Author details

Full Name

Matthew E Ritchie

Affiliation

The University of Melbourne

ORCID

Career Start Year

2006

Papers

115

H Index

Expertise

CM4AI Collaborator

Gloria M Sheynkman (CM4AI)

PMID	Paper Title	Journal Title	Published Year
38059347	Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR.	Nucleic Acids Res	2024
38059347	Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR.	Nucleic Acids Res	2024
36725870	Identification and control for the effects of bioinformatic globin depletion on human RNA-seq differential expression analysis.	Sci Rep	2023
38079450	Hookworms dynamically respond to loss of Type 2 immune pressure.	PLoS Pathog	2023
37783886	Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.	Nat Methods	2023
38053127	FGF-independent MEK1/2 signalling in the developing foetal testis is essential for male germline differentiation in mice.	BMC Biol	2023
38046273	scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor.	NAR Genom Bioinform	2023
36521105	Venetoclax treatment in patients with cancer has limited impact on circulating T and NK cells.	Blood Adv	2023
36840716	Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions.	Nucleic Acids Res	2023
37147723	Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data.	Genome Biol	2023
37173797	Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data.	Genome Biol	2023
36725870	Identification and control for the effects of bioinformatic globin depletion on human RNA-seq differential expression analysis.	Sci Rep	2023
37546854	Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.	bioRxiv	2023
38079450	Hookworms dynamically respond to loss of Type 2 immune pressure.	PLoS Pathog	2023
37546854	Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.	bioRxiv	2023
38053127	FGF-independent MEK1/2 signalling in the developing foetal testis is essential for male germline differentiation in mice.	BMC Biol	2023
37783886	Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.	Nat Methods	2023
38046273	scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor.	NAR Genom Bioinform	2023
37147723	Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data.	Genome Biol	2023
37173797	Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data.	Genome Biol	2023
36521105	Venetoclax treatment in patients with cancer has limited impact on circulating T and NK cells.	Blood Adv	2023
36840716	Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions.	Nucleic Acids Res	2023
35127999	A transcriptomic dataset evaluating the effect of radiotherapy injury on cells of skin and soft tissue.	Data Brief	2022
35843975	Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation.	Epigenetics Chromatin	2022
35709339	Single-cell multiomics reveal the scale of multilayered adaptations enabling CLL relapse during venetoclax therapy.	Blood	2022
35965451	NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells.	MAbs	2022
36355065	A method for stabilising the XX karyotype in female mESC cultures.	Development	2022
35831623	Epigenetic modulators of B cell fate identified through coupled phenotype-transcriptome analysis.	Cell Death Differ	2022
35761990	Corrigendum to 'A transcriptomic dataset evaluating the effect of radiotherapy injury on cells of skin and soft tissue' Data in Brief 41 (2022) 107828.	Data Brief	2022
36129434	A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells.	J Cell Biol	2022
35351876	BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation.	Nat Commun	2022
35127999	A transcriptomic dataset evaluating the effect of radiotherapy injury on cells of skin and soft tissue.	Data Brief	2022
35843975	Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation.	Epigenetics Chromatin	2022
35709339	Single-cell multiomics reveal the scale of multilayered adaptations enabling CLL relapse during venetoclax therapy.	Blood	2022
35351876	BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation.	Nat Commun	2022
35831623	Epigenetic modulators of B cell fate identified through coupled phenotype-transcriptome analysis.	Cell Death Differ	2022
35761990	Corrigendum to 'A transcriptomic dataset evaluating the effect of radiotherapy injury on cells of skin and soft tissue' Data in Brief 41 (2022) 107828.	Data Brief	2022
35965451	NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells.	MAbs	2022
36129434	A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells.	J Cell Biol	2022
36355065	A method for stabilising the XX karyotype in female mESC cultures.	Development	2022
33278564	Single-Cell Transcriptomic Analysis Reveals BCMA CAR-T Cell Dynamics in a Patient with Refractory Primary Plasma Cell Leukemia.	Mol Ther	2021
33862015	Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development.	Immunity	2021
33590862	long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data.	Gigascience	2021
34289356	Homeostatic apoptosis prevents competition-induced atrophy in follicular B cells.	Cell Rep	2021
34172588	CD36 family members are TCR-independent ligands for CD1 antigen-presenting molecules.	Sci Immunol	2021
34121118	A functional genetic screen identifies aurora kinase b as an essential regulator of Sox9-positive mouse embryonic lung progenitor cells.	Development	2021
33937765	The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools.	NAR Genom Bioinform	2021
33660333	The impact of influenza pulmonary infection and inflammation on vagal bronchopulmonary sensory neurons.	FASEB J	2021
33649477	Single-cell analyses reveal the clonal and molecular aetiology of Flt3L-induced emergency dendritic cell development.	Nat Cell Biol	2021
34353350	Community-wide hackathons to identify central themes in single-cell multi-omics.	Genome Biol	2021

1 - 50 of 230

Rhonda Bacher

University of Florida

Career Start Year 2016

Number of shared co-authors 0

Hailiang Mei

Leiden University Medical Center

Career Start Year 2014

Number of shared co-authors 1

Travers Ching

Adaptive Biotechnologies

Career Start Year 2014

Number of shared co-authors 1

Stephanie C Hicks

Johns Hopkins Bloomberg School of Public Health

Career Start Year 2011

Number of shared co-authors 10

H??ctor Corrada Bravo

University of Maryland College Park, College Park

Career Start Year 2009

Number of shared co-authors 16

Akira Hasegawa

RIKEN Center for Integrative Medical Sciences

Career Start Year 2008

Number of shared co-authors 4

Ludwig Geistlinger

Center for Computational Biomedicine, Harvard Medical School

Career Start Year 2008

Number of shared co-authors 12

Oliver Stegle

Wellcome Sanger Institute

Career Start Year 2008

Number of shared co-authors 11

Lana X Garmire

University of Michigan ann arbor

Career Start Year 2007

Number of shared co-authors 4

Jonathan E Bard

University at Buffalo

Career Start Year 2007

Number of shared co-authors 0

Altuna Akalin

Berlin Institute for Medical Systems Biology

Career Start Year 2006

Number of shared co-authors 4

Simon Anders

Heidelberg University

Career Start Year 2006

Number of shared co-authors 11

Joshua W K Ho

The University of Hong Kong

Career Start Year 2006

Number of shared co-authors 0

Jessica C Mar

Australian Institute for Bioengineering and Nanotechnology, University of Queensland

Career Start Year 2005

Number of shared co-authors 6

Yongjun Zhao

Canada British Columbia Cancer Research Centre, University of British Columbia

Career Start Year 2005

Number of shared co-authors 2

John C Marioni

Cancer Research UK Cambridge Institute, University of Cambridge

Career Start Year 2004

Number of shared co-authors 11

Zhandong Liu

Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital

Career Start Year 2003

Number of shared co-authors 0

Gerald Quon

University of California davis

Career Start Year 2003

Number of shared co-authors 0

Terence P Speed

Walter and Eliza Hall Institute of Medical Research

Career Start Year 2003

Number of shared co-authors 2

Shintaro Katayama

Folkhalsan Research Center

Career Start Year 2003

Number of shared co-authors 4

Carsten O Daub

International Institute of Molecular and Cell Biology in Warsaw

Career Start Year 2002

Number of shared co-authors 5

Mikhail G Dozmorov

Virginia Commonwealth University

Career Start Year 2001

Number of shared co-authors 1

Jean Yee Hwa Yang

The University of Sydney

Career Start Year 2001

Number of shared co-authors 5

Shujun Luo

Predicine Inc.

Career Start Year 2000

Number of shared co-authors 2

Gregory R Grant

Perelman School of Medicine, University of Pennsylvania Philadelphia

Career Start Year 1999

Number of shared co-authors 4

Christina Kendziorski

University of Wisconsin-Madison

Career Start Year 1999

Number of shared co-authors 2

Mark D Robinson

University of Zurich

Career Start Year 1997

Number of shared co-authors 8

Alistair R R Forrest

RIKEN Center for Integrative Medical Sciences

Career Start Year 1994

Number of shared co-authors 4

Jean-Pierre A Kocher

Mayo Clinic

Career Start Year 1991

Number of shared co-authors 1

Aviv Regev

Broad Institute of MIT and Harvard

Career Start Year 1987

Number of shared co-authors 8

row(s) 1 - 30 of 30

Gordon K Smyth

The University of Melbourne

Co-authored papers 28

Shian Su

The Walter and Eliza Hall Institute of Medical Research

Co-authored papers 19

Charity W Law

The Walter and Eliza Hall Institute of Medical Research

Co-authored papers 17

Ruijie Liu

Co-authored papers 11

Peter F Hickey

The Walter and Eliza Hall Institute of Medical Research

Co-authored papers 11

Simon Tavar??

Irving Institute for Cancer Dynamics, Columbia University

Co-authored papers 8

Mark J Dunning

The Medical School, The University of Sheffield

Co-authored papers 7

Andy G Lynch

University of St Andrews

Co-authored papers 6

Rafael A Irizarry

Dana-Farber Cancer Institute

Co-authored papers 4

Panos Deloukas

William Harvey Research Institute, Queen Mary University of London

Co-authored papers 3

Benilton S Carvalho

Brazilian Institute of Neuroscience and Neurotechnology (BRAINN)

Co-authored papers 3

Vincent J Carey

Brigham and Women's Hospital, Harvard Medical School

Co-authored papers 3

Kim-Anh L?? Cao

University of Melbourne

Co-authored papers 3

Emmanouil T Dermitzakis

University of Geneva

Co-authored papers 3

Vera Pancaldi

Universite de Toulouse, Inserm, CNRS, Universite Toulouse III-Paul Sabatier

Co-authored papers 2

Gavin M Wright

St. Vincent's Hospital, University of Melbourne

Co-authored papers 2

Aedin C Culhane

Dana-Farber Cancer Institute & Harvard School of Public Health

Co-authored papers 2

Arshi Arora

Memorial Sloan Kettering Cancer Center

Co-authored papers 2

Dario Righelli

University of Padova

Co-authored papers 2

Casey S Greene

Dartmouth College Geisel School of Medicine, Princeton University, University of Colorado Anschutz Medical Campus, University of Pennsylvania Perelman School of Medicine

Co-authored papers 2

Michael I Love

University of North Carolina at Chapel Hill

Co-authored papers 2

Terence P Speed

Co-authored papers 2

Ayshwarya Subramanian

Broad Institute of MIT and Harvard

Co-authored papers 2

Huei San Leong

Peter MacCallum Cancer Centre

Co-authored papers 2