Marchionni, Luigi

Publications

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selected publications

Optimal fluid volume for detecting malignancy in serous effusions: a single institution experience. Journal of the American Society of Cytopathology. 2023 Academic Article GET IT
MultiNEP: a multi-omics network enhancement framework for prioritizing disease genes and metabolites simultaneously. Bioinformatics (Oxford, England). 2023 Academic Article GET IT
Times cited: 12
CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species. Patterns (New York, N.Y.). 2023 Academic Article GET IT
Times cited: 78
Distinct mesenchymal cell states mediate prostate cancer progression. bioRxiv : the preprint server for biology. 2023 Article GET IT
REPAC: analysis of alternative polyadenylation from RNA-sequencing data. Genome biology. 2023 Academic Article GET IT
Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer. JCI insight. 2023 Academic Article GET IT
Using biological constraints to improve prediction in precision oncology. iScience. 2023 Academic Article GET IT
Times cited: 606
A Phase 1 Trial of Durvalumab in Combination with Bacillus Calmette-Guerin (BCG) or External Beam Radiation Therapy in Patients with BCG-unresponsive Non-muscle-Invasive Bladder Cancer: The Hoosier Cancer Research Network GU16-243 ADAPT-BLADDER Study. European urology. 2023 Academic Article GET IT
Times cited: 1
Recurrent germline variant in ATM associated with familial myeloproliferative neoplasms. Leukemia. 2022 Academic Article GET IT
A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas. The Journal of clinical investigation. 2022 Academic Article GET IT
Times cited: 1
Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a vulnerability in mesenchymal colorectal cancer. Cancer cell. 2022 Academic Article GET IT
Times cited: 3
Donor-derived acute myeloid leukemia in solid organ transplantation. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2022 Academic Article GET IT
ZNF92, an unexplored transcription factor with remarkably distinct breast cancer over-expression associated with prognosis and cell-of-origin. NPJ breast cancer. 2022 Academic Article GET IT
Times cited: 12
Rapid detection of SARS-CoV-2 variants of concern by single nucleotide polymorphism genotyping using TaqMan assays. Diagnostic microbiology and infectious disease. 2022 Academic Article GET IT
Times cited: 1
Precision health diagnostic and surveillance network uses S gene target failure (SGTF) combined with sequencing technologies to track emerging SARS-CoV-2 variants. Immunity, inflammation and disease. 2022 Academic Article GET IT
Times cited: 3
Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology. Molecular cancer research : MCR. 2021 Academic Article GET IT
Times cited: 6
Hobotnica: exploring molecular signature quality. F1000Research. 2021 Academic Article GET IT
Times cited: 2
Host Blood Gene Signatures Can Detect the Progression to Severe and Cerebral Malaria. Frontiers in cellular and infection microbiology. 2021 Academic Article GET IT
Times cited: 2
A robust and interpretable gene signature for predicting the lymph node status of primary T1/T2 oral cavity squamous cell carcinoma. International journal of cancer. 2021 Academic Article GET IT
Times cited: 3
A field guide to cultivating computational biology. PLoS biology. 2021 Academic Article GET IT
Times cited: 4
Transcriptional landscape of PTEN loss in primary prostate cancer. BMC cancer. 2021 Review GET IT
Times cited: 10
RNA-sequencing highlights differential regulated pathways involved in cell cycle and inflammation in orbitofacial neurofibromas. Brain pathology (Zurich, Switzerland). 2021 Academic Article GET IT
Efficient representations of tumor diversity with paired DNA-RNA aberrations. PLoS computational biology. 2021 Academic Article GET IT
covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data. Database : the journal of biological databases and curation. 2021 Academic Article GET IT
Influenza Vaccination and COVID-19 Mortality in the USA: An Ecological Study. Vaccines. 2021 Academic Article GET IT
Times cited: 122
An R package for divergence analysis of omics data. PloS one. 2021 Academic Article GET IT
Plasma cells are enriched in localized prostate cancer in Black men and are associated with improved outcomes. Nature communications. 2021 Academic Article GET IT
Times cited: 42
Newly Identified Members of FGFR1 Splice Variants Engage in Cross-talk with AXL/AKT Axis in Salivary Adenoid Cystic Carcinoma. Cancer research. 2021 Academic Article GET IT
Times cited: 7
Identifying Personalized Metabolic Signatures in Breast Cancer. Metabolites. 2020 Academic Article GET IT
Times cited: 1869
GULP1 regulates the NRF2-KEAP1 signaling axis in urothelial carcinoma. Science signaling. 2020 Academic Article GET IT
Times cited: 12
Comparative transcriptomics of primary cells in vertebrates. Genome research. 2020 Academic Article GET IT
Times cited: 17
Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome research. 2020 Academic Article GET IT
Times cited: 73
Global microRNA profiling identified miR-10b-5p as a regulator of neurofibromatosis 1 (NF1)-glioma migration. Neuropathology and applied neurobiology. 2020 Academic Article GET IT
Times cited: 7
Influenza Vaccination and COVID19 Mortality in the USA. medRxiv : the preprint server for health sciences. 2020 Article GET IT
Times cited: 1170
Correction to: Differential gene methylation and expression of HOX transcription factor family in orbitofacial neurofibroma. Acta neuropathologica communications. 2020 Academic Article GET IT
Times cited: 1
Differential gene methylation and expression of HOX transcription factor family in orbitofacial neurofibroma. Acta neuropathologica communications. 2020 Academic Article GET IT
Times cited: 4
Genetic Analysis of Small Well-differentiated Pancreatic Neuroendocrine Tumors Identifies Subgroups With Differing Risks of Liver Metastases. Annals of surgery. 2020 Academic Article GET IT
Times cited: 55
Recounting the FANTOM CAGE-Associated Transcriptome. Genome research. 2020 Academic Article GET IT
Times cited: 12
Look for methods, not conclusions. Cell death & disease. 2019 Letter GET IT
Combined extracts of Echinacea angustifolia DC. and Zingiber officinale Roscoe in softgel capsules: Pharmacokinetics and immunomodulatory effects assessed by gene expression profiling. Phytomedicine : international journal of phytotherapy and phytopharmacology. 2019 Academic Article GET IT
Times cited: 11
PTEN Loss with ERG Negative Status is Associated with Lethal Disease after Radical Prostatectomy. The Journal of urology. 2019 Academic Article GET IT
Times cited: 9
CDK12 inactivation across solid tumors: an actionable genetic subtype. Oncoscience. 2019 Academic Article GET IT
Times cited: 42
JAK3 Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients. Cancer prevention research (Philadelphia, Pa.). 2019 Academic Article GET IT
Times cited: 12
Ezrin Promotes Stem Cell Properties in Pancreatic Ductal Adenocarcinoma. Molecular cancer research : MCR. 2019 Academic Article GET IT
Times cited: 10
PDCD4 Is an Androgen-Repressed Tumor Suppressor that Regulates Prostate Cancer Growth and Castration Resistance. Molecular cancer research : MCR. 2018 Academic Article GET IT
Times cited: 21
Hypomethylation, endogenous retrovirus expression, and interferon signaling in testicular germ cell tumors. Proceedings of the National Academy of Sciences of the United States of America. 2018 Letter GET IT
Times cited: 9
Hedgehog/GLI1 activation leads to leukemic transformation of myelodysplastic syndrome in vivo and GLI1 inhibition results in antitumor activity. Oncogene. 2018 Academic Article GET IT
Times cited: 17
Epigenetically regulated PAX6 drives cancer cells toward a stem-like state via GLI-SOX2 signaling axis in lung adenocarcinoma. Oncogene. 2018 Academic Article GET IT
Times cited: 36
Cell-type specific expression of oncogenic and tumor suppressive microRNAs in the human prostate and prostate cancer. Scientific reports. 2018 Academic Article GET IT
Times cited: 31
PD-L1 Expression Heterogeneity in Non-Small Cell Lung Cancer: Defining Criteria for Harmonization between Biopsy Specimens and Whole Sections. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer. 2018 Academic Article GET IT
Times cited: 121
Genome-Wide Somatic Copy Number Alterations and Mutations in High-Grade Pancreatic Intraepithelial Neoplasia. The American journal of pathology. 2018 Academic Article GET IT
Times cited: 24
Digitizing omics profiles by divergence from a baseline. Proceedings of the National Academy of Sciences of the United States of America. 2018 Academic Article GET IT
Times cited: 11
Cell-autonomous and cell non-autonomous downregulation of tumor suppressor DAB2IP by microRNA-149-3p promotes aggressiveness of cancer cells. Cell death and differentiation. 2018 Academic Article GET IT
Times cited: 24
Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy. Nature communications. 2018 Academic Article GET IT
Times cited: 197
Arsenic promotes the COX2/PGE2-SOX2 axis to increase the malignant stemness properties of urothelial cells. International journal of cancer. 2018 Academic Article GET IT
Times cited: 22
YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells. Cancer research. 2017 Academic Article GET IT
Times cited: 70
Pharmacodynamic and pharmacokinetic neoadjuvant study of hedgehog pathway inhibitor Sonidegib (LDE-225) in men with high-risk localized prostate cancer undergoing prostatectomy. Oncotarget. 2017 Academic Article GET IT
Times cited: 20
High-resolution microbiome profiling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation. Oncotarget. 2017 Academic Article GET IT
Times cited: 57
MicroRNAs, promising biomarkers in the diagnosis of Xp11 translocation RCC-reply. Human pathology. 2017 Letter GET IT
The extracellular matrix and focal adhesion kinase signaling regulate cancer stem cell function in pancreatic ductal adenocarcinoma. PloS one. 2017 Academic Article GET IT
Times cited: 57
Correction: Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma. Cancer prevention research (Philadelphia, Pa.). 2017 Academic Article GET IT
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. Bioinformatics (Oxford, England). 2017 Academic Article GET IT
Times cited: 16
Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer. Nature communications. 2017 Academic Article GET IT
Times cited: 162
Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques. PloS one. 2017 Academic Article GET IT
Times cited: 1
MicroRNA expression profiling of Xp11 renal cell carcinoma. Human pathology. 2017 Review GET IT
Times cited: 23
Analysis of differential gene expression mediated by clozapine in human postmortem brains. Schizophrenia research. 2016 Review GET IT
Times cited: 13
Identification of miR-30b-3p and miR-30d-5p as direct regulators of androgen receptor signaling in prostate cancer by complementary functional microRNA library screening. Oncotarget. 2016 Academic Article GET IT
Times cited: 60
Expression of HIV-1 matrix protein p17 and association with B-cell lymphoma in HIV-1 transgenic mice. Proceedings of the National Academy of Sciences of the United States of America. 2016 Academic Article GET IT
Times cited: 21
Human Th17 Cells Lack HIV-Inhibitory RNases and Are Highly Permissive to Productive HIV Infection. Journal of virology. 2016 Academic Article GET IT
Times cited: 42
Dysregulation of EGFR Pathway in EphA2 Cell Subpopulation Significantly Associates with Poor Prognosis in Colorectal Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research. 2016 Academic Article GET IT
Times cited: 51
Summary and Recommendations from the National Cancer Institute's Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer. Bladder cancer (Amsterdam, Netherlands). 2016 Academic Article GET IT
Times cited: 135
Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma. Cancer prevention research (Philadelphia, Pa.). 2016 Academic Article GET IT
Times cited: 68
Correction: Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma. PloS one. 2015 Article GET IT
Times cited: 40
A multi-omic analysis of human naïve CD4+ T cells. BMC systems biology. 2015 Academic Article GET IT
Times cited: 32
Alterations in cellular metabolome after pharmacological inhibition of Notch in glioblastoma cells. International journal of cancer. 2015 Academic Article GET IT
Times cited: 30
Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research. 2015 Academic Article GET IT
Times cited: 24
Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA. Nature communications. 2015 Academic Article GET IT
Times cited: 113
Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma. PloS one. 2015 Academic Article GET IT
Times cited: 40
Neutrophil to lymphocyte ratio (NLR) improves the risk assessment of ISS staging in newly diagnosed MM patients treated upfront with novel agents. Annals of hematology. 2015 Academic Article GET IT
Times cited: 42
Erratum for the Research Article: "Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia" by Y. Lim, L. Gondek, L. Li, Q. Wang, H. Ma, E. Chang, D. L. Huso, S. Foerster, L. Marchionni, K. McGovern, D. N. Watkins, C. D. Peacock, M. Levis, B. D. Smith, A. A. Merchant, D. Small, W. Matsui. Science translational medicine. 2015 Article GET IT
Removal of Abnormal Myofilament O-GlcNAcylation Restores Ca2+ Sensitivity in Diabetic Cardiac Muscle. Diabetes. 2015 Academic Article GET IT
Times cited: 73
Integration of Hedgehog and mutant FLT3 signaling in myeloid leukemia. Science translational medicine. 2015 Academic Article GET IT
Times cited: 48
Tissue-based Genomics Augments Post-prostatectomy Risk Stratification in a Natural History Cohort of Intermediate- and High-Risk Men. European urology. 2015 Academic Article GET IT
Times cited: 175
HES6 promotes prostate cancer aggressiveness independently of Notch signalling. Journal of cellular and molecular medicine. 2015 Academic Article GET IT
Times cited: 18
Notch signaling activation in pediatric low-grade astrocytoma. Journal of neuropathology and experimental neurology. 2015 Academic Article GET IT
Times cited: 6
Only three driver gene mutations are required for the development of lung and colorectal cancers. Proceedings of the National Academy of Sciences of the United States of America. 2014 Academic Article GET IT
Times cited: 250
Identification of miR-145 targets through an integrated omics analysis. Molecular bioSystems. 2014 Academic Article GET IT
Times cited: 19
switchBox: an R package for k-Top Scoring Pairs classifier development. Bioinformatics (Oxford, England). 2014 Academic Article GET IT
Times cited: 29
Key tumor suppressor genes inactivated by "greater promoter" methylation and somatic mutations in head and neck cancer. Epigenetics. 2014 Academic Article GET IT
Times cited: 109
Clear cell papillary renal cell carcinoma: micro-RNA expression profiling and comparison with clear cell renal cell carcinoma and papillary renal cell carcinoma. Human pathology. 2014 Academic Article GET IT
Times cited: 47
Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma. Clinical cancer research : an official journal of the American Association for Cancer Research. 2014 Academic Article GET IT
Times cited: 48
Hydrogen sulfide [corrected] increases survival during sepsis: protective effect of CHOP inhibition. Journal of immunology (Baltimore, Md. : 1950). 2014 Academic Article GET IT
Times cited: 67
Association of promoter methylation of VGF and PGP9.5 with ovarian cancer progression. PloS one. 2013 Academic Article GET IT
Times cited: 34
Next-generation sequence analysis of cancer xenograft models. PloS one. 2013 Academic Article GET IT
Times cited: 21
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors. Epigenetics. 2013 Academic Article GET IT
Times cited: 33
High levels of CD2 expression identify HIV-1 latently infected resting memory CD4+ T cells in virally suppressed subjects. Journal of virology. 2013 Academic Article GET IT
Times cited: 66
A simple and reproducible breast cancer prognostic test. BMC genomics. 2013 Academic Article GET IT
Times cited: 38
ERK phosphorylation is predictive of resistance to IGF-1R inhibition in small cell lung cancer. Molecular cancer therapeutics. 2013 Academic Article GET IT
Times cited: 30
Combination treatment with ABT-737 and chloroquine in preclinical models of small cell lung cancer. Molecular cancer. 2013 Academic Article GET IT
Times cited: 42
Isolation of microarray-quality RNA from primary human cells after intracellular immunostaining and fluorescence-activated cell sorting. Journal of immunological methods. 2013 Academic Article GET IT
Times cited: 10
MicroRNA profiling in pediatric pilocytic astrocytoma reveals biologically relevant targets, including PBX3, NFIB, and METAP2. Neuro-oncology. 2012 Academic Article GET IT
Times cited: 53
Wnt signaling though beta-catenin is required for prostate lineage specification. Developmental biology. 2012 Academic Article GET IT
Times cited: 39
Secreted protein, acidic and rich in cysteine-like 1 (SPARCL1) is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome. Proceedings of the National Academy of Sciences of the United States of America. 2012 Academic Article GET IT
Times cited: 42
Sox9 is required for prostate development and prostate cancer initiation. Oncotarget. 2012 Academic Article GET IT
Times cited: 48
Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification. Breast cancer research and treatment. 2012 Academic Article GET IT
Times cited: 51
Regulation of lipid metabolism by Dicer revealed through SILAC mice. Journal of proteome research. 2012 Academic Article GET IT
Times cited: 24
MYC is activated by USP2a-mediated modulation of microRNAs in prostate cancer. Cancer discovery. 2012 Academic Article GET IT
Times cited: 71
Integrating diverse genomic data using gene sets. Genome biology. 2011 Academic Article GET IT
Times cited: 44
Effects of age and heart failure on human cardiac stem cell function. The American journal of pathology. 2011 Academic Article GET IT
Times cited: 159
In vivo liver regeneration potential of human induced pluripotent stem cells from diverse origins. Science translational medicine. 2011 Academic Article GET IT
Times cited: 187
An EGFR-ERK-SOX9 signaling cascade links urothelial development and regeneration to cancer. Cancer research. 2011 Academic Article GET IT
Times cited: 94
Molecular effects of genistein on male urethral development. The Journal of urology. 2011 Academic Article GET IT
Times cited: 25
Gene expression pathways of high grade localized prostate cancer. The Prostate. 2011 Academic Article GET IT
Times cited: 69
Dimeric naphthoquinones, a novel class of compounds with prostate cancer cytotoxicity. BJU international. 2010 Academic Article GET IT
Times cited: 16
The Notch target Hes1 directly modulates Gli1 expression and Hedgehog signaling: a potential mechanism of therapeutic resistance. Clinical cancer research : an official journal of the American Association for Cancer Research. 2010 Academic Article GET IT
Times cited: 140
A novel role of IL-17-producing lymphocytes in mediating lytic bone disease in multiple myeloma. Blood. 2010 Academic Article GET IT
Times cited: 166
Methylation profiles of endometrioid and serous endometrial cancers. Endocrine-related cancer. 2010 Academic Article GET IT
Times cited: 28
Downregulation of homologous recombination DNA repair genes by HDAC inhibition in prostate cancer is mediated through the E2F1 transcription factor. PloS one. 2010 Academic Article GET IT
Times cited: 129
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. BMC bioinformatics. 2009 Academic Article GET IT
Times cited: 31
Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma. Stem cells (Dayton, Ohio). 2009 Academic Article GET IT
Times cited: 109
A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. Cancer research. 2009 Academic Article GET IT
Times cited: 362
Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer. Oncogene. 2008 Academic Article GET IT
Times cited: 138
Are short-term or long-term recurrence rates more important in breast cancer screening?. Annals of internal medicine. 2008 Letter GET IT
Systematic review: gene expression profiling assays in early-stage breast cancer. Annals of internal medicine. 2008 Review GET IT
Times cited: 131
Impact of gene expression profiling tests on breast cancer outcomes. Evidence report/technology assessment. 2007 Review GET IT
Times cited: 39
The transcriptional landscape of the mammalian genome. Science (New York, N.Y.). 2005 Academic Article GET IT
Times cited: 2835
Discovery of 342 putative new genes from the analysis of 5'-end-sequenced full-length-enriched cDNA human transcripts. Genomics. 2005 Academic Article GET IT
Times cited: 4
Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2. Oncogene. 2004 Academic Article GET IT
Times cited: 77
hGTSE-1 expression stimulates cytoplasmic localization of p53. The Journal of biological chemistry. 2004 Academic Article GET IT
Times cited: 44
LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome. Comptes rendus biologies. 2003 Academic Article GET IT
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Academic Article GET IT
Times cited: 1412
Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Academic Article GET IT
Times cited: 574

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Research

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Funding awarded

Collaborative Research: SCH: Integrated Analysis of Single-Cell and Spatially Resolved Omics Data awarded by National Science Foundation Principal Investigator 2021 - 2025

Investigating cell-intrinsic and extrinsic interactions in prostate cancer at the single cell level ("Core A: Pathobiology") awarded by National Institute of Environmental Health Sciences Co-Investigator 2022 - 2027

Radiation Oncology-Biology Integration Network on Oligometastasis (ROBIN OligoMET) Center (Shared Resources Core) awarded by National Cancer Institute Principal Investigator Subaward 2022 - 2027
Bioinformatic-Chemical Approach to Credential Molecular Targets to Combat Rapid Chemo-Radiation Resistance in SCLC awarded by Commonwealth Fund Principal Investigator Subaward 2020 - 2023

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Background

education and training

Ph.D., Scuola Internazionale Superiore di Studi Avanzati (Italy) 2004
M.D., University of Turin Faculty of Medicine and Surgery (Italy) 1998

Contact

full name

Luigi Marchionni

primary email

lum4003@med.cornell.edu

VIVO Weill Cornell Medical College

Luigi Marchionni Associate Professor of Pathology and Laboratory Medicine

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email

Phone

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email