A/Prof Lachlan Coin
Featured projects | Duration |
---|---|
Assembly of complex genome (Macadamia) using single molecule sequencing Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2019 |
Journal Articles
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
Khan, Nemat, Kumar, Vinod, Li, Pengcheng, RAPIDS Study Group, Raman, Sainath (RSG member), Sharp, Natalie (RSG member), Irwin, Adam (RSG member), Phillips, Natalie (RSG member), George, Shane (RSG member), Grimwood, Keith (RSG member), Snelling, Peter (RSG member), Chavan, Arjun (RSG member), Hempenstall, Allison (RSG member), Gibbons, Kristen (RSG member), Le Marsney, Renate (RSG member), Blumenthal, Antje (RSG member), Ganesamoorthy, Devika (RSG member), Coin, Lachlan (RSG member), Schlapbach, Luregn J., Boyd, Andrew W., Coulthard, Mark G. and Woodruff, Trent M. (2024). Inhibiting Eph/ephrin signaling reduces vascular leak and endothelial cell dysfunction in mice with sepsis. Science Translational Medicine, 16 (744) eadg5768, 1-15. doi: 10.1126/scitranslmed.adg5768
Chai, Ming G., Tu, Quyen, Cotta, Menino O., Bauer, Michelle J., Balch, Ross, Okafor, Charles, Comans, Tracy, Kruger, Peter, Meyer, Jason, Shekar, Kiran, Brady, Kara, Fourie, Cheryl, Sharp, Natalie, Vlad, Luminita, Whiley, David, Ungerer, Jacobus P. J., Mcwhinney, Brett C., Farkas, Andras, Paterson, David L., Clark, Julia E., Hajkowicz, Krispin, Raman, Sainath, Bialasiewicz, Seweryn, Lipman, Jeffrey, Forde, Brian M., Harris, Patrick N. A., Schlapbach, Luregn J., Coin, Lachlan, Roberts, Jason A. and Irwin, Adam D. (2024). Correction: Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsis. Intensive Care Medicine, 50 (5), 810-810. doi: 10.1007/s00134-024-07393-9
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
Chai, Gene G., Tu, Quyen, Cotta, Menino O., Bauer, Michelle J., Balch, Ross, Okafor, Charles, Comans, Tracy, Kruger, Peter, Meyer, Jason, Shekar, Kiran, Brady, Kara, Fourie, Cheryl, Sharp, Natalie, Vlad, Luminita, Whiley, David, Ungerer, Jacobus P. J., McWhinney, Brett C., Farkas, Andras, Paterson, David L., Clark, Julia E., Hajkowicz, Krispin, Raman, Sainath, Bialasiewicz, Seweryn, Lipman, Jeffrey, Forde, Brian M., Harris, Patrick N. A., Schlapbach, Luregn J., Coin, Lachlan, Roberts, Jason A. and Irwin, Adam D. (2024). Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsis. Intensive Care Medicine, 50 (4), 1-9. doi: 10.1007/s00134-024-07353-3
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
Habgood-Coote, Dominic, Wilson, Clare, Shimizu, Chisato, Barendregt, Anouk M., Philipsen, Ria, Galassini, Rachel, Calle, Irene Rivero, Workman, Lesley, Agyeman, Philipp K.A., Ferwerda, Gerben, Anderson, Suzanne T., van den Berg, J. Merlijn, Emonts, Marieke, Carrol, Enitan D., Fink, Colin G., de Groot, Ronald, Hibberd, Martin L., Kanegaye, John, Nicol, Mark P., Paulus, Stéphane, Pollard, Andrew J., Salas, Antonio, Secka, Fatou, Schlapbach, Luregn J., Tremoulet, Adriana H., Walther, Michael, Zenz, Werner, Van der Flier, Michiel, Zar, Heather J. ... Kaforou, Myrsini (2023). Diagnosis of childhood febrile illness using a multi-class blood RNA molecular signature. Med, 4 (9), 635-654.e5. doi: 10.1016/j.medj.2023.06.007
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
Chen, Andrew, Sun, Jiaman, Viljoen, Altus, Mostert, Diane, Xie, Yucong, Mangila, Leroy, Bothma, Sheryl, Lyons, Rebecca, Hřibová, Eva, Christelová, Pavla, Uwimana, Brigitte, Amah, Delphine, Pearce, Stephen, Chen, Ning, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav, Crisp, Peter, Brown, Allan F., Martin, Guillaume, Yahiaoui, Nabila, D’Hont, Angelique, Coin, Lachlan, Swennen, Rony and Aitken, Elizabeth A. B. (2023). Genetic mapping, candidate gene identification and marker validation for host plant resistance to the race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis. Pathogens, 12 (6) 820, 820. doi: 10.3390/pathogens12060820
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
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, 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
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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
Chambers, John C., Zhang, Weihua, Sehmi, Joban, Li, Xinzhong, Wass, Mark N., Van der Harst, Pim, Holm, Hilma, Sanna, Serena, Kavousi, Maryam, Baumeister, Sebastian E., Coin, Lachlan J., Deng, Guohong, Gieger, Christian, Heard-Costa, Nancy L., Hottenga, Jouke-Jan, Kuhnel, Brigitte, Kumar, Vinod, Lagou, Vasiliki, Liang, Liming, Luan, Jian’an, Marques Vidal, Pedro, Leach, Irene Mateo, O'Reilly, Paul F., Peden, John F., Rahmioglu, Nilufer, Soininen, Pasi, Speliotes, Elizabeth K., Yuan, Xin, Thorleifsson, Gudmar ... Kooner, Jaspal S. (2011). Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nature Genetics, 43 (11), 1131-1138. doi: 10.1038/ng.970
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
Strawbridge, Rona J., Dupuis, Josee, Prokopenko, Iinga, Barker, Adam, Ahlqvist, Emma, Petrie, John R., Travers, Mary E., Bouatia-Naji, Nabila, Dimas, Antigone S., Nica, Alexandra, Wheeler, Eleanor, Chen, Han, Voight, Benjamin F., Taneera, Jalal, Kanoni, Stavroula, Peden, John F., Turrini, Fabiola, Gustafsson, Stefan, Zabena, Carina, Almgren, Peter, Barker, David J. P., Barnes, Daniel, Dennison, Elaine M., Eriksson, Johan G., Eriksson, Per, Eury, Elodie, Folkersen, Lasse, Fox, Caroline S., Frayling, Timothy M. ... . (2011). Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. Diabetes, 60 (10), 2624-2634. doi: 10.2337/db11-0415
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
Heid, Iris M., Jackson, Anne U., Randall, Joshua C., Winkler, Thomas W., Qi, Lu, Steinthorsdottir, Valgerdur, Thorleifsson, Gudmar, Zillikens, M. Carola, Speliotes, Elizabeth K., Maegi, Reedik, Workalemahu, Tsegaselassie, White, Charles C., Bouatia-Naji, Nabila, Harris, Tamara B., Berndt, Sonja I., Ingelsson, Erik, Willer, Cristen J., Weedon, Michael N., Luan, Jianan, Vedantam, Sailaja, Esko, Tonu, Kilpelaeinen, Tuomas O., Kutalik, Zoltan, Li, Shengxu, Monda, Keri L., Dixon, Anna L., Holmes, Christopher C., Kaplan, Lee M., Liang, Liming ... Lindgren, Cecilia M. (2010). Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nature Genetics, 42 (11), 949-962. doi: 10.1038/ng.685
Elizabeth K Speliotes, Cristen J Willer, Sonja I Berndt, Keri L Monda, Gudmar Thorleifsson, Anne U Jackson, Hana Lango Allen, Cecilia M Lindgren, Jian'an Luan, Reedik Magi, Joshua C Randall, Sailaja Vedantam, Thomas W Winkler, Lu Qi, Tsegaselassie Workalemahu, Iris M Heid, Valgerdur Steinthorsdottir, Heather M Stringham, Michael N Weedon, Eleanor Wheeler, Andrew R Wood, Teresa Ferreira, Robert J Weyant, Ayellet V Segre, Karol Estrada, Liming Liang, James Nemesh, Ju-Hyun Park, Stefan Gustafsson ... Ruth J F Loos (2010). Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nature Genetics, 42 (11), 937-948. doi: 10.1038/ng.686
Dupuis, Josée, Langenberg, Claudia, Prokopenko, Inga, Saxena, Richa, Soranzo, Nicole, Jackson, Anne U., Wheeler, Eleanor, Glazer, Nicole L., Bouatia-Naji, Nabila, Gloyn, Anna L., Lindgren, Cecilia M., Mägi, Reedik, Morris, Andrew P., Randall, Joshua, Johnson, Toby, Elliott, Paul, Rybin, Denis, Thorleifsson, Gudmar, Steinthorsdottir, Valgerdur, Henneman, Peter, Grallert, Harald, Dehghan, Abbas, Hottenga, Jouke Jan, Franklin, Christopher S., Navarro, Pau, Song, Kijoung, Goel, Anuj, Perry, John R.B., Egan, Josephine M. ... Barroso, Inês (2010). Erratum: New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk (Nature Genetics (2010) 42 (105-116)). Nature Genetics, 42 (5), 464-464. doi: 10.1038/ng0510-464a
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
Freathy, Rachel M., Mook-Kanamor, Dennis O., Sovio, Ulla, Prokopenko, Inga, Timpson, Nicholas J., Berry, Diane J., Warrington, Nicole M., Widen, Elisabeth, Hottenga, Jouke Jan, Kaakinen, Marika, Lange, Leslie A., Bradfield, Jonathan P., Kerkhof, Marjan, Marsh, Julie A., Magi, Reedik, Chen, Chih-Mei, Lyon, Helen N., Kirin, Mirna, Adair, Linda S., Aulchenko, Yurii S., Bennett, Amanda J., Borja, Judith B., Bouatia-Naji, Nabila, Charoen, Pimphen, Coin, Lachlan ..J. M., Cousminer, Diana L., De Geus, Eco J. C., Deloukas, Panos, Elliott, Paul ... McCarthy, Mark I. (2010). Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight. Nature Genetics, 42 (5), 430-435. doi: 10.1038/ng.567
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