Search Results - "Gurtowski, James"

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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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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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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Genome and transcriptome of the regeneration-competent flatworm,Macrostomum lignano by Wasik, Kaja, Gurtowski, James, Zhou, Xin, Ramos, Olivia Mendivil, Delás, M. Joaquina, Battistoni, Giorgia, Demerdash, Osama El, Falciatori, Ilaria, Vizoso, Dita B., Smith, Andrew D., Ladurner, Peter, Schärer, Lukas, McCombie, W. Richard, Hannon, Gregory J., Schatz, Michael

“…The free-living flatworm,Macrostomum lignanohas an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism…”
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Hybrid assembly with long and short reads improves discovery of gene family expansions by Miller, Jason R, Zhou, Peng, Mudge, Joann, Gurtowski, James, Lee, Hayan, Ramaraj, Thiruvarangan, Walenz, Brian P, Liu, Junqi, Stupar, Robert M, Denny, Roxanne, Song, Li, Singh, Namrata, Maron, Lyza G, McCouch, Susan R, McCombie, W Richard, Schatz, Michael C, Tiffin, Peter, Young, Nevin D, Silverstein, Kevin A T

“…Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate…”
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Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano by Zhou, Xin, Battistoni, Giorgia, El Demerdash, Osama, Gurtowski, James, Wunderer, Julia, Falciatori, Ilaria, Ladurner, Peter, Schatz, Michael C, Hannon, Gregory J, Wasik, Kaja A

“…PIWI proteins and piRNA pathways are essential for transposon silencing and some aspects of gene regulation during animal germline development. In contrast to…”
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Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes by Kent, Clement F, Dey, Alivia, Patel, Harshilkumar, Tsvetkov, Nadejda, Tiwari, Tanushree, MacPhail, Victoria J, Gobeil, Yann, Harpur, Brock A, Gurtowski, James, Schatz, Michael C, Colla, Sheila R, Zayed, Amro

“…The yellow-banded bumblebee was common in North America but has recently declined and is now on the IUCN Red List of threatened species. The causes of s…”
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Antibiotic Spacer Arthroplasty for Revision MTP Arthrodesis: A Novel Means to Build the Implant: A Case Report by Bitterman, Adam, Mathew, Cristin, Patel, Milap, Gurtowski, James P

“…Metatarsophalangeal (MTP) joint osteoarthritis (OA), also known as hallux rigidus (HR), is the most common degenerative arthropathy of the foot and is often…”
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Geoseq: a tool for dissecting deep-sequencing datasets by Gurtowski, James, Cancio, Anthony, Shah, Hardik, Levovitz, Chaya, George, Ajish, Homann, Robert, Sachidanandam, Ravi

“…Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read…”
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KBase: The United States Department of Energy Systems Biology Knowledgebase by Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong

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The pineapple genome and the evolution of CAM photosynthesis by Ming, Ray, VanBuren, Robert, Wai, Ching Man, Tang, Haibao, Schatz, Michael C, Bowers, John E, Lyons, Eric, Wang, Ming-Li, Chen, Jung, Biggers, Eric, Zhang, Jisen, Huang, Lixian, Zhang, Lingmao, Miao, Wenjing, Zhang, Jian, Ye, Zhangyao, Miao, Chenyong, Lin, Zhicong, Wang, Hao, Zhou, Hongye, Yim, Won C, Priest, Henry D, Zheng, Chunfang, Woodhouse, Margaret, Edger, Patrick P, Guyot, Romain, Guo, Hao-Bo, Guo, Hong, Zheng, Guangyong, Singh, Ratnesh, Sharma, Anupma, Min, Xiangjia, Zheng, Yun, Lee, Hayan, Gurtowski, James, Sedlazeck, Fritz J, Harkess, Alex, McKain, Michael R, Liao, Zhenyang, Fang, Jingping, Liu, Juan, Zhang, Xiaodan, Zhang, Qing, Hu, Weichang, Qin, Yuan, Wang, Kai, Chen, Li-Yu, Shirley, Neil, Lin, Yann-Rong, Liu, Li-Yu, Hernandez, Alvaro G, Wright, Chris L, Bulone, Vincent, Tuskan, Gerald A, Heath, Katy, Zee, Francis, Moore, Paul H, Sunkar, Ramanjulu, Leebens-Mack, James H, Mockler, Todd, Bennetzen, Jeffrey L, Freeling, Michael, Sankoff, David, Paterson, Andrew H, Zhu, Xinguang, Yang, Xiaohan, Smith, J Andrew C, Cushman, John C, Paull, Robert E, Yu, Qingyi

“…Ray Ming, Robert Paull, Qingyi Yu and colleagues report the genome sequences of two cultivated pineapple varieties and one wild pineapple relative. Their…”
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Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae by Simner, Patricia J, Antar, Annukka A R, Hao, Stephanie, Gurtowski, James, Tamma, Pranita D, Rock, Clare, Opene, Belita N A, Tekle, Tsigereda, Carroll, Karen C, Schatz, Michael C, Timp, Winston

“…Abstract Objectives In this study, we characterize a concurrent disseminated infection with a virulent hypermucoviscous (HMV) Klebsiella pneumoniae and an…”
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Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica by Schatz, Michael C, Maron, Lyza G, Stein, Joshua C, Hernandez Wences, Alejandro, Gurtowski, James, Biggers, Eric, Lee, Hayan, Kramer, Melissa, Antoniou, Eric, Ghiban, Elena, Wright, Mark H, Chia, Jer-ming, Ware, Doreen, McCouch, Susan R, McCombie, W Richard

“…The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important…”
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Genotyping in the cloud with Crossbow by Gurtowski, James, Schatz, Michael C, Langmead, Ben

“…Crossbow is a scalable, portable, and automatic cloud computing tool for identifying SNPs from high-coverage, short-read resequencing data. It is built on…”
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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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Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis by MacColl, Elisabeth, Therkelsen, Matthew D., Sherpa, Tshering, Ellerbrock, Hannah, Johnston, Lily A., Jariwala, Ravi H., Chang, WeiShu, Gurtowski, James, Schatz, Michael C., Mozammal Hossain, M., Cassidy-Hanley, Donna M., Clark, Theodore G., Chang, Wei-Jen

“…[Display omitted] •Mitochondrial sequences can be used to characterize isolates of I. multifiliis.•At least two genetically distinct groups of I. multifiliis…”
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KBase: The United States Department of Energy Systems Biology Knowledgebase by Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong

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Answering the demands of digital genomics by Titmus, Matthew A., Gurtowski, James, Schatz, Michael C.

“…SUMMARY The continuing revolution in DNA sequencing and biological sensor technologies is driving a digital transformation to our approaches for observation,…”
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Antibiotic Spacer Arthroplasty for Revision MTP Arthrodesis: A Novel Means to Build the Implant: A Case Report by Bitterman, Adam, Mathew, Cristin, Patel, Milap, Gurtowski, James P

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Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa , document novel gene space of aus and indica by Schatz, Michael C, Maron, Lyza G, Stein, Joshua C, Wences, Alejandro, Gurtowski, James, Biggers, Eric, Lee, Hayan, Kramer, Melissa, Antoniou, Eric, Ghiban, Elena, Wright, Mark H, Chia, Jer-ming, Ware, Doreen, McCouch, Susan R, McCombie, William

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