Search Results - "Miller, Brendan F"

Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data by Miller, Brendan F., Huang, Feiyang, Atta, Lyla, Sahoo, Arpan, Fan, Jean

“…Recent technological advancements have enabled spatially resolved transcriptomic profiling but at multi-cellular pixel resolution, thereby hindering the…”
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Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression by Huang, Di, Petrykowska, Hanna M, Miller, Brendan F, Elnitski, Laura, Ovcharenko, Ivan

“…Compared to enhancers, silencers are notably difficult to identify and validate experimentally. In search for human silencers, we utilized H3K27me3-DNase I…”
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Assessing ZNF154 methylation in patient plasma as a multicancer marker in liquid biopsies from colon, liver, ovarian and pancreatic cancer patients by Miller, Brendan F., Petrykowska, Hanna M., Elnitski, Laura

“…One epigenetic hallmark of many cancer types is differential DNA methylation occurring at multiple loci compared to normal tissue. Detection and assessment of…”
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Repair of naturally occurring mismatches can induce mutations in flanking DNA by Chen, Jia, Miller, Brendan F, Furano, Anthony V

“…'Normal' genomic DNA contains hundreds of mismatches that are generated daily by the spontaneous deamination of C (U/G) and methyl-C (T/G). Thus, a mutagenic…”
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Transient reduction of DNA methylation at the onset of meiosis in male mice by Gaysinskaya, Valeriya, Miller, Brendan F, De Luca, Chiara, van der Heijden, Godfried W, Hansen, Kasper D, Bortvin, Alex

“…Meiosis is a specialized germ cell cycle that generates haploid gametes. In the initial stage of meiosis, meiotic prophase I (MPI), homologous chromosomes pair…”
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Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities by Miller, Brendan F, Bambah-Mukku, Dhananjay, Dulac, Catherine, Zhuang, Xiaowei, Fan, Jean

“…Recent technological advances have enabled spatially resolved measurements of expression profiles for hundreds to thousands of genes in fixed tissues at…”
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The Emergence of Pan-Cancer CIMP and Its Elusive Interpretation by Miller, Brendan F, Sánchez-Vega, Francisco, Elnitski, Laura

“…Epigenetic dysregulation is recognized as a hallmark of cancer. In the last 16 years, a CpG island methylator phenotype (CIMP) has been documented in tumors…”
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SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis by Aihara, Gohta, Clifton, Kalen, Chen, Mayling, Li, Zhuoyan, Atta, Lyla, Miller, Brendan F, Satija, Rahul, Hickey, John W, Fan, Jean

“…Spatial omics data demand computational analysis but many analysis tools have computational resource requirements that increase with the number of cells…”
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Evaluating Stacked Methylation Markers for Blood-Based Multicancer Detection by Funderburk, Karen, Bang-Christensen, Sara R, Miller, Brendan F, Tan, Hua, Margolin, Gennady, Petrykowska, Hanna M, Baugher, Catherine, Farney, S Katie, Grimm, Sara A, Jameel, Nader, Holland, David O, Altman, Naomi S, Elnitski, Laura

“…The ability to detect several types of cancer using a non-invasive, blood-based test holds the potential to revolutionize oncology screening. We mined tumor…”
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Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers by Miller, Brendan F, Pisanic Ii, Thomas R, Margolin, Gennady, Petrykowska, Hanna M, Athamanolap, Pornpat, Goncearenco, Alexander, Osei-Tutu, Akosua, Annunziata, Christina M, Wang, Tza-Huei, Elnitski, Laura

“…Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based…”
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Structure-Based Mutagenesis Reveals Critical Residues in the Transferrin Receptor Participating in the Mechanism of pH-Induced Release of Iron from Human Serum Transferrin by Steere, Ashley N, Chasteen, N. Dennis, Miller, Brendan F, Smith, Valerie C, MacGillivray, Ross T. A, Mason, Anne B

“…The recent crystal structure of two monoferric human serum transferrin (FeNhTF) molecules bound to the soluble portion of the homodimeric transferrin receptor…”
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Ionic Residues of Human Serum Transferrin Affect Binding to the Transferrin Receptor and Iron Release by Steere, Ashley N, Miller, Brendan F, Roberts, Samantha E, Byrne, Shaina L, Chasteen, N. Dennis, Smith, Valerie C, MacGillivray, Ross T. A, Mason, Anne B

“…Efficient delivery of iron is critically dependent on the binding of diferric human serum transferrin (hTF) to its specific receptor (TFR) on the surface of…”
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Abstract 4666: DREAMing as a simple and low cost alternative for the assessment of methylation in ultra rare DNA by Pisanic, Thomas R., Athamanolap, Pornpat, Miller, Brendan F., Wu, Vincent, Elnitski, Laura, Wang, Tza-Huei

“…Abstract Background: Current approaches for the assessment of methylation, such as methylation-specific PCR (MSP) and next-generation bisulfite sequencing…”
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Structure-based mutagenesis reveals critical residues in the transferrin receptor participating in the mechanism of pH-induced iron release from human serum transferrin by Steere, Ashley N., Chasteen, N. Dennis, Miller, Brendan F., Smith, Valerie C., MacGillivray, Ross T.A., Mason, Anne B.

“…The recent crystal structure of two monoferric human serum transferrin (Fe N hTF) molecules bound to the soluble portion of the homodimeric transferrin…”
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