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Centre for Computational Biology

Chothani Sonia Pankaj

Research Fellow


Contact: 66016936

Sonia is a computational biologist working in the area of small open reading frames and RNA translation in human diseases. She completed her PhD with A/Prof Owen Rackham’s, Prof Stuart Cook’s and Prof. Sebastian Schafer’s research groups at Duke-NUS medicine school. Prior to which she has worked across industry and research institutes such as Philips Research and A*STAR after completing her bachelors and masters from Indian Institute of Technology Madras and Carnegie Mellon University respectively.

She has developed approaches to identify novel targets in human disease by integrating several different next-generation sequencing technologies (Ribo-seq, RNA-seq, CLIP-seq, single-cell RNA-seq). She has applied these approaches to changes in human cardiac fibrosis and identified the RNA-binding protein network in cardiac scarring which was further shown to be active in patients with cardiac fibrosis.

She is currently working on developing an atlas of human micropeptides across various human cell-types and tissues. This work involves integrating large amounts of data, applying multiple algorithms and developing an easily available resource for researchers.

  1. Chothani S,*, Schafer S*, Adami E*, Viswanathan S, Widjaja AA, Langley SR, Tan J, Wang M, Quaife NM, Pua CJ, D'Agostino G, Shekeran SG, George BL, Lim S, Cao EY, van Heesch S, Witte F, Felkin LE, Christodoulou EG, Dong J, Blachut S, Patone G, Barton PJR, Hubner N, Cook SA+, Rackham OJL+. Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins. Circulation. 2019 Sep 10; 140(11):937-951; Publication highlighted in Nature Reviews Cardiology, "Cardiac  brosis research: Two steps forward".
  2. Chothani S, Adami, E., Ouyang, J.F., Viswanathan, S., Hubner, N., Cook, S.A., Schafer, S., and Rackham, O.J.L. deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo-seq and RNA-seq Data. Current Protocols in Molecular Biology. 2019. V129.
  3. Ng B, Dong J, Viswanathan S, DAgostino G, Widjaja A, Lim W, Ko N, Tan J, Chothani S, Huang B, Xie C, Chacko AM, Guimaraes-Camboa N, Evans S, Byrne A, Maher T, Liang J, Noble P, Schafer S, Cook S. IL-11 is a therapeutic target in idiopathic pulmonary  brosis. Sci Transl Med. 2019 Sep 25;11(511)
  4. WidjajaA, SinghB, AdamiE, ViswanathanS, DongJ, D'AgostinoGA, NgB, LimWW, TanJ, PalejaBS, TripathiM, LimSY, ShekeranSG, Chothani S, RabesA, SombetzkiM, BruinstroopE, MinLP, SinhaRA, AlbaniS, YenPM, SchaferS, CookSA. Inhibiting Interleukin 11 Signaling Reduces Hepatocyte Death and Liver Fibrosis, Inflammation, and Steatosis in Mouse Models of Non-Alcoholic Steatohepatitis. Gastroenterology. 2019 Sep;157(3):777-792.e14
  5. Zhou, J., Ng, B., Ko, N.S.J., Fiedler, L.R., Khin, E., Lim, A., Sahib, N.E., Wu, Y., Chothani, S.P., Schafer, S., et al.. Titin truncations lead to impaired cardiomyocyte autophagy and mitochondrial function in vivo. Hum. Mol. Genet. 2019 Jun 15;28(12):1971-1981
  6. Whi n, N., Karczewski, K.J., Zhang, X., Chothani, S., Smith, M.J., Gareth Evans, D., Roberts, A.M., Quaife, N.M., Schafer, S., Rackham, O., et al. Characterising the loss-of-function impact of 5' untranslated region variants in whole genome sequence data from 15,708 individuals. Accepted Nature Communications. 2019
  7. Schafer S, Viswanathan S, Widjaja AA, Lim WW, Moreno-Moral A, DeLaughter DM, Ng B, Patone G, Chow K, Khin E, Tan J, Chothani SP, Ye L, Rackham OJL, Ko NSJ, Sahib NE, Pua CJ, Zhen NTG, Xie C, Wang M, Maatz H, Lim S, Saar K, Blachut S, Petretto E, Schmidt S, Putoczki T, Guimar~aes-Camboa N, Wakimoto H, van Heesch S, Sigmundsson K, Lim SL, Soon JL, Chao VTT, Chua YL, Tan TE, Evans SM, Loh YJ, Jamal MH, Ong KK, Chua KC, Ong BH, Chakaramakkil MJ, Seidman JG, Seidman CE, Hubner N, Sin KYK, Cook SA. IL-11 is a crucial determinant of cardiovascular  brosis. Nature. 2017 Dec 7;552(7683):110-115.
  8. Taliun, D., Chothani, S.P., Schonherr, S., Forer, L., Boehnke, M., Abecasis, G.R., and Wang, C.. LASER server: ancestry tracing with genotypes or sequence reads. Bioinformatics 2017 Jul 1;33(13):2056-2058
  9. Nagarajan, R., Chothani, S.P., Ramakrishnan, C., Sekijima, M., and Gromiha, M.M. Structure based approach for understanding organism speci c recognition of protein-RNA complexes. Biol. Direct. 2015 Mar 7;10:8
  10. Banerjee, N., Chothani, S., Harris, L., and Dimitrova, N. (2013). Identifying RNAseq-based coding-noncoding coexpression interactions in breast cancer. In 2013 IEEE International Workshop on Genomic Signal Processing and Statistics,.