A/Prof Lachlan Coin

Featured projects	Duration
Assembly of complex genome (Macadamia) using single molecule sequencing Genome Innovation Hub Collaborative Project (UQ infrastructure)	2019

Hall, Michael B, Wick, Ryan R, Judd, Louise M, Nguyen, An N, Steinig, Eike J, Xie, Ouli, Davies, Mark, Seemann, Torsten, Stinear, Timothy P and Coin, Lachlan (2024). Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. eLife, 13 ARTN RP98300. doi: 10.7554/elife.98300.3

Wu, Jiangping, Chen, Yan, Zhao, Jiawei, Prosun, Tanjila Alam, O’Brien, Jake William, Coin, Lachlan, Hai, Faisal I., Sanderson-Smith, Martina and Jiang, Guangming (2024). Wastewater Microbiome Analysis for Population Alcohol Abuse. Water, 16 (15) 2149, 2149. doi: 10.3390/w16152149

Bainomugisa, Arnold, Pandey, Sushil, O'Connor, Bridget, Syrmis, Melanie, Whiley, David, Sintchenko, Vitali, Coin, Lachlan J.M., Marais, Ben J. and Coulter, Christopher (2024). Sustained transmission over two decades of a previously unrecognised MPT64 negative Mycobacterium tuberculosis strain in Queensland, Australia: a whole genome sequencing study. The Lancet Regional Health - Western Pacific, 47 101105, 101105. doi: 10.1016/j.lanwpc.2024.101105

Schlapbach, Luregn J., Ganesamoorthy, Devika, Wilson, Clare, Raman, Sainath, George, Shane, Snelling, Peter J., Phillips, Natalie, Irwin, Adam, Sharp, Natalie, Le Marsney, Renate, Chavan, Arjun, Hempenstall, Allison, Bialasiewicz, Seweryn, MacDonald, Anna D., Grimwood, Keith, Cling, Jessica C., McPherson, Stephen J., Blumenthal, Antje, Kaforou, Myrsini, Levin, Michael, Herberg, Jethro A., Gibbons, Kristen S., Coin, Lachlan J. M., EUCLIDS consortium and RAPIDS Study Group (2024). Host gene expression signatures to identify infection type and organ dysfunction in children evaluated for sepsis: a multicentre cohort study. The Lancet Child and Adolescent Health, 8 (5), 325-338. doi: 10.1016/S2352-4642(24)00017-8

Chang, Jessie J.-Y., Grimley, Samantha, Tran, Bang M., Deliyannis, Georgia, Tumpach, Carolin, Nguyen, An N.T., Steinig, Eike, Zhang, JianShu, Schröder, Jan, Caly, Leon, McAuley, Julie, Wong, Sharon L., Waters, Shafagh A., Stinear, Timothy P., Pitt, Miranda E., Purcell, Damian, Vincan, Elizabeth and Coin, Lachlan J.M. (2024). Uncovering strain- and age-dependent innate immune responses to SARS-CoV-2 infection in air-liquid-interface cultured nasal epithelia. iScience, 27 (6) 110009, 110009. doi: 10.1016/j.isci.2024.110009

Wu, Jiangping, Chen, Yan, Zhao, Jiawei, Prosun, Tanjila, O'Brien, Jake William, Coin, Lachlan, Hai, Faisal I., Sanderson-Smith, Martina, Bi, Peng and Jiang, Guangming (2024). Associations between the wastewater microbiome and community obesity rates: A study in Australia. Soil & Environmental Health, 2 (2) 100081, 100081. doi: 10.1016/j.seh.2024.100081

He, Zhijie, Wang, Cong, Guo, Xudong, Sun, Heyun, Bi, Yue, Pitt, Miranda E, Li, Chen, Song, Jiangning, Coin, Lachlan J M and Li, Fuyi (2024). MERITS: a web-based integrated mycobacterial PE/PPE protein database. Bioinformatics Advances, 4 (1) vbae035, vbae035. doi: 10.1093/bioadv/vbae035

Yeoh, Sophya, Estrada-Rivadeneyra, Diego, Jackson, Heather, Keren, Ilana, Galassini, Rachel, Cooray, Samantha, Shah, Priyen, Agyeman, Philipp, Basmaci, Romain, Carrol, Enitan, Emonts, Marieke, Fink, Colin, Kuijpers, Taco, Martinon-Torres, Federico, Mommert-Tripon, Marine, Paulus, Stephane, Pokorn, Marko, Rojo, Pablo, Romani, Lorenza, Schlapbach, Luregn, Schweintzger, Nina, Shen, Ching-Fen, Tsolia, Maria, Usuf, Effua, van der Flier, Michiel, Vermont, Clementien, von Both, Ulrich, Yeung, Shunmay, Zavadska, Dace ... DIAMONDS and UK KD Genetic Consortia (2024). Plasma Protein Biomarkers Distinguish Multisystem Inflammatory Syndrome in Children From Other Pediatric Infectious and Inflammatory Diseases. Pediatric Infectious Disease Journal, 43 (5), 444-53. doi: 10.1097/inf.0000000000004267

Harris, Patrick N. A., Bauer, Michelle J., Lüftinger, Lukas, Beisken, Stephan, Forde, Brian M., Balch, Ross, Cotta, Menino, Schlapbach, Luregn, Raman, Sainath, Shekar, Kiran, Kruger, Peter, Lipman, Jeff, Bialasiewicz, Seweryn, Coin, Lachlan, Roberts, Jason A., Paterson, David L. and Irwin, Adam D. (2024). Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis. Microbiology spectrum, 12 (2) e0306523, e0306523. doi: 10.1128/spectrum.03065-23

Wang, Cong, He, Zhijie, Jia, Runchang, Pan, Shirui, Coin, Lachlan JM, Song, Jiangning and Li, Fuyi (2024). PLANNER: a multi-scale deep language model for the origins of replication site prediction. IEEE Journal of Biomedical and Health Informatics, 28 (4), 1-10. doi: 10.1109/JBHI.2024.3349584

Hall, Michael B and Coin, Lachlan J M (2024). Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data. GigaScience, 13 giae010. doi: 10.1093/gigascience/giae010

Zhang, Shuxin, Shi, Jiahua, Li, Xuan, Tiwari, Ananda, Gao, Shuhong, Zhou, Xu, Sun, Xiaoyan, O'Brien, Jake W., Coin, Lachlan, Hai, Faisal and Jiang, Guangming (2023). Wastewater-based epidemiology of Campylobacter spp.: A systematic review and meta-analysis of influent, effluent, and removal of wastewater treatment plants. Science of The Total Environment, 903 166410, 1-13. doi: 10.1016/j.scitotenv.2023.166410

Li, Fuyi, Wang, Cong, Guo, Xudong, Akutsu, Tatsuya, Webb, Geoffrey I., Coin, Lachlan J.M., Kurgan, Lukasz and Song, Jiangning (2023). ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction. Briefings in Bioinformatics, 24 (6) bbad372. doi: 10.1093/bib/bbad372

Jackson, Heather R., Zandstra, Judith, Menikou, Stephanie, Hamilton, Melissa Shea, McArdle, Andrew J., Fischer, Roman, Thorne, Adam M., Huang, Honglei, Tanck, Michael W., Jansen, Machiel H., De, Tisham, Agyeman, Philipp K A, Von Both, Ulrich, Carrol, Enitan D., Emonts, Marieke, Eleftheriou, Irini, Van der Flier, Michiel, Fink, Colin, Gloerich, Jolein, De Groot, Ronald, Moll, Henriette A., Pokorn, Marko, Pollard, Andrew J., Schlapbach, Luregn J. (PERFORM consortium), Tsolia, Maria N., Usuf, Effua, Wright, Victoria J., Yeung, Shunmay, Zavadska, Dace ... Kaforou, Myrsini (2023). A multi-platform approach to identify a blood-based host protein signature for distinguishing between bacterial and viral infections in febrile children (PERFORM): a multi-cohort machine learning study. The Lancet. Digital health, 5 (11), e774-e785. doi: 10.1016/S2589-7500(23)00149-8

Wu, Jiangping, Zhang, Shuxin, Chen, Yan, Zhao, Jiawei, Prosun, Tanjila, O’Brien, Jake William, Mueller, Jochen F., Tscharke, Ben J., Coin, Lachlan J.M, Luby, Stephen P., Hai, Faisal I., Buchanan, Tanya and Jiang, Guangming (2023). Associations between wastewater microbiome and population smoking rate identified using wastewater-based epidemiology. Environment and Health, 1 (6), 394-404. doi: 10.1021/envhealth.3c00105

Zhang, Shuxin, Shi, Jiahua, Li, Xuan, Coin, Lachlan, O'Brien, Jake W., Sivakumar, Muttucumaru, Hai, Faisal and Jiang, Guangming (2023). Triplex qPCR assay for Campylobacter jejuni and Campylobacter coli monitoring in wastewater. Science of The Total Environment, 892 164574, 1-8. doi: 10.1016/j.scitotenv.2023.164574

Li, Fuyi, Guo, Xudong, Bi, Yue, Jia, Runchang, Pitt, Miranda E., Pan, Shirui, Li, Shuqin, Gasser, Robin B., Coin, Lachlan J. M. and Song, Jiangning (2023). Digerati – a multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins. Computers in Biology and Medicine, 163 107155, 1-11. doi: 10.1016/j.compbiomed.2023.107155

Hall, Michael B., Lima, Leandro, Coin, Lachlan J. M. and Iqbal, Zamin (2023). Drug resistance prediction for Mycobacterium tuberculosis with reference graphs. Microbial Genomics, 9 (8) 001081, 1-14. doi: 10.1099/mgen.0.001081

Bader, Stefanie M., Cooney, James P., Sheerin, Dylan, Taiaroa, George, Harty, Leigh, Davidson, Kathryn C., Mackiewicz, Liana, Dayton, Merle, Wilcox, Stephen, Whitehead, Lachlan, Rogers, Kelly L., Georgy, Smitha Rose, Coussens, Anna K., Grimley, Samantha L., Corbin, Vincent, Pitt, Miranda, Coin, Lachlan, Pickering, Raelene, Thomas, Merlin, Allison, Cody C., McAuley, Julie, Purcell, Damian F. J., Doerflinger, Marcel and Pellegrini, Marc (2023). SARS-CoV-2 mouse adaptation selects virulence mutations that cause TNF-driven age-dependent severe disease with human correlates. Proceedings of the National Academy of Sciences, 120 (32) e2301689120, e2301689120. doi: 10.1073/pnas.2301689120

Zhu, Yan, Li, Fuyi, Guo, Xudong, Wang, Xiaoyu, Coin, Lachlan J. M., Webb, Geoffrey I., Song, Jiangning and Jia, Cangzhi (2023). TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters. Briefings in Bioinformatics, 24 (4) bbad209, 1-12. doi: 10.1093/bib/bbad209

Quah, Pin Shie, Tran, Bang M., Corbin, Vincent D. A., Chang, Jessie J.-Y., Wong, Chinn Yi, Diaz-Méndez, Andrés, Hartley, Carol A., Zeng, Weiguang, Hanssen, Eric, Trifunovic, Zlatan, Reading, Patrick C., Jackson, David C., Vincan, Elizabeth, Coin, Lachlan J. M. and Deliyannis, Georgia (2023). Development of matrix-embedded bovine tracheal organoids to study the innate immune response against bovine respiratory disease. Organoids, 2 (2), 82-101. doi: 10.3390/organoids2020007

Chen, Ruyi, Li, Fuyi, Guo, Xudong, Bi, Yue, Li, Chen, Pan, Shirui, Coin, Lachlan J M and Song, Jiangning (2023). ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Briefings in Bioinformatics, 24 (3) bbad170. doi: 10.1093/bib/bbad170

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

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

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

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) ARTN btac454, 4053-4061. doi: 10.1093/bioinformatics/btac454

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

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), e645. doi: 10.1016/S2666-5247(22)00151-3

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

Steinig, Eike and Coin, Lachlan (2022). Nanoq: ultra-fast quality control for nanopore reads. Journal of Open Source Software, 7 (69), 2991. doi: 10.21105/joss.02991

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

Halliday, Alice, Jain, Pooja, Hoang, Long, Parker, Robert, Tolosa-Wright, Mica, Masonou, Tereza, Green, Nathan, Boakye, Aime, Takwoingi, Yemisi, Hamilton, Shea, Mandagere, Vinay, Fries, Anastasia, Coin, Lachlan, Deeks, Jon, White, Peter J, Levin, Michael, Beverley, Peter, Kon, Onn Min and Lalvani, Ajit (2021). New technologies for diagnosing active TB: the VANTDET diagnostic accuracy study. Efficacy and Mechanism Evaluation, 8 (5), 1-160. doi: 10.3310/eme08050

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

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

Chaisson, Mark J. P., Sanders, Ashley D., Zhao, Xuefang, Malhotra, Ankit, Porubsky, David, Rausch, Tobias, Gardner, Eugene J., Rodriguez, Oscar L., Guo, Li, Collins, Ryan L., Fan, Xian, Wen, Jia, Handsaker, Robert E., Fairley, Susan, Kronenberg, Zev N., Kong, Xiangmeng, Hormozdiari, Fereydoun, Lee, Dillon, Wenger, Aaron M., Hastie, Alex R., Antaki, Danny, Anantharaman, Thomas, Audano, Peter A., Brand, Harrison, Cantsilieris, Stuart, Cao, Han, Cerveira, Eliza, Chen, Chong, Chen, Xintong ... Lee, Charles (2019). Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications, 10 (1) 1784, 1-16. doi: 10.1038/s41467-018-08148-z

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) ARTN 000147. 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

Bachenheimer, Lou, Scherzer, Ryan, Elliott, Paul, Stagon, Stephen, Gasparov, Lev and Huang, Hanchen (2017). Degradation Mechanism of Ag Nanorods for Surface Enhanced Raman Spectroscopy. Scientific Reports, 7 (1) ARTN 16282. doi: 10.1038/s41598-017-16580-2

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

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

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

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

Genovese, Giulio, Handsaker, Robert E., Li, Heng, Kenny, Eimear E. and McCarroll, Steven A. (2013). Mapping the Human Reference Genome's Missing Sequence by Three-Way Admixture in Latino Genomes. American Journal of Human Genetics, 93 (3), 411-421. doi: 10.1016/j.ajhg.2013.07.002

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

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

Genovese, Giulio, Handsaker, Robert E., Li, Heng, Altemose, Nicolas, Lindgren, Amelia M., Chambert, Kimberly, Pasaniuc, Bogdan, Price, Alkes L., Reich, David, Morton, Cynthia C., Pollak, Martin R., Wilson, James G. and McCarroll, Steven A. (2013). Using population admixture to help complete maps of the human genome. Nature Genetics, 45 (4), 406-414. doi: 10.1038/ng.2565

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

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

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

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

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) R120. 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

Dastani, Zari, Hivert, Marie-France, Timpson, Nicholas, Perry, John R. B., Yuan, Xin, Scott, Robert A., Henneman, Peter, Heid, Iris M., Kizer, Jorge R., Lyytikäinen, Leo-Pekka, Fuchsberger, Christian, Tanaka, Toshiko, Morris, Andrew P., Small, Kerrin, Isaacs, Aaron, Beekman, Marian, Coassin, Stefan, Lohman, Kurt, Qi, Lu, Kanoni, Stavroula, Pankow, James S., Uh, Hae-Won, Wu, Ying, Bidulescu, Aurelian, Rasmussen-Torvik, Laura J., Greenwood, Celia M. T., Ladouceur, Martin, Grimsby, Jonna, Manning, Alisa K. ... MuTHER Consortium (2012). Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: A multi-ethnic meta-analysis of 45,891 individuals. PloS Genetics, 8 (3) e1002607, e1002607.1-e1002607.23. doi: 10.1371/journal.pgen.1002607

Coin, Lachlan J. M., Cao, Dandan, Ren, Jingjing, Zuo, Xianbo, Sun, Liangdan, Yang, Sen, Zhang, Xuejun, Cui, Yong, Li, Yingrui, Jin, Xin and Wang, Jun (2012). An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. Bioinformatics, 28 (18) bts379, I370-I374. doi: 10.1093/bioinformatics/bts379

Costelloe, Sean J., El-Sayed Moustafa, Julia S., Drenos, Fotions, Palmen, Jutta, Qiao, Li, Whiting, Stephen, Thomas, Michael, Kivimaki, Mika, Kumari, Meena, Hingorani, Aroon D., Tzoulaki, Ioanna, Marjo-Riitta, Jarvelin, Aimo, Ruokonen, Hartikainen, Anna-Liisa, Pouta, A., Walters, Robin G., Blakemore, Alexandra I. F., Humphries, Steve E., Coin, Lachlan J. M. and Talmud, Philippa J. (2012). Gene-targeted analysis of copy number variants identifies 3 novel associations with coronary heart disease traits. Circulation: Cardiovascular Genetics, 5 (5), 555-560. doi: 10.1161/CIRCGENETICS.111.961037

Hoggart, Clive J., O'Reilly, Paul F., Kaakinen, Marika, Zhang, Weihua, Chambers, John C., Kooner, Jaspal S., Coin, Lachlan J. M. and Jarvelin, Marjo-Riitta (2012). Fine-scale estimation of location of birth from genome-wide single-nucleotide polymorphism data. Genetics, 190 (2), 669-677. doi: 10.1534/genetics.111.135657

Bown, Matthew J., Jones, Gregory T., Harrison, Seamus C., Wright, Benjamin J., Bumpstead, Suzannah, Baas, Annette F., Gretarsdottir, Solveig, Badger, Stephen A., Bradley, Declan T., Burnand, Kevin, Child, Anne H., Clough, Rachel E., Cockerill, Gillian, Hafez, Hany, Scott, D Julian A., Futers, Simon, Johnson, Anne, Sohrabi, Soroush, Smith, Alberto, Thompson, Matthew M., van Bockxmeer, Frank M., Waltham, Matthew, Matthiasson, Stefan E., Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Blankensteijn, Jan D., Teijink, Joep A.W., Wijmenga, Cisca, de Graaf, Jacqueline ... Yu, Grace (2011). Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1. American Journal of Human Genetics, 89 (5), 619-627. doi: 10.1016/j.ajhg.2011.10.002

Zhu, Hao, Shyh-Chang, Ng, Segrè, Ayellet V., Shinoda, Gen, Shah, Samar P., Einhorn, William S., Takeuchi, Ayumu, Engreitz, Jesse M., Hagan, John P., Kharas, Michael G., Urbach, Achia, Thornton, James E., Triboulet, Robinson, Gregory, Richard I., DIAGRAM Consortium, MAGIC Investigators, Altshuler, David, Daley, George Q. and Coin, Lachlan J. M. (2011). The Lin28/let-7 axis regulates glucose metabolism. Cell, 147 (1), 81-94. doi: 10.1016/j.cell.2011.08.033

Eleftherohorinou, Hariklia, Andersson-Assarsson, Johanna C., Walters, Robin G., Moustafa, Julia S. El-Sayed, Coin, Lachlan, Jacobson, Peter, Carlsson, Lena M. S., Blakemore, Alexandra I. F., Froguel, Philippe, Walley, Andrew J. and Falchi, Mario (2011). famCNV: copy number variant association for quantitative traits in families. Bioinformatics, 27 (13) btr264, 1873-1875. doi: 10.1093/bioinformatics/btr264

Schumann, Gunter, Coin, Lachlan J., Lourdusamy, Anbarasu, Charoen, Pimphen, Berger, Karen H., Stacey, David, Desrivieres, Sylvane, Aliev, Fazil A., Khan, Anokhi A., Amin, Najaf, Aulchenko, Yurii S., Bakalkin, Georgy, Bakker, Stephan J., Balkau, Beverley, Beulens, Joline W., Bilbao, Ainhoa, de Boer, Rudolf A., Beury, Delphine, Bots, Michiel L., Breetvelt, Elemi J., Cauchi, Stephane, Cavalcanti-Proenca, Christine, Chambers, John C., Clarke, Toni-Kim, Dahmen, Norbert, de Geus, Eco J., Dick, Danielle, Ducci, Francesca, Easton, Alanna ... Elliott, Paul (2011). Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption (vol 108, pg 7119, 2011). Proceedings of the National Academy of Sciences of the United States of America, 108 (22), 9316-9316. doi: 10.1073/pnas.1106917108

Schumann, Gunter, Coin, Lachlan J., Lourdusamy, Anbarasu, Charoen, Pimphen, Berger, Karen H., Stacey, David, Desrivieres, Sylvane, Aliev, Fazil A., Khan, Anokhi A., Amin, Najaf, Aulchenko, Yurii S., Bakalkin, Georgy, Bakker, Stephan J., Balkau, Beverley, Beulens, Joline W., Bilbao, Ainhoa, de Boer, Rudolf A., Beury, Delphine, Bots, Michiel L., Breetvelt, Elemi J., Cauchi, Stéphane, Cavalcanti-Proenca, Christine, Chambers, John C., Clarke, Toni-Kim, Dahmen, Norbert, de Geus, Eco J., Dick, Danielle, Ducci, Francesca, Easton, Alanna ... Elliott, Paul (2011). Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption. Proceedings of the National Academy of Sciences of the United States of America, 108 (17), 7119-7124. doi: 10.1073/pnas.1017288108

Kilpelainen T.O., Den Hoed M., Ong K.K., Grontved A., Brage S., Jameson K., Cooper C., Khaw K.-T., Ekelund U., Wareham N.J., Loos R.J.F., Freathy R.M., Mook-Kanamori D.O., Sovio U., Prokopenko I., Timpson N.J., Berry D.J., Warrington N.M., Widen E., Hottenga J.J., Kaakinen M., Lange L.A., Bradfield J.P., Kerkhof M., Marsh J.A., Magi R., Chen C.-M., Lyon H.N., Kirin M. ... McCarthy M.I. (2011). Obesity-susceptibility loci have a limited influence on birth weight: A meta-analysis of up to 28,219 individuals. American Journal of Clinical Nutrition, 93 (4), 851-860. doi: 10.3945/ajcn.110.000828

Ducci, Francesca, Kaakinen, Marika, Pouta, Anneli, Hartikainen, Anna-Liisa, Veijola, Juha, Isohanni, Matti, Charoen, Pimphen, Coin, Lachlan, Hoggart, Clive, Ekelund, Jesper, Peltonen, Leena, Freimer, Nelson, Elliott, Paul, Schumann, Gunter and Jurvelin, Marjo-Riitta (2011). TTC12-ANKK1-DRD2 and CHRNA5-CHRNA3-CHRNB4 influence different pathways leading to smoking behavior from adolescence to mid-adulthood. Biological Psychiatry, 69 (7), 650-660. doi: 10.1016/j.biopsych.2010.09.055

Shimizu, Chisato, Jain, Sonia, Davila, Sonia, Hibberd, Martin L., Lin, Kevin O., Molkara, Delaram, Frazer, Jeffrey R., Sun, Shelly, Baker, Annette L., Newburger, Jane W., Rowley, Anne H., Shulman, Stanford T., Burgner, David, Breunis, Willemijn B., Kuijpers, Taco W., Wright, Victoria J., Levin, Michael, Eleftherohorinou, Hariklia, Coin, Lachlan, Popper, Stephen J., Relman, David A., Fury, Wen, Lin, Calvin, Mellis, Scott, Tremoulet, Adriana H. and Burns, Jane C. (2011). Erratum: Transforming growth factor-β signaling pathway in patients with Kawasaki disease (Circulation: Cardiovascular Genetics (2011) 4 (16-25)). Circulation: Cardiovascular Genetics, 4 (2). doi: 10.1161/HCG.0b013e31821bbda9

Speliotes, Elizabeth K., Yerges-Armstrong, Laura M., Wu, Jun, Hernaez, Ruben, Kim, Lauren J., Palmer, Cameron D., Gudnason, Vilmundur, Eiriksdottir, Gudny, Garcia, Melissa E., Launer, Lenore J., Nalls, Michael A., Clark, Jeanne M., Mitchell, Braxton D., Shuldiner, Alan R., Butler, Johannah L., Tomas, Marta, Hoffmann, Udo, Hwang, Shih-Jen, Massaro, Joseph M., O'Donnell, Christopher J., Sahani, Dushyant V., Salomaa, Veikko, Schadt, Eric E., Schwartz, Stephen M., Siscovick, David S., NASH CRN, GIANT Consortium, MAGIC Investigators, Voight, Benjamin F. ... Coin, Lachlan (2011). Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits. PLoS Genetics, 7 (3) e1001324, e1001324.1-e1001324.14. doi: 10.1371/journal.pgen.1001324

Turro, Ernest, Su, Shu-Yi, Goncalves, Ângela, Coin, Lachlan J. M., Richardson, Sylvia and Lewin, Alex (2011). Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biology, 12 (2) R13, R13.1-R13.15. doi: 10.1186/gb-2011-12-2-r13

Ramasamy, Adaikalavan, Curjuric, Ivan, Coin, Lachlan J., Kumar, Ashish, McArdle, Wendy L., Imboden, Medea, Leynaert, Benedicte, Kogevinas, Manolis, Schmid-Grendelmeier, Peter, Pekkanen, Juha, Wjst, Matthias, Bircher, Andreas J., Sovio, Ulla, Rochat, Thierry, Hartikainen, Anna-Liisa, Balding, David J., Jarvelin, Marjo-Riitta, Probst-Hensch, Nicole, Strachan, David P. and Jarvis, Deborah L. (2011). A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order. Journal of Allergy and Clinical Immunology, 128 (5), 996-1005. doi: 10.1016/j.jaci.2011.08.030

Li, Yingrui, Zheng, Hancheng, Luo, Ruibang, Wu, Honglong, Zhu, Hongmei, Li, Ruiqiang, Cao, Hongzhi, Wu, Boxin, Huang, Shujia, Shao, Haojing, Ma, Hanzhou, Zhang, Fan, Feng, Shuijian, Zhang, Wei, Du, Hongli, Tian, Geng, Li, Jingxiang, Zhang, Xiuqing, Li, Songgang, Bolund, Lars, Kristiansen, Karsten, de Smith, Adam J., Blakemore, Alexandra I. F., Coin, Lachlan J. M., Yang, Huanming, Wang, Jian and Wang, Jun (2011). Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology, 29 (8), 723-730. doi: 10.1038/nbt.1904

Fernando, Michelle M. A., de Smith, Adam J., Coin, Lachlan, Morris, David L., Froguel, Philippe, Mangion, Jonathan, Blakemore, Alexandra I. F., Graham, Robert R., Behrens, Timothy W. and Vyse, Timothy J. (2011). Investigation of the HIN200 locus in UK SLE families identifies novel copy number variants. Annals of Human Genetics, 75 (3), 383-397. doi: 10.1111/j.1469-1809.2011.00641.x

Shimizu, Chisato, Jain, Sonia, Davila, Sonia, Hibberd, Martin L., Lin, Kevin O., Molkara, Delaram, Frazer, Jeffrey R., Sun, Shelly, Baker, Annette L., Newburger, Jane W., Rowley, Anne H., Shulman, Stanford T., Burgner, David, Breunis, Willemijn B. B, Kuijpers, Taco W., Wright, Victoria J., Levin, Michael, Eleftherohorinou, Hariklia, Coin, Lachlan, Popper, Stephen J., Relman, David A., Fury, Wen, Lin, Calvin, Mellis, Scott, Tremoulet, Adriana H. and Burns, Jane C. (2011). Transforming growth factor-β signaling pathway in patients with Kawasaki disease. Circulation: Cardiovascular Genetics, 4 (1), 16-25. doi: 10.1161/CIRCGENETICS.110.940858

Eleftherohorinou, Hariklia, Hoggart, Clive J., Wright, Victoria J., Levin, Michael and Coin, Lachlan J. M. (2011). Pathway-driven gene stability selection of two rheumatoid arthritis GWAS identifies and validates new susceptibility genes in receptor mediated signalling pathways. Human Molecular Genetics, 20 (17) ddr248, 3494-3506. doi: 10.1093/hmg/ddr248

Trewick, Anne L., El-Sayed Moustafa, Julia S., De Smith, Adam J., Froguel, Philippe, Greve, Gottfried, Njolstad, Pal R., Coin, Lachlan J. M. and Blakemore, A.I.F. (2011). Accurate single-nucleotide polymorphism allele assignment in trisomic or duplicated regions by using a single base-extension assay with MALDI-TOF mass spectrometry. Clinical Chemistry, 57 (8), 1188-1195. doi: 10.1373/clinchem.2010.159558

Su, Shu-Yi, Asher, Julian E., Jarvelin, Marjo-Riita, Froguel, Phillipe, Blakemore, Alexandra I. F., Balding, David J. and Coin, Lachlan J. M. (2010). Inferring combined CNV/SNP haplotypes from genotype data. Bioinformatics, 26 (11) btq157, 1437-1445. doi: 10.1093/bioinformatics/btq157

Walters, R. G., Jacquemont, S., Valsesia, A., De Smith, A. J., Martinet, D., Andersson, J., Falchi, M., Chen, F., Andrieux, J., Lobbens, S., Delobel, B., Stutzmann, F., El-Sayed Moustafa, J. S., Chevre, J.-C., Lecoeur, C., Vatin, V., Bouquillon, S., Buxton, J. L., Boute, O., Holder-Espinasse, M., Cuisset, J.-M., Lemaitre, M.-P., Ambresin, A.-E., Brioschi, A., Gaillard, M., Giusti, V., Fellmann, F., Ferrarini, A., Hadjikhani, N. ... Beckmann, J. S. (2010). A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature, 463 (7281), 671-675. doi: 10.1038/nature08727

O'Reilly, Paul F., Coin, Lachlan J. M. and Hoggart, Clive J. (2010). invertFREGENE: software for simulating inversions in population genetic data. Bioinformatics, 26 (6) btq029, 838-840. doi: 10.1093/bioinformatics/btq029

Pillas, Demetris, Hoggart, Clive J., Evans, David M., O'Reilly, Paul F., Sipila, Kirsi, Lahdesmaki, Raija, Millwood, Iona Y., Kaakinen, Marika., Netuveli, Gopalakrishnan, Blane, David, Charoen, Pimphen, Sovio, Ulla, Pouta, Anneli, Freimer, Nelson, Hartikainen, Anna-Lisa., Laitinen, Jaana, Vaara, Sarianna, Glaser, Beate, Crawford, Peter, Timpson, Nicholas J., Ring, Susan M., Deng, Guohong, Zhang, Weihua, McCarthy, Mark I., Deloukas, Panos, Peltonen, Leena, Elliott, Paul, Coin, Lachlan J. M., Smith, George D. and Jarvelin, Marjo-Riita (2010). Genome-wide association study reveals multiple loci associated with primary tooth development during infancy. PLoS Genetics, 6 (2) e1000856, e1000856.1-e1000856.7. doi: 10.1371/journal.pgen.1000856

Coin, Lachlan J. M., Asher, Julian E., Walters, Robin G., El-Sayed Moustafa, Julia S., de Smith, Adam J., Sladek, Rob, Balding, David J., Froguel, Philippe and Blakemore, Alexandra I. F. (2010). CnvHap: An integrative population and haplotype-based multiplatform model of SNPs and CNVs. Nature Methods, 7 (7), 541-546. doi: 10.1038/nmeth.1466

Eleftherohorinou, Hariklia, Wright, Victoria, Hoggart, Clive, Hartikainen, Anna-Liisa, Jarvelin, Marjo-Riitta, Balding, David, Coin, Lachlan and Levin, Michael (2009). Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases. PLoS ONE, 4 (11) e0008068, e8068.1-e8068.11. doi: 10.1371/journal.pone.0008068

Elliott, Paul, Chambers, John C., Zhang, Weihua, Clarke, Robert, Hopewell, Jemma C., Peden, John F., Erdmann, Jeanette, Braund, Peter, Engert, James C., Bennett, Derrick, Coin, Lachlan, Ashby, Deborah, Tzoulaki, Ioanna, Brown, Ian J., Mt-Isa, Shahrul, McCarthy, Mark I., Peltonen, Leena, Freimer, Nelson B., Farrall, Martin, Ruokonen, Aimo, Hamsten, Anders, Lim, Noha, Froguel, Philippe, Waterworth, Dawn M., Vollenweider, Peter, Waeber, Gerard, Jarvelin, Marjo-Riitta, Mooser, Vincent, Scott, James ... Kooner, Jaspal S. (2009). Genetic loci associated with C-reactive protein levels and risk of coronary heart disease. JAMA: The Journal of the American Medical Association, 302 (1), 37-48. doi: 10.1001/jama.2009.954

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

Burton, Paul R., Hansell, Anna L., Fortier, Isabel, Manolio, Teri A., Khoury, Muin J., Little, Julian and Elliott, Paul (2009). Size matters: just how big is BIG? Quantifying realistic sample size requirements for human genome epidemiology. International Journal of Epidemiology, 38 (1), 263-273. doi: 10.1093/ije/dyn147

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

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

Caulfield, Mark J., Munroe, Patricia B., O'Neill, Deb, Witkowska, Kate, Charchar, Fadi J., Doblado, Manuel, Evans, Sarah, Eyheramendy, Susana, Onipinla, Abiodun, Howard, Philip, Shaw-Hawkins, Sue, Dobson, Richard J., Wallace, Chris, Newhouse, Stephen J., Brown, Morris, Connell, John M., Dominiczak, Anna, Farrall, Martin, Lathrop, G. Mark, Samani, Nilesh J., Kumari, Meena, Marmot, Michael, Brunner, Eric, Chambers, John, Elliott, Paul, Kooner, Jaspal, Laan, Maris, Org, Elin, Veldre, Gudrun ... Cheeseman, Chris (2008). SLC2A9 Is a High-Capacity Urate Transporter in Humans. Plos Medicine, 5 (10) ARTN E197, 1509-1523. doi: 10.1371/journal.pmed.0050197

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 (1) 56. 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

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, L. and Durbin, R. (2004). Improved techniques for the identification of pseudogenes. Bioinformatics, 20 (SUPPL. 1), 94-100. doi: 10.1093/bioinformatics/bth942

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

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.

Shimizu, Chisato, Kim, Jihoon, Eleftherohorinou, Hariklia, Wright, Victoria, Hoang, Long, Tremoulet, Adriana, Franco, Alessandra, Hibberd, Martin, Takahashi, Atsushi, Kubo, Michiaki, Ito, Kaoru, Tanaka, Toshihiro, Onouchi, Yoshihiro, Coin, Lachlan, Levin, Michael, Burns, Jane and Shike, Hiroko (2017). Genetic Variants in HLA-C and Class I Pathway Genes Influence Susceptibility to Kawasaki Disease. 81st Annual Meeting of the American-College-of-Rheumatology (ACR) / Association-of-Rheumatology-Health-Professionals (ARHP), San Diego Ca, Nov 03-08, 2017. HOBOKEN: WILEY.

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.

Cao, Minh Duc, Nguyen, Hoang Son, Ganesamoorthy, Devika, Elliott, Alysha, Cooper, Matthew and Coin, Lachlan J. M. (2016). Scaffolding and completing genome assemblies in real-time with nanopore sequencing.

Ganesamoorthy, Devika and Coin, Lachlan (2024). Paediatric sepsis whole blood transcriptomics. The University of Queensland. (Dataset) doi: 10.48610/7f1ad77

Coin, Lachlan (2019). Sputum Metagenomics. The University of Queensland. (Dataset) doi: 10.48610/1dd1c4b

Coin, Lachlan (2014). Genomics of development and disease. The University of Queensland. (Collection) doi: 10.14264/uql.2016.583

A/Prof Lachlan Coin

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