Valentine Murigneux

Computational biologist

Genome Innovation Hub

Bioinformatician

QCIF Facility for Advanced Bioinformatics

v.murigneux@uq.edu.au

Expertise

Analysis of next-generation sequencing data
Analysis of long-read sequencing data (Oxford Nanopore Technology, Pacific Biosciences)
Development of bioinformatics workflows

Researcher biography

Valentine graduated in 2010 with a Master of Engineering in Bioinformatics and Modelling at the National Institute of Applied Sciences of Lyon, France. There she positioned herself at the interface between life sciences, computer sciences and mathematics. Valentine then honed her ability to work collaboratively within a wet lab research team, leading the data analysis of human and mouse transcriptome sequencing projects aimed at identifying the RNA binding sites of a multiprotein complex and the role of this complex in the regulation of alternative splicing. In 2013, she joined the Genome Integrity, Immunity and Cancer group at the Pasteur Institute where she was in charge of the development of cancer genomics pipelines to identify mutations and chromosomal rearrangements in mouse models of lymphoid cancers. In 2016 she moved to Australia as a Bioinformatics Officer at the UQ Diamantina Institute where she analyzed genomics data in collaboration with eight research teams on a variety of cancer types and diseases. In 2018, she started a joint appointment between the UQ Genome Innovation Hub and the QCIF Facility for Advanced Bioinformatics.

Featured projects	Duration
A genomic dissection of metaorganisms: molecular approaches for teasing apart the hologenome Genome Innovation Hub Collaborative Project (UQ infrastructure)	2020
TraDIS-Vault: an interactive searchable genome browser and repository for TraDIS data Genome Innovation Hub Collaborative Project (UQ infrastructure)	2020
Genome-Phaser: protocol for fully phasing whole genome variants using haplotagging Genome Innovation Hub Collaborative Project (UQ infrastructure)	2021
Deciphering the epitranscriptome machinery using direct native RNA sequencing Genome Innovation Hub Collaborative Project (UQ infrastructure)	2021
Assessing DNA Replication Dynamics in Cancer Genome Innovation Hub Collaborative Project (UQ infrastructure)	2021
Multi-contact Pore-C Genome Innovation Hub Collaborative Project (UQ infrastructure)	2022
Adaptive sequencing for metagenomic sequencing of low biomass samples Genome Innovation Hub Collaborative Project (UQ infrastructure)	2022
Proximity ligation sequencing of mixed bacterial communities Genome Innovation Hub Collaborative Project (UQ infrastructure)	2023
Discovery of new regulatory networks with long-read transcriptomics Genome Innovation Hub Collaborative Project (UQ infrastructure)	2019
Applying long-read sequencing technology to understand telomere repair and DNA replication Genome Innovation Hub Collaborative Project (UQ infrastructure)	2019
Assembly of complex genome (Macadamia) using single molecule sequencing Genome Innovation Hub Collaborative Project (UQ infrastructure)	2019
Using transposon-sequencing to probe whole cell protein-protein interactions Genome Innovation Hub Collaborative Project (UQ infrastructure)	2019

Publications

Journal Articles (25)

Conference Papers (9)

Journal Articles

Wong, Ho Yi, Lee, Ruby C., Chong, Sharene, Kapadia, Stuti, Freeman, Michael, Murigneux, Valentine, Brown, Susan, Soyer, H. Peter, Roy, Edwige and Khosrotehrani, Kiarash (2023). Epidermal mutation accumulation in photodamaged skin is associated with skin cancer burden and can be targeted through ablative therapy. Science Advances, 9 (19) eadf2384, 1-13. doi: 10.1126/sciadv.adf2384

Wong, H., Lee, R., Chong, S., Kapadia, S., Murigneux, V., Freeman, M., Soyer, H., Roy, E. and Khosrotehrani, K. (2023). 232 Epidermal mutation accumulation in photodamaged skin is associated with skin cancer burden and can be targeted through ablative therapy. Journal of Investigative Dermatology, 143 (5), S40. doi: 10.1016/j.jid.2023.03.236

Wong, H., Lee, R., Roy, E., Kapadia, S., Murigneux, V., Chong, S., Freeman, M. and Khosrotehrani, K. (2022). 435 Epidermal ablation reduces keratinocyte cancer burden by lowering skin mutation load. Journal of Investigative Dermatology, 142 (12), S255. doi: 10.1016/j.jid.2022.09.449

Sharma, Priyanka, Murigneux, Valentine, Haimovitz, Jasmine, Nock, Catherine J., Tian, Wei, Kharabian Masouleh, Ardashir, Topp, Bruce, Alam, Mobashwer, Furtado, Agnelo and Henry, Robert J. (2021). The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding. Plant Direct, 5 (12) e364, e364. doi: 10.1002/pld3.364

Villani, Rehan, Murigneux, Valentine, Alexis, Josue, Sim, Seen-Ling, Wagels, Michael, Saunders, Nicholas, Soyer, H. Peter, Parmentier, Laurent, Nikolaev, Sergey, Fink, J. Lynn, Roy, Edwige and Khosrotehrani, Kiarash (2021). Subtype specific analyses reveal infiltrative basal cell carcinoma are highly interactive with their environment. The Journal of Investigative Dermatology, 141 (10), 2380-2390. doi: 10.1016/j.jid.2021.02.760

Murigneux, Valentine, Roberts, Leah W., Forde, Brian M., Phan, Minh-Duy, Nhu, Nguyen Thi Khanh, Irwin, Adam D., Harris, Patrick N. A., Paterson, David L., Schembri, Mark A., Whiley, David M. and Beatson, Scott A. (2021). MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction. BMC Genomics, 22 (1) 474, 474. doi: 10.1186/s12864-021-07767-z

Sharma, Priyanka, Al-Dossary, Othman, Alsubaie, Bader, Al-Mssallem, Ibrahim, Nath, Onkar, Mitter, Neena, Rodrigues Alves Margarido, Gabriel, Topp, Bruce, Murigneux, Valentine, Kharabian Masouleh, Ardashir, Furtado, Agnelo and Henry, Robert J. (2021). Improvements in the sequencing and assembly of plant genomes. Gigabyte, 2021, 1-10. doi: 10.46471/gigabyte.24

Kobayashi, Takumi, Lam, Pui Yeng, Jiang, Hui, Bednarska, Karolina, Gloury, Renee Elyse, Murigneux, Valentine, Tay, Joshua, Jacquelot, Nicolas, Li, Rui, Tuong, Zewen Kelvin, Leggatt, Graham, Gandhi, Maher K., Hill, Michelle M, Belz, Gabrielle T., Ngo, Shyuan, Kallies, Axel and Mattarollo, Stephen R. (2020). Increased lipid metabolism impairs NK cell function and mediates adaptation to the lymphoma environment. Blood, 136 (26), 3004-3017. doi: 10.1182/blood.2020005602

Murigneux, Valentine, Rai, Subash Kumar, Furtado, Agnelo, Bruxner, Timothy J. C., Tian, Wei, Harliwong, Ivon, Wei, Hanmin, Yang, Bicheng, Ye, Qianyu, Anderson, Ellis, Mao, Qing, Drmanac, Radoje, Wang, Ou, Peters, Brock A, Xu, Mengyang, Wu, Pei, Topp, Bruce, Coin, Lachlan J. M. and Henry, Robert J. (2020). Comparison of long-read methods for sequencing and assembly of a plant genome. GigaScience, 9 (12) giaa146. doi: 10.1093/gigascience/giaa146

Gunawardana, Jay, Lee, Justina N., Bednarska, Karolina, Murigneux, Valentine, Long, Lilia Merida, Sabdia, Muhammed B., Birch, Simone, Tobin, Joshua W. D. and Gandhi, Maher K. (2020). Genetic aberrations of NLRC5 are associated with downregulated MHC‐I antigen presentation and impaired T‐cell immunity in follicular lymphoma. eJHaem, 1 (2) jha2.116, 517-526. doi: 10.1002/jha2.116

Ganesamoorthy, Devika, Yan, Mengjia, Murigneux, Valentine, Zhou, Chenxi, Cao, Minh Duc, Duarte, Tania P. S. and Coin, Lachlan J. M. (2020). High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing. F1000Research, 9, 1084. doi: 10.12688/f1000research.25693.1

Roy, Edwige, Wong, Ho Yi, Villani, Rehan, Rouille, Thomas, Salik, Basit, Sim, Seen Ling, Murigneux, Valentine, Stark, Mitchell S., Fink, J. Lynn, Soyer, H. Peter, Walker, Graeme, Lyons, J. Guy, Saunders, Nicholas and Khosrotehrani, Kiarash (2020). Regional Variation in Epidermal Susceptibility to UV-Induced Carcinogenesis Reflects Proliferative Activity of Epidermal Progenitors. Cell Reports, 31 (9) 107702, 107702. doi: 10.1016/j.celrep.2020.107702

Tobin, Joshua W. D., Keane, Colm, Gunawardana, Jay, Mollee, Peter, Birch, Simone, Hoang, Thanh, Lee, Justina, Li, Li, Huang, Li, Murigneux, Valentine, Fink, J. Lynn, Matigian, Nicholas, Vari, Frank, Francis, Santiyagu, Kridel, Robert, Weigert, Oliver, Haebe, Sarah, Jurinovic, Vindi, Klapper, Wolfram, Steidl, Christian, Sehn, Laurie H., Law, Soi-Cheng, Wykes, Michelle N. and Gandhi, Maher K. (2019). Progression of disease within 24 months in follicular lymphoma is associated with reduced intratumoral immune infiltration. Journal of Clinical Oncology, 37 (34), 3300-3309. doi: 10.1200/JCO.18.02365

Bianchi, Joy J., Murigneux, Valentine, Bedora-Faure, Marie, Lescale, Chloé and Deriano, Ludovic (2019). Breakage-fusion-bridge events trigger complex genome rearrangements and amplifications in developmentally arrested T cell lymphomas. Cell Reports, 27 (10), 2847-2858.e4. doi: 10.1016/j.celrep.2019.05.014

Bahin, Mathieu, Noel, Benoit F., Murigneux, Valentine, Bernard, Charles, Bastianelli, Leila, Le Hir, Herve, Lebreton, Alice and Genovesio, Auguste (2019). ALFA: annotation landscape for aligned reads. BMC Genomics, 20 (1) 250, 250. doi: 10.1186/s12864-019-5624-2

Donovan, Prudence, Patel, Jatin, Dight, James, Wong, Ho Yi, Sim, Seen-Ling, Murigneux, Valentine, Francois, Mathias and Khosrotehrani, Kiarash (2019). Endovascular progenitors infiltrate melanomas and differentiate towards a variety of vascular beds promoting tumor metastasis. Nature Communications, 10 (1) 18, 18. doi: 10.1038/s41467-018-07961-w

Williams, Sarah M., An, Joon Yong, Edson, Janette, Watts, Michelle, Murigneux, Valentine, Whitehouse, Andrew J. O., Jackson, Colin J., Bellgrove, Mark A., Cristino, Alexandre S. and Claudianos, Charles (2018). An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder. Molecular Psychiatry, 24 (11), 1-13. doi: 10.1038/s41380-018-0049-x

Cardoso, Ana, Gil Castro, Antonio, Martins, Ana Catarina, Carriche, Guilhermina M, Murigneux, Valentine, Castro, Isabel, Cumano, Ana, Vieira, Paulo and Saraiva, Margarida (2018). The Dynamics of Interleukin-10-Afforded Protection during Dextran Sulfate Sodium-Induced Colitis. Frontiers in Immunology, 9, 1-10. doi: 10.3389/fimmu.2018.00400

Lescale, Chloe, Abramowski, Vincent, Bedora-Faure, Marie, Murigneux, Valentine, Vera, Gabriella, Roth, David B., Revy, Patrick, de Villartay, Jean-Pierre and Deriano, Ludovic (2016). RAG2 and XLF/Cernunnos interplay reveals a novel role for the RAG complex in DNA repair. Nature Communications, 7 (1) 10529, 10529.1-10529.13. doi: 10.1038/ncomms10529

Murigneux, Valentine, Dufour, Anne-Beatrice, Lobry, Jean R. and Pene, Laurent (2014). Analysis of positive control STR experiments reveals that results obtained for FGA, D3S1358, and D13S317 condition the success rate of the analysis of routine reference samples. Journal of Forensic Sciences, 59 (4), 1074-1079. doi: 10.1111/1556-4029.12360

Wang, Zhen, Murigneux, Valentine and Le Hir, Herve (2014). Transcriptome-wide modulation of splicing by the exon junction complex. Genome Biology, 15 (12) 551. doi: 10.1186/s13059-014-0551-7

Murigneux, Valentine, Sauliere, Jerome, Crollius, Hugues Roest and Le Hir, Helve (2013). Transcriptome-wide identification of RNA binding sites by CLIP-seq. Methods, 63 (1), 32-40. doi: 10.1016/j.ymeth.2013.03.022

Sauliere, Jerome, Murigneux, Valentine, Wang, Zhen, Marquenet, Emelie, Barbosa, Isabelle, Le Tonqueze, Olivier, Audic, Yann, Paillard, Luc, Crollius, Hugues Roest and Le Hir, Herve (2012). CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. Nature Structural and Molecular Biology, 19 (11), 1124-1131. doi: 10.1038/nsmb.2420

Conference Papers

Wong, H., Lee, R., Chong, S., Kapadia, S., Murigneux, V., Freeman, M., Soyer, H., Roy, E. and Khosrotehrani, K. (2023). Epidermal mutation accumulation in photodamaged skin is associated with skin cancer burden and can be targeted through ablative therapy. 1st International Societies for Investigative Dermatology Meeting, Tokyo Japan, May 12-13, 2023. NEW YORK: ELSEVIER SCIENCE INC.

Gandhi, M.K., Hoang, T., Tobin, J.W., Law, S.C., Talaulikar, D., Jain, S., Vari, F., Murigneux, V., Fink, L., Gunawardana, J., Gould, C., Oey, H., Delecluse, S., Trappe, R.U., Merida de Long, L., Sabdia, M.B., Bhagat, G., Hapgood, G., Blyth, E., Clancy, L., Casey, J., Wight, J., Hawkes, E. and Keane, C. (2019). EBV+ CNS lymphomas have a distinctive tumor microenvironment and genetic profile, which is amenable to combination 3rd party EBV-specific CTL and Ibrutinib therapy. 15th International Conference on Malignant Lymphoma, Lugano, Switzerland, 18–22 June 2019. Oxford, United Kingdom: John Wiley & Sons. doi: 10.1002/hon.91_2629

Villani, R., Roy, E., Murigneux, V., Sim, S., Malapitan, C., Galbraith, J., Kapadia, S., Fink, L. and Khosrotehrani, K. (2019). Cancer associated fibroblast profiling reveals endothelin signalling as a novel mediator of niche to tumour cross-talk in Basal Cell Carcinoma. 49th Annual Meeting of the European Society for Dermatological Research (ESDR), Bordeaux, France, 18-21 September 2019. New York, NY United States: Elsevier. doi: 10.1016/j.jid.2019.07.507

Wong, H., Roy, E., Kapadia, S., Murigneux, V., Chong, S. and Khosrotehrani, K. (2019). Laser dermabrasion: a potential treatment for non-melanoma skin cancers. 49th Annual Meeting of the European Society for Dermatological Research (ESDR), Bordeaux, France, 18-21 September, 2019. Oxford, United Kingdom: Elsevier. doi: 10.1016/j.jid.2019.07.567

Gould, Clare, Keane, Colm, Murigneux, Valentine, Oey, Harald, Ellis, Jonathan, Birch, Simone, Gunawardana, Jay, Talaulikar, Dipti, Hertzberg, Mark S., Jones, Kimberley and Gandhi, Maher K. (2019). B2M Gene Expression Reflects an Immunologically Active Tumor Microenvironment in DLBCL. ASH Annual Meeting, Orlando, FL, United States, 7-10 December 2019. Washington, DC, United States: American Society of Hematology. doi: 10.1182/blood-2019-126537

Tobin, J., Keane, C., Mollee, P., Birch, S., Gould, C., Gunawardana, J., Hoang, T., Savarimuthu, S., Ma, T., Li, L., Murigneux, V. , Fink, L., Matigian, N. and Gandhi, M. K. (2018). The Tumour Microenvironment as an Independent Prognostic Biomarker in Follicular Lymphoma. RACP Congress 2018, Disruption for Healthy Futures, Sydney, NSW Australia, 14–16 May 2018. Hoboken, NJ United States: Wiley. doi: 10.1111/imj.2_13826

Tobin, Joshua W. D., Keane, Colm, Mollee, Peter, Birch, Simone, Gould, Clare, Gunawardana, Jay, Hoang, Thanh , Ma, Ti, Abro, Emad Uddin, Shanavas, Mohamed, Yoo, Hyung, Li, Li, Scuffham, Paul, Murigneux, Valentine, Fink, Lynn, Matigian, Nicholas, Vari, Frank, Francis, Santiyagu and Gandhi, Maher K. (2017). The tumor microenvironment is independently prognostic of conventional and clinicogenetic risk models in follicular lymphoma. 59th Annual Meeting of the American-Society-of-Hematology (ASH), Atlanta, GA United States, 9-12 December 2017. Washington, DC United States: American Society of Hematology. doi: 10.1182/blood.V130.Suppl_1.728.728

Gandhi, Maher K., Keane, Colm, Tobin, Joshua W. D., Talaulikar, Dipti, Jain, Sanjiv, Vari, Frank, Kruze, Lutz, Murigneux, Valentine, Fink, Lynn, Gunawardana, Jithendra, Gould, Clare, Oey, Harold, Fink, Susanne, Trappe, Ralf Ulrich, Mathews, Marina, Francis, Santiyagu and Hoang, Thanh (2017). The impact of EBV upon the tumor microenvironment and mutational profile of primary CNS lymphoma in PTLD. 59th Annual Meeting of the American-Society-of-Hematology (ASH), Atlanta, GA, United States, 9-12 December 2017. Washington, DC, United States: American Society of Hematology.

Roy, E., Wong, H., Murigneux, V., Fink, L. and Khosrotehrani, K. (2017). Regional variation in epidermal susceptibility to ultraviolet induced carcinogenesis reflects proliferative activity of epidermal progenitors. 47th Annual Meeting of the European-Society-for-Dermatological-Research (ESDR), Salzburg Austria, 27-30 September 2017. London, United Kingdom: Nature Publishing Group. doi: 10.1016/j.jid.2017.07.721

Areas of research

Bioinformatics

GIH collaborative project

Genomics

Long-read

Short read/Next Gen sequencing