Search Results - "Bauer, Denis C."

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

“…Precise genomic modification using prime editing (PE) holds enormous potential for research and clinical applications. In this study, we generated all-in-one…”
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A comparative study of techniques for differential expression analysis on RNA-Seq data 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

“…Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in…”
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Predicting CRISPR-Cas12a guide efficiency for targeting using machine learning by O'Brien, Aidan, Bauer, Denis C, Burgio, Gaetan

“…Genome editing through the development of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)–Cas technology has revolutionized many fields in…”
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Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data by Buske, Fabian A, Bauer, Denis C, Mattick, John S, Bailey, Timothy L

“…Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand in its major groove. This sequence-specific process…”
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The Current State and Future of CRISPR-Cas9 gRNA Design Tools by Wilson, Laurence O W, O'Brien, Aidan R, Bauer, Denis C

“…Recent years have seen the development of computational tools to assist researchers in performing CRISPR-Cas9 experiment optimally. More specifically, these…”
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Blue: correcting sequencing errors using consensus and context by Greenfield, Paul, Duesing, Konsta, Papanicolaou, Alexie, Bauer, Denis C

“…Bioinformatics tools, such as assemblers and aligners, are expected to produce more accurate results when given better quality sequence data as their starting…”
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Evaluation of computational programs to predict HLA genotypes from genomic sequencing data by Bauer, Denis C, Zadoorian, Armella, Wilson, Laurence O W, Thorne, Natalie P

“…Abstract Motivation Despite being essential for numerous clinical and research applications, high-resolution human leukocyte antigen (HLA) typing remains…”
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Assigning roles to DNA regulatory motifs using comparative genomics by Buske, Fabian A., Bodén, Mikael, Bauer, Denis C., Bailey, Timothy L.

“…Motivation: Transcription factors (TFs) are crucial during the lifetime of the cell. Their functional roles are defined by the genes they regulate. Uncovering…”
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Novel Alzheimer’s disease genes and epistasis identified using machine learning GWAS platform by Lundberg, Mischa, Sng, Letitia M. F., Szul, Piotr, Dunne, Rob, Bayat, Arash, Burnham, Samantha C., Bauer, Denis C., Twine, Natalie A.

“…Alzheimer’s disease (AD) is a complex genetic disease, and variants identified through genome-wide association studies (GWAS) explain only part of its…”
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Fast and accurate exhaustive higher-order epistasis search with BitEpi by Bayat, Arash, Hosking, Brendan, Jain, Yatish, Hosking, Cameron, Kodikara, Milindi, Reti, Daniel, Twine, Natalie A., Bauer, Denis C.

“…Complex genetic diseases may be modulated by a large number of epistatic interactions affecting a polygenic phenotype. Identifying these interactions is…”
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The inequity of targeted cystic fibrosis reproductive carrier screening tests in Australia 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

“…Objective European and Australian guidelines for cystic fibrosis (CF) reproductive carrier screening recommend testing a small number of high frequency CF…”
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Evolutionary Insights from Association Rule Mining of Co-Occurring Mutations in Influenza Hemagglutinin and Neuraminidase by Galeone, Valentina, Lee, Carol, Monaghan, Michael T, Bauer, Denis C, Wilson, Laurence O W

“…Seasonal influenza viruses continuously evolve via antigenic drift. This leads to recurring epidemics, globally significant mortality rates, and the need for…”
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Adenosine monophosphate deaminase 3 activation shortens erythrocyte half-life and provides malaria resistance in mice by Hortle, Elinor, Nijagal, Brunda, Bauer, Denis C., Jensen, Lora M., Ahn, Seong Beom, Cockburn, Ian A., Lampkin, Shelley, Tull, Dedreia, McConville, Malcolm J., McMorran, Brendan J., Foote, Simon J., Burgio, Gaetan

“…The factors that determine red blood cell (RBC) lifespan and the rate of RBC aging have not been fully elucidated. In several genetic conditions, including…”
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Cpipe: a shared variant detection pipeline designed for diagnostic settings 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, Taylor, Graham, Gaff, Clara, Oshlack, Alicia, Thorne, Natalie P

“…The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines…”
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VARSCOT: variant-aware detection and scoring enables sensitive and personalized off-target detection for CRISPR-Cas9 by Wilson, Laurence O W, Hetzel, Sara, Pockrandt, Christopher, Reinert, Knut, Bauer, Denis C

“…Natural variations in a genome can drastically alter the CRISPR-Cas9 off-target landscape by creating or removing sites. Despite the resulting potential…”
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Genome-wide analysis of chemically induced mutations in mouse in phenotype-driven screens by Bauer, Denis C, McMorran, Brendan J, Foote, Simon J, Burgio, Gaetan

“…N-ethyl-N-nitrosourea (ENU) mutagen has become the method of choice for inducing random mutations for forward genetics applications. However, distinguishing…”
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AAVolve: Concatenated long-read deep sequencing enables whole capsid tracking during shuffled AAV library selection by Scott, Suzanne, Westhaus, Adrian, Nazareth, Deborah, Cabanes-Creus, Marti, Navarro, Renina Gale, Chandra, Deborah, Zhu, Erhua, Venkateswaran, Aravind, Alexander, Ian E., Bauer, Denis C., Wilson, Laurence O.W., Lisowski, Leszek

“…Gene therapies using recombinant adeno-associated virus (AAV) vectors have demonstrated considerable clinical success in the treatment of genetic disorders…”
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Genetic Analysis of Tryptophan Metabolism Genes in Sporadic Amyotrophic Lateral Sclerosis 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

“…The essential amino acid tryptophan (TRP) is the initiating metabolite of the kynurenine pathway (KP), which can be upregulated by inflammatory conditions in…”
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Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach by Dunne, Robert, Reguant, Roc, Ramarao-Milne, Priya, Szul, Piotr, Sng, Letitia M.F., Lundberg, Mischa, Twine, Natalie A., Bauer, Denis C.

“…Random forests (RFs) are a widely used modelling tool capable of feature selection via a variable importance measure (VIM), however, a threshold is needed to…”
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Synsor: a tool for alignment-free detection of engineered DNA sequences by Tay, Aidan P, Didi, Kieran, Wickramarachchi, Anuradha, Bauer, Denis C, Wilson, Laurence O W, Maselko, Maciej

“…DNA sequences of nearly any desired composition, length, and function can be synthesized to alter the biology of an organism for purposes ranging from the…”
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