Denis C. Bauer

发表

Assigning roles to DNA regulatory motifs using comparative genomics

Mikael Bodén, Fabian A. Buske, Denis C. Bauer, 2010, Bioinform..

Unlocking HDR-mediated Nucleotide Editing by identifying high-efficiency target sites using machine learning

Denis C. Bauer, Aidan R. O’Brien, Laurence O. W. Wilson, 2018 .

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster

Mikael Bodén, Fabian A. Buske, Denis C. Bauer, 2010, Neurocomputing.

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

Denis C. Bauer, Timothy L. Bailey, T. Bailey, 2008, BMC Bioinformatics.

Artificial Intelligence and Machine Learning in Bioinformatics

Yi Guo, Denis C. Bauer, Aidan R. O’Brien, 2019, Encyclopedia of Bioinformatics and Computational Biology.

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

Sebastian Maurer-Stroh, Alejandro Metke-Jimenez, Denis C. Bauer, 2020, Transboundary and emerging diseases.

Australia's precision medicine is powered by ultra-high dimensional machine learning and serverless cloud-architecture

Robert Dunne, Denis C. Bauer, Piotr Szul, 2019 .

Blue: correcting sequencing errors using consensus and context

Paul Greenfield, Denis C. Bauer, Alexie Papanicolaou, 2014, Bioinform..

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

Fabian A. Buske, Denis C. Bauer, Timothy L. Bailey, 2013, Bioinform..

Optimizing static thermodynamic models of transcriptional regulation

Denis C. Bauer, Timothy L. Bailey, T. Bailey, 2009, Bioinform..

Predicting SUMOylation Sites

Mikael Bodén, Fabian A. Buske, Denis C. Bauer, 2008, PRIB.

Ten Simple Rules for Searching and Organizing the Scientific Literature

Denis C. Bauer, 2009 .

STREAM: Static Thermodynamic REgulAtory Model of transcription

Denis C. Bauer, Timothy L. Bailey, 2008, Bioinform..

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

Denis C. Bauer, Laurence O. W. Wilson, Natalie P. Thorne, 2016, Briefings Bioinform..

Cpipe: a shared variant detection pipeline designed for diagnostic settings

Clara Gaff, Andrew Lonie, Denis C. Bauer, 2015 .

Sorting the nuclear proteome

Mikael Bodén, Kim-Anh Lê Cao, Fabian A. Buske, 2011, Bioinform..

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

Denis C. Bauer, Aidan R. O’Brien, Laurence O. W. Wilson, 2018, Front. Pharmacol..

VariantSpark, A Random Forest Machine Learning Implementation for Ultra High Dimensional Data

Robert Dunne, Denis C. Bauer, Piotr Szul, 2019, bioRxiv.

STAR: predicting recombination sites from amino acid sequence

Mikael Bodén, Denis C. Bauer, Ricarda Thier, 2006, BMC Bioinformatics.

Predicting Structural Disruption of Proteins Caused by Crossover

Mikael Bodén, Zheng Yuan, Denis C. Bauer, 2005, 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

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

Fabian A. Buske, Denis C. Bauer, Timothy L. Bailey, 2010, BMC Bioinformatics.

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

Fabian A. Buske, Denis C. Bauer, Martin A. Smith, 2014, Bioinform..

BitEpi: A Fast and Accurate Exhaustive Higher-Order Epistasis Search

Denis C. Bauer, Arash Bayat, Brendan Hosking, 2019 .

VariantSpark: population scale clustering of genotype information

Fabian A. Buske, Denis C. Bauer, Aidan R. O’Brien, 2015, BMC Genomics.

A comparative study of techniques for differential expression analysis on RNA-Seq data

Denis C. Bauer, N. Wray, J. Edson, 2014, bioRxiv.

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

Denis C. Bauer, N. Wray, J. Edson, 2014, bioRxiv.

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

Martin S. Taylor, Denis C. Bauer, Andrew M. Waterhouse, 2009, Nature Genetics.

Cpipe: a shared variant detection pipeline designed for diagnostic settings

Denis C. Bauer, N. Thorne, A. Oshlack, 2015, bioRxiv.

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

Aaron T. L. Lun, Fabian A. Buske, Denis C. Bauer, 2016, Genome research.

Gene expression Optimizing static thermodynamic models of transcriptional regulation

Denis C. Bauer, T. Bailey, 2009 .

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

Knut Reinert, Denis C. Bauer, Laurence O. W. Wilson, 2019, BMC Biotechnology.

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

Denis C. Bauer, Laurence O. W. Wilson, Cameron Hosking, 2020, Transboundary and emerging diseases.

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

Chikako Ragan, Denis C. Bauer, B. Mowry, 2012, Nucleic acids research.

Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes

Denis C. Bauer, Timothy J. Peters, E. Zotenko, 2019, Scientific Reports.

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

Denis C. Bauer, L. Henden, M. Kiernan, 2020, Journal of Medical Genetics.

Genetic analysis of GLT8D1 and ARPP21 in Australian familial and sporadic amyotrophic lateral sclerosis

Denis C. Bauer, L. Henden, M. Kiernan, 2021, Neurobiology of Aging.

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

Denis C. Bauer, L. Henden, M. Kiernan, 2020, npj Genomic Medicine.

IBD analysis of Australian amyotrophic lateral sclerosis SOD1-mutation carriers identifies five founder events and links sporadic cases to existing ALS families

Denis C. Bauer, L. Henden, M. Kiernan, 2019, bioRxiv.

Mutation analysis of MATR3 in Australian familial amyotrophic lateral sclerosis

Denis C. Bauer, K. Williams, I. Blair, 2015, Neurobiology of Aging.

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene in and for Therapeutic

Timothy A. Miller, Denis C. Bauer, Shankaracharya, 2018 .

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

Denis C. Bauer, Laurence O. W. Wilson, G. I. Godahewa, 2021, bioRxiv.

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

Denis C. Bauer, Patrick M. Lelliott, L. Tilley, 2017, G3: Genes, Genomes, Genetics.

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

Denis C. Bauer, Patrick M. Lelliott, S. Foote, 2016, Scientific Reports.

Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data

Fabian A. Buske, Denis C. Bauer, Timothy L Bailey, 2012, Genome research.

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

Anita Sathyanarayanan, Rohit Gupta, Denis C. Bauer, 2019, Briefings Bioinform..

A Critical Review of the Impact of Candidate Copy Number Variants on Autism Spectrum Disorders

Denis C. Bauer, R. Alizadehsani, S. S. Abedini, 2023, 2302.03211.

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

Robert Dunne, Denis C. Bauer, Aidan R. O’Brien, 2020, GigaScience.

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

Denis C. Bauer, D. Rowe, K. Williams, 2017, Neurodegenerative Diseases.

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

Denis C. Bauer, Desma M. Grice, G. N. Hannan, 2015, Critical reviews in microbiology.

Genetic correlation between amyotrophic lateral sclerosis and schizophrenia

Denis C. Bauer, Annelot M. Dekker, Ashley R. Jones, 2017, Nature Communications.

Gut permeability, its interaction with gut microflora and effects on metabolic health are mediated by the lymphatics system, liver and bile acid.

Denis C. Bauer, Desma M. Grice, G. N. Hannan, 2015, Future microbiology.

Genomics and personalised whole-of-life healthcare.

Clara Gaff, Lynne Cobiac, Fabian A. Buske, 2014, Trends in molecular medicine.

A Critical Review of the Impact of Candidate Copy Number Variants on Autism Spectrum Disorders

Denis C. Bauer, R. Alizadehsani, S. S. Abedini, 2023, 2302.03211.

Genetic and immunopathological analysis of CHCHD10 in Australian amyotrophic lateral sclerosis and frontotemporal dementia and transgenic TDP-43 mice

Denis C. Bauer, J. Hodges, G. Halliday, 2019, Journal of Neurology, Neurosurgery, and Psychiatry.

Genetic Analysis of Tryptophan Metabolism Genes in Sporadic Amyotrophic Lateral Sclerosis

Denis C. Bauer, G. Guillemin, M. Kiernan, 2021, Frontiers in Immunology.

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

Denis C. Bauer, R. Scott, A. Spigelman, 2016, Cancer medicine.

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression

Denis C. Bauer, Timothy J. Peters, S. Clark, 2019, Scientific Reports.

High Activity Target-Site Identification Using Phenotypic Independent CRISPR-Cas9 Core Functionality.

Denis C. Bauer, Aidan R. O’Brien, Laurence O. W. Wilson, 2018, The CRISPR journal.

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

Denis C. Bauer, S. Foote, M. McConville, 2016, Blood.

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

Denis C. Bauer, S. Foote, G. Burgio, 2015, BMC Genomics.

Breaking the Curse of Dimensionality for Machine Learning on Genomic Data

Robert Dunne, Denis C. Bauer, Piotr Szul, 2017, BAI@IJCAI.

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

Denis C. Bauer, L. Henden, M. Kiernan, 2020, NPJ genomic medicine.

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

Denis C. Bauer, Aidan R. O’Brien, Laurence O. W. Wilson, 2018, bioRxiv.

Predicting CRISPR-Cas12a guide efficiency for targeting using machine learning

Denis C. Bauer, Aidan R. O’Brien, G. Burgio, 2023, bioRxiv.

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

Denis C. Bauer, S. Foote, E. Di Pierro, 2019, bioRxiv.

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

Sebastian Maurer-Stroh, Alejandro Metke-Jimenez, Denis C. Bauer, 2020, Transboundary and emerging diseases.

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

Denis C. Bauer, S. Foote, G. Burgio, 2015, BMC Genomics.

Variant calling comparison CASAVA1.8 and GATK

Denis C. Bauer, 2011 .

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

Denis C. Bauer, Aidan R. O’Brien, Laurence O. W. Wilson, 2018, Scientific Reports.

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression

Denis C. Bauer, Timothy J. Peters, S. Clark, 2019, Scientific Reports.

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

Martin S. Taylor, Denis C. Bauer, Ariel S. Schwartz, 2009, Nature Genetics.

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

Denis C. Bauer, Aidan R. O’Brien, Gaetan Burgio, 2020, Briefings Bioinform..

Interacting with Genomic Data: Clinician Requirements and Prototype Structure

Melissa Martyn, Clara Gaff, Dana Bradford, 2017, HIC.

Cpipe: a shared variant detection pipeline designed for diagnostic settings

Denis C. Bauer, N. Thorne, A. Oshlack, 2015, Genome Medicine.

TRIBES: A user-friendly pipeline for relatedness detection and disease gene discovery

Denis C. Bauer, L. Henden, K. Williams, 2019, bioRxiv.