Nikolay Shirokikh is a molecular and RNA biologist. He leads the RNA Multi-Omics and Design Laboratory (RMODEL) at the Australian Centre for RNA Therapeutics in Cancer, School of Human Sciences, where he is Group Leader and Senior Lecturer, and co-leads Biocodecs group (https://biocodecs.org/) together with Alice Cleynen.

His work asks how cells read messenger RNA, how fast, and what happens when that reading goes wrong. He produced the first genome-wide evidence of ribosomal scanning, the step in which a ribosome inspects a messenger RNA to find where a gene begins, published as first author in Nature in 2016. To make that observation possible he developed translation complex profile sequencing (TCP-seq), released as a protocol in Nature Protocols in 2017 and since taken up by laboratories worldwide in yeast, mammalian cells and plants.

He has 34 peer reviewed publications, all in Q1 journals, including Nature, Molecular Cell, PNAS, Genes and Development, EMBO Journal, Nucleic Acids Research, Nature Protocols and Nature Communications. He is first, co-first or corresponding author on over half of them, and his work has attracted more than 2,200 citations.

He completed his PhD in Biology at M.V. Lomonosov Moscow State University in 2011 and trained at the State University of New York Downstate Medical Center and the Institute of Protein Research, Russian Academy of Sciences. He built his independent group at the John Curtin School of Medical Research, Australian National University, where he holds an Honorary Fellowship, and moved to UWA in 2025. He held an NHMRC Emerging Leadership Fellowship from 2020 to 2025.

Nikolay Shirokikh studies RNA level control of gene expression: how messenger RNA is translated into protein, how stable it is, how it is chemically modified, and how those properties change when a cell is stressed, ageing, or resisting a drug.

His interests span six areas:

• Regulation of RNA translation and stability, including during cell stress

• RNA control of the onset of drug resistance in cancer

• RNA control of immune activation

• Transcriptomic signatures and mechanisms of ageing and longevity

• Transcriptome and epitranscriptome of environmental adaptation

• New fundamental and clinical RNA interrogation methods, with a focus on accessible high-throughput technologies, including for personalised medicine

The approach is deliberately trans-disciplinary. It joins molecular and cell biology to bioinformatics, machine learning and mathematical modelling, using in-house expertise alongside collaborations built to supply what the group does not hold itself.

Work in the group runs along five connected lines.

Fundamental principles of translational control. Using yeast and mammalian cells, the group investigates how small ribosomal subunits select the correct messenger RNAs, which initiation factors are used where, and how scanning works as the central regulatory step (Molecular Cell 2020, Nucleic Acids Research 2024).

Rapid cell responses to stimuli and stress. In yeast the group has found translation level responses within seconds-to-minutes of an environmental change. In mammalian and cancer cells it examines translation level responses to anti-cancer drugs within minutes, to explain how malignant cells survive chemotherapy.

RNA and protein interactions in development and disease. With Minna-Liisa Änkö, the lab develops dirCLIP and derived methods for direct detection of RNA-protein interactions without RNA amplification, based on the nanopore sequencing, to more precisely understand how RNA and protein interactions shape development, homeostasis and disease.

Advanced transcriptome and epitranscriptome methods. With Alice Cleynen, the group uses Oxford Nanopore direct RNA sequencing to reach single-molecule principles of translation and stability, including the INDEGRA method which allows instant stability assessment and degradation-corrected RNA abundance measurements, and SWARM basecaller for detecting m6A, m5C, ac4C and pseudouridine in individual RNA molecules, inclusive of historic 002 chemistry data.

Modelling and artificial intelligence. The group builds and maintains tools for biological RNA processes modelling and quantification, including based on AI methods, and software for RNA data operation and visualisation, such as T2GD and VX (see more in https://biocodecs.org/tools).

New ways to suppress the adaptation of cancer, and to promote the survival of normal cells, are needed. Almost any cancer treatment can produce resistance. Oxidative and hypoxic stresses drive ageing and shorten lifespan. Failures of rapid cellular activation or suppression underlie defects in immunity and cognition.

These problems share a root: how quickly a cell copes with a change in its metabolism, and how it decides whether to repair itself or be eliminated. Both decisions are made faster than the nucleus can respond, and both run through control of messenger RNA translation in the cytoplasm. Which messenger RNAs and which RNA regulatory elements are engaged in those first moments is still largely unknown genome-wide.

Nikolay Shirokikh plans to map the RNA elements of control that matter in malignancy, drug resistance, immune activation, development and ageing. Five aims follow from this:

1. Identify translation control mechanisms in malignant cells and their response to anti-cancer drug treatment

2. Identify translation control mechanisms in cells of different mitotic age and differentiation stage, and their response to oxidative and hypoxic stress

3. Identify translation control mechanisms behind rapid reprogramming of immune and neuronal cells

4. Develop new ways to detect and quantify RNA based gene control by translation

5. Devise AI based tools and platform technologies to diagnose the phenotypic state of cells and to design RNA of improved function.

Nikolay Shirokikh has secured more than $8M in Chief Investigator roles across more than ten successful applications, spanning national competitive schemes, international agencies and industry contracts.

He held an NHMRC Emerging Leadership Fellowship from 2020 to 2025. He is a Chief Investigator on ARC Discovery Project, “The Evolutionary Landscape of RNA Modification in Mammals” (2024). He is a Chief Investigator, key application lead and Pillar 1 head on the 2024 MRFF National Therapeutic RNA Platform grant, and 2026 MRFF ROBUST grant, altogether >$6M, connecting Australian research with more than 20 national and international partners.

Internationally he holds two CNRS awards, through the MITI and Postes Rouges schemes, for mathematical modelling of RNA degradation. He served as a Lead Chief Investigator and Project Director on a contracted company-driven R&D program.

Earlier support includes a Group of Eight European Fellowship in 2013, which laid the foundation for the Nature 2016 work, ARC Discovery Project funding and grants supporting national scientific events from the Australian Academy of Science and the NSW Government.

Nikolay Shirokikh treats the identification and education of younger scientists as part of the research role rather than separate from it.

He is primary supervisor to three current PhD students. He has taken two PhD students to completion as primary supervisor and six as co-supervisor, four of those with day to day supervision. He has mentored more than six further PhD candidates and served on more than ten PhD panels. He trains two to three Masters and Honours students each year and has trained more than ten in total. He has supervised or mentored eight post-doctoral researchers and six research officers.

He convened the advanced third year course “Genetics of Human Disease 2” and coordinated the Bachelor of Philosophy (Honours) program for the College of Health and Medicine at the Australian National University, matching students to supervisors and following projects to completion.

At UWA, he reads the Epigenetics and Epitranscriptomics lectures in SCIE5003 Advanced Bioinformatics and Data Analysis for Genomics course and Ageing and Senescence lectures in IMED3020 / PODI3115 Body Systems 2 course.

Students and mentees publish as first authors in journals including Nucleic Acids Research and Nature Communications, win awards, and move into positions at leading laboratories.

Nikolay Shirokikh chairs Viva Voce examinations at UWA in 2026 and facilitates seminars and visits for RNA-centric events and activities such as the WA RNA Salon. WA RNA Salon brings the Perth RNA community together across UWA, the Harry Perkins Institute, The Kids Research Institute Australia and Curtin University.

In 2026 he hosted Professor Sophie Lebre of CNRS and the University of Montpellier at UWA as a Robert and Maude Gledden Visiting Fellow of the Institute of Advanced Studies. The visit produced a laboratory seminar, an ACRTC seminar and a public RNA Salon lecture, together with collaborative meetings across UWA and partner institutes. It also produced several research projects and collaborative initiatives.

His service to the discipline is long running. He has been an ARC External Assessor since 2017, with more than 50 applications assessed, and an NHMRC panel member since 2021 for Investigator Grants and since 2023 for Ideas Grants, with more than 20 assessed. He provides expertise to the European Commission in biochemistry and molecular biology, and reviews grants for the Swiss National Science Foundation, the Health Research Council of New Zealand, the French National Research Agency, the Czech Science Foundation and the U.S.-Israel Binational Science Foundation. He is a national PhD thesis examiner and an international senior promotion examiner in France.

Nikolay Shirokikh is a co-founder of the A-RNA Conference, which also spun the Australasian RNA Biology and Biotechnology Association. He led ACT-based RNA Salon under The RNA Society in 2018-2024.

He organises public science events, such as lectures by Nobel laureates Craig Mello in 2024 and Peter Doherty in 2022. He has chaired sessions at events such as ASBMB, A-RNA, CHARM and Regensburg and Canberra RNP Biology meetings, and organised the 2024 Canberra RNA Emerging Leaders Symposium and the 2024 AI in Science Conference.

He is a member of The RNA Society and A-RNA Association.

Nikolay Shirokikh works at the point where RNA science becomes product.

He holds PCT/AU2023/050168 covering Stochastic Translation Efficiency, a method to quantify absolute translation rates from footprinting data, enabled by the machine learning approach published in Nucleic Acids Research in 2024.

He is a qualified patent expert (USPTO and RUPTO, 2013) and has reviewed more than 20 United States and international patent applications in biochemistry through to acceptance or rejection.

He served as a Project Director of a contracted R&D program with the contract following his 2023 Bridge Industry Fellowship. He also completed the MTPConnect Bridge (2021) and BridgeTech (2023) programs and the CSIRO On Prime program (2022).

He has brought industry sponsorship into Australian RNA science, including Oxford Nanopore Technologies, New England Biolabs, Merck, Lexogen, ATA Scientific and Custom Science.

• 2021 to 2025, Group Leader and Academic Level C, Protein Biosynthesis and Homeostatic Control group, John Curtin School of Medical Research, Australian National University

• 2020 to 2025, NHMRC Emerging Leadership Fellow

• 2022 to 2025, Founder and Chair, Early-Mid Career Research Committee, College of Health and Medicine, Australian National University

• 2022 to 2025, Co-Chair, ANU Network for Early Career Academics (NECTAR)

• 2021 to 2025, Coordinator, Bachelor of Philosophy (Honours) program, College of Health and Medicine, Australian National University

• 2020 to 2025, Member, College of Health and Medicine Research Committee

• 2017 to 2019, Academic Level B, RNA Biology Laboratory, John Curtin School of Medical Research, Australian National University

• 2015 to 2017, Academic Level A, RNA Biology Laboratory, John Curtin School of Medical Research, Australian National University

• 2011 to 2017, Associate Professor (lecturing, part time), State Socio-Humanitarian University, Russia

• 2012, State Intellectual Property Expert in Biochemistry (part time), Federal Institute of Industrial Property, Moscow

• 2011 to 2012, Research Scientist, Institute of Protein Research, Russian Academy of Sciences

• 2008 to 2011, Principal Engineer, Institute of Protein Research, Russian Academy of Sciences

• 2004 to 2005, Visiting Postgraduate Student, State University of New York Downstate Medical Center, Brooklyn, New York