Yang Liao

Sex-specific adipose tissue imprinting of regulatory T cells

Ajithkumar Vasanthakumar, David Chisanga, Jonas Blume, Renee Gloury, Kara Britt, Darren C Henstridge, Yifan Zhan, Santiago Valle Torres, Sebastian Liene, Nicholas Collins, Enyuan Cao, Tom Sidwell, Chaoran Li, Raul German Spallanzani, Yang Liao, Paul A Beavis, Thomas Gebhardt, Natalie Trevaskis, Stephen L Nutt, Jeffrey D Zajac, et al.

Journal article  |  2020  |  Nature

Adipose tissue is an energy store and a dynamic endocrine organ1,2. In particular, visceral adipose tissue (VAT) is critical for t..

Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis

Tom Sidwell, Yang Liao, Alexandra L Garnham, Ajithkumar Vasanthakumar, Renee Gloury, Jonas Blume, Peggy P Teh, David Chisanga, Christoph Thelemann, Fabian de Labastida Rivera, Christian R Engwerda, Lynn Corcoran, Kohei Kometani, Tomohiro Kurosaki, Gordon K Smyth, Wei Shi, Axel Kallies

Journal article  |  2020  |  Nature Communications

Differentiation and homeostasis of Foxp3+ regulatory T (Treg) cells are strictly controlled by T-cell receptor (TCR) signals; howe..

IRF4 Activity Is Required in Established Plasma Cells to Regulate Gene Transcription and Mitochondrial Homeostasis

Michael Sze Yuan Low, Erica J Brodie, Pasquale L Fedele, Yang Liao, George Grigoriadis, Andreas Strasser, Axel Kallies, Simon N Willis, Julie Tellier, Wei Shi, Sarah Gabriel, Kristy O'Donnell, Catherine Pitt, Stephen L Nutt, David Tarlinton

Journal article  |  2019  |  Cell Reports

The transcription factor interferon regulatory factor 4 (IRF4) is critical for the development, maintenance, and function of plasm..

Transcription Factor T-bet in B Cells Modulates Germinal Center Polarization and Antibody Affinity Maturation in Response to Malaria

Ann Ly, Yang Liao, Halina Pietrzak, Lisa J Ioannidis, Tom Sidwell, Renee Gloury, Marcel Doerflinger, Tony Triglia, Raymond Z Qin, Joanna R Groom, Gabrielle T Belz, Kim L Good-Jacobson, Wei Shi, Axel Kallies, Diana S Hansen

Journal article  |  2019  |  Cell Reports

Despite the key role that antibodies play in protection, the cellular processes mediating the acquisition of humoral immunity agai..

TCF-1 limits the formation of Tc17 cells via repression of the MAF-ROR gamma t axis

Lisa A Mielke, Yang Liao, Ella Bridie Clemens, Matthew A Firth, Brigette Duckworth, Qiutong Huang, Francisca F Almeida, Michael Chopin, Hui-Fern Koay, Carolyn A Bell, Soroor Hediyeh-Zadeh, Simone L Park, Dinesh Raghu, Jarny Choi, Tracy L Putoczki, Philip D Hodgkin, Ashley E Franks, Laura K Mackay, Dale Godfrey, Melissa J Davis, et al.

Journal article  |  2019  |  Journal of Experimental Medicine

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

Yang Liao, Gordon K Smyth, Wei Shi

Journal article  |  2019  |  Nucleic Acids Research

c-Maf-dependent T-reg cell control of intestinal T(H)17 cells and IgA establishes host-microbiota homeostasis

Christian Neumann, Jonas Blume, Urmi Roy, Peggy P Teh, Ajithkumar Vasanthakumar, Alexander Beller, Yang Liao, Frederik Heinrich, Teresita L Arenzana, Jason A Hackney, Celine Eidenschenk, Eric JC Galvez, Christina Stehle, Gitta A Heinz, Patrick Maschmeyer, Tom Sidwell, Yifang Hu, Derk Amsen, Chiara Romagnani, Hyun-Dong Chang, et al.

Journal article  |  2019  |  Nature Immunology

Tailored NEOadjuvant epirubicin, cyclophosphamide and Nanoparticle Albumin-Bound paclitaxel for breast cancer: The phase II NEONAB trial-Clinical outcomes and molecular determinants of response

Caitlin Murphy, Andrea Muscat, David Ashley, Violet Mukaro, Linda West, Yang Liao, David Chisanga, Wei Shi, Ian Collins, Sally Baron-Hay, Sujata Patil, Geoffrey Lindeman, Mustafa Khasraw

Journal article  |  2019  |  PloS one

IMiDs prime myeloma cells for daratumumab-mediated cytotoxicity through loss of Ikaros and Aiolos

Pasquale L Fedele, Simon N Willis, Yang Liao, Michael S Low, Jai Rautela, David H Segal, Jia-Nan Gong, Nicholas D Huntington, Wei Shi, David CS Huang, George Grigoriadis, Julie Tellier, Stephen L Nutt

Journal article  |  2018  |  Blood

Plasmacytoid dendritic cell heterogeneity is defined by CXCL10 expression following TLR7 stimulation

Casper Marsman, Fanny Lafouresse, Yang Liao, Tracey M Baldwin, Lisa A Mielke, Yifang Hu, Matthias Mack, Paul J Hertzog, Carolyn A de Graaf, Wei Shi, Joanna R Groom

Journal article  |  2018  |  Immunology and Cell Biology

Mining the Plasma Cell Transcriptome for Novel Cell Surface Proteins

Stephanie Trezise, Alexander Karnowski, Pasquale L Fedele, Sridurga Mithraprabhu, Yang Liao, Kathy D'Costa, Andrew J Kueh, Matthew P Hardy, Catherine M Owczarek, Marco J Herold, Andrew Spencer, Wei Shi, Simon N Willis, Stephen L Nutt, Lynn M Corcoran

Journal article  |  2018  |  International Journal of Molecular Sciences

Chimeric antigen receptor T cells form nonclassical and potent immune synapses driving rapid cytotoxicity

AJ Davenport, RS Cross, KA Watson, Y Liao, W Shi, HM Prince, PA Beavis, JA Trapani, MH Kershaw, DS Ritchie, PK Darcy, PJ Neeson, MR Jenkins

Journal article  |  2018  |  Proceedings of the National Academy of Sciences

A point mutation in the Ncr1 signal peptide impairs the development of innate lymphoid cell subsets

Francisca F Almeida, Sara Tognarelli, Antoine Marcais, Andrew J Kueh, Miriam E Friede, Yang Liao, Simon N Willis, Kylie Luong, Fabrice Faure, Francois E Mercier, Justine Galluso, Matthew Firth, Emilie Narni-Mancinelli, Bushra Rais, David T Scadden, Francesco Spallotta, Sandra Weil, Ariane Giannattasio, Franziska Kalensee, Tobias Zoeller, et al.

Journal article  |  2018  |  OncoImmunology

Transcription Factor IRF4 Promotes CD8( ) T Cell Exhaustion and Limits the Development of Memory-like T Cells during Chronic Infection

Kevin Man, Sarah S Gabriel, Yang Liao, Renee Gloury, Simon Preston, Darren C Henstridge, Marc Pellegrini, Dietmar Zehn, Friederike Berberich-Siebelt, Mark A Febbraio, Wei Shi, Axel Kallies

Journal article  |  2017  |  Immunity

Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB

Simon N Willis, Julie Tellier, Yang Liao, Stephanie Trezise, Amanda Light, Kristy O'Donnell, Lee Ann Garrett-Sinha, Wei Shi, David M Tarlinton, Stephen L Nutt

Journal article  |  2017  |  Nature Communications

An update on using CRISPR/Cas9 in the one-cell stage mouse embryo for generating complex mutant alleles

Andrew J Kueh, Martin Pal, Lin Tai, Yang Liao, Gordon K Smyth, Wei Shi, Marco J Herold

Journal article  |  2017  |  Cell Death & Differentiation

The TNF Receptor Superfamily-NF-kappa B Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues

Ajithkumar Vasanthakumar, Yang Liao, Peggy Teh, Maria F Pascutti, Anna E Oja, Alexandra L Garnham, Renee Gloury, Jessica C Tempany, Tom Sidwell, Eloy Cuadrado, Paul Tuijnenburg, Taco W Kuijpers, Najoua Lalaoui, Lisa A Mielke, Vanessa L Bryant, Philip D Hodgkin, John Silke, Gordon K Smyth, Martijn A Nolte, Wei Shi, et al.

Journal article  |  2017  |  Cell Reports

Effector Regulatory T Cell Differentiation and Immune Homeostasis Depend on the Transcription Factor Myb

Sheila Dias, Angela D'Amico, Erika Cretney, Yang Liao, Julie Tellier, Christine Bruggeman, Francisca F Almeida, Jamie Leahy, Gabrielle T Belz, Gordon K Smyth, Wei Shi, Stephen L Nutt

Journal article  |  2017  |  Immunity

Dynamic changes in Id3 and E-protein activity orchestrate germinal center and plasma cell development

Renee Gloury, Dimitra Zotos, Malou Zuidscherwoude, Frederick Masson, Yang Liao, Jhaguaral Hasbold, Lynn M Corcoran, Phil D Hodgkin, Gabrielle T Belz, Wei Shi, Stephen L Nutt, David M Tarlinton, Axel Kallies

Journal article  |  2016  |  The Journal of Experimental Medicine

Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes

Laura K Mackay, Martina Minnich, Natasja AM Kragten, Yang Liao, Benjamin Nota, Cyril Seillet, Ali Zaid, Kevin Man, Simon Preston, David Freestone, Asolina Braun, Erica Wynne-Jones, Felix M Behr, Regina Stark, Daniel G Pellicci, Dale I Godfrey, Gabrielle T Belz, Marc Pellegrini, Thomas Gebhardt, Meinrad Busslinger, et al.

Journal article  |  2016  |  Science

A molecular threshold for effector CD8( ) T cell differentiation controlled by transcription factors Blimp-1 and T-bet

Annie Xin, Frederick Masson, Yang Liao, Simon Preston, Tianxia Guan, Renee Gloury, Moshe Olshansky, Jian-Xin Lin, Peng Li, Terence P Speed, Gordon K Smyth, Matthias Ernst, Warren J Leonard, Marc Pellegrini, Susan M Kaech, Stephen L Nutt, Wei Shi, Gabrielle T Belz, Axel Kallies

Journal article  |  2016  |  Nature Immunology

Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response

Julie Tellier, Wei Shi, Martina Minnich, Yang Liao, Simon Crawford, Gordon K Smyth, Axel Kallies, Meinrad Busslinger, Stephen L Nutt

Journal article  |  2016  |  Nature Immunology

Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells

Wei Shi, Yang Liao, Simon N Willis, Nadine Taubenheim, Michael Inouye, David M Tarlinton, Gordon K Smyth, Philip D Hodgkin, Stephen L Nutt, Lynn M Corcoran

Journal article  |  2015  |  Nature Immunology

The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue-resident regulatory T cells

Ajithkumar Vasanthakumar, Kazuyo Moro, Annie Xin, Yang Liao, Renee Gloury, Shimpei Kawamoto, Sidonia Fagarasan, Lisa A Mielke, Shoukat Afshar-Sterle, Seth L Masters, Susumu Nakae, Hirohisa Saito, John M Wentworth, Peng Li, Wei Liao, Warren J Leonard, Gordon K Smyth, Wei Shi, Stephen L Nutt, Shigeo Koyasu, et al.

Journal article  |  2015  |  Nature Immunology

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

Sarah A Munro, Steven P Lund, P Scott Pine, Hans Binder, Djork-Arne Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixiao Hong, Nadereh Jafari, David P Kreil, Pawel P Labaj, Sheng Li, Yang Liao, Simon M Lin, Joseph Meehan, Christopher E Mason, Javier Santoyo-Lopez, Robert A Setterquist, et al.

Journal article  |  2014  |  Nature Communications

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

Zhenqiang Su, Pawel P Labaj, Sheng Li, Jean Thierry-Mieg, Danielle Thierry-Mieg, Wei Shi, Charles Wang, Gary P Schroth, Robert A Setterquist, John F Thompson, Wendell D Jones, Wenzhong Xiao, Weihong Xu, Roderick V Jensen, Reagan Kelly, Joshua Xu, Ana Conesa, Cesare Furlanello, Hanlin Gao, Huixiao Hong, et al.

Journal article  |  2014  |  Nature Biotechnology

Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia

Grace J Liu, Luisa Cimmino, Julian G Jude, Yifang Hu, Matthew T Witkowski, Mark D McKenzie, Mutlu Kartal-Kaess, Sarah A Best, Laura Tuohey, Yang Liao, Wei Shi, Charles G Mullighan, Michael A Farrar, Stephen L Nutt, Gordon K Smyth, Johannes Zuber, Ross A Dickins

Journal article  |  2014  |  Genes & Development

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Yang Liao, Gordon K Smyth, Wei Shi

Journal article  |  2014  |  Bioinformatics

Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain

Laura F Dagley, Carl A White, Yang Liao, Wei Shi, Gordon K Smyth, Jacqueline M Orian, Andrew Emili, Anthony W Purcell

Journal article  |  2014  |  Proteomics

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

Yang Liao, Gordon K Smyth, Wei Shi

Journal article  |  2013  |  Nucleic Acids Research