Anton Valouev

Professional Education

• Doctor of Philosophy, University of Southern California (2006)

Faculty Advisor

• Arend Sidow

Web Site Links

• My research web page

Research Interests

My research mainly addresses various aspects of chromatin function. One example is how local organization of chromatin affects its transcriptional and regulatory state. Answering these kind of question typically involves understanding interactions between different aspects of chromtain such as nucleosome-mediated packaging of DNA, local occupancy by the transcription factors, and presence of epigenetic signatures such as DNA methylation and histone modifications at individual loci .

In addressing these questions, I leverage data from high-throughput sequencing assays to build and analyze genome-wide high resolution maps of chromatin state that provide global and local insights into chromatin function and how it changes over time.

Publications

• Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Valouev A,  Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A.  Nat Methods.  2008;
• A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Valouev A,  Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM.  Genome Res.  2008; 18 (7): 1051-63
• A quantile method for sizing optical maps. Li H,  Valouev A, Schwartz DC, Waterman MS, Li LM.  J Comput Biol.  2007; 14 (3): 255-66
• An algorithm for assembly of ordered restriction maps from single DNA molecules. Valouev A,  Schwartz DC, Zhou S, Waterman MS.  Proc Natl Acad Sci U S A.  2006; 103 (43): 15770-5
• Alignment of optical maps. Valouev A,  Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y, Waterman MS.  J Comput Biol.  2006; 13 (2): 442-62
• Refinement of optical map assemblies. Valouev A,  Zhang Y, Schwartz DC, Waterman MS.  Bioinformatics.  2006; 22 (10): 1217-24