S
Shalima S. Nair
Researcher at Garvan Institute of Medical Research
Publications - 37
Citations - 2210
Shalima S. Nair is an academic researcher from Garvan Institute of Medical Research. The author has contributed to research in topics: DNA methylation & Epigenome. The author has an hindex of 22, co-authored 36 publications receiving 1795 citations. Previous affiliations of Shalima S. Nair include Tata Institute of Fundamental Research & University of New South Wales.
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Journal ArticleDOI
Quantitative comparison of DNA methylation assays for biomarker development and clinical applications
Christoph Bock,Florian Halbritter,Francisco J. Carmona,Sascha Tierling,Paul Datlinger,Yassen Assenov,María Berdasco,Anke K. Bergmann,Keith Booher,Florance Busato,Mihaela Campan,Christina Dahl,Christina M. Dahmcke,Dinh Diep,Agustín F. Fernández,Clarissa Gerhäuser,Andrea Haake,Katharina Heilmann,Thomas Holcomb,Dianna Hussmann,Mitsuteru Ito,Ruth Kläver,Martin Kreutz,Marta Kulis,Virginia Lopez,Shalima S. Nair,Dirk S. Paul,Nongluk Plongthongkum,Wenija Qu,Ana C. Queirós,Frank Reinicke,Guido Sauter,Thorsten Schlomm,Aaron L. Statham,Clare Stirzaker,Ruslan Strogantsev,Rocío G. Urdinguio,Kimberly Walter,Dieter Weichenhan,Daniel J. Weisenberger,Stephan Beck,Susan J. Clark,Manel Esteller,Anne C. Ferguson-Smith,Mario F. Fraga,Per Guldberg,Lise Lotte Hansen,Peter W. Laird,José I. Martín-Subero,Anders O. H. Nygren,Ralf Peist,Christoph Plass,David S. Shames,Reiner Siebert,Xueguang Sun,Jörg Tost,Jörn Walter,Kun Zhan +57 more
TL;DR: The results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use are described, with amplicon bisulfite sequencing and bisulfITE pyrosequencing showing the best all-round performance.
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Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias
Shalima S. Nair,Marcel W. Coolen,Clare Stirzaker,Jenny Z. Song,Aaron L. Statham,Dario Strbenac,Mark D. Robinson,Susan J. Clark +7 more
TL;DR: Two commonly used approaches to enrich for methylated DNA regions of the genome are compared, namely methyl-DNA immunoprecipitation (MeDIP) that is based on enrichment with antibodies specific for 5′-methylcytosine (5MeC), and capture of methylatedDNA using a methyl-CpG binding domain-based (MBD) protein to discover differentially methylated regions (DMRs) in cancer.
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Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer
Fatima Valdes-Mora,Jenny Z. Song,Aaron L. Statham,Dario Strbenac,Mark D. Robinson,Mark D. Robinson,Shalima S. Nair,Kate I. Patterson,David J. Tremethick,Clare Stirzaker,Susan J. Clark,Susan J. Clark +11 more
TL;DR: This work finds that H2A.Z is enriched in a bimodal distribution at nucleosomes, surrounding the transcription start sites (TSSs) of both active and poised gene promoters, and shows for the first time, that acetylation of H 2A.
Journal ArticleDOI
Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value.
Clare Stirzaker,Elena Zotenko,Jenny Z. Song,Wenjia Qu,Shalima S. Nair,Warwick J. Locke,Andrew Stone,Nicola J. Armstong,Mark D. Robinson,Alexander Dobrovic,Kelly A. Avery-Kiejda,Kate M. Peters,Juliet D. French,Sandra Stein,Darren Korbie,Matt Trau,John F. Forbes,Rodney J. Scott,Melissa A. Brown,Glenn Francis,Susan J. Clark +20 more
TL;DR: The data reveal that coordinated hypermethylation can occur in oestrogen receptor-negative disease, and that characterizing the epigenetic framework provides a potential signature to stratify TNBCs, demonstrating the feasibility of profiling the cancer methylome with limited archival tissue to identify regulatory regions associated with cancer.
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MicroRNA alterations and associated aberrant DNA methylation patterns across multiple sample types in oral squamous cell carcinoma
Erik D Wiklund,Erik D Wiklund,Shan Gao,Toby Hulf,Tennille Sibbritt,Shalima S. Nair,Daniela Elena Costea,Sune B. Villadsen,Vivi Bakholdt,Jesper B. Bramsen,Jens Ahm Sørensen,Annelise Krogdahl,Susan J. Clark,Jørgen Kjems +13 more
TL;DR: Although overall activated in OSCC, miR-200/miR-205 suppression in oral CSCs indicate that cell specific silencing of these miRNAs may drive tumor expansion and progression, and are suggested as promising candidates for future investigations.