Dr Lachlan Coin
Deputy Director, IMB Centre for Superbug Solutions
Honorary Associate Professor
Institute for Molecular Bioscience
+61 7 334 62649
Highlights
Associate Professor Lachlan Coin is a mathematician with a research focus on developing genomics and bioinformatics tools in infectious disease and cancer. He was originally drawn by the rigour and intellectual challenge of pure mathematics but now uses his maths background as a toolkit for solving complex problems in analysing high throughput biological data.
Associate Professor Coin is best known for using approaches borrowed from machine learning, statistics and probability theory to interrogate genomic data.
In particular, Associate Professor Coin has focussed on using these approaches to uncover genomic deletions and amplifications and has identified changes that are associated with increased risk of obesity and diabetes.
He has also developed approaches for finding minimal biomarker signatures associated with disease, and has applied these approaches to find biomarkers that distinguish bacterial from viral infection, and for the presence of active tuberculosis infection. He is also applying his methodology to develop a diagnostic tool for cancer from cell free DNA
Ultimately, Associate Professor Coin is motivated by making discoveries that are routinely used in clinical practice and to inform public policy to improve health outcomes.
Connect
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Journal Articles
Zhang, Shuxin, Shi, Jiahua, Sharma, Elipsha, Li, Xuan, Gao, Shuhong, Zhou, Xu, O'Brien, Jake, Coin, Lachlan, Liu, Yanchen, Sivakumar, Muttucumaru, Hai, Faisal and Jiang, Guangming (2023). In-sewer decay and partitioning of Campylobacter jejuni and Campylobacter coli and implications for their wastewater surveillance. Water Research, 233 119737, 1-9. doi: 10.1016/j.watres.2023.119737
Davies, Mark R., Keller, Nadia, Brouwer, Stephan, Jespersen, Magnus G., Cork, Amanda J., Hayes, Andrew J., Pitt, Miranda E., De Oliveira, David M. P., Harbison-Price, Nichaela, Bertolla, Olivia M., Mediati, Daniel G., Curren, Bodie F., Taiaroa, George, Lacey, Jake A., Smith, Helen V., Fang, Ning-Xia, Coin, Lachlan J. M., Stevens, Kerrie, Tong, Steven Y. C., Sanderson-Smith, Martina, Tree, Jai J., Irwin, Adam D., Grimwood, Keith, Howden, Benjamin P., Jennison, Amy V. and Walker, Mark J. (2023). Detection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA. Nature Communications, 14 (1) 1051, 1-12. doi: 10.1038/s41467-023-36717-4
Chen, Andrew, Sun, Jiaman, Martin, Guillaume, Gray, Lesley-Ann, Hřibová, Eva, Christelová, Pavla, Yahiaoui, Nabila, Rounsley, Steve, Lyons, Rebecca, Batley, Jacqueline, Chen, Ning, Hamill, Sharon, Rai, Subash K., Coin, Lachlan, Uwimana, Brigitte, D’Hont, Angelique, Doležel, Jaroslav, Edwards, David, Swennen, Rony and Aitken, Elizabeth A. B. (2023). Identification of a major QTL-controlling resistance to the Subtropical Race 4 of Fusarium oxysporum f. sp. cubense in Musa acuminata ssp. malaccensis. Pathogens, 12 (2) 289, 1-13. doi: 10.3390/pathogens12020289
Blaskovich, Mark A.T., Hansford, Karl A., Butler, Mark S., Ramu, Soumya, Kavanagh, Angela M., Jarrad, Angie M., Prasetyoputri, Anggia, Pitt, Miranda E., Huang, Johnny X., Lindahl, Fredrik, Ziora, Zyta M., Bradford, Tanya, Muldoon, Craig, Rajaratnam, Premraj, Pelingon, Ruby, Edwards, David J., Zhang, Bing, Amado, Maite, Elliott, Alysha G., Zuegg, Johannes, Coin, Lachlan, Woischnig, Anne-Kathrin, Khanna, Nina, Breidenstein, Elena, Stincone, Anna, Mason, Clive, Khan, Nawaz, Cho, Hye-Kyung, Karau, Melissa J. ... Cooper, Matthew A. (2022). A lipoglycopeptide antibiotic for Gram-positive biofilm-related infections. Science Translational Medicine, 14 (662) abj2381. doi: 10.1126/scitranslmed.abj238
Blaskovich, Mark A.T., Hansford, Karl A., Butler, Mark S., Ramu, Soumya, Kavanagh, Angela M., Jarrad, Angie M., Prasetyoputri, Anggia, Pitt, Miranda E., Huang, Johnny X., Lindahl, Fredrik, Ziora, Zyta M., Bradford, Tanya, Muldoon, Craig, Rajaratnam, Premraj, Pelingon, Ruby, Edwards, David J., Zhang, Bing, Amado, Maite, Elliott, Alysha G., Zuegg, Johannes, Coin, Lachlan, Woischnig, Anne-Kathrin, Khanna, Nina, Breidenstein, Elena, Stincone, Anna, Mason, Clive, Khan, Nawaz, Cho, Hye-Kyung, Karau, Melissa J. ... Cooper, Matthew A. (2022). A lipoglycopeptide antibiotic for Gram-positive biofilm-related infections. Science Translational Medicine, 14 (662) abj2381, 1-16. doi: 10.1126/scitranslmed.abj2381
Liu, Quanzhong, Fang, Honglin, Wang, Xiao, Wang, Miao, Li, Shuqin, Coin, Lachlan J M, Li, Fuyi and Song, Jiangning (2022). DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions. Bioinformatics (Oxford, England), 38 (17), 4053-4061. doi: 10.1093/bioinformatics/btac454
Hall, Michael B and Coin, Lachlan J M (2022). Assessment of the 2021 WHO Mycobacterium tuberculosis drug resistance mutation catalogue on an independent dataset. The Lancet Microbe, 3 (9). doi: 10.1016/S2666-5247(22)00151-3
Kumar, Vikrant, Pouw, Richard B., Autio, Matias I., Sagmeister, Manfred G., Phua, Zai Yang, Borghini, Lisa, Wright, Victoria J., Hoggart, Clive, Pan, Bangfen, Tan, Antson Kiat Yee, Binder, Alexander, Brouwer, Mieke C., Pinnock, Ellie, De Groot, Ronald, Hazelzet, Jan, Emonts, Marieke, Van Der Flier, Michiel, Reiter, Karl, Nöthen, Markus M., Hoffmann, Per, Schlapbach, Luregn J., Bellos, Evangelos, Anderson, Suzanne, Secka, Fatou, Martinón-Torres, Federico, Salas, Antonio, Fink, Colin, Carrol, Enitan D., Pollard, Andrew J. ... Davila, Sonia (2022). Variation in CFHR3 determines susceptibility to meningococcal disease by controlling factor H concentrations. American Journal of Human Genetics, 109 (9), 1680-1691. doi: 10.1016/j.ajhg.2022.08.001
Bainomugisa, Arnold, Lavu, Evelyn, Pandey, Sushil, Majumdar, Suman, Banamu, Jennifer, Coulter, Chris, Marais, Ben, Coin, Lachlan, Graham, Stephen M. and du Cros, Philipp (2022). Evolution and spread of a highly drug resistant strain of Mycobacterium tuberculosis in Papua New Guinea. BMC Infectious Diseases, 22 (1) 437. doi: 10.1186/s12879-022-07414-2
Chang, Jessie J.-Y., Gleeson, Josie, Rawlinson, Daniel, De Paoli-Iseppi, Ricardo, Zhou, Chenxi, Mordant, Francesca L., Londrigan, Sarah L., Clark, Michael B., Subbarao, Kanta, Stinear, Timothy P., Coin, Lachlan J. M. and Pitt, Miranda E. (2022). Long-read RNA sequencing identifies polyadenylation elongation and differential transcript usage of host transcripts during SARS-CoV-2 in vitro infection. Frontiers in Immunology, 13 832223, 832223. doi: 10.3389/fimmu.2022.832223
Steinig, Eike, Duchêne, Sebastián, Aglua, Izzard, Greenhill, Andrew, Ford, Rebecca, Yoannes, Mition, Jaworski, Jan, Drekore, Jimmy, Urakoko, Bohu, Poka, Harry, Wurr, Clive, Ebos, Eri, Nangen, David, Manning, Laurens, Laman, Moses, Firth, Cadhla, Smith, Simon, Pomat, William, Tong, Steven Y. C, Coin, Lachlan, McBryde, Emma and Horwood, Paul (2022). Phylodynamic inference of bacterial outbreak parameters using nanopore sequencing. Molecular Biology and Evolution, 39 (3) msac040. doi: 10.1093/molbev/msac040
Zhang, Meng, Jia, Cangzhi, Li, Fuyi, Li, Chen, Zhu, Yan, Akutsu, Tatsuya, Webb, Geoffrey I., Zou, Quan, Coin, Lachlan J. M. and Song, Jiangning (2022). Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. Briefings in Bioinformatics, 23 (2) bbab551, 1-25. doi: 10.1093/bib/bbab551
Schlapbach, Luregn J and Coin, Lachlan (2022). Understanding detrimental host response to infection: the promise of transcriptomics. Pediatric critical care medicine, 23 (2), 133-135. doi: 10.1097/PCC.0000000000002870
Ganesamoorthy, Devika, Robertson, Alan James, Chen, Wenhan, Hall, Michael B., Cao, Minh Duc, Ferguson, Kaltin, Lakhani, Sunil R., Nones, Katia, Simpson, Peter T. and Coin, Lachlan J. M. (2022). Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content. BMC Cancer, 22 (1) 85, 85. doi: 10.1186/s12885-021-09160-1
Li, Fuyi, Dong, Shuangyu, Leier, André, Han, Meiya, Guo, Xudong, Xu, Jing, Wang, Xiaoyu, Pan, Shirui, Jia, Cangzhi, Zhang, Yang, Webb, Geoffrey I., Coin, Lachlan J M, Li, Chen and Song, Jiangning (2022). Positive-unlabeled learning in bioinformatics and computational biology: a brief review. Briefings in Bioinformatics, 23 (1) bbab461, 1-13. doi: 10.1093/bib/bbab461
Li, Fuyi, Guo, Xudong, Xiang, Dongxu, Pitt, Miranda E., Bainomugisa, Arnold and Coin, Lachlan J.M. (2022). Computational analysis and prediction of PE_PGRS proteins using machine learning. Computational and Structural Biotechnology Journal, 20, 662-674. doi: 10.1016/j.csbj.2022.01.019
Zhang, Shuxin, Li, Xuan, Wu, Jiangping, Coin, Lachlan, O’Brien, Jake, Hai, Faisal and Jiang, Guangming (2021). Molecular methods for pathogenic bacteria detection and recent advances in wastewater analysis. Water, 13 (24) 3551, 3551. doi: 10.3390/w13243551
Li, Fuyi, Guo, Xudong, Jin, Peipei, Chen, Jinxiang, Xiang, Dongxu, Song, Jiangning and Coin, Lachlan J. M. (2021). Porpoise: a new approach for accurate prediction of RNA pseudouridine sites. Briefings in Bioinformatics, 22 (6) bbab245. doi: 10.1093/bib/bbab245
Li, Xuan, Kulandaivelu, Jagadeeshkumar, Zhang, Shuxin, Shi, Jiahua, Sivakumar, Muttucumaru, Mueller, Jochen, Luby, Stephen, Ahmed, Warish, Coin, Lachlan and Jiang, Guangming (2021). Data-driven estimation of COVID-19 community prevalence through wastewater-based epidemiology. Science of the Total Environment, 789 147947, 147947. doi: 10.1016/j.scitotenv.2021.147947
De, Tisham, Goncalves, Angela, Speed, Doug, Froguel, Philippe, NFBC Consortium, Gaffney, Daniel J., Johnson, Michael R., Jarvelin, Marjo-Riitta and Coin, Lachlan JM. (2021). Signatures of TSPAN8 variants associated with human metabolic regulation and diseases. iScience, 24 (8) 102893, 102893. doi: 10.1016/j.isci.2021.102893
Parry, Rhys, Gifford, Robert J., Lytras, Spyros, Ray, Stuart C. and Coin, Lachlan J. M. (2021). No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues. Proceedings of the National Academy of Sciences, 118 (33) e2109066118, e2109066118. doi: 10.1073/pnas.2109066118
Irwin, Adam D., Coin, Lachlan J. M., Harris, Patrick N. A., Cotta, Menino Osbert, Bauer, Michelle J., Buckley, Cameron, Balch, Ross, Kruger, Peter, Meyer, Jason, Shekar, Kiran, Brady, Kara, Fourie, Cheryl, Sharp, Natalie, Vlad, Luminita, Whiley, David, Beatson, Scott A., Forde, Brian M., Paterson, David, Clark, Julia, Hajkowicz, Krispin, Raman, Sainath, Bialasiewicz, Seweryn, Lipman, Jeffrey, Schlapbach, Luregn J. and Roberts, Jason A. (2021). Optimising treatment outcomes for children and adults through rapid genome sequencing of sepsis pathogens. A study protocol for a prospective, multi-centre trial (DIRECT). Frontiers in Cellular and Infection Microbiology, 11 667680, 1-8. doi: 10.3389/fcimb.2021.667680
Chang, Jessie J.-Y., Rawlinson, Daniel, Pitt, Miranda E., Taiaroa, George, Gleeson, Josie, Zhou, Chenxi, Mordant, Francesca L., De Paoli-Iseppi, Ricardo, Caly, Leon, Purcell, Damian F.J., Stinear, Timothy P., Londrigan, Sarah L., Clark, Michael B., Williamson, Deborah A., Subbarao, Kanta and Coin, Lachlan J.M. (2021). Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection. Cell Reports, 35 (6) 109108, 1-18. doi: 10.1016/j.celrep.2021.109108
Bainomugisa, Arnold, Meumann, Ella M., Rajahram, Giri Shan, Ong, Rick Twee-Hee, Coin, Lachlan, Paul, Dawn Carmel, William, Timothy, Coulter, Christopher and Ralph, Anna P. (2021). Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses. Microbial Genomics, 7 (5) 000573, 1-12. doi: 10.1099/mgen.0.000573
Gliddon, Harriet D., Kaforou, Myrsini, Alikian, Mary, Habgood-Coote, Dominic, Zhou, Chenxi, Oni, Tolu, Anderson, Suzanne T., Brent, Andrew J., Crampin, Amelia C., Eley, Brian, Heyderman, Robert, Kern, Florian, Langford, Paul R., Ottenhoff, Tom H. M., Hibberd, Martin L., French, Neil, Wright, Victoria J., Dockrell, Hazel M., Coin, Lachlan J., Wilkinson, Robert J., Levin, Michael and on behalf of the ILULU Consortium (2021). Identification of reduced host transcriptomic signatures for tuberculosis disease and digital PCR-based validation and quantification. Frontiers in Immunology, 12 637164, 1-13. doi: 10.3389/fimmu.2021.637164
Nguyen, Son Hoang, Cao, Minh Duc and Coin, Lachlan (2021). Real-time resolution of short-read assembly graph using ONT long reads. PLoS Computational Biology, 17 (1) e1008586, e1008586. doi: 10.1371/journal.pcbi.1008586
Murigneux, Valentine, Rai, Subash Kumar, Furtado, Agnelo, Bruxner, Timothy J. C., Tian, Wei, Harliwong, Ivon, Wei, Hanmin, Yang, Bicheng, Ye, Qianyu, Anderson, Ellis, Mao, Qing, Drmanac, Radoje, Wang, Ou, Peters, Brock A, Xu, Mengyang, Wu, Pei, Topp, Bruce, Coin, Lachlan J. M. and Henry, Robert J. (2020). Comparison of long-read methods for sequencing and assembly of a plant genome. GigaScience, 9 (12) giaa146. doi: 10.1093/gigascience/giaa146
Zhou, Chenxi, Olukolu, Bode, Gemenet, Dorcus C., Wu, Shan, Gruneberg, Wolfgang, Cao, Minh Duc, Fei, Zhangjun, Zeng, Zhao-Bang, George, Andrew W., Khan, Awais, Yencho, G. Craig and Coin, Lachlan J. M. (2020). Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations. Nature Genetics, 52 (11), 1256-1264. doi: 10.1038/s41588-020-00717-7
Ganesamoorthy, Devika, Yan, Mengjia, Murigneux, Valentine, Zhou, Chenxi, Cao, Minh Duc, Duarte, Tania P. S. and Coin, Lachlan J. M. (2020). High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing. F1000Research, 9, 1084. doi: 10.12688/f1000research.25693.1
Zhang, Ping, Ganesamoorthy, Devika, Nguyen, Son Hoang, Au, Raymond, Coin, Lachlan J. and Tey, Siok-Keen (2020). Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy. Journal for ImmunoTherapy of Cancer, 8 (1) e000299, 1-13. doi: 10.1136/jitc-2019-000299
Pitt, Miranda E., Nguyen, Son H., Duarte, Tânia P. S., Roddam, Louise F., Blaskovich, Mark A. T., Cooper, Matthew A. and Coin, Lachlan J. M. (2020). Complete genome sequences of clinical Pandoraea fibrosis isolates. Microbiology Resource Announcements, 9 (13) e00060-20. doi: 10.1128/mra.00060-20
Pitt, Miranda E., Nguyen, Son H., Duarte, Tânia P. S., Teng, Haotian, Blaskovich, Mark A. T., Cooper, Matthew A. and Coin, Lachlan J. M. (2020). Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing. GigaScience, 9 (2), 1-14. doi: 10.1093/gigascience/giaa002
Xu, Jun, Falconer, Caitlin, Nguyen, Quan, Crawford, Joanna, McKinnon, Brett D., Mortlock, Sally, Senabouth, Anne, Andersen, Stacey, Chiu, Han Sheng, Jiang, Longda, Palpant, Nathan J., Yang, Jian, Mueller, Michael D., Hewitt, Alex W., Pébay, Alice, Montgomery, Grant W., Powell, Joseph E. and Coin, Lachlan J. M. (2019). Genotype-free demultiplexing of pooled single-cell RNA-seq. Genome Biology, 20 (1) 290, 290. doi: 10.1186/s13059-019-1852-7
Raftery, Lyndon J., Howard, Christopher B., Grewal, Yadveer S., Vaidyanathan, Ramanathan, Jones, Martina L., Anderson, Will, Korbie, Darren, Duarte, Tania, Duc Cao, Minh, Nguyen, Son Hoang, Coin, Lachlan JM, Mahler, Stephen M and Trau, Matt (2019). Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing. Lab on a Chip, 19 (24), 4083-4092. doi: 10.1039/c9lc00978g
Gemenet, Dorcus C., da Silva Pereira, Guilherme, De Boeck, Bert, Wood, Joshua C., Mollinari, Marcelo, Olukolu, Bode A., Diaz, Federico, Mosquera, Veronica, Ssali, Reuben T., David, Maria, Kitavi, Mercy N., Burgos, Gabriela, Felde, Thomas Zum, Ghislain, Marc, Carey, Edward, Swanckaert, Jolien, Coin, Lachlan J. M., Fei, Zhangjun, Hamilton, John P., Yada, Benard, Yencho, G. Craig, Zeng, Zhao-Bang, Mwanga, Robert O. M., Khan, Awais, Gruneberg, Wolfgang J. and Buell, C. Robin (2019). Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]. Theoretical and Applied Genetics, 133 (1), 23-36. doi: 10.1007/s00122-019-03437-7
Couto Alves, Alexessander, De Silva, N. Maneka G., Karhunen, Ville, Sovio, Ulla, Das, Shikta, Taal, H. Rob, Warrington, Nicole M., Lewin, Alexandra M., Kaakinen, Marika, Cousminer, Diana L., Thiering, Elisabeth, Timpson, Nicholas J., Bond, Tom A., Lowry, Estelle, Brown, Christopher D., Estivill, Xavier, Lindi, Virpi, Bradfield, Jonathan P., Geller, Frank, Speed, Doug, Coin, Lachlan J. M., Loh, Marie, Barton, Sheila J., Beilin, Lawrence J., Bisgaard, Hans, Bønnelykke, Klaus, Alili, Rohia, Hatoum, Ida J., Schramm, Katharina ... Early Growth Genetics (EGG) Consortium (2019). GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI. Science Advances, 5 (9) eaaw3095, eaaw3095. doi: 10.1126/sciadv.aaw3095
Bialasiewicz, Seweryn, Duarte, Tania P. S., Nguyen, Son H., Sukumaran, Vichitra, Stewart, Alexandra, Appleton, Sally, Pitt, Miranda E., Bainomugisa, Arnold, Jennison, Amy V., Graham, Rikki, Coin, Lachlan J. M. and Hajkowicz, Krispin (2019). Rapid diagnosis of Capnocytophaga canimorsus septic shock in an immunocompetent individual using real-time Nanopore sequencing: a case report. BMC Infectious Diseases, 19 (1) 660, 1-5. doi: 10.1186/s12879-019-4173-2
McCart Reed, Amy E., Lal, Samir, Kutasovic, Jamie R., Wockner, Leesa, Robertson, Alan, de Luca, Xavier M., Kalita-de Croft, Priyakshi, Dalley, Andrew J., Coorey, Craig P., Kuo, Luyu, Ferguson, Kaltin, Niland, Colleen, Miller, Gregory, Johnson, Julie, Reid, Lynne E., Males, Renique, Saunus, Jodi M., Chenevix-Trench, Georgia, Coin, Lachlan, Lakhani, Sunil R. and Simpson, Peter T. (2019). LobSig is a multigene predictor of outcome in invasive lobular carcinoma. npj Breast Cancer, 5 (1) 18, 18. doi: 10.1038/s41523-019-0113-y
Georgiadou, Athina, Lee, Hyun Jae, Walther, Michael, van Beek, Anna E., Fitriani, Fadlila, Wouters, Diana, Kuijpers, Taco W., Nwakanma, Davis, D’Alessandro, Umberto, Riley, Eleanor M., Otto, Thomas D., Ghani, Azra, Levin, Michael, Coin, Lachlan J., Conway, David J., Bretscher, Michael T. and Cunnington, Aubrey J. (2019). Modelling pathogen load dynamics to elucidate mechanistic determinants of host–Plasmodium falciparum interactions. Nature Microbiology, 4 (9), 1592-1602. doi: 10.1038/s41564-019-0474-x
Shimizu, Chisato, Kim, Jihoon, Eleftherohorinou, Hariklia, Wright, Victoria J., Hoang, Long T., Tremoulet, Adriana H., Franco, Alessandra, Hibberd, Martin L., Takahashi, Atsushi, Kubo, Michiaki, Ito, Kaoru, Tanaka, Toshihiro, Onouchi, Yoshihiro, Coin, Lachlan J. M., Levin, Michael, Burns, Jane C. and Shike, Hiroko (2019). HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki disease. Human Immunology, 80 (9), 731-738. doi: 10.1016/j.humimm.2019.04.020
Borghini, Lisa, Png, Eileen, Binder, Alexander, Wright, Victoria J., Pinnock, Ellie, de Groot, Ronald, Hazelzet, Jan, Emonts, Marieke, Van der Flier, Michiel, Schlapbach, Luregn J., Anderson, Suzanne, Secka, Fatou, Salas, Antonio, Fink, Colin, Carrol, Enitan D., Pollard, Andrew J., Coin, Lachlan J., Kuijpers, Taco W., Martinon-Torres, Federico, Zenz, Werner, Levin, Michael, Hibberd, Martin L., Davila, Sonia and EUCLIDS consortium (2019). Identification of regulatory variants associated with genetic susceptibility to meningococcal disease. Scientific Reports, 9 (1) 6966, 6966. doi: 10.1038/s41598-019-43292-6
Teng, Haotian, Cao, Minh Duc, Hall, Michael B., Duarte, Tania, Wang, Sheng and Coin, Lachlan J M (2019). Correction to: Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning. GigaScience, 8 (5). doi: 10.1093/gigascience/giz049
Bainomugisa, Arnold, Pandey, Sushi, Donnan, Ellen, Simpson, Graham, Foster, J'Belle, Lavu, Evelyn, Hiasihri, Stenard, McBryde, Emma S., Moke, Rendi, Vincent, Steven, Sintchenko, Vitali, Marais, Ben J., Coin, Lachlan J. M. and Coulter, Christopher (2019). Cross-border movement of highly drug-resistant Mycobacterium tuberculosis from Papua New Guinea to Australia through Torres Strait Protected Zone, 2010-2015. Emerging Infectious Diseases, 25 (3), 406-415. doi: 10.3201/eid2503.181003
Zhang, Ping, Raju, Jyothy, Ullah, Md Ashik, Au, Raymond, Varelias, Antiopi, Gartlan, Kate H, Olver, Stuart D., Samson, Luke D., Sturgeon, Elise, Zomerdijk, Nienke, Avery, Judy, Gargett, Tessa, Brown, Michael P., Coin, Lachlan J., Ganesamoorthy, Devika, Hutchins, Cheryl, Pratt, Gary R, Kennedy, Glen A., Morton, A. James, Curley, Cameron I., Hill, Geoffrey R. and Tey, Siok-Keen (2019). Phase I trial of inducible caspase 9 T cells in adult stem cell transplant demonstrates massive clonotypic proliferative potential and long-term persistence of transgenic T cells. Clinical Cancer Research, 25 (6), 1749-1755. doi: 10.1158/1078-0432.CCR-18-3069
Pitt, Miranda E., Cao, Minh Duc, Butler, Mark S., Ramu, Soumya, Ganesamoorthy, Devika, Blaskovich, Mark A. T., Coin, Lachlan J. M. and Cooper, Matthew A. (2018). Octapeptin C4 and polymyxin resistance occur via distinct pathways in an epidemic XDR Klebsiella pneumoniae ST258 isolate. The Journal of Antimicrobial Chemotherapy, 74 (3), 582-593. doi: 10.1093/jac/dky458
Shao, Haojing, Zhou, Chenxi, Cao, Minh Duc and Coin, Lachlan J. M. (2018). Ongoing human chromosome end extension revealed by analysis of BioNano and nanopore data. Scientific Reports, 8 (1) 16616, 16616. doi: 10.1038/s41598-018-34774-0
Wu, Shan, Lau, Kin H., Cao, Qinghe, Hamilton, John P., Sun, Honghe, Zhou, Chenxi, Eserman, Lauren, Gemenet, Dorcus C., Olukolu, Bode A., Wang, Haiyan, Crisovan, Emily, Godden, Grant T., Jiao, Chen, Wang, Xin, Kitavi, Mercy, Manrique-Carpintero, Norma, Vaillancourt, Brieanne, Wiegert-Rininger, Krystle, Yang, Xinsun, Bao, Kan, Schaff, Jennifer, Kreuze, Jan, Gruneberg, Wolfgang, Khan, Awais, Ghislain, Marc, Ma, Daifu, Jiang, Jiming, Mwanga, Robert O. M., Leebens-Mack, Jim ... Fei, Zhangjun (2018). Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nature Communications, 9 (1) 4580, 4580. doi: 10.1038/s41467-018-06983-8
Wright, Victoria J., Herberg, Jethro A., Kaforou, Myrsini, Shimizu, Chisato, Eleftherohorinou, Hariklia, Shailes, Hannah, Barendregt, Anouk M., Menikou, Stephanie, Gormley, Stuart, Berk, Maurice, Hoang, Long Truong, Tremoulet, Adriana H., Kanegaye, John T., Coin, Lachlan J. M., Glodé, Mary P., Hibberd, Martin, Kuijpers, Taco W., Hoggart, Clive J., Burns, Jane C. and Levin, Michael (2018). Diagnosis of Kawasaki Disease using a minimal whole-blood gene expression signature. JAMA Pediatrics, 172 (10), e182293. doi: 10.1001/jamapediatrics.2018.2293
Zhou, Chenxi, Duarte, Tania, Silvestre, Rocio, Rossel, Genoveva, Mwanga, Robert O. M., Khan, Awais, George, Andrew W., Fei, Zhangjun, Yencho, G. Craig, Ellis, David and Coin, Lachlan J. M. (2018). Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes. Gates Open Research, 2 41, 41. doi: 10.12688/gatesopenres.12856.1
Lu, Ji, Jin, Min, Nguyen, Son Hoang, Mao, Likai, Li, Jie, Coin, Lachlan J.M., Yuan, Zhiguo and Guo, Jianhua (2018). Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation. Environment International, 118, 257-265. doi: 10.1016/j.envint.2018.06.004
Ganesamoorthy, Devika, Cao, Minh Duc, Duarte, Tania, Chen, Wenhan and Coin, Lachlan (2018). GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing. BMC Bioinformatics, 19 (1) 267, 267. doi: 10.1186/s12859-018-2282-3
Shao, Haojing, Ganesamoorthy, Devika, Duarte, Tania, Cao, Minh Duc, Hoggart, Clive J. and Coin, Lachlan J. M. (2018). npInv: accurate detection and genotyping of inversions using long read sub-alignment. BMC Bioinformatics, 19 (1) 261, 261. doi: 10.1186/s12859-018-2252-9
Lee, Hyun Jae, Georgiadou, Athina, Walther, Michael, Nwakanma, Davis, Stewart, Lindsay B., Levin, Michael, Otto, Thomas D., Conway, David J., Coin, Lachlan J. and Cunnington, Aubrey J. (2018). Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. Science Translational Medicine, 10 (447) eaar3619, eaar3619. doi: 10.1126/scitranslmed.aar3619
Bainomugisa, Arnold, Duarte, Tania, Lavu, Evelyn, Pandey, Sushil, Coulter, Chris, Marais, Ben J. and Coin, Lachlan M. (2018). A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions. Microbial Genomics, 4 (7) 000188. doi: 10.1099/mgen.0.000188
Lee, Hyun Jae, Georgiadou, Athina, Otto, Thomas D., Levin, Michael, Coin, Lachlan J., Conway, David J. and Cunnington, Aubrey J. (2018). Transcriptomic studies of malaria: a paradigm for investigation of systemic host-pathogen interactions. Microbiology and Molecular Biology Reviews, 82 (2) e00071-17, e00071-17. doi: 10.1128/MMBR.00071-17
Martinón-Torres, Federico, Salas, Antonio, Rivero-Calle, Irene, Cebey-López, Miriam, Pardo-Seco, Jacobo, Herberg, Jethro A, Boeddha, Navin P, Klobassa, Daniela S, Secka, Fatou, Paulus, Stephane, de Groot, Ronald, Schlapbach, Luregn J, Driessen, Gertjan J, Anderson, Suzanne T, Emonts, Marieke, Zenz, Werner, Carrol, Enitan D, Van der Flier, Michiel, Levin, Michael, Levin, Michael, Coin, Lachlan, Gormley, Stuart, Hamilton, Shea, Herberg, Jethro, Hourmat, Bernardo, Hoggart, Clive, Kaforou, Myrsini, Sancho-Shimizu, Vanessa, Wright, Victoria ... EUCLIDS Consortium (2018). Life-threatening infections in children in Europe (the EUCLIDS Project): a prospective cohort study. The Lancet Child and Adolescent Health, 2 (6), 404-414. doi: 10.1016/S2352-4642(18)30113-5
Teng, Haotian, Cao, Minh Duc, Hall, Michael B., Duarte, Tania, Wang, Sheng and Coin, Lachlan J. M. (2018). Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning. GigaScience, 7 (5). doi: 10.1093/gigascience/giy037
Pitt, Miranda E., Elliott, Alysha G., Cao, Minh Duc, Ganesamoorthy, Devika, Karaiskos, Ilias, Giamarellou, Helen, Abboud, Cely S., Blaskovich, Mark A. T., Cooper, Matthew A. and Coin, Lachlan J. M. (2018). Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae. Microbial Genomics, 4 (3) 000158. doi: 10.1099/mgen.0.000158
von Both, Ulrich, Berk, Maurice, Agapow, Paul-Michael, Wright, Joseph D, Git, Anna, Hamilton, Melissa Shea, Goldgof, Greg, Siddiqui, Nazneen, Bellos, Evangelos, Wright, Victoria J, Coin, Lachlan J, Newton, Sandra M and Levin, Michael (2018). Mycobacterium tuberculosis exploits a molecular off switch of the immune system for intracellular survival. Scientific reports, 8 (1) 661, 661. doi: 10.1038/s41598-017-18528-y
Bainomugisa, Arnold, Lavu, Evelyn, Hiashiri, Stenard, Majumdar, Suman, Honjepari, Alice, Moke, Rendi, Dakulala, Paison, Hill-Cawthorne, Grant A, Pandey, Sushil, Marais, Ben J, Coulter, Chris and Coin, Lachlan (2018). Multi-clonal evolution of multi-drug-resistant/extensively drug-resistant Mycobacterium tuberculosis in a high-prevalence setting of Papua New Guinea for over three decades. Microbial Genomics, 4 (2). doi: 10.1099/mgen.0.000147
Lu, Ji, Wang, Yue, Li, Jie, Mao, Likai, Nguyen, Son Hoang, Duarte, Tania, Coin, Lachlan, Bond, Philip, Yuan, Zhiguo and Guo, Jianhua (2018). Triclosan at environmentally relevant concentrations promotes horizontal transfer of multidrug resistance genes within and across bacterial genera. Environment International, 121 (Pt 2), 1217-1226. doi: 10.1016/j.envint.2018.10.040
Hemingway, Cheryl, Berk, Maurice, Anderson, Suzanne T., Wright, Victoria J., Hamilton, Shea, Eleftherohorinou, Hariklia, Kaforou, Myrsini, Goldgof, Greg M., Hickman, Katy, Kampmann, Beate, Schoeman, Johan, Eley, Brian, Beatty, David, Pienaar, Sandra, Nicol, Mark P., Griffiths, Michael J., Waddell, Simon J., Newton, Sandra M., Coin, Lachlan J., Relman, David A., Montana, Giovanni and Levin, Michael (2017). Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function. PLoS One, 12 (11) e0185973, e0185973. doi: 10.1371/journal.pone.0185973
Cao, Minh Duc, Ganesamoorthy, Devika, Zhou, Chenxi and Coin, Lachlan J M (2017). Simulating the Dynamics of Targeted Capture Sequencing with CapSim. Bioinformatics (Oxford, England), 34 (5), 873-874. doi: 10.1093/bioinformatics/btx691
Couto Alves, A., Valcarcel, B., Mäkinen, V. P., Morin-Papunen, L., Sebert, S., Kangas, A. J., Soininen, P., Das, S., De Iorio, M., Coin, L., Ala-Korpela, M., Järvelin, M. R. and Franks, S. (2017). Metabolic profiling of polycystic ovary syndrome reveals interactions with abdominal obesity. International Journal of Obesity, 41 (9), 1331-1340. doi: 10.1038/ijo.2017.126
Nguyen, Son Hoang, Duarte, Tania, Coin, Lachlan and Cao, Minh Duc (2017). Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode. Bioinformatics (Oxford, England), 33 (24), 3988-3990. doi: 10.1093/bioinformatics/btx537
Kaforou, Myrsini, Herberg, Jethro A., Wright, Victoria J., Coin, Lachlan J. M. and Levin, Michael (2017). Diagnosis of bacterial infection using a 2-transcript host RNA signature in febrile infants 60 days or younger. Journal of the American Medical Association, 317 (15), 1577-1578. doi: 10.1001/jama.2017.1365
Chen, Wenhan, Robertson, Alan J., Ganesamoorthy, Devika and Coin, Lachlan J. M. (2017). sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors. Nucleic Acids Research, 45 (5) 1086, e34-e34. doi: 10.1093/nar/gkw1086
Cao, Minh Duc, Nguyen, Son Hoang, Ganesamoorthy, Devika, Elliott, Alysha G., Cooper, Matthew A. and Coin, Lachlan J. M. (2017). Scaffolding and completing genome assemblies in real-time with nanopore sequencing. Nature Communications, 8 (1) 14515, 14515. doi: 10.1038/ncomms14515
Shimizu, Chisato, Eleftherohorinou, Hariklia, Wright, Victoria J., Kim, Jihoon, Alphonse, Martin P., Perry, James C., Cimaz, Rolando, Burgner, David, Dahdah, Nagib, Hoang, Long T., Khor, Chiea Chuen, Salgado, Andrea, Tremoulet, Adriana H., Davila, Sonia, Kuijpers, Taco W., Hibberd, Martin L., Johnson, Todd A., Takahashi, Atsushi, Tsunoda, Tatsuhiko, Kubo, Michiaki, Tanaka, Toshihiro, Onouchi, Yoshihiro, Yeung, Rae S. M., Coin, Lachlan J. M., Levin, Michael and Burns, Jane C. (2016). Genetic variation in the SLC8A1 calcium signaling pathway is associated with susceptibility to Kawasaki disease and coronary artery abnormalities. Circulation: Cardiovascular Genetics, 9 (6), 559-568. doi: 10.1161/CIRCGENETICS.116.001533
Martinon-Torres, Federico, Png, Eileen, Khor, Chiea Chuen, Davila, Sonia, Wright, Victoria J., Sim, Kar Seng, Vega, Ana, Fachal, Laura, Inwald, David, Nadel, Simon, Carrol, Enitan D., Martinon-Torres, Nazareth, Marcos Alonso, Sonia, Carracedo, Angel, Morteruel, Elvira, Lopez-Bayon, Julio, Concha Torre, Andres, Calvo Monge, Cristina, Gonzalez de Aguilar, Pilar Azcon, Esteban Torne, Elisabeth, del Carmen Martinez-Padilla, Maria, Maria Martinon-Sanchez, Jose, Levin, Michael, Hibberd, Martin L., Salas, Antonio, ESIGEM network, ESPID meningococcal consortium, Coin, Lachlan and EUCLIDS consortium (2016). Natural resistance to meningococcal disease related to CFH loci: meta-analysis of genome-wide association studies. Scientific Reports, 6 (1) 35842, 35842.1-35842.9. doi: 10.1038/srep35842
Herberg, Jethro A., Kaforou, Myrsini, Wright, Victoria J., Shailes, Hannah, Eleftherohorinou, Hariklia, Hoggart, Clive J., Cebey-Lopez, Miriam, Carter, Michael J., Janes, Victoria A., Gormley, Stuart, Shimizu, Chisato, Tremoulet, Adriana H., Barendregt, Anouk M., Salas, Antonio, Kanegaye, John, Pollard, Andrew J., Faust, Saul N., Patel, Sanjay, Kuijpers, Taco, Martinon-Torres, Federico, Burns, Jane C., Coin, Lachlan J. M. and Levin, Michael (2016). Diagnostic test accuracy of a 2-transcript host RNA signature for discriminating bacterial vs viral infection in febrile children. The Journal of the American Medical Association, 316 (8), 835-845. doi: 10.1001/jama.2016.11236
Cao, Minh Duc, Ganesamoorthy, Devika, Elliott, Alysha G., Zhang, Huihui, Cooper, Matthew A. and Coin, Lachlan J. M. (2016). Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION (TM) sequencing. Gigascience, 5 (1) 32, 32. doi: 10.1186/s13742-016-0137-2
Poznik, G. David, Xue, Yali, Mendez, Fernando L., Willems, Thomas F., Massaia, Andrea, Sayres, Melissa A. Wilson, Ayub, Qasim, McCarthy, Shane A., Narechania, Apurva, Kashin, Seva, Chen, Yuan, Banerjee, Ruby, Rodriguez-Flores, Juan L., Cerezo, Maria, Shao, Haojing, Gymrek, Melissa, Malhotra, Ankit, Louzada, Sandra, Desalle, Rob, Ritchie, Graham R. S., Cerveira, Eliza, Fitzgerald, Tomas W., Garrison, Erik, Marcketta, Anthony, Mittelman, David, Romanovitch, Mallory, Zhang, Chengsheng, Zheng-Bradley, Xiangqun, Abecasis, Goncalo R. ... Tyler-Smith, Chris (2016). Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nature Genetics, 48 (6), 593-599. doi: 10.1038/ng.3559
Elliott, Alysha G., Ganesamoorthy, Devika, Coin, Lachlan, Cooper, Matthew A. and Cao, Minh Duc (2016). Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae strain ATCC 700603. Genome Announcements, 4 (3) e00438-16. doi: 10.1128/genomeA.00438-16
Li, Jun, Woods, Susan L., Healey, Sue, Beesley, Jonathan, Chen, Xiaoqing, Lee, Jason S., Sivakumaran, Haran, Wayte, Nicci, Nones, Katia, Waterfall, Joshua J., Pearson, John, Patch, Anne-Marie, Senz, Janine, Ferreira, Manuel A., Kaurah, Pardeep, Mackenzie, Robertson, Heravi-Moussavi, Alireza, Hansford, Samantha, Lannagan, Tamsin R. M., Spurdle, Amanda B., Simpson, Peter T., da Silva, Leonard, Lakhani, Sunil R., Clouston, Andrew D., Bettington, Mark, Grimpen, Florian, Busuttil, Rita A., Di Costanzo, Natasha, Boussioutas, Alex ... Chenevix-Trench, Georgia (2016). Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. American Journal of Human Genetics, 98 (5), 830-842. doi: 10.1016/j.ajhg.2016.03.001
Cao, Minh Duc, Ganesamoorthy, Devika, Cooper, Matthew A. and Coin, Lachlan J.M. (2015). Realtime analysis and visualisation of MinION sequencing data with npReader. Bioinformatics, 32 (5), 764-766. doi: 10.1093/bioinformatics/btv658
The 1000 Genomes Project Consortium and Coin, Lachlan (2015). A global reference for human genetic variation. Nature, 526 (7571), 68-74. doi: 10.1038/nature15393
Bellos, Evangelos, Kumar, Vikrant, Lin, Clarabelle, Maggi, Jordi, Yang Phua, Zai Yang, Cheng, Ching-Yu, Cheung, Chui Ming Gemmy, Hibberd, Martin L., Wong, Tien Yin, Coin, Lachlan J. M. and Davila, Sonia (2014). cnvCapSeq: detecting copy number variation in long-range targeted resequencing date. Nucleic Acids Research, 42 (20), e158-e158. doi: 10.1093/nar/gku849
Ramasamy, Adaikalavan, Trabzuni, Daniah, Guelfi, Sebastian, Varghese, Vibin, Smith, Colin, Walker, Robert, De, Tisham, Coin, Lachlan, de Silva, Rohan, Cookson, Mark R., Singleton, Andrew B., Hardy, John, Ryten, Mina and Weale, Michael E. (2014). Genetic variability in the regulation of gene expression in ten regions of the human brain. Nature Neuroscience, 17 (10), 1418-1428. doi: 10.1038/nn.3801
Bellos, Evangelos and Coin, Lachlan J. M. (2014). cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data. Bioinformatics, 30 (17), i639-i645. doi: 10.1093/bioinformatics/btu475
Colonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., Garrison, E., Xue, Y., Tyler-Smith, C., The 1000 Genomes Project Consortium, Abecasis, G. R., Auton, A., Brooks, L. D., Depristo, M. A., Durbin, R. M., Handsaker, R. E., Kang, H. M., Marth, G. T., McVean, Ga, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Donnelly, P., Eichler, E. E., Flicek, P., Gabriel, S. B. ... Peterson, J. L. (2014). Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biology, 15 (6) R88. doi: 10.1186/gb-2014-15-6-r88
Anderson, Suzanne T., Kaforou, Myrsini, Brent, Andrew J., Wright, Victoria J., Banwell, Claire M., Chagaluka, George, Crampin, Amelia C., Dockrell, Hazel M., French, Neil, Hamilton, Melissa S., Hibberd, Martin L., Kern, Florian, Langford, Paul R., Ling, Ling, Mlotha, Rachel, Ottenhoff, Tom H. M., Pienaar, Sandy, Pillay, Vashini, Scott, J. Anthony G., Twahir, Hemed, Wilkinson, Robert J., Coin, Lachlan J., Heyderman, Robert S., Levin, Michael, Eley, Brian and for the ILULU Consortium and KIDS TB Study Group (2014). Diagnosis of childhood tuberculosis and host RNA expression in Africa. New England Journal of Medicine, 370 (18), 1712-1723. doi: 10.1056/NEJMoa1303657
Zhang, Fan, Chen, Ruoyan, Liu, Dongbing, Yao, Xiaotian, Li, Guoqing, Jin, Yabin, Yu, Chang, Li, Yingrui and Coin, Lachlan J. M. (2013). YHap: A population model for probabilistic assignment of Y haplogroups from re-sequencing data. BMC Bioinformatics, 14 (1) 331, 331.1-331.4. doi: 10.1186/1471-2105-14-331
Alves, Alexessander Couto, Bruhn, Soren, Ramasamy, Adaikalavan, Wang, Hui, Holloway, John W., Hartikainen, Anna-Liisa, Jarvelin, Marjo-Riitta, Benson, Mikael, Balding, David J. and Coin, Lachlan J. M. (2013). Dysregulation of complement system and CD4+T cell activation pathways implicated in allergic response. PLoS One, 8 (10) e74821, e74821.1-e74821.15. doi: 10.1371/journal.pone.0074821
Munhoz, Renato Puppi, Teive, Hélio A., Eleftherohorinou, Hariklia, Coin, Lachlan J., Lees, Andrew J. and Silveira-Moriyama, Laura (2013). Demographic and motor features associated with the occurrence of neuropsychiatric and sleep complications of Parkinson's disease. Journal of Neurology, Neurosurgery and Psychiatry, 84 (8), 883-887. doi: 10.1136/jnnp-2012-304440
Bønnelykke, Klaus, Matheson, Melanie C., Pers, Tune H., Granell, Raquel, Strachan, David P., Alves, Alexessander Couto, Linneberg, Allan, Curtin, John A., Warrington, Nicole M., Standl, Marie, Kerkhof, Marjan, Jonsdottir, Ingileif, Bukvic, Blazenka K., Kaakinen, Marika, Sleimann, Patrick, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Schramm, Katharina, Baltic, Svetlana, Kreiner-Møller, Eskil, Simpson, Angela, St Pourcain, Beate, Coin, Lachlan, Hui, Jennie, Walters, Eugene H., Tiesler, Carla M. T., Duffy, David L., Jones, Graham, Ring, Susan M. ... Brown, Matthew A. (2013). Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization. Nature Genetics, 45 (8), 902-906. doi: 10.1038/ng.2694
Couto-Alves, Alexessander, Wright, Victoria J., Perumal, Karnan, Binder, Alexander, Carrol, Enitan D., Emonts, Marieke, de Groot, Ronald, Hazelzet, Jan, Kuijpers, Taco, Nadel, Simon, Zenz, Werner, Ramnarayan, Padmanabhan, Levin, Michael, Coin, Lachlan and Inwald, David P. (2013). A new scoring system derived from base excess and platelet count at presentation predicts mortality in paediatric meningococcal sepsis. Critical Care, 17 (2) R68. doi: 10.1186/cc12609
Ramasamy, Adaikalavan, Kuokkanen, Mikko, Vedantam, Sailaja, Gajdos, Zofia K., Alves, Alexessander Couto, Lyon, Helen N., Ferreira, Manuel A. R., Strachan, David P., Zhao, Jing Hua, Abramson, Michael J., Brown, Matthew A., Coin, Lachlan, Dharmage, Shyamali C., Duffy, David L., Haahtela, Tari, Heath, Andrew C., Janson, Christer, Kähönen, Mika, Khaw, Kay-Tee, Laitinen, Jaana, Souef, Peter Le, Lehtimäki, Terho, Madden, Pamela A. F., Marks, Guy B., Martin, Nicholas G., Matheson, Melanie C., Palmer, Cameron D., Palotie, Aarno, Pouta, Anneli ... Hirschhorn, Joel N. (2013). Correction: Genome-wide association studies of asthma in population-based cohorts confirm known and suggested loci and identify an additional association near HLA (PLoS ONE). PLoS ONE, 8 (3), 1-1. doi: 10.1371/annotation/9630862b-4676-4b82-9869-8d8fbb2a2e65
Walters, Robin G., Coin, Lachlan J. M., Ruokonen, Aimo, de Smith, Adam J., Moustafa, Julia S. El-Sayed, Jacquemont, Sebastien, Elliott, Paul, Esko, Tonu, Hartikainen, Anna-Liisa, Laitinen, Jaana, Maennik, Katrin, Martinet, Danielle, Meyre, David, Nauck, Matthias, Schurmann, Claudia, Sladek, Rob, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Valsesia, Armand, Waeber, Gerard, Zufferey, Flore, Balkau, Beverley, Pattou, Francois, Metspalu, Andres, Voelzke, Henry, Vollenweider, Peter, Stefansson, Kari, Jarvelin, Marjo-Riitta, Beckmann, Jacques S. ... Blakemore, Alexandra I. F. (2013). Rare Genomic Structural Variants in Complex Disease: Lessons from the Replication of Associations with Obesity. Plos One, 8 (3) e58048, e58048.1-e58048.11. doi: 10.1371/journal.pone.0058048
Vimaleswaran, Karani S., Berry, Diane J., Lu, Chen, Tikkanen, Emmi, Pilz, Stefan, Hiraki, Linda T., Cooper, Jason D., Dastani, Zari, Li, Rui, Houston, Denise K., Wood, Andrew R., Michaëlsson, Karl, Vandenput, Liesbeth, Zgaga, Lina, Yerges-Armstrong, Laura M., McCarthy, Mark I., Dupuis, Josée, Kaakinen, Marika, Kleber, Marcus E., Jameson, Karen, Arden, Nigel, Raitakari, Olli, Viikari, Jorma, Lohman, Kurt K., Ferrucci, Luigi, Melhus, Håkan, Ingelsson, Erik, Byberg, Liisa, Lind, Lars ... Hirschhorn, J. N. (2013). Causal relationship between obesity and vitamin D status: bi-directional Mendelian randomization analysis of multiple cohorts. PLoS Medicine, 10 (2) e1001383, e1001383. doi: 10.1371/journal.pmed.1001383
Shao, Haojing, Bellos, Evangelos, Yin, Hanjiudai, Liu , Xiao, Zou, Jing, Li, Yingrui, Wang, Jun and Coin, Lachlan J. M. (2013). A population model for genotyping indels from next-generation sequence data. Nucleic Acids Research, 41 (3), e46.1-e46.6. doi: 10.1093/nar/gks1143
Seich al Basatena N.-K., Hoggart C.J., Coin L.J. and O'Reilly P.F. (2013). The effect of genomic inversions on estimation of population genetic parameters from SNP data. Genetics, 193 (1), 243-253. doi: 10.1534/genetics.112.145599
Kaforou, Myrsini, Wright, Victoria J., Oni, Tolu, French, Neil, Anderson, Suzanne T., Bangani, Nonzwakazi, Banwell, Claire M., Brent, Andrew J., Crampin, Amelia C., Dockrell, Hazel M., Eley, Brian, Heyderman, Robert S., Hibberd, Martin L., Kern, Florian, Langford, Paul R., Ling, Ling, Mendelson, Marc, Ottenhoff, Tom H., Zgambo, Femia, Wilkinson, Robert J., Coin, Lachlan J. and Levin, Michael (2013). Detection of tuberculosis in HIV-infected and -uninfected African adults using whole blood RNA expression signatures: a case-control study. PLoS Medicine, 10 (10) e1001538, e1001538.1-e1001538.17. doi: 10.1371/journal.pmed.1001538
Bellos, Evangelos, Johnson, Michael R. and Coin, Lachlan J. M. (2012). cnvHiTSeq: Integrative models for high-resolution copy number variation detection and genotyping using population sequencing data. Genome Biology, 13 (12). doi: 10.1186/gb-2012-13-12-r120
The 1000 Genomes Project Consortium, Coin, L. J. M. and Li, Yingrui (2012). An integrated map of genetic variation from 1,092 human genomes. Nature, 491 (7422), 56-65. doi: 10.1038/nature11632
Bellos, Evangelos, Coin, Lachlan J. M. and Kaforou, Myrsini (2012). Bioinformatics: living on the edge. Genome Biology, 13 (10). doi: 10.1186/gb-2012-13-10-321
Ramasamy, Adaikalavan, Kuokkanen, Mikko, Vedantam, Sailaja, Gajdos, Zofia K., Alves, Alexessander Couto, Lyon, Helen N., Ferreira, Manuel A. R., Strachan, David P., Zhao, Jing Hua, Abramson, Michael J., Brown, Matthew A., Coin, Lachlan, Dharmage, Shyamali C., Duffy, David L., Haahtela, Tari, Heath, Andrew C., Janson, Christer, Kahonen, Mika, Khaw, Kay-Tee, Laitinen, Jaana, Le Souef, Peter, Lehtimaki, Terho, Madden, Pamela A. F., Marks, Guy B., Martin, Nicholas G., Matheson, Melanie C., Palmer, Cameron D., Palotie, Aarno, Pouta, Anneli ... Hirschhorn, Joel N. (2012). Genome-Wide Association Studies of Asthma in Population-Based Cohorts Confirm Known and Suggested Loci and Identify an Additional Association near HLA. PLoS One, 7 (9 Article No. e44008) e44008, e44008-1-e44008-10. doi: 10.1371/journal.pone.0044008
Okada, Y., Sim, X., Go, M. J., Wu, J. Y., Gu, D., Takeuchi, F., Takahashi, A., Maeda, S., Tsunoda, T., Chen, P., Lim, S. C., Wong, T. Y., Liu, J., Young, T. L., Aung, T., Seielstad, M., Teo, Y. Y., Kim, Y. J., Lee, J. Y., Han, B. g., Kang, D., Chen, C. h., Tsai, F. j., Chang, L. c., Fann, S. j., Mei, H., Rao, D. c., Hixson, J. e., Chen, S. ... Gieger, C. (2012). Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations. Nature Genetics, 44 (8), 904-909. doi: 10.1038/ng.2352
Barrenas, Fredrik, Chavali, Sreenivas, Couto Alves, Alexessander, Coin, Lachlan, Jarvelin, Marjo-Riitta, Jornsten, Rebecka, Langston, Michael A., Ramasamy, Adaikalavan, Rogers, Gary, Wang, Hui and Benson, Mikael (2012). Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms. Genome Biology, 13 (6) R46, R46.1-R46.9. doi: 10.1186/gb-2012-13-6-r46
O'Reilly, Paul F., Hoggart, Clive J., Pomyen, Yotsawat, Calboli, Federico C. F., Elliott, Paul, Jarvelin, Marjo- Riitta and Coin, Lachlan J. M. (2012). MultiPhen: Joint model of multiple phenotypes can increase discovery in GWAS. PLoS ONE, 7 (5) e34861, e34861.1-e34861.12. doi: 10.1371/journal.pone.0034861
Taal, H. Rob, St Pourcain, Beate, Thiering, Elisabeth, Das, Shikta, Mook-Kanamori, Dennis O., Warrington, Nicole M., Kaakinen, Marika, Kreiner-Møller, Eskil, Bradfield, Jonathan P., Freathy, Rachel M., Geller, Frank, Guxens, Mònica, Cousminer, Diana L., Kerkhof, Marjan, Timpson, Nicholas J., Ikram, M. Arfan, Beilin, Lawrence J., Bønnelykke, Klaus, Buxton, Jessica L., Charoen, Pimphen, Chawes, Bo Lund Krogsgaard, Eriksson, Johan, Evans, David M., Hofman, Albert, Kemp, John P., Kim, Cecilia E., Klopp, Norman, Lahti, Jari, Lye, Stephen J. ... Middeldorp, Christel (2012). Common variants at 12q15 and 12q24 are associated with infant head circumference. Nature Genetics, 44 (5), 532-538. doi: 10.1038/ng.2238
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Lindgren, Cecilia M., Heid, Iris M., Randall, Joshua C., Lamina, Claudia, Steinthorsdottir, Valgerdur, Qi, Lu, Speliotes, Elizabeth K, Thorleifsson,Gudmar, Willer, Cristen J., Herrera, Blanca M., Jackson, Anne U., Lim, Noha, Scheet, Paul, Soranzo, Nicole, Amin, Najaf, Aulchenko, Yurii S., Chambers, John C., Drong, Alexander, Luan, Jian'an, Lyon, Helen N., Rivadeneira, Fernando, Sanna, Serena, Timpson, Nicholas J., Zillikens, M. Carola, Zhao, Jing Hua, Almgren, Peter, Bandinelli, Stefania, Bennett, Amanda J., Bergman, Richard N. ... Bradbury, Linda (2009). Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution. PLoS Genetics, 5 (6) e1000508, e1000508-1-e1000508-13. doi: 10.1371/journal.pgen.1000508
Newton-Chen, C., Johnson, T., Gateva, V., Tobin, M. D., Bochud, M., Coin, L., Najjar, S. S., Zhao, J. H., et al, Wellcome Trust Case Control Consortium, Brown, Matthew A., Bradbury, Linda and Evans, David (2009). Genome-wide association study identifies eight loci associated with blood pressure.. Nature Genetics, 41 (6), 666-676. doi: 10.1038/ng.361
Sovio, Ulla, Bennett, Amanda J., Millwood, Iona Y., Molitor, John, O'Reilly, Paul F., Timpson, Nicholas J., Kaakinen, Marika, Laitinen, Jaana, Haukka, Jari, Pillas, Demetris, Tzoulaki, Ioanna, Molitor, Jassy, Hoggart, Clive, Coin, Lachlan J. M., Whittaker, John, Pouta, Anneli, Hartikainen, Anna-Liisa, Freimer, Nelson B., Widen, Elisabeth, Peltonen, Leena, Elliott, Paul, Mccarthy, Mark I. and Jarvelin, Marjo-Riitta (2009). Genetic determinants of height growth assessed longitudinally from infancy to adulthood in the northern Finland birth cohort 1966. PLoS Genetics, 5 (3), e1000409.1-e1000409.8. doi: 10.1371/journal.pgen.1000409
Meyre, David, Delplanque, Jerome, Chevre, Jean-Claude, Lecoeur, Cecile, Lobbens, Stephane, Gallina, Sophie, Durand, Emmanuelle, Vatin, Vincent, Degraeve, Franck, Proenca, Christine, Gaget, Stefan, Korner, Antje, Kovacs, Peter, Kiess, Wieland, Tichet, Jean, Marre, Michel, Hartikainen, Anna-Liisa, Horber, Fritz, Potoczna, Natascha, Hercberg, Serge, Levy-Marchal, Claire, Pattou, Francois, Heude, Barbara, Tauber, Maithe´, McCarthy, Mark I., Blakemore, Alexandra I. F., Montpetit, Alexandre, Polychronakos, Constantin, Weill, Jacques ... Froguel, Philippe (2009). Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations. Nature Genetics, 41 (2), 157-159. doi: 10.1038/ng.301
Sabatti, Chiara, Service, Susan K., Hartikainen, Anna-Liisa, Pouta, Anneli, Ripatti, Samuli, Brodsky, Jae, Jones, Chris G., Zaitlen, Noah A., Varilo, Teppo, Kaakinen, Marika, Sovio, Ulla, Ruokonen, Aimo, Laitinen, Jaana, Jakkula, Eveliina, Coin, Lachlan, Hoggart, Clive, Collins, Andrew, Turunen, Hannu, Gabriel, Stacey, Elliot, Paul, McCarthy, Mark I., Daly, Mark J., Jarvelin, Marjo-Riitta, Freimer, Nelson B. and Peltonen, Leena (2009). Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nature Genetics, 41 (1), 35-46. doi: 10.1038/ng.271
Willer, Cristen J., Speliotes, Elizabeth K., Loos, Ruth J. F., Li, Shengxu, Lindgren, Cecilia M., Heid, Iris M., Berndt, Sonja I., Elliot, Amanda L., Jackson, Anne U., Lamina, Claudia, Lettre, Guillaume, Lim, Noha, Lyon, Helen N., McCarroll, Steven N., Papadakis, Konstantinos, Qi, Lu, Randall, Joshua C., Roccasecca, Rosa Maria, Sanna, Serena, Scheet, Paul, Weedon, Michael N., Wheeler, Eleanor, Zhao, Jing Hua, Jacobs, Leonie C., Prokopenko,, Soranzo, Nicole, Tanaka, Toshiko, Timpson, Nicholas J., Almgran, Peter ... GIANT consortium (2009). Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nature Genetics, 41 (1), 25-34. doi: 10.1038/ng.287
Prokopenko, Inga, Langenberg, Claudia, Florez, Jose C., Saxena, Richa, Soranzo, Nicole, Thorleifsson, Gudmar, Loos, Ruth J. F., Manning, Alisa K., Jackson, Anne U., Aulchenko, Yurii, Potter, Simon C., Erdos, Michael R., Sanna, Serena, Hottenga, Jouke-Jan, Wheeler, Eleanor, Kaakinen, Marika, Lyssenko, Valeriya, Chen, Wei-Min, Ahmadi, Kourosh, Beckmann, Jacques S., Bergman, Richard N., Bochud, Murielle, Bonnycastle, Lori L., Buchanan, Thomas A., Cao, Antonio, Cervino, Alessandra, Coin, Lachlan, Collins, Francis S., Crisponi, Laura ... Abecasis, Goncalo R. (2009). Variants in MTNR1B influence fasting glucose levels. Nature Genetics, 41 (1), 77-81. doi: 10.1038/ng.290
Su, Shu-Yi, White, Jonathan, Balding, David J. and Coin, Lachlan J. M. (2008). Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions. BMC Bioinformatics, 9 (1) 513, 513.1-513.9. doi: 10.1186/1471-2105-9-513
de Smith, Adam J., Walters, Robin G., Coin, Lachlan J. M., Steinfeld, Israel, Yakhini, Zohar, Sladek, Rob, Froguel, Philippe and Blakemore, Alexandra I. F. (2008). Small deletion variants have stable breakpoints commonly associated with Alu elements. PLoS ONE, 3 (8) e3104, e3104.1-e3104.11. doi: 10.1371/journal.pone.0003104
Su, Shu-Yi, Balding, David J. and Coin, Lachlan J. M. (2008). Disease association tests by inferring ancestral haplotypes using a hidden markov model. Bioinformatics, 24 (7), 972-978. doi: 10.1093/bioinformatics/btn071
Ruan, Jue, Li, Heng, Chen, Zhongzhong, Coghlan, Avril, Coin, Lachlan James M., Guo, Yiran, Heacute;riché, Jean-Karim, Hu, Yafeng, Kristiansen, Karsten, Li, Ruiqiang, Liu, Tao, Moses, Alan, Qin, Junjie, Vang, Søren, Vilella, Albert J., Ureta-Vidal, Abel, Bolund, Lars, Wang, Jun and Durbin, Richard (2008). TreeFam: 2008 Update. Nucleic Acids Research, 36 (SUPPL. 1), D735-D740. doi: 10.1093/nar/gkm1005
Li, Heng, Coghlan, Avril, Ruan, Jue, Coin, Lachlan James, Heriche, Jean-Karim, Osmotherly, Lara, Li, Ruiqiang, Liu, Tao, Zhang, Zhang, Bolund, Lars, Wong, Gane Ka-Shu, Zheng, Weimou, Dehal, Paramvir, Wang, Jun and Durbin, Richard (2006). TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Research, 34 (Database issue), D572-D580. doi: 10.1093/nar/gkj118
Goeb, J, Leblanc-Deshayes, M, Coin, L, Malka, J, Bouderlique, C and Duverger, R (2004). Neonatal death of a newborn twin. Archives De Pediatrie, 11 (9), 1135-1138. doi: 10.1016/S0929-693X(04)00061-2
Coin L., Bateman A. and Durbin R. (2004). Enhanced protein domain discovery using taxonomy. BMC Bioinformatics, 5. doi: 10.1186/1471-2105-5-56
Futreal, PA, Coin, L, Marshall, M, Down, T, Hubbard, T, Wooster, R, Rahman, N and Stratton, MR (2004). A census of human cancer genes. Nature Reviews Cancer, 4 (3), 177-183. doi: 10.1038/nrc1299
Coin, L. and Durbin, R. (2004). Improved techniques for the identification of pseudogenes. Bioinformatics, 20 (SUPPL. 1), 94-100. doi: 10.1093/bioinformatics/bth942
Bateman, A, Coin, L, Durbin, R, Finn, RD, Hollich, V, Griffiths-Jones, S, Khanna, A, Marshall, M, Moxon, S, Sonnhammer, ELL, Studholme, DJ, Yeats, C and Eddy, SR (2004). The Pfam protein families database. Nucleic Acids Research, 32 (DATABASE ISS.), D138-D141. doi: 10.1093/nar/gkh121
Coin, Lachlan, Bateman, Alex and Durbin, Richard (2003). Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proceedings of the National Academy of Sciences of the United States of America, 100 (8), 4516-4520. doi: 10.1073/pnas.0737502100
Conference Papers
Ngo, Ha, Crew, Kathy S., Vance, Megan, Thomas, John, Nguyen, Son, Duarte, Tania, Coin, Lachlan and Geering, Andrew (2019). New achievements for diagnostics of banana streak virus. Australasian Plant Pathology Society 22nd Biennial Conference, Melbourne, Australia, 26-28 November 2019. Melbourne, Australia:
Georgiadou, Athina, Bretscher, Michael, Lee, Hyun, Walther, Michael, van Beek, Anna, Fitriani, Fadlila, Wouters, Diana, Kuijpers, Taco, Nwakanma, Davis, Riley, Eleanor, Levin, Michael, Coin, Lachlan, Ghani, Azra, Conway, David and Cunnington, Aubrey (2018). COMBINING RNA-SEQUENCING AND MATHEMATICAL MODELLING TO IDENTIFY MECHANISTIC CORRELATES OF PROTECTION IN MALARIA. 67th Annual Meeting of the American-Society-of-Tropical-Medicine-and-Hygiene (ASTHM), New Orleans La, Oct 28-Nov 01, 2018. MCLEAN: AMER SOC TROP MED & HYGIENE.
De, T., Prokopenko, I., Jarvelin, M. -R. and Coin, L. (2015). Metabonomic Signatures of CNVs in TSPAN8 Exonic Regions Associated with Type 2 Diabetes. 43rd European Mathematical Genetics Meeting (EMGM), Brest, France, 16-17 April 2015. Basel, Switzerland: S. Karger AG. doi: 10.1159/000381109
Schumann, G., Coin, L., Lourdusamy, A., Charoen, P., Stacey, D., Desrivieres, S., Jarvelin, M. R. and Elliott, P. (2010). Identification of Genes Associated with Alcohol Consumption. World Congress on International-Society-for-Biomedical-Research-on-Alcoholism, Paris France, Sep 13-16, 2010.
Munhoz, Renato P., Teive, Helio A., Eleftherohorinou, Hariklia, Coin, Lachlan J., Lees, Andrew, Werneck, Lineu and Silveira-Moriyama, Laura (2010). Can Motor Features of Parkinson's Disease Be Used To Predict Occurrence of Non-Motor Symptoms of the Disease?. 62nd Annual Meeting of the American-Academy-of-Neurology, Toronto Canada, Apr 10-17, 2010. LIPPINCOTT WILLIAMS & WILKINS.
Trewick, Anne L., Froguel, P., Coin, L. J. M. and Blakemore, A. I. F. (2009). Assignment of trisomic genotypes using the Sequenom iPLEX MALDI TOF assay reveals transmission disequilibrium of two SNP loci in the Type VI Collagen gene cluster associated with CHD in Down's Syndrome.. British Human Genetics Conference, York England, Aug 31-Sep 02, 2009. LONDON: B M J PUBLISHING GROUP.
Buxton, Jessica, Coin, L. J. M., Walters, R. G., Andersson, J., de Smith, A. J., Moustafa, J. S. El-Sayed, Sladek, R., Froguel, P. and Blakemore, A. I. F. (2009). Identification and validation of novel genomic CNVs associated with Type 2 diabetes. British Human Genetics Conference, York England, Aug 31-Sep 02, 2009. LONDON: B M J PUBLISHING GROUP.
Moustafa, Julia Sarah El-Sayed, Coin, L. J. M., de Smith, A. J., Walters, R. G., Buxton, J. L., Asher, J. E., Meyre, D., Dina, C., Froguel, P. and Blakemore, A. I. F. (2009). CNVs in Obesity: Uncovering a New Level of Genomic Variation. British Human Genetics Conference, York England, Aug 31-Sep 02, 2009. B M J PUBLISHING GROUP.
Elliott, P., Chambers, J. C., Zhang, W., Clarke, R., Peden, J. F., Erdmann, J., Braund, P., Engert, J., Hopewell, J., Coin, Lachlan, Ashby, D., McCarthy, M. I., Farrall, M., Jarvelin, Marjo-Riitta, Scott, J., Hall, A. S., Schunkert, H., Anand, S. S., Collins, R., Samani, N., Watkins, H. and Kooner, J. S. (2009). Genetic Loci Influencing C-Reactive Protein Levels and Coronary Heart Disease Risk: Results of Genetic Association and Mendelian Randomisation Study with Meta-Analysis in 80 614 People. Annual Scientific Conference of the British-Cardiovascular-Society, London England, Jun 01-03, 2009. LONDON: B M J PUBLISHING GROUP.
Su, S.-Y., Balding, D. J. and Coin, L. (2007). Using haplotype clustering techniques to perform genome-wide disease association studies. 16th Annual Meeting of the International-Genetic-Epidemiology-Society, York England, Sep 07-10, 2007. HOBOKEN: WILEY-LISS.
Preprint
Dataset Collection
Coin, Lachlan (2014). Genomics of development and disease. The University of Queensland. (Collection) doi: 10.14264/uql.2016.583