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Publications 2011

Yildirim O, Li R, Hung J, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ+, Fazzio TG+. (2011) 
Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells. 
Cell. Dec 23;147(7):1498-510 (PMCID: PMC3252821).

Khurana JS*, Wang J*, Xu J, Koppetsch BS, Thomson TC, Nowosielska A, Li C, Zamore PD, Weng Z+, Theurkauf WE+. (2011) 
Adaptation to P Element Transposon Invasion in Drosophila melanogaster.  
Cell. Dec 23;147(7):1551-63. (PMCID: PMC3246748) *Joint first authors. 
+Co-corresponding authors.

Fleishman SJ, Hwang H, Vreven T, Pierce BG, Weng Z, Baker D. (2011) 
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
J Mol Biol. Nov 25;414(2):289-302. Epub 2011 Sep 29. (PMCID: PMC3839241).

Han BW, Hung JH, Weng Z, Zamore PD+, Ameres SL+. (2011) 
The 3'-to-5' Exoribonuclease Nibbler Shapes the 3' Ends of MicroRNAs Bound to Drosophila Argonaute1. 
Current Biology.  21, 1878-1887. (PMCID: PMC3236499) 
+Co-corresponding authors.

Zhang Z, Xu J, Koppetsch B.S., Wang J, Tipping C, Ma S, Weng Z+, Theurkauf WE+, Zamore PD+. (2011) 
Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3-ligase and Tudor Domains. 
Molecular Cell. 44, 572-584. (PMCID: PMC3236501) 
+Co-corresponding authors.

Shulha H*, Cheung I*, Whittle C, Wang J, Virgil D, Lin C, Guo Y, Lessard A, Akbarian S+ and Weng Z+. (2011) 
Epigenetic signatures of autism: trimethylated H3K4 landscapes in prefrontal neurons. 
Arch Gen Psychiatry  Supplementary Materials Mar; 69(3):314-24.  (NIHMSID: NIHMS549209)  
*Joint first authors. +Co-corresponding authors.

Pierce BG, Hourai Y, Weng Z. (2011) 
Accelerating protein docking in ZDOCK using an advanced 3D convolution library. 
PLoS One. 2011 Sep 19; 6(9): e24657. (PMCID: PMC3176283).

Hung J, Yang TH, Hu Z, Weng Z+, Delisi C+. (2011) 
Gene set enrichment analysis: performance evaluation and usage guidelines. 
Brief Bioinform. Sep 7. (PMCID: PMC3357488) 
+Co-corresponding authors.

Bonsor DA, Postel S, Pierce BG, Wang N, Zhu P, Buonpane RA, Weng Z, Kranz DM, Sundberg EJ. (2011) 
Molecular Basis of a Million-Fold Affinity Maturation Process in a Protein-Protein Interaction. 
J Mol BiolAug 12;411(2):321-8.(PMCID: PMC3143254).

Hwang H*, Vreven T*, Whitfield TW, Wiehe K, Weng Z.(2011) 
A machine learning approach for the prediction of protein surface loop flexibility. 
Proteins 2011 Aug;79(8):2467-74. doi: 10.1002/prot.23070 (PMCID: PMC3341935)
*Joint first authors.

Vreven T, Hwang H, Weng Z.(2011) 
Integrating atom-based and residue-based scoring functions for protein-protein docking. 
Protein SciJul 7. Doi: 10.1002/pro.687 (PMCID: PMC3190152).

Jee J*, Rozowsky J*, Yip KY*, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M (2011) 
ACT: aggregation and correlation toolbox for analyses of genome tracks. 
Bioinformatics 2011 Apr 15; 27(8):1152-4 (PMCID: PMC3072554)
*Joint first authors.

Myers RM, ENCODE Project Consortium, Dekker J, Lajoie BR, Sanyal A, Weng Z, Whitfield TW, Wang J. et. al (2011)
A User’s Guide to the Encyclopedia of DNA Elements (ENCODE). 
Plos Biol 2011;9(4):e1001046. doi:10.1371/journal.pbio.1001046. (PMCID: PMC3079585).

Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung J, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC. (2011) 
Deep annotation of Drosophila melanogaster micro RNAs yields insights into their processing, modification, and emergence. 
Genome Res. Feb;21(2):203-15. (PMCID: PMC3032924).