About

 

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My name is Jesper Maag. I am a Swedish scientist with a Ph.D. in Medicine (Computational Biology) from the Garvan Institute of Medical Research/UNSW, Sydney, Australia. I did a postdoctoral fellowship in Computational Biology at NYU School of Medicine. Currently, I am working as a Senior Computational Biologist at Memorial Sloan Kettering Cancer Center (MSKCC) in New York City.

I am a highly motivated and productive Computational Biologist experienced in next generation sequencing analysis. Through my Ph.D. and postdoc, I have developed analysis pipelines, conducted data and statistical analysis of complex genomic datasets, visualised and successfully communicated the results in multiple peer-reviewed publications and presentations at both national and international conferences. I have effectively and successfully led, managed, and worked in collaborative, multi-national, research teams. I am highly adaptable, a quick learner, and a self-taught coder — all of which have made me successful in analysing the complexity of the genome.

Curriculum Vitae

Education

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PhD in Medicine (Computational Biology)

2013-2017. UNSW and Garvan Institute of Medical Research. Sydney, Australia.

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Master’s of Pharmaceutical Sciences

2007-2012. Uppsala University. Uppsala, Sweden.

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Master’s thesis research in pharmacology

2011. University of Adelaide, Adelaide, Australia

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Exchange year

2010. Flinders University, Adelaide, University.

Experience

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Senior Computational Biologist

May 2018 – Present. Center for Epigenetics Research. MSKCC


Post-doctoral fellow in Computational Biology

Dec 2016 – May 2018. Institute of Systems Genetics. NYU Medical School

Skills

Computational

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Genomic

RNA-seq

RNA-seq

ATAC/DNase-seq

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ChIP-seq

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HiC

HiC

Mutation calling

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Publications

Google Scholar

CCR6 Defines Memory B Cell Precursors in Mouse and Human Germinal Centers, Revealing Light-Zone Location and Predominant Low Antigen Affinity

Suan_ImmunityFrontDan Suan, Nike J Kräutler, Jesper LV Maag, Danyal Butt, Katherine Bourne, Jana R Hermes, Danielle T Avery, Clara Young, Aaron Statham, Michael Elliott, Marcel E Dinger, Antony Basten, Stuart G Tangye, Robert Brink (2017). Immunity, 47: 1142–1153.

Novel Aberrations Uncovered in Barrett’s Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing

MCR_EACJesper LV Maag and Oliver M Fisher, Angelique J Levert-Mignon, Dominik C Kaczorowski, Melissa L Thomas, Damian Hussey, David, Watson, Antony Wettstein, Yuri V Bobryshev, Melanie Edwards, Marcel E Dinger and Reginald V Lord (2017). Molecular Cancer Research5: 11.

Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo

BCMgenFrontJesper LV Maag, Dominik C Kaczorowski, Debabrata Panja, Timothy J Peters, Clive R Bramham, Karin Wibrand, Marcel E Dinger (2017). BMC Genomics, 18: (1) 250.

Intergenic disease-associated regions are abundant in novel transcripts.
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Nenad Bartonicek, Mike B Clark  Xiu Cheng Quek, James Torpy, Antonia L Pritchard, Jesper LV Maag, Brian S Gloss, Joanna Crawford, Ryan J Taft, Nicholas K Hayward, Grant W Montgomery, John S Mattick, Tim R Mercer, Marcel E Dinger (2017). Genome Biology, 18: 241.

Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity

DynamicFrontJesper LV Maag, Debabrata Panja, Ida Sporild, Sudarshan Patil, Dominik C Kaczorowski, Clive R Bramham, Marcel E Dinger, Karin Wibrand (2015). Frontiers in Neuroscience, 9: 351.

Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data

SciRepRNACeline Everaert, Manuel Luypaert, Jesper LV Maag, Quek Xiu Cheng, Marcel E Dinger, Jan Hellemans, Pieter Mestdagh (2017). Scientific Reports, 7.

The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states

sciRepNeatGuy Barry, James A Briggs, Sam P Nayler Do Won Hwang, Patrick RJ Fortuna, Nicky Jonkhout, Fabien Dachet, Jesper LV Maag, Pieter Mestdagh, Erin M Singh, Lotta Avesson, Dominik C Kaczorowski, Ezgi Ozturk, Nigel C Jones, Irina Vetter, Luis Arriola-Martinez, Jianfei Hu, Gloria R Franco, Victoria M Warn, Andrew Gong, Marcel E Dinger, Frank Rigo, Leonard Lipovich, Margaret J Morris, Terence J O’Brien, Dong Soo Lee, Jeffrey A Loeb, Seth Blackshaw, John S Mattick, Ernst J Wolvetang (2017). Scientific Reports, 7.

CD151 Gene and Protein Expression Provides Independent Prognostic Information for Patients with Adenocarcinoma of the Esophagus and Gastroesophageal Junction Treated by Esophagectomy

AnnOncDrontOliver M Fisher, Angelique J Levert-Mignon, Christopher W Lehane, Natalia K Botelho, Jesper LV Maag, Melissa L Thomas, Melanie Edwards, Sarah J Lord, Yuri V Bobryshev, David C Whiteman, Reginald V Lord (2016). Annals of surgical oncology, 23: (5) 745-754.

Long noncoding RNAs in cancer: mechanisms of action and technological advancements

molcanFrontNenad Bartonicek and Jesper LV Maag , Marcel E Dinger (2016). Molecular Cancer, 15: (1) 43.

lncRNAdb v2. 0: expanding the reference database for functional long noncoding RNAss

NucleFrontXiu Cheng Quek, Daniel W Thomson, Jesper LV Maag, Nenad Bartonicek, Bethany Signal, Michael B Clark, Brian S Gloss, Marcel E Dinger (2014). Nucleic acids research, 43: (D1) 168-173.

Cannabinoid effects on β amyloid fibril and aggregate formation, neuronal and microglial-activated neurotoxicity in vitro

CannFrontEmelie Janefjord, Jesper LV Maag, Benjamin S Harvey, Scott D Smid (2014). Cellular and molecular neurobiology, 34: (1) 31-42.

Contrasting protective effects of cannabinoids against oxidative stress and amyloid-β evoked neurotoxicity in vitro

NurotoxFrontBenjamin S Harvey, Katharina S Ohlsson, Jesper LV Maag, Ian F Musgrave, Scott D Smid (2012). Neurotoxicology, 3: (1) 138-146.

Dietary polyphenol-derived protection against neurotoxic β-amyloid protein: from molecular to clinical

FoodFrontScott D Smid, Jesper LV Maag, Ian F Musgrave (2012). Food & function, 3: (12) 1242-1250.