Associate Professor Lutz Krause

Principal Research Fellow

The University of Queensland Diamantina Institute
Faculty of Medicine
l.krause@uq.edu.au
+61 7 344 37052

Overview

Associate Professor Lutz Krause undertook undergraduate studies in Applied Computer science and completed his PhD in Bioinformatics and Genome Research in 2007 at Bielefeld University in Germany. During his graduate studies his primary research interests were in sequence analysis, metagenomics, machine-learning and development of efficient algorithms for next-generation sequencing. He also investigated the composition and function of natural microbial communities from diverse ecosystems, including biogas fermenters, coral reefs and waste water treatment plants. Lutz joined the Nestlé Research Center in Lausanne, Switzerland in 2008, where he studied the role of the gut microbiota in health and disease, in particular in obesity and diabetes. In 2010 he moved to Brisbane to take up the role as head of the Bioinformatics laboratory at the QIMR Berghofer Medical Research Institute. His team developed and applied bioinformatics methods in the context of biomedical research with a focus on the genetics and epigenetics of complex disorders and infectious diseases.

In 2014 Lutz joined the UQ Diamantina Institute to pursue his research on cancer genetics, biomarker discovery, genetics and epigenetics of complex diseases and parasite genomics. His group analyses heterogeneous data-sets, including copy-number variations, expression data, genomic mutations, structural variations and genome-wide methylation. In collaboration with the Princess Alexandra Hospital, Lutz research aims at the identification of biomarkers that help clinicians choosing the optimal treatment for individual OAC patients. In the field of infectious diseases, he is interested in discovering novel drug and vaccine targets against human parasites, based on the sequencing and comparative analysis of multiple parasite genomes. In collaboration with the Prince Charles Hospital our group is studying the genetics of lung cancer.

Research Interests

  • Parasite genome-sequencing and comparative analysis
    Parasitic infections by blood flukes (schistosomes) cause highly significant human diseases. Schistosomiasis, a chronic disease caused by Schistosoma spp., is considered by the World Health Organization as the second most socioeconomically devastating and second most common parasitic disease afflicting humans, affecting 200 million people worldwide. No vaccines are available and treatment relies on only one drug, praziquantel. We apply whole-genome sequencing and comparative analysis of parasite genomes to study genome evolution and to identify novel drug and vaccine targets.
  • Cancer genomics
    We have a main interest in the discovery of biomarkers for disease onset, progression and personalised treatment in cancer. We analyse heterogeneous datasets, including genomic variations, epigenetic modifications, gene expression changes and copy number variations.
  • Role of the human microbiome in health and disease
    We develop data-mining methods, machine learning techniques and algorithms for the analysis of microbial and viral metagenomes, including the Calypso software for the higher-level analysis of 16S rDNA samples: http://cgenome.net/calypso/
  • Bioinformatics
    We develop and apply bioinformatics methods in the context of biomedical research. Our group specialises in genetics and epigenetics of complex disorders, biomarker discovery, parasite genomics, the human microbiota, and machine learning.
  • Genome-wide epigenetic association studies
    The emerging field of epigenetics studies heritable changes of our genome, which switch genes on or off without altering the genetic code. Epigenetics allows organisms to dynamically respond to environmental factors like diet, stress or prenatal experiences. Failure of epigenetic regulation can lead to important diseases, including cancer and mental disorders. Examples of epigenetic changes are the methylation of cysteine or histone modifications. These marks can be studied on a whole genome scale using recently developed next-generation DNA sequencing techniques, for example by Chip-Seq or Medip-Seq. We are involved in several epigenome-wide association studies investigating the role of epigenetics in complex diseases, in particular cancer and psychological disorders.
  • Cancer whole-genome sequencing
    We analyse whole-genome sequence data of cancer to identify somatic mutations, structural variations and copy-number changes associated with tumorigenesis and resistance to chemotherapy.

Qualifications

  • PhD, University of Bielefeld

Publications

  • Giacomin, Paul, Zakrzewski, Martha, Croese, John, Su, Xiaopei, Sotillo, Javier, McCann, Leisa, Navarro, Severine, Mitreva, Makedonka, Krause, Lutz, Loukas, Alex and Cantacessi, Cinzia (2015) Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects. Scientific Reports, 5 Art No.: 13797: . doi:10.1038/srep13797

  • Giacomin, Paul, Croese, John, Krause, Lutz, Loukas, Alex and Cantacessi, Cinzia (2015) Suppression of inflammation by helminths: a role for the gut microbiota?. Philosophical Transactions of the Royal Society B: Biological Sciences, 370 1675: . doi:10.1098/rstb.2014.0296

  • Cantacessi, Cinzia, Giacomin, Paul, Croese, John, Zakrzewski, Martha, Sotillo, Javier, McCann, Leisa, Nolan, Matthew J., Mitreva, Makedonka, Krause, Lutz and Loukas, Alex (2014) Impact of experimental hookworm infection on the human gut microbiota. The Journal of Infectious Diseases, 210 9: 1431-1434. doi:10.1093/infdis/jiu256

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

  • Swe, Pearl M., Zakrzewski, Martha, Kelly, Andrew, Krause, Lutz and Fischer, Katja (2014) Scabies mites alter the skin microbiome and promote growth of opportunistic pathogens in a porcine model. PLoS Neglected Tropical Diseases, 8 5: 1-12. doi:10.1371/journal.pntd.0002897

  • Davies, Matthew N., Krause, Lutz, Bell, Jordana T., Gao, Fei, Ward, Kirsten J., Wu, Honglong, Lu, Hanlin, Liu, Yuan, Tsai, Pei-Chein, Collier, David A., Murphy, Therese, Dempster, Emma, Mill, Jonathan, UK Brain Expression Consortium, Battle, Alexis, Mostafavi, Sara, Zhu, Xiaowei, Henders, Anjali, Byrne, Enda, Wray, Naomi R., Martin, Nicholas G., Spector, Tim D. and Wang, Jun (2014) Hypermethylation in the ZBTB20 gene is associated with major depressive disorder. Genome Biology, 15 4: R56.1-R56.12. doi:10.1186/gb-2014-15-4-r56

View all Publications

Supervision

  • (2017) Doctor Philosophy

  • (2017) Doctor Philosophy

  • Doctor Philosophy

View all Supervision

Available Projects

  • Parasitic infections by blood flukes (schistosomes) cause highly significant human diseases. Schistosomiasis, a chronic disease caused by Schistosoma spp., is considered by the World Health Organization as the second most socioeconomically devastating and second most common parasitic disease afflicting humans, affecting 200 million people worldwide. No vaccines are available and treatment relies on only one drug, praziquantel. The genomes of three Schistosoma species infecting humans have recently become publicly available. We are sequencing several further parasite genomes, which allows us to do a comprehensive comparative genome analysis of multiple parasites and free-living flatworms. Using bioinformatics methods, we identify genes important for host-parasite interaction and novel drug and vaccine targets. This project will provide important information for preventing and controlling human parasite infections by Schistosoma spp. affecting more than 200 million people every year. The study will provide novel insights into the evolution of human parasite genomes, identify gene functions and pathways important for the parasite-host interaction and reveal novel candidate drug and vaccine targets.

  • We have a main interest in the discovery of biomarkers for disease onset, progression and personalised treatment. In collaboration with Dr. Andrew Barbour for example, we are aiming at developing biomarkers for prognosis, progression and personalised treatment in oesophageal adenocarcinoma. Heterogeneous datasets are used and integrated, including genomic variations, epigenetic modifications, gene expression changes and copy number variations. For the discovery of novel biomarkers we employ various machine learning and data-mining methods, such as Support Vector Machines, Cox models, generalised linear models, supervised and unsupervised clustering, and multivariate techniques.

  • The emerging field of epigenetics studies heritable changes of our genome, which switch genes on or off without altering the genetic code. Epigenetics allows organisms to dynamically respond to environmental factors like diet, stress or prenatal experiences. Failure of epigenetic regulation can lead to important diseases, including cancer and mental disorders. Examples of epigenetic changes are the methylation of cysteine or histone modifications. These marks can be studied on a whole genome scale using recently developed next-generation DNA sequencing techniques, for example by Chip-Seq or Medip-Seq. In light of the huge amounts of data generated and the size of the human genome, the analysis of Chip-Seq and Medip-Seq data poses a considerable computational challenge. The Bionformatics Laboratory is involved in several projects investigating the role of epigenetics in complex diseases, in particular cancer and psychological disorders.

View all Available Projects

Publications

Featured Publications

  • Giacomin, Paul, Zakrzewski, Martha, Croese, John, Su, Xiaopei, Sotillo, Javier, McCann, Leisa, Navarro, Severine, Mitreva, Makedonka, Krause, Lutz, Loukas, Alex and Cantacessi, Cinzia (2015) Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects. Scientific Reports, 5 Art No.: 13797: . doi:10.1038/srep13797

  • Giacomin, Paul, Croese, John, Krause, Lutz, Loukas, Alex and Cantacessi, Cinzia (2015) Suppression of inflammation by helminths: a role for the gut microbiota?. Philosophical Transactions of the Royal Society B: Biological Sciences, 370 1675: . doi:10.1098/rstb.2014.0296

  • Cantacessi, Cinzia, Giacomin, Paul, Croese, John, Zakrzewski, Martha, Sotillo, Javier, McCann, Leisa, Nolan, Matthew J., Mitreva, Makedonka, Krause, Lutz and Loukas, Alex (2014) Impact of experimental hookworm infection on the human gut microbiota. The Journal of Infectious Diseases, 210 9: 1431-1434. doi:10.1093/infdis/jiu256

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

  • Swe, Pearl M., Zakrzewski, Martha, Kelly, Andrew, Krause, Lutz and Fischer, Katja (2014) Scabies mites alter the skin microbiome and promote growth of opportunistic pathogens in a porcine model. PLoS Neglected Tropical Diseases, 8 5: 1-12. doi:10.1371/journal.pntd.0002897

  • Davies, Matthew N., Krause, Lutz, Bell, Jordana T., Gao, Fei, Ward, Kirsten J., Wu, Honglong, Lu, Hanlin, Liu, Yuan, Tsai, Pei-Chein, Collier, David A., Murphy, Therese, Dempster, Emma, Mill, Jonathan, UK Brain Expression Consortium, Battle, Alexis, Mostafavi, Sara, Zhu, Xiaowei, Henders, Anjali, Byrne, Enda, Wray, Naomi R., Martin, Nicholas G., Spector, Tim D. and Wang, Jun (2014) Hypermethylation in the ZBTB20 gene is associated with major depressive disorder. Genome Biology, 15 4: R56.1-R56.12. doi:10.1186/gb-2014-15-4-r56

Journal Article

Conference Publication

  • Daniels, Marissa G., Krause, Lutz, Ellis, Jonathan J., Yang, Ian A., Bowman, Rayleen V., Relan, Vandana, Chee, Kelly, Goh, Felicia, Parris, Brielle, Morrison, Leanne, Martins, Maria, Passmore, Linda, McCaul, Elizabeth, Courtney, Deborah, Duhig, Edwina, Windsor, Morgan, Naidoo, Rishendran and Fong, Kwun M. (2016). Intratumoral genomic heterogeneity of primary pulmonary adenocarcinoma in never smokers. In: Meeting of the American-Association-for-Cancer-Research (AACR) Precision Medicine Series - Integrating Clinical Genomics and Cancer Therapy, Salt Lake, UT, United States, (). 13-16 June 2015.

  • Daniels, Marissa, Krause, Lutz, Ellis, Jonathan, Yang, Ian A., Bowman, Rayleen V., Relan, Vandana, Chee, Kelly, Goh, Felicia, Parris, Brielle, Morrison, Leanne, Martins, Maria, Mccaul, Elizabeth, Passmore, Linda, Courtney, Deborah, Duhig, Edwina, Naidoo, Rishendran, Fong, Kwun and Windsor, Morgan (2015). Inter-, and Intratumoural Genomic Heterogeneity of Primary Pulmonary Adenocarcinoma in Never Smokers. In: Unknown, Unknown, (S217-S217). Unknown.

  • Smith, D. J., Badrick, A. C., Krause, L., Bell, S. C., Anderson, G. J. and Reid, D. W. (2013). Perturbation of Sputum Microbiota by Intravenous Antibiotics in Cystic Fibrosis Is Short-Lived. In: Special Issue: Abstracts of the Thoracic Society of Australia and New Zealand and the Australian and New Zealand Society of Respiratory Science 2013 Annual Scientific Meetings. 2013 Annual Scientific Meetings of The Thoracic Society of Australia and New Zealand and the Australian and New Zealand Society of Respiratory Science, Darwin, NT Australia, (62-62). 22 - 27 March 2013. doi:10.1111/resp.12046

  • Krause, Lutz, Diaz, Naryttza N., Bartels, Daniela, Edwards, Robert A., Puehler, Alfred, Rohwer, Forest, Meyer, Folker and Stoye, Jens (2006). Finding novel genes in bacterial communities isolated from the environment. In: 14th Conference on Intelligent Systems for Molecular Biology, Fortaleza Brazil, (E281-E289). Aug 06-10, 2006. doi:10.1093/bioinformatics/btl247

PhD and MPhil Supervision

Current Supervision

Completed Supervision

  • (2017) Doctor Philosophy — Principal Advisor

  • (2017) Doctor Philosophy — Associate Advisor

Possible Research Projects

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

  • Parasitic infections by blood flukes (schistosomes) cause highly significant human diseases. Schistosomiasis, a chronic disease caused by Schistosoma spp., is considered by the World Health Organization as the second most socioeconomically devastating and second most common parasitic disease afflicting humans, affecting 200 million people worldwide. No vaccines are available and treatment relies on only one drug, praziquantel. The genomes of three Schistosoma species infecting humans have recently become publicly available. We are sequencing several further parasite genomes, which allows us to do a comprehensive comparative genome analysis of multiple parasites and free-living flatworms. Using bioinformatics methods, we identify genes important for host-parasite interaction and novel drug and vaccine targets. This project will provide important information for preventing and controlling human parasite infections by Schistosoma spp. affecting more than 200 million people every year. The study will provide novel insights into the evolution of human parasite genomes, identify gene functions and pathways important for the parasite-host interaction and reveal novel candidate drug and vaccine targets.

  • We have a main interest in the discovery of biomarkers for disease onset, progression and personalised treatment. In collaboration with Dr. Andrew Barbour for example, we are aiming at developing biomarkers for prognosis, progression and personalised treatment in oesophageal adenocarcinoma. Heterogeneous datasets are used and integrated, including genomic variations, epigenetic modifications, gene expression changes and copy number variations. For the discovery of novel biomarkers we employ various machine learning and data-mining methods, such as Support Vector Machines, Cox models, generalised linear models, supervised and unsupervised clustering, and multivariate techniques.

  • The emerging field of epigenetics studies heritable changes of our genome, which switch genes on or off without altering the genetic code. Epigenetics allows organisms to dynamically respond to environmental factors like diet, stress or prenatal experiences. Failure of epigenetic regulation can lead to important diseases, including cancer and mental disorders. Examples of epigenetic changes are the methylation of cysteine or histone modifications. These marks can be studied on a whole genome scale using recently developed next-generation DNA sequencing techniques, for example by Chip-Seq or Medip-Seq. In light of the huge amounts of data generated and the size of the human genome, the analysis of Chip-Seq and Medip-Seq data poses a considerable computational challenge. The Bionformatics Laboratory is involved in several projects investigating the role of epigenetics in complex diseases, in particular cancer and psychological disorders.

  • Our gut microbiota is an integral part of our body and increasing evidence indicates that it plays an essential role in diverse diseases such as allergies, cancer, mental illness, and metabolic and gastrointestinal disorders. While considerable efforts have been dedicated to find a cure for these diseases, their causes still remain poorly understood. The Bioinformatics Laboratory is involved in various projects investigating the role of bacteria in the development of diseases and disorders, including diabetes, obesity, gastrointestinal disorders and bacterial infections. The obtained results form a valuable basis for the development of novel treatment and prevention options and for the identification of biomarkers for disease risk. We also develop novel computational tools for mining, comparing and visualising large and complex metagenomic and 16S rDNA datasets.

  • We are analysing whole-genome sequening data of cancer to identify mutations, strucutral variations and copy-number variations inovlved in tumorigenesis and response to chemotherapy.