Dr Lynn Fink

Senior Research Fellow

The University of Queensland Diamantina Institute
Faculty of Medicine
l.fink@uq.edu.au
+61 7 344 37946

Overview

Research Interests

  • Genomic Medicine
  • Cancer Genomics

Qualifications

  • Bachelor of Science, Ariz.
  • Doctor of Philosophy, University of California

Publications

  • Scarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie , Bailey, Peter, Lawlor, Rita T., Johns, Amber L. , Miller, David K. , Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano , Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye , Quinn, Michael C. J., Bruxner, Timothy J. C. , Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J. , Fink, J. Lynn, Newell, Felicity, Waddell, Nick , Holmes, Oliver , Kazakoff, Stephen H. , Leonard, Conrad, Wood, Scott, Xu, Qinying, Nagaraj, Shivashankar Hiriyur, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P., Capelli, Paola, Davi, Maria Vittoria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L. J. , Leggett, Barbara A. , Harris, Janelle L. , Harris, Jonathan, Jones, Marc D. , Humphris, Jeremy, Chantrill, Lorraine A. , Chin, Venessa, Nagrial, Adnan M. , Pajic, Marina, Scarlett, Christopher J. , Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S. , Colvin, Emily K. , Chou, Angela, Lovell, Jessica A. , Jamieson, Nigel B. , Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E. , Dagg, Rebecca A. , Lau, Loretta M. S. , Lee, Michael, Pickett, Hilda A. , Reddel, Roger R. , Samra, Jaswinder S. , Kench, James G. , Merrett, Neil D. , Epari, Krishna, Nguyen, Nam Q. , Zeps, Nikolajs, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J. , Wheeler, David A. , Gibbs, Richard A. , Musgrove, Elizabeth A., Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V. , Waddell, Nicola, Biankin, Andrew V. and Grimmond, Sean M. (2017) Whole-genome landscape of pancreatic neuroendocrine tumours. Nature, 543 7643: 65-71. doi:10.1038/nature21063

  • Humphris, Jeremy L., Patch, Ann-Marie, Nones, Katia, Bailey, Peter J., Johns, Amber L., McKay, Skye, Chang, David K., Miller, David K., Pajic, Marina, Kassahn, Karin S., Quinn, Michael C. J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Stone, Andrew, Wilson, Peter J., Anderson, Matthew, Fink, J. Lynn, Holmes, Oliver, Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Mead, Ronald S., Xu, Qinying, Wu, Jianmin, Pinese, Mark, Cowley, Mark J., Jones, Marc D., Nagrial, Adnan M., Chin, Venessa T., Chantrill, Lorraine A., Mawson, Amanda, Chou, Angela, Scarlett, Christopher J., Pinho, Andreia V., Rooman, Ilse, Giry-Laterriere, Marc, Samra, Jaswinder S., Kench, James G., Merrett, Neil D., Toon, Christopher W., Epari, Krishna, Nguyen, Nam Q., Barbour, Andrew, Zeps, Nikolajs, Jamieson, Nigel B., McKay, Colin J., Carter, C. Ross, Dickson, Euan J., Graham, Janet S., Duthie, Fraser, Oien, Karin, Hair, Jane, Morton, Jennifer P., Sansom, Owen J., Grutzmann, Robert, Hruban, Ralph H., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Schulick, Richard D., Wolfgang, Christopher L., Morgan, Richard A., Lawlor, Rita T., Rusev, Borislav, Corbo, Vincenzo, Salvia, Roberto, Cataldo, Ivana, Tortora, Giampaolo, Tempero, Margaret A., Hofmann, Oliver, Eshleman, James R., Pilarsky, Christian, Scarpa, Aldo, Musgrove, Elizabeth A., Gill, Anthony J., Pearson, John V., Grimmond, Sean M., Waddell, Nicola and Biankin, Andrew V. (2017) Hypermutation in pancreatic cancer. Gastroenterology, 152 1: 68-74.e2. doi:10.1053/j.gastro.2016.09.060

  • Baile, Peter, Chang, David K., Nones, Katia, Johns, Amber L., Patch, Ann-Marie, Gingras, Marie-Claude, Miller, David K., Christ, Angelika N., Bruxner, Tim J. C., Quinn, Michael C., Nourse, Craig, Murtaugh, L. Charles, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourbakhsh, Ehsan, Wani, Shivangi, Fink, Lynn, Holmes, Oliver, Chin, Vencssa, Anderson, Matthew J., Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Xu, Qinying, Wilson, Peter J., Cloonan, Nicole, Kassahn, Karin S., Taylor, Darrin, Quek, Kelly, Robertson, Alan, Pantano, Lorena, Mincarelli, Laura, Sanchez, Luis N., Evers, Lisa, Wu, Jianmin, Pinese, Mark, Cowley, Mark J., Jones, Marc D., Colvin, Emily K., Nagrial, Adnan M., Humphrey, Emily S., Chantrill, Lorraine A., Mawson, Amanda, Humphris, Jeremy, Chou, Angela, Pajic, Marina, Scarlett, Christopher J., Pinho, Andreia V., Giry-Laterriere, Marc, Rooman, Ilse, Samra, Jaswinder S., Kench, James G., Lovell, Jessica A., Merrett, Neil D., Toon, Christopher W., Epari, Krishna, Nguyen, Nam Q., Barbour, Andrew, Zeps, Nikolajs, Moran-Jones, Kim, Jamieson, Nigel B., Graham, Janet S., Duthie, Fraser, Oien, Karin, Hair, Jane, Gruetzmann, Robert, Maitra, Anirban, Iacobuzio-Donahue, Christine A., Wolfgang, Christopher L., Morgan, Richard A., Lawlor, Rita T., Corbo, Vincenzo, Bassi, Claudio, Rusev, Borislav, Capelli, Paola, Salvia, Roberto, Tortora, Giampaolo, Mukhopadhyay, Debabrata, Petersen, Gloria M., Munzy, Donna M., Fisher, William E., Karim, Saadia A., Eshleman, James R., Hruban, Ralph H., Pilarsky, Christian, Morton, Jennifer R., Sansom, Owen J., Scarpa, Aldo, Musgrove, Elizabeth A., Bailey, Ulla-Maja Hagbo, Hofmann, Oliver, Sutherland, Robert L., Wheeler, David A., Gill, Anthony J., Gibbs, Richard A., Pearson, John V., Waddell, Nicola, Biankin, Andrew V. and Grimmond, Sean M. (2016) Genomic analyses identify molecular subtypes of pancreatic cancer. Nature, 531 7592: 47-52. doi:10.1038/nature16965

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Supervision

  • Doctor Philosophy

  • Doctor Philosophy

View all Supervision

Available Projects

  • Projects based on the topics described below can be adjusted to your skill level and degree program.

    Interest from Honours students, Masters students, and PhD students is welcome. As this is a computational lab, students who have some knowledge of UNIX, programming or scripting languages, and basic statistics will have the most enriching experience.

  • With Professor Andrew Zannettino

  • With Dr Andrew Moore

View all Available Projects

Publications

Journal Article

  • Scarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie , Bailey, Peter, Lawlor, Rita T., Johns, Amber L. , Miller, David K. , Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano , Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye , Quinn, Michael C. J., Bruxner, Timothy J. C. , Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J. , Fink, J. Lynn, Newell, Felicity, Waddell, Nick , Holmes, Oliver , Kazakoff, Stephen H. , Leonard, Conrad, Wood, Scott, Xu, Qinying, Nagaraj, Shivashankar Hiriyur, Amato, Eliana, Dalai, Irene, Bersani, Samantha, Cataldo, Ivana, Dei Tos, Angelo P., Capelli, Paola, Davi, Maria Vittoria, Landoni, Luca, Malpaga, Anna, Miotto, Marco, Whitehall, Vicki L. J. , Leggett, Barbara A. , Harris, Janelle L. , Harris, Jonathan, Jones, Marc D. , Humphris, Jeremy, Chantrill, Lorraine A. , Chin, Venessa, Nagrial, Adnan M. , Pajic, Marina, Scarlett, Christopher J. , Pinho, Andreia, Rooman, Ilse, Toon, Christopher, Wu, Jianmin, Pinese, Mark, Cowley, Mark, Barbour, Andrew, Mawson, Amanda, Humphrey, Emily S. , Colvin, Emily K. , Chou, Angela, Lovell, Jessica A. , Jamieson, Nigel B. , Duthie, Fraser, Gingras, Marie-Claude, Fisher, William E. , Dagg, Rebecca A. , Lau, Loretta M. S. , Lee, Michael, Pickett, Hilda A. , Reddel, Roger R. , Samra, Jaswinder S. , Kench, James G. , Merrett, Neil D. , Epari, Krishna, Nguyen, Nam Q. , Zeps, Nikolajs, Falconi, Massimo, Simbolo, Michele, Butturini, Giovanni, Van Buren, George, Partelli, Stefano, Fassan, Matteo, Khanna, Kum Kum, Gill, Anthony J. , Wheeler, David A. , Gibbs, Richard A. , Musgrove, Elizabeth A., Bassi, Claudio, Tortora, Giampaolo, Pederzoli, Paolo, Pearson, John V. , Waddell, Nicola, Biankin, Andrew V. and Grimmond, Sean M. (2017) Whole-genome landscape of pancreatic neuroendocrine tumours. Nature, 543 7643: 65-71. doi:10.1038/nature21063

  • Humphris, Jeremy L., Patch, Ann-Marie, Nones, Katia, Bailey, Peter J., Johns, Amber L., McKay, Skye, Chang, David K., Miller, David K., Pajic, Marina, Kassahn, Karin S., Quinn, Michael C. J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Stone, Andrew, Wilson, Peter J., Anderson, Matthew, Fink, J. Lynn, Holmes, Oliver, Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Mead, Ronald S., Xu, Qinying, Wu, Jianmin, Pinese, Mark, Cowley, Mark J., Jones, Marc D., Nagrial, Adnan M., Chin, Venessa T., Chantrill, Lorraine A., Mawson, Amanda, Chou, Angela, Scarlett, Christopher J., Pinho, Andreia V., Rooman, Ilse, Giry-Laterriere, Marc, Samra, Jaswinder S., Kench, James G., Merrett, Neil D., Toon, Christopher W., Epari, Krishna, Nguyen, Nam Q., Barbour, Andrew, Zeps, Nikolajs, Jamieson, Nigel B., McKay, Colin J., Carter, C. Ross, Dickson, Euan J., Graham, Janet S., Duthie, Fraser, Oien, Karin, Hair, Jane, Morton, Jennifer P., Sansom, Owen J., Grutzmann, Robert, Hruban, Ralph H., Maitra, Anirban, Iacobuzio-Donahue, Christine A., Schulick, Richard D., Wolfgang, Christopher L., Morgan, Richard A., Lawlor, Rita T., Rusev, Borislav, Corbo, Vincenzo, Salvia, Roberto, Cataldo, Ivana, Tortora, Giampaolo, Tempero, Margaret A., Hofmann, Oliver, Eshleman, James R., Pilarsky, Christian, Scarpa, Aldo, Musgrove, Elizabeth A., Gill, Anthony J., Pearson, John V., Grimmond, Sean M., Waddell, Nicola and Biankin, Andrew V. (2017) Hypermutation in pancreatic cancer. Gastroenterology, 152 1: 68-74.e2. doi:10.1053/j.gastro.2016.09.060

  • Baile, Peter, Chang, David K., Nones, Katia, Johns, Amber L., Patch, Ann-Marie, Gingras, Marie-Claude, Miller, David K., Christ, Angelika N., Bruxner, Tim J. C., Quinn, Michael C., Nourse, Craig, Murtaugh, L. Charles, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourbakhsh, Ehsan, Wani, Shivangi, Fink, Lynn, Holmes, Oliver, Chin, Vencssa, Anderson, Matthew J., Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Xu, Qinying, Wilson, Peter J., Cloonan, Nicole, Kassahn, Karin S., Taylor, Darrin, Quek, Kelly, Robertson, Alan, Pantano, Lorena, Mincarelli, Laura, Sanchez, Luis N., Evers, Lisa, Wu, Jianmin, Pinese, Mark, Cowley, Mark J., Jones, Marc D., Colvin, Emily K., Nagrial, Adnan M., Humphrey, Emily S., Chantrill, Lorraine A., Mawson, Amanda, Humphris, Jeremy, Chou, Angela, Pajic, Marina, Scarlett, Christopher J., Pinho, Andreia V., Giry-Laterriere, Marc, Rooman, Ilse, Samra, Jaswinder S., Kench, James G., Lovell, Jessica A., Merrett, Neil D., Toon, Christopher W., Epari, Krishna, Nguyen, Nam Q., Barbour, Andrew, Zeps, Nikolajs, Moran-Jones, Kim, Jamieson, Nigel B., Graham, Janet S., Duthie, Fraser, Oien, Karin, Hair, Jane, Gruetzmann, Robert, Maitra, Anirban, Iacobuzio-Donahue, Christine A., Wolfgang, Christopher L., Morgan, Richard A., Lawlor, Rita T., Corbo, Vincenzo, Bassi, Claudio, Rusev, Borislav, Capelli, Paola, Salvia, Roberto, Tortora, Giampaolo, Mukhopadhyay, Debabrata, Petersen, Gloria M., Munzy, Donna M., Fisher, William E., Karim, Saadia A., Eshleman, James R., Hruban, Ralph H., Pilarsky, Christian, Morton, Jennifer R., Sansom, Owen J., Scarpa, Aldo, Musgrove, Elizabeth A., Bailey, Ulla-Maja Hagbo, Hofmann, Oliver, Sutherland, Robert L., Wheeler, David A., Gill, Anthony J., Gibbs, Richard A., Pearson, John V., Waddell, Nicola, Biankin, Andrew V. and Grimmond, Sean M. (2016) Genomic analyses identify molecular subtypes of pancreatic cancer. Nature, 531 7592: 47-52. doi:10.1038/nature16965

  • Saunus, Jodi M., Quinn, MIchael C. J., Patch, Ann-Marie, Pearson, John V., Bailey, Peter J., Nones, Katia, McCart Reed, Amy E., Miller, David, Peter J. Wilson, Al-Ejeh, Fares, Mariasegaram, Mythily, Lau, Queenie, Withers, Teresa, Jeffree, Rosalind L., Reid, Lynne E., Da Silva, Leonard, Matsika, Admire, Niland, Colleen M., Cummings, Margaret C., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Anderson, Matthew J., Fink, J. Lynn, Holmes, Oliver, Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Taylor, Darrin, Wood, Scott, Xu, Qinying, Kassahn, Karin S., Narayanan, Vairavan, Taib, Nur Aishah, Teo, Soo-Hwang, Chow, Yock Ping, kConFab, Jat, Parmjit S., Brandner, Sebastian, Flanagan, Adrienne M., Khanna, KumKum, Chenevix-Trench, Georgia, Grimmond, Sean M., Simpson, Peter T., Waddell, Nicola and Lakhani, Sunil R. (2015) Integrated genomic and transcriptomic analysis of human brain metastases identifies recurrently altered pathways of potential clinical significance. Journal of Pathology, 237 3: 363-378. doi:10.1002/path.4583

  • Patch, Ann-Marie, Christie, Elizabeth L., Etemadmoghadam, Dariush, Garsed, Dale W., George, Joshy, Fereday, Sian, Nones, Katia, Cowin, Prue, Alsop, Kathryn, Bailey, Peter J., Kassahn, Karin S., Newell, Felicity, Quinn, Michael C. J., Kazakoff, Stephen, Quek, Kelly, Wilhelm-Benartzi, Charlotte, Curry, Ed, Leong, Huei San, The Australian Ovarian Cancer Study Group, Hamilton, Anne, Mileshkin, Linda, Au-Yeung, George, Kennedy, Catherine, Hung, Jillian, Chiew, Yoke-Eng, Harnett, Paul, Friedlander, Michael, Quinn, Michael, Pyman, Jan, Cordner, Stephen, O'Brien, Patricia, Leditschke, , Jodie, Young, Greg, Strachan, Kate, Waring, Paul, Azar, Walid, Mitchell, Chris, Traficante, Nadia, Hendley, Joy, Thorne, Heather, Shackleton, Mark, Miller, David K., Arnau, Gisela Mir, Tothill, Richard W., Holloway, Timothy P., Semple, Timothy, Harliwong, Ivon, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Idrisoglu, Senel, Bruxner, Timothy J. C., Christ, Angelika N., Poudel, Barsha, Holmes, Oliver, Anderson, Matthew, Leonard, Conrad, Lonie, Andrew, Hall, Nathan, Wood, Scott, Taylor, Darrin F., Xu, Qinying, Fink, J. Lynn, Waddell, Nick, Drapkin, Ronny, Stronach, Euan, Gabra, Hani, Brown, Robert, Jewell, Andrea, Nagaraj, Shivashankar H., Markham, Emma, Wilson, Peter J., Ellul, Jason, McNally, Orla, Doyle, Maria A., Vedururu, Ravikiran, Stewart, Collin, Lengyel, Ernst, Pearson, John V., Waddell, Nicola, Defazio, Anna, Grimmond, Sean M. and Bowtell, David D. L. (2015) Whole-genome characterization of chemoresistant ovarian cancer. Nature, 521 7553: 489-494. doi:10.1038/nature14410

  • Waddell, Nicola, Pajic, Marina, Patch, Anne-Marie, Chang, David K, Kassahn, Karin S, Bailey, Peter, Johns, Amber L, Miller, David, Nones, Katia, Quek, Kelly, Quinn, Michael C. J, Robertson, Alan J, Fadlullah, Muhammad Z.H, Bruxner, Tim J.C, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Wilson, Peter J, Markham, Emma, Cloonan, Nicole, Anderson, Matthew J, Fink, J. Lynn, Holmes, Oliver, Kazakoff, Stephen H, Leonard, Conrad, Newell, Felicity, Poudel, Barsha, Song, Sarah, Taylor, Darrin, Waddell, Nick, Wood, Scott, Xu, Qinying, Wu, Jianmin, Pinese, Mark, Cowley, Mark J, Lee, Hong C, Jones, Marc D, Nagrial, Adnan M, Humphris, Jeremy, Chantrill, Lorraine A, Chin, Venessa, Steinmann, Angela M, Mawson, Amanda, Humphrey, Emily S, Colvin, Emily K, Chou, Angela, Scarlett, Christopher J, Pinho, Andreia V, Giry-Laterriere, Marc, Rooman, Ilse, Samra, Jaswinder S, Kench, James G, Pettitt, Jessica A, Merrett, Neil D, Toon, Christopher, Epari, Krishna, Nguyen, Nam Q, Barbour, Andrew, Zeps, Nikolajs, Jamieson, Nigel B, Graham, Janet S, Niclou, Simone P, Bjerkvig, Rolf, Grutzmann, Robert, Aust, Daniela, Hruban, Ralph H, Maitra, Anirban, Iacobuzio-Donahue, Christine A, Wolfgang, Christopher L, Morgan, Richard A, Lawlor, Rita T, Corbo, Vincenzo, Bassi, Claudio, Falconi, Massimo, Zamboni, Giuseppe, Tortora, Giampaolo, Tempero, Margaret A, Gill, Anthony J, Eshleman, James R, Pilarsky, Christian, Scarpa, Aldo, Musgrove, Elizabeth A, Pearson, John V, Biankin, Andrew V and Grimmond, Sean M (2015) Whole genomes redefine the mutational landscape of pancreatic cancer. Nature, 518 7540: 495-501. doi:10.1038/nature14169

  • Nones, Katia, Waddell, Nicola, Wayte, Nicci, Patch, Ann-Marie, Bailey, Peter, Newell, Felicity, Holmes, Oliver, Fink, J. Lynn, Quinn, Michael C. J., Tang, Yue Hang, Lampe, Guy, Quek, Kelly, Loffler, Kelly A., Manning, Suzanne, Idrisoglu, Senel, Miller, David, Xu, Qinying, Waddell, Nick, Wilson, Peter J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Nourse, Craig, Nourbakhsh, Ehsan, Anderson, Matthew, Kazakoff, Stephen, Leonard, Conrad, Wood, Scott, Simpson, Peter T., Reid, Lynne E., Krause, Lutz, Hussey, Damian J., Watson, David I., Lord, Reginald V., Nancarrow, Derek, Phillips, Wayne A., Gotely, David, Smithers, B. Mark, Whiteman, David C., Hayward, Nicholas K., Campbell, Peter J., Pearson, John V., Grimmond, Sean M. and Barbour, Andrew P. (2014) Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nature Communications, 5 5224.1-5224.9. doi:10.1038/ncomms6224

  • Nones, Katia, Waddell, Nic, Song, Sarah, Patch, Ann-Marie, Miller, David, Johns, Amber, Wu, Jianmin, Kassahn, Karin S., Wood, David, Bailey, Peter, Fink, Lynn, Manning, Suzanne, Christ, Angelika N., Nourse, Craig, Kazakoff, Stephen, Taylor, Darrin, Leonard, Conrad, Chang, David K., Jones, Marc D., Thomas, Michelle, Watson, Clare, Pinese, Mark, Cowley, Mark, Rooman, Ilse, Pajic, Marina, Butturini, Giovanni, Malpaga, Anna, Corbo, Vincenzo, Crippa, Stefano, Falconi, Massimo, Zamboni, Guiseppe, Castelli, Paola, APGI, Lawlor, Rita T., Gill, Anthony J., Scarpa, Aldo, Pearson, John V., Biankin, Andrew V. and Grimmond, Sean M. (2014) Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling. International Journal of Cancer, 2014 5: 1110-1118. doi:10.1002/ijc.28765

  • Quek, Kelly, Nones, Katia, Patch, Ann-Marie, Fink, J. Lynn, Newell, Felicity, Cloonan, Nicole, Miller, David, Fadlullah, Muhammad Z. H., Kassahn, Karin, Christ, Angelika N., Bruxner, Timothy J. C., Manning, Suzanne, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Steptoe, Anita, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Australian Pancreatic Cancer Genome Initiative, Wilson, Peter, Biankin, Andrew V., Pearson, John V., Waddell, Nic and Grimmond, Sean M. (2014) A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing. BioTechniques, 57 1: 31-38. doi:10.2144/000114189

  • Kassahn, Karin S., Holmes, Oliver, Nones, Katia, Patch, Ann-Marie, Miller, David K., Christ, Angelika K., Harliwong, Ivon, Bruxner, Timothy J., Xu, Qinying, Anderson, Matthew, Wood, Scott, Leonard, Conrad, Taylor, Darrin, Newell, Felicity, Song, Sarah, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Steptoe, Anita, Pajic, Marina, Cowley, Mark J., Pinese, Mark, Chang, David K., Gill, Anthony J., Johns, Amber L., Wu, Jianmin, Wilson, Peter J., Fink, Lynn, Biankin, Andrew V., Waddell, Nicola, Grimmond, Sean M. and Pearson, John V. (2013) Somatic point mutation calling in low cellularity tumors. PloS One, 8 11: e74380.1-e74380.10. doi:10.1371/journal.pone.0074380

  • Gonzalez-Perez, Abel, Mustonen, Ville, Reva, Boris, Ritchie, Graham R. S., Creixell, Pau, Karchin, Rachel, Vazquez, Miguel, Fink, J. Lynn, Kassahn, Karin S., Pearson, John V., Bader, Gary D., Boutros, Paul C., Muthuswamy, Lakshmi, Ouellette, B. F. Francis, Reimand, Jüri, Linding, Rune, Shibata, Tatsuhiro, Valencia, Alfonso, Butler, Adam, Dronov, Serge, Flicek, Paul, Shannon, Nick B., Carter, Hannah, Ding, Li, Sander, Chris, Stuart, Josh M., Stein, Lincoln D. and Lopez-Bigas, Nuria (2013) Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods, 10 8: 723-729. doi:10.1038/nmeth.2562

  • Biankin, Andrew V., Waddell, Nicola, Kassahn, Karin S., Gingras, Marie-Claude, Muthuswamy, Lakshmi B., Johns, Amber L., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Wu, Jianmin, Chang, David K., Cowley, Mark J., Gardiner, Brooke B., Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Pajic, Marina, Scarlett, Christopher J., Gill, Anthony J., Pinho, Andreia V., Rooman, Ilse, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Fink, J. Lynn, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Kolle, Gabriel, Newell, Felicity, Pinese, Mark, Mead, R. Scott, Humphris, Jeremy L., Kaplan, Warren, Jones, Marc D., Colvin, Emily K., Nagrial, Adnan M., Humphrey, Emily S., Chou, Angela, Chin, Venessa T., Chantrill, Lorraine A., Mawson, Amanda, Samra, Jaswinder S., Kench, James G., Lovell, Jessica A., Daly, Roger J., Merrett, Neil D., Toon, Christopher, Epari, Krishna, Nguyen, Nam Q., Barbour, Andrew, Zeps, Nikolajs, Australian Pancreatic Cancer Genome Initiative, Pearson, John V. and Grimmond, Sean M. (2012) Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature, 491 7424: 399-405. doi:10.1038/nature11547

  • Song, Sarah, Nones, Katia, Miller, David, Harliwong, Ivon, Kassahn, Karin S., Pinese, Mark, Pajic, Marina, Gill, Anthony J., Johns, Amber L., Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Newell, Felicity, Cowley, Mark J., Wu, Jianmin, Wilson, Peter, Fink, Lynn, Biankin, Andrew V., Waddell, Nic, Grimmond, Sean M. and Pearson, John V. (2012) qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS One, 7 9: e45835.1-e45835.7. doi:10.1371/journal.pone.0045835

  • Mann, Karen M., Ward, Jerrold M., Yew, Christopher Chin Kuan, Kovochich, Anne, Dawson, David W., Black, Michael A., Brett, Benjamin T., Sheetz, Benjamin T., Dupuy, Adam J., Chang, David K., Biankin, Andrew V., Waddell, Nicola, Kassahn, Karin S., Grimmond, Sean M., Rust, Alistair G., Adams, David J., Jenkins, Nancy A., Copeland, Neal G., Australian Pancreatic Cancer Genome Initiative, Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Christina, Nones, Katia, Fink, J. Lynn, Christ, Angelika, Bruxner, Tim, Cloonan, Nicole, Newell, Felicity and Pearson, John V. (2012) Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. Proceedings of the National Academy of Sciences of the United States of America, 109 16: 5934-5941. doi:10.1073/pnas.1202490109

  • Prlic, Andreas, Martinez, Marco A., Dimitropoulos, Dimitris, Beran, Bojan, Yukich, Benjamin T., Rose, Peter W., Bourne, Philip E. and Fink, J. Lynn (2010) Integration of Open Access Literature into the Protein Data Bank Using BioLit. Bmc Bioinformatics, 11 . doi:10.1186/1471-2105-11-220

  • Fink, J. Lynn, Fernicola, Pablo, Chandran, Rahul, Parastatidis, Savas, Wade, Alex, Naim, Oscar, Quinn, Gregory B. and Bourne, Philip E. (2010) Word add-in for ontology recognition: semantic enrichment of scientific literature. Bmc Bioinformatics, 11 24: Article number 103. doi:10.1186/1471-2105-11-103

  • Suzuki, H, Forrest, ARR, van Nimwegen, E, Daub, CO, Balwierz, PJ, Irvine, KM, Lassmann, T, Ravasi, T, Hasegawa, Y, de Hoon, MJL, Katayama, S, Schroder, K, Carninci, P, Tomaru, Y, Kanamori-Katayama, M, Kubosaki, A, Akalin, A, Ando, Y, Arner, E, Asada, M, Asahara, H, Bailey, T, Bajic, VB, Bauer, D, Beckhouse, AG, Bertin, N, Bjorkegren, J, Brombacher, F, Bulger, E, Chalk, AM, Chiba, J, Cloonan, N, Dawe, A, Dostie, J, Engstrom, PG, Essack, M, Faulkner, GJ, Fink, JL, Fredman, D, Fujimori, K, Furuno, M, Gojobori, T, Gough, J, Grimmond, SM, Gustafsson, M, Hashimoto, M, Hashimoto, T, Hatakeyama, M, Heinzel, S, Hide, W, Hofmann, O, Hornquist, M, Huminiecki, L, Ikeo, K, Imamoto, N, Inoue, S, Inoue, Y, Ishihara, R, Iwayanagi, T, Jacobsen, A, Kaur, M, Kawaji, H, Kerr, MC, Kimura, R, Kimura, S, Kimura, Y, Kitano, H, Koga, H, Kojima, T, Kondo, S, Konno, T, Krogh, A, Kruger, A, Kumar, A, Lenhard, B, Lennartsson, A, Lindow, M, Lizio, M, MacPherson, C, Maeda, N, Maher, CA, Maqungo, M, Mar, J, Matigian, NA, Matsuda, H, Mattick, JS, Meier, S, Miyamoto, S, Miyamoto-Sato, E, Nakabayashi, K, Nakachi, Y, Nakano, M, Nygaard, S, Okayama, T, Okazaki, Y, Okuda-Yabukami, H, Orlando, V, Otomo, J, Pachkov, M, Petrovsky, N, Plessy, C, Quackenbush, J, Radovanovic, A, Rehli, M, Saito, R, Sandelin, A, Schmeier, S, Schonbach, C, Schwartz, AS, Semple, CA, Sera, M, Severin, J, Shirahige, K, Simons, C, Laurent, GS, Suzuki, M, Suzuki, T, Sweet, MJ, Taft, RJ, Takeda, S, Takenaka, Y, Tan, K, Taylor, MS, Teasdale, RD, Tegner, J, Teichmann, S, Valen, E, Wahlestedt, C, Waki, K, Waterhouse, A, Wells, Christine A., Winther, O, Wu, L, Yamaguchi, K, Yanagawa, H, Yasuda, J, Zavolan, M, Hume, DA, Arakawa, T, Fukuda, S, Imamura, K, Kai, C, Kaiho, A, Kawashima, T, Kawazu, C, Kitazume, Y, Kojima, M, Miura, H, Murakami, K, Murata, M, Ninomiya, N, Nishiyori, H, Noma, S, Ogawa, C, Sano, T, Simon, C, Tagami, M, Takahashi, Y, Kawai, J, Hayashizaki, Y, FANTOM Consortium and Riken Omics Science Center (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41 5: 553-562. doi:10.1038/ng.375

  • Bourne, Philip E. and Fink, J. Lynn (2008) I am not a scientist, I am a number. PLoS Computational Biology, 4 12: Article number: e1000247. doi:10.1371/journal.pcbi.1000247

  • Fink, J. Lynn, Kushch, Sergey, Williams, Parker R. and Bourne, Philip E. (2008) BioLit: Integrating biological literature with databases. Nucleic Acids Research, 36 Supp. 2: W385-W389. doi:10.1093/nar/gkn317

  • Veretnik, Stella, Fink, J. Lynn and Bourne, Philip E. (2008) Computational biology resources lack persistence and usability. PLoS Computational Biology, 4 7: e1000136.1-e1000136.3. doi:10.1371/journal.pcbi.1000136

  • Bourne, Philip E., Fink, J. Lynn and Gerstein, Mark (2008) Open access: Taking full advantage of the content. PLoS Computational Biology, 4 3: Article number: e1000037. doi:10.1371/journal.pcbi.1000037

  • Fink, J. Lynn, Karunaratne, Seetha, Mittal, Amit, Gardiner, Donald M., Hamilton, Nicholas, Mahony, Donna, Kai, Chikatoshi, Suzuki, Harukazu, Hayashizaki, Yosihide and Teasdale, Rohan D. (2008) Towards defining the nuclear proteome. Genome Biology, 9 1: 1-15. doi:10.1186/gb-2008-9-1-r15

  • Sprenger, J., Fink, L., Karunaratne, S., Hanson, K., Hamilton, N. A. and Teasdale, R. D. (2008) LOCATE: A mammalian protein subcellular localization database. Nucleic Acids Research, 36 Database issue: D230-D233. doi:10.1093/nar/gkm950

  • Fink, J. Lynn and Hamilton, Nicholas (2007) DomainDraw: A macromolecular feature drawing program. In Silico Bilogy, 7 2: 145-150.

  • Davis, Melissa J., Hanson, Kelly A., Clark, Francis, Fink, J. Lynn, Zhang, Fasheng, Kasukawa, Takeya, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide and Teasdale, Rohan D. (2006) Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. Plos Genetics, 2 4: 554-563. doi:10.1371/journal.pgen.0020046

  • Forrest, Alistair R. R., Taylor, Darrin F., Fink, J. Lynn, Gongora, M. Milena, Flegg, Cameron, Teasdale, Rohan D., Suzuki, Harukazu, Kanamori, Mutsumi, Kai, Chikatoshi, Hayashizaki, Yoshihide and Grimmond, Sean M. (2006) PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. BMC Bioinformatics, 7 82: 1-11. doi:10.1186/1471-2105-7-82

  • Fink, J. Lynn, Aturaliya, Rajith N., Davis, Melissa J., Zhang, Fasheng, Hanson, Kelly, Teasdale, Melvena S., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide and Teasdale, Rohan D. (2006) LOCATE: a mouse protein subcellular localization database. Nucleic Acids Research, 34 Supp. 1: D213-D217. doi:10.1093/nar/gkj069

  • Aturaliya,Rajith N., Fink, J. Lynn, Davis, Melissa J., Hanson, Kelly A., Miranda,Kevin C., Forrest,Alistair R. R., Grimmond, Sean M., Suzuki,Harukazu, Kanamori,Mutsumi, Kai,Chikatoshi, Kawai,Jun, Carninci,Piero, Hayashizaki,Yoshihide and Teasdale,Rohan D. (2006) Subcellular localization of mammalian type II membrane proteins. Traffic, 7 5: 613-625. doi:10.1111/j.1600-0854.2006.00407.x

  • Fung, M. M., Chu, Y. L., Fink, J. L., Wallace, A. and McGuire, K. L. (2005) IL-2- and STAT5-regulated cytokine gene expression in cells expressing the Tax protein of HTLV-1. Oncogene, 24 29: 4624-4633. doi:10.1038/sj.onc.1208507

  • Fink, J. L., Drewes, S., Patel, H., Welsh, J. B., Masys, D. R., Corbeil, J. and Gribskov, M. R. (2003) 2HAPI: a microarray data analysis system. Bioinformatics, 19 11: 1443-1445. doi:10.1093/bioinformatics/btg169

  • Nair, T. M., Zheng, C. L., Fink, J. L., Stuart, R. O. and Gribskov, M. (2003) Rival penalized competitive learning (RPCL): a topology-determining algorithm for analyzing gene expression data. Computational Biology And Chemistry, 27 6: 565-574. doi:10.1016/j.compbiolchem.2003.09.006

  • Tchieu, J. H., Fana, F., Fink, J. L., Harper, J., Nair, T. M., Niedner, R. H., Smith, D. W., Steube, K., Tam, T. M., Veretnik, S., Wang, D. G. and Gribskov, M. (2003) The PlantsP and PlantsT functional Genomics Databases. Nucleic Acids Research, 31 1: 342-344. doi:10.1093/nar/gkg023

  • Corbeil, Jacques, Sheeter, Dennis, Genini, Davide, Rought, Steffney, Leoni, Lorenzo, Du, Pinyi, Ferguson, Mark, Masys, Daniel R., Welsh, John B., Fink, J. Lynn, Sasik, Roman, Huang, David, Drenkow, Jorg, Richman, Douglas D. and Gingeras, Thomas (2001) Temporal gene regulation during HIV-1 infection of human CD4(+) T cells. Genome Research, 11 7: 1198-1204. doi:10.1101/gr.180201

  • Masys, D. R., Welsh, J. B., Fink, J. L., Gribskov, M., Klacansky, I. and Corbeil, J. (2001) Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics, 17 4: 319-326. doi:10.1093/bioinformatics/17.4.319

  • Kurdi-Haidar, B, Hom, DK, Flittner, DE, Heath, D, Fink, L, Naredi, P and Howell, SB (1998) Dual cytoplasmic and nuclear distribution of the novel arsenite-stimulated human ATPase (hASNA-I). Journal of Cellular Biochemistry, 71 1: 1-10. doi:10.1002/(SICI)1097-4644(19981001)71:1<1::AID-JCB1>3.0.CO;2-#

  • Aebi, S, Fink, D, Gordon, R, Kim, HK, Zheng, H, Fink, JL and Howell, SB (1997) Resistance to cytotoxic drugs in DNA mismatch repair-deficient cells. Clinical Cancer Research, 3 10: 1763-1767.

  • Jiang, J, Sharma, SD, Hruby, VJ, Fink, JL and Hadley, ME (1997) Human epidermal melanocyte and keratinocyte melanotropin receptors: Visualization by melanotropic peptide conjugated macrospheres (polyamide beads). Experimental Dermatology, 6 1: 6-12. doi:10.1111/j.1600-0625.1997.tb00139.x

  • Jiang, JW, Sharma, SD, Hruby, VJ, Bentley, DL, Fink, JL and Hadley, ME (1996) Human epidermal melanocyte and keratinocyte melanocortin receptors: Visualization by melanotropic peptide conjugated microspheres (latex beads). Pigment Cell Research, 9 5: 240-247. doi:10.1111/j.1600-0749.1996.tb00113.x

  • Hadley, ME, Hruby, VJ, Jiang, JW, Sharma, SD, Fink, JL, HaskellLuevano, C, Bentley, DL, AlObeidi, F and Sawyer, TK (1996) Melanocortin receptors: Identification and characterization by melanotropic peptide agonists and antagonists. Pigment Cell Research, 9 5: 213-234. doi:10.1111/j.1600-0749.1996.tb00111.x

  • Jiang, Jinwen, Sharma, Shudh D., Fink, Jody L., Hadley, Mac E. and Hruby, Victor J. (1996) Melanotropic peptide receptors: membrane markers of human melanoma cells. Experimental Dermatology, 5 6: 325-333. doi:10.1111/j.1600-0625.1996.tb00136.x

  • Jiang, JW, Sharma, SD, Nakamura, S, Lai, JY, Fink, JL, Hruby, VJ and Hadley, ME (1995) The melanotropic peptide, [Nle(4),D-Phe(7)]alpha-MSH, stimulates human melanoma tyrosinase activity and inhibits cell proliferation. Pigment Cell Research, 8 6: 314-323. doi:10.1111/j.1600-0749.1995.tb00680.x

Conference Publication

  • Caporaso, J. Gregory, Deshpande, Nita, Fink, J. Lynn, Bourne, Philip E., Cohen, K. Bretonnel and Hunter, Lawrence (2008). Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. In: Russ B. Altman, Keith Dunker, Lawrence Hunter, Tiffany Murray and Teri E. Klein, Pacific Symposium on Biocomputing. PSB 2008: Pacific Symposium on Biocomputing, Hawai'i, HI, United States, (640-651). 4-8 January 2008.

  • Hamilton, A, Pantelic, S, Hanson,, Fink, L, Karunaratne, M and Teasdale, R D (2006). Automated subcellar phenotype classification : An introduction and recent results. In: Mikael Boden and Timothy Bailey, Conferences in research and practice in information technology online. 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006). 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006), Hobart, Australia, (67-72). 4/12/2006.

  • Sprenger, Josefine, Fink, J. Lynn and Teasdale, Rohan D. (2006). Evaluation and comparison of mammalian subcellular localization prediction methods. In: BMC bioinformatics. International Conference in Bioinformatics- InCoB2006, New Delhi, India, (1-7). 18-20 December, 2006. doi:10.1186/1471-2105-7-S5-S3

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Joint Principal Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

    Other advisors:

Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • Projects based on the topics described below can be adjusted to your skill level and degree program.

    Interest from Honours students, Masters students, and PhD students is welcome. As this is a computational lab, students who have some knowledge of UNIX, programming or scripting languages, and basic statistics will have the most enriching experience.

  • With Professor Andrew Zannettino

  • With Dr Andrew Moore

  • With Associate Professor Kiarash Khosrotehrani

  • With Associate Professor Nicholas Saunders and Professor Mark Ragan

  • With Dr Darren Korbie