Work with Dr. Justin Whalley, Ph.D | NotedSource
Dr. Justin P. Whalley was educated in the UK (M.Sci.
Mathematics, University of Bristol) and France (Ph.D.
Bioinformatics, University of Évry). He moved to Spain to
work as a postdoc at the National Center for Genomic
Analysis (CNAG). During his time there, he ran the Quality
Control working group for the Pan-Cancer Analysis of Whole
Genomes project to assess the data coming in and reduce
batch effects. This involved collaboration with
researchers from the Broad Institute of MIT and Harvard,
the German Cancer Research Center and the Wellcome Sanger
Institute in the UK. He returned to the UK to work as a
[Senior Bioinformatician at the University of
Oxford](https://www.well.ox.ac.uk/people/jpw/). His time
there coincided with the global pandemic and he was deeply
involved in the COvid-19 Multi-omics Blood ATlas (COMBAT)
consortium as the lead for the Integration (Tensor)
working group. Dr. Whalley became a member of the [faculty
of the Chicago Medical School at Rosalind Franklin
University of Medicine and
Science](https://www.rosalindfranklin.edu/academics/faculty/justin-p-whalley/)
in January 2023.
https://cv.notedsource.io/me/1PLK52ZJ
Dr. Justin Whalley, Ph.D
Assistant Professor of Bioinformatics, with experience in finding the quintessential features in large, multi-layered 'omic datasets.
North Chicago, Illinois, United States of
America
Research Expertise
Genomics
Bioinformatics
Immunity
Tensor decomposition
Cancer
Cancer Research
Oncology
Genetics
Immunology and Allergy
Computational Theory and Mathematics
Cellular and Molecular Neuroscience
Molecular Biology
Modeling and Simulation
Ecology, Evolution, Behavior and Systematics
Critical Care and Intensive Care Medicine
Cardiology and Cardiovascular Medicine
Genetics (clinical)
Molecular Medicine
Biotechnology
About
Dr. Justin P. Whalley was educated in the UK
(M.Sci. Mathematics, University of Bristol)
and France (Ph.D. Bioinformatics, University
of Évry). He moved to Spain to work as a
postdoc at the National Center for Genomic
Analysis (CNAG). During his time there, he ran
the Quality Control working group for the
Pan-Cancer Analysis of Whole Genomes project
to assess the data coming in and reduce batch
effects. This involved collaboration with
researchers from the Broad Institute of MIT
and Harvard, the German Cancer Research Center
and the Wellcome Sanger Institute in the UK.
He returned to the UK to work as a [Senior
Bioinformatician at the University of
Oxford](https://www.well.ox.ac.uk/people/jpw/).
His time there coincided with the global
pandemic and he was deeply involved in the
COvid-19 Multi-omics Blood ATlas (COMBAT)
consortium as the lead for the Integration
(Tensor) working group. Dr. Whalley became a
member of the [faculty of the Chicago Medical
School at Rosalind Franklin University of
Medicine and
Science](https://www.rosalindfranklin.edu/academics/faculty/justin-p-whalley/)
in January 2023.
Legacy Map
Full ViewPublications
The Repertoire of Mutational Signatures in
Human Cancer
Unknown Venue
2018
Cancer Gets a Global Genomic Map: The
Pan-Cancer Analysis of Whole Genomes
incorporated 2,658 whole genomes, 38 tumor
types, 1,188 transcriptomes, and 1,300
scientists from 37 countries
Clinical OMICs
2020
TrackSig: reconstructing evolutionary
trajectories of mutations in cancer
Unknown Venue
2018
Patterns of structural variation in human
cancer
Unknown Venue
2017
Abstract LB-378: Comprehensive analysis of
chromothripsis in 2,658 human cancers
using whole-genome sequencing
Cancer Research
2018
The whole-genome panorama of cancer
drivers
Unknown Venue
2017
Pan-cancer analysis of whole genomes
reveals driver rearrangements promoted by
LINE-1 retrotransposition in human tumours
Unknown Venue
2017
The landscape of viral associations in
human cancers
Unknown Venue
2018
Genomic basis for RNA alterations revealed
by whole-genome analyses of 27 cancer
types
Unknown Venue
2017
Publisher Correction: Comprehensive
molecular characterization of
mitochondrial genomes in human cancers
Nature Genetics
2020
Spatial Genome Organization as a Framework
for Somatic Alterations in Human Cancer
Unknown Venue
2017
A deep learning system can accurately
classify primary and metastatic cancers
based on patterns of passenger mutations
Unknown Venue
2017
Unique genomic features and
deeply-conserved functions of long
non-coding RNAs in the Cancer LncRNA
Census (CLC)
Unknown Venue
2017
Integrative pathway enrichment analysis of
multivariate omics data
Unknown Venue
2018
ABO blood group association and COVID-19.
COVID-19 susceptibility and severity: a
review
Hematology, Transfusion and Cell
Therapy
2022
Genomic footprints of activated telomere
maintenance mechanisms in cancer
Unknown Venue
2017
Divergent mutational processes distinguish
hypoxic and normoxic tumours
Unknown Venue
2019
Pathway and network analysis of more than
2,500 whole cancer genomes
Unknown Venue
2018
Sex Differences in Oncogenic Mutational
Processes
Unknown Venue
2019
Whole genome and RNA sequencing of 1,220
cancers reveals hundreds of genes
deregulated by rearrangement of
cis-regulatory elements
Unknown Venue
2017
DriverPower: Combined burden and
functional impact tests for cancer driver
discovery
Unknown Venue
2017
Accelerated somatic mutation calling for
whole-genome and whole-exome sequencing
data from heterogenous tumor samples
Unknown Venue
2023
SVclone: inferring structural variant
cancer cell fraction
Unknown Venue
2017
Enabling rapid cloud-based analysis of
thousands of human genomes via Butler
Unknown Venue
2017
Constructing custom-made
radiotranscriptomic signatures from CT
angiograms: an application in COVID-19
vascular inflammation
European Heart Journal
2022
Mapping the epigenomic landscape of human
monocytes following innate immune
activation reveals context-specific
mechanisms driving endotoxin tolerance
BMC Genomics
2023
Genetic Manipulation of Animals for
Modeling Disease and Investigating Gene
Function
Human Molecular Genetics
2018
SARS-CoV-2 infection induces a long-lived
pro-inflammatory transcriptional profile
Genome Medicine
2023
A Transcriptomic Approach to Understand
Patient Susceptibility to Pneumonia After
Abdominal Surgery
Annals of Surgery
2023
A transcriptomic approach to understand
patient susceptibility to pneumonia after
abdominal surgery
Unknown Venue
2023
Unbiased single cell spatial analysis
localises inflammatory clusters of
immature neutrophils-CD8 T cells to
alveolar progenitor cells in fatal
COVID-19 lungs
Unknown Venue
2022
Coronavirus disease 2019 subphenotypes and
differential treatment response to
convalescent plasma in critically ill
adults: secondary analyses of a randomized
clinical trial
Intensive Care Medicine
2022
High-throughput mass spectrometry maps the
sepsis plasma proteome and differences in
response
Unknown Venue
2022
Constructing custom-made
radiotranscriptomic signatures of vascular
inflammation from routine CT angiograms: a
prospective outcomes validation study in
COVID-19
The Lancet Digital Health
2022
Natural Killer cells demonstrate distinct
eQTL and transcriptome-wide disease
associations, highlighting their role in
autoimmunity
Nature Communications
2022
Epigenomic analysis reveals a dynamic and
context-specific macrophage enhancer
landscape associated with innate immune
activation and tolerance
Genome Biology
2022
A blood atlas of COVID-19 defines
hallmarks of disease severity and
specificity
Cell
2022
Using de novo assembly to identify
structural variation of eight complex
immune system gene regions
PLOS Computational Biology
2021
A blood atlas of COVID-19 defines
hallmarks of disease severity and
specificity
Unknown Venue
2021
Natural Killer cells demonstrate distinct
eQTL and transcriptome-wide disease
associations, highlighting their role in
autoimmunity
Unknown Venue
2021
Genome-wide CRISPR/Cas9-knockout in human
induced Pluripotent Stem Cell
(iPSC)-derived macrophages
Scientific Reports
2021
Using de novo assembly to identify
structural variation of complex immune
system gene regions
Unknown Venue
2021
Framework for quality assessment of whole
genome cancer sequences
Nature Communications
2020
Retrospective evaluation of whole exome
and genome mutation calls in 746 cancer
samples
Nature Communications
2020
Sex differences in oncogenic mutational
processes
Nature Communications
2020
Comprehensive analysis of chromothripsis
in 2,658 human cancers using whole-genome
sequencing
Nature Genetics
2020
Comprehensive molecular characterization
of mitochondrial genomes in human cancers
Nature Genetics
2020
Disruption of chromatin folding domains by
somatic genomic rearrangements in human
cancer
Nature Genetics
2020
Pan-cancer analysis of whole genomes
identifies driver rearrangements promoted
by LINE-1 retrotransposition
Nature Genetics
2020
Butler enables rapid cloud-based analysis
of thousands of human genomes
Nature Biotechnology
2020
The landscape of viral associations in
human cancers
Nature Genetics
2020
The evolutionary history of 2,658 cancers
Nature
2020
A deep learning system accurately
classifies primary and metastatic cancers
using passenger mutation patterns
Nature Communications
2020
Analyses of non-coding somatic drivers in
2,658 cancer whole genomes
Nature
2020
Cancer LncRNA Census reveals evidence for
deep functional conservation of long
noncoding RNAs in tumorigenesis
Communications Biology
2020
Combined burden and functional impact
tests for cancer driver discovery using
DriverPower
Nature Communications
2020
Divergent mutational processes distinguish
hypoxic and normoxic tumours
Nature Communications
2020
Genomic basis for RNA alterations in
cancer
Nature
2020
Genomic footprints of activated telomere
maintenance mechanisms in cancer
Nature Communications
2020
High-coverage whole-genome analysis of
1220 cancers reveals hundreds of genes
deregulated by rearrangement-mediated
cis-regulatory alterations
Nature Communications
2020
Inferring structural variant cancer cell
fraction
Nature Communications
2020
Integrative pathway enrichment analysis of
multivariate omics data
Nature Communications
2020
Pathway and network analysis of more than
2500 whole cancer genomes
Nature Communications
2020
Patterns of somatic structural variation
in human cancer genomes
Nature
2020
Reconstructing evolutionary trajectories
of mutation signature activities in cancer
using TrackSig
Nature Communications
2020
The repertoire of mutational signatures in
human cancer
Nature
2020
Pan-cancer analysis of whole genomes
Nature
2020
Recurrent somatic mutations reveal new
insights into consequences of mutagenic
processes in cancer
PLOS Computational Biology
2019
Framework for quality assessment of whole
genome, cancer sequences
Unknown Venue
2017
Education
Université d'Évry Val-d'Essonne
Ph.D., Bioinformatics / May, 2015
Évry
University of Bristol
M.Sci., Mathematics / June, 2008
Bristol
Experience
University of Oxford
Senior Bioinformatician / 2017 — 2022
Rosalind Franklin University of Medicine and Science Chicago Medical School
Assistant Professor of Bioinformatics / 2023 — Present
CNAG
Postdoctoral Researcher / 2014 — 2017
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