Research

The Phipson laboratory works on both novel bioinformatics methods development as well as collaborative analysis projects with scientists within and external to the Institute. We use sophisticated statistical modelling to reveal insights into normal development and disease.

A major research focus of the Phipson laboratory is on developing new bioinformatics methods for data generated from single cell technologies. We also work on genomic data generated from other high-throughput technologies including RNA-seq and DNA methylation. Our novel bioinformatics methods are implemented as publicly available open source software through the Bioconductor project.

Current research areas of interest include:

– Developing statistical methods for designed single cell experiments with biological replication

– Advancing DNA methylation analysis for current and emerging technologies

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2023

Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7

Andrew J. Kueh, Maria I. Bergamasco, Anna Quaglieri, Belinda Phipson, Connie S.N. Li-Wai-Suen, …, Michael P. Snyder, Gordon K. Smyth, Terence P. Speed, Tim Thomas, Anne K. Voss

Cell Reports  ·  01 Jan 2023  ·  doi:10.1016/j.celrep.2022.111980

2022

Heterotopic reduction of forelimb progenitors underpins development of the vestigial emu wing; implications for vertebrate limb evolution

Axel H Newton, Sarah M Williams, Belinda Phipson, Andrew J Pask, Andrew T Major, Craig A Smith

Cold Spring Harbor Laboratory  ·  25 Nov 2022  ·  doi:10.1101/2022.11.23.516993

propeller: testing for differences in cell type proportions in single cell data

Belinda Phipson, Choon Boon Sim, Enzo R Porrello, Alex W Hewitt, Joseph Powell, Alicia Oshlack

Bioinformatics  ·  14 Oct 2022  ·  doi:10.1093/bioinformatics/btac582

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Manuscript Source

Website

open-science collaboration

Defining the Fetal Gene Program at Single-Cell Resolution in Pediatric Dilated Cardiomyopathy

Neda R. Mehdiabadi, Choon Boon Sim, Belinda Phipson, Ravi K.R. Kalathur, Yuliangzi Sun, …, Robert G. Weintraub, Igor E. Konstantinov, Nathan J. Palpant, David A. Elliott, Enzo R. Porrello

Circulation  ·  04 Oct 2022  ·  doi:10.1161/CIRCULATIONAHA.121.057763

2021

Gene set enrichment analysis for genome-wide DNA methylation data

Jovana Maksimovic, Alicia Oshlack, Belinda Phipson

Genome Biology  ·  08 Jun 2021  ·  doi:10.1186/s13059-021-02388-x

Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor

Choon Boon Sim, Belinda Phipson, Mark Ziemann, Haloom Rafehi, Richard J. Mills, …, David A. Elliott, Assam El-Osta, Alicia Oshlack, James E. Hudson, Enzo R. Porrello

Circulation  ·  20 Apr 2021  ·  doi:10.1161/circulationaha.120.051921

2019

Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk.

Alexander N Combes, Belinda Phipson, Kynan T Lawlor, Aude Dorison, Ralph Patrick, Luke Zappia, Richard P Harvey, Alicia Oshlack, Melissa H Little

Development (Cambridge, England)  ·  12 Jun 2019  ·  pmid:31118232

2018

Evaluation of variability in human kidney organoids

Belinda Phipson, Pei X. Er, Alexander N. Combes, Thomas A. Forbes, Sara E. Howden, …, Jane Sun, Ernst Wolvetang, Minoru Takasato, Alicia Oshlack, Melissa H. Little

Nature Methods  ·  20 Dec 2018  ·  doi:10.1038/s41592-018-0253-2

Evaluation of variability in human kidney organoids.

Belinda Phipson, Pei X Er, Alexander N Combes, Thomas A Forbes, Sara E Howden, …, Jane Sun, Ernst Wolvetang, Minoru Takasato, Alicia Oshlack, Melissa H Little

Nature methods  ·  20 Dec 2018  ·  pmid:30573816

3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening.

Lorna J Hale, Sara E Howden, Belinda Phipson, Andrew Lonsdale, Pei X Er, …, Shahnaz Khan, Alicia Oshlack, Catherine Quinlan, Rachel Lennon, Melissa H Little

Nature communications  ·  04 Dec 2018  ·  pmid:30514835

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period

Ramona H. Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael M. Cheung, Joseph J. Smolich, Salvatore Pepe

PLOS ONE  ·  19 Sep 2018  ·  doi:10.1371/journal.pone.0204038

STRetch: detecting and discovering pathogenic short tandem repeat expansions

Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, …, Phillipa Lamont, Joshua S. Clayton, Nigel G. Laing, Daniel G. MacArthur, Alicia Oshlack

Genome Biology  ·  21 Aug 2018  ·  doi:10.1186/s13059-018-1505-2

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Luke Zappia, Belinda Phipson, Alicia Oshlack

PLOS Computational Biology  ·  25 Jun 2018  ·  doi:10.1371/journal.pcbi.1006245

Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms

Thomas A. Forbes, Sara E. Howden, Kynan Lawlor, Belinda Phipson, Jovana Maksimovic, …, Alicia Oshlack, Chirag Patel, Andrew Mallett, Cas Simons, Melissa H. Little

The American Journal of Human Genetics  ·  01 May 2018  ·  doi:10.1016/j.ajhg.2018.03.014

Haploinsufficiency for the Six2 gene increases nephron progenitor proliferation promoting branching and nephron number

Alexander N. Combes, Sean Wilson, Belinda Phipson, Brandon B. Binnie, Adler Ju, …, Ian M. Smyth, Karen M. Moritz, Raphael Kopan, Alicia Oshlack, Melissa H. Little

Kidney International  ·  01 Mar 2018  ·  doi:10.1016/j.kint.2017.09.015

2017

Splatter: simulation of single-cell RNA sequencing data

Luke Zappia, Belinda Phipson, Alicia Oshlack

Genome Biology  ·  12 Sep 2017  ·  doi:10.1186/s13059-017-1305-0

Gene length and detection bias in single cell RNA sequencing protocols

Belinda Phipson, Luke Zappia, Alicia Oshlack

F1000Research  ·  28 Apr 2017  ·  doi:10.12688/f1000research.11290.1

A cross-package Bioconductor workflow for analysing methylation array data

Jovana Maksimovic, Belinda Phipson, Alicia Oshlack

F1000Research  ·  05 Apr 2017  ·  doi:10.12688/f1000research.8839.3

2016

Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros

Elizabeth S Ng, Lisa Azzola, Freya F Bruveris, Vincenzo Calvanese, Belinda Phipson, …, Katja Schenke-Layland, Alicia Oshlack, Hanna K A Mikkola, Edouard G Stanley, Andrew G Elefanty

Nature Biotechnology  ·  17 Oct 2016  ·  doi:10.1038/nbt.3702

Functionally distinct roles for different miR-155 expression levels through contrasting effects on gene expression, in acute myeloid leukaemia

N Narayan, L Morenos, B Phipson, S N Willis, G Brumatti, …, D Catchpoole, R Saffery, A Oshlack, G J Goodall, P G Ekert

Leukemia  ·  14 Oct 2016  ·  doi:10.1038/leu.2016.279

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

Belinda Phipson, Stanley Lee, Ian J. Majewski, Warren S. Alexander, Gordon K. Smyth

The Annals of Applied Statistics  ·  01 Jun 2016  ·  doi:10.1214/16-aoas920

2015

missMethyl: an R package for analyzing data from Illumina’s HumanMethylation450 platform

Belinda Phipson, Jovana Maksimovic, Alicia Oshlack

Bioinformatics  ·  30 Sep 2015  ·  doi:10.1093/bioinformatics/btv560

Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model

Ashley P. Ng, Yifang Hu, Donald Metcalf, Craig D. Hyland, Helen Ierino, …, Hiu Kiu, Ladina Di Rago, Douglas J. Hilton, Gordon K. Smyth, Warren S. Alexander

PLOS Genetics  ·  14 May 2015  ·  doi:10.1371/journal.pgen.1005211

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo

Bilal N. Sheikh, Natalie L. Downer, Belinda Phipson, Hannah K. Vanyai, Andrew J. Kueh, Davis J. McCarthy, Gordon K. Smyth, Tim Thomas, Anne K. Voss

Proceedings of the National Academy of Sciences  ·  14 Apr 2015  ·  doi:10.1073/pnas.1422872112

MOZ (MYST3, KAT6A) inhibits senescence via the INK4A-ARF pathway

B N Sheikh, B Phipson, F El-Saafin, H K Vanyai, N L Downer, …, A J Kueh, R E May, G K Smyth, A K Voss, T Thomas

Oncogene  ·  16 Mar 2015  ·  doi:10.1038/onc.2015.33

limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E. Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W. Law, Wei Shi, Gordon K. Smyth

Nucleic Acids Research  ·  20 Jan 2015  ·  doi:10.1093/nar/gkv007

2014

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging

Belinda Phipson, Alicia Oshlack

Genome Biology  ·  01 Sep 2014  ·  doi:10.1186/s13059-014-0465-4

2013

Polycomb repressive complex 2 (PRC2) suppresses Eμ-myc lymphoma

Stanley C. W. Lee, Belinda Phipson, Craig D. Hyland, Huei San Leong, Rhys S. Allan, …, Stephen L. Nutt, Marnie E. Blewitt, Gordon K. Smyth, Warren S. Alexander, Ian J. Majewski

Blood  ·  10 Oct 2013  ·  doi:10.1182/blood-2013-02-484055

2012

Bcl-2, Bcl-xL, and Bcl-w are not equivalent targets of ABT-737 and navitoclax (ABT-263) in lymphoid and leukemic cells

Delphine Mérino, Seong L. Khaw, Stefan P. Glaser, Daniel J. Anderson, Lisa D. Belmont, …, Suzanne Cory, Andrew W. Roberts, Mary J. C. Ludlam, David C. S. Huang, Philippe Bouillet

Blood  ·  14 Jun 2012  ·  doi:10.1182/blood-2011-12-400929

Proteomic and Metabolomic Analyses of Mitochondrial Complex I-deficient Mouse Model Generated by Spontaneous B2 Short Interspersed Nuclear Element (SINE) Insertion into NADH Dehydrogenase (Ubiquinone) Fe-S Protein 4 (Ndufs4) Gene

Dillon W. Leong, Jasper C. Komen, Chelsee A. Hewitt, Estelle Arnaud, Matthew McKenzie, …, Albert Sickmann, Michael T. Ryan, Gordon K. Smyth, David R. Thorburn, Hamish S. Scott

Journal of Biological Chemistry  ·  01 Jun 2012  ·  doi:10.1074/jbc.M111.327601

Neither loss of Bik alone, nor combined loss of Bik and Noxa, accelerate murine lymphoma development or render lymphoma cells resistant to DNA damaging drugs

L Happo, B Phipson, G K Smyth, A Strasser, C L Scott

Cell Death & Disease  ·  10 May 2012  ·  doi:10.1038/cddis.2012.42

2011

Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance

François-Xavier Hubert, Sarah A. Kinkel, Gayle M. Davey, Belinda Phipson, Scott N. Mueller, …, Li Wu, Christopher C. Goodnow, Francis R. Carbone, Hamish S. Scott, William R. Heath

Blood  ·  01 Sep 2011  ·  doi:10.1182/blood-2010-06-286393

Targeting Antigen to Mouse Dendritic Cells via Clec9A Induces Potent CD4 T Cell Responses Biased toward a Follicular Helper Phenotype

Mireille H. Lahoud, Fatma Ahmet, Susie Kitsoulis, Soo San Wan, David Vremec, …, Scott N. Mueller, Gayle M. Davey, William R. Heath, Ken Shortman, Irina Caminschi

The Journal of Immunology  ·  15 Jul 2011  ·  doi:10.4049/jimmunol.1101176

2010

Maximal killing of lymphoma cells by DNA damage–inducing therapy requires not only the p53 targets Puma and Noxa, but also Bim

Lina Happo, Mark S. Cragg, Belinda Phipson, Jon M. Haga, Elisa S. Jansen, …, Cassandra J. Vandenberg, Gordon K. Smyth, Andreas Strasser, Suzanne Cory, Clare L. Scott

Blood  ·  09 Dec 2010  ·  doi:10.1182/blood-2010-04-280818

A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility

Iris K.L. Tan, Leanne Mackin, Nancy Wang, Anthony T. Papenfuss, Colleen M. Elso, …, Melanie Bahlo, Terence P. Speed, Gordon K. Smyth, Grant Morahan, Thomas C. Brodnicki

Genome Research  ·  04 Nov 2010  ·  doi:10.1101/gr.101881.109

Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells

Ian J. Majewski, Matthew E. Ritchie, Belinda Phipson, Jason Corbin, Miha Pakusch, …, Yifang Hu, Gordon K. Smyth, Warren S. Alexander, Douglas J. Hilton, Marnie E. Blewitt

Blood  ·  05 Aug 2010  ·  doi:10.1182/blood-2009-12-260760

Pro-Inflammatory CD11c+CD206+ Adipose Tissue Macrophages Are Associated With Insulin Resistance in Human Obesity

John M. Wentworth, Gaetano Naselli, Wendy A. Brown, Lisa Doyle, Belinda Phipson, Gordon K. Smyth, Martin Wabitsch, Paul E. O’Brien, Leonard C. Harrison

Diabetes  ·  31 Mar 2010  ·  doi:10.2337/db09-0287

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

Belinda Phipson, Gordon K Smyth

Statistical Applications in Genetics and Molecular Biology  ·  31 Jan 2010  ·  doi:10.2202/1544-6115.1585

2009

Murine hematopoietic blast colony-forming cells and their progeny have distinctive membrane marker profiles

Donald Metcalf, Ashley P. Ng, Stephen J. L. Loughran, Belinda Phipson, Gordon K. Smyth, Ladina Di Rago, Sandra Mifsud

Proceedings of the National Academy of Sciences  ·  10 Nov 2009  ·  doi:10.1073/pnas.0910354106

Molecular dissection of the pea shoot apical meristem*

Dacheng Liang, Chui E. Wong, Mohan B. Singh, Christine A. Beveridge, Belinda Phipson, Gordon K. Smyth, Prem L. Bhalla

Journal of Experimental Botany  ·  25 Aug 2009  ·  doi:10.1093/jxb/erp254