Publications
Our research contributions to computational biology, single-cell analysis, and network biology. Lab members are highlighted in bold in the author lists.
2010
The Evolution and Structure Prediction of Coiled Coils across All Genomes
Journal of Molecular Biology (2010) DOI: 10.1016/j.jmb.2010.08.032
A Ca2+-based computational model for NDMA receptor-dependent synaptic plasticity at individual post-synaptic spines in the hippocampus
Frontiers in Synaptic Neuroscience (2010) DOI: 10.3389/fnsyn.2010.00031
2011
SUPERFAMILY 1.75 including a domain-centric gene ontology method
Nucleic Acids Research (2011) DOI: 10.1093/nar/gkq1130
2012
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Nucleic Acids Research (2012) DOI: 10.1093/nar/gks1266
2013
A daily-updated tree of (sequenced) life as a reference for genome research
Scientific Reports (2013) DOI: 10.1038/srep02015
2014
An atlas of active enhancers across human cell types and tissues
Nature (2014) DOI: 10.1038/nature12787
A promoter-level mammalian expression atlas
Nature (2014) DOI: 10.1038/nature13182
Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation
Proceedings of the National Academy of Sciences (2014) DOI: 10.1073/pnas.1312717110
The Evolution of Human Cells in Terms of Protein Innovation
Molecular Biology and Evolution (2014) DOI: 10.1093/molbev/mst139
2015
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution
Biochimie (2015) DOI: 10.1016/j.biochi.2015.05.003
The statistical geometry of transcriptome divergence in cell-type evolution and cancer
Nature Communications (2015) DOI: 10.1038/ncomms7066
WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools
Bioinformatics (2015) DOI: 10.1093/bioinformatics/btv114
EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization
Nucleic Acids Research (2015) DOI: 10.1093/nar/gku1322
The SUPERFAMILY 1.75 database in 2014: a doubling of data
Nucleic Acids Research (2015) DOI: 10.1093/nar/gku1041
Genome3D: exploiting structure to help users understand their sequences
Nucleic Acids Research (2015) DOI: 10.1093/nar/gku973
A <scp>P</scp> roteome <scp>Q</scp> uality <scp>I</scp> ndex
Environmental Microbiology (2015) DOI: 10.1111/1462-2920.12622
Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body
PLOS ONE (2015) DOI: 10.1371/journal.pone.0117581
2016
A predictive computational framework for direct reprogramming between human cell types
Nature Genetics (2016) DOI: 10.1038/ng.3487
Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease
Nature Neuroscience (2016) DOI: 10.1038/nn.4205
Computational methods for direct cell conversion
Cell Cycle (2016) DOI: 10.1080/15384101.2016.1238119
Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data
Bioinformatics (2016) DOI: 10.1093/bioinformatics/btv598
A Bayesian approach for analysis of whole-genome bisulphite sequencing data identifies disease-associated changes in DNA methylation
Preprint (2016) DOI: 10.1101/041715
2017
Cell Type of Origin Dictates the Route to Pluripotency
Cell Reports (2017) DOI: 10.1016/j.celrep.2017.11.029
An atlas of human long non-coding RNAs with accurate 5′ ends
Nature (2017) DOI: 10.1038/nature21374
IL-11 is a crucial determinant of cardiovascular fibrosis
Nature (2017) DOI: 10.1038/nature24676
Titin-truncating variants affect heart function in disease cohorts and the general population
Nature Genetics (2017) DOI: 10.1038/ng.3719
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals
Nucleic Acids Research (2017) DOI: 10.1093/nar/gkw995
Reliable detection of translational regulation with Ribo-seq
Preprint (2017) DOI: 10.1101/234344
<scp>RNA</scp> polymerase <scp>II</scp> primes Polycomb‐repressed developmental genes throughout terminal neuronal differentiation
Molecular Systems Biology (2017) DOI: 10.15252/msb.20177754
A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation
Genetics (2017) DOI: 10.1534/genetics.116.195008
2018
Translational control of cardiac fibrosis
Preprint (2018) DOI: 10.1101/451666
2019
Integrated systems‐genetic analyses reveal a network target for delaying glioma progression
Annals of Clinical and Translational Neurology (2019) DOI: 10.1002/acn3.50850
deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo‐seq and RNA‐seq Data
Current Protocols in Molecular Biology (2019) DOI: 10.1002/cpmb.108
Molecular Interaction Networks to Select Factors for Cell Conversion
Methods in Molecular Biology (2019) DOI: 10.1007/978-1-4939-9224-9_16
WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling
Nature Communications (2019) DOI: 10.1038/s41467-019-11551-9
A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation
Nature Neuroscience (2019) DOI: 10.1038/s41593-019-0539-4
Characterising the loss-of-function impact of 5’ untranslated region variants in whole genome sequence data from 15,708 individuals
Preprint (2019) DOI: 10.1101/543504
A single cell brain atlas in human Alzheimer’s disease
Preprint (2019) DOI: 10.1101/628347
Mouse and human microglial phenotypes in Alzheimer’s disease are controlled by amyloid plaque phagocytosis through Hif1α
Preprint (2019) DOI: 10.1101/639054
Identification of drugs for leukaemia differentiation therapy by network pharmacology
Preprint (2019) DOI: 10.1101/676106
Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping
Preprint (2019) DOI: 10.1101/700864
<i>GeneSwitches</i> : Ordering gene-expression and functional events in single-cell experiments
Preprint (2019) DOI: 10.1101/832626
Potassium channel dysfunction in human neuronal models of Angelman syndrome
Science (2019) DOI: 10.1126/science.aav5386
Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins
Circulation (2019) DOI: 10.1161/circulationaha.119.039596
Let it <scp>RE</scp> : <scp>IN</scp> : integrating experimental observations to predict pluripotency network behaviour
The EMBO Journal (2019) DOI: 10.15252/embj.2018101133
2020
EpiMogrify Models H3K4me3 Data to Identify Signaling Molecules that Improve Cell Fate Control and Maintenance
Cell Systems (2020) DOI: 10.1016/j.cels.2020.09.004
Clonal myelopoiesis in the UK Biobank cohort: ASXL1 mutations are strongly associated with smoking
Leukemia (2020) DOI: 10.1038/s41375-020-0896-8
Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals
Nature Communications (2020) DOI: 10.1038/s41467-019-10717-9
Reprogramming roadmap reveals route to human induced trophoblast stem cells
Nature (2020) DOI: 10.1038/s41586-020-2734-6
GeneSwitches: ordering gene expression and functional events in single-cell experiments
Bioinformatics (2020) DOI: 10.1093/bioinformatics/btaa099
ShinyCell: Simple and sharable visualisation of single-cell gene expression data
Preprint (2020) DOI: 10.1101/2020.10.25.354100
Functional annotation of human long noncoding RNAs via molecular phenotyping
Genome Research (2020) DOI: 10.1101/gr.254219.119
Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy
Journal of the American Society of Nephrology (2020) DOI: 10.1681/ASN.2019030289
2021
Genome-wide association study identifies novel susceptibility loci for KIT D816V positive mastocytosis
The American Journal of Human Genetics (2021) DOI: 10.1016/j.ajhg.2020.12.007
Computational Stem Cell Biology: Open Questions and Guiding Principles
Cell Stem Cell (2021) DOI: 10.1016/j.stem.2020.12.012
Challenges for Computational Stem Cell Biology: A Discussion for the Field
Stem Cell Reports (2021) DOI: 10.1016/j.stemcr.2020.12.015
Evaluating Capture Sequence Performance for Single-Cell CRISPR Activation Experiments
ACS Synthetic Biology (2021) DOI: 10.1021/acssynbio.0c00499
Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity
Nature Communications (2021) DOI: 10.1038/s41467-021-22397-5
Modelling human blastocysts by reprogramming fibroblasts into iBlastoids
Nature (2021) DOI: 10.1038/s41586-021-03372-y
ShinyCell: simple and sharable visualization of single-cell gene expression data
Bioinformatics (2021) DOI: 10.1093/bioinformatics/btab209
Cardiomyocyte BRAF and type 1 RAF inhibitors promote cardiomyocyte and cardiac hypertrophy in mice <i>in vivo</i>
Preprint (2021) DOI: 10.1101/2021.08.14.455637
CLIPreg: Constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq
Preprint (2021) DOI: 10.1101/2021.12.06.470871
Synthetic biology: at the crossroads of genetic engineering and human therapeutics—a Keystone Symposia report
Annals of the New York Academy of Sciences (2021) DOI: 10.1111/nyas.14710
2022
A high-resolution map of human RNA translation
Molecular Cell (2022) DOI: 10.1016/j.molcel.2022.06.023
Clonal myelopoiesis promotes adverse outcomes in chronic kidney disease
Leukemia (2022) DOI: 10.1038/s41375-021-01382-3
A novel network pharmacology approach for leukaemia differentiation therapy using Mogrify®
Oncogene (2022) DOI: 10.1038/s41388-022-02505-5
Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential
npj Regenerative Medicine (2022) DOI: 10.1038/s41536-022-00226-7
CLIPreg: constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq
Bioinformatics (2022) DOI: 10.1093/bioinformatics/btac363
2023
LINC01013 Is a Determinant of Fibroblast Activation and Encodes a Novel Fibroblast-Activating Micropeptide
Journal of Cardiovascular Translational Research (2023) DOI: 10.1007/s12265-022-10288-z
Deep learning models will shape the future of stem cell research
Stem Cell Reports (2023) DOI: 10.1016/j.stemcr.2022.11.007
DNA methylation is associated with codon degeneracy in a species of bumblebee
Heredity (2023) DOI: 10.1038/s41437-023-00591-z
Single cell analysis in head and neck cancer reveals potential immune evasion mechanisms during early metastasis
Nature Communications (2023) DOI: 10.1038/s41467-023-37379-y
Transient naive reprogramming corrects hiPS cells functionally and epigenetically
Nature (2023) DOI: 10.1038/s41586-023-06424-7
Discovering microproteins: making the most of ribosome profiling data
RNA Biology (2023) DOI: 10.1080/15476286.2023.2279845
Differences in 5’untranslated regions highlight the importance of translational regulation of dosage sensitive genes
Preprint (2023) DOI: 10.1101/2023.05.15.540809
Striatin plays a major role in angiotensin II-induced cardiomyocyte and cardiac hypertrophy in mice <i>in vivo</i>
Preprint (2023) DOI: 10.1101/2023.10.21.563397
Age-related loss of chromosome Y is associated with levels of sex hormone binding globulin and clonal hematopoiesis defined by <i>TET2</i> , <i>TP53</i> , and <i>CBL</i> mutations
Science Advances (2023) DOI: 10.1126/sciadv.ade9746
A Single-cell Atlas Identifies Pretreatment Features of Primary Imatinib Resistance in Chronic Myeloid Leukemia
Blood (2023) DOI: 10.1182/blood.2022017295
2024
Striatin plays a major role in angiotensin II-induced cardiomyocyte and cardiac hypertrophy in mice <i>in vivo</i>
Clinical Science (2024) DOI: 10.1042/cs20240496
Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes
Genome Biology (2024) DOI: 10.1186/s13059-024-03248-0
2025
Global analysis of ligand-gated ion channel conservation across Platyhelminthes
General and Comparative Endocrinology (2025) DOI: 10.1016/j.ygcen.2025.114718
High-Capacity Optical Fingerprinting Using Dual-Peak Photoluminescence of Quantum Dots
ACS Applied Materials & Interfaces (2025) DOI: 10.1021/acsami.5c19508
Microprotein SMIM26 drives oxidative metabolism via serine-responsive mitochondrial translation
Molecular Cell (2025) DOI: 10.1016/j.molcel.2025.05.033
Personalized uncertainty quantification in artificial intelligence
Nature Machine Intelligence (2025) DOI: 10.1038/s42256-025-01024-8
taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level
PHAGE: Therapy, Applications, and Research (2025) DOI: 10.1089/phage.2024.0050
ShinyCell2: An extended library for simple and sharable visualisation of spatial, peak-based and multi-omic single-cell data
Preprint (2025) DOI: 10.1101/2025.04.22.650045
Loss of chromosome Y shapes the immune cell fate with aging in men
Preprint (2025) DOI: 10.1101/2025.06.01.25328624
Genome-wide analysis defines genetic determinants of MPN subtypes and identifies a sex-specific association at <i>CDH22</i> / <i>CD40</i>
Blood (2025) DOI: 10.1182/blood.2025028489
2026
Genome-scale Identification of Microprotein Regulators of Mitochondrial Metabolism
Preprint (2026) DOI: 10.2139/ssrn.6460221
PathPinpointR: Predicting the progression of sc-RNAseq samples through reference trajectories.
TBC (2026) DOI: TBC
Abstract
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to analyse cellular heterogeneity, enabling detailed mapping of cellular progression. Trajectory inference tools construct trajectories from scRNA-seq data, facilitating the tracing of cellular progression through developmental pathways. PathPinpointR (PPR) is a lightweight and user-friendly R package developed to predict and compare the positions of scRNA-seq samples along reference biological trajectories, such as those created from large cell atlas projects. PPR utilises sets of switching-gene events from reference trajectories as indicators of cellular progression. By applying these positional indicators to query datasets, each cell can be accurately assigned a pseudo-time value, providing predictive insight into its position along a trajectory. This information can be used to stage cells within an established developmental process, or to evaluate how different patient samples compare when mapped onto reference disease or drug response trajectories.
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