Publications by authors named "Denis Bauer"

44Publications

Host Porphobilinogen Deaminase Deficiency Confers Malaria Resistance in but Not in or During Intraerythrocytic Growth.

Front Cell Infect Microbiol 2020 3;10:464. Epub 2020 Sep 3.

Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.

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http://dx.doi.org/10.3389/fcimb.2020.00464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7495142PMC
September 2020

A Navigation System for Base Editing: Are We There Yet?

CRISPR J 2020 Aug;3(4):224-225

Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, North Ryde, Australia; and Macquarie University, Macquarie Park, Australia.

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http://dx.doi.org/10.1089/crispr.2020.29097.dcbDOI Listing
August 2020

Identity by descent analysis identifies founder events and links familial and sporadic ALS cases.

NPJ Genom Med 2020 7;5:32. Epub 2020 Aug 7.

Macquarie University Centre for Motor Neuron Disease Research, Department of Biological Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW Australia.

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http://dx.doi.org/10.1038/s41525-020-00139-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414871PMC
August 2020

VariantSpark: Cloud-based machine learning for association study of complex phenotype and large-scale genomic data.

Gigascience 2020 Aug;9(8)

Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave North Ryde NSW 2113 Australia.

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http://dx.doi.org/10.1093/gigascience/giaa077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7407261PMC
August 2020

Evidence for polygenic and oligogenic basis of Australian sporadic amyotrophic lateral sclerosis.

J Med Genet 2020 May 14. Epub 2020 May 14.

Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia

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http://dx.doi.org/10.1136/jmedgenet-2020-106866DOI Listing
May 2020

Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing.

Brief Bioinform 2020 Feb 2. Epub 2020 Feb 2.

Health and Biosecurity, CSIRO, Sydney, NSW, Australia.

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http://dx.doi.org/10.1093/bib/bbz145DOI Listing
February 2020

A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping.

Brief Bioinform 2019 Nov 27. Epub 2019 Nov 27.

School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.

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http://dx.doi.org/10.1093/bib/bbz121DOI Listing
November 2019

The Current State and Future of CRISPR-Cas9 gRNA Design Tools.

Front Pharmacol 2018 12;9:749. Epub 2018 Jul 12.

Commonwealth Scientific and Industrial Research Organisation, Sydney, NSW, Australia.

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http://dx.doi.org/10.3389/fphar.2018.00749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6052051PMC
July 2018

Genetic and Pathological Assessment of hnRNPA1, hnRNPA2/B1, and hnRNPA3 in Familial and Sporadic Amyotrophic Lateral Sclerosis.

Neurodegener Dis 2017 11;17(6):304-312. Epub 2017 Nov 11.

Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.

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http://dx.doi.org/10.1159/000481258DOI Listing
July 2018

Interacting with Genomic Data: Clinician Requirements and Prototype Structure.

Stud Health Technol Inform 2017 ;239:1-7

Melbourne Genomics Health Alliance, Victoria, Australia.

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April 2018

Ankyrin-1 Gene Exhibits Allelic Heterogeneity in Conferring Protection Against Malaria.

G3 (Bethesda) 2017 09 7;7(9):3133-3144. Epub 2017 Sep 7.

Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia

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http://dx.doi.org/10.1534/g3.117.300079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592938PMC
September 2017

A novel ENU-induced ankyrin-1 mutation impairs parasite invasion and increases erythrocyte clearance during malaria infection in mice.

Sci Rep 2016 11 16;6:37197. Epub 2016 Nov 16.

Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, ACT, Australia.

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http://dx.doi.org/10.1038/srep37197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111128PMC
November 2016

Evaluation of computational programs to predict HLA genotypes from genomic sequencing data.

Brief Bioinform 2018 03;19(2):179-187

Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia.

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http://dx.doi.org/10.1093/bib/bbw097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019030PMC
March 2018

Adenosine monophosphate deaminase 3 activation shortens erythrocyte half-life and provides malaria resistance in mice.

Blood 2016 09 27;128(9):1290-301. Epub 2016 Jul 27.

Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia;

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http://dx.doi.org/10.1182/blood-2015-09-666834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009516PMC
September 2016

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.

Genome Res 2016 06 6;26(6):719-31. Epub 2016 Apr 6.

Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia;

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http://dx.doi.org/10.1101/gr.201517.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889976PMC
June 2016

Targeted next-generation sequencing of 22 mismatch repair genes identifies Lynch syndrome families.

Cancer Med 2016 05 25;5(5):929-41. Epub 2016 Jan 25.

School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia.

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http://doi.wiley.com/10.1002/cam4.628
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http://dx.doi.org/10.1002/cam4.628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864822PMC
May 2016

VariantSpark: population scale clustering of genotype information.

BMC Genomics 2015 Dec 10;16:1052. Epub 2015 Dec 10.

CSIRO, Health & Biosecurity Flagship, 11 Julius Av, Sydney, 2113, Australia.

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http://dx.doi.org/10.1186/s12864-015-2269-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676146PMC
December 2015

Genome-wide analysis of chemically induced mutations in mouse in phenotype-driven screens.

BMC Genomics 2015 Oct 26;16:866. Epub 2015 Oct 26.

Australian School of Advanced Medicine, Macquarie University, 2 technology place, Sydney, 2109, Australia.

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http://dx.doi.org/10.1186/s12864-015-2073-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623266PMC
October 2015

Cpipe: a shared variant detection pipeline designed for diagnostic settings.

Genome Med 2015 10;7(1):68. Epub 2015 Jul 10.

Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, 3052 Australia ; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010 Australia ; Melbourne Genomics Health Alliance, Melbourne, Australia ; Walter and Eliza Hall Institute, Parkville, VIC 3052 Australia.

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http://dx.doi.org/10.1186/s13073-015-0191-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515933PMC
July 2015

Mutation analysis of MATR3 in Australian familial amyotrophic lateral sclerosis.

Neurobiol Aging 2015 Mar 20;36(3):1602.e1-2. Epub 2014 Nov 20.

Australian School of Advanced Medicine, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.neurobiolaging.2014.11.010DOI Listing
March 2015

Blue: correcting sequencing errors using consensus and context.

Bioinformatics 2014 Oct 11;30(19):2723-32. Epub 2014 Jun 11.

CSIRO Computational Informatics, School of IT, University of Sydney, CSIRO Animal, Food and Health Sciences, Sydney, NSW 2113, and CSIRO Ecosystem Sciences, Canberra, ACT 2601, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btu368DOI Listing
October 2014

Genomics and personalised whole-of-life healthcare.

Trends Mol Med 2014 Sep 4;20(9):479-86. Epub 2014 May 4.

CSIRO Preventative Health National Research Flagship, Adelaide, SA 5000, Australia.

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http://dx.doi.org/10.1016/j.molmed.2014.04.001DOI Listing
September 2014

Early life events influence whole-of-life metabolic health via gut microflora and gut permeability.

Crit Rev Microbiol 2015 19;41(3):326-40. Epub 2014 Mar 19.

Preventative Health Flagship, CSIRO , North Ryde , Australia .

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http://dx.doi.org/10.3109/1040841X.2013.837863DOI Listing
April 2016

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

Bioinformatics 2014 May 26;30(10):1471-2. Epub 2014 Jan 26.

Cancer Epigenetics Program, Cancer Research Division, Kinghorn Cancer Centre, Garvan Institute of Medical Research, RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, St Vincent's Clinical School, University of NSW, Sydney 2010, Australia and Division of Computational Informatics, CSIRO, Sydney 2113, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btu036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016703PMC
May 2014

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

Bioinformatics 2013 Aug 5;29(15):1895-7. Epub 2013 Jun 5.

Division of Genomics and Computational Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btt315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712220PMC
August 2013

Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.

Nucleic Acids Res 2012 Sep 16;40(16):7633-43. Epub 2012 Jun 16.

The University of Queensland, Queensland Brain Institute, Brisbane, Qld. 4072, Australia.

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http://dx.doi.org/10.1093/nar/gks505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439898PMC
September 2012

Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data.

Genome Res 2012 Jul 1;22(7):1372-81. Epub 2012 May 1.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia.

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http://dx.doi.org/10.1101/gr.130237.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396377PMC
July 2012

Sorting the nuclear proteome.

Bioinformatics 2011 Jul;27(13):i7-14

Queensland Brain Institute, School of Chemistry and Molecular Biosciences, Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117375PMC
July 2011

Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster.

BMC Bioinformatics 2010 Jul 2;11:366. Epub 2010 Jul 2.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072 Australia.

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http://dx.doi.org/10.1186/1471-2105-11-366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912886PMC
July 2010

Assigning roles to DNA regulatory motifs using comparative genomics.

Bioinformatics 2010 Apr 10;26(7):860-6. Epub 2010 Feb 10.

Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia.

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http://bioinformatics.oxfordjournals.org/content/early/2010/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btq049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844991PMC
April 2010

Optimizing static thermodynamic models of transcriptional regulation.

Bioinformatics 2009 Jul 27;25(13):1640-6. Epub 2009 Apr 27.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btp283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732318PMC
July 2009

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

STREAM: Static Thermodynamic REgulAtory Model of transcription.

Bioinformatics 2008 Nov 6;24(21):2544-5. Epub 2008 Sep 6.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld. 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btn467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732279PMC
November 2008

Studying the functional conservation of cis-regulatory modules and their transcriptional output.

BMC Bioinformatics 2008 Apr 29;9:220. Epub 2008 Apr 29.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld. 4072 Australia.

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http://dx.doi.org/10.1186/1471-2105-9-220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386823PMC
April 2008

STAR: predicting recombination sites from amino acid sequence.

BMC Bioinformatics 2006 Oct 8;7:437. Epub 2006 Oct 8.

Institute for Molecular Bioscience, The University of Queensland, QLD 4072, Australia.

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http://dx.doi.org/10.1186/1471-2105-7-437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624854PMC
October 2006