and packages: R, SAS, S.A.G.E., Merlin, NCBI power scripting

Parallel computing, I have experience with different cluster designs, I have setup and administered linux clusters and I'm familiar with Rocks, Sun Grid Engine, Hadoop, Map/Reduce and Map/Reduce databases.

Honors

1994 B.S. Summa Cum Laude

1995-1998 M.S. Scholarship for Graduate Studies

1998-1999. Fellowship (National Institute of Health, sponsored John E. Fogarty International Center) to work in the National Cancer Institute.

Publications

Mathias RA, Kim Y, Sung H, Yanek LR, Mantese VJ, Hererra-Galeano JE, Ruczinski I, Wilson AF, Faraday N, Becker LC, Becker DM. A combined genome-wide linkage and association approach to find susceptibility loci for platelet function phenotypes in European American and African American families with coronary artery disease. BMC Med Genomics. 2010 Jun 7;3:22

Sun H, Swaim A, Herrera JE, Becker D, Becker L, Srivastava K, Thompson LE, Shero MR, Perez-Tamayo A, Suktitipat B, Mathias R, Contractor A, Faraday N, Morrell CN. Platelet kainate receptor signaling promotes thrombosis by stimulating cyclooxygenase activation. Circ Res. 2009 Sep 11;105(6):595-603.

Faraday N, Yanek LR, Vaidya D, Kral B, Qayyum R, Herrera-Galeano JE, Moy TF, Becker DM, Becker LC. Leukocyte count is associated with increased platelet reactivity and diminished response to aspirin in healthy individuals with a family history of coronary artery disease. Thromb Res. 2009 Jul;124(3):311-7.

J. E Herrera, Lisa R Yanek, Rasika Mathias, Alexander F Wilson, Taryn F Moy, Lewis C Becker, and Diane M Becker. Abstract 5091: Genome-Wide Association Study Identifies Loci Associated with a Global Measure of Well-Being Circulation, Oct 2008; 118: S_1143 - S_1144. Oral Presentation.

J. E Herrera, Rehan Qayyum, Nauder Faraday, Lisa R Yanek, Dhananjay Vaidya, Diane M Becker, and Lewis C Becker. Abstract 1440: Platelet Response to Aspirin is Under Polygenic Control of Variants in the VAV3 and Phospholipase C Gamma 2 (PLCG2) Genes Circulation, Oct 2008; 118: S_326. Oral Presentation.

Dhananjay Vaidya, J E Herrera-Galeano, Lisa R Yanek, Taryn F Moy, Nauder Faraday, Lewis C Becker, and Diane M Becker. Abstract 3140: A Variant in the von Willebrand Factor Gene is Associated with Differences in Circulating Protein Levels and Platelet Function Circulation, Oct 2008; 118: S_1101.

Brian G Kral, Nauder Faraday, J. E Herrera-Galeano, Dhananjay Vaidya, Lisa R Yanek, Taryn F Moy,Diane M Becker, and Lewis C Becker. Abstract 1811: Novel Variants in Mitogen-Activated Protein Kinase (MAPK) Genes are Associated with Platelet Responsiveness to Aspirin Circulation, Oct 2008; 118: S_390.

J. Enrique Herrera-Galeano; Diane M. Becker; Alexander F. Wilson; Lisa R. Yanek; Paul Bray; Dhananjay Vaidya; Nauder Faraday; Lewis C. Becker. A Novel Variant in the Platelet Endothelial Aggregation Receptor-1 Gene Is Associated With Increased Platelet Aggregability. Arterioscler Thromb Vasc Biol. 2008 Aug;28(8):1484-90. Epub 2008 May 29.

Faraday N, Yanek LR, Mathias R, Herrera-Galeano JE, Vaidya D, Moy TF, Fallin MD, Wilson AF, Bray PF, Becker LC, Becker DM. Heritability of platelet responsiveness to aspirin in activation pathways directly and indirectly related to cyclooxygenase-1. Circulation. 2007 May 15;115(19):2490-6.

Herrera-Galeano JE, Mathias RA, Sung H, Faraday N, Sorant A, Becker DM, Becker LC, Wilson AF, Low correlation among association tests for quantitative traits. ASHG meeting, 2007

Herrera-Galeano JE, Faraday N, Yanek LR, Moy TF, Becker DM, and Becker LC. Genetic Variants in ALOX5 and ALOX5AP are Associated with Reduced Response to Aspirin in African American Families with Premature Coronary Artery Disease. Circulation 116: II_56-a, 2007

Herrera-Galeano JE, Wilson AF, Faraday N, Yanek LR, Moy TF, Becker DM, and Becker LC. Genetic Contribution to Collagen-Induced Platelet Aggregation Following Low-Dose Aspirin in Families with Premature Coronary Artery Disease. Circulation 116: II_807-d-808II , 2007

Diane M. Becker; Jodi Segal; Dhananjay Vaidya; Lisa R. Yanek; J. Enrique Herrera-Galeano, Paul F. Bray; Taryn F. Moy; Lewis C. Becker; Nauder Faraday Sex Differences in Platelet Reactivity and Response to Low-Dose Aspirin Therapy, JAMA. 2006;295:1420-1427.

Faraday N, Becker DM, Yanek LR, Herrera-Galeano JE, Segal JB, Moy TF, Bray PF, Becker LC. Relation between atherosclerosis risk factors and aspirin resistance in a primary prevention population. Am J Cardiol. 2006 Sep 15;98(6):774-9.

Herrera-Galeano JE, Vaidya D, Faraday N, Yanek LR, Moy TF, Becker DM, Becker LC. A genome wide scan supports linkage of collagen-induced platelet aggregation following aspirin therapy to the D15S1005 locus. Circulation, 114(18):II-488 (2380), 2006.

Herrera-Galeano JE, Becker DM, Yanek LR, Moy TF, Faraday N, Becker LC. A novel variant in the platelet endothelial aggregation receptor-1 gene is associated with decreased response to aspirin. Circulation, 114(18):II-55 (399), 2006.

Faraday N, Herrera-Galeano JE, Yanek LR, Moy TF, Bray PF, Becker DM, Becker LC. Gene variants in collagen signaling alter platelet function and response to aspirin. Circulation, 114(18):II- 105 (638), 2006.

Paul F Bray, Rasika A Mathias, Jesus E Herrera-Galeano, Lisa R Yanek, Nauder Faraday, Ahmed A Hasan, Lewis C Becker, Diane M Becker Heritability of Platelet Reactivity in White and African American Subjects at Moderately High Risk of Coronary Artery Disease, Circulation, 112(17):II-74(443), 2005.

Jodi B Segal, Jesus E. Herrera-Galeano, Nauder Faraday, Lisa R Yanek, Taryn F Moy, Lewis C Becker, Diane M Becker Platelet Responsiveness to Aspirin Differs by Sex in Families with a History of Premature Coronary Artery Disease, Circulation 112(17):II-814(3771), 2005.

Faraday N, Becker D, Herrera-Galeano JE, Fallin D, Yanek LR, Robarts P, McFillin A, Chen LP, Becker LC High Throughput Screening Identifies Genetic Variants Associated with Variability in Platelet Function, Circulation, 110(17):III-719(3329), 2004.

El-Omar EM, Carrington M, Chow WH, McColl KE, Bream JH, Young HA, Herrera-Galeano JE, Lissowska Y, et al. Interleukin-1 Polymorphisms Associated with Increased Risk of Gastric Cancer, Nature 404: 398 - 402, 2000.

Hildesheim A, Schiffman M, Brinton LA, Fraumeni JF Jr, Herrero R, Bratti MC,Schwartz P, Mortel R, Barnes W, Greenberg M, McGowan L, Scott DR, Martin M, Herrera JE, Carrington M P53 Polymorphism and Risk of Cervical Cancer, Nature 396:531-2, 1998.

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