From bec64928f9f194845b38a66c5dc6866ed66dd548 Mon Sep 17 00:00:00 2001 From: geryan Date: Tue, 11 Jun 2024 11:52:46 +1000 Subject: [PATCH] If you have lost an object inside Charles de Gaulle Airport, you must first complete the loss form online --- docs/index.html | 2 +- docs/publications.html | 9 ++++-- docs/search.json | 4 +-- publications.qmd | 73 +++++++++++++++++++++--------------------- 4 files changed, 45 insertions(+), 43 deletions(-) diff --git a/docs/index.html b/docs/index.html index 3e437d8..aaf9f23 100644 --- a/docs/index.html +++ b/docs/index.html @@ -2,7 +2,7 @@ - + diff --git a/docs/publications.html b/docs/publications.html index dce5b5d..7ce1bd4 100644 --- a/docs/publications.html +++ b/docs/publications.html @@ -2,7 +2,7 @@ - + @@ -154,19 +154,22 @@

Publications

Pre-prints

+

Eales, O., Teo, M., Price, D.J., Hao, T., Ryan, G.E., Senior, K.L., Carlson, S., Dalton, C., Dawson, P., Golding, N., McCaw, J.M., and Shearer, F.M. Temporal trends in test-seeking behaviour during the COVID-19 pandemic medRxiv 2024.06.06.24308566

Ryan, G.E., Nicholson, E., Baker, C.M., and McCarthy, M. A. (2024). The costs and benefits of publicising species discoveries. EcoEvoRxiv 10.32942/X2Q02W

Le, T.P., Conway, E., Akpan, E., Abell, I., Abraham, P., Baker, C.M., Campbell, P.T., Cromer, D., Lydeamore, M.J., McDonough, Y., Mueller, I., Ryan, G., Walker, C., Wang, Y., Carvalho, N., and McVernon, J. (2023). Cost-effective boosting allocations in the post-Omicron era of COVID-19 management. medRxiv 2023.11.14.23298536.

Peer-reviewed articles

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20. Shearer, F.M., McCaw, J.M., Ryan, G.E., Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2024). Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia. Epidemics 47(2024): 100764

+

20. Shearer, F.M., McCaw, J.M., Ryan, G.E., Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2024). Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia. Epidemics 47(2024): 100764

19. Ryan, G.E., Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2024). Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening. Epidemics 47(2024): 100763

18. Zachreson, C., Tobin, R., Szanyi, J., Walker, C., Cromer, D., Shearer, F.M., Conway, E., Ryan, G., Cheng, A., McCaw, J.M. and Geard, N., (2023). Individual variation in vaccine immune response can produce bimodal distributions of protection. Vaccine 41(45): 6630–6636.

17. Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., Ryan, G.E., Campbell, T., Miller, J.C., Rebuli, N., Yeung, M., Kabashima, G., Geard, N., Wood, J., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2023). COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting. Proceedings of the Royal Society B, 290(2005): 20231437.

16. Golding, N., Price, D.J., Ryan, G., McVernon, J., McCaw, J.M. and Shearer, F.M., (2023). A modelling approach to estimate the transmissibility of SARS-CoV-2 during periods of high, low, and zero case incidence. eLife, 12: e78089.

15. Borzée, A., McNeely, J., Magellan, K., Miller, J.R., Porter, L., Dutta, T., Kadinjappalli, K.P., Sharma, S., Shahabuddin, G., Aprilinayati, F., Ryan, G.E and others (2020). COVID-19 Highlights the Need for More Effective Wildlife Trade Legislation. Trends in Ecology and Evolution 35: 1052–1055 pdf

14. Brownell RL Jr, Reeves RR, Read AJ, Smith BD, Thomas PO, Ralls K, Amano M, Berggren P, Chit AM, Collins T, Currey R, Dolar L, Genov T, Hobbs R, Kreb D, Marsh H, Zhigang M, Perrin WF, Phay S, Rojas-Bracho L, Ryan GE, Shelden KEW, Slooten E, Taylor BL, Vidal O, Ding W, Whitty TS, & Wang JY (2019). Bycatch in gillnet fisheries threatens Critically Endangered small cetaceans and other aquatic megafauna. Endangered Species Research 40: 285–296

-

13. Thomas, PO, Gulland, FMD, Reeves, RR, Kreb, D, Ding, W, Smith, B, Malik, MI, Ryan, GE, & Phay, S (2019). A review of electrofishing as a potential threat to freshwater cetaceans. Endangered Species Research 39: 207–220

+
    +
  1. Thomas, PO, Gulland, FMD, Reeves, RR, Kreb, D, Ding, W, Smith, B, Malik, MI, Ryan, GE, & Phay, S (2019). A review of electrofishing as a potential threat to freshwater cetaceans. Endangered Species Research 39: 207–220
    2. +

12. Ryan, GE, Nicholson, E, Eames, JC, Gray, TNE, Loveridge, R, Mahood, SP, Sum P, & McCarthy, MA (2019). Simultaneous‐count models to estimate abundance from counts of unmarked individuals with imperfect detection. Conservation Biology 33(3): 697–708

11. Ryan, GE, & Baker, CM (2019). Corrigendum to “A general method for assessing the risks and benefits of secrecy in conserving ’Lazarus species” [Biol. Cons. 203, 186–187]. Biological Conservation 230: 47

10. Loveridge, R, Ryan, GE, Sum P, Grey-Read, O, Mahood, SP, Mould, A, Harrison, S, Crouthers, R, Ko, S., Clements, T, Eames, JC, & Pruvot, M. (2018). Poisoning causing the decline in South-East Asia’s largest vulture population. Bird Conservation International 29(1): 41–54

diff --git a/docs/search.json b/docs/search.json index 662577f..b889373 100644 --- a/docs/search.json +++ b/docs/search.json @@ -11,14 +11,14 @@ "href": "publications.html#pre-prints", "title": "Publications", "section": "Pre-prints", - "text": "Pre-prints\nRyan, G.E., Nicholson, E., Baker, C.M., and McCarthy, M. A. (2024). The costs and benefits of publicising species discoveries. EcoEvoRxiv 10.32942/X2Q02W\nLe, T.P., Conway, E., Akpan, E., Abell, I., Abraham, P., Baker, C.M., Campbell, P.T., Cromer, D., Lydeamore, M.J., McDonough, Y., Mueller, I., Ryan, G., Walker, C., Wang, Y., Carvalho, N., and McVernon, J. (2023). Cost-effective boosting allocations in the post-Omicron era of COVID-19 management. medRxiv 2023.11.14.23298536." + "text": "Pre-prints\nEales, O., Teo, M., Price, D.J., Hao, T., Ryan, G.E., Senior, K.L., Carlson, S., Dalton, C., Dawson, P., Golding, N., McCaw, J.M., and Shearer, F.M. Temporal trends in test-seeking behaviour during the COVID-19 pandemic medRxiv 2024.06.06.24308566\nRyan, G.E., Nicholson, E., Baker, C.M., and McCarthy, M. A. (2024). The costs and benefits of publicising species discoveries. EcoEvoRxiv 10.32942/X2Q02W\nLe, T.P., Conway, E., Akpan, E., Abell, I., Abraham, P., Baker, C.M., Campbell, P.T., Cromer, D., Lydeamore, M.J., McDonough, Y., Mueller, I., Ryan, G., Walker, C., Wang, Y., Carvalho, N., and McVernon, J. (2023). Cost-effective boosting allocations in the post-Omicron era of COVID-19 management. medRxiv 2023.11.14.23298536." }, { "objectID": "publications.html#peer-reviewed-articles", "href": "publications.html#peer-reviewed-articles", "title": "Publications", "section": "Peer-reviewed articles", - "text": "Peer-reviewed articles\n20. Shearer, F.M., McCaw, J.M., Ryan, G.E., Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2024). Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia. Epidemics 47(2024): 100764\n19. Ryan, G.E., Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2024). Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening. Epidemics 47(2024): 100763\n18. Zachreson, C., Tobin, R., Szanyi, J., Walker, C., Cromer, D., Shearer, F.M., Conway, E., Ryan, G., Cheng, A., McCaw, J.M. and Geard, N., (2023). Individual variation in vaccine immune response can produce bimodal distributions of protection. Vaccine 41(45): 6630–6636.\n17. Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., Ryan, G.E., Campbell, T., Miller, J.C., Rebuli, N., Yeung, M., Kabashima, G., Geard, N., Wood, J., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2023). COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting. Proceedings of the Royal Society B, 290(2005): 20231437.\n16. Golding, N., Price, D.J., Ryan, G., McVernon, J., McCaw, J.M. and Shearer, F.M., (2023). A modelling approach to estimate the transmissibility of SARS-CoV-2 during periods of high, low, and zero case incidence. eLife, 12: e78089.\n15. Borzée, A., McNeely, J., Magellan, K., Miller, J.R., Porter, L., Dutta, T., Kadinjappalli, K.P., Sharma, S., Shahabuddin, G., Aprilinayati, F., Ryan, G.E and others (2020). COVID-19 Highlights the Need for More Effective Wildlife Trade Legislation. Trends in Ecology and Evolution 35: 1052–1055 pdf\n14. Brownell RL Jr, Reeves RR, Read AJ, Smith BD, Thomas PO, Ralls K, Amano M, Berggren P, Chit AM, Collins T, Currey R, Dolar L, Genov T, Hobbs R, Kreb D, Marsh H, Zhigang M, Perrin WF, Phay S, Rojas-Bracho L, Ryan GE, Shelden KEW, Slooten E, Taylor BL, Vidal O, Ding W, Whitty TS, & Wang JY (2019). Bycatch in gillnet fisheries threatens Critically Endangered small cetaceans and other aquatic megafauna. Endangered Species Research 40: 285–296\n13. Thomas, PO, Gulland, FMD, Reeves, RR, Kreb, D, Ding, W, Smith, B, Malik, MI, Ryan, GE, & Phay, S (2019). A review of electrofishing as a potential threat to freshwater cetaceans. Endangered Species Research 39: 207–220\n12. Ryan, GE, Nicholson, E, Eames, JC, Gray, TNE, Loveridge, R, Mahood, SP, Sum P, & McCarthy, MA (2019). Simultaneous‐count models to estimate abundance from counts of unmarked individuals with imperfect detection. Conservation Biology 33(3): 697–708\n11. Ryan, GE, & Baker, CM (2019). Corrigendum to “A general method for assessing the risks and benefits of secrecy in conserving ’Lazarus species” [Biol. Cons. 203, 186–187]. Biological Conservation 230: 47\n10. Loveridge, R, Ryan, GE, Sum P, Grey-Read, O, Mahood, SP, Mould, A, Harrison, S, Crouthers, R, Ko, S., Clements, T, Eames, JC, & Pruvot, M. (2018). Poisoning causing the decline in South-East Asia’s largest vulture population. Bird Conservation International 29(1): 41–54\n9. Krutzen, M, Beasley I, Ackermann, CY, Lieckfeldt, D, Ludwig, A, Ryan, GE, Bejder, L, Parra, GJ, Wolfensberger, R, & Spencer, PBS (2018). Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River. PLoS ONE 13(1): e0189200\n8. Brownell, RL, Reeves, RR, Thomas, PO, Smith, BD, & Ryan, GE (2017). Dams threaten rare Mekong dolphins. Science 355(6327): 805\n7. Mustika, PLK, Welters, R, Ryan, GE, D’Lima, C, Sorongon-Yap, P, Jutapruet S, & Peter, C (2017). A rapid assessment of wildlife tourism risk posed to cetaceans in Asia. Journal of Sustainable Tourism 25(8): 1138–115\n6. Ryan, GE, & Baker, CM (2016). A general method for assessing the risks and benefits of secrecy in conserving ‘Lazarus species’. Biological Conservation 203: 186–187. See also Corrigendum, Ryan & Baker (2019)\n5. Singh, R. Phan C, Prum S, Pin C, Ryan, G, & Wright, M (2013). The Serengeti of Asia: current status of the Eastern Plains Landscape protected area complex, Cambodia. PARKS 19(2): 23-32\n4. Ryan, GE (2012). Brahminy kites Haliastur indus fishing with Irrawaddy dolphins Orcaella brevirostris in the Mekong River. Forktail 28: 161-162\n3. Sok K, Claassen, AH, Wright, HL, & Ryan, GE (2012). Waterbird nest protection on the Mekong River: a preliminary evaluation, with notes on the recovery and release of white-shouldered ibis Pseudibis davisoni chicks. Cambodian Journal of Natural History 2012(1): 29-41\n2. McCarthy, MA, Garrard, GE, Moore, AL, Parris, KM, Regan, TJ, & Ryan, GE (2011). The SAFE index should not be used for prioritization. Frontiers in Ecology and the Environment 9(9): 486–487\n1. Ryan, GE, Dove, V, Trujillo, F, & Doherty, PF (2011). Irrawaddy dolphin demography in the Mekong River: an application of mark-resight models. Ecosphere 2(5): art58" + "text": "Peer-reviewed articles\n20. Shearer, F.M., McCaw, J.M., Ryan, G.E., Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2024). Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia. Epidemics 47(2024): 100764\n19. Ryan, G.E., Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2024). Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening. Epidemics 47(2024): 100763\n18. Zachreson, C., Tobin, R., Szanyi, J., Walker, C., Cromer, D., Shearer, F.M., Conway, E., Ryan, G., Cheng, A., McCaw, J.M. and Geard, N., (2023). Individual variation in vaccine immune response can produce bimodal distributions of protection. Vaccine 41(45): 6630–6636.\n17. Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., Ryan, G.E., Campbell, T., Miller, J.C., Rebuli, N., Yeung, M., Kabashima, G., Geard, N., Wood, J., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2023). COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting. Proceedings of the Royal Society B, 290(2005): 20231437.\n16. Golding, N., Price, D.J., Ryan, G., McVernon, J., McCaw, J.M. and Shearer, F.M., (2023). A modelling approach to estimate the transmissibility of SARS-CoV-2 during periods of high, low, and zero case incidence. eLife, 12: e78089.\n15. Borzée, A., McNeely, J., Magellan, K., Miller, J.R., Porter, L., Dutta, T., Kadinjappalli, K.P., Sharma, S., Shahabuddin, G., Aprilinayati, F., Ryan, G.E and others (2020). COVID-19 Highlights the Need for More Effective Wildlife Trade Legislation. Trends in Ecology and Evolution 35: 1052–1055 pdf\n14. Brownell RL Jr, Reeves RR, Read AJ, Smith BD, Thomas PO, Ralls K, Amano M, Berggren P, Chit AM, Collins T, Currey R, Dolar L, Genov T, Hobbs R, Kreb D, Marsh H, Zhigang M, Perrin WF, Phay S, Rojas-Bracho L, Ryan GE, Shelden KEW, Slooten E, Taylor BL, Vidal O, Ding W, Whitty TS, & Wang JY (2019). Bycatch in gillnet fisheries threatens Critically Endangered small cetaceans and other aquatic megafauna. Endangered Species Research 40: 285–296\n\nThomas, PO, Gulland, FMD, Reeves, RR, Kreb, D, Ding, W, Smith, B, Malik, MI, Ryan, GE, & Phay, S (2019). A review of electrofishing as a potential threat to freshwater cetaceans. Endangered Species Research 39: 207–220\n\n12. Ryan, GE, Nicholson, E, Eames, JC, Gray, TNE, Loveridge, R, Mahood, SP, Sum P, & McCarthy, MA (2019). Simultaneous‐count models to estimate abundance from counts of unmarked individuals with imperfect detection. Conservation Biology 33(3): 697–708\n11. Ryan, GE, & Baker, CM (2019). Corrigendum to “A general method for assessing the risks and benefits of secrecy in conserving ’Lazarus species” [Biol. Cons. 203, 186–187]. Biological Conservation 230: 47\n10. Loveridge, R, Ryan, GE, Sum P, Grey-Read, O, Mahood, SP, Mould, A, Harrison, S, Crouthers, R, Ko, S., Clements, T, Eames, JC, & Pruvot, M. (2018). Poisoning causing the decline in South-East Asia’s largest vulture population. Bird Conservation International 29(1): 41–54\n9. Krutzen, M, Beasley I, Ackermann, CY, Lieckfeldt, D, Ludwig, A, Ryan, GE, Bejder, L, Parra, GJ, Wolfensberger, R, & Spencer, PBS (2018). Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River. PLoS ONE 13(1): e0189200\n8. Brownell, RL, Reeves, RR, Thomas, PO, Smith, BD, & Ryan, GE (2017). Dams threaten rare Mekong dolphins. Science 355(6327): 805\n7. Mustika, PLK, Welters, R, Ryan, GE, D’Lima, C, Sorongon-Yap, P, Jutapruet S, & Peter, C (2017). A rapid assessment of wildlife tourism risk posed to cetaceans in Asia. Journal of Sustainable Tourism 25(8): 1138–115\n6. Ryan, GE, & Baker, CM (2016). A general method for assessing the risks and benefits of secrecy in conserving ‘Lazarus species’. Biological Conservation 203: 186–187. See also Corrigendum, Ryan & Baker (2019)\n5. Singh, R. Phan C, Prum S, Pin C, Ryan, G, & Wright, M (2013). The Serengeti of Asia: current status of the Eastern Plains Landscape protected area complex, Cambodia. PARKS 19(2): 23-32\n4. Ryan, GE (2012). Brahminy kites Haliastur indus fishing with Irrawaddy dolphins Orcaella brevirostris in the Mekong River. Forktail 28: 161-162\n3. Sok K, Claassen, AH, Wright, HL, & Ryan, GE (2012). Waterbird nest protection on the Mekong River: a preliminary evaluation, with notes on the recovery and release of white-shouldered ibis Pseudibis davisoni chicks. Cambodian Journal of Natural History 2012(1): 29-41\n2. McCarthy, MA, Garrard, GE, Moore, AL, Parris, KM, Regan, TJ, & Ryan, GE (2011). The SAFE index should not be used for prioritization. Frontiers in Ecology and the Environment 9(9): 486–487\n1. Ryan, GE, Dove, V, Trujillo, F, & Doherty, PF (2011). Irrawaddy dolphin demography in the Mekong River: an application of mark-resight models. Ecosphere 2(5): art58" }, { "objectID": "publications.html#grey-literature", diff --git a/publications.qmd b/publications.qmd index 8ffb558..462c918 100644 --- a/publications.qmd +++ b/publications.qmd @@ -2,80 +2,83 @@ title: "Publications" --- - *Most articles are free to read, but contact me for pdfs:* - +[gerard.ryan\@telethonkids.org.au](mailto:gerard.ryan@telethonkids.org.au){.email} + + + + - + ## Pre-prints -**Ryan, G.E.**, Nicholson, E., Baker, C.M., and McCarthy, M. A. (2024). [The costs and benefits of publicising species discoveries](https://doi.org/10.32942/X2Q02W){target="_blank"}. **EcoEvoRxiv** 10.32942/X2Q02W - -Le, T.P., Conway, E., Akpan, E., Abell, I., Abraham, P., Baker, C.M., Campbell, P.T., Cromer, D., Lydeamore, M.J., McDonough, Y., Mueller, I., **Ryan, G.**, Walker, C., Wang, Y., Carvalho, N., and McVernon, J. (2023). [Cost-effective boosting allocations in the post-Omicron era of COVID-19 management]( https://doi.org/10.1101/2023.11.14.23298536){target="_blank"}. **medRxiv** 2023.11.14.23298536. +Eales, O., Teo, M., Price, D.J., Hao, T., **Ryan, G.E.**, Senior, K.L., Carlson, S., Dalton, C., Dawson, P., Golding, N., McCaw, J.M., and Shearer, F.M. [Temporal trends in test-seeking behaviour during the COVID-19 pandemic](https://doi.org/10.1101/2024.06.06.24308566) medRxiv 2024.06.06.24308566 +**Ryan, G.E.**, Nicholson, E., Baker, C.M., and McCarthy, M. A. (2024). [The costs and benefits of publicising species discoveries](https://doi.org/10.32942/X2Q02W){target="_blank"}. **EcoEvoRxiv** 10.32942/X2Q02W +Le, T.P., Conway, E., Akpan, E., Abell, I., Abraham, P., Baker, C.M., Campbell, P.T., Cromer, D., Lydeamore, M.J., McDonough, Y., Mueller, I., **Ryan, G.**, Walker, C., Wang, Y., Carvalho, N., and McVernon, J. (2023). [Cost-effective boosting allocations in the post-Omicron era of COVID-19 management](https://doi.org/10.1101/2023.11.14.23298536){target="_blank"}. **medRxiv** 2023.11.14.23298536. ## Peer-reviewed articles -20.\ Shearer, F.M., McCaw, J.M., **Ryan, G.E.**, Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2024). [Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia](https://doi.org/10.1016/j.epidem.2024.100764){target="_blank"}. **Epidemics ** 47(2024): 100764 -19.\ **Ryan, G.E.**, Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2024). [Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening](https://doi.org/10.1016/j.epidem.2024.100763){target="_blank"}. **Epidemics** 47(2024): 100763 +20. Shearer, F.M., McCaw, J.M., **Ryan, G.E.**, Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2024). [Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia](https://doi.org/10.1016/j.epidem.2024.100764){target="_blank"}. **Epidemics** 47(2024): 100764 -18.\ Zachreson, C., Tobin, R., Szanyi, J., Walker, C., Cromer, D., Shearer, F.M., Conway, E., **Ryan, G.**, Cheng, A., McCaw, J.M. and Geard, N., (2023). [Individual variation in vaccine immune response can produce bimodal distributions of protection](https://doi.org/10.1016/j.vaccine.2023.09.025){target="_blank"}. **Vaccine** 41(45): 6630--6636. +19. **Ryan, G.E.**, Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2024). [Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening](https://doi.org/10.1016/j.epidem.2024.100763){target="_blank"}. **Epidemics** 47(2024): 100763 -17.\ Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., **Ryan, G.E.**, Campbell, T., Miller, J.C., Rebuli, N., Yeung, M., Kabashima, G., Geard, N., Wood, J., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2023). [COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting](https://doi.org/10.1098/rspb.2023.1437){target="_blank"}. **Proceedings of the Royal Society B**, 290(2005): 20231437. +18. Zachreson, C., Tobin, R., Szanyi, J., Walker, C., Cromer, D., Shearer, F.M., Conway, E., **Ryan, G.**, Cheng, A., McCaw, J.M. and Geard, N., (2023). [Individual variation in vaccine immune response can produce bimodal distributions of protection](https://doi.org/10.1016/j.vaccine.2023.09.025){target="_blank"}. **Vaccine** 41(45): 6630--6636. -16.\ Golding, N., Price, D.J., **Ryan, G.**, McVernon, J., McCaw, J.M. and Shearer, F.M., (2023). [A modelling approach to estimate the transmissibility of SARS-CoV-2 during periods of high, low, and zero case incidence](https://doi.org/10.7554/eLife.78089){target="_blank"}. **eLife**, 12: e78089. +17. Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., **Ryan, G.E.**, Campbell, T., Miller, J.C., Rebuli, N., Yeung, M., Kabashima, G., Geard, N., Wood, J., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2023). [COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting](https://doi.org/10.1098/rspb.2023.1437){target="_blank"}. **Proceedings of the Royal Society B**, 290(2005): 20231437. -15.\ Borzée, A., McNeely, J., Magellan, K., Miller, J.R., Porter, L., Dutta, T., Kadinjappalli, K.P., Sharma, S., Shahabuddin, G., Aprilinayati, F., **Ryan, G.E** and others (2020). [COVID-19 Highlights the Need for More Effective Wildlife Trade Legislation](https://doi.org/10.1016/j.tree.2020.10.001){target="_blank"}. **Trends in Ecology and Evolution** 35: 1052--1055 [pdf](publications/TREE_35(12)1052–1055_Boruzee&al_2020.pdf){target="_blank"} +16. Golding, N., Price, D.J., **Ryan, G.**, McVernon, J., McCaw, J.M. and Shearer, F.M., (2023). [A modelling approach to estimate the transmissibility of SARS-CoV-2 during periods of high, low, and zero case incidence](https://doi.org/10.7554/eLife.78089){target="_blank"}. **eLife**, 12: e78089. -14.\ Brownell RL Jr, Reeves RR, Read AJ, Smith BD, Thomas PO, Ralls K, Amano M, Berggren P, Chit AM, Collins T, Currey R, Dolar L, Genov T, Hobbs R, Kreb D, Marsh H, Zhigang M, Perrin WF, Phay S, Rojas-Bracho L, **Ryan GE**, Shelden KEW, Slooten E, Taylor BL, Vidal O, Ding W, Whitty TS, & Wang JY (2019). [Bycatch in gillnet fisheries threatens Critically Endangered small cetaceans and other aquatic megafauna](https://doi.org/10.3354/esr00994){target="_blank"}. **Endangered Species Research** 40: 285--296 +15. Borzée, A., McNeely, J., Magellan, K., Miller, J.R., Porter, L., Dutta, T., Kadinjappalli, K.P., Sharma, S., Shahabuddin, G., Aprilinayati, F., **Ryan, G.E** and others (2020). [COVID-19 Highlights the Need for More Effective Wildlife Trade Legislation](https://doi.org/10.1016/j.tree.2020.10.001){target="_blank"}. **Trends in Ecology and Evolution** 35: 1052--1055 [pdf](publications/TREE_35(12)1052–1055_Boruzee&al_2020.pdf){target="_blank"} -13.\ Thomas, PO, Gulland, FMD, Reeves, RR, Kreb, D, Ding, W, Smith, B, Malik, MI, **Ryan, GE**, & Phay, S (2019). [A review of electrofishing as a potential threat to freshwater cetaceans](https://doi.org/10.3354/esr00962){target="_blank"}. **Endangered Species Research** 39: 207--220 +14. Brownell RL Jr, Reeves RR, Read AJ, Smith BD, Thomas PO, Ralls K, Amano M, Berggren P, Chit AM, Collins T, Currey R, Dolar L, Genov T, Hobbs R, Kreb D, Marsh H, Zhigang M, Perrin WF, Phay S, Rojas-Bracho L, **Ryan GE**, Shelden KEW, Slooten E, Taylor BL, Vidal O, Ding W, Whitty TS, & Wang JY (2019). [Bycatch in gillnet fisheries threatens Critically Endangered small cetaceans and other aquatic megafauna](https://doi.org/10.3354/esr00994){target="_blank"}. **Endangered Species Research** 40: 285--296 -12.\ **Ryan, GE**, Nicholson, E, Eames, JC, Gray, TNE, Loveridge, R, Mahood, SP, Sum P, & McCarthy, MA (2019). [Simultaneous‐count models to estimate abundance from counts of unmarked individuals with imperfect detection](https://doi.org/10.1111/cobi.13261){target="_blank"}. **Conservation Biology** 33(3): 697--708 +13. Thomas, PO, Gulland, FMD, Reeves, RR, Kreb, D, Ding, W, Smith, B, Malik, MI, **Ryan, GE**, & Phay, S (2019). [A review of electrofishing as a potential threat to freshwater cetaceans](https://doi.org/10.3354/esr00962){target="_blank"}. **Endangered Species Research** 39: 207--220 -11.\ **Ryan, GE**, & Baker, CM (2019). [Corrigendum to "A general method for assessing the risks and benefits of secrecy in conserving 'Lazarus species" \[Biol. Cons. 203, 186--187\]](https://doi.org/10.1016/j.biocon.2018.12.003){target="_blank"}. **Biological Conservation** 230: 47 +12. **Ryan, GE**, Nicholson, E, Eames, JC, Gray, TNE, Loveridge, R, Mahood, SP, Sum P, & McCarthy, MA (2019). [Simultaneous‐count models to estimate abundance from counts of unmarked individuals with imperfect detection](https://doi.org/10.1111/cobi.13261){target="_blank"}. **Conservation Biology** 33(3): 697--708 -10.\ Loveridge, R, **Ryan, GE**, Sum P, Grey-Read, O, Mahood, SP, Mould, A, Harrison, S, Crouthers, R, Ko, S., Clements, T, Eames, JC, & Pruvot, M. (2018). [Poisoning causing the decline in South-East Asia's largest vulture population](https://doi.org/10.1017/S0959270918000126){target="_blank"}. **Bird Conservation International** 29(1): 41--54 +11. **Ryan, GE**, & Baker, CM (2019). [Corrigendum to "A general method for assessing the risks and benefits of secrecy in conserving 'Lazarus species" \[Biol. Cons. 203, 186--187\]](https://doi.org/10.1016/j.biocon.2018.12.003){target="_blank"}. **Biological Conservation** 230: 47 -9.\ Krutzen, M, Beasley I, Ackermann, CY, Lieckfeldt, D, Ludwig, A, **Ryan, GE**, Bejder, L, Parra, GJ, Wolfensberger, R, & Spencer, PBS (2018). [Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River](https://doi.org/10.1371/journal.pone.0189200){target="_blank"}. PLoS ONE 13(1): e0189200 +10. Loveridge, R, **Ryan, GE**, Sum P, Grey-Read, O, Mahood, SP, Mould, A, Harrison, S, Crouthers, R, Ko, S., Clements, T, Eames, JC, & Pruvot, M. (2018). [Poisoning causing the decline in South-East Asia's largest vulture population](https://doi.org/10.1017/S0959270918000126){target="_blank"}. **Bird Conservation International** 29(1): 41--54 -8.\ Brownell, RL, Reeves, RR, Thomas, PO, Smith, BD, & **Ryan, GE** (2017). [Dams threaten rare Mekong dolphins](https://doi.org/10.1126/science.aam6406){target="_blank"}. **Science** 355(6327): 805 +9. Krutzen, M, Beasley I, Ackermann, CY, Lieckfeldt, D, Ludwig, A, **Ryan, GE**, Bejder, L, Parra, GJ, Wolfensberger, R, & Spencer, PBS (2018). [Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River](https://doi.org/10.1371/journal.pone.0189200){target="_blank"}. PLoS ONE 13(1): e0189200 -7.\ Mustika, PLK, Welters, R, **Ryan, GE**, D'Lima, C, Sorongon-Yap, P, Jutapruet S, & Peter, C (2017). [A rapid assessment of wildlife tourism risk posed to cetaceans in Asia](http://dx.doi.org/10.1080/09669582.2016.1257012){target="_blank"}. **Journal of Sustainable Tourism** 25(8): 1138--115 +8. Brownell, RL, Reeves, RR, Thomas, PO, Smith, BD, & **Ryan, GE** (2017). [Dams threaten rare Mekong dolphins](https://doi.org/10.1126/science.aam6406){target="_blank"}. **Science** 355(6327): 805 -6.\ **Ryan, GE**, & Baker, CM (2016). [A general method for assessing the risks and benefits of secrecy in conserving 'Lazarus species'](http://dx.doi.org/10.1016/j.biocon.2016.09.022){target="_blank"}. **Biological Conservation** 203: 186--187. See also Corrigendum, Ryan & Baker (2019) +7. Mustika, PLK, Welters, R, **Ryan, GE**, D'Lima, C, Sorongon-Yap, P, Jutapruet S, & Peter, C (2017). [A rapid assessment of wildlife tourism risk posed to cetaceans in Asia](http://dx.doi.org/10.1080/09669582.2016.1257012){target="_blank"}. **Journal of Sustainable Tourism** 25(8): 1138--115 -5.\ Singh, R. Phan C, Prum S, Pin C, **Ryan, G**, & Wright, M (2013). [The Serengeti of Asia: current status of the Eastern Plains Landscape protected area complex, Cambodia](https://doi.org/10.2305/IUCN.CH.2013.PARKS-19-2.RS.en){target="_blank"}. **PARKS** 19(2): 23-32 +6. **Ryan, GE**, & Baker, CM (2016). [A general method for assessing the risks and benefits of secrecy in conserving 'Lazarus species'](http://dx.doi.org/10.1016/j.biocon.2016.09.022){target="_blank"}. **Biological Conservation** 203: 186--187. See also Corrigendum, Ryan & Baker (2019) -4.\ **Ryan, GE** (2012). [Brahminy kites Haliastur indus fishing with Irrawaddy dolphins Orcaella brevirostris in the Mekong River](https://www.researchgate.net/publication/289744193_Brahminy_Kites_Haliastur_indus_fishing_with_Irrawaddy_dolphins_Orcaella_brevirostris_in_the_Mekong_River){target="_blank"}. **Forktail** 28: 161-162 +5. Singh, R. Phan C, Prum S, Pin C, **Ryan, G**, & Wright, M (2013). [The Serengeti of Asia: current status of the Eastern Plains Landscape protected area complex, Cambodia](https://doi.org/10.2305/IUCN.CH.2013.PARKS-19-2.RS.en){target="_blank"}. **PARKS** 19(2): 23-32 -3.\ Sok K, Claassen, AH, Wright, HL, & **Ryan, GE** (2012). [Waterbird nest protection on the Mekong River: a preliminary evaluation, with notes on the recovery and release of white-shouldered ibis Pseudibis davisoni chicks](https://www.fauna-flora.org/wp-content/uploads/2023/05/FFI_201207_Cambodian-Journal-of-Natural-History.pdf){target="_blank"}. **Cambodian Journal of Natural History** 2012(1): 29-41 +4. **Ryan, GE** (2012). [Brahminy kites Haliastur indus fishing with Irrawaddy dolphins Orcaella brevirostris in the Mekong River](https://www.researchgate.net/publication/289744193_Brahminy_Kites_Haliastur_indus_fishing_with_Irrawaddy_dolphins_Orcaella_brevirostris_in_the_Mekong_River){target="_blank"}. **Forktail** 28: 161-162 -2.\ McCarthy, MA, Garrard, GE, Moore, AL, Parris, KM, Regan, TJ, & **Ryan, GE** (2011). [The SAFE index should not be used for prioritization](https://doi.org/10.1890/11.WB.027){target="_blank"}. **Frontiers in Ecology and the Environment** 9(9): 486--487 +3. Sok K, Claassen, AH, Wright, HL, & **Ryan, GE** (2012). [Waterbird nest protection on the Mekong River: a preliminary evaluation, with notes on the recovery and release of white-shouldered ibis Pseudibis davisoni chicks](https://www.fauna-flora.org/wp-content/uploads/2023/05/FFI_201207_Cambodian-Journal-of-Natural-History.pdf){target="_blank"}. **Cambodian Journal of Natural History** 2012(1): 29-41 -1.\ **Ryan, GE**, Dove, V, Trujillo, F, & Doherty, PF (2011). [Irrawaddy dolphin demography in the Mekong River: an application of mark-resight models](https://doi.org/10.1890/ES10-00171.1){target="_blank"}. **Ecosphere** 2(5): art58 +2. McCarthy, MA, Garrard, GE, Moore, AL, Parris, KM, Regan, TJ, & **Ryan, GE** (2011). [The SAFE index should not be used for prioritization](https://doi.org/10.1890/11.WB.027){target="_blank"}. **Frontiers in Ecology and the Environment** 9(9): 486--487 +1. **Ryan, GE**, Dove, V, Trujillo, F, & Doherty, PF (2011). [Irrawaddy dolphin demography in the Mekong River: an application of mark-resight models](https://doi.org/10.1890/ES10-00171.1){target="_blank"}. **Ecosphere** 2(5): art58 ## Grey Literature -Select grey literature. +Select grey literature. [Series of weekly COVID-19 epidemic situational assessment reports submitted to the Australian Government Department of Health Office of Health Protection from April 2020 to December 2023.](https://doi.org/10.26188/24845328.v1){target="_blank"} McCaw, JM, R Moss, DJ Price, FM Shearer, R Tobin, N Golding, T Hao, **G Ryan**, A Adekunle, P Dawson, M Teo, D Morris, JV Ross, T South, R Hyndman, M Lydeamore, M O'Hara-Wild, and J Wood (2022). [Situational assessment of COVID-19 in Australia Technical Report 22 May 2022 (released 12 August 2022)](https://mspgh.unimelb.edu.au/__data/assets/pdf_file/0003/4256103/2022-05-22-Technical-report-public-release.pdf){target="_blank"} -[Doherty Modelling – Final Report to National Cabinet](https://www.doherty.edu.au/uploads/content_doc/ Synthesis_DohertyModelling_FinalReport__NatCab05Nov.pdf){target="_blank"}. 5th November 2021. (2021) +[Doherty Modelling – Final Report to National Cabinet](https://www.doherty.edu.au/uploads/content_doc/%20Synthesis_DohertyModelling_FinalReport__NatCab05Nov.pdf){target="_blank"}. 5th November 2021. (2021) Nick Golding, Freya M. Shearer, Robert Moss, Peter Dawson, Dennis Liu, Joshua V. Ross, Rob Hyndman, Pablo Montero-Manso, **Gerry Ryan**, Tobin South, Jodie McVernon, David J. Price, and James M. McCaw, (2021). [Situational assessment of COVID-19 in Australia Technical Report 15 March 2021 (released 28 May 2021)](https://mspgh.unimelb.edu.au/__data/assets/pdf_file/0004/4230643/2021-03-15-Technical-report-public-release.pdf){target="_blank"} @@ -99,20 +102,17 @@ Cowling, V, & **Ryan, G** (2014). Can trans-boundary management save the dolphin Rodgers, M, Nash, E, Blate, G, Congdon, G, & **Ryan, GE** (2012). Resilience on the Mekong: A vulnerability and adaptation assessment in North-East Cambodia. WWF-Cambodia Technical Report, WWF-Cambodia, Phnom Penh, Cambodia - ## Data -**Ryan, G**, Nicholson, E, & McCarthy, M (2024). Data and questionnaire for "The costs and benefits of publicising species discoveries". The University of Melbourne. Dataset. Figshare DOI [10.26188/11357126](https://doi.org/10.26188/11357126){target="_blank"} - +**Ryan, G**, Nicholson, E, & McCarthy, M (2024). Data and questionnaire for "The costs and benefits of publicising species discoveries". The University of Melbourne. Dataset. Figshare DOI [10.26188/11357126](https://doi.org/10.26188/11357126){target="_blank"} ## Archived code -**Ryan, G**. (2024). geryan/publicising_species_discoveries. Zenodo. {target="_blank"} +**Ryan, G**. (2024). geryan/publicising_species_discoveries. Zenodo. [https://zenodo.org/doi/10.5281/zenodo.10622196](https://zenodo.org/doi/10.5281/zenodo.10622196){target="_blank"} -**Ryan GE**, & Golding, N. (2022). geryan/nat_plan_figs: Citable version for national plan paper (Version v1). Zenodo. {target="_blank"} - -**Ryan, G.** (2018). geryan/simultaneous_count_models: Archiving release of SCM code (Version 1). Zenodo. {target="_blank"} +**Ryan GE**, & Golding, N. (2022). geryan/nat_plan_figs: Citable version for national plan paper (Version v1). Zenodo. [https://doi.org/10.5281/zenodo.7117840](https://doi.org/10.5281/zenodo.7117840){target="_blank"} +**Ryan, G.** (2018). geryan/simultaneous_count_models: Archiving release of SCM code (Version 1). Zenodo. [https://doi.org/10.5281/zenodo.1473876](https://doi.org/10.5281/zenodo.1473876){target="_blank"} ## Published pre-prints @@ -120,7 +120,6 @@ Shearer, F.M., McCaw, J.M., **Ryan, G.E.**, Hao, T., Tierney, N., Lydeamore, M., **Ryan, G.E.**, Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2022). [Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening](https://doi.org/10.1101/2022.12.15.22282869){target="_blank"}. **medRxiv** 12.15.22282869 *Now Ryan et al. 2024 Epidemics 47(2024): 100763* -Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., **Ryan, G.E.**, Campbell, T., Miller, J.C., Yeung, M., Kabashima, G., Wood, J., Rebuli, N., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2022) [COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting](https://doi.org/10.1101/2022.12.04.22282996){target="_blank"} medRxiv 2022.12.04.22282996 *Now Conway et al.2024 Proc. Roy. Soc. B. 290(2005): 20231437* +Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., **Ryan, G.E.**, Campbell, T., Miller, J.C., Yeung, M., Kabashima, G., Wood, J., Rebuli, N., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2022) [COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting](https://doi.org/10.1101/2022.12.04.22282996){target="_blank"} medRxiv 2022.12.04.22282996 *Now Conway et al.2024 Proc. Roy. Soc. B. 290(2005): 20231437* Golding, N., Price, D.J., **Ryan, G.**, McVernon, J., McCaw, J.M. and Shearer, F.M. (2021) [Estimating the transmissibility of SARS-CoV-2 during periods of high, low and zero case incidence](https://doi.org/10.1101/2021.11.28.21264509){target="_blank"} medRxiv 2021.11.28.21264509 *Now Golding et al. 2023 eLife 12:e78089* -