Search Results - "Nattestad, Maria"

Assemblytics: a web analytics tool for the detection of variants from an assembly by Nattestad, Maria, Schatz, Michael C

“…Assemblytics is a web app for detecting and analyzing variants from a de novo genome assembly aligned to a reference genome. It incorporates a unique anchor…”
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Accurate detection of complex structural variations using single-molecule sequencing by Sedlazeck, Fritz J., Rescheneder, Philipp, Smolka, Moritz, Fang, Han, Nattestad, Maria, von Haeseler, Arndt, Schatz, Michael C.

“…Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule…”
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GenomeScope: fast reference-free genome profiling from short reads by Vurture, Gregory W, Sedlazeck, Fritz J, Nattestad, Maria, Underwood, Charles J, Fang, Han, Gurtowski, James, Schatz, Michael C

“…GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat…”
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Ribbon: intuitive visualization for complex genomic variation by Nattestad, Maria, Aboukhalil, Robert, Chin, Chen-Shan, Schatz, Michael C

“…Ribbon is an alignment visualization tool that shows how alignments are positioned within both the reference and read contexts, giving an intuitive view that…”
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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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BigTop: a three-dimensional virtual reality tool for GWAS visualization by Westreich, Samuel T, Nattestad, Maria, Meyer, Christopher

“…Genome-wide association studies (GWAS) are typically visualized using a two-dimensional Manhattan plot, displaying chromosomal location of SNPs along the…”
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Local read haplotagging enables accurate long-read small variant calling by Kolesnikov, Alexey, Cook, Daniel, Nattestad, Maria, Brambrink, Lucas, McNulty, Brandy, Gorzynski, John, Goenka, Sneha, Ashley, Euan A., Jain, Miten, Miga, Karen H., Paten, Benedict, Chang, Pi-Chuan, Carroll, Andrew, Shafin, Kishwar

“…Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical…”
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Phased diploid genome assembly with single-molecule real-time sequencing by Chin, Chen-Shan, Peluso, Paul, Sedlazeck, Fritz J, Nattestad, Maria, Concepcion, Gregory T, Clum, Alicia, Dunn, Christopher, O'Malley, Ronan, Figueroa-Balderas, Rosa, Morales-Cruz, Abraham, Cramer, Grant R, Delledonne, Massimo, Luo, Chongyuan, Ecker, Joseph R, Cantu, Dario, Rank, David R, Schatz, Michael C

“…The open-source FALCON and FALCON-Unzip software utilize long-read sequencing data to generate contiguous, accurate and phased diploid assemblies, even from…”
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Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads by Shafin, Kishwar, Pesout, Trevor, Chang, Pi-Chuan, Nattestad, Maria, Kolesnikov, Alexey, Goel, Sidharth, Baid, Gunjan, Kolmogorov, Mikhail, Eizenga, Jordan M., Miga, Karen H., Carnevali, Paolo, Jain, Miten, Carroll, Andrew, Paten, Benedict

“…Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent…”
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DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer by Baid, Gunjan, Cook, Daniel E., Shafin, Kishwar, Yun, Taedong, Llinares-López, Felipe, Berthet, Quentin, Belyaeva, Anastasiya, Töpfer, Armin, Wenger, Aaron M., Rowell, William J., Yang, Howard, Kolesnikov, Alexey, Ammar, Waleed, Vert, Jean-Philippe, Vaswani, Ashish, McLean, Cory Y., Nattestad, Maria, Chang, Pi-Chuan, Carroll, Andrew

“…Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10–25 kilobases), accurate ‘HiFi’ reads by combining serial…”
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Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting by Gorzynski, John E, Goenka, Sneha D, Shafin, Kishwar, Jensen, Tanner D, Fisk, Dianna G, Grove, Megan E, Spiteri, Elizabeth, Pesout, Trevor, Monlong, Jean, Baid, Gunjan, Bernstein, Jonathan A, Ceresnak, Scott, Chang, Pi-Chuan, Christle, Jeffrey W, Chubb, Henry, Dalton, Karen P, Dunn, Kyla, Garalde, Daniel R, Guillory, Joseph, Knowles, Joshua W, Kolesnikov, Alexey, Ma, Michael, Moscarello, Tia, Nattestad, Maria, Perez, Marco, Ruzhnikov, Maura R.Z, Samadi, Mehrzad, Setia, Ankit, Wright, Chris, Wusthoff, Courtney J, Xiong, Katherine, Zhu, Tong, Jain, Miten, Sedlazeck, Fritz J, Carroll, Andrew, Paten, Benedict, Ashley, Euan A

“…Because a genetic diagnosis can guide clinical management and improve prognosis in critically ill patients, much effort has gone into developing methods that…”
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Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing by Goenka, Sneha D., Gorzynski, John E., Shafin, Kishwar, Fisk, Dianna G., Pesout, Trevor, Jensen, Tanner D., Monlong, Jean, Chang, Pi-Chuan, Baid, Gunjan, Bernstein, Jonathan A., Christle, Jeffrey W., Dalton, Karen P., Garalde, Daniel R., Grove, Megan E., Guillory, Joseph, Kolesnikov, Alexey, Nattestad, Maria, Ruzhnikov, Maura R. Z., Samadi, Mehrzad, Sethia, Ankit, Spiteri, Elizabeth, Wright, Christopher J., Xiong, Katherine, Zhu, Tong, Jain, Miten, Sedlazeck, Fritz J., Carroll, Andrew, Paten, Benedict, Ashley, Euan A.

“…Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use…”
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The effect of α-mating factor secretion signal mutations on recombinant protein expression in Pichia pastoris by Lin-Cereghino, Geoff P., Stark, Carolyn M., Kim, Daniel, Chang, Jennifer, Shaheen, Nadia, Poerwanto, Hansel, Agari, Kimiko, Moua, Pachai, Low, Lauren K., Tran, Namphuong, Huang, Amy D., Nattestad, Maria, Oshiro, Kristin T., Chang, John William, Chavan, Archana, Tsai, Jerry W., Lin-Cereghino, Joan

“…The methylotrophic yeast, Pichia pastoris, has been genetically engineered to produce many heterologous proteins for industrial and research purposes. In order…”
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Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing by Vembar, Shruthi Sridhar, Seetin, Matthew, Lambert, Christine, Nattestad, Maria, Schatz, Michael C, Baybayan, Primo, Scherf, Artur, Smith, Melissa Laird

“…The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging…”
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Abstract 850: Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing by Nattestad, Maria, Ng, Karen, Goodwin, Sara, Baslan, Timour, Sedlazeck, Fritz, Gurtowski, James, Hutton, Elizabeth, Sundaravadanam, Yogi, Garvin, Tyler, Alford, Marley, Tseng, Elizabeth, Rescheneder, Philipp, Chin, Jason, Beck, Timothy, Kramer, Melissa, McPherson, John, Hicks, James, Schatz, Michael C., McCombie, William R.

“…Abstract Genomic instability is one of the hallmarks of cancer, leading to widespread copy number variations, chromosomal fusions, and other structural…”
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Analysis of the 5′ untranslated region (5′UTR) of the alcohol oxidase 1 (AOX1) gene in recombinant protein expression in Pichia pastoris by Staley, Chris A., Huang, Amy, Nattestad, Maria, Oshiro, Kristin T., Ray, Laura E., Mulye, Tejas, Li, Zhiguo Harry, Le, Thu, Stephens, Justin J., Gomez, Seth R., Moy, Allison D., Nguyen, Jackson C., Franz, Andreas H., Lin-Cereghino, Joan, Lin-Cereghino, Geoff P.

“…Pichia pastoris is a methylotrophic yeast that has been genetically engineered to express over one thousand heterologous proteins valued for industrial,…”
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PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions by Olson, Nathan D, Wagner, Justin, McDaniel, Jennifer, Stephens, Sarah H, Westreich, Samuel T, Prasanna, Anish G, Johanson, Elaine, Boja, Emily, Maier, Ezekiel J, Serang, Omar, Jáspez, David, Lorenzo-Salazar, José M, Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A, Flores, Carlos, Kyriakidis, Konstantinos, Malousi, Andigoni, Shafin, Kishwar, Pesout, Trevor, Jain, Miten, Paten, Benedict, Chang, Pi-Chuan, Kolesnikov, Alexey, Nattestad, Maria, Baid, Gunjan, Goel, Sidharth, Yang, Howard, Carroll, Andrew, Eveleigh, Robert, Bourgey, Mathieu, Bourque, Guillaume, Li, Gen, Ma, ChouXian, Tang, LinQi, Du, YuanPing, Zhang, ShaoWei, Morata, Jordi, Tonda, Raúl, Parra, Genís, Trotta, Jean-Rémi, Brueffer, Christian, Demirkaya-Budak, Sinem, Kabakci-Zorlu, Duygu, Turgut, Deniz, Kalay, Özem, Budak, Gungor, Narcı, Kübra, Arslan, Elif, Brown, Richard, Johnson, Ivan J, Dolgoborodov, Alexey, Semenyuk, Vladimir, Jain, Amit, Tetikol, H Serhat, Jain, Varun, Ruehle, Mike, Lajoie, Bryan, Roddey, Cooper, Catreux, Severine, Mehio, Rami, Ahsan, Mian Umair, Liu, Qian, Wang, Kai, Ebrahim Sahraeian, Sayed Mohammad, Fang, Li Tai, Mohiyuddin, Marghoob, Hung, Calvin, Jain, Chirag, Feng, Hanying, Li, Zhipan, Chen, Luoqi, Sedlazeck, Fritz J, Zook, Justin M

“…The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge…”
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Knowledge distillation for fast and accurate DNA sequence correction by Belyaeva, Anastasiya, Shor, Joel, Cook, Daniel E, Shafin, Kishwar, Liu, Daniel, Töpfer, Armin, Wenger, Aaron M, Rowell, William J, Yang, Howard, Kolesnikov, Alexey, McLean, Cory Y, Nattestad, Maria, Carroll, Andrew, Chang, Pi-Chuan

“…Learning Meaningful Representations of Life, NeurIPS 2022 workshop oral paper Accurate genome sequencing can improve our understanding of biology and the…”
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