Paragraph: a graph-based structural variant genotyper for short-read sequence data von 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

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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions von 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

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ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data von 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.

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A Poly(vinyl alcohol) Coating Method for a Tilted‐Fiber Bragg‐Grating‐Assisted Fiber Hygrometer von Dolzhenko, Egor I., Tomyshev, Kirill, Butov, Oleg V.

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A deep population reference panel of tandem repeat variation von 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

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RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci von 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

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Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions von Rajan-Babu, Indhu-Shree, Pen, Junran J., Chiu, Readman, Li, Chenkai, Mohajeri, Arezoo, Dolzhenko, Egor, Eberle, Michael A., Birol, Inanc, Friedman, Jan M.

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P819: Genome-wide resolution of highly homologous genes using long-read PacBio HiFi sequencing von 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 von 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

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TRGT-ing the dark genome to accurately characterize tandem repeats at scale

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Large scale in silico characterization of repeat expansion variation in human genomes von Fazal, Sarah, Danzi, Matt C., Cintra, Vivian P., Bis-Brewer, Dana M., Dolzhenko, Egor, Eberle, Michael A., Zuchner, Stephan

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Biogeographic conservation of the cytosine epigenome in the globally important marine, nitrogen‐fixing cyanobacterium Trichodesmium von Walworth, Nathan G., Hutchins, David A., Dolzhenko, Egor, Lee, Michael D., Fu, Feixue, Smith, Andrew D., Webb, Eric A.

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lncRNA requirements for mouse acute myeloid leukemia and normal differentiation von 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

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Genome-wide detection of tandem DNA repeats expanded in autism von 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.

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P478: Simultaneous analysis of 50+ different repeat expansions with twist target enrichment and PacBio HiFi sequencing von Han, Tina, Corbitt, Holly, Dolzhenko, Egor, Gonzaludo, Nina, Kingan, Sarah, Tung, Po-Yuan, Toro, Esteban, Locklear, Chad

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P293: Long read sequencing analysis of 120 samples with known and challenging-to-detect clinical variants von Devaney, Joseph, Noya, Jessica, Berlyoung, April, Johnson, Aaron, Spangler, Julianna, Brandon, Rhonda, Hruska, Kathleen, Lochovsky, Lucas, Dolzhenko, Egor, Chen, Xiao, Eberle, Michael, Robertson, Alexander, Kruszka, Paul, Stolovitzky, Gustavo, Newman, Scott

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STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data von Halman, Andreas, Dolzhenko, Egor, Oshlack, Alicia

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Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing von Alvarez Jerez, Pilar, Daida, Kensuke, Grenn, Francis P., Malik, Laksh, Miano-Burkhardt, Abigail, Makarious, Mary B., Ding, Jinhui, Gibbs, J. Raphael, Moore, Anni, Reed, Xylena, Nalls, Mike A., Shah, Syed, Mahmoud, Medhat, Sedlazeck, Fritz J., Dolzhenko, Egor, Park, Morgan, Iwaki, Hirotaka, Casey, Bradford, Ryten, Mina, Blauwendraat, Cornelis, Singleton, Andrew B., Billingsley, Kimberley J.

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LUCApedia: a database for the study of ancient life von Goldman, Aaron David, Bernhard, Tess M., Dolzhenko, Egor, Landweber, Laura F.

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Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study von Ibañez, Kristina, Polke, James, Hagelstrom, R Tanner, Dolzhenko, Egor, Pasko, Dorota, Thomas, Ellen Rachel Amy, Smith, Katherine R, McDonagh, Ellen M, Polychronopoulos, Dimitris, Chan, Georgia, Davison, James E, Festenstein, Richard, Fratta, Pietro, Giunti, Paola, Howard, Robin, Venkata, Laxmi, Laurá, Matilde, Morris, Huw, Robinson, Robert, Rosser, Elisabeth, Faravelli, Francesca, Schrag, Anette, Schott, Jonathan M, Wood, Nicholas W, Bourn, David, Eggleton, Kelly, Twiss, Philip, Almheiri, Ghareesa, Sheikh, Isabella, Vandrovcova, Jana, Brittain, Helen, Baple, Emma, Moutsianas, Loukas, Deshpande, Viraj, Perry, Denise L, Ajay, Subramanian S., Rajan, Vani, Oprych, Kathryn, Chinnery, Patrick F, Wilson, Gill, Ellard, Sian, Temple, I Karen, McMullan, Dom, Naresh, Kikkeri, Flinter, Frances A, Taylor, Jenny C, Greenhalgh, Lynn, Newman, William, Brennan, Paul, Sayer, John A, Raymond, F Lucy, Deans, Zandra C, Hill, Sue, Fowler, Tom, Scott, Richard H, Chinnery, Patrick F, Rendon, Augusto, Eberle, Michael A, Taft, Ryan J, Arumugam, Prabhu, Bleda, Marta, Boardman-Pretty, Freya, Boissiere, Jeanne M., Devereau, Andrew, Elgar, Greg, Foulger, Rebecca E., Furió-Tarí, Pedro, Hackett, Joanne, Hamblin, Angela, Holman, James, Hubbard, Tim J.P., Jones, Louise J., Kayikci, Melis, Lawson, Kay, Leigh, Sarah E.A., Leong, Ivonne U.S., Maleady-Crowe, Fiona, Mason, Joanne, Mueller, Michael, Murugaesu, Nirupa, Odhams, Chris A., Perez-Gil, Daniel, Pullinger, John, Rahim, Tahrima, Riesgo-Ferreiro, Pablo, Ryten, Mina, Savage, Kevin, Sawant, Kushmita, Sieghart, Alexander, Smedley, Damian, Sosinsky, Alona, Spooner, William, Stevens, Helen E., Stuckey, Alexander, Sultana, Razvan, Tregidgo, Carolyn, Walsh, Emma, Watters, Sarah A., Williams, Eleanor, Zarowiecki, Magdalena

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