Eczema Model (Chng et al, 2016)

Malassezia Phylogeny (Wu et al, 2015)

1. Post-doctoral Fellowship in Skin Microbiome Studies

We are looking for genomics researchers with a keen interest in studying the role of microbes in skin diseases. The Nagarajan lab in the Genome Institute of Singapore, in collaboration with the Epithelial Biology group in the Institute of Medical Biology are seeking candidates to lead multiple projects studying the role of the microbiome in inflammatory diseases of the skin (e.g. eczema, psoriasis etc.). Successful candidates will have the opportunity to design new studies in close interaction with doctors and domain experts, applying nextgen omics and analytical approaches to understand the complex host-microbiome interactions that lead to skin disease [1].

The role that microbes play on human skin is still poorly understood despite characterization of the diversity of habitats and niches that they occupy [2]. This is particularly the case for skin diseases which can affect a large proportion of the population and have a significant impact on their quality of life. We recently conducted a metagenome-wide association study for eczema, identifying key microbes and their likely functional roles [1]. We are interested in extending this work in several directions including (i) characterizing the utility of pre-/probiotic therapies (ii) developing in vitro and in silico models for host-microbiome interactions [3] and (iii) studying the role of fungi (e.g. Malassezia) on human skin [4].

References

1. Chng KR, Tay ASL, Li C, Ng AHQ, Wang J, Suri BK, Matta AS, McGovern N, Janela B, Wong XFC, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MBY, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JEA#, Nagarajan N# "Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare" Nature Microbiology 2016 1:16106 doi:10.1038/nmicrobiol.2016.106
2. Oh, J. et al. "Biogeography and individuality shape function in the human skin metagenome." Nature 2014 514, 59–64
3. Li C, Lim KM, Chng KR, Nagarajan N# "Predicting microbial interactions through computational approaches." Methods 2016 Jun 1 ; 102 : 12-9 Epub 2016 Mar 26
4. Wu G, Zhao H, Li C, Rajapakse MP, Wong WC, Xu J, Saunders CW, Reeder NL, Reilman RA, Scheynius A, Sun S, Billmyre BR, Li W, Averette AF, Mieczkowski P, Heitman J, Theelen B, Schröder MS, De Sessions PF, Butler G, Maurer-Stroh S, Boekhout T, Nagarajan N#, Dawson TL# "Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin." PLoS Genet 2015 Nov ; 11(11) : e1005614 Epub 2015 Nov 5

Qualifications

• PhD in Computational Biology/Computer Science/Applied Mathematics/Genomics
• Strong analytical and programming skills (C/C++, perl/python, UNIX environment). Candidates with significant experience in Microbiome Studies or Skin Biology will be strongly preferred.

How To Apply: E-mail cover letter, research statement, curriculum vitae, and contact details of at least three referees to Niranjan Nagarajan (nagarajann@gis.a-star.edu.sg)

2. Bioinformatic Specialist

We seek motivated candidates who are interested in exploring a career in data science to apply for the position of bioinformatics specialist in our group. We are a team of experimental and computational scientists, passionate about biology and medical research, committed to developing smart analytics and innovative biotechnologies for resolving complex biological research questions. Leveraging on systems biology frameworks, we seek to unravel the complex relationship of the human host, it’s resident (e.g. skin and gut) microbial communities and the resulting health phenotype, with the ultimate goal to develop interventions that improve quality of life.

Job Scope

1. Process and perform integrative analysis on biological datasets, including but not limited to metagenomics, metatranscriptomics, proteomics and metabolomics.
2. Perform both descriptive and inferential statistical analyses to elucidate biological significance from experimental observations.
3. Implement modelling and machine learning classifiers for predictive analytics.
4. Create, maintain and manage databases and pipelines for cataloguing and analyzing large biological datasets.

Qualifications

• A degree or masters related to Computational Biology/Computer Science/Applied Mathematics/Applied Statistics/Genomics
• Good analytical, statistical and programming skills (Python/R/C++)
• Comfortable working in Unix environment
• Familiarity with NGS data and/or microbiome biology would be an advantage
• Familiarity with AI and machine learning would be an advantage

How To Apply: E-mail cover letter, curriculum vitae, and contact details of at least three referees to Niranjan Nagarajan (nagarajann@gis.a-star.edu.sg)

SPLASH Graphical Abstract (Aw et al, 2016)

PARTE Graphical Abstract (Wan et al, 2012)

3. Post-doctoral Fellowship in RNA Structural Genomics

We are seeking highly qualified computational scientists with expertise/interest in RNA structure and biology. The Nagarajan Lab, in collaboration with the Wan Lab at the Genome Institute of Singapore are looking for applicants to direct collaborative projects involving the development of new algorithms and the analyis of novel high-throughput, genome-scale RNA structure datasets. Successfull candidates will work in a highly inter-disciplinary environment to apply cutting edge techniques in computational and experimental genomics for achieving breakthrough discoveries that significantly advance human health and well-being.

RNA structure is fundamental to its function in almost every cellular process and for understanding disease biology. We have developed new approaches to probe RNA secondary and tertiary structure genome-wide [1-4] and are applying these for a range of applications including (i) identification of new targets for developing antibiotics against extremely drug-resistant pathogens (ii) understanding host-microbial interactions in diseases and (iii) identifying structural switches that control gene regulation during stem-cell differentiation and oncogenesis. We are seeking exceptional researchers who will join us in leveraging this unique opportunity for significant basic and translational advances in RNA genomics.

References

1. Kertesz M*, Wan Y*, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E "Genome-wide measurement of RNA secondary structure in yeast." Nature 2010 Sep 2 ; 467(7311) : 103-7
2. Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Makino DL, Nutter RC, Segal E, Chang HY "Genome-wide measurement of RNA folding energies." Mol Cell 2012 Oct 26 ; 48(2) : 169-81 Epub 2012 Sep 13
3. Wan Y.*, Qu K.*, Zhang QF, Manor O, Ouyang Z, Zhang J, Snyder MP, Segal E and Chang HY "Landscape and variation of RNA secondary structure across the human transcriptome." Nature 2014 ; 505, 706–709
4. Aw JG, Shen Y, Wilm A, Sun M, Lim XN, Boon KL, Tapsin S, Chan YS, Tan CP, Sim AY, Zhang T, Susanto TT, Fu Z, Nagarajan N#, Wan Y# "In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation." Mol Cell 2016 May 19 ; 62(4) : 603-17 Epub 2016 May 12

Qualifications

• PhD in Computational Biology/Computer Science/Applied Mathematics/Genomics
• Strong analytical and programming skills (C/C++, perl/python, UNIX environment). Candidates with significant experience in RNA structure prediction will be strongly preferred.

How To Apply: E-mail cover letter, research statement, curriculum vitae, and contact details of at least three referees to Niranjan Nagarajan (nagarajann@gis.a-star.edu.sg) and Wan Yue (wany@gis.a-star.edu.sg)