Journal Publications


1. Dufourt J, Bontonou G, Chartier A, Jahan C, Meunier A, Pierson S, Harrison P, Papin C, Beilharz T and Simonelig M. (2017), “piRNAs and Aubergine cooperate with Wispy poly (A) polymerase to stabilize mRNAs in the germ plasm”, Nature Communications, Vol. 8 No. 1, p. 1305.

2. Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WW, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND and Schneider MV. (2017), “Best practice data life cycle approaches for the life sciences”, F1000Research, Vol. 6, p. 1618.

3. Gujar H, Liang JW, Wong NC and Mozhui K. (2017), “Profiling DNA Methylation Differences Between Inbred Mouse Strains on the Illumina Human Infinium MethylationEPIC Microarray”, BioRxiv, p. 194464.

4. Harrison PF. (2017), “Varistran: Anscombe’s variance stabilizing transformation for RNA-seq gene expression data”, The Journal of Open Source Software, Vol. 2017.

5. Hayward J, Sanchez J, Perry A, Huang C, Rodriguez Valle M, Canals M, Payne R and Stone M. (2017), “Ticks from diverse genera encode chemokine-inhibitory evasin proteins”, Journal of Biological Chemistry, Vol. 292 No. 38, pp. 15670–15680.

6. Jiménez R, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí J, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin P, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz D, Leskošek B, López Gómez F, Oliveira L, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider M, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik H, Todorov I, Treloar A, Tyagi S, Gompel M van, Vaughan D, Via A, Wang X, Watson-Haigh N and Crouch S. (2017), “Four simple recommendations to encourage best practices in research software”, F1000Research, Vol. 6, available at:

7. Li C, Ramarathinam S, Revote J, Khoury G, Song J and Purcell A. (2017), “HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency”, Scientific Reports, Vol. 7, p. 45509.

8. Liu X, Nefzger C, Rossello F, Chen J, Knaupp A, Firas J, Ford E, Pflueger J, Paynter J, Chy H, O’Brien C, Huang C, Mishra K, Hodgson-Garms M, Jansz N, Williams S, Blewitt M, Nilsson S, Schittenhelm R, Laslett A, Lister R and Polo J. (2017), “Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming”, Nature Methods, Vol. 14 No. 11, pp. 1055–1062.

9. Mamrot J, Legaie R, Ellery S, Wilson T, Seemann T, Powell D, Gardner D, Walker D, Temple-Smith P, Papenfuss A and Dickinson H. (2017), “De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)”, Scientific Reports, Vol. 7 No. 1, p. 8996.

10. Murray G, Tsyganov K, Kostoulias X, Bulach D, Powell D, Creek D, Boyce J, Paulsen I and Peleg A. (2017), “Global Gene Expression Profile of Acinetobacter baumannii During Bacteremia”, The Journal of Infectious Diseases, Vol. 215 No. suppl_1, pp. S52–S57.

11. Nefzger C, Rossello F, Chen J, Liu X, Knaupp A, Firas J, Paynter J, Pflueger J, Buckberry S, Lim S, Williams B, Alaei S, Faye-Chauhan K, Petretto E, Nilsson S, Lister R, Ramialison M, Powell D, Rackham O and Polo J. (2017), “Cell type of origin dictates the route to pluripotency”, Cell Reports, Vol. 21 No. 10, pp. 2649–2660.

12. Schneider M, Griffin P, Tyagi S, Flannery M, Dayalan S, Gladman S, Watson-Haigh N, Bayer P, Charleston M, Cooke I, Cook R, Edwards R, Edwards D, Gorse D, McConville M, Powell D, Wilkins M and Lonie A. (2017), “Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia”, Briefings in Bioinformatics.

13. Shirokikh NE, Archer SK, Beilharz TH, Powell D and Preiss T. (2017), “Translation complex profile sequencing to study the in vivo dynamics of mRNA-ribosome interactions during translation initiation, elongation and termination”, Nature Protocols, Vol. 12 No. 4, pp. 697–731.

14. Sibbritt T, Jones V, Ip CK, Wilkie E, Studdert J, Archer S, Ramialison M, Fossat N and Tam P. (2017), “Deciphering the gene regulatory network for head formation”, Mechanisms of Development, Vol. 145, p. S143.

15. Srikhanta Y, Gorrell R, Power P, Tsyganov K, Boitano M, Clark T, Korlach J, Hartland E, Jennings M and Kwok T. (2017), “Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori”, Scientific Reports, Vol. 7 No. 1, p. 16140.

16. Tamura T, Lu W, Song J and Akutsu T. (2017), “Computing Minimum Reaction Modifications in a Boolean Metabolic Network”, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

17. Tsiloulis T, Pike J, Powell D, Rossello F, Canny B, Meex R and Watt M. (2017), “Impact of endurance exercise training on adipocyte microRNA expression in overweight men”, The FASEB Journal, Vol. 31 No. 1, pp. 161–171.

18. Wang X, Goodrich K, Gooding A, Naeem H, Archer S, Paucek R, Youmans D, Cech T and Davidovich C. (2017), “Targeting of Polycomb Repressive Complex 2 to RNA by Short Repeats of Consecutive Guanines”, Molecular Cell, Vol. 65 No. 6, pp. 1056–1067.


19. Archer S, Shirokikh N, Beilharz T and Preiss T. (2016), “Dynamics of ribosome scanning and recycling revealed by translation complex profiling”, Nature.

20. Beilharz T, Harrison P, Miles D, See M, Le U, Kalanon M, Curtis M, Hasan Q, Saksouk J, Margaritis T, Holstege F, Geli V and Dichtl B. (2016), “Coordination of Cell Cycle Progression and Mitotic Spindle Assembly Involves Histone H3 Lysine 4 Methylation by Set1/COMPASS”, Genetics, p. genetics.116.194852.

21. Li C, Androulakis S, Buckle A and Song J. (2016a), “KinetochoreDB: A comprehensive online resource for the kinetochore and its related proteins”, Database, Vol. 2016.

22. Li C, Nagel J, Androulakis S, Song J and Buckle AM. (2016b), “PolyQ 2.0: An improved version of PolyQ, a database of human polyglutamine proteins”, Database: The Journal of Biological Databases and Curation, Vol. 2016, available at:

23. Liepelt A, Naarmann-de Vries I, Simons N, Eichelbaum K, Föhr S, Archer S, Castello A, Usadel B, Krijgsveld J, Preiss T, Marx G, Hentze M, Ostareck D and Ostareck-Lederer A. (2016), “Identification of RNA-binding proteins in macrophages by interactome capture”, Molecular & Cellular Proteomics, Vol. 15 No. 8, pp. 2699–2714.

24. Liu Q, Song J and Li J. (2016), “Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes”, Scientific Reports, Vol. 6, p. 21223.

25. Low L, Harrison P, Lin Y, Boyce J, Rood J and Cheung J. (2016), “RNA-seq analysis of virR and revR mutants of Clostridium perfringens”, BMC Genomics, Vol. 17 No. 1, p. 391.

26. Messina N, Fulford T, O’Reilly L, Loh W, Motyer J, Ellis D, McLean C, Naeem H, Lin A, Gugasyan R, Slattery R, Grumont R and Gerondakis S. (2016), “The NF-κB transcription factor RelA is required for the tolerogenic function of Foxp3+ regulatory T cells”, Journal of Autoimmunity, Vol. 70, pp. 52–62.

27. Mégroz M, Kleifeld O, Wright A, Powell D, Harrison P, Adler B, Harper M and Boyce JD. (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, Vol. 84 No. 5, pp. 1361–1370.

28. Nefzger C, Jardé T, Rossello F, Horvay K, Knaupp A, Powell D, Chen J, Abud H and Polo J. (2016), “A versatile strategy for isolating a highly enriched population of intestinal stem cells”, Stem Cell Reports, Vol. 6 No. 3, pp. 321–329.

29. Soetanto R, Hynes C, Patel H, Humphreys D, Evers M, Duan G, Parker B, Archer S, Clancy J, Graham R, Beilharz T, Smith N and Preiss T. (2016), “Role of miRNAs and alternative mRNA 3′-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy”, Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, Vol. 1859 No. 5, pp. 744–756.

30. Wong Q, Vaz C, Lee Q, Zhao T, Luo R, Archer S, Preiss T, Tanavde V and Vardy L. (2016), “Embryonic stem cells exhibit mRNA isoform specific translational regulation”, PloS One, Vol. 11 No. 1, p. e0143235.


31. Archer S, Shirokikh N and Preiss T. (2015), “Probe-Directed Degradation (PDD) for Flexible Removal of Unwanted cDNA Sequences from RNA-Seq Libraries”, Current Protocols in Human Genetics, pp. 11–15.

32. Harrison PF, Powell DR, Clancy JL, Preiss T, Boag PR, Traven A, Seemann T and Beilharz TH. (2015), “PAT-seq: A method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome”, RNA, Vol. 21 No. 8, pp. 1502–1510.

33. Hasan M, Zhou Y, Lu X, Li J, Song J and Zhang Z. (2015), “Computational identification of protein pupylation sites by using profile-based composition of k-spaced amino acid pairs”, PloS One, Vol. 10 No. 6, p. e0129635.

34. Kumar N, Cheong K, Powell D, Fonseca Pereira C da, Anderson J, Evans V, Lewin S and Cameron P. (2015), “The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4+ T-cells”, Retrovirology, Vol. 12 No. 1, p. 76.

35. Li C, Ching Han Chang C, Nagel J, Porebski B, Hayashida M, Akutsu T, Song J and Buckle A. (2015), “Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins”, Briefings in Bioinformatics, Vol. 17 No. 2, pp. 270–282.

36. Verma-Gaur J, Qu Y, Harrison P, Lo T, Quenault T, Dagley M, Bellousoff M, Powell D, Beilharz T and Traven A. (2015), “Integration of posttranscriptional gene networks into metabolic adaptation and biofilm maturation in Candida albicans”, PLoS Genetics, Vol. 11 No. 10, p. e1005590.

37. Zhou Z, Zhao S, Wang S, Li X, Su L, Ma Y, Li J and Song J. (2015), “Extracellular overexpression of chitosanase from Bacillus sp. TS in Escherichia coli”, Applied Biochemistry and Biotechnology, Vol. 175 No. 7, pp. 3271–3286.


38. Chen Z, Zhou Y, Zhang Z and Song J. (2014), “Towards more accurate prediction of ubiquitination sites: A comprehensive review of current methods, tools and features”, Briefings in Bioinformatics, Vol. 16 No. 4, pp. 640–657.

39. Meyer G, Aragão D, Mudie N, Caradoc-Davies T, McGowan S, Bertling P, Groenewegen D, Quenette S, Bond C, Buckle A and Androulakis S. (2014), “Operation of the Australian Store. Synchrotron for macromolecular crystallography”, Acta Crystallographica Section D: Biological Crystallography, Vol. 70 No. 10, pp. 2510–2519.

Conference/Meetings Talks


  • 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"


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


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

Conference posters


  • 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.


  • 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.


  • 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"