Fios clients often feature the bioinformatics analysis we have performed for them in their publications. The following publications are the outcome of our team and co-founders’ collaboration with clients from pharmaceutical, biotechnological companies and research organisations.
You can find our publications sorted by Research Area, Research Stage, and Data Type.
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By Research Area
Microarray profiling predicts early neurological and immune phenotypic traits in advance of CNS disease
2021 – Paul Montague, Barbara Bradley, Jean Rodgers, Peter G. E. Kennedy
Human African trypanosomiasis (HAT), also known as sleeping sickness, is a major cause of mortality and morbidity in sub-Saharan Africa. We hypothesised that recent findings of neurological features and parasite brain infiltration occurring at much earlier stages in HAT than previously thought could be explained by early activation of host genetic programmes controlling CNS disease.
Central nervous system regeneration is driven by microglia necroptosis and repopulation
2019 – Amy F. Lloyd, Claire L. Davies, Rebecca K. Holloway, et al.
This study shows our collaboration with the Medical Research Council Centre for Reproductive Health, The Queen’s Medical Research Institute, The University of Edinburgh as well as other collaborators.
Failed regeneration of CNS myelin contributes to clinical decline in neuroinflammatory and neurodegenerative diseases, for which there is an unmet therapeutic need. Impaired microglia death and/or repopulation may underpin dysregulated microglia activation in neurological diseases, and therapeutic targets to promote white matter regeneration were revealed.
Microbe-host interplay in atopic dermatitis and psoriasis
2019 – Nanna Fyhrquist, Gareth Muirhead, Stefanie Prast-Nielsen, et al.
This study shows our collaboration with several organisations for the MAARS FP7 project.
Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis.
- A multi-tissue age prediction model based on DNA methylation analysis
Hussain Alsaleh, Nicola A. McCallum, Daniel L. Halligan, Penelope R. Haddrill. Forensic Science International: Genetics Supplement Series (2017). - Stress perception impacts on clinical signs of skin ageing and modifies the epigenome
R. Pattinson, C. Bundy, L. Cordingley, et al. Journal of Investigative Dermatology, 062 (2016).
Differential sensitivity of mucosal organs to transient exposure to hydrogen sulphide in post-smolt Atlantic salmon (Salmo salar)
2023 – Carlo Lazado, Hanna Ross D. Alipio, Julie Hansen Bergstedt
The study demonstrates the physiological consequences of transient exposure of post-smolt Atlantic salmon to H2S. The fish were exposed to one of three levels of H2S for 1 h: 0 μM (unexposed), 0.6 μM (low exposure), and 1.2 μM (high exposure). Fish were allowed to recover for 24 hours and then sampled for gene expression, histology, and metabolomics analyses. Molecular profiling was performed on a subset of genes with known functions in sulphide detoxification, mucins, immunity, and stress responses, which focused on the gills, olfactory organ, skin, and distal gut.
Genome-wide analysis clarifies the population genetic structure of wild Gilthead Sea Bream (Sparus aurata)
2021 – Francesco Maroso, Konstantinos Gkagkavouzis, Sabina De Innocentiis, et al.
The study below shows our collaboration with the Aquatrace Consortium.
Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry.
(Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
Consequences of continuous ozonation on the health and welfare of Atlantic salmon post-smolts in a brackish water recirculating aquaculture system
2021 – Lazado Carlo, Kevin T. Stiller, Britt-Kristin Megård Reiten, João Osório, Jelena Kolarevic, Lill-Heidi Johansen
This study investigated the biological consequences of 45-day continuous ozonation on Atlantic salmon (Salmo salar) post-smolts in a brackish water recirculating aquaculture system (RAS). Microarray analysis revealed that the gills and liver were more responsive to the oxidant than the skin, with the gills being the most sensitive. Moreover, the magnitude of the transcriptomic modifications depended on the exposure duration. A functional analysis showed that genes involved in immunity and ribosomal functions were significantly affected in the gills. In contrast, genes crucial for the oxidation-reduction process were mainly targeted in the liver.
Multiomics Provide Insights into the Key Molecules and Pathways Involved in the Physiological Adaptation of Atlantic Salmon (Salmo salar) to Chemotherapeutic-Induced Oxidative Stress
2021 – Lazado C., Timmerhaus G., Breiland M., Pittman K., Hytterød S.
In this study, multiomics analysis helped understanding how a chemical oxidative stressor alters salmon physiology at both the systemic and mucosal levels. This knowledge will be pivotal in developing an evidence-driven approach to the use of oxidative therapeutics in fish, with some of the molecules and pathways identified as potential biomarkers and targets for assessing the physiological cost of these treatments.
Sonic hedgehog specifies flight feather positional information in avian wings
2020 – Lara Busby, Cristina Aceituno, Caitlin McQueen, et al.
The study below shows our collaboration with The University of Sheffield.
Classical tissue recombination experiments performed in the chick embryo provide evidence that signals operating during early limb development specify the position and identity of feathers. Sonic hedgehog (Shh) signalling in the embryonic chick wing bud specifies positional information required for the formation of adult flight feathers in a defined spatial and temporal sequence that reflects their different identities.
- An intrinsic cell cycle timer terminates limb bud outgrowth
Joseph Pickering, Constance A. Rich, Holly Stainton, et al. Developmental Biology, 7:e37429 (2018). - Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)
Fernanda Dotti do Prado, Manuel Vera, Miguel Hermida et al. Evolutionary Applications, 11:1322–1341 (2018). - A gene expression atlas of the domestic pig
Freeman, T.C., Ivens, A., Baillie, J.K., et al. BMC Biology. 10, 90-111 (2012).
Structural and functional annotation of the porcine immunome
2013 – Dawson, H.D., Loveland, J.E., Pascal, G., et al.
The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, 3,472 transcripts were annotated. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. Gene duplications for 18 genes were found, including 13 immune response genes and five non-immune response genes discovered in the annotation process.
- A gene expression atlas of the domestic pig
Freeman, T.C., Ivens, A., Baillie, J.K., et al. BMC Biology, 10, 90-111 (2012).
Exploring the transcriptomic changes underlying recombinant vaccine efficacy against Teladorsagia circumcincta in 3-month-old lambs
2023 – Tara Pérez-Hernández, Julia N. Hernández, Stewart T.G. Burgess, et al.
Teladorsagia circumcincta is an abomasal parasitic nematode that can cause serious issues in small ruminant production, which are aggravated by drug resistance. Vaccines have been suggested as a feasible, long-lasting alternative for control since adaptation to the host’s immune mechanisms by helminths develops at a much slower pace than anthelmintic resistance. Recently, a T. circumcincta recombinant subunit vaccine yielded over a 60% reduction in egg excretion and worm burden and induced strong humoral and cellular anti-helminth responses in vaccinated 3-month-old Canaria Hair Breed (CHB) lambs, but Canaria Sheep (CS) of a similar age were not protected by the vaccine. Here, we compared the transcriptomic profiles in the abomasal lymph nodes of such 3-month-old CHB and CS vaccinates 40 days after infection with T. circumcincta to understand differences in responsiveness at the molecular level.
Structural and functional annotation of the porcine immunome
2013 – Dawson, H.D., Loveland, J.E., Pascal, G., et al.
The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, 3,472 transcripts were annotated. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. Gene duplications for 18 genes were found, including 13 immune response genes and five non-immune response genes discovered in the annotation process.
(Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
- IFITM3 restricts the morbidity and mortality associated with influenza
Everitt, A.R., Clare, S., Pertel, T., et al. Nature, 484, 519-U146 (2012). - Macrophages.com: an on-line community resource for innate immunity research
Robert C., Lu X., Law A., et al. Immunobiology, 216, 1203-11 (2011). - Microarray analyses of mouse responses to infection by Neospora caninum identifies disease associated cellular pathways in the host response
Ellis, J., Sinclair, D., Morrison, D., et al. Molecular and Biochemical Parasitology, 174(2):117-27 (2010). - RamA, a member of the AraC/XylS family, influences both virulence and efflux in Salmonella enterica serovar Typhimurium
Bailey, A.M. Ivens, A., Kingsley, R., et al. Journal of Bacteriology, 192, 1607 (2010). - Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts
DeMarco, R. Mathieson, W., Manuel, S.J., et al. Genome Research, 20(8):1112-21 (2010).
Ritonavir reverses resistance to docetaxel and cabazitaxel in prostate cancer cells with acquired resistance to docetaxel
2024 – Eric van der Putten, Katja Wosikowski, Jos H.Beijnen, et al.
This study investigates the mechanisms of acquired resistance to docetaxel in prostate cancer cells, focusing on the role of P-glycoprotein (P-gp) drug transporters.
Enitociclib, a Selective CDK9 Inhibitor, Induces Complete Regression of MYC+ Lymphoma by Downregulation of RNA Polymerase II Mediated Transcription
2023 – Melanie M. Frigault, Arushi Mithal, Harvey Wong, et al.
This study investigates the pharmacodynamic (PD) effect of CDK9 inhibition in preclinical models and in blood samples from patients (DH-DLBCL [n=10] and MYC+ NHL [n=5]) treated with 30 mg i.v. QW enitociclib.
The menin inhibitor revumenib in KMT2A-rearranged or NPM1-mutant leukaemia
2023 – Issa, G.C., Aldoss, I., DiPersio, J, et al.
This study shows our collaboration with Syndax Pharmaceuticals.
Here, we describe the results of the first-in-human phase 1 clinical trial investigating revumenib (SNDX-5613), a potent and selective oral inhibitor of the menin–KMT2A interaction, in patients with relapsed or refractory acute leukaemia (ClinicalTrials.gov, NCT04065399).
Anti-cancer activity of ST101, a novel antagonist of CCAAT/enhancer binding protein β
2022 – Emma Darvishi, Lila Ghamsari, Siok F. Leong, Ricardo Ramirez, Jim A. Rotolo, et al.
This study shows our collaboration with Sapience Therapeutics.
CCAAT/Enhancer Binding Protein β (C/EBPβ) is a basic leucine zipper (bZIP) family transcription factor that is upregulated or overactivated in many cancers, resulting in gene transactivation that drives oncogenesis. C/EBPβ dimerization regulates binding to DNA at the canonical TTGCGCAA motif and subsequent transcriptional activity, suggesting that disruption of dimerization represents a powerful approach to inhibit this previously ‘undruggable’ oncogenic target. Here we describe the mechanism of action and anti-tumor activity of ST101, a novel and selective peptide antagonist of C/EBPβ that is currently in clinical evaluation in patients with advanced solid tumors.
Outcomes based on plasma biomarkers in METEOR, a randomized phase 3 trial of cabozantinib vs everolimus in advanced renal cell carcinoma
2021 – Thomas Powles, Toni K. Choueiri, Robert J. Motzer, Eric Jonasch, et al.
This study shows our collaboration with several organisations including Queen Mary University of London, Memorial Sloan Kettering Cancer Center, University of Texas
In this exploratory analysis, plasma biomarkers from baseline and week 4 from 621 of 658 randomized patients were analysed for CA9, HGF, MET, GAS6, AXL, VEGF, VEGFR2, and IL-8. PFS and OS were analysed by baseline biomarker levels as both dichotomized and continuous variables using univariate and multivariable methods.
ctDNA guiding adjuvant immunotherapy in urothelial carcinoma
2021 – Thomas Powles, Zoe June Assaf, et al.
This study shows our collaboration with Genentech.
Minimally invasive approaches to detect residual disease after surgery are needed to identify patients with cancer who are at risk for metastatic relapse. Circulating tumour DNA (ctDNA) holds promise as a biomarker for molecular residual disease and relapse. This study evaluated outcomes in 581 patients who had undergone surgery and were evaluable for ctDNA from a randomized phase III trial of adjuvant atezolizumab versus observation in operable urothelial cancer.
Serum Alpha-fetoprotein Levels and Clinical Outcomes in the Phase III CELESTIAL Study of Cabozantinib versus Placebo in Patients with Advanced Hepatocellular Carcinoma
2020 – Robin Kate Kelley, Tim Meyer, Lorenza Rimassa, et al.
This study shows our collaboration with Exelixis.
The phase III CELESTIAL study demonstrated improved overall survival (OS) and progression-free survival (PFS) with cabozantinib versus placebo in patients with previously treated, advanced hepatocellular carcinoma (HCC). We analyzed outcomes by baseline alpha-fetoprotein (AFP) and on-treatment AFP changes.
CDK4/6 inhibition enhances antitumor efficacy of chemotherapy and immune checkpoint inhibitor combinations in preclinical models and enhances T-cell activation in patients with SCLC receiving chemotherapy
2020 – Anne Lai, Jessica Sorrentino, Konstantin Dragnev, et al.
This study shows our collaboration with G1 Therapeutics.
Combination treatment with chemotherapy and immune checkpoint inhibitors (ICIs) has demonstrated meaningful clinical benefit to patients. Transient CDK4/6 inhibition by trilaciclib was sufficient to enhance and prolong the duration of the antitumor response by chemotherapy/ICI combinations, suggesting a role for the transient cell cycle arrest of tumor immune infiltrates in remodeling the tumor microenvironment.
Development of a gene expression–based prognostic signature for IDH wild-type glioblastoma
2020 – Radia M. Johnson, Heidi S. Phillips, Carlos Bais, et al.
This study shows our collaboration with Genentech.
We aimed to develop a gene expression–based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations.
Comprehensive Profiling of Poor-Risk Paired Primary and Recurrent Triple-Negative Breast Cancers Reveals Immune Phenotype Shifts
2020 – Katherine E. Hutchinson, Susan E. Yost, Ching-Wei Chang, et al.
This study shows our collaboration with Genentech.
Emerging data suggest immune checkpoint inhibitors have reduced efficacy in heavily pretreated triple-negative breast cancers (TNBC), but underlying mechanisms are poorly understood. To better understand the phenotypic evolution of TNBCs, we studied the genomic and transcriptomic profiles of paired tumors from patients with TNBC.
(Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
Tumor Fusion Burden as a Hallmark of Immune Infiltration in Prostate Cancer
2020 – Marie-Claire Wagle, Joseph Castillo, Shrividhya Srinivasan, et al.
This study shows our collaboration with Genentech.
Prostate cancer is the second leading cause of cancer-related death in men. Our findings suggest that high tumor fusion burden may be a more appropriate biomarker than tumor mutational burden in prostate cancer, as it more closely associates with immunogenicity, and suggests that tumors with high fusion burden could be potential candidates for immunotherapeutic agents.
- Rintodestrant (G1T48), an oral selective estrogen receptor degrader, in ER+/HER2 locally advanced or metastatic breast cancer: updated phase 1 results and dose selection
Philippe Aftimos, Patrick Neven, Mark Pegram, et al. San Antonio Breast Cancer Symposium 2020 Poster. - Pharmacodynamic analysis from a phase 1 study of rintodestrant (G1T48), an oral selective estrogen receptor degrader, in ER+/HER 2 locally advanced or metastatic breast cancer
Philippe Aftimos, Marina Maglakeidze, Andor W.J.M. Glaudemans, et al. San Antonio Breast Cancer Symposium 2020 Poster. - Trilaciclib improves overall survival when given with gemcitabine/carboplatin in patients with metastatic triple negative breast cancer: final analysis of a randomized phase 2 trial
Joyce O’Shaughnessy, Gail S. Wright, Anu R. Thummala, et al. San Antonio Breast Cancer Symposium 2020 Poster. - Transcriptome profiling of ST3GAL4 and FUT7 in multiple tumor types and prognostic value in adult acute myeloid leukemia
William E. Fogler, Vince Deng, David Stewart, et al. AACR Virtual Meeting II 2020 Poster. - Lerociclib (G1T38), a continuously dosed oral CDK4/6 inhibitor, with fulvestrant in HR+/HER2- advanced breast cancer patients: updated Phase 2 results and dose selection
Iurie Bulat, Marina Maglakeidze, Boris Krastev, et al. ESMO Congress 2020 Poster. - Trilaciclib plus chemotherapy versus chemotherapy alone in patients with metastatic triple-negative breast cancer: a multicentre, randomised, open-label, phase 2 trial
Antoinette R Tan, Gail S Wright, Anu R Thummala, et al. The Lancet Oncology (2019). - P300/CBP inhibitor CCS1477 targets 22RV1 prostate tumor AR and C-MYC gene expression in vivo
Paul Elvin, Neil Pegg, Simone Daminelli, et al. AACR Annual Meeting 2019 Poster. - Association of tumor fusion burden with immune presence and androgen sensitivity in prostate cancer
Marie Wagle, Kobe Yuen, Edward E. Kadel, III, et al. AACR Annual Meeting 2019 Poster. - First-in-human dose-escalation study of G1T48, an oral selective estrogen receptor degrader (SERD), in postmenopausal women with ER+/HER2- locally advanced or metastatic breast cancer (ABC)
E. Claire Dees, Philippe Aftimos, Catharina Willemien Menke-van der Houven van Oordt, et al. ESMO Congress 2019 Poster. - Lerociclib (G1T38), an oral CDK4/6 inhibitor, dosed continuously in combination with osimertinib for EGFRmut non−small cell lung cancer: initial Phase 1b results
David Berz, Alexander I. Spira, Shirish M. Gadgeel, et al. ESMO Congress 2019 Poster. - TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells
Sanjeev Mariathasan, Shannon J. Turley, Dorothee Nickles et al. Nature (2018). - Survival prediction in mesothelioma using a scalable Lasso regression model: instructions for use and initial performance using clinical predictors
Andrew C Kidd, Michael McGettrick, Selina Tsim, et al. BMJ Open Respiratory Research (2018). - Transient exposure to trilaciclib, a CDK4/6 inhibitor, modulates gene expression in tumor immune infiltrates and promotes a pro-inflammatory tumor microenvironment
Anne Y. Lai, Jessica A. Sorrentino, Jay C. Strum, Patrick J. Roberts. AACR Annual Meeting 2018 Poster. - The CDK4/6 inhibitor, G1T38, enhances response to targeted therapies in preclinical models of non-small cell lung cancer
Jessica A. Sorrentino, Daniel M. Freed, John E. Bisi, et al. AACR Annual Meeting 2018 Poster. - Trilaciclib preserves and enhances immune system function in extensive-stage small cell lung cancer (SCLC) patients receiving first-line chemotherapy
J.A. Sorrentino, A.Y. Lai, C.R. Hall, et al. ESMO Congress 2018 Poster. - Trilaciclib, a C4/6 inhibitor, dosed with gemcitabine, carboplatin in metastatic triple negative breast cancer (MTNBC) patients: preliminary phase 2 results
Joyce OʼShaughnessy, Gail S. Wright, Anu R. Thummala, et al. San Antonio Breast Cancer Symposium 2018 Poster. - Gene mutational analyses in 154 ovarian cancer (OC) samples from the ROSiA study of front-line bevacizumab (BEV)-containing therapy for OC 950P
et al.Annals of Oncology (2017). (Just one of several genomics publications featuring bioinformatics research from Fios Genomics.) - Analysis of stroma and immune-related gene expression patterns during breast cancer (BC) progression
Luciana Molinero, Joan Albanell, Hartmut Koeppen, et al. ESMO Congress 2017 Poster. - Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment
Doig T.N., Hume D.A., Theocharidis T. et al. BMC Genomics, 14, 469 (2013). - Cyclin G1 regulates the outcome of taxane-induced mitotic checkpoint arrest
Russell, P., Hennessy, B.T., Li, J. et al. Oncogene 31, 2450-2460 (2012). - Oligonucleotide microarray expression profiling of contrasting invasive phenotypes in colorectal cancer
Thorn C.C., Williams D. and Freeman T.C. Methods in Molecular Biology 755, 203-21 (2011). - Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer Using Formalin-Fixed Paraffin-Embedded Tissue
Kennedy RD, Bylesjo M, Kerr P, et al. J Clin Oncol, 29, 4620-4626 (2011). - Microarray analyses of mouse responses to infection by Neospora caninum identifies disease associated cellular pathways in the host response
Ellis, J. et al. Molecular and Biochemical Parasitology (2010).
Application of pharmacogenomics and bioinformatics to exemplify the utility of human ex vivo organoculture models in the field of precision medicine
2019 – Karen Cowan, Graeme Macluskie, Michael Finch, et al.
This study shows our collaboration with REPROCELL.
Here we describe a collaboration between industry, the National Health Service (NHS) and academia that sought to demonstrate how early understanding of both pharmacology and genomics can improve strategies for the development of precision medicines.
(Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
- TGFβ and IL-13 Induce Pro-Fibrotic Changes in the 3DBioBarrierTM Airway Epithelial/Fibroblast Model System
Sam J. Wadsworth, Catherine Overed-Sayers, Lynne Murray et al. ATS Journals (2016). - USP18 restricts PRRSV growth through alteration of nuclear translocation of NF-κB p65 and p50 in MARC-145 cells
Xu D, Lillico SG, Barnett MW, et al. Virus Research 169, 264-7 (2012).
Gene expression profiling of placentae from women with obesity and obstructive sleep apnoea
2022 – Emma C Johns, Daniel L Halligan, Triin Tammsalu, et al.
This study shows our collaboration with Queen’s Medical Research Institute.
Obstructive sleep apnoea (OSA), a condition characterised by intermittent hypoxia and reoxygenation during sleep, is associated with an increased risk of adverse pregnancy outcomes including gestational diabetes and hypertensive disorders of pregnancy. The biological mechanisms of these associations are poorly understood. The impact of OSA on placental function has not been well characterised. 3′ mRNA sequencing on placenta from women with obesity and OSA (n = 11) and women with obesity and no OSA (n = 9) were performed.
Discovery through Machine Learning and Preclinical Validation of Novel Anti-Diabetic Peptides
2021 – Rory Casey, Alessandro Adelfio, Martin Connolly, Audrey Wall, Ian Holyer and Nora Khaldi
This study shows our collaboration with Nuritas Ltd.
Using machine learning, we present novel anti-diabetic peptides which are less than 16 amino acids in length, distinct from human signalling peptides. We validate the capacity of these peptides to stimulate glucose uptake and Glucose transporter type 4 (GLUT4) translocation in vitro. In obese insulin-resistant mice, predicted peptides significantly lower plasma glucose, reduce glycated haemoglobin and even improve hepatic steatosis when compared to treatments currently in use in a clinical setting.
By Research Stage
Integration of genomic and transcriptomic data of inbred mouse models for polygenic obesity and leanness revealed “obese” and “lean” candidate alleles in polyadenylation signals
2024 – Martin Simon, Špela Mikec, Nicholas M. Morton, et al.
This study investigates the association between genetic variations in polyadenylation signals (PAS-SNPs) and obesity in inbred mouse models.
Enitociclib, a Selective CDK9 Inhibitor, Induces Complete Regression of MYC+ Lymphoma by Downregulation of RNA Polymerase II Mediated Transcription
2023 – Melanie M. Frigault, Arushi Mithal, Harvey Wong, et al.
This study investigates the pharmacodynamic (PD) effect of CDK9 inhibition in preclinical models and in blood samples from patients (DH-DLBCL [n=10] and MYC+ NHL [n=5]) treated with 30 mg i.v. QW enitociclib.
Microarray profiling predicts early neurological and immune phenotypic traits in advance of CNS disease
2021 – Paul Montague, Barbara Bradley, Jean Rodgers, Peter G. E. Kennedy
Human African trypanosomiasis (HAT), also known as sleeping sickness, is a major cause of mortality and morbidity in sub-Saharan Africa. We hypothesised that recent findings of neurological features and parasite brain infiltration occurring at much earlier stages in HAT than previously thought could be explained by early activation of host genetic programmes controlling CNS disease.
Multiomics Provide Insights into the Key Molecules and Pathways Involved in the Physiological Adaptation of Atlantic Salmon (Salmo salar) to Chemotherapeutic-Induced Oxidative Stress
2021 – Lazado C., Timmerhaus G., Breiland M., Pittman K., Hytterød S.
In this study, multiomics analysis helped understanding how a chemical oxidative stressor alters salmon physiology at both the systemic and mucosal levels. This knowledge will be pivotal in developing an evidence-driven approach to the use of oxidative therapeutics in fish, with some of the molecules and pathways identified as potential biomarkers and targets for assessing the physiological cost of these treatments.
Consequences of continuous ozonation on the health and welfare of Atlantic salmon post-smolts in a brackish water recirculating aquaculture system
2021 – Lazado Carlo, Kevin T.Stiller, Britt-Kristin Megård Reiten, João Osório, Jelena Kolarevic, Lill-Heidi Johansen
This study investigated the biological consequences of 45-day continuous ozonation on Atlantic salmon (Salmo salar) post-smolts in a brackish water recirculating aquaculture system (RAS). Microarray analysis revealed that the gills and liver were more responsive to the oxidant than the skin, with the gills being the most sensitive. Moreover, the magnitude of the transcriptomic modifications depended on the exposure duration. A functional analysis showed that genes involved in immunity and ribosomal functions were significantly affected in the gills. In contrast, genes crucial for the oxidation-reduction process were mainly targeted in the liver.
Discovery through Machine Learning and Preclinical Validation of Novel Anti-Diabetic Peptides
2021 – Rory Casey, Alessandro Adelfio, Martin Connolly, Audrey Wall, Ian Holyer and Nora Khaldi
This study shows our collaboration with Nuritas Ltd.
Using machine learning, we present novel anti-diabetic peptides which are less than 16 amino acids in length, distinct from human signalling peptides. We validate the capacity of these peptides to stimulate glucose uptake and Glucose transporter type 4 (GLUT4) translocation in vitro. In obese insulin-resistant mice, predicted peptides significantly lower plasma glucose, reduce glycated haemoglobin and even improve hepatic steatosis when compared to treatments currently in use in a clinical setting.
Central nervous system regeneration is driven by microglia necroptosis and repopulation
2019 – Amy F. Lloyd, Claire L. Davies, Rebecca K. Holloway, et al.
This study shows our collaboration with the Medical Research Council Centre for Reproductive Health, The Queen’s Medical Research Institute, The University of Edinburgh as well as other collaborators.
Failed regeneration of CNS myelin contributes to clinical decline in neuroinflammatory and neurodegenerative diseases, for which there is an unmet therapeutic need. Impaired microglia death and/or repopulation may underpin dysregulated microglia activation in neurological diseases, and therapeutic targets to promote white matter regeneration were revealed.
- P300/CBP inhibitor CCS1477 targets 22RV1 prostate tumor AR and C-MYC gene expression in vivo
Paul Elvin, Neil Pegg, Simone Daminelli, et al. AACR Annual Meeting 2019 Poster. (Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
- Association of tumor fusion burden with immune presence and androgen sensitivity in prostate cancer
Marie Wagle, Kobe Yuen, Edward E. Kadel, III, et al. AACR Annual Meeting 2019 Poster. - TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells
Sanjeev Mariathasan, Shannon J. Turley, Dorothee Nickles et al. Nature (2018). - Species-specific regulation of angiogenesis by glucocorticoids reveals contrasting effects on inflammatory and angiogenic pathways
Ruth Morgan, John Keen, Daniel Halligan, et al. PLoS ONE (2018). - Transient exposure to trilaciclib, a CDK4/6 inhibitor, modulates gene expression in tumor immune infiltrates and promotes a pro-inflammatory tumor microenvironment
Anne Y. Lai, Jessica A. Sorrentino, Jay C. Strum, Patrick J. Roberts. AACR Annual Meeting 2019 Poster. (Just one of several genomics publications featuring bioinformatics research from Fios Genomics.) - The CDK4/6 inhibitor, G1T38, enhances response to targeted therapies in preclinical models of non-small cell lung cancer
Jessica A. Sorrentino, Daniel M. Freed, John E. Bisi, et al. AACR Annual Meeting 2018 Poster. - TGFβ and IL-13 Induce Pro-Fibrotic Changes in the 3DBioBarrierTM Airway Epithelial/Fibroblast Model System
Sam J. Wadsworth, Catherine Overed-Sayers, Lynne Murray, et al. ATS Journals (2016). - Assessing Recent Selection and Functionality at Long Non-Coding RNA Loci in the Mouse Genome
R. Axel W. Wiberg, Daniel L. Halligan, Rob W. Ness, et al. Genome Biology and Evolution (2015). - IFITM3 restricts the morbidity and mortality associated with influenza
Everitt, A.R., Clare, S., Pertel, T., et al. Nature 484, 519-U146 (2012). - Cyclin G1 regulates the outcome of taxane-induced mitotic checkpoint arrest
Russell, P., Hennessy, B.T., Li, J., et al. Oncogene 31, 2450-2460 (2012). - Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer Using Formalin-Fixed Paraffin-Embedded Tissue
Kennedy RD, Bylesjo M, Kerr P, et al. J Clin Oncol, 29, 4620-4626 (2011). - The genome of the blood fluke Schistosoma mansoni
Berriman, M. et al. Nature 460, 352–358 (2009).
(Just one of several genomics publications featuring bioinformatics.)
Genetics of vegetarianism: A genome-wide association study
2023 – Nabeel R. Yaseen, Catriona L.K. Barnes, Lingwei Sun, et al.
In this study, a genome-wide association study (GWAS) was used to identify loci associated with strict vegetarianism in UK Biobank participants. Comparing 5,324 strict vegetarians to 329,455 controls, one SNP on chromosome 18 that is associated with vegetarianism at the genome-wide significant level (rs72884519, β = -0.11, P = 4.997 x 10−8) was identified, along with an additional 201 suggestively significant variants.
Hepatotoxicity of AKR1C3 Inhibitor BAY1128688: Findings from an Early Terminated Phase IIa Trial for the Treatment of Endometriosis
2023 – Jan Hilpert, Esther Groettrup-Wolfers, Hristiyan Kosturski, Laura Bennett, Catriona L K Barnes, et al.
This manuscript reports the results of a clinical trial (AKRENDO1) assessing the effects of BAY1128688 in adult premenopausal women with endometriosis-related pain symptoms over a 12-week treatment period.
Defects in sperm capacitation/fertilizing ability are equally prevalent across ages in men seeking fertility assistance
2023 – Fady I. Sharara, G. Charles Ostemeier and Alexander J. Travis
This study shows our collaboration with Androvia LifeSciences.
The aim of this study was to determine how capacitation ability, measured by Cap-Score™, and traditional semen analysis measures (volume, concentration, motility) changes with age in men questioning their fertility (MQF).
Anti-cancer activity of ST101, a novel antagonist of CCAAT/enhancer binding protein β
2022 – Emma Darvishi, Lila Ghamsari, Siok F. Leong, Ricardo Ramirez, Jim A. Rotolo, et al.
This study shows our collaboration with Sapience Therapeutics.
CCAAT/Enhancer Binding Protein β (C/EBPβ) is a basic leucine zipper (bZIP) family transcription factor that is upregulated or overactivated in many cancers, resulting in gene transactivation that drives oncogenesis. C/EBPβ dimerization regulates binding to DNA at the canonical TTGCGCAA motif and subsequent transcriptional activity, suggesting that disruption of dimerization represents a powerful approach to inhibit this previously ‘undruggable’ oncogenic target. Here we describe the mechanism of action and anti-tumor activity of ST101, a novel and selective peptide antagonist of C/EBPβ that is currently in clinical evaluation in patients with advanced solid tumors.
Gene expression profiling of placentae from women with obesity and obstructive sleep apnoea
2022 – Emma C Johns, Daniel L Halligan, Triin Tammsalu, et al.
This study shows our collaboration with Queen’s Medical Research Institute.
Obstructive sleep apnoea (OSA), a condition characterised by intermittent hypoxia and reoxygenation during sleep, is associated with an increased risk of adverse pregnancy outcomes including gestational diabetes and hypertensive disorders of pregnancy. The biological mechanisms of these associations are poorly understood. The impact of OSA on placental function has not been well characterised. 3′ mRNA sequencing on placenta from women with obesity and OSA (n = 11) and women with obesity and no OSA (n = 9) were performed.
ctDNA guiding adjuvant immunotherapy in urothelial carcinoma
2021 – Thomas Powles, Zoe June Assaf, et al.
This study shows our collaboration with Genentech.
Minimally invasive approaches to detect residual disease after surgery are needed to identify patients with cancer who are at risk for metastatic relapse. Circulating tumour DNA (ctDNA) holds promise as a biomarker for molecular residual disease and relapse. This study evaluated outcomes in 581 patients who had undergone surgery and were evaluable for ctDNA from a randomized phase III trial of adjuvant atezolizumab versus observation in operable urothelial cancer.
Serum Alpha-fetoprotein Levels and Clinical Outcomes in the Phase III CELESTIAL Study of Cabozantinib versus Placebo in Patients with Advanced Hepatocellular Carcinoma
2020 – Robin Kate Kelley, Tim Meyer, Lorenza Rimassa, et al.
This study shows our collaboration with Exelixis.
The phase III CELESTIAL study demonstrated improved overall survival (OS) and progression-free survival (PFS) with cabozantinib versus placebo in patients with previously treated, advanced hepatocellular carcinoma (HCC). We analyzed outcomes by baseline alpha-fetoprotein (AFP) and on-treatment AFP changes.
CDK4/6 inhibition enhances antitumor efficacy of chemotherapy and immune checkpoint inhibitor combinations in preclinical models and enhances T-cell activation in patients with SCLC receiving chemotherapy
2020 – Anne Lai, Jessica Sorrentino, Konstantin Dragnev, et al.
This study shows our collaboration with G1 Therapeutics.
Combination treatment with chemotherapy and immune checkpoint inhibitors (ICIs) has demonstrated meaningful clinical benefit to patients. Transient CDK4/6 inhibition by trilaciclib was sufficient to enhance and prolong the duration of the antitumor response by chemotherapy/ICI combinations, suggesting a role for the transient cell cycle arrest of tumor immune infiltrates in remodeling the tumor microenvironment.
Development of a gene expression–based prognostic signature for IDH wild-type glioblastoma
2020 – Radia M. Johnson, Heidi S. Phillips, Carlos Bais, et al.
This study shows our collaboration with Genentech.
We aimed to develop a gene expression–based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations.
Comprehensive Profiling of Poor-Risk Paired Primary and Recurrent Triple-Negative Breast Cancers Reveals Immune Phenotype Shifts
2020 – Katherine E. Hutchinson, Susan E. Yost, Ching-Wei Chang, et al.
This study shows our collaboration with Genentech.
Emerging data suggest immune checkpoint inhibitors have reduced efficacy in heavily pretreated triple-negative breast cancers (TNBC), but underlying mechanisms are poorly understood. To better understand the phenotypic evolution of TNBCs, we studied the genomic and transcriptomic profiles of paired tumors from patients with TNBC.
(Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
Tumor Fusion Burden as a Hallmark of Immune Infiltration in Prostate Cancer
2020 – Marie-Claire Wagle, Joseph Castillo, Shrividhya Srinivasan, et al.
This study shows our collaboration with Genentech.
Prostate cancer is the second leading cause of cancer-related death in men. Our findings suggest that high tumor fusion burden may be a more appropriate biomarker than tumor mutational burden in prostate cancer, as it more closely associates with immunogenicity, and suggests that tumors with high fusion burden could be potential candidates for immunotherapeutic agents.
Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC
2020 – A.K. Sorial, I.M.J. Hofer, M. Tselepi, et al.
This study highlights the expertise of our team.
In cartilage, the osteoarthritis (OA) associated single nucleotide polymorphism (SNP) rs11780978 correlates with differential expression of PLEC, and with differential methylation of PLEC CpG dinucleotides, forming eQTLs and mQTLs respectively. We sought to assess whether these PLEC functional effects were cartilage specific.
DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA
2020 – Laura J. Smyth, Christopher C. Patterson, Elizabeth J. Swan, et al.
This study shows our collaboration with Queen’s University Belfast.
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
- Rintodestrant (G1T48), an oral selective estrogen receptor degrader, in ER+/HER2 locally advanced or metastatic breast cancer: updated phase 1 results and dose selection
Philippe Aftimos, Patrick Neven, Mark Pegram, et al. San Antonio Breast Cancer Symposium 2020 Poster. - Pharmacodynamic analysis from a phase 1 study of rintodestrant (G1T48), an oral selective estrogen receptor degrader, in ER+/HER 2 locally advanced or metastatic breast cancer
Philippe Aftimos, Marina Maglakeidze, Andor W.J.M. Glaudemans, et al. San Antonio Breast Cancer Symposium 2020 Poster. - Trilaciclib improves overall survival when given with gemcitabine/carboplatin in patients with metastatic triple negative breast cancer: final analysis of a randomized phase 2 trial
Joyce O’Shaughnessy, Gail S. Wright, Anu R. Thummala, et al. San Antonio Breast Cancer Symposium 2020 Poster. - Transcriptome profiling of ST3GAL4 and FUT7 in multiple tumor types and prognostic value in adult acute myeloid leukemia.
William E. Fogler, Vince Deng, David Stewart, et al. AACR Virtual Meeting II 2020 Poster. - Lerociclib (G1T38), a continuously dosed oral CDK4/6 inhibitor, with fulvestrant in HR+/HER2- advanced breast cancer patients: updated Phase 2 results and dose selection
Iurie Bulat, Marina Maglakeidze, Boris Krastev, et al. ESMO Congress 2020 Poster. - Microbe-host interplay in atopic dermatitis and psoriasis
Nanna Fyhrquist, Gareth Muirhead, Stefanie Prast-Nielsen, et al. Nature Communications, 4703 (2019). - Central nervous system regeneration is driven by microglia necroptosis and repopulation
Amy F. Lloyd, Claire L. Davies, Rebecca K. Holloway, et al. Nature Neuroscience, 22, 1046 –1052, (2019). - Durable responses observed in elderly AML patients unfit for intensive chemotherapy with first-in-class selective AXL inhibitor bemcentinib (BGB324) in combination with LDAC: phase II open-label study
Sonja Loges, Michael Heuser, Jörg Chromik, et al. ASH Annual Meeting 2019 Poster. - First-in-human dose-escalation study of G1T48, an oral selective estrogen receptor degrader (SERD), in postmenopausal women with ER+/HER2- locally advanced or metastatic breast cancer (ABC)
E. Claire Dees, Philippe Aftimos, Catharina Willemien Menke-van der Houven van Oordt, et al. ESMO Congress 2019 Poster. - Lerociclib (G1T38), an oral CDK4/6 inhibitor, dosed continuously in combination with osimertinib for EGFRmut non−small cell lung cancer: initial Phase 1b results
David Berz, Alexander I. Spira, Shirish M. Gadgeel, et al. ESMO Congress 2019 Poster. - Application of pharmacogenomics and bioinformatics to exemplify the utility of human ex vivo organoculture models in the field of precision medicine
Karen Cowan, Graeme Macluskie, Michael Finch, et al. PLOS One, 14(12) (2019). (Just one of several genomics publications featuring bioinformatics research from Fios Genomics.) - Trilaciclib plus chemotherapy versus chemotherapy alone in patients with metastatic triple-negative breast cancer: a multicentre, randomised, open-label, phase 2 trial
Antoinette R. Tan, Gail S. Wright, Anu R. Thummala, et al. The Lancet Oncology, 20(11) 1587-1601. (2019). - TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells
Sanjeev Mariathasan, Shannon J. Turley, Dorothee Nickles et al. Nature (2018). - Trilaciclib preserves and enhances immune system function in extensive-stage small cell lung cancer (SCLC) patients receiving first-line chemotherapy
J.A. Sorrentino, A.Y. Lai, C.R. Hall, et al. ESMO Congress 2018 Poster. - Trilaciclib, a C4/6 inhibitor, dosed with gemcitabine, carboplatin in metastatic triple negative breast cancer (MTNBC) patients: preliminary phase 2 results
Joyce OʼShaughnessy, Gail S. Wright, Anu R. Thummala, et al. San Antonio Breast Cancer Symposium 2018 Poster. - Survival prediction in mesothelioma using a scalable Lasso regression model: instructions for use and initial performance using clinical predictors
Andrew C Kidd, Michael McGettrick, Selina Tsim, et al. BMJ Open Respiratory Research (2018). - Transient exposure to trilaciclib, a CDK4/6 inhibitor, modulates gene expression in tumor immune infiltrates and promotes a pro-inflammatory tumor microenvironment
Anne Y. Lai, Jessica A. Sorrentino, Jay C. Strum, Patrick J. Roberts. AACR Annual Meeting 2018 Poster. - Analysis of stroma and immune-related gene expression patterns during breast cancer (BC) progression
Luciana Molinero, Joan Albanell, Hartmut Koeppen, et al. ESMO Congress 2017 Poster. - A multi-tissue age prediction model based on DNA methylation analysis
Hussain Alsaleh, Nicola A. McCallum, Daniel L. Halligan, Penelope R. Haddrill. Forensic Science International: Genetics Supplement Series (2017). - Gene mutational analyses in 154 ovarian cancer (OC) samples from the ROSiA study of front-line bevacizumab (BEV)-containing therapy for OC
et al.Annals of Oncology (2017). - Stress perception impacts on clinical signs of skin ageing and modifies the epigenome
R. Pattinson, C. Bundy, L. Cordingley, et al. 062. Journal of Investigative Dermatology (2016). - Whole blood gene expression profiling of neonates with confirmed bacterial sepsis
Dickinson P., Smith C.L., Forster T., et al. Genomics Data 3, 41-48 (2015). - Uterine NK Cells Regulate Endometrial Bleeding in Women and are Suppressed by the Progesterone Receptor Modulator Asoprisnil
Wilkens J., Male V., Ghazal P., et al. J. Immunology Aug (2) (2013).
Characterization of the xenobiotic response of Caenorhabditis elegans to the anthelmintic drug albendazole and the indentification of novel drug glucoside metabolites
2010 – Laing, S.T. et al.
This study investigated how the model nematode Caenorhabditis elegans responds to and metabolizes albendazole, one of the most important anthelmintic drugs for human and animal use. Using a mutant strain lacking the β-tubulin drug target to minimize generalized stress responses, we show that the transcriptional response is dominated by genes encoding XMEs (xenobiotic-metabolizing enzymes), particularly cytochrome P450s and UGTs (UDP-glucuronosyl transferases).
Hepatotoxicity of AKR1C3 Inhibitor BAY1128688: Findings from an Early Terminated Phase IIa Trial for the Treatment of Endometriosis
2023 – Jan Hilpert, Esther Groettrup-Wolfers, Hristiyan Kosturski, Laura Bennett, Catriona L K Barnes, et al.
This manuscript reports the results of a clinical trial (AKRENDO1) assessing the effects of BAY1128688 in adult premenopausal women with endometriosis-related pain symptoms over a 12-week treatment period.
Outcomes based on plasma biomarkers in METEOR, a randomized phase 3 trial of cabozantinib vs everolimus in advanced renal cell carcinoma
2021 – Thomas Powles, Toni K. Choueiri, Robert J. Motzer, Eric Jonasch, et al.
This study shows our collaboration several organisations including Queen Mary University of London, Memorial Sloan Kettering Cancer Center, University of Texas
In this exploratory analysis, plasma biomarkers from baseline and week 4 from 621 of 658 randomized patients were analyzed for CA9, HGF, MET, GAS6, AXL, VEGF, VEGFR2, and IL-8. PFS and OS were analyzed by baseline biomarker levels as both dichotomized and continuous variables using univariate and multivariable methods.
Tumor Fusion Burden as a Hallmark of Immune Infiltration in Prostate Cancer
2020 – Marie-Claire Wagle, Joseph Castillo, Shrividhya Srinivasan, et al.
This study shows our collaboration with Genentech.
Prostate cancer is the second leading cause of cancer-related death in men. Our findings suggest that high tumor fusion burden may be a more appropriate biomarker than tumor mutational burden in prostate cancer, as it more closely associates with immunogenicity, and suggests that tumors with high fusion burden could be potential candidates for immunotherapeutic agents.
Application of pharmacogenomics and bioinformatics to exemplify the utility of human ex vivo organoculture models in the field of precision medicine
2019 – Karen Cowan, Graeme Macluskie, Michael Finch, et al.
This study shows our collaboration with REPROCELL.
Here we describe a collaboration between industry, the National Health Service (NHS) and academia that sought to demonstrate how early understanding of both pharmacology and genomics can improve strategies for the development of precision medicines. (Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
Microbe-host interplay in atopic dermatitis and psoriasis
2019 – Nanna Fyhrquist, Gareth Muirhead, Stefanie Prast-Nielsen, et al.
This study shows our collaboration with several organisations for the MAARS FP7 project
Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis.
- Analysis of stroma and immune-related gene expression patterns during breast cancer (BC) progression
Luciana Molinero, Joan Albanell, Hartmut Koeppen, et al. ESMO Congress 2017 Poster. - Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer Using Formalin-Fixed Paraffin-Embedded Tissue
Kennedy RD, Bylesjo M, Kerr P, et al. J Clin Oncol, 29, 4620-4626 (2011).
By Data Type
Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC
2020 – A.K. Sorial, I.M.J. Hofer, M. Tselepi, et al.
This study highlights the expertise of our team.
In cartilage, the osteoarthritis (OA) associated single nucleotide polymorphism (SNP) rs11780978 correlates with differential expression of PLEC, and with differential methylation of PLEC CpG dinucleotides, forming eQTLs and mQTLs respectively. We sought to assess whether these PLEC functional effects were cartilage specific.
Functional testing of thousands of osteoarthritis-associated variants for regulatory activity
2019 – Jason C. Klein, Aidan Keith, Sarah J. Rice, et al.
This study highlights the expertise of our team.
To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signaling in osteoarthritis pathogenesis.
Genetics of vegetarianism: A genome-wide association study
2023 – Nabeel R. Yaseen, Catriona L.K. Barnes, Lingwei Sun, et al.
In this study, a genome-wide association study (GWAS) was used to identify loci associated with strict vegetarianism in UK Biobank participants. Comparing 5,324 strict vegetarians to 329,455 controls, one SNP on chromosome 18 that is associated with vegetarianism at the genome-wide significant level (rs72884519, β = -0.11, P = 4.997 x 10−8) was identified, along with an additional 201 suggestively significant variants.
Development of a gene expression–based prognostic signature for IDH wild-type glioblastoma
2020 – Radia M. Johnson, Heidi S. Phillips, Carlos Bais, et al.
This study shows our collaboration with Genentech.
We aimed to develop a gene expression–based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations.
- Structural and functional annotation of the porcine immunome
Dawson, H.D., Loveland, J.E., Pascal, G., et al. BMC Genomics 14, 332 (2013). - Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment
Doig T.N., Hume D.A., Theocharidis T., et al. BMC Genomics, 14, 469 (2013). - An expression atlas of human primary cells: inference of gene function from coexpression networks
Mabott N.A., Baillie J.K., Brown H., et al. BMC Genomics 14, 632 (2013). - Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations
Kobayashi, A., Donaldson, D.S., Kanaya, T., et al. DNA Research. 19, 407-422 (2012). - Extending signaling pathways with protein-interaction networks. Application to apoptosis
Joan Planas-Iglesias, Emre Guney, Javier García-García, et al. OMICS, 16(5):245-56 (2012). - Macrophages.com: an on-line community resource for innate immunity research
Robert C., Lu X., Law A., Freeman T.C. and Hume D.A. Immunobiology 216, 1203-11 (2011). - Expression of mesenchyme-specific gene signatures by follicular dendritic cells: insights from the meta-analysis of microarray data from multiple mouse cell populations
Mabbott N.A., Baillie J.K., Kobayashi A., et al. Immunology 133, 482-498 (2011).
DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA
2020 – Laura J. Smyth, Christopher C. Patterson, Elizabeth J. Swan, et al.
This study shows our collaboration with Queen’s University Belfast.
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
Application of pharmacogenomics and bioinformatics to exemplify the utility of human ex vivo organoculture models in the field of precision medicine
2019 – Karen Cowan, Graeme Macluskie, Michael Finch, et al.
This study shows our collaboration with REPROCELL.
Here we describe a collaboration between industry, the National Health Service (NHS) and academia that sought to demonstrate how early understanding of both pharmacology and genomics can improve strategies for the development of precision medicines. (Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
- First-in-human dose-escalation study of G1T48, an oral selective estrogen receptor degrader (SERD), in postmenopausal women with ER+/HER2- locally advanced or metastatic breast cancer (ABC)
E. Claire Dees, Philippe Aftimos, Catharina Willemien Menke-van der Houven van Oordt, et al. ESMO Congress 2019 Poster. - Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)
Fernanda Dotti do Prado, Manuel Vera, Miguel Hermida et al. Evolutionary Applications (2018). - Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer Using Formalin-Fixed Paraffin-Embedded Tissue
Kennedy RD, Bylesjo M, Kerr P, et al. J Clin Oncol, 29, 4620-4626 (2011). - Somatic retrotransposition alters the genetic landscape of the human brain
Baillie J.K., Barnett M.W., Upton K.R., et al. Nature 479, 534-7 (2011). - Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host
Parker-Manuel, S.J., Ivens, A.C., Dillon, G.P. & Wilson, R.A. PLoS Negl Trop Dis 5, e1274 (2011). - Genetic diversity amongst isolates of Neospora caninum, and the development of a multiplex assay for the detection of distinct strains
Al-Qassab, S., Reichel, M.P., Ivens, A. & Ellis, J.T. Molecular and Cellular Probes, 23, 132–139 (2009). - Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport
Pan, Z. et al. Microbiology 155, 3200 (2009).
DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA
2020 – Laura J. Smyth, Christopher C. Patterson, Elizabeth J. Swan, et al.
This study shows our collaboration with Queen’s University Belfast.
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC
2020 – A.K. Sorial, I.M.J. Hofer, M. Tselepi, et al.
This study highlights the expertise of our team.
In cartilage, the osteoarthritis (OA) associated single nucleotide polymorphism (SNP) rs11780978 correlates with differential expression of PLEC, and with differential methylation of PLEC CpG dinucleotides, forming eQTLs and mQTLs respectively. We sought to assess whether these PLEC functional effects were cartilage specific.
- A multi-tissue age prediction model based on DNA methylation analysis
Hussain Alsaleh, Nicola A. McCallum, Daniel L. Halligan, Penelope R. Haddrill. Forensic Science International: Genetics Supplement Series (2017). - Stress perception impacts on clinical signs of skin ageing and modifies the epigenome
R. Pattinson, C. Bundy, L. Cordingley, et al. 062. Journal of Investigative Dermatology (2016).
Integration of genomic and transcriptomic data of inbred mouse models for polygenic obesity and leanness revealed “obese” and “lean” candidate alleles in polyadenylation signals
2024 – Martin Simon, Špela Mikec, Nicholas M. Morton, et al.
This study investigates the association between genetic variations in polyadenylation signals (PAS-SNPs) and obesity in inbred mouse models.
Genetics of vegetarianism: A genome-wide association study
2023 – Nabeel R. Yaseen, Catriona L.K. Barnes, Lingwei Sun, et al.
In this study, a genome-wide association study (GWAS) was used to identify loci associated with strict vegetarianism in UK Biobank participants. Comparing 5,324 strict vegetarians to 329,455 controls, one SNP on chromosome 18 that is associated with vegetarianism at the genome-wide significant level (rs72884519, β = -0.11, P = 4.997 x 10−8) was identified, along with an additional 201 suggestively significant variants.
Microarray profiling predicts early neurological and immune phenotypic traits in advance of CNS disease
2021 – Paul Montague, Barbara Bradley, Jean Rodgers, Peter G. E. Kennedy
Human African trypanosomiasis (HAT), also known as sleeping sickness, is a major cause of mortality and morbidity in sub-Saharan Africa. We hypothesised that recent findings of neurological features and parasite brain infiltration occurring at much earlier stages in HAT than previously thought could be explained by early activation of host genetic programmes controlling CNS disease.
Discovery through Machine Learning and Preclinical Validation of Novel Anti-Diabetic Peptides
2021 – Rory Casey, Alessandro Adelfio, Martin Connolly, Audrey Wall, Ian Holyer and Nora Khaldi
This study shows our collaboration with Nuritas Ltd
Using machine learning, we present novel anti-diabetic peptides which are less than 16 amino acids in length, distinct from human signalling peptides. We validate the capacity of these peptides to stimulate glucose uptake and Glucose transporter type 4 (GLUT4) translocation in vitro. In obese insulin-resistant mice, predicted peptides significantly lower plasma glucose, reduce glycated haemoglobin and even improve hepatic steatosis when compared to treatments currently in use in a clinical setting.
Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC
2020 – A.K. Sorial, I.M.J. Hofer, M. Tselepi, et al.
This study highlights the expertise of our team.
In cartilage, the osteoarthritis (OA) associated single nucleotide polymorphism (SNP) rs11780978 correlates with differential expression of PLEC, and with differential methylation of PLEC CpG dinucleotides, forming eQTLs and mQTLs respectively. We sought to assess whether these PLEC functional effects were cartilage specific.
Development of a gene expression–based prognostic signature for IDH wild-type glioblastoma
2020 – Radia M. Johnson, Heidi S. Phillips, Carlos Bais, et al.
This study shows our collaboration with Genentech.
We aimed to develop a gene expression–based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations.
DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA
2020 – Laura J. Smyth, Christopher C. Patterson, Elizabeth J. Swan, et al.
This study shows our collaboration with Queen’s University Belfast.
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
Functional testing of thousands of osteoarthritis-associated variants for regulatory activity
2019 – Jason C. Klein, Aidan Keith, Sarah J. Rice, et al.
This study highlights the expertise of our team.
To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signalling in osteoarthritis pathogenesis.
- Serum Alpha-fetoprotein Levels and Clinical Outcomes in the Phase III CELESTIAL Study of Cabozantinib versus Placebo in Patients with Advanced Hepatocellular Carcinoma
2020 – Robin Kate Kelley, Tim Meyer, Lorenza Rimassa, et al. - Comprehensive Profiling of Poor-Risk Paired Primary and Recurrent Triple-Negative Breast Cancers Reveals Immune Phenotype Shifts
2020 – Katherine E. Hutchinson, Susan E. Yost, Ching-Wei Chang,et al. - Sonic hedgehog specifies flight feather positional information in avian wings
2020 – Lara Busby, Cristina Aceituno, Caitlin McQueen, et al. - Association of tumor fusion burden with immune presence and androgen sensitivity in prostate cancer
Marie Wagle, Kobe Yuen, Edward E. Kadel, III, et al.AACR Annual Meeting 2019 Poster.
- Microbe-host interplay in atopic dermatitis and psoriasis
Nanna Fyhrquist, Gareth Muirhead, Stefanie Prast-Nielsen, et al. Nature Communications, 4703 (2019). - Central nervous system regeneration is driven by microglia necroptosis and repopulation
Amy F. Lloyd, Claire L. Davies, Rebecca K. Holloway, et al. Nature Neuroscience, 22, 1046 –1052, (2019). - Application of pharmacogenomics and bioinformatics to exemplify the utility of human ex vivo organoculture models in the field of precision medicine
Karen Cowan, Graeme Macluskie, Michael Finch, et al. PLOS One, 14(12) (2019). - Trilaciclib plus chemotherapy versus chemotherapy alone in patients with metastatic triple-negative breast cancer: a multicentre, randomised, open-label, phase 2 trial
2019 – Antoinette R Tan, Gail S Wright, Anu R Thummala, et al. - First-in-human dose-escalation study of G1T48, an oral selective estrogen receptor degrader (SERD), in postmenopausal women with ER+/HER2- locally advanced or metastatic breast cancer (ABC)
E. Claire Dees, Philippe Aftimos, Catharina Willemien Menke-van der Houven van Oordt, et al. ESMO Congress 2019 Poster.
- P300/CBP inhibitor CCS1477 targets 22RV1 prostate tumor AR and C-MYC gene expression in vivo
Paul Elvin, Neil Pegg, Simone Daminelli, et al. AACR Annual Meeting 2019 Poster. - Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)
Fernanda Dotti do Prado, Manuel Vera, Miguel Hermida et al. Evolutionary Applications (2018). - An intrinsic cell cycle timer terminates limb bud outgrowth
Joseph Pickering, Constance A Rich, Holly Stainton, et al. Developmental Biology (2018). - Species-specific regulation of angiogenesis by glucocorticoids reveals contrasting effects on inflammatory and angiogenic pathways
Ruth Morgan, John Keen, Daniel Halligan, et al. PLoS ONE (2018). - Survival prediction in mesothelioma using a scalable Lasso regression model: instructions for use and initial performance using clinical predictors
Andrew C Kidd, Michael McGettrick, Selina Tsim, et al. BMJ Open Respiratory Research (2018). - Gene mutational analyses in 154 ovarian cancer (OC) samples from the ROSiA study of front-line bevacizumab (BEV)-containing therapy for OC 950P
R. Deurloo, N. Colombo, C. Mendiola, et al. Annals of Oncology (2017). - Transcriptional changes in chick wing bud polarization induced by retinoic acid
Joseph Pickering, Neha Wali, Matthew Towers. Developmental Dynamics (2017). - A multi-tissue age prediction model based on DNA methylation analysis
Hussain Alsaleh, Nicola A. McCallum, Daniel L. Halligan, Penelope R. Haddrill. Forensic Science International: Genetics Supplement Series (2017). - TGFβ and IL-13 Induce Pro-Fibrotic Changes in the 3DBioBarrierTM Airway Epithelial/Fibroblast Model System
Sam J. Wadsworth, Catherine Overed-Sayers, Lynne Murray, et al. ATS Journals (2016). - Stress perception impacts on clinical signs of skin ageing and modifies the epigenome
R. Pattinson, C. Bundy, L. Cordingley, et al. 062. Journal of Investigative Dermatology (2016). - Whole blood gene expression profiling of neonates with confirmed bacterial sepsis
Dickinson P., Smith C.L., Forster T., et al. Genomics Data 3, 41-48 (2015). - Assessing Recent Selection and Functionality at Long Non-Coding RNA Loci in the Mouse Genome
R. Axel W. Wiberg, Daniel L. Halligan, Rob W. Ness, et al. Genome Biology and Evolution (2015). - Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family
Keightley P.D., Ness R.W., Halligan D.L., Haddrill P.R. Genetics 196, 313-320 (2014). - Faster-X Adaptive Protein Evolution in House Mice
Kousathanas A., Halligan D.L., Keightley P.D. Genetics, 196, 1131-1143 (2014). - Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents
Halligan D.L., Kousathanas A., Ness R.W., et al. PLoS Genetics 9(12) (2013). - Uterine NK Cells Regulate Endometrial Bleeding in Women and are Suppressed by the Progesterone Receptor Modulator Asoprisnil
Wilkens J., Male V., Ghazal P., et al. J. Immunology Aug (2) (2013). - Cyclin G1 regulates the outcome of taxane-induced mitotic checkpoint arrest
- Structural and functional annotation of the porcine immunome
Dawson, H.D., Loveland, J.E., Pascal, G., et al. BMC Genomics 14, 332 (2013). - Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment
Doig T.N., Hume D.A., Theocharidis T., et al. BMC Genomics, 14, 469 (2013).
- An expression atlas of human primary cells: inference of gene function from coexpression networks
Mabott N.A., Baillie J.K., Brown H., et al. BMC Genomics 14, 632 (2013). - Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations
Kobayashi, A., Donaldson, D.S., Kanaya, T., et al. DNA Research. 19, 407-422 (2012). - Cyclin G1 regulates the outcome of taxane-induced mitotic checkpoint arrest
Russell, P., Hennessy, B.T., Li, J., et al. Oncogene 31, 2450-2460 (2012). - A gene expression atlas of the domestic pig
Freeman, T.C., Ivens, A., Baillie, J.K., et al. BMC Biology. 10, 90-111 (2012). - Extending signaling pathways with protein-interaction networks. Application to apoptosis
Joan Planas-Iglesias, Emre Guney, Javier García-García, et al. OMICS, 16(5):245-56 (2012). - USP18 restricts PRRSV growth through alteration of nuclear translocation of NF-κB p65 and p50 in MARC-145 cells
Xu D, Lillico SG, Barnett MW, et al. Virus Research 169, 264-7 (2012). - SynGAP isoforms exert opposing effects on synaptic strength
McMahon AC, Barnett MW, O’Leary TS, et al. Nature Communications 3, 900 (2012). - Oligonucleotide microarray expression profiling of contrasting invasive phenotypes in colorectal cancer
Thorn C.C., Williams D. and Freeman T.C. Methods in Molecular Biology 755, 203-21 (2011). - Macrophages.com: an on-line community resource for innate immunity research
Robert C., Lu X., Law A., Freeman T.C. and Hume D.A. Immunobiology 216, 1203-11 (2011). - Expression of mesenchyme-specific gene signatures by follicular dendritic cells: insights from the meta-analysis of microarray data from multiple mouse cell populations
Mabbott N.A., Baillie J.K., Kobayashi A., et al. Immunology 133, 482-498 (2011). - Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer Using Formalin-Fixed Paraffin-Embedded Tissue
Kennedy RD, Bylesjo M, Kerr P, et al. J Clin Oncol, 29, 4620-4626 (2011). - Somatic retrotransposition alters the genetic landscape of the human brain
Baillie J.K., Barnett M.W., Upton K.R., et al. Nature 479, 534-7 (2011). - Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host
Parker-Manuel, S.J., Ivens, A.C., Dillon, G.P. & Wilson, R.A. PLoS Negl Trop Dis 5, e1274 (2011). - RamA, a member of the AraC/XylS family, influences both virulence and efflux in Salmonella enterica serovar Typhimurium
Bailey, A.M. et al. Journal of bacteriology 192, 1607 (2010). - Comparative expression profiling of Leishmania: modulation in gene expression between species and in different host genetic backgrounds
Depledge, D.P. et al. PLoS neglected tropical diseases 3, e476 (2009). - The global consequence of disruption of the AcrAB-TolC efflux pump in Salmonella enterica includes reduced expression of SPI-1 and other attributes required to infect the host
Webber, M.A. et al. Journal of bacteriology 191, 4276 (2009). - Genetic diversity amongst isolates of Neospora caninum, and the development of a multiplex assay for the detection of distinct strains
Al-Qassab, S., Reichel, M.P., Ivens, A. & Ellis, J.T. Molecular and Cellular Probes, 23, 132–139 (2009). - Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport
Pan, Z. et al. Microbiology 155, 3200 (2009).
Microarray profiling predicts early neurological and immune phenotypic traits in advance of CNS disease
2021 – Paul Montague, Barbara Bradley, Jean Rodgers, Peter G. E. Kennedy
Human African trypanosomiasis (HAT), also known as sleeping sickness, is a major cause of mortality and morbidity in sub-Saharan Africa. We hypothesised that recent findings of neurological features and parasite brain infiltration occurring at much earlier stages in HAT than previously thought could be explained by early activation of host genetic programmes controlling CNS disease.
Discovery through Machine Learning and Preclinical Validation of Novel Anti-Diabetic Peptides
2021 – Rory Casey, Alessandro Adelfio, Martin Connolly, Audrey Wall, Ian Holyer and Nora Khaldi
This study shows our collaboration with Nuritas Ltd
Using machine learning, we present novel anti-diabetic peptides which are less than 16 amino acids in length, distinct from human signalling peptides. We validate the capacity of these peptides to stimulate glucose uptake and Glucose transporter type 4 (GLUT4) translocation in vitro. In obese insulin-resistant mice, predicted peptides significantly lower plasma glucose, reduce glycated haemoglobin and even improve hepatic steatosis when compared to treatments currently in use in a clinical setting.
Microbe-host interplay in atopic dermatitis and psoriasis
2019 – Nanna Fyhrquist, Gareth Muirhead, Stefanie Prast-Nielsen, et al.
This study shows our collaboration with several organisations for the MAARS FP7 project
Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis.
- P300/CBP inhibitor CCS1477 targets 22RV1 prostate tumor AR and C-MYC gene expression in vivo
Paul Elvin, Neil Pegg, Simone Daminelli, et al. AACR Annual Meeting 2019 Poster. - Transcriptional changes in chick wing bud polarization induced by retinoic acid
Joseph Pickering, Neha Wali, Matthew Towers. Developmental Dynamics (2017). - A multi-tissue age prediction model based on DNA methylation analysis
Hussain Alsaleh, Nicola A. McCallum, Daniel L. Halligan, Penelope R. Haddrill. Forensic Science International: Genetics Supplement Series (2017). - TGFβ and IL-13 Induce Pro-Fibrotic Changes in the 3DBioBarrierTM Airway Epithelial/Fibroblast Model System
Sam J. Wadsworth, Catherine Overed-Sayers, Lynne Murray, et al. ATS Journals (2016). - Stress perception impacts on clinical signs of skin ageing and modifies the epigenome
R. Pattinson, C. Bundy, L. Cordingley, et al. 062. Journal of Investigative Dermatology (2016). - Whole blood gene expression profiling of neonates with confirmed bacterial sepsis
Dickinson P., Smith C.L., Forster T., et al. Genomics Data 3, 41-48 (2015). - Faster-X Adaptive Protein Evolution in House Mice
Kousathanas A., Halligan D.L., Keightley P.D. Genetics, 196, 1131-1143 (2014). - Uterine NK Cells Regulate Endometrial Bleeding in Women and are Suppressed by the Progesterone Receptor Modulator Asoprisnil
Wilkens J., Male V., Ghazal P., et al. J. Immunology Aug (2) (2013). - Structural and functional annotation of the porcine immunome
Dawson, H.D., Loveland, J.E., Pascal, G., et al. BMC Genomics 14, 332 (2013). - Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment
Doig T.N., Hume D.A., Theocharidis T., et al. BMC Genomics, 14, 469 (2013). - An expression atlas of human primary cells: inference of gene function from coexpression networks
Mabott N.A., Baillie J.K., Brown H., et al. BMC Genomics 14, 632 (2013). - Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations
Kobayashi, A., Donaldson, D.S., Kanaya, T., et al. DNA Research. 19, 407-422 (2012). - Cyclin G1 regulates the outcome of taxane-induced mitotic checkpoint arrest
Russell, P., Hennessy, B.T., Li, J., et al. Oncogene 31, 2450-2460 (2012). - A gene expression atlas of the domestic pig
Freeman, T.C., Ivens, A., Baillie, J.K., et al. BMC Biology. 10, 90-111 (2012).
Differential sensitivity of mucosal organs to transient exposure to hydrogen sulphide in post-smolt Atlantic salmon (Salmo salar)
2023 – Carlo Lazado, Hanna Ross D. Alipio, Julie Hansen Bergstedt
The study demonstrates the physiological consequences of transient exposure of post-smolt Atlantic salmon to H2S. The fish were exposed to one of three levels of H2S for 1 h: 0 μM (unexposed), 0.6 μM (low exposure), and 1.2 μM (high exposure). Fish were allowed to recover for 24 h and then sampled for gene expression, histology, and metabolomics analyses. Molecular profiling was performed on a subset of genes with known functions in sulphide detoxification, mucins, immunity, and stress responses, which focused on the gills, olfactory organ, skin, and distal gut.
The circulating plasma metabolome of Neoparamoeba perurans-infected Atlantic salmon (Salmo salar))
2022 – Carlo C. Lazado, Mette W. Breiland, Francisco Furtado et al.
The study reports the circulating plasma metabolome of Atlantic salmon (Salmo salar) experimentally infected with Neoparamoeba perurans—the causative agent of amoebic gill disease (AGD).
Integrated Analysis of Transcript, Protein and Metabolite Data To Study Lignin Biosynthesis in Hybrid Aspen
2009- Bylesjo M, Nilsson R et al.
In this paper, a strategy is outlined for informative data generation and integrated modeling of systematic changes in transcript, protein and metabolite profiles measured from hybrid aspen samples.
Enitociclib, a Selective CDK9 Inhibitor, Induces Complete Regression of MYC+ Lymphoma by Downregulation of RNA Polymerase II Mediated Transcription
2023 – Melanie M. Frigault, Arushi Mithal, Harvey Wong, et al.
This study investigates the pharmacodynamic (PD) effect of CDK9 inhibition in preclinical models and in blood samples from patients (DH-DLBCL [n=10] and MYC+ NHL [n=5]) treated with 30 mg i.v. QW enitociclib.
Serum Alpha-fetoprotein Levels and Clinical Outcomes in the Phase III CELESTIAL Study of Cabozantinib versus Placebo in Patients with Advanced Hepatocellular Carcinoma
2020 – Robin Kate Kelley, Tim Meyer, Lorenza Rimassa, et al.
This study shows our collaboration with Exelixis.
The phase III CELESTIAL study demonstrated improved overall survival (OS) and progression-free survival (PFS) with cabozantinib versus placebo in patients with previously treated, advanced hepatocellular carcinoma (HCC). We analyzed outcomes by baseline alpha-fetoprotein (AFP) and on-treatment AFP changes.
Development of a gene expression–based prognostic signature for IDH wild-type glioblastoma
2020 – Radia M. Johnson, Heidi S. Phillips, Carlos Bais, et al.
This study shows our collaboration with Genentech.
We aimed to develop a gene expression–based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations.
Comprehensive Profiling of Poor-Risk Paired Primary and Recurrent Triple-Negative Breast Cancers Reveals Immune Phenotype Shifts
2020 – Katherine E. Hutchinson, Susan E. Yost, Ching-Wei Chang, et al.
This study shows our collaboration with Genentech.
Emerging data suggest immune checkpoint inhibitors have reduced efficacy in heavily pretreated triple-negative breast cancers (TNBC), but underlying mechanisms are poorly understood. To better understand the phenotypic evolution of TNBCs, we studied the genomic and transcriptomic profiles of paired tumors from patients with TNBC. (Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC
2020 – A.K. Sorial, I.M.J. Hofer, M. Tselepi, et al.
This study highlights the expertise of our team.
In cartilage, the osteoarthritis (OA) associated single nucleotide polymorphism (SNP) rs11780978 correlates with differential expression of PLEC, and with differential methylation of PLEC CpG dinucleotides, forming eQTLs and mQTLs respectively. We sought to assess whether these PLEC functional effects were cartilage specific.
Sonic hedgehog specifies flight feather positional information in avian wings
2020 – Lara Busby, Cristina Aceituno, Caitlin McQueen, et al.
The study below shows our collaboration with The University of Sheffield.
Classical tissue recombination experiments performed in the chick embryo provide evidence that signals operating during early limb development specify the position and identity of feathers. Sonic hedgehog (Shh) signalling in the embryonic chick wing bud specifies positional information required for the formation of adult flight feathers in a defined spatial and temporal sequence that reflects their different identities.
- Association of tumor fusion burden with immune presence and androgen sensitivity in prostate cancer
Marie Wagle, Kobe Yuen, Edward E. Kadel, III, et al. AACR Annual Meeting 2019 Poster. - Microbe-host interplay in atopic dermatitis and psoriasis
Nanna Fyhrquist, Gareth Muirhead, Stefanie Prast-Nielsen, et al. Nature Communications, 4703 (2019). - Central nervous system regeneration is driven by microglia necroptosis and repopulation
Amy F. Lloyd, Claire L. Davies, Rebecca K. Holloway, et al. Nature Neuroscience, 22, 1046 –1052, (2019). - Application of pharmacogenomics and bioinformatics to exemplify the utility of human ex vivo organoculture models in the field of precision medicine
Karen Cowan, Graeme Macluskie, Michael Finch, et al. PLOS One, 14(12) (2019). - An intrinsic cell cycle timer terminates limb bud outgrowth
Joseph Pickering, Constance A Rich, Holly Stainton, et al. Developmental Biology (2018). - Species-specific regulation of angiogenesis by glucocorticoids reveals contrasting effects on inflammatory and angiogenic pathways
Ruth Morgan, John Keen, Daniel Halligan, et al. PLoS ONE (2018). - TGFβ and IL-13 Induce Pro-Fibrotic Changes in the 3DBioBarrierTM Airway Epithelial/Fibroblast Model System
Sam J. Wadsworth, Catherine Overed-Sayers, Lynne Murray, et al. ATS Journals (2016). - Assessing Recent Selection and Functionality at Long Non-Coding RNA Loci in the Mouse Genome
R. Axel W. Wiberg, Daniel L. Halligan, Rob W. Ness, et al. Genome Biology and Evolution (2015). - Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family
Keightley P.D., Ness R.W., Halligan D.L., Haddrill P.R. Genetics 196, 313-320 (2014). - Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents
Halligan D.L., Kousathanas A., Ness R.W., et al. PLoS Genetics 9(12) (2013). - Uterine NK Cells Regulate Endometrial Bleeding in Women and are Suppressed by the Progesterone Receptor Modulator Asoprisnil
Wilkens J., Male V., Ghazal P., Fet al. J. Immunology Aug (2) (2013). - USP18 restricts PRRSV growth through alteration of nuclear translocation of NF-κB p65 and p50 in MARC-145 cells
Xu D, Lillico SG, Barnett MW, et al. Virus Research 169, 264-7 (2012). - A gene expression atlas of the domestic pig
Freeman, T.C., Ivens, A., Baillie, J.K., et al. BMC Biology. 10, 90-111 (2012). - SynGAP isoforms exert opposing effects on synaptic strength
McMahon AC, Barnett MW, O’Leary TS, et al. Nature Communications 3, 900 (2012). - Oligonucleotide microarray expression profiling of contrasting invasive phenotypes in colorectal cancer
Thorn C.C., Williams D. and Freeman T.C. Methods in Molecular Biology 755, 203-21 (2011). - RamA, a member of the AraC/XylS family, influences both virulence and efflux in Salmonella enterica serovar Typhimurium
Bailey, A.M. et al. Journal of bacteriology 192, 1607 (2010). - Comparative expression profiling of Leishmania: modulation in gene expression between species and in different host genetic backgrounds
Depledge, D.P. et al. PLoS neglected tropical diseases 3, e476 (2009). - The global consequence of disruption of the AcrAB-TolC efflux pump in Salmonella enterica includes reduced expression of SPI-1 and other attributes required to infect the host
Webber, M.A. et al. Journal of bacteriology 191, 4276 (2009). - Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport
Pan, Z. et al. Microbiology 155, 3200 (2009).
Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)
2018 – Fernanda Dotti do Prado, Manuel Vera, Miguel Hermida, et al.
The study below shows our collaboration with the Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Lugo, Spain.
This study evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing.
- Extending signaling pathways with protein-interaction networks. Application to apoptosis
Joan Planas-Iglesias, Emre Guney, Javier García-García, et al. OMICS, 16(5):245-56 (2012).
- SynGAP isoforms exert opposing effects on synaptic strength
McMahon AC, Barnett MW, O’Leary TS, et al. Nature Communications 3, 900 (2012). - Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts
DeMarco, R. et al. Genome research 20, 1112 (2010). - Integrated Analysis of Transcript, Protein and Metabolite Data To Study Lignin Biosynthesis in Hybrid Aspen
Bylesjo M, Nilsson R et al. J Proteome Res, 8, 199-210 (2009).
Ritonavir reverses resistance to docetaxel and cabazitaxel in prostate cancer cells with acquired resistance to docetaxel
2024 – Eric van der Putten, Katja Wosikowski, Jos H.Beijnen, et al.
This study investigates the mechanisms of acquired resistance to docetaxel in prostate cancer cells, focusing on the role of P-glycoprotein (P-gp) drug transporters.
Enitociclib, a Selective CDK9 Inhibitor, Induces Complete Regression of MYC+ Lymphoma by Downregulation of RNA Polymerase II Mediated Transcription
2023 – Melanie M. Frigault, Arushi Mithal, Harvey Wong, et al.
This study investigates the pharmacodynamic (PD) effect of CDK9 inhibition in preclinical models and in blood samples from patients (DH-DLBCL [n=10] and MYC+ NHL [n=5]) treated with 30 mg i.v. QW enitociclib.
Anti-cancer activity of ST101, a novel antagonist of CCAAT/enhancer binding protein β
2022 – Emma Darvishi, Lila Ghamsari, Siok F. Leong, Ricardo Ramirez, Jim A. Rotolo, et al.
This study shows our collaboration with Sapience Therapeutics.
CCAAT/Enhancer Binding Protein β (C/EBPβ) is a basic leucine zipper (bZIP) family transcription factor that is upregulated or overactivated in many cancers, resulting in gene transactivation that drives oncogenesis. C/EBPβ dimerization regulates binding to DNA at the canonical TTGCGCAA motif and subsequent transcriptional activity, suggesting that disruption of dimerization represents a powerful approach to inhibit this previously ‘undruggable’ oncogenic target. Here we describe the mechanism of action and anti-tumor activity of ST101, a novel and selective peptide antagonist of C/EBPβ that is currently in clinical evaluation in patients with advanced solid tumors.
Comprehensive Profiling of Poor-Risk Paired Primary and Recurrent Triple-Negative Breast Cancers Reveals Immune Phenotype Shifts
2020 – Katherine E. Hutchinson, Susan E. Yost, Ching-Wei Chang, Radia Marie Johnson, Adrian R. Carr, Paul R. McAdam, Daniel L. Halligan, Chun-Chieh Chang, Daniel Schmolze, Jackson Liang, and Yuan Yuan.
This study shows our collaboration with Genentech.
Development of a gene expression–based prognostic signature for IDH wild-type glioblastoma
2020 – Radia M. Johnson, Heidi S. Phillips, Carlos Bais, Cameron W. Brennan, Timothy F. Cloughesy, Anneleen Daemen, Ulrich Herrlinger, Robert B. Jenkins, Albert Lai, Christoph Mancao, Michael Weller, Wolfgang Wick, Richard Bourgon, and Josep Garcia.
This study shows our collaboration with Genentech.
Serum Alpha-fetoprotein Levels and Clinical Outcomes in the Phase III CELESTIAL Study of Cabozantinib versus Placebo in Patients with Advanced Hepatocellular Carcinoma
2020 –Robin Kate Kelley, Tim Meyer, Lorenza Rimassa, Philippe Merle, Joong-Won Park, Thomas Yau, Stephen L. Chan, Jean-Frederic Blanc, Vincent C. Tam, Albert Tran, Vincenzo Dadduzio, David W. Markby, Rajesh Kaldate, Ann-Lii Cheng, Anthony B. El-Khoueiry, and Ghassan K. Abou-Alfa.
This study shows our collaboration with Exelixis.
Trilaciclib plus chemotherapy versus chemotherapy alone in patients with metastatic triple-negative breast cancer: a multicentre, randomised, open-label, phase 2 trial
2019 – Antoinette R Tan, Gail S Wright, Anu R Thummala, et al.
This study shows our collaboration with G1 Therapeutics.
Trilaciclib is an intravenous cell-cycle inhibitor that transiently maintains immune cells and haemopoietic stem and progenitor cells in G1 arrest. By protecting the immune cells and bone marrow from chemotherapy-induced damage, trilaciclib has the potential to optimise antitumour activity while minimising myelotoxicity.
- First-in-human dose-escalation study of G1T48, an oral selective estrogen receptor degrader (SERD), in postmenopausal women with ER+/HER2- locally advanced or metastatic breast cancer (ABC)
E. Claire Dees, Philippe Aftimos, Catharina Willemien Menke-van der Houven van Oordt, et al. ESMO Congress 2019 Poster. - Survival prediction in mesothelioma using a scalable Lasso regression model: instructions for use and initial performance using clinical predictors
Andrew C Kidd, Michael McGettrick, Selina Tsim, et al. BMJ Open Respiratory Research (2018). - Gene mutational analyses in 154 ovarian cancer (OC) samples from the ROSiA study of front-line bevacizumab (BEV)-containing therapy for OC 950P
et alAnnals of Oncology (2017). - RamA, a member of the AraC/XylS family, influences both virulence and efflux in Salmonella enterica serovar Typhimurium
Bailey, A.M. et al. Journal of Bacteriology 192, 1607 (2010).
Integration of genomic and transcriptomic data of inbred mouse models for polygenic obesity and leanness revealed “obese” and “lean” candidate alleles in polyadenylation signals
2024 – Martin Simon, Špela Mikec, Nicholas M. Morton, et al.
This study investigates the association between genetic variations in polyadenylation signals (PAS-SNPs) and obesity in inbred mouse models.
Enitociclib, a Selective CDK9 Inhibitor, Induces Complete Regression of MYC+ Lymphoma by Downregulation of RNA Polymerase II Mediated Transcription
2023 – Melanie M. Frigault, Arushi Mithal, Harvey Wong, et al.
This study investigates the pharmacodynamic (PD) effect of CDK9 inhibition in preclinical models and in blood samples from patients (DH-DLBCL [n=10] and MYC+ NHL [n=5]) treated with 30 mg i.v. QW enitociclib.
Exploring the transcriptomic changes underlying recombinant vaccine efficacy against Teladorsagia circumcincta in 3-month-old lambs
2023 – Tara Pérez-Hernández, Julia N. Hernández, Stewart T.G. Burgess, et al.
Teladorsagia circumcincta is an abomasal parasitic nematode that can cause serious issues in small ruminant production, which are aggravated by drug resistance. Vaccines have been suggested as a feasible, long-lasting alternative for control since adaptation to the host’s immune mechanisms by helminths develops at a much slower pace than anthelmintic resistance. Recently, a T. circumcincta recombinant subunit vaccine yielded over a 60% reduction in egg excretion and worm burden and induced strong humoral and cellular anti-helminth responses in vaccinated 3-month-old Canaria Hair Breed (CHB) lambs, but Canaria Sheep (CS) of a similar age were not protected by the vaccine. Here, we compared the transcriptomic profiles in the abomasal lymph nodes of such 3-month-old CHB and CS vaccinates 40 days after infection with T. circumcincta to understand differences in responsiveness at the molecular level.
Variability in the Response against Teladorsagia circumcincta in Lambs of Two Canarian Sheep Breeds
2022 – Pérez-Hernández T., Hernández J., Machín C., McNeilly T. , Nisbet A. et al.
The increasing resistance to anthelmintics has necessitated the exploration of alternative control strategies of gastrointestinal nematode (GIN) infections. A sustainable option is genetic selection based on differences in susceptibility to GIN infection between and within breeds of sheep. Here, three-month-old Canaria Hair breed (GIN-resistant) and Canaria Sheep breed (GIN-susceptible) showed no significant between-breed differences after trickle infection with Teladorsagia circumcincta, whereas considerable individual variability was found in both breeds. Next, data from lambs of both breeds were used to explore the relationships between parasitological variables and T. circumcincta-specific IgA levels, local immune cell populations, and abomasal lymph node gene expression to understand the possible mechanisms underlying resistance. Mucosal IgA levels as well as numbers of globular leukocytes and MHC-II+ cells were associated with protection. Analysis of lymph node gene expression revealed the associations between lower parasite numbers and cumulative fecal egg counts and several immune pathways, such as leukocyte cell adhesion, activation and differentiation of T cells, in particular CD4+ and IL-4 production. The data obtained here may inform on the relationship between phenotypic resistance variability and protective responses at the humoral, cellular, and transcriptomic levels, thus contributing to identifying immune responses in young lambs that could be used as markers for selection.
(Just one of several genomics publications featuring bioinformatics research from Fios Genomics).
Gene expression profiling of placentae from women with obesity and obstructive sleep apnoea
2022 – Emma C Johns, Daniel L Halligan, Triin Tammsalu, et al.
This study shows our collaboration with Queen’s Medical Research Institute.
Obstructive sleep apnoea (OSA), a condition characterised by intermittent hypoxia and reoxygenation during sleep, is associated with an increased risk of adverse pregnancy outcomes including gestational diabetes and hypertensive disorders of pregnancy. The biological mechanisms of these associations are poorly understood. The impact of OSA on placental function has not been well characterised. 3′ mRNA sequencing on placenta from women with obesity and OSA (n = 11) and women with obesity and no OSA (n = 9) were performed.
Multiomics Provide Insights into the Key Molecules and Pathways Involved in the Physiological Adaptation of Atlantic Salmon ( Salmo salar) to Chemotherapeutic-Induced Oxidative Stress
2021 – Lazado C., Timmerhaus G., Breiland M., Pittman K., Hytterød S.
In this study, multiomics analysis helped understanding how a chemical oxidative stressor alters salmon physiology at both the systemic and mucosal levels. This knowledge will be pivotal in developing an evidence-driven approach to the use of oxidative therapeutics in fish, with some of the molecules and pathways identified as potential biomarkers and targets for assessing the physiological cost of these treatments.
Consequences of continuous ozonation on the health and welfare of Atlantic salmon post-smolts in a brackish water recirculating aquaculture system
2021 – Lazado Carlo, Kevin T.Stiller, Britt-Kristin Megård Reiten, João Osório, Jelena Kolarevic, Lill-Heidi Johansen
This study investigated the biological consequences of 45-day continuous ozonation on Atlantic salmon (Salmo salar) post-smolts in a brackish water recirculating aquaculture system (RAS). Microarray analysis revealed that the gills and liver were more responsive to the oxidant than the skin, with the gills being the most sensitive. Moreover, the magnitude of the transcriptomic modifications depended on the exposure duration. A functional analysis showed that genes involved in immunity and ribosomal functions were significantly affected in the gills. In contrast, genes crucial for the oxidation-reduction process were mainly targeted in the liver.
ctDNA guiding adjuvant immunotherapy in urothelial carcinoma
2021 – Thomas Powles, Zoe June Assaf, et al.
This study shows our collaboration with Genentech.
Minimally invasive approaches to detect residual disease after surgery are needed to identify patients with cancer who are at risk for metastatic relapse. Circulating tumour DNA (ctDNA) holds promise as a biomarker for molecular residual disease and relapse. This study evaluated outcomes in 581 patients who had undergone surgery and were evaluable for ctDNA from a randomized phase III trial of adjuvant atezolizumab versus observation in operable urothelial cancer.
Genome-wide analysis clarifies the population genetic structure of wild Gilthead Sea Bream (Sparus aurata)
2021 – Francesco Maroso, Konstantinos Gkagkavouzis, Sabina De Innocentiis, et al.
The study below shows our collaboration with the Aquatrace Consortium.
Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry. (Just one of several genomics publications featuring bioinformatics research from Fios Genomics.)
Serum Alpha-fetoprotein Levels and Clinical Outcomes in the Phase III CELESTIAL Study of Cabozantinib versus Placebo in Patients with Advanced Hepatocellular Carcinoma
2020 – Robin Kate Kelley, Tim Meyer, Lorenza Rimassa, et al.
This study shows our collaboration with Exelixis.
The phase III CELESTIAL study demonstrated improved overall survival (OS) and progression-free survival (PFS) with cabozantinib versus placebo in patients with previously treated, advanced hepatocellular carcinoma (HCC). We analyzed outcomes by baseline alpha-fetoprotein (AFP) and on-treatment AFP changes.
Tumor Fusion Burden as a Hallmark of Immune Infiltration in Prostate Cancer
2020 – Marie-Claire Wagle, Joseph Castillo, Shrividhya Srinivasan, et al.
This study shows our collaboration with Genentech.
Prostate cancer is the second leading cause of cancer-related death in men. Our findings suggest that high tumor fusion burden may be a more appropriate biomarker than tumor mutational burden in prostate cancer, as it more closely associates with immunogenicity, and suggests that tumors with high fusion burden could be potential candidates for immunotherapeutic agents.
- Microbe-host interplay in atopic dermatitis and psoriasis
Nanna Fyhrquist, Gareth Muirhead, Stefanie Prast-Nielsen, et al. Nature Communications (2019) - Central nervous system regeneration is driven by microglia necroptosis and repopulation
Amy F. Lloyd, Claire L. Davies, Rebecca K. Holloway, et al. Nature Neuroscience (2019) - Lerociclib (G1T38), an oral CDK4/6 inhibitor, dosed continuously in combination with osimertinib for EGFRmut non−small cell lung cancer: initial Phase 1b results
David Berz, Alexander I. Spira, Shirish M. Gadgeel, et al. ESMO Congress 2019 Poster. - An intrinsic cell cycle timer terminates limb bud outgrowth
Joseph Pickering, Constance A Rich, Holly Stainton, et al. Developmental Biology (2018) - Species-specific regulation of angiogenesis by glucocorticoids reveals contrasting effects on inflammatory and angiogenic pathways
Ruth Morgan, John Keen, Daniel Halligan, et al. PLoS ONE (2018) - Transcriptional changes in chick wing bud polarization induced by retinoic acid
Joseph Pickering, Neha Wali, Matthew Towers. Developmental Dynamics (2017) - Whole blood gene expression profiling of neonates with confirmed bacterial sepsis
Dickinson P., Smith C.L., Forster T., et al. Genomics Data 3, 41-48 (2015). - Uterine NK Cells Regulate Endometrial Bleeding in Women and are Suppressed by the Progesterone Receptor Modulator Asoprisnil
Wilkens J., Male V., Ghazal P., et al. J. Immunology Aug (2) (2013). - Structural and functional annotation of the porcine immunome
Dawson, H.D., Loveland, J.E., Pascal, G., et al. BMC Genomics 14, 332 (2013). - Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment
Doig T.N., Hume D.A., Theocharidis T., et al. BMC Genomics, 14, 469 (2013). - An expression atlas of human primary cells: inference of gene function from coexpression networks
Mabott N.A., Baillie J.K., Brown H., et al. BMC Genomics 14, 632 (2013). - Reprogramming Pig Fetal Fibroblasts Reveals a Functional LIF Signaling Pathway
Thomson, A.J., Pierart, H., Meek, S., et al. Cellular Reprogramming. 14, 112-122 (2012). - USP18 restricts PRRSV growth through alteration of nuclear translocation of NF-κB p65 and p50 in MARC-145 cells
Xu D, Lillico SG, Barnett MW, et al. Virus Research 169, 264-7 (2012). - A gene expression atlas of the domestic pig
Freeman, T.C., Ivens, A., Baillie, J.K., et al. BMC Biology. 10, 90-111 (2012). - SynGAP isoforms exert opposing effects on synaptic strength
McMahon AC, Barnett MW, O’Leary TS, et al. Nature Communications 3, 900 (2012). - Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations
Kobayashi, A., Donaldson, D.S., Kanaya, T., et al. DNA Research. 19, 407-422 (2012). - Expression of mesenchyme-specific gene signatures by follicular dendritic cells: insights from the meta-analysis of microarray data from multiple mouse cell populations
Mabbott N.A., Baillie J.K., Kobayashi A., et al. Immunology 133, 482-498 (2011). - Oligonucleotide microarray expression profiling of contrasting invasive phenotypes in colorectal cancer
Thorn C.C., Williams D. and Freeman T.C. Methods in Molecular Biology 755, 203-21 (2011). - RamA, a member of the AraC/XylS family, influences both virulence and efflux in Salmonella enterica serovar Typhimurium
Bailey, A.M. et al. Journal of bacteriology 192, 1607 (2010). - Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations
Mabbott, N.A., Baillie, J.K., Hume, D.A. & Freeman, T.C. Immunobiology 215, 724-736 (2010). - Integrated Analysis of Transcript, Protein and Metabolite Data To Study Lignin Biosynthesis in Hybrid Aspen
Bylesjo M, Nilsson R et al. J Proteome Res, 8, 199-210 (2009). - Exposure of Escherichia coli and Salmonella enterica serovar Typhimurium to triclosan induces a species-specific response, including drug detoxification
Andrew M Bailey, Chrystala Constantinidou, Al Ivens, et al. J Antimicrob Chemother, 64(5):973-85 (2009). - Anti-schistosomal intervention targets identified by lifecycle transcriptomic analyses
Fitzpatrick, J.M. et al. PLoS neglected tropical diseases, 3, (2009). - The global consequence of disruption of the AcrAB-TolC efflux pump in Salmonella enterica includes reduced expression of SPI-1 and other attributes required to infect the host
Webber, M.A. et al. Journal of bacteriology 191, 4276 (2009).
Integration of genomic and transcriptomic data of inbred mouse models for polygenic obesity and leanness revealed “obese” and “lean” candidate alleles in polyadenylation signals
2024 – Martin Simon, Špela Mikec, Nicholas M. Morton, et al.
This study investigates the association between genetic variations in polyadenylation signals (PAS-SNPs) and obesity in inbred mouse models.
Microbe-host interplay in atopic dermatitis and psoriasis
2019 – Nanna Fyhrquist, Gareth Muirhead, Stefanie Prast-Nielsen, et al.
This study shows our collaboration with several organisations for the MAARS FP7 project
Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis.
- Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family
Keightley P.D., Ness R.W., Halligan D.L., Haddrill P.R. Genetics 196, 313-320 (2014). - Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents
Halligan D.L., Kousathanas A., Ness R.W., et al. PLoS Genetics 9(12) (2013). - A gene expression atlas of the domestic pig
Freeman, T.C., Ivens, A., Baillie, J.K., et al. BMC Biology. 10, 90-111 (2012). - Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport
Pan, Z. et al. Microbiology 155, 3200 (2009).
