Professor Caleb Webber

2025

• Li, Z. et al. 2025. Changes in neural progenitor lineage composition during astrocytic differentiation of human iPSCs. eLife 13 RP96423. (10.7554/eLife.96423.3)
• Maguire, E. et al. 2025. Modeling common Alzheimer’s disease with high and low polygenic risk in human iPSC: A large-scale research resource. Stem Cell Reports 20 (8) 102570. (10.1016/j.stemcr.2025.102570)

2024

• Kurtyka, M. et al., 2024. The solute carrier SLC7A1 may act as a protein transporter at the blood-brain barrier. European Journal of Cell Biology 103 (2) 151406. (10.1016/j.ejcb.2024.151406)
• Li, Z. et al. 2024. Differential growth and transcriptomic profile of stem cell-derived midbrain astrocytes. eLife 13 RP96423. (10.7554/eLife.96423.1)
• Nassiri, I. et al., 2024. Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression. Bioinformatics Advances 4 (1) vbae085. (10.1093/bioadv/vbae085)
• Tsartsalis, S. et al., 2024. A single nuclear transcriptomic characterisation of mechanisms responsible for impaired angiogenesis and blood-brain barrier function in Alzheimer’s disease. Nature Communications 15 2243. (10.1038/s41467-024-46630-z)

2023

• Cameron, D. et al. 2023. Single nuclei RNA sequencing of 5 regions of the human prenatal brain implicates developing neuron populations in genetic risk for schizophrenia. Biological Psychiatry 93 , pp.157-166. (10.1016/j.biopsych.2022.06.033)
• Fernandez Cardo, L. et al. 2023. Single-cell transcriptomics and In vitro lineage tracing reveals differential susceptibility of human iPSC-derived midbrain dopaminergic neurons in a cellular model of Parkinson's Disease. Cells 12 (24) 2860. (10.3390/cells12242860)
• Keefe, F. et al. 2023. Single-cell transcriptomics reveals conserved regulatory networks in human and mouse interneuron development. International Journal of Molecular Sciences 24 (9) 8122. (10.3390/ijms24098122)
• Sri, S. et al., 2023. A multi-disciplinary commentary on preclinical research to investigate vascular contributions to dementia. Cerebral Circulation - Cognition & Behavior 5 100189. (10.1016/j.cccb.2023.100189)

2022

• Monzón-Sandoval, J. et al. 2022. Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models. Disease Models and Mechanisms 15 (10) dmm049349. (10.1242/dmm.049349)
• Pokhilko, A. et al., 2022. Targeted single-cell RNA sequencing of transcription factors facilitates biological insights from human cell experimental models. Genome Research 31 , pp.1069-1081. (10.1101/gr.273961.120)
• Sandor, C. et al. 2022. Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation. Genome Medicine 14 129. (10.1186/s13073-022-01132-9)

2021

• Meijboom, K. et al., 2021. Combining multi-omics and drug perturbation profiles to identify muscle-specific treatments for spinal muscular atrophy. JCI Insight 6 (13) e149446. (10.1172/jci.insight.149446)

2020

• Agarwal, D. et al., 2020. A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders. Nature Communications 11 (1) 4183. (10.1038/s41467-020-17876-0)
• Carling, P. J. et al., 2020. Deep phenotyping of peripheral tissue facilitates mechanistic disease stratification in sporadic Parkinson's disease. Progress in Neurobiology 187 101772. (10.1016/j.pneurobio.2020.101772)
• Hedegaard, A. et al., 2020. Pro-maturational effects of human iPSC-derived cortical astrocytes upon iPSC-derived cortical neurons. Stem Cell Reports 15 , pp.1-14. (10.1016/j.stemcr.2020.05.003)
• Mencacci, N. et al., 2020. Dystonia genes functionally converge in specific neurons and share neurobiology with psychiatric disorders. Brain 143 (9), pp.2771-2787. (10.1093/brain/awaa217)
• Monzón‐Sandoval, J. et al., 2020. Human‐specific transcriptome of ventral and dorsal midbrain dopamine neurons. Annals of Neurology 87 (6), pp.853-868. (10.1002/ana.25719)
• Volpato, V. and Webber, C. 2020. Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility. Disease Models and Mechanisms 13 (1) dmm042317. (10.1242/dmm.042317)
• Ward, J. et al., 2020. The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function. Molecular Psychiatry 25 , pp.3091-3099. (10.1038/s41380-019-0439-8)
• Williams, N. M. et al. 2020. Genome‐wide association study of pain in Parkinson's disease implicates TRPM8 as a risk factor. Movement Disorders 35 (4), pp.705-707. (10.1002/mds.28001)

2019

• Booth, H. D. et al., 2019. RNA sequencing reveals MMP2 and TGFB1 downregulation in LRRK2 G2019S Parkinson's iPSC-derived astrocytes. Neurobiology of Disease 129 , pp.56-66. (10.1016/j.nbd.2019.05.006)
• Collins, S. C. et al., 2019. Large-scale neuroanatomical study uncovers 198 gene associations in mouse brain morphogenesis. Nature Communications 10 (1) 3465. (10.1038/s41467-019-11431-2)
• Lang, C. et al., 2019. Single-cell sequencing of iPSC-Dopamine neurons reconstructs disease progression and identifies HDAC4 as a regulator of Parkinson cell phenotypes. Cell Stem Cell 24 (1), pp.93-106.e6. (10.1016/j.stem.2018.10.023)
• Mancuso, R. et al., 2019. CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. Brain 142 (10), pp.3243-3264. (10.1093/brain/awz241)

2018

• Anttila, V. et al., 2018. Analysis of shared heritability in common disorders of the brain. Science 360 (6395) eaap8757. (10.1126/science.aap8757)
• Eddowes, L. A. et al., 2018. Antiviral activity of bone morphogenetic proteins and activins. Nature Microbiology 4 , pp.339-351. (10.1038/s41564-018-0301-9)
• Nash, A. et al., 2018. Headache and type 2 diabetes association: a US national ambulatory case-control study. [Online].bioRxiv. (10.1101/336586)Available at: https://doi.org/10.1101/336586.
• Volpato, V. et al., 2018. Reproducibility of molecular phenotypes after long-term differentiation to uuman iPSC-derived neurons: a multi-site omics study. Stem Cell Reports 11 (4), pp.897-911. (10.1016/j.stemcr.2018.08.013)
• Yang, Y. et al., 2018. Molecular genetic overlap between migraine and major depressive disorder. European Journal of Human Genetics 26 (8), pp.1202-1216. (10.1038/s41431-018-0150-2)

2017

• Baud, A. et al., 2017. Multiplex high-throughput targeted proteomic assay to identify induced pluripotent stem cells. Analytical Chemistry 89 (4), pp.2440-2448. (10.1021/acs.analchem.6b04368)
• Sandor, C. , Beer, N. L. and Webber, C. 2017. Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network. PLoS Computational Biology 13 (10) e1005816. (10.1371/journal.pcbi.1005816)
• Sandor, C. et al. 2017. Whole-exome sequencing of 228 patients with sporadic Parkinson's disease. Scientific Reports 7 41188. (10.1038/srep41188)
• Sandor, C. et al. 2017. Transcriptomic profiling of purified patient-derived dopamine neurons identifies convergent perturbations and therapeutics for Parkinson's disease. Human Molecular Genetics 26 (3), pp.552-566. (10.1093/hmg/ddw412)
• Webber, C. 2017. Epistasis in neuropsychiatric disorders. Trends in Genetics 33 (4), pp.256-265. (10.1016/j.tig.2017.01.009)

2016

• Gormley, P. et al., 2016. Corrigendum: Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine. Nature Genetics 48 (10), pp.1296. (10.1038/ng1016-1296c)
• Gormley, P. et al., 2016. Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine. Nature Genetics 48 (8), pp.856-866. (10.1038/ng.3598)
• Kochinke, K. et al., 2016. Systematic phenomics analysis deconvolutes genes mutated in intellectual disability into biologically coherent modules. American Journal of Human Genetics 98 (1), pp.149-164. (10.1016/j.ajhg.2015.11.024)

2015

• Andrews, T. et al., 2015. The clustering of functionally related genes contributes to CNV-mediated disease. Genome Research 25 (6), pp.802-813. (10.1101/gr.184325.114)
• Andrews, T. et al., 2015. Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders. PLoS Genetics 11 (3) e1005012. (10.1371/journal.pgen.1005012)
• Grice, S. J. , Liu, J. and Webber, C. 2015. Synergistic interactions between Drosophila orthologues of genes spanned by De Novo human CNVs support multiple-hit models of autism. PLoS Genetics 11 (3) e1004998. (10.1371/journal.pgen.1004998)
• Steinberg, J. et al., 2015. Haploinsufficiency predictions without study bias. Nucleic Acids Research 43 (15) e101. (10.1093/nar/gkv474)
• Tan, J. Y. et al., 2015. Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells. Genome Research 25 (9) 1410.1. (10.1101/gr.196568.115)
• Tan, J. Y. et al., 2015. Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells. Genome Research 25 (5), pp.655-666. (10.1101/gr.181974.114)
• Taylor, A. et al., 2015. GeneNet toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks. Bioinformatics 31 (3), pp.442-444. (10.1093/bioinformatics/btu669)
• Taylor, A. , Steinberg, J. and Webber, C. 2015. Duplications in ADHD patients harbour neurobehavioural genes that are co-expressed with genes associated with hyperactivity in the mouse. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 168 (2), pp.97-107. (10.1002/ajmg.b.32285)

2014

• Ferry, Q. et al., 2014. Diagnostically relevant facial gestalt information from ordinary photos. eLife 2014 (3) e02020. (10.7554/eLife.02020.001)
• Honti, F. , Meader, S. and Webber, C. 2014. Unbiased functional clustering of gene variants with a phenotypic-linkage network. PLoS Computational Biology 10 (8) e1003815. (10.1371/journal.pcbi.1003815)
• Robinson, P. N. and Webber, C. 2014. Phenotype ontologies and cross-species analysis for translational research. PLoS Genetics 10 (4) e1004268. (10.1371/journal.pgen.1004268)

2013

• Brandler, W. M. et al., 2013. Common variants in left/right asymmetry genes and pathways are associated with relative hand skill. PLoS Genetics 9 (9) e1003751. (10.1371/journal.pgen.1003751)
• Heger, A. et al., 2013. GAT: A simulation framework for testing the association of genomic intervals. Bioinformatics 29 (16), pp.2046-2048. (10.1093/bioinformatics/btt343)
• Hoerder-Suabedissen, A. et al., 2013. Expression profiling of mouse subplate reveals a dynamic gene network and disease association with autism and schizophrenia. Proceedings of the National Academy of Sciences 110 (9), pp.3555-3560. (10.1073/pnas.1218510110)
• Noh, H. J. et al., 2013. Network topologies and convergent aetiologies arising from deletions and duplications observed in individuals with autism. PLoS Genetics 9 (6) e1003523. (10.1371/journal.pgen.1003523)
• Steinberg, J. and Webber, C. 2013. The roles of FMRP-regulated genes in autism spectrum disorder: single- and multiple-hit genetic etiologies. American Journal of Human Genetics 93 (5), pp.825-839. (10.1016/j.ajhg.2013.09.013)
• Vulto-van Silfhout, A. T. et al., 2013. Clinical significance of de novo and inherited copy-number variation. Human Mutation 34 (12), pp.1679-1687. (10.1002/humu.22442)

2012

• Boulding, H. and Webber, C. 2012. Large-scale objective association of mouse phenotypes with human symptoms through structural variation identified in patients with developmental disorders. Human Mutation 33 (5), pp.874-883. (10.1002/humu.22069)

2011

• Mills, R. E. et al., 2011. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Research 21 (6), pp.830-839. (10.1101/gr.115907.110)
• Shaikh, T. H. et al., 2011. Genes and biological processes commonly disrupted in rare and heterogeneous developmental delay syndromes. Human Molecular Genetics 20 (5), pp.880-893. (10.1093/hmg/ddq527)
• Webber, C. 2011. Functional enrichment analysis with structural variants: pitfalls and strategies. Cytogenetic and Genome Research 135 (3-4), pp.277-285. (10.1159/000331670)

2010

• Agam, A. et al., 2010. Elusive copy number variation in the mouse genome. PLoS ONE 5 (9), pp.1-13. (10.1371/journal.pone.0012839)
• Hehir-Kwa, J. Y. et al., 2010. Accurate distinction of pathogenic from benign CNVs in mental retardation. PLoS Computational Biology 6 (4) e1000752. (10.1371/journal.pcbi.1000752)
• Pinto, D. et al., 2010. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466 (7304), pp.368-372. (10.1038/nature09146)

2009

• Webber, C. et al. 2009. Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PLoS Genetics 5 (6) e1000531. (10.1371/journal.pgen.1000531)

2008

• Nguyen, D. et al., 2008. Reduced purifying selection prevails over positive selection in human copy number variant evolution. Genome Research 18 (11), pp.1711-1723. (10.1101/gr.077289.108)
• Walsh, T. P. et al., 2008. SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser.. Nucleic Acids Research 36 (Supple), pp.W25-W29. (10.1093/nar/gkn320)
• Warren, W. C. et al., 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453 , pp.175-183. (10.1038/nature06936)

2007

• Goodstadt, L. et al., 2007. An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes. Genome Research 17 (7), pp.969-981. (10.1101/gr.6093907)
• Mikkelsen, T. S. et al., 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447 (7141), pp.167-177. (10.1038/nature05805)

2006

• Nguyen, D. , Webber, C. and Ponting, C. P. 2006. Bias of selection on human copy-number variants. PLoS Genetics 2 (2) e20. (10.1371/journal.pgen.0020020)

2005

• Lindblad-Toh, K. et al., 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438 (7069), pp.803-819. (10.1038/nature04338)
• Webber, C. and Ponting, C. P. 2005. Hotspots of mutation and breakage in dog and human chromosomes. Genome Research 15 (12), pp.1787-1797. (10.1101/gr.3896805)

2004

• Abdellah, Z. , International Human Genome Sequencing Consortium, and Webber, C. 2004. Finishing the euchromatic sequence of the human genome.. Nature 431 , pp.931-945. (10.1038/nature03001)
• Gibbs, R. A. et al., 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428 (6982), pp.493-521. (10.1038/nature02426)
• Hiller, L. W. , International Chicken Genome Sequencing Consortium, and Webber, C. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.. Nature 432 , pp.659-716. (10.1038/nature03154)
• Webber, C. and Ponting, C. P. 2004. Genes and homology. Current Biology 14 (9), pp.R332-R333. (10.1016/j.cub.2004.04.016)
• Wong, G. K. et al., 2004. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432 (7018), pp.717-722. (10.1038/nature03156)

2003

• Webber, C. and Barton, G. J. 2003. Increased coverage obtained by combination of methods for protein sequence database searching. Bioinformatics 19 (11), pp.1397-1403. (10.1093/bioinformatics/btg156)

2001

• Webber, C. and Barton, G. J. 2001. Estimation of p-values for global alignments of protein sequences. Bioinformatics 17 (12), pp.1158-1167. (10.1093/bioinformatics/17.12.1158)

2000

• McCarthy, L. C. et al., 2000. A whole-genome radiation hybrid panel and framework map of the rat genome. Mammalian Genome 11 (9), pp.791-795. (10.1007/s003350010132)

1999

• Watanabe, T. K. et al., 1999. A radiation hybrid map of the rat genome containing 5,255 markers. Nature Genetics 22 , pp.27-36. (10.1038/8737)

1998

• Deloukas, P. et al., 1998. A physical map of 30,000 human genes. Science 282 (5389), pp.744-746. (10.1126/science.282.5389.744)