PIOTR Z - Marta & Piotr Kozbial

PIOTR Z. KOZBIAL, PH.D.
3177 Via Alicante, Unit 149  La Jolla, CA 92037
Cell: (858) 260-1005  pkozbial@gmail.com  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:
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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
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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
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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.
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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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