Publications 2015

Labadorf A, Hoss AG, Lagomarsino V, Latourelle JC, Hadzi TC, Bregu J, MacDonald ME, Gusella JF, Chen JF, Akbarian S, Weng Z, Myers RH. (2015)
RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression.
Plos OneDec 4;10(12):e0143563. doi: 10.1371/journal.pone.0143563. (PMCID: PMC4670106)

Dong X*Tsuji J*, Labadorf A, Roussos P, Chen JF+, Myers RH+, Akbarian S+Weng Z+. (2015) 
The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington’s Disease. 
Plos OneDec 4;10(12):e0144398. doi: 10.1371/journal.pone.0144398. (PMCID: PMC4670094). 
*Joint first authors. +Co-corresponding authors.

Tsuji JWeng Z. (2015) 
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data
Brief Bioinform  Dec 1. pii: bbv103. [Epub ahead of print].

Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Weng Z, Senthil G+, Lehner T+, Sklar P+, Sestan N+.et.al. (2015) 
The PsychENCODE Project. 
Nat Neursci Nov 25;18(12):1707-12. doi: 10.1038/nn.4156. (PMCID: PMC4675669)

Tran H, Almeida S, Moore J, Gendron TF, Chalasani U, Lu Y, Du X, Nickerson JA, Petrucelli L, Weng Z, Gao FB (2015) 
Differential Toxicity of Nuclear RNA Foci versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS. 
Neuron Sep 23;87(6):1207-14. doi: 110.1016/j.neuron.2015.09.015. (PMCID: PMC4589299)[Available on 2016-09-23].

Wang W*, Han BW*, Tipping C, Ge DT, Zhang Z, Weng Z+Zamore PD+. (2015) Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms. 
Mol CellSept 3;59(5):819-30. doi: 10.1016/j.molcel.2015.08.007. (PMCID: PMC4560842)[Available on 2016-09-03] *Joint first authors. +Co-corresponding authors.

Tu S*, Wu MZ*, Wang J, Cutter AD, Weng Z+, Claycomb J+. (2015) 
Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes
Nucleic Acids Res Jan;43(1):208-24. doi: 10.1093/nar/gku1308. (PMCID: PMC4288196) 
*Joint first authors. +Co-corresponding authors.

Zhuang JWeng Z (2015) 
Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes. 
Nucleic Acids ResAug 17. pii:gkv831. (PMCID: PMC4787836).

Vreven T*, Moal IH*, Vangone A*, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jimenez-Garcia B, Bates PA+, Fernandez-Recio J+, Bonvin AM+, Weng Z+. (2015)
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version2.
J Mol Biol Sep 25;427(19):3031-41. doi: 10.1016/j.jmb.2015.07.016. (PMCID: PMC4677049)
*Joint first authors. +Co-corresponding authors.

Wang D*, Mou H*, Li S*, Li Y, Hough S, Tran K, Li J, Yin H, Anderson DG, Sontheimer EJ, Weng Z+, Gao G+, Xue W+. (2015) 
Adenvirus-Mediated Somatic Genome Editing of Pten by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses. 
Human Gene Ther. Jul;26/(7):432-42. doi: 10.1089/hum.2015.087. (PMCID: PMC4509492)
*Joint first authors. +Co-corresponding authors.

Li Y, Park A, Mou H, Cansu C, Bizhanova A, Akama-Garren E, Joshi N, Hendrickson EA, Feldser D, Yin H, Anderson DG, Jacks T, Weng Z+, and Xue W+. (2015)
A versatile reporter system for CRISPR-mediated chromosomal rearrangements.
Genome Biology. May 28;16:111.doi:10.1186/s13059-015-0680-7 (PMCID: PMC4465146)
+Co-corresponding authors.

Chou MT*, Han BW*, Hsiao CP, Zamore PD, Weng Z, Hung JH. (2015) 
Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
Nucleic Acids Res. May 24; pii: gkv537. (PMCID: PMC4632877) *Joint first authors.

Hoss AG, Labadorf A, Latourelle JC, Kartha VK, Hadzi TC, Gusella JF, MacDonald ME, Chen JF, Akbarian S, Weng Z, Vonsattel JP, Myers RH (2015) 
miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement. 
BMC Med Genomics 8(1):10. (PMCID: PMC4349621).

Marinov GK*, Wang J*, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF (2015) Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi's Genomic Targets Still Not Identified.
Dev. Cell Mar 23; 32(6):765-71. (PMCID: PMC4494788)
*Joint first authors.

Han BW*, Wang W*, Li C, Weng Z+, Zamore PD+. (2015) 
Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. 
Science May 15;348 (6236):817-21. (PMCID: PMC 4545291) *Joint first authors. +Co-corresponding authors.

Gao M*, Thomson TC*, Creed TM, Tu S, Loganathan SN, Jackson CA, McCluskey P, Lin Y, Collier SE, Weng Z,  Lasko P, Ohi MD, Arkov AL. (2015) 
Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements. 
EMBO Rep18: pii: e201439694. (PMCID: PMC4364877).

Han BW*, Wang W*, Zamore PD+, Weng Z+. (2015)
piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and
CAGE-seq, ChIP-seq and genomic DNA sequencing.

Bioinformatics Feb 15; 31(4):593-5. (PMCID: PMC 4325541)
*Joint first authors. +Co-corresponding authors.

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