Search Results - "Goodwin, Sara"

Coming of age: ten years of next-generation sequencing technologies by Goodwin, Sara, McPherson, John D., McCombie, W. Richard

“…Key Points There are two major paradigms in next-generation sequencing (NGS) technology: short-read sequencing and long-read sequencing. Short-read sequencing…”
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RaGOO: fast and accurate reference-guided scaffolding of draft genomes by Alonge, Michael, Soyk, Sebastian, Ramakrishnan, Srividya, Wang, Xingang, Goodwin, Sara, Sedlazeck, Fritz J, Lippman, Zachary B, Schatz, Michael C

“…We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve…”
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Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome by Goodwin, Sara, Gurtowski, James, Ethe-Sayers, Scott, Deshpande, Panchajanya, Schatz, Michael C, McCombie, W Richard

“…Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a…”
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Machine learning to predict occult nodal metastasis in early oral squamous cell carcinoma by Bur, Andrés M., Holcomb, Andrew, Goodwin, Sara, Woodroof, Janet, Karadaghy, Omar, Shnayder, Yelizaveta, Kakarala, Kiran, Brant, Jason, Shew, Matthew

“…•Prediction of occult nodal metastasis can be used to guide surgical treatment.•Improved predictive methods may personalize treatment of early oral…”
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Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line by Nattestad, Maria, Goodwin, Sara, Ng, Karen, Baslan, Timour, Sedlazeck, Fritz J, Rescheneder, Philipp, Garvin, Tyler, Fang, Han, Gurtowski, James, Hutton, Elizabeth, Tseng, Elizabeth, Chin, Chen-Shan, Beck, Timothy, Sundaravadanam, Yogi, Kramer, Melissa, Antoniou, Eric, McPherson, John D, Hicks, James, McCombie, W Richard, Schatz, Michael C

“…The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be…”
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Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing by Aganezov, Sergey, Goodwin, Sara, Sherman, Rachel M, Sedlazeck, Fritz J, Arun, Gayatri, Bhatia, Sonam, Lee, Isac, Kirsche, Melanie, Wappel, Robert, Kramer, Melissa, Kostroff, Karen, Spector, David L, Timp, Winston, McCombie, W Richard, Schatz, Michael C

“…Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic…”
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High resolution copy number inference in cancer using short-molecule nanopore sequencing by Baslan, Timour, Kovaka, Sam, Sedlazeck, Fritz J, Zhang, Yanming, Wappel, Robert, Tian, Sha, Lowe, Scott W, Goodwin, Sara, Schatz, Michael C

“…Abstract Genome copy number is an important source of genetic variation in health and disease. In cancer, Copy Number Alterations (CNAs) can be inferred from…”
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Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria by Hegelmeyer, Nuri K, Parkin, Lia A, Previti, Mary L, Andrade, Joshua, Utama, Raditya, Sejour, Richard J, Gardin, Justin, Muller, Stephanie, Ketchum, Steven, Yurovsky, Alisa, Futcher, Bruce, Goodwin, Sara, Ueberheide, Beatrix, Seeliger, Jessica C

“…( ) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to…”
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Transcriptional Silencing of ALDH2 Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia by Yang, Zhaolin, Wu, Xiaoli S, Wei, Yiliang, Polyanskaya, Sofya A, Iyer, Shruti V, Jung, Moonjung, Lach, Francis P, Adelman, Emmalee R, Klingbeil, Olaf, Milazzo, Joseph P, Kramer, Melissa, Demerdash, Osama E, Chang, Kenneth, Goodwin, Sara, Hodges, Emily, McCombie, W Richard, Figueroa, Maria E, Smogorzewska, Agata, Vakoc, Christopher R

“…Hundreds of genes become aberrantly silenced in acute myeloid leukemia (AML), with most of these epigenetic changes being of unknown functional consequence…”
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MinION Analysis and Reference Consortium: Phase 1 data release and analysis by Ip, Camilla L C, Loose, Matthew, Tyson, John R, de Cesare, Mariateresa, Brown, Bonnie L, Jain, Miten, Leggett, Richard M, Eccles, David A, Zalunin, Vadim, Urban, John M, Piazza, Paolo, Bowden, Rory J, Paten, Benedict, Mwaigwisya, Solomon, Batty, Elizabeth M, Simpson, Jared T, Snutch, Terrance P, Birney, Ewan, Buck, David, Goodwin, Sara, Jansen, Hans J, O'Grady, Justin, Olsen, Hugh E

“…The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale…”
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Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata by Oppenheim, Sara, Cao, Xiaolong, Rueppel, Olav, Krongdang, Sasiprapa, Phokasem, Patcharin, DeSalle, Rob, Goodwin, Sara, Xing, Jinchuan, Chantawannakul, Panuwan, Rosenfeld, Jeffrey A

“…Abstract The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently,…”
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Associations between circulating interferon and kynurenine/tryptophan pathway metabolites: support for a novel potential mechanism for cognitive dysfunction in SLE by Anderson, Erik W, Jin, Ying, Shih, Andrew, Arazi, Arnon, Goodwin, Sara, Roeser, Julien, Furie, Richard A, Aranow, Cynthia, Volpe, Bruce, Diamond, Betty, Mackay, Meggan

“…ObjectiveQuinolinic acid (QA), a kynurenine (KYN)/tryptophan (TRP) pathway metabolite, is an N-methyl-D-aspartate receptor agonist that can produce excitotoxic…”
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621 The Association of Interferon with Kynurenine/Tryptophan Pathway Activation in Systemic Lupus Erythematosus by Anderson, Erik W, Jin, Ying, Shih, Andrew, Arazi, Arnon, Goodwin, Sara, Roeser, Julien, Furie, Richard A, Aranow, Cynthia, Volpe, Bruce T, Diamond, Betty, Mackay, Meggan

“…BackgroundCognitive dysfunction (CD) is highly prevalent in systemic lupus erythematosus (SLE) with significant impact on quality of life, yet SLE-mediated…”
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Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud by Wang, Liya, Lu, Zhenyuan, delaBastide, Melissa, Van Buren, Peter, Wang, Xiaofei, Ghiban, Cornel, Regulski, Michael, Drenkow, Jorg, Xu, Xiaosa, Ortiz-Ramirez, Carlos, Marco, Cristina F, Goodwin, Sara, Dobin, Alexander, Birnbaum, Kenneth D, Jackson, David P, Martienssen, Robert A, McCombie, William R, Micklos, David A, Schatz, Michael C, Ware, Doreen H, Gingeras, Thomas R

“…MaizeCODE is a project aimed at identifying and analyzing functional elements in the maize genome. In its initial phase, MaizeCODE assayed up to five tissues…”
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Next-Generation Sequencing as Input for Chemometrics in Differential Sensing Routines by Goodwin, Sara, Gade, Alexandra M., Byrom, Michelle, Herrera, Baine, Spears, Camille, Anslyn, Eric V., Ellington, Andrew D.

“…Differential sensing (DS) methods traditionally use spatially arrayed receptors and optical signals to create score plots from multivariate data which classify…”
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Abstract 5136: Adapting long read sequencing technologies for targeted and single cell applications by Iyer, Shruti, Goodwin, Sara, McCombie, W. Richard

“…Abstract Structural variations (SV), a hallmark of genomic instability in cancer, include insertions, deletions, duplications, inversions, or translocations…”
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Abstract LB201: Understanding genetic variation in cancer using nanopore targeted sequencing by Iyer, Shruti V., Kramer, Melissa, Goodwin, Sara, McCombie, W. Richard

“…Abstract Structural variations (SV), a hallmark of genomic instability in cancer can either activate oncogenes or inactivate tumor suppressor genes. SVs tend…”
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Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding by Gladman, Nicholas, Goodwin, Sara, Chougule, Kapeel, Richard McCombie, William, Ware, Doreen

“…Whole-genome sequencing and assembly have revolutionized plant genetics and molecular biology over the last two decades. However, significant shortcomings in…”
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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato by Alonge, Michael, Wang, Xingang, Benoit, Matthias, Soyk, Sebastian, Pereira, Lara, Zhang, Lei, Suresh, Hamsini, Ramakrishnan, Srividya, Maumus, Florian, Ciren, Danielle, Levy, Yuval, Harel, Tom Hai, Shalev-Schlosser, Gili, Amsellem, Ziva, Razifard, Hamid, Caicedo, Ana L., Tieman, Denise M., Klee, Harry, Kirsche, Melanie, Aganezov, Sergey, Ranallo-Benavidez, T. Rhyker, Lemmon, Zachary H., Kim, Jennifer, Robitaille, Gina, Kramer, Melissa, Goodwin, Sara, McCombie, W. Richard, Hutton, Samuel, Van Eck, Joyce, Gillis, Jesse, Eshed, Yuval, Sedlazeck, Fritz J., van der Knaap, Esther, Schatz, Michael C., Lippman, Zachary B.

“…Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of…”
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Abstract 1360: Understanding genetic variation in cancer using targeted nanopore long read sequencing by Iyer, Shruti V., Goodwin, Sara, Kramer, Melissa, McCombie, W. Richard

“…Abstract Structural variations (SV), a hallmark of genomic instability in cancer can either activate oncogenes or inactivate tumor suppressor genes. SVs tend…”
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