Search Results - "Dolzhenko, Egor"

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments by Dolzhenko, Egor, Smith, Andrew D

“…Whole-genome bisulfite sequencing currently provides the highest-precision view of the epigenome, with quantitative information about populations of cells down…”
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Paragraph: a graph-based structural variant genotyper for short-read sequence data by Chen, Sai, Krusche, Peter, Dolzhenko, Egor, Sherman, Rachel M, Petrovski, Roman, Schlesinger, Felix, Kirsche, Melanie, Bentley, David R, Schatz, Michael C, Sedlazeck, Fritz J, Eberle, Michael A

“…Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical…”
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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions by Dolzhenko, Egor, Deshpande, Viraj, Schlesinger, Felix, Krusche, Peter, Petrovski, Roman, Chen, Sai, Emig-Agius, Dorothea, Gross, Andrew, Narzisi, Giuseppe, Bowman, Brett, Scheffler, Konrad, van Vugt, Joke J F A, French, Courtney, Sanchis-Juan, Alba, Ibáñez, Kristina, Tucci, Arianna, Lajoie, Bryan R, Veldink, Jan H, Raymond, F Lucy, Taft, Ryan J, Bentley, David R, Eberle, Michael A

“…Abstract Summary We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to…”
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Length of Uninterrupted CAG, Independent of Polyglutamine Size, Results in Increased Somatic Instability, Hastening Onset of Huntington Disease by Wright, Galen E.B., Collins, Jennifer A., Kay, Chris, McDonald, Cassandra, Dolzhenko, Egor, Xia, Qingwen, Bečanović, Kristina, Drögemöller, Britt I., Semaka, Alicia, Nguyen, Charlotte M., Trost, Brett, Richards, Fiona, Bijlsma, Emilia K., Squitieri, Ferdinando, Ross, Colin J.D., Scherer, Stephen W., Eberle, Michael A., Yuen, Ryan K.C., Hayden, Michael R.

“…Huntington disease (HD) is caused by a CAG repeat expansion in the huntingtin (HTT) gene. Although the length of this repeat is inversely correlated with age…”
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ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data by Dolzhenko, Egor, Bennett, Mark F, Richmond, Phillip A, Trost, Brett, Chen, Sai, van Vugt, Joke J F A, Nguyen, Charlotte, Narzisi, Giuseppe, Gainullin, Vladimir G, Gross, Andrew M, Lajoie, Bryan R, Taft, Ryan J, Wasserman, Wyeth W, Scherer, Stephen W, Veldink, Jan H, Bentley, David R, Yuen, Ryan K C, Bahlo, Melanie, Eberle, Michael A

“…Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods…”
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The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development by Chen, Xiao, Bracht, John R., Goldman, Aaron David, Dolzhenko, Egor, Clay, Derek M., Swart, Estienne C., Perlman, David H., Doak, Thomas G., Stuart, Andrew, Amemiya, Chris T., Sebra, Robert P., Landweber, Laura F.

“…Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This…”
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A Poly(vinyl alcohol) Coating Method for a Tilted‐Fiber Bragg‐Grating‐Assisted Fiber Hygrometer by Dolzhenko, Egor I., Tomyshev, Kirill, Butov, Oleg V.

“…A new technique of depositing a poly(vinyl alcohol) (PVA) coating with an airbrush on the cylindrical surface of an optical fiber with real‐time spectral…”
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A deep population reference panel of tandem repeat variation by Ziaei Jam, Helyaneh, Li, Yang, DeVito, Ross, Mousavi, Nima, Ma, Nichole, Lujumba, Ibra, Adam, Yagoub, Maksimov, Mikhail, Huang, Bonnie, Dolzhenko, Egor, Qiu, Yunjiang, Kakembo, Fredrick Elishama, Joseph, Habi, Onyido, Blessing, Adeyemi, Jumoke, Bakhtiari, Mehrdad, Park, Jonghun, Javadzadeh, Sara, Jjingo, Daudi, Adebiyi, Ezekiel, Bafna, Vineet, Gymrek, Melissa

“…Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep…”
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RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci by Fazal, Sarah, Danzi, Matt C, Xu, Isaac, Kobren, Shilpa Nadimpalli, Sunyaev, Shamil, Reuter, Chloe, Marwaha, Shruti, Wheeler, Matthew, Dolzhenko, Egor, Lucas, Francesca, Wuchty, Stefan, Tekin, Mustafa, Züchner, Stephan, Aguiar-Pulido, Vanessa

“…Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will…”
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Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease by Gross, Andrew M., Ajay, Subramanian S., Rajan, Vani, Brown, Carolyn, Bluske, Krista, Burns, Nicole J., Chawla, Aditi, Coffey, Alison J., Malhotra, Alka, Scocchia, Alicia, Thorpe, Erin, Dzidic, Natasa, Hovanes, Karine, Sahoo, Trilochan, Dolzhenko, Egor, Lajoie, Bryan, Khouzam, Amirah, Chowdhury, Shimul, Belmont, John, Roller, Eric, Ivakhno, Sergii, Tanner, Stephen, McEachern, Julia, Hambuch, Tina, Eberle, Michael, Hagelstrom, R. Tanner, Bentley, David R., Perry, Denise L., Taft, Ryan J.

“…Purpose Current diagnostic testing for genetic disorders involves serial use of specialized assays spanning multiple technologies. In principle, genome…”
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Molecular characterization of the transition from acute to chronic kidney injury following ischemia/reperfusion by Liu, Jing, Kumar, Sanjeev, Dolzhenko, Egor, Alvarado, Gregory F, Guo, Jinjin, Lu, Can, Chen, Yibu, Li, Meng, Dessing, Mark C, Parvez, Riana K, Cippà, Pietro E, Krautzberger, A Michaela, Saribekyan, Gohar, Smith, Andrew D, McMahon, Andrew P

“…Though an acute kidney injury (AKI) episode is associated with an increased risk of chronic kidney disease (CKD), the mechanisms determining the transition…”
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An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland by dos Santos, Camila O., Dolzhenko, Egor, Hodges, Emily, Smith, Andrew D., Hannon, Gregory J.

“…Pregnancy is the major modulator of mammary gland activity. It induces a tremendous expansion of the mammary epithelium and the generation of alveolar…”
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Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions by Rajan-Babu, Indhu-Shree, Peng, Junran J, Chiu, Readman, Li, Chenkai, Mohajeri, Arezoo, Dolzhenko, Egor, Eberle, Michael A, Birol, Inanc, Friedman, Jan M

“…Screening for short tandem repeat (STR) expansions in next-generation sequencing data can enable diagnosis, optimal clinical management/treatment, and accurate…”
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P819: Genome-wide resolution of highly homologous genes using long-read PacBio HiFi sequencing by Chen, Xiao, Dolzhenko, Egor, Farrow, Emily, Thiffault, Isabelle, Hoischen, Alexander, Pastinen, Tomi, Eberle, Michael

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REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats by Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F, Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C, Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A, Saunders, Christopher T, Scheffler, Konrad, van Vugt, Joke J F A, Zwamborn, Ramona R A J, Chong, Samuel S, Friedman, Jan M, Tucci, Arianna, Rehm, Heidi L, Eberle, Michael A

“…Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many…”
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Large scale in silico characterization of repeat expansion variation in human genomes by Fazal, Sarah, Danzi, Matt C., Cintra, Vivian P., Bis-Brewer, Dana M., Dolzhenko, Egor, Eberle, Michael A., Zuchner, Stephan

“…Significant progress has been made in elucidating single nucleotide polymorphism diversity in the human population. However, the majority of the variation…”
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Biogeographic conservation of the cytosine epigenome in the globally important marine, nitrogen‐fixing cyanobacterium Trichodesmium by Walworth, Nathan G., Hutchins, David A., Dolzhenko, Egor, Lee, Michael D., Fu, Feixue, Smith, Andrew D., Webb, Eric A.

“…Summary Cytosine methylation has been shown to regulate essential cellular processes and impact biological adaptation. Despite its evolutionary importance,…”
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lncRNA requirements for mouse acute myeloid leukemia and normal differentiation by Delás, M Joaquina, Sabin, Leah R, Dolzhenko, Egor, Knott, Simon Rv, Munera Maravilla, Ester, Jackson, Benjamin T, Wild, Sophia A, Kovacevic, Tatjana, Stork, Eva Maria, Zhou, Meng, Erard, Nicolas, Lee, Emily, Kelley, David R, Roth, Mareike, Barbosa, Inês Am, Zuber, Johannes, Rinn, John L, Smith, Andrew D, Hannon, Gregory J

“…A substantial fraction of the genome is transcribed in a cell-type-specific manner, producing long non-coding RNAs (lncRNAs), rather than protein-coding…”
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Genome-wide detection of tandem DNA repeats expanded in autism by Trost, Brett, Engchuan, Worrawat, Nguyen, Charlotte M., Thiruvahindrapuram, Bhooma, Dolzhenko, Egor, Backstrom, Ian, Mirceta, Mila, Mojarad, Bahareh A., Yin, Yue, Dov, Alona, Chandrakumar, Induja, Prasolava, Tanya, Shum, Natalie, Hamdan, Omar, Pellecchia, Giovanna, Howe, Jennifer L., Whitney, Joseph, Klee, Eric W., Baheti, Saurabh, Amaral, David G., Anagnostou, Evdokia, Elsabbagh, Mayada, Fernandez, Bridget A., Hoang, Ny, Suzanne Lewis, M. E., Liu, Xudong, Sjaarda, Calvin, Smith, Isabel M., Szatmari, Peter, Zwaigenbaum, Lonnie, Glazer, David, Hartley, Dean, Stewart, A. Keith, Eberle, Michael A., Sato, Nozomu, Pearson, Christopher E., Scherer, Stephen W., Yuen, Ryan K. C.

“…Tandem DNA repeats vary by the size and sequence of each unit (motif). When expanded, they have been associated with >40 monogenic disorders 1 . Their…”
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P478: Simultaneous analysis of 50+ different repeat expansions with twist target enrichment and PacBio HiFi sequencing by Han, Tina, Corbitt, Holly, Dolzhenko, Egor, Gonzaludo, Nina, Kingan, Sarah, Tung, Po-Yuan, Toro, Esteban, Locklear, Chad

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