Publications

1. Tellier J, Shi W, Minnich M, Liao Y, Crawford S, Smyth GK, Kallies A, Busslinger M and Nutt SL. Blimp1 controls plasma cell function through regulation of immunoglobulin secretion and the unfolded protein response. Nature Immunology. Accepted on 30 September 2015
2. Vasanthakumar A, Moro K, Xin A, Liao Y, Gloury R, Kawamoto S, Fagarasan S, Mielke LA, Afshar-Sterle S, Masters SL, Nakae S, Saito H, Wentworth JM, Li P, Liao W, Leonard WJ, Smyth GK, Shi W, Nutt SL, Koyasu S and Kallies A. The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue-resident regulatory T cells. Nature Immunology. 2015 Mar;16(3):276-85. PMID: 25599561
3. Shi W, Liao Y, Willis SN, Taubenheim, N, Inouye M, Tarlinton DM, Smyth GK, Hodgkin PD, Nutt SL and Corcoran LM. Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells. Nature Immunology, 2015 Jun;16(6):663-73. PMID: 25894659
4. Su Z, Łabaj PP, Li S, Thierry-Mieg J, Thierry-Mieg D, Shi W, Wang C, Schroth GP, Setterquist RA, Thompson JF, et al. (162 authors ,SEQC/MAQC-III Consortium). A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology. 2014 Sep;32(9):903-14. PMID: 25150838
5. Liao Y, Smyth GK and Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. PMID: 24227677
6. Tang JZ, Carmichael CL, Shi W, Metcalf D, Ng AP, Hyland CD, Jenkins NA, Copeland NG, Howell VM, Zhao ZJ, Smyth GK, Kile BT and Alexander WS. Transposon mutagenesis reveals cooperation of ETS family transcription factors with signaling pathways in erythro-megakaryocytic leukemia. Proceedings of the National Academy of Sciences of the United States of America. 2013 Apr 9;110(15):6091-6. PMID: 23533276
7. Liao Y, Smyth GK and Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research. 2013 May 1;41(10):e108. PMID: 23558742
8. Shi W, Oshlack A and Smyth GK. Optimizing the noise versus bias trade-off for Illumina Whole Genome Expression BeadChips. Nucleic Acids Research. 2010 Dec;38(22):e204. PMID: 20929874
9. Shi W, de Graaf CA, Kinkel SA, Achtman AH, Baldwin T, Schofield L, Scott HS, Hilton DJ and Smyth GK. Estimating the proportion of microarray probes expressed in an RNA sample. Nucleic Acids Research. 2010 Apr;38(7):2168-76. PMID: 20056656
10. Shi W, Banerjee A, Ritchie ME, Gerondakis S and Smyth GK. Illumina WG-6 BeadChip strips should be normalized separately. BMC Bioinformatics. 2009 Nov 11;10:372. PMID: 19903361