Annaïck Carles

Position/Role


Computational Biologist

Field of Research

Bioinformatics, next-generation sequencing data management and quality control analysis, cancer genomics and epigenomics

Major research activities/interests

I am operating a next-generation sequencing data quality control analysis pipeline dedicated to genome wide DNA methylation data. It generates integrated genome browse tracks for visualization and further data analysis. DNA methylation is an epigenetic mark known to be deregulated across different types of cancer. My research aims to participate in the understanding of the epigenetic regulation of gene expression in normal development and human diseases.

Selected publications

Nguyen LV, Makarem M, Kannan N, Carles A, Balani S, Moksa M, Hirst M, Eaves CJ. Clonal Analysis of Mouse Mammary Luminal Epithelial Cell Transplants. Stem Cells Dev. 2019 Mar

Giambra V, Gusscott S, Gracias D, Song R, Lam SH, Panelli P, Tyshchenko K, Jenkins CE, Hoofd C, Lorzadeh A, Carles A, Hirst M, Eaves CJ, Weng AP. Epigenetic Restoration of Fetal-like IGF1 Signaling Inhibits Leukemia Stem Cell Activity. Cell Stem Cell. 2018 Sep 19. pii: S1934-5909(18)30436-3. doi: 10.1016/j.stem.2018.08.018.PMID: 30269902

Siu C, Wiseman S, Gakkhar S, Heravi-Moussavi A, Bilenky M, Carles A, Sierocinski T, Tam A, Zhao E, Kasaian K, Moore RA, Mungall AJ, Walker B, Thomson T, Marra MA, Hirst M, Jones SJM. Characterization of the human thyroid epigenome. J Endocrinol. 2017 Nov;235(2):153-165. doi: 10.1530/JOE-17-0145. Epub 2017 Aug 14. PMID: 28808080

Lan X, Jörg DJ, Cavalli FMG, Richards LM, Nguyen LV, Vanner RJ, Guilhamon P, Lee L, Kushida MM, Pellacani D, Park NI, Coutinho FJ, Whetstone H, Selvadurai HJ, Che C, Luu B, Carles A, Moksa M, Rastegar N, Head R, Dolma S, Prinos P, Cusimano MD, Das S, Bernstein M, Arrowsmith CH, Mungall AJ, Moore RA, Ma Y, Gallo M, Lupien M, Pugh TJ, Taylor MD, Hirst M, Eaves CJ, Simons BD, Dirks PB. Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy. Nature. 2017 Sep 14;549(7671):227-232.PMID: 28854171

Sloma I, Mitjavila-Garcia MT, Feraud O, Griscelli F, Oudrhiri N, El Marsafy S, Gobbo E, Divers D, Proust A, Smadja DM, Desterke C, Carles A, Ma Y, Hirst M, Marra MA, Eaves CJ, Bennaceur-Griscelli A, Turhan AG. Whole-genome analysis reveals unexpected dynamics of mutant subclone development in a patient with JAK2-V617F-positive chronic myeloid leukemia. Exp Hematol. 2017 Sep;53:48-58. PMID: 28602946

Alireza Lorzadeh, Misha Bilenky, Colin Hammond, David J.H.F. Knapp, Luolan Li, Paul H. Miller, Annaick Carles, Alireza Heravi-Moussavi, Sitanshu Gakkhar, Michelle Moksa, Connie J. Eaves and Martin Hirst. Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility. Cell Reports 17, 2112–2124, November 15, 2016

Hye-Jung E. Chun, Emilia L. Lim, Alireza Heravi-Moussavi, Saeed Saberi, Karen L. Mungall, Mikhail Bilenky, Annaick Carles, Kane Tse, Inna Shlafman, Kelsey Zhu, Jenny Q. Qian, Diana L. Palmquist, An He, William Long, Rodrigo Goya, Michelle Ng, Veronique G. LeBlanc, Erin Pleasance, Nina Thiessen, Tina Wong, Eric Chuah, Yong-Jun Zhao, Jacquie E. Schein, Daniela S. Gerhard, Michael D. Taylor, Andrew J. Mungall, Richard A. Moore, Yussanne Ma, Steven J.M. Jones. Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways. Cancer Cell. 2016 Mar 14

Nguyen LV, Pellacani D, Lefort S, Kannan N, Osako T, Makarem M, Cox CL, Kennedy W, Beer P, Carles A, Moksa M, Bilenky M, Balani S, Babovic S, Sun I, Rosin M, Aparicio S, Hirst M, Eaves CJ.Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells.  Nature. 2015 Dec 10

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19

Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O’Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M. Epigenetic and transcriptional determinants of the human breast. Nat Commun. 2015 Feb 18

Long Nguyen, Claire Cox, Peter Eirew, David Knapp, Davide Pellacani, Nagarajan Kannan, Annaick Carles, Michelle Moksa, Sneha Balani, Sohrab Shah, Martin Hirst, Sam Aparicio, and Connie Eaves. DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts. Nature Communications. November 2014

Nguyen LV, Makarem M, Carles A, Moksa M, Kannan N, Pandoh P, Eirew P, Osako T, Kardel M, Cheung AM, Kennedy W, Tse K, Zeng T, Zhao Y, Humphries R, Aparicio S, Eaves CJ, Hirst M. Clonal Analysis via Barcoding Reveals Diverse Growth and Differentiation of Transplanted Mouse and Human Mammary Stem Cells. Cell Stem Cell. 2014 Jan 15.

Cheung AM, Nguyen LV, Carles A, Beer P, Miller PH, Knapp DJ, Dhillon K, Hirst M, Eaves CJ. Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice. Blood. 2013 Oct 31