Selected publications (2018-2021)

A list of our peer-reviewed publications can be accessed via Google Scholar.

  1. Chen, T., Abadi A.J., Lecao K.A., Tyagi, S. A user-friendly multi-omics data harmonisation R pipeline. (Accepted) F1000Research 2021 (https://doi.org/10.12688/f1000research.53453.1).
  2. Philip M.Chen, T.,  Tyagi, S. A Survey of Current Resources to Study lncRNA-protein Interactions. Non-Coding RNA 7, no. 2: 33. (https://doi.org/10.3390/ncrna7020033)
  3. Chen, T., Philip M., Lecao K.A., Tyagi, S. A multimodal data harmonisation approach for discovery of COVID-19 drug targets. Briefings in Bioinformatics 2021 (DOI: 10.1093/bib/bbab185)
  4. Ramakrishnaiah, Y., Kuhlmann, L., Tyagi, S. linc2function: A deep learning model to identify and assign a function to long noncoding RNA (lncRNA) bioRxiv 2021, https://doi.org/10.1101/2021.01.29.42878
  5. M Saaristo, JA Craft, S Tyagi, CP Johnstone, M Allinson… Transcriptome-wide changes associated with the reproductive behaviour of male guppies exposed to 17α-ethinyl estradiol Environmental Pollution, 2021.
  6. Ramakrishnaiah, Y.Kuhlmann, L., Tyagi, S. Towards a Comprehensive Pipeline to Functionally Annotate Long non-coding RNA (lncRNA). Computers in Biology and Medicine 2020 Dec;127:104028. doi: 10.1016/j.compbiomed.2020.104028.
    (An older version of this manuscript was available as a preprint: Computational approaches to functionally annotate long non-coding RNA (lncRNA) 2020, https://europepmc.org/article/ppr/ppr17354)
  7.  Chen, T. and Tyagi, S. Integrative computational epigenomics to build data-driven gene regulation hypotheses. GigaScience, Volume 9, Issue 6, June 2020 (https://doi.org/10.1093/gigascience/giaa064).
  8.  Van Horn, J., S. Abe, J.L. Ambite, T.K. Attwood, N. Beard, L. Bellis, A. Bhattrai, A. Bui, G. Burns, L. Fierro, J. Gordon, J. Grethe, J. Kamdar, X. Lei, K. Lerman, A. McGrath, N. Mulder, C. O'Driscoll, C. Stewart, and S. Tyagi, Advancing the international data science workforce through shared training and education. F1000Research, 2019.
  9.  Schneider, M.V., P.C. Griffin, S. Tyagi, M. Flannery, S. Dayalan, S. Gladman, N. Watson-Haigh, P.E. Bayer, M. Charleston, I. Cooke, R. Cook, R.J. Edwards, D. Edwards, D. Gorse, M. McConville, D. Powell, M.R. Wilkins, and A. Lonie, Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics, 2019. 20(2): p. 384-389.
  10. Delay, C., K. Chapman, M. Taleski, Y. Wang, S. Tyagi, Y. Xiong, N. Imin, and M.A. Djordjevic, CEP3 levels affect starvation-related growth responses of the primary root. Journal of Experimental Botany, 2019. 70(18): p. 4763-4774. [Equal senior author]
  11. Dang, T.H.Y., S. Tyagi, G. D’Cunha, M. Bhave, R. Crawford, and E.P. Ivanova, Computational prediction of microRNAs in marine bacteria of the genus Thalassospira. PLoS ONE, 2019. 14(3).
  12. Chan, E.C., S. Tyagi, and R. Smith. Using RNAseq to Dissect the Transformation of the Human Myometrium for Labor. in REPRODUCTIVE SCIENCES. 2019. SAGE PUBLICATIONS INC 2455 TELLER RD, THOUSAND OAKS, CA 91320 USA.
  13. Chahal, G., S. Tyagi, and M. Ramialison, Navigating the non-coding genome in heart development and Congenital Heart Disease. Differentiation, 2019. 107: p. 11-23. [Equal senior author]
  14. Tsai, T.S., S. Tyagi, and J.C. St John, The molecular characterisation of mitochondrial DNA deficient oocytes using a pig model. Human Reproduction, 2018. 33(5): p. 942-953.
  15. Stefanidis, A., N.M. Wiedmann, S. Tyagi, A.M. Allen, M.J. Watt, and B.J. Oldfield, Insights into the neurochemical signature of the Innervation of Beige Fat. Molecular Metabolism, 2018. 11: p. 47-58.
  16.  Griffin, P.C., J. Khadake, K.S. LeMay, S.E. Lewis, S. Orchard, A. Pask, B. Pope, U. Roessner, K. Russell, T. Seemann, A. Treloar, S. Tyagi, J.H. Christiansen, S. Dayalan, S. Gladman, S.B. Hangartner, H.L. Hayden, W.W.H. Ho, G. Keeble-Gagnère, P.K. Korhonen, P. Neish, P.R. Prestes, M.F. Richardson, N.S. Watson-Haigh, K.L. Wyres, N.D. Young, and M.V. Schneider, Best practice data life cycle approaches for the life sciences. F1000Research, 2018. 6.
  17. Fahey, J.K., S.M. Williams, S. Tyagi, D.R. Powell, J.C. Hallab, G. Chahal, M.S.M. Ramialison, and A.J. White, The Intercellular Tight Junction and Spontaneous Coronary Artery Dissection. Journal of the American College of Cardiology, 2018. 72(14): p. 1752-1753.


Selected conference attendance

  1. Organising member, program chair, and presenter at the virtual Australian Bioinformatics Society conference ABACBS2020.
  2. Oral talk at Deep Learning Symposium in Medical Biology (DLiMB) 2020, WEHI Melbourne Australia
  3. TyagiLab presents at the virtual ISMB 2020.
  4. The scientific committee member and presenter at the virtual Bioinformatics Community Conference & Galaxy Community Conference 2020 #bcc2020 (July 2020)
  5. Invited delegate at the virtual Education Summit 2020 organized by EMBL-EBI and ELIXIR (May 2020.)
  6. Invited talk at InBix'20, an International Bioinformatics Conference December 2020 India.
  7. Keynote talk at APBionet Symposium on Bioinformatics, Dec 2019.
  8. Invited talk on "Integrative Approaches to Computational Epigenomics" at the Children Medical Research Institute Sydney 2019.
  9. The program committee member of the joint ABACBS/GIW2019 Sydney Australia.
  10. Invited Computational Biology session chair at Lorne Genome 2019 Australia.
  11. Invited talk on "Exploring epigenome using ChIPseq and ATACseq" at the Bioinformatics Winter school 2018  at UQ Brisbane.
  12. Invited Bioinformatics session chair, and presented a poster on "Identification of mature miRNA using feed-forward neural network" Lorne Genome 2018 Australia.
  13. Organizing of Bioinfosummer 2017 Monash University Melbourne Australia
  14. ISMB-ECCB 2017, Prague: Tyagi S, Schneider MV, Morgan SL, et al. GOBLET Standards Committee: our activities and forward vision F1000Research 2017.
  15. GAMe 2017: Scientific Committee chair, session chair, and RADseq workshop lead at the first Galaxy Australasia Meeting, Melbourne, Australia.
  16. Festival of Bioinformatics 2016. Presentation on "Small RNA Profiling Using Different Sample Preparation Protocols and Input Amounts" 
  17. Festival of Bioinformatics 2016: Presentation on "Global Mapping of Bioinformatics Training in Australia".
  18. Invited talk on "Minion brings the power of genomics to the palm of your hand" at the 'Back to future Computational Biology Conference' JNU New Delhi Dec 2015.
  19. Invited talk on "NGS Data Analysis Toolkit" at LaTrobe University Bioinformatics User Group Meeting Australia. 2015.
  20. Invited talk on "Best practices in RNAseq data analysis" at the annual BioinfoSummer 2014, Monash University.
  21. Invited talk on "Are we in the era of personalized medicine ?" at an international conference on 'Future Challenges of Computational and Integrated Sciences' Nov 2014.
  22. Invited AGRF Special User Group Talk on "RNA sequencing: Challenges and Opportunities" at ARMI, Monash University 2013.