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Publications 2012

Shulha HP*, Crisci JL*, Reshetov D*, Tushir JS*, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI+, Jensen JD+, Weng Z+ and Akbarian S+. (2012) 
Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. 
PLoS Biol. Nov;10(11):e1001427. (PMCID: PMC3502543) 
*Joint first authors. Co-corresponding authors.

Zhang F*, Wang J*, Xu J, Zhang Z, Koppetsch BS, Schultz N, Vreven T, Meignin C, Davis I, Zamore PD, Weng Z+and Theurkauf WE+. (2012) 
UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery. 
Cell. Nov 9;151(4):871-84. (PMCID: PMC3499805) *Joint first authors.  +Co-corresponding authors.

Singh G*, Kucukural A*, Cenik C, Leszyk JD, Shaffer SA, Weng Z and Moore MJ. (2012)
The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus. 
Cell. Nov 9;151(4):750-64. (PMCID: PMC3522173) *Joint first authors.

Fukunaga R, Han BW, Hung JH, Xu J, Weng Z and Zamore PD. (2012)
Dicer partner proteins tune the length of mature miRNAs in flies and mammals.
Cell. Oct 26;151(3):533-46. (PMCID: PMC3609031).

Zhang Z, Theurkauf WE, Weng Z, Zamore PD. (2012) 
Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. 
Silence Dec 28; 3(1)9. doi:10.1186/1758-907X-3-9. (PMCID: PMC3552703).

The ENCODE Project Consortium (2012) 
An integrated encyclopedia of DNA elements in the human genome. 
Nature Sep 6;489(7414):57-74. doi: 10.1038/nature11247. (PMCID: PMC3439153).

Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carnici P, Lassman T,Gingeras TR, Guigo R, Birney E, Weng Z, Snyder M, Gerstein M. (2012) 
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. 
Genome ResSep;22(9): 1658-67. (PMCID: PMC3431483).

Hawse WF, Champion MM, Joyce MV, Hellman LM, Houssain M, Ryan V, Pierce BG+, Weng Z+, Baker BM. (2012) 
Cutting Edge: Evidence for a dynamically driven T cell signaling mechanism. 
Journal of Immunology. (PMCID: PMC3375328).

Dong XGreven M, Kundaje A, Djebali S, Brown JB, Cheng C, Gerstein M, Guigó Serra R, Birney E, Weng Z. (2012) 
Modeling gene expression using chromatin features in various cellular contexts. 
Genome BiologyCode and Data  Sep 5;13(9):R50. (PMCID: PMC3491397).

Whitfield T, Wang J, Collins PJ, Partridge CE, Trinklein ND, Myers RM, Weng Z. (2012) 
Functional analysis of transcription factor binding sites in human promoters. 
Genome Biology. Sep 5;13(9):R50. (PMCID: PMC3491394).

Wang J*, ZhuangJ*, Iyer S*, Lin XY*, Whitfield TW, Greven M, Pierce BG, DongX, Kundaje  A, ChengY, Rando OJ, BirneyE, MyersRM, NobleWS, SnyderM, Weng Z. (2012) 
Sequence Features and Chromatin Structure around the Genomic Regions Bound by 119 Human Transcription Factors. 
Genome Research. Sep;22(9):1798-812. (PMCID: PMC3431495) *Joint first authors.

Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. (2012) 
Exploring the DNA-recognition potential of homeodomains. 
Genome Research.  Apr 26. (PMCID: PMC3460184).

Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P+, Weng Z+, Rhind N+. (2012) 
Genome-wide identification and characterization of replication origins by deep sequencing. 
Genome Biology. Apr 24;13(4):R27. (PMCID: PMC3446301) 
+Co-corresponding authors.

Vreven T, Hwang H, Pierce BG+, Weng Z+. (2012) 
Prediction of protein-protein binding free energies. 
Protein Science. Mar:21(2) 396-404. (PMCID:3375440) 
+Co-corresponding authors.

Hoffman M, Buske O, Wang J, Weng Z, Blimes J, Noble W. (2012).
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. 
Nature Methods. Mar 18;9(5):473-6. (PMCID: PMC3340533).

Xie J, Ameres SL, Friedline R, Hung JH, Zhang Y, Xie Q, Zhong L, Su Q, He R, Li M, Li H, Mu X, Zhang H, Broderick JA, Kim JK, Weng Z, Flotte TR, Zamore PD+, Gao G+. (2012).
Long-term, efficient inhibition of microRNA function in mice using rAAV vectors.
Nature Methods. Mar 4;9(4):403-9. (PMCID: PMC3420816) 
+Co-corresponding authors.