Journal Publications

2017

  1. Hayward, J., Sanchez, J., Perry, A., Huang, C., Rodriguez Valle, M., Canals, M., … Stone, M. J. (2017). Ticks from diverse genera encode chemokine-inhibitory evasin proteins. Journal of Biological Chemistry, jbc.M117.807255. http://doi.org/10.1074/jbc.M117.807255.

  2. Wang X, Goodrich K, Gooding A, Naeem H, Archer S, Paucek R, Cech TR, Davidovich C. (2017). Targeting of Polycomb Repressive Complex 2 (PRC2) to RNA by Short Repeats of Consecutive Guanines, Molecular Cell, 65(6):1056-1067.e5.

  3. Griffin P. et. al, Tyagi S. et al. 2017. Best Practice Data Life Cycle Approaches for the Life Sciences bioRxiv preprint  http://dx.doi.org/10.1101/167619

  4. Maria Victoria Schneider, Philippa C. Griffin, Sonika Tyagi, Madison Flannery, Saravanan Dayalan, Simon Gladman, Nathan Watson-Haigh, Philipp E. Bayer, Michael Charleston, Ira Cooke, Rob Cook, Richard J. Edwards, David Edwards, Dominique Gorse, Malcolm McConville, David Powell, Marc R. Wilkins, Andrew Lonie; Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Brief Bioinform 2017 bbx071. doi: 10.1093/bib/bbx071

  5. Jiménez RC, Kuzak M, Alhamdoosh M et al. Tyagi S. et al. Four simple recommendations to encourage best practices in research software [version 1; referees: 3 approved]. F1000Research 2017, 6:876 (doi: 10.12688/f1000research.11407.1)

  6. Jerico Revote, Nathan S. Watson-Haigh, Steve Quenette, Blair Bethwaite, Annette McGrath, Catherine A. Shang; Remote Desktop Development of a cloud-based Workshop Bioinformatics Training Platform. Brief Bioinform 2017; 18 (3): 537-544. doi: 10.1093/bib/bbw032

2016

  1. Liu, Q., Song, J. & Li, J., 2016. Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes. Scientific reports, 6, p.21223. Available at: http://dx.doi.org/10.1038/srep21223.
  2. Li, C., Androulakis, S., et al., 2016. KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. Database: the journal of biological databases and curation, 2016. Available at: http://dx.doi.org/10.1093/database/baw01
  3. Li, C., Nagel, J., et al., 2016. PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. Database: the journal of biological databases and curation, 2016. Available at: http://dx.doi.org/10.1093/database/baw050.
  4. Messina N, Fulford T, Reilly LO, Loh WX, Motyer JM, Ellis D, MacLean C, Naeem H, Gugasyan R et al. (2016) . The NF-κB transcription factor RelA is required for the tolerigenic function of Foxp3+ CD4 Regulatory T cells. Journal of Autoimmunity, 70:52-62. Available at: http://dx.doi.org/10.1016/j.jaut.2016.03.017
  5. Soetanto, R. et al., 2016. Role of miRNAs and alternative mRNA 3’-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy. Biochimica et biophysica acta, 1859(5), pp.744–756. Available at: http://dx.doi.org/10.1016/j.bbagrm.2016.03.010.
  6. Low, L.-Y. et al., 2016. RNA-seq analysis of virR and revR mutants of Clostridium perfringens. BMC genomics, 17(1), p.391. Available at: http://dx.doi.org/10.1186/s12864-016-2706-2.
  7. Archer, S.K. et al., 2016. Dynamics of ribosome scanning and recycling revealed by translation complex profiling. Nature, 535(7613), pp.570–574. Available at: http://dx.doi.org/10.1038/nature18647.
  8. Murphy, N.M. et al., 2016. Haplotyping the human leukocyte antigen system from single chromosomes. Scientific reports, 6, p.30381. Available at: http://dx.doi.org/10.1038/srep30381.
  9. Mégroz, M. et al., 2016. The RNA-Binding Chaperone Hfq Is an Important Global Regulator of Gene Expression in Pasteurella multocida and Plays a Crucial Role in Production of a Number of Virulence Factors, Including Hyaluronic Acid Capsule. Infection and immunity, 84(5), pp.1361–1370. Available at: http://dx.doi.org/10.1128/iai.00122-16.
  10. Nefzger, C.M. et al., 2016. A Versatile Strategy for Isolating a Highly Enriched Population of Intestinal Stem Cells. Stem cell reports, 6(3), pp.321–329. Available at: http://dx.doi.org/10.1016/j.stemcr.2016.01.014.
  11. Guirguis, A.A. et al., 2016. PUMA promotes apoptosis of hematopoietic progenitors driving leukemic progression in a mouse model of myelodysplasia. Cell death and differentiation, 23(6), pp.1049–1059. Available at: http://dx.doi.org/10.1038/cdd.2015.159.

2015

  1. Verma-Gaur, J. et al., 2015. Integration of Posttranscriptional Gene Networks into Metabolic Adaptation and Biofilm Maturation in Candida albicans. PLoS genetics, 11(10), p.e1005590. Available at: http://dx.doi.org/10.1371/journal.pgen.1005590.

  2. Kumar, N.A. et al., 2015. The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4(+) T-cells. Retrovirology, 12, p.76. Available at: http://dx.doi.org/10.1186/s12977-015-0204-2.

  3. Harrison, P.F. et al., 2015. PAT-seq: a method to study the integration of 3’-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA , 21(8), pp.1502–1510. Available at: http://dx.doi.org/10.1261/rna.048355.114.

2014

  1. Meyer, G.R. et al., 2014. Operation of the Australian Store.Synchrotron for macromolecular crystallography. Acta crystallographica. Section D, Biological crystallography, 70(Pt 10), pp.2510–2519. Available at: http://dx.doi.org/10.1107/S1399004714016174.

 

Conference/Meetings Talks

2016

  • ICBCSB 2016 : 18th International Conference on Bioinformatics, Computational and Systems Biology, Rio de Janeiro, Brazil - 01/02 February 2016. Roxane Legaie  “The importance of including all data in a linear model for the analysis of RNAseq data“
  • Brave New World - Innovation in Diagnostic Testing, Melbourne, Australia July 2016. Roxane Legaie “The role of Bioinformatics in Clinical Genomics”
  • AB3ACBS conference; November 2016. Stuart Archer "Regulation of mRNA translation initiation revealed by TCP-seq"
  • Australasian Genomic Technology Association meeting; October 2016. Stuart Archer "Mechanisms and regulation of mRNA translation initiation revealed by TCP-seq"
  • Lorne Genome Conference, February 2016. Stuart Archer. "Making Bioinformatics Work"

2015

  • 4th French Researchers in Australia Network (FRAN) Forum, Brisbane, Australia, August 2015. Roxane Legaie “Monash Bioinformatics Platform in the ‘clinical research’ space”

2014

  • BioInfoSummer, Melbourne, Australia;  November, 2014. Stuart Archer, Steve Androulakis. "Introduction to Python"


Conference posters

2017

  • ISMB/ECCB Prague July 2017: Tyagi S, Schneider MV, Morgan SL et al. GOBLET Standards Committee: our activities and forward vision [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1305 (poster) (doi: 10.7490/f1000research.1114554.1)
  • ISMB/ECCB Prague, July 2017: Scaling bioinformatics trainers: A Train-the-Trainer Instructor Course. Annette Mcgrath, Konsta Duesing, Paul Greenfield, Sean McWilliam, Paula Moolhuijzen, Ann-Marie Patch, Erdahl Teber, Sonika Tyagi, Sarah L Morgan.

2016

  • ABACBS November 2016 Brisbane, Australia. Sarah M Williams, Belinda J Goldie, Janette Edson, Michelle Watts, Charles Claudianos, Alexandre Cristino. Differences in non-seed pairing between miR-324-3p and miR-1913-3p account for binding and functional differences   
  • ABACBS November 2016 Brisbane, Australia.  Kirill Tsyganov, Hilaria Amuzu, David Powell, Rosemarie I. Herbert, Cassandra Koh, Elizabeth McGraw. Bioinformatic investigation into effects of Wolbachia pipientis on insect-specific Flaviviruses in populations of mosquitoes.

2015

  • ABACBS October 2015 Sydney, Australia:  Paul Harrison "Anscombe's 1948 variance stabilizing transformation for the negative binomial distribution is well suited to RNA-Seq expression data" doi: 10.7490/f1000research.1110757.1
  • ABACBS October 2015 Sydney, Australia: Stuart Archer "One in a million: choice of immune cell receptor dictates T-cell fate"
  • AGTA October 2015 Hunter Valley, Australia. Stuart Archer. "Small ribosomal subunit profiling quantifies conformational changes in initiating and terminating ribosomes"