Curriculum Vitae

I was born in Sofia, Bulgaria.

199991 German Language School 'Prof. Konstantin Galabov' in Sofia, Bulgaria.
1999 - 2000Computer science at the University of Sofia 'St. Kliment Ohridski', Bulgaria.
2000 - 2002Computer science at the Technical University in Berlin, Germany. (Vordiplom)
2002 - 2006Computer science at the Free University in Berlin, Germany. (Diplom, which is equivalent to a MSc degree)
2007 - 2011MA Electronic Media at the University of Sofia 'St. Kliment Ohridski', Sofia, Bulgaria.
2011 - presentworking on my PhD in Bioinformatics at the University of California, Los Angeles.

1999 - 2000State Scholar at the University of Sofia (high GPA)
2003RECOMB Travel Fellowship for presenting a poster
2011 - 20121st year Bioinformatics IDP Fellowship, UCLA
2013 - 2014Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research Pre-doctoral Fellowship in Stem Cell Science
2014 - 2015California Institute for Regenerative Medicine Pre-doctoral Fellowship
2015 - presentEli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research Pre-doctoral Fellowship in Stem Cell Science

Professional Experience
2/2001 - 9/2002: Bioinformatician at metaGen Pharmaceuticals GmbH
I was part of the sequence analysis group in metaGen Pharmaceuticals GmbH, a spin-off company of Schering AG focused on cancer research. During this time I worked with Dr. Artemis Hatzigeorgiou on three pieces of software that use artificial neural networks to predict coding regions in DNA, translation initiation sites in ESTs and stretches of signal peptides in proteins. Later, I continued to work with Dr. Eike Staub and Dr. Bernd Hinzmann on various other projects in the field of gene and protein annotation.

4/2002 - 9/2002: Research assistant at the Free University of Berlin
I worked with Jurgen Kleffe at the Free University in Berlin on a piece of gene prediction software based on Markov chains. From September 2001 to February 2002 I worked with him also on a small project about suffix trees and their application in clustering expressed sequence tags.

10/2002 - 4/2003: Research scholar at the Penn Center for Bioinformatics, University of Pennsylvania
I worked with Dr. Artemis Hatzigeorgiou on two projects about microRNA genetics and posttranscriptional gene regulation by microRNAs. We developed one of the first software tools for micro-RNA target prediction (DIANA-MicroT Analyzer).

4/2003 - 8/2004: Research assistant at the Max Planck Institute for Molecular Genetics
I worked in the Gene Regulation Group lead by Prof. Martin Vingron with Dr. Stephan Ropcke. My job was to find new RNA editing sites using computational approaches. Within this project we developed a web interface for structured visualization of sequence conservation.

4/2005 - 4/2006: Research assistant at the Max Planck Institute for Molecular Genetics
I joined again the CMB department this time to work on my diploma thesis. In the summer of 2005 I visited Harvard Medical School in Boston, where I collaborated with Debora Marks on a project about understanding the networks of microRNA - mRNA interactions. This gave rise to the subject of my diploma thesis, which was the uniform generation of random directed graphs with prescribed degree sequence. This work was supervised by Prof. Martin Vingron.

3/2007 - 3/2008: Software developer at Metalife Bulgaria
I developed software for the biotech industry that integrates multiple public and proprietary databases and allows versatile algorithmic analysis.

2007 - 2009: Adjunct Lecturer at the University of Sofia
I lectured parts of the class "Introduction to Computational Biology" for three semesters at the Faculty of Mathematics and Informatics of the University of Sofia "St. Kliment Ohridski".

4/2008 - 8/2011: Software developer at Blue Edge Bulgaria
I worked on natural language processing projects and did web development for the online gambling industry using Django, Tornado, Google App Engine and other cool Python stuff.

9/2011 - present: doing my PhD in Bioinformatics at UCLA
Currently I am a member of Jason Ernst's lab where I work on machine learning methods for chromatin states dynamics.

Programming languages C, C++, C#, Java, Perl, Python, Ruby, Javascript, SQL.
Databases MS SQL, mySQL, Oracle.
Operating systems Windows, Linux, Solaris, Minix.
Web technologies (D)HTML, Django and the like, JQuery, CGI, ASP, ASP.NET, Google App Engine.
Other Matlab, interfaces for parallel programming (MPI, JPVM), administration of local networks, office software.

1. Artemis G. Hatzigeorgiou, Petko Fiziev, Martin Reczko: DIANA-EST: a statistical analysis. Bioinformatics 17(10): 913-919 (2001)

2. Martin Reczko, Petko Fiziev, Eike Staub, Artemis G. Hatzigeorgiou: Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networks. WABI 2002: 60-67

3. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A.: A combined computational-experimental approach predicts human microRNA targets.Genes Dev. 2004 May 15;18(10):1165-78. Epub 2004 May 06.

4. Staub E, Fiziev P, Rosenthal A, Hinzmann B.: Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.Bioessays, 2004 May;26(5):567-81

5. Staub, E., Fiziev, P., Rosenthal, A. and Hinzmann, B. The nucleolar proteome and the (endosymbiotic) origin of the nucleus - Response. Bioessays, 2004, 26, 1145-1147.

6. Stefan Roepcke, Petko Fiziev, Peter Seeburg, Martin Vingron: SVC: Structured Visualization of Evolutionary Sequence Conservation. Nucleic Acids Res. 2005 Jul 1;33(Web Server Issue):W271-3.

7. Petko Fiziev: Uniform generation of random directed graphs with prescribed degree sequence. Diploma Thesis.

8. Petko Fiziev: Pseudoscientific theories and practices. (in Bulgarian) Business Magazine, June 2008.

9. Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun, Michael Q Zhang, Pao-Yang Chen and Matteo Pellegrini. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data BMC Genomics, 2013.

10. Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, Heffernan TP, Horner JW, Ekmekcioglu S, Lazar A, Ernst J, Chin L. Dual Roles of RNF2 in Melanoma Progression. Cancer Discovery, 2015.

11. Constantinos Chronis*, Petko Fiziev*, Bernadett Papp, Stefan Butz, Giancarlo Bonora, Shan Sabri, Jason Ernst, Kathrin Plath. Cooperative Binding of Transcription Factors Orchestrates Reprogramming. Cell, 2017. (UCLA press release, CIRM highlights)

12. Petko Fiziev*, Kadir C. Akdemir*, John P. Miller, Emily Z. Keung, Neha S. Samant, Sneha Sharma, Christopher A. Natale, Christopher J. Terranova, Mayinuer Maitituoheti, Samirkumar B. Amin, Emmanuel Martinez-Ledesma, Mayura Dhamdhere, Jacob B. Axelrad, Amiksha Shah, Christine S. Cheng, Harshad Mahadeshwar, Sahil Seth, Michelle C. Barton, Alexei Protopopov, Kenneth Y. Tsai, Michael A. Davies, Benjamin A. Garcia, Ido Amit, Lynda Chin, Jason Ernst, Kunal Rai. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Reports, 2017.

* Co-first author

Conference Talks
1. Systematic detection and analysis of epigenomic changes during melanoma cancer progression. 2013 RECOMB/ISCB conference on Regulatory and Systems Genomics, with DREAM Challenges in Toronto, Canada.
2. Systematic Detection of Spatio-temporal Patterns of Epigenetic Changes. 2014 RECOMB/ISCB conference on Regulatory and Systems Genomics, with DREAM Challenges in San Diego, USA, and UC Bioengineering Symposium 2015, Santa Cruz, USA.

Conferences Posters
1. Finding signal peptides in human protein sequences using recurrent neural networks, RECOMB 2003 in Berlin, Germany.
2. BS Seeker 2: Enhanced algorithmic pipeline for analysis of large scale bisulfite sequencing and reduced representation bisulfite sequencing data, ISMB 2012 in Long Beach, USA.
3. Systematic detection of differential chromatin from multiple epigenomic maps with application to stem cell reprogramming in mouse. ISMB 2014 in Boston, USA.
4. Computational method for detecting patterns of epigenetic changes from time series ChIP-seq data. ISMB 2015 in Dublin, Ireland (Wiley Poster Prize).

Bulgarian, German, English, Russian.

petko.fiziev [at]
(interpret "[at]" as @, an action against web-robots collecting email adresses for spam mail)

Petko Fiziev's personal blog