Works by Bauer, Denis C.

Results: 46

The inequity of targeted cystic fibrosis reproductive carrier screening tests in Australia.

Published in:

Prenatal Diagnosis, 2023, v. 43, n. 1, p. 109, doi. 10.1002/pd.6285

By:

Shum, Bennett O. V.;
Sng, Letitia M. F.;
Ruseckaite, Rasa;
Henner, Ilya;
Twine, Natalie;
Bauer, Denis C.;
Wilgen, Urs;
Pretorius, Carel;
Barahona, Paulette;
Ungerer, Jacobus P. J.;
Bennett, Glenn

Publication type:

Article

Blue: correcting sequencing errors using consensus and context.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2723, doi. 10.1093/bioinformatics/btu368

By:

Greenfield, Paul;
Duesing, Konsta;
Papanicolaou, Alexie;
Bauer, Denis C.

Publication type:

Article

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

Published in:

Bioinformatics, 2014, v. 30, n. 10, p. 1471, doi. 10.1093/bioinformatics/btu036

By:

Buske, Fabian A.;
French, Hugh J.;
Smith, Martin A.;
Clark, Susan J.;
Bauer, Denis C.

Publication type:

Article

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

Published in:

Bioinformatics, 2013, v. 29, n. 15, p. 1895, doi. 10.1093/bioinformatics/btt315

By:

Buske, Fabian A.;
Bauer, Denis C.;
Mattick, John S.;
Bailey, Timothy L.

Publication type:

Article

Sorting the nuclear proteome.

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. i7, doi. 10.1093/bioinformatics/btr217

By:

Bauer, Denis C.;
Willadsen, Kai;
Buske, Fabian A.;
Lê Cao, Kim-Anh;
Bailey, Timothy L.;
Dellaire, Graham;
Bodén, Mikael

Publication type:

Article

Assigning roles to DNA regulatory motifs using comparative genomics.

Published in:

Bioinformatics, 2010, v. 26, n. 7, p. 860, doi. 10.1093/bioinformatics/btq049

By:

Buske, Fabian A.;
Bodén, Mikael;
Bauer, Denis C.;
Bailey, Timothy L.

Publication type:

Article

Optimizing static thermodynamic models of transcriptional regulation.

Published in:

Bioinformatics, 2009, v. 25, n. 13, p. 1640, doi. 10.1093/bioinformatics/btp283

By:

Denis C. Bauer;
Timothy L. Bailey

Publication type:

Article

STREAM: Static Thermodynamic REgulAtory Model of transcription.

Published in:

Bioinformatics, 2008, v. 24, n. 21, p. 2544, doi. 10.1093/bioinformatics/btn467

By:

Denis C. Bauer;
Timothy L. Bailey

Publication type:

Article

Fast and accurate exhaustive higher-order epistasis search with BitEpi.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-94959-y

By:

Bayat, Arash;
Hosking, Brendan;
Jain, Yatish;
Hosking, Cameron;
Kodikara, Milindi;
Reti, Daniel;
Twine, Natalie A.;
Bauer, Denis C.

Publication type:

Article

A Pangenomic Approach to Improve Population Genetics Analysis and Reference Bias in Underrepresented Middle Eastern and Horn of Africa Populations.

Published in:

Biomolecules (2218-273X), 2025, v. 15, n. 4, p. 582, doi. 10.3390/biom15040582

By:

Oliva, Adrien;
Foare, Rachel;
Campbell, Peter;
Twine, Natalie A.;
Bauer, Denis C.;
Johar, Angad Singh

Publication type:

Article

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data.

Published in:

PLoS ONE, 2014, v. 9, n. 8, p. 1, doi. 10.1371/journal.pone.0103207

By:

Zhang, Zong Hong;
Jhaveri, Dhanisha J.;
Marshall, Vikki M.;
Bauer, Denis C.;
Edson, Janette;
Narayanan, Ramesh K.;
Robinson, Gregory J.;
Lundberg, Andreas E.;
Bartlett, Perry F.;
Wray, Naomi R.;
Zhao, Qiong-Yi

Publication type:

Article

Applying a risk governance approach to examine how professionals perceive the benefits and risks of clinical genomics in Australian healthcare.

Published in:

New Genetics & Society, 2023, v. 42, n. 1, p. 1, doi. 10.1080/14636778.2023.2192472

By:

Malakar, Yuwan;
Lacey, Justine;
Twine, Natalie A.;
Bauer, Denis C.

Publication type:

Article

Novel Alzheimer's disease genes and epistasis identified using machine learning GWAS platform.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-44378-y

By:

Lundberg, Mischa;
Sng, Letitia M. F.;
Szul, Piotr;
Dunne, Rob;
Bayat, Arash;
Burnham, Samantha C.;
Bauer, Denis C.;
Twine, Natalie A.

Publication type:

Article

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

Published in:

Scientific Reports, 2016, p. 37197, doi. 10.1038/srep37197

By:

Huang, Hong Ming;
Bauer, Denis C.;
Lelliott, Patrick M.;
Greth, Andreas;
McMorran, Brendan J.;
Foote, Simon J.;
Burgio, Gaetan

Publication type:

Article

Identity by descent analysis identifies founder events and links SOD1 familial and sporadic ALS cases.

Published in:

NPJ Genomic Medicine, 2020, v. 5, n. 1, p. 1, doi. 10.1038/s41525-020-00139-8

By:

Henden, Lyndal;
Twine, Natalie A.;
Szul, Piotr;
McCann, Emily P.;
Nicholson, Garth A.;
Rowe, Dominic B.;
Kiernan, Matthew C.;
Bauer, Denis C.;
Blair, Ian P.;
Williams, Kelly L.

Publication type:

Article

Synsor: a tool for alignment-free detection of engineered DNA sequences.

Published in:

Frontiers in Bioengineering & Biotechnology, 2024, p. 1, doi. 10.3389/fbioe.2024.1375626

By:

Tay, Aidan P.;
Didi, Kieran;
Wickramarachchi, Anuradha;
Bauer, Denis C.;
Wilson, Laurence O. W.;
Maselko, Maciej

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 1, p. 308, doi. 10.1093/bib/bbz145

By:

O'Brien, Aidan R;
Burgio, Gaetan;
Bauer, Denis C

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2020, v. 21, n. 6, p. 1920, doi. 10.1093/bib/bbz121

By:

Sathyanarayanan, Anita;
Gupta, Rohit;
Thompson, Erik W;
Nyholt, Dale R;
Bauer, Denis C;
Nagaraj, Shivashankar H

Publication type:

Article

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

Published in:

Briefings in Bioinformatics, 2018, v. 19, n. 2, p. 179, doi. 10.1093/bib/bbw097

By:

Bauer, Denis C.;
Zadoorian, Armella;
Wilson, Laurence O. W.;
Thorne, Natalie P.

Publication type:

Article

Interoperable medical data: The missing link for understanding COVID‐19.

Published in:

Transboundary & Emerging Diseases, 2021, v. 68, n. 4, p. 1753, doi. 10.1111/tbed.13892

By:

Bauer, Denis C.;
Metke‐Jimenez, Alejandro;
Maurer‐Stroh, Sebastian;
Tiruvayipati, Suma;
Wilson, Laurence O. W.;
Jain, Yatish;
Perrin, Amandine;
Ebrill, Kate;
Hansen, David P.;
Vasan, Seshadri S.

Publication type:

Article

Supporting pandemic response using genomics and bioinformatics: A case study on the emergent SARS‐CoV‐2 outbreak.

Published in:

Transboundary & Emerging Diseases, 2020, v. 67, n. 4, p. 1453, doi. 10.1111/tbed.13588

By:

Bauer, Denis C.;
Tay, Aidan P.;
Wilson, Laurence O. W.;
Reti, Daniel;
Hosking, Cameron;
McAuley, Alexander J.;
Pharo, Elizabeth;
Todd, Shawn;
Stevens, Vicky;
Neave, Matthew J.;
Tachedjian, Mary;
Drew, Trevor W.;
Vasan, Seshadri S.

Publication type:

Article

Cover Image.

Published in:

Transboundary & Emerging Diseases, 2020, v. 67, n. 4, p. i, doi. 10.1111/tbed.13242

By:

Bauer, Denis C.;
Tay, Aidan P.;
Wilson, Laurence O. W.;
Reti, Daniel;
Hosking, Cameron;
McAuley, Alexander J.;
Pharo, Elizabeth;
Todd, Shawn;
Stevens, Vicky;
Neave, Matthew J.;
Tachedjian, Mary;
Drew, Trevor W.;
Vasan, Seshadri S.

Publication type:

Article

VariantSpark: population scale clustering of genotype information.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2269-7

By:

O'Brien, Aidan R.;
Saunders, Neil F. W.;
Yi Guo;
Buske, Fabian A.;
Scott, Rodney J.;
Bauer, Denis C.

Publication type:

Article

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

Published in:

BMC Genomics, 2015, v. 16, p. 866, doi. 10.1186/s12864-015-2073-4

By:

Bauer, Denis C.;
McMorran, Brendan J.;
Foote, Simon J.;
Burgio, Gaetan

Publication type:

Article

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

Published in:

Critical Reviews in Microbiology, 2015, v. 41, n. 3, p. 326, doi. 10.3109/1040841X.2013.837863

By:

Kerr, Caroline A.;
Grice, Desma M.;
Tran, Cuong D.;
Bauer, Denis C.;
Li, Dongmei;
Hendry, Phil;
Hannan, Garry N.

Publication type:

Article

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

Published in:

Cancer Medicine, 2016, v. 5, n. 5, p. 929, doi. 10.1002/cam4.628

By:

Talseth‐Palmer, Bente A.;
Bauer, Denis C.;
Sjursen, Wenche;
Evans, Tiffany J.;
McPhillips, Mary;
Proietto, Anthony;
Otton, Geoffrey;
Spigelman, Allan D.;
Scott, Rodney J.

Publication type:

Article

Genetic Analysis of Tryptophan Metabolism Genes in Sporadic Amyotrophic Lateral Sclerosis.

Published in:

Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.701550

By:

Fifita, Jennifer A.;
Chan Moi Fat, Sandrine;
McCann, Emily P.;
Williams, Kelly L.;
Twine, Natalie A.;
Bauer, Denis C.;
Rowe, Dominic B.;
Pamphlett, Roger;
Kiernan, Matthew C.;
Tan, Vanessa X.;
Blair, Ian P.;
Guillemin, Gilles J.

Publication type:

Article

Predicting CRISPR-Cas12a guide efficiency for targeting using machine learning.

Published in:

PLoS ONE, 2023, v. 18, n. 10, p. 1, doi. 10.1371/journal.pone.0292924

By:

O'Brien, Aidan;
Bauer, Denis C.;
Burgio, Gaetan

Publication type:

Article

Optimizing UK biobank cloud-based research analysis platform to fine-map coronary artery disease loci in whole genome sequencing data.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-95286-2

By:

Sng, Letitia M.F.;
Kaphle, Anubhav;
O'Brien, Mitchell J.;
Hosking, Brendan;
Reguant, Roc;
Verjans, Johan;
Jain, Yatish;
Twine, Natalie A.;
Bauer, Denis C.

Publication type:

Article

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

Published in:

Frontiers in Pharmacology, 2018, p. N.PAG, doi. 10.3389/fphar.2018.00749

By:

Wilson, Laurence O. W.;
O’Brien, Aidan R.;
Bauer, Denis C.

Publication type:

Article

Host Porphobilinogen Deaminase Deficiency Confers Malaria Resistance in Plasmodium chabaudi but Not in Plasmodium berghei or Plasmodium falciparum During Intraerythrocytic Growth.

Published in:

Frontiers in Cellular & Infection Microbiology, 2020, v. 10, p. N.PAG, doi. 10.3389/fcimb.2020.00464

By:

Schnider, Cilly Bernardette;
Yang, Hao;
Starrs, Lora;
Ehmann, Anna;
Rahimi, Farid;
Di Pierro, Elena;
Graziadei, Giovanna;
Matthews, Kathryn;
De Koning-Ward, Tania;
Bauer, Denis C.;
Foote, Simon J.;
Burgio, Gaetan;
McMorran, Brendan J.

Publication type:

Article

Optimized nickase- and nuclease-based prime editing in human and mouse cells.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 18, p. 10785, doi. 10.1093/nar/gkab792

By:

Adikusuma, Fatwa;
Lushington, Caleb;
Arudkumar, Jayshen;
Godahewa, Gelshan I;
Chey, Yu C J;
Gierus, Luke;
Piltz, Sandra;
Geiger, Ashleigh;
Jain, Yatish;
Reti, Daniel;
Wilson, Laurence O W;
Bauer, Denis C;
Thomas, Paul Q

Publication type:

Article

Evolutionary Insights from Association Rule Mining of Co-Occurring Mutations in Influenza Hemagglutinin and Neuraminidase.

Published in:

Viruses (1999-4915), 2024, v. 16, n. 10, p. 1515, doi. 10.3390/v16101515

By:

Galeone, Valentina;
Lee, Carol;
Monaghan, Michael T.;
Bauer, Denis C.;
Wilson, Laurence O. W.

Publication type:

Article

Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. 1, doi. 10.1038/s41598-019-39142-0

By:

O'Brien, Aidan R.;
Wilson, Laurence O. W.;
Burgio, Gaetan;
Bauer, Denis C.

Publication type:

Article

Dual-functioning transcription factors in thedevelopmental gene network of Drosophilamelanogaster.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 366, doi. 10.1186/1471-2105-11-366

By:

Bauer, Denis C;
Buske, Fabian A.;
Bailey, Timothy L.

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-220

By:

Bauer, Denis C.;
Bailey, Timothy L.

Publication type:

Article

AskBeacon—performing genomic data exchange and analytics with natural language.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf079

By:

Wickramarachchi, Anuradha;
Tonni, Shakila;
Majumdar, Sonali;
Karimi, Sarvnaz;
Kõks, Sulev;
Hosking, Brendan;
Rambla, Jordi;
Twine, Natalie A;
Jain, Yatish;
Bauer, Denis C

Publication type:

Article

Novel Alzheimer’s disease genes and epistasis identified using machine learning GWAS platform.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-44378-y

By:

Lundberg, Mischa;
Sng, Letitia M. F.;
Szul, Piotr;
Dunne, Rob;
Bayat, Arash;
Burnham, Samantha C.;
Bauer, Denis C.;
Twine, Natalie A.

Publication type:

Article

Future-proofing genomic data and consent management: a comprehensive review of technology innovations.

Published in:

GigaScience, 2024, v. 13, n. 1, p. 1, doi. 10.1093/gigascience/giae021

By:

Oliva, Adrien;
Kaphle, Anubhav;
Reguant, Roc;
Sng, Letitia M F;
Twine, Natalie A;
Malakar, Yuwan;
Wickramarachchi, Anuradha;
Keller, Marcel;
Ranbaduge, Thilina;
Chan, Eva K F;
Breen, James;
Buckberry, Sam;
Guennewig, Boris;
Haas, Matilda;
Brown, Alex;
Cowley, Mark J;
Thorne, Natalie;
Jain, Yatish;
Bauer, Denis C

Publication type:

Article

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

Published in:

GigaScience, 2020, v. 9, n. 8, p. 1, doi. 10.1093/gigascience/giaa077

By:

Bayat, Arash;
Szul, Piotr;
O'Brien, Aidan R;
Dunne, Robert;
Hosking, Brendan;
Jain, Yatish;
Hosking, Cameron;
Luo, Oscar J;
Twine, Natalie;
Bauer, Denis C

Publication type:

Article

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

Published in:

Genome Medicine, 2015, v. 7, n. 1, p. 1, doi. 10.1186/s13073-015-0191-x

By:

Sadedin, Simon P.;
Dashnow, Harriet;
James, Paul A.;
Bahlo, Melanie;
Bauer, Denis C.;
Lonie, Andrew;
Lunke, Sebastian;
Macciocca, Ivan;
Ross, Jason P.;
Siemering, Kirby R.;
Stark, Zornitza;
White, Susan M.;
Alliance, Melbourne Genomics Health;
Taylor, Graham;
Gaff, Clara;
Oshlack, Alicia;
Thorne, Natalie P.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2012, v. 40, n. 16, p. 7633, doi. 10.1093/nar/gks505

By:

Ragan, Chikako;
Mowry, Bryan J.;
Bauer, Denis C.

Publication type:

Article

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

Published in:

G3: Genes | Genomes | Genetics, 2017, v. 7, n. 9, p. 3133, doi. 10.1534/g3.117.300079

By:

Hong Ming Huang;
Bauer, Denis C.;
Lelliott, Patrick M.;
Dixon, Matthew W. A.;
Tilley, Leann;
McMorran, Brendan J.;
Foote, Simon J.;
Burgio, Gaetan

Publication type:

Article

Scalable genomic data exchange and analytics with sBeacon.

Published in:

2023

By:

Wickramarachchi, Anuradha;
Hosking, Brendan;
Jain, Yatish;
Grimes, John;
O'Brien, Mitchell J.;
Wright, Tracey;
Burgess, Mark A.;
Lin, Victor San Kho;
Reisinger, Florian;
Hofmann, Oliver;
Lawley, Michael;
Wilson, Laurence O. W.;
Twine, Natalie A.;
Bauer, Denis C.

Publication type:

Letter

VARSCOT: variant-aware detection and scoring enables sensitive and personalized off-target detection for CRISPR-Cas9.

Published in:

BMC Biotechnology, 2019, v. 19, n. 1, p. N.PAG, doi. 10.1186/s12896-019-0535-5

By:

Wilson, Laurence O. W.;
Hetzel, Sara;
Pockrandt, Christopher;
Reinert, Knut;
Bauer, Denis C.

Publication type:

Article

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

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-015-2073-4

By:

Bauer, Denis C.;
McMorran, Brendan J.;
Foote, Simon J.;
Burgio, Gaetan

Publication type:

Article