Anton Valouev

Ph.D.

E-mail: valouev@stanford.edu

I am currently a postdoctoral researcher at Arend Sidow's lab at the Dept. of Pathology at Stanford.

Resume [pdf]

Current Projects

1. High-resolution maps of nucleosome organization of chromatin in purified human blood cells. (with Andy Fire and Steve Johnson)

2. Regulatory circutry of cellular reprogramming (with Ziyang Ma and Joanna Wysocka)

Software Tools

1. QuEST: ChIP-Seq data analysis software incorporating UCSC browser data visulization

Papers

1. Gracey LE, Chen ZY, Maniar JM, Valouev A , Sidow A, Kay MA, Fire AZ
“An in vitro-identified high affinity nucleosome positioning signal is capable of transiently positioning nucleosome in vivo”
for submission, Nov 2009

2. Peng J, Valouev A , Swigut T, Zhang J, Zhao Y, Sidow A, and Wysocka J
“Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells”
Cell, Nov 2009 (in press)

3. Brunner^* AL, Johnson^* DS, Kim^* SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM.
“Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver"
Genome Research, Jun 2009 [ pdf ]

4. Valouev^* A, Johnson^* DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM and Sidow A.
“Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data”
Nature Methods, Sep 2008 [ pdf ] [ web page ]

5. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, and Johnson SM.
“A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning”
Genome Research, Jul 2008 [ pdf ]

6. Li H, Valouev A, Schwartz DC, Waterman MS and Li L.
“A quantile method for sizing optical maps”
Journal of Computational Biology, Apr 2007 [ pdf ]

7. Valouev A, Schwartz DC, Zhou S, and Waterman MS.
“An algorithm for assembly of ordered restriction maps from single DNA molecules”
PNAS, Oct 2006 [ pdf ][ software ]

8. Valouev^* A, Zhang^* Y, Schwartz DC, and Waterman MS.
“Refinement of optical map assemblies”
Bioinformatics, May 2006 [ pdf ][ software ]

9. Valouev A, Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y, and Waterman MS.
“Alignment of optical maps”
Journal of Computational Biology, Mar 2006 [ pdf ][ software ]

Thesis

1. Anton Valouev
“Shotgun optical mapping: a comprehensive statistical and computational analysis”
Ph.D. Thesis 2006 [ pdf ]

Last modified: 11-05-2009