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Publications 2014

Zhuang J, Wang J, Theurkauf W+, Weng Z+. (2014) 
TEMP: a computational method for analyzing transposable element polymorphism in populations. 
Nucleic Acids ResApr 21. (PMCID: PMC4066757) +Co-corresponding authors.

Pierce BG, Weng Z+, Baker BM+. (2014) 
Computational design of the affinity and specificity of a therapeutic T cell receptor. 
Plos Comput Biol Feb 13;10(2):e1003478. doi: 10.1371/journal.pcbi.1003478. eCollection (PMCID:PMC3923660). +Co-corresponding authors.

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC+, Snyder MP+. (2014) 
Principles of regulatory information conservation between mouse and human. 
Nature.  Nov 20; 515(7527):371-5. (PMCID: PMC4343047).

Bai G, Cheung I, Shulha HP, Coelho JE, Li P, Dong X, Jakovcevski M, Wang Y, Grigorenko A, Jiang Y,  Hoss A, Patel K,
Zheng M, Rogaev E, Myers RH+, Weng Z+, Akbarian S+, Chen JF+. (2014) 
Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains. 
Hum Mol Genet2015 Mar 1; 24(5) 1441-56 doi:10.1093/hmg/ddu561 Epub Dec 5. (PMCID: PMC4321450) 
+Co-corresponding authors.

Wang W*, Yoshikawa M*, Han BW, Izumi N, Tomari Y+, Weng Z+, Zamore PD+.(2014) 
The Initial Uridine of Primary piRNAs Does Not Create the Tenth Adenine that Is the Hallmark of Secondary piRNAs. 
Mol Cell. Dec 4; 56(5):708-16. (PMCID: PMC 4337030) *Joint first authors. +Co-corresponding authors.

Pierce BG+, Vreven T, Weng Z+. (2014) 
Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. 
BMC Bioinformatics. 15(1):319. (PMCID: PMC4261541) +Co-corresponding authors.

Shen E, Shulha H, Weng Z, Akbarian S. (2014) 
Regulation of histone H3K4 methylation in brain development and disease. 
Philos Trans R Soc Lond B Biol Sci. Sep 26; 369(1652). (PMCID: PMC4142035).

Kellis M+, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC+. (2014) 
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. 
Proc Natl Acad Sci USA. Aug 19; 111(33):E3366. (PMCID: PMC4143047).

Yildirim O, Hung JH, Cedeno RJ, Weng Z, Lengner CJ, Rando OJ. (2014) 
A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters
PLoS Genet. Aug; 10(8):e1004515. (PMCID: PMC4125098).

Carone BR, Hung JH, Hainer SJ, Chou MT, Carone DM, Weng Z, Fazzio TG, Rando OJ. (2014) 
High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. 
Dev Cell. Jul 14; 30(1):11-22. (PMCID: PMC4184102).

Babcock GJ*, Iyer S*, Smith HL*, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. (2014) 
High-throughput sequencing analysis of post-liver transplantation HCV e2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody.
PLoS One.  9(6):e100325. (PMCID: PMC4067308) *Joint first authors.

Pierce BG+, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z+. (2014) 
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. 
BioinformaticsJune 15;30(12):1771-3.doi:10.1093. Epub Feb 14. (PMCID: PMC4058926). +Co-corresponding authors.

Zhang Z, Wang J, Schultz N, Zhang F, Parhad S, Tu SVreven T, Zamore P, Weng Z+, Theurkauf W+. (2014) 
The HP1 Homolog Rhino Anchors a Nuclear Complex that Supresses piRNA Precursor Splicing. 
Cell June 5: 157(6):1353-1363 (PMCID: PMC4167631) +Co-corresponding authors.

Trastoy B, Lomino JV, Pierce BG, Carter LG, Günther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang LX, Sundberg EJ. (2014) 
Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. 
Proc Natl Acad Sci U S A.  May 6; 111(18):6714-9. (PMCID: PMC4020096).

Kellis M+, Wold B, Snyder MP, Bernstein BE, Kundaje A*, Marinov GK*, Ward LD*, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC+. (2014) 
Defining functional DNA elements in the human genome. 
Proc Natl Acad Sci U S A. Apr 29; 111(17):6131-8. (PMCID: PMC4035993).

Haidar JN+, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z+. (2014)
Backbone Flexibility of CDR3 and Immune Recognition of Antigens. 
J Mol Biol. Apr 3; 426(7):1583-99. (PMID: 24380763) [Pub Med – Indexed for MEDLINE] 
+Co-corresponding authors.

Zhang Z, Koppetsch BS, Wang J, Tipping C, Weng Z, Theurkauf WE, Zamore PD. (2014) 
Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin. 
EMBO J. Mar 18; 33(6):536-9. (PMCID: PMC3989648).

Chen W, Shulha HP, Patel AA, Yan J, Green KM, Query CC, Rhind N, Weng Z, Moore MJ. (2014) 
Endogenous U2· U5· U6 snRNA complexes in S. pombe are intron lariat spliceosomes. 
RNAMar;20(3):308-20. Doi: 10.1261/rna.040980.113.  (PMCID: PMC3923126).

Hoss AG, Kartha VK, Dong X, Latourelle JC, Dumitriu A, Hadzi TC, Macdonald ME, Gusella JF, Akbarian S, Chen JF, Weng Z, Myers RH. (2014) 
Micro RNAs Located in the Hox Gene Clusters Are Implicated in Huntington's Disease Pathogenesis. 
PLoS Genet.  Feb; 10(2):e1004188. (PMCID: PMC3937267).

Pierce BG*, Hellman LM*, Hossain M, Singh NK, Vander Kooi CW, Weng Z+, Baker BM+. (2014) 
Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor. 
PLoS Comput Biol. Feb 13;10(2):e1003478. doi: 10.1371/journal.pcbi.1003478. (PMCID: PMC3923660).   
*Joint first authors. +Co-corresponding authors.