PIOTR Z. KOZBIAL, PH.D. 3177 Via Alicante, Unit 149  La Jolla, CA 92037 Cell: (858) 260-1005  [email protected]  http://www.linkedin.com/in/piotrkozbial I have a strong combination of biology and genetics background coupled with excellent bioinformatics skills. I published 34 peer-reviewed research papers since 2007 and my latest manuscript about a novel molecular mechanism that operates at functional enhancers was accepted for publication in Cell. Given the importance of non-coding RNA and DNA damage in innate immunity and cancers, a deeper understanding of the crosstalk between these factors has important therapeutic implications, including their potential utility as biomarkers, therapeutic targets, or immune modulators. About 83% of common diseases and traits-associated non-coding SNPs occur in enhancer regions. EDUCATION  Ph.D. in Molecular Biology, “Differential analysis of gene expression in N. tabacum with a reduced level of major histone H1 variants.” Research supervisor: Andrzej Jerzmanowski, Howard Hughes Medical Institute International Research Scholar, University of Warsaw, Poland, 2003  Master Degree in Molecular Biology, “Transient freezing regulates expression of extensin-type genes in winter rapeseed.” University of Warsaw, Poland, 1995 WORK EXPERIENCE UNIVERSITY OF CALIFORNIA – SAN DIEGO, La Jolla, CA 6/2009 to present Bioinformatics Scientist, Department of Medicine, Laboratory of Michael Geoff Rosenfeld  Investigation of the regulatory, architectural, and integrative genome-wide transcriptional responses involved in orchestrating nuclear programs of diverse signaling pathways. Analysis of high throughput sequencing data from human/mouse cell lines and macrophages (2120 ChIP-seq, 648 GRO-seq, 81 RNA-seq, and 18 PRO-cap datasets).  Experienced in supervisory and interpersonal relations. Well-organized, analytical, deadline-oriented, stresstolerant, self-motivated, team player, adept at multi-project management with technical expertise in:         Next Generation Sequencing (NGS) 370 Bioinformatics software tools R programming / Bioconductor Linux, AWS (EC2, S3), Apache HTML, AWK, Bash scripting PERL / Python software workflows GEO, TCGA, ArrayExpress databases Expression analysis: NGS / microarray             SANFORD | BURNHAM MEDICAL RESEARCH INSTITUTE, La Jolla, CA 4/2006 to 4/2009 Postdoctoral Associate, Joint Center for structural Genomics, Bioinformatics Core Industry level experience in annotation of 160 novel proteins through large-scale structural analysis. Generated annotated protein structure entries at www.topsan.org for more than 120 proteins. Development and deployment of a computational pipeline to analyze protein structures. Co-authored 30 research papers. Human non-coding RNA (ncRNA) Cancer genomics / transcriptomics GO term enrichment analysis Chromatin remodeling / modifications Gene activation pathways RNA-binding complexes DNA damage and repair Protein structure-function and MOA         Molecular biology techniques RNA-based biomarkers Human / mouse epigenetics RNA-Seq (polyA+, total) CLIP-Seq/PAR-CLIP RIP-Seq, ChIRP-Seq Ribo-Seq, MeDIP-seq Creative problem solving STOWERS INSTITUTE FOR MEDICAL RESEARCH, Kansas City, MO 6/2003 to 4/2006 Postdoctoral Research Associate, Bioinformatics Center  Prediction of conserved non-coding regions in fungal genomes.  Computational comparison of sequences and structures of various S-adenosylmethionine-binding proteins through evolutionary trajectories of these enzymes.  Investigations of chromatin remodeling and epigenetic regulators of development. PIOTR Z. KOZBIAL, PH.D.     RESUME, PAGE 2 UNIVERSITY OF WARSAW, Poland Predoctoral Teaching and Research Position, Laboratory of Plant Molecular Biology Lectured students in molecular biology. Advised and supervised three graduate students pursuing their Master of Science degrees. Administered Linux/Windows computer network. Designed and developed Internet portal for the Polish Biochemical Society. 10/1995 to 5/2003 SELECTED PUBLICATIONS (OUT OF 37) 1. Puc J, Kozbial P, Li W, Tan Y, Liu Z, Suter T, Ohgi K, Zhang J, Aggarwal A, and Rosenfeld MG (2015). 'LigandDependent Enhancer Activation Regulated by Topoisomerase-I Activity', Cell 160, 367–380, January 29, 2015 2. Axelrod HL, Kozbial P, et al. (2010) 'Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris.' Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 10):1347-53. 3. Das D, Kozbial P, et al. (2010) 'The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.' Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 10):125460. 4. Das D, Kozbial P, et al. (2009) 'Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution.' Proteins: Structure, Function, and Bioinformatics. Proteins. 75(2):296-307. 5. Xu Q, et al. (2009) 'A Structural Basis for the Regulatory Inactivation of DnaA.' J Mol Biol. 385(2):368-380. 6. Kozbial P, Xu Q, Chiu HJ, et al. (2008) 'Crystal structures of MW1337R and lin2004: Representatives of a novel protein family that adopt a four-helical bundle fold.' Proteins: Structure, Function, and Bioinformatics. 71(3):1589-1596. 7. Xu Q, Kozbial P, et al. (2008) 'Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritime at 2.70 Å resolution.' Proteins: Structure, Function, and Bioinformatics. 71(3):1546-1552. 8. Zubieta C, Krishna SS, Kapoor M, Kozbial P, et al. (2007) 'Crystal Structures of Two Novel Dye-decolorizing Peroxidases Reveal a β-barrel Fold with a Conserved Heme-binding Motif.' Proteins: Structure, Function, and Bioinformatics. 69(2):223-33. 9. Kozbial PZ, and Mushegian AR. (2005) 'Natural history of S-adenosylmethionine-binding proteins.' BMC Struct Biol. 5:19. 10. Sarnowski TJ, et al. (2005) 'SWI3 Subunits of Putative SWI/SNF Chromatin-Remodeling Complexes Play Distinct Roles during Arabidopsis Development. ' Plant Cell. (9):2454-72. Presented at international conferences in: Bethesda, MD  San Diego, CA Ventura, CA Lawrence, KS Vienna, Austria  Berlin, Germany Heidelberg, Germany Poznan, Poland. 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