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Start Over Author "Levy, Shawn" Journal nature biotechnology
8 results on '"Levy, Shawn"'

1. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Arslan, Sinan, primary, Garcia, Francisco J., additional, Guo, Minghao, additional, Kellinger, Matthew W., additional, Kruglyak, Semyon, additional, LeVieux, Jake A., additional, Mah, Adeline H., additional, Wang, Haosen, additional, Zhao, Junhua, additional, Zhou, Chunhong, additional, Altomare, Andrew, additional, Bailey, John, additional, Byrne, Matthew B., additional, Chang, Chiting, additional, Chen, Steve X., additional, Cho, Byungrae, additional, Dennler, Claudia N., additional, Dien, Vivian T., additional, Fuller, Derek, additional, Kelley, Ryan, additional, Khandan, Omid, additional, Klein, Michael G., additional, Kim, Michael, additional, Lajoie, Bryan R., additional, Lin, Bill, additional, Liu, Yu, additional, Lopez, Tyler, additional, Mains, Peter T., additional, Price, Andrew D., additional, Robertson, Samantha R., additional, Taylor-Weiner, Hermes, additional, Tippana, Ramreddy, additional, Tomaney, Austin B., additional, Zhang, Su, additional, Abtahi, Minna, additional, Ambroso, Mark R., additional, Bajari, Rosita, additional, Bellizzi, Ava M., additional, Benitez, Chris B., additional, Berard, Daniel R., additional, Berti, Lorenzo, additional, Blease, Kelly N., additional, Blum, Angela P., additional, Boddicker, Andrew M., additional, Bondar, Leo, additional, Brown, Chris, additional, Bui, Chris A., additional, Calleja-Aguirre, Juan, additional, Cappa, Kevin, additional, Chan, Joshua, additional, Chang, Victor W., additional, Charov, Katherine, additional, Chen, Xiyi, additional, Constandse, Rodger M., additional, Damron, Weston, additional, Dawood, Mariam, additional, DeBuono, Nicole, additional, Dimalanta, John D., additional, Edoli, Laure, additional, Elango, Keerthana, additional, Faustino, Nikka, additional, Feng, Chao, additional, Ferrari, Matthew, additional, Frankie, Keith, additional, Fries, Adam, additional, Galloway, Anne, additional, Gavrila, Vlad, additional, Gemmen, Gregory J., additional, Ghadiali, James, additional, Ghorbani, Arash, additional, Goddard, Logan A., additional, Guetter, Adriana Roginski, additional, Hendricks, Garren L., additional, Hentschel, Jendrik, additional, Honigfort, Daniel J., additional, Hsieh, Yun-Ting, additional, Hwang Fu, Yu-Hsien, additional, Im, Scott K., additional, Jin, Chaoyi, additional, Kabu, Shradha, additional, Kincade, Daniel E., additional, Levy, Shawn, additional, Li, Yu, additional, Liang, Vincent K., additional, Light, William H., additional, Lipsher, Jonathan B., additional, Liu, Tsung-li, additional, Long, Grace, additional, Ma, Rui, additional, Mailloux, John M., additional, Mandla, Kyle A., additional, Martinez, Anyssa R., additional, Mass, Max, additional, McKean, Daniel T., additional, Meron, Michael, additional, Miller, Edmund A., additional, Moh, Celyne S., additional, Moore, Rachel K., additional, Moreno, Juan, additional, Neysmith, Jordan M., additional, Niman, Cassandra S., additional, Nunez, Jesus M., additional, Ojeda, Micah T., additional, Ortiz, Sara Espinosa, additional, Owens, Jenna, additional, Piland, Geoffrey, additional, Proctor, Daniel J., additional, Purba, Josua B., additional, Ray, Michael, additional, Rong, Daisong, additional, Saade, Virginia M., additional, Saha, Sanchari, additional, Tomas, Gustav Santo, additional, Scheidler, Nicholas, additional, Sirajudeen, Luqmanal H., additional, Snow, Samantha, additional, Stengel, Gudrun, additional, Stinson, Ryan, additional, Stone, Michael J., additional, Sundseth, Keoni J., additional, Thai, Eileen, additional, Thompson, Connor J., additional, Tjioe, Marco, additional, Trejo, Christy L., additional, Trieger, Greg, additional, Truong, Diane Ni, additional, Tse, Ben, additional, Voiles, Benjamin, additional, Vuong, Henry, additional, Wong, Jennifer C., additional, Wu, Chiung-Ting, additional, Yu, Hua, additional, Yu, Yingxian, additional, Yu, Ming, additional, Zhang, Xi, additional, Zhao, Da, additional, Zheng, Genhua, additional, He, Molly, additional, and Previte, Michael, additional

Published
2023
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2. Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Author

Foox, Jonathan, primary, Tighe, Scott W., additional, Nicolet, Charles M., additional, Zook, Justin M., additional, Byrska-Bishop, Marta, additional, Clarke, Wayne E., additional, Khayat, Michael M., additional, Mahmoud, Medhat, additional, Laaguiby, Phoebe K., additional, Herbert, Zachary T., additional, Warner, Derek, additional, Grills, George S., additional, Jen, Jin, additional, Levy, Shawn, additional, Xiang, Jenny, additional, Alonso, Alicia, additional, Zhao, Xia, additional, Zhang, Wenwei, additional, Teng, Fei, additional, Zhao, Yonggang, additional, Lu, Haorong, additional, Schroth, Gary P., additional, Narzisi, Giuseppe, additional, Farmerie, William, additional, Sedlazeck, Fritz J., additional, Baldwin, Don A., additional, and Mason, Christopher E., additional

Published
2021
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3. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Author

Foox, Jonathan, primary, Tighe, Scott W., additional, Nicolet, Charles M., additional, Zook, Justin M., additional, Byrska-Bishop, Marta, additional, Clarke, Wayne E., additional, Khayat, Michael M., additional, Mahmoud, Medhat, additional, Laaguiby, Phoebe K., additional, Herbert, Zachary T., additional, Warner, Derek, additional, Grills, George S., additional, Jen, Jin, additional, Levy, Shawn, additional, Xiang, Jenny, additional, Alonso, Alicia, additional, Zhao, Xia, additional, Zhang, Wenwei, additional, Teng, Fei, additional, Zhao, Yonggang, additional, Lu, Haorong, additional, Schroth, Gary P., additional, Narzisi, Giuseppe, additional, Farmerie, William, additional, Sedlazeck, Fritz J., additional, Baldwin, Don A., additional, and Mason, Christopher E., additional

Published
2021
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4. The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing

Author

MacKay, Matthew J., primary, Hooker, Anna C., additional, Afshinnekoo, Ebrahim, additional, Salit, Marc, additional, Kelly, Jason, additional, Feldstein, Jonathan V., additional, Haft, Nick, additional, Schenkel, Doug, additional, Nambi, Subhalaxmi, additional, Cai, Yizhi, additional, Zhang, Feng, additional, Church, George, additional, Dai, Junbiao, additional, Wang, Cliff L., additional, Levy, Shawn, additional, Huber, Jeff, additional, Ji, Hanlee P., additional, Kriegel, Alison, additional, Wyllie, Anne L., additional, and Mason, Christopher E., additional

Published
2020
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5. Erratum: Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

Author

Li, Sheng, primary, Tighe, Scott W, additional, Nicolet, Charles M, additional, Grove, Deborah, additional, Levy, Shawn, additional, Farmerie, William, additional, Viale, Agnes, additional, Wright, Chris, additional, Schweitzer, Peter A, additional, Gao, Yuan, additional, Kim, Dewey, additional, Boland, Joe, additional, Hicks, Belynda, additional, Kim, Ryan, additional, Chhangawala, Sagar, additional, Jafari, Nadereh, additional, Raghavachari, Nalini, additional, Gandara, Jorge, additional, Garcia-Reyero, Natàlia, additional, Hendrickson, Cynthia, additional, Roberson, David, additional, Rosenfeld, Jeffrey, additional, Smith, Todd, additional, Underwood, Jason G, additional, Wang, May, additional, Zumbo, Paul, additional, Baldwin, Don A, additional, Grills, George S, additional, and Mason, Christopher E, additional

Published
2014
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6. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

Author

Li, Sheng, primary, Tighe, Scott W, additional, Nicolet, Charles M, additional, Grove, Deborah, additional, Levy, Shawn, additional, Farmerie, William, additional, Viale, Agnes, additional, Wright, Chris, additional, Schweitzer, Peter A, additional, Gao, Yuan, additional, Kim, Dewey, additional, Boland, Joe, additional, Hicks, Belynda, additional, Kim, Ryan, additional, Chhangawala, Sagar, additional, Jafari, Nadereh, additional, Raghavachari, Nalini, additional, Gandara, Jorge, additional, Garcia-Reyero, Natàlia, additional, Hendrickson, Cynthia, additional, Roberson, David, additional, Rosenfeld, Jeffrey A, additional, Smith, Todd, additional, Underwood, Jason G, additional, Wang, May, additional, Zumbo, Paul, additional, Baldwin, Don A, additional, Grills, George S, additional, and Mason, Christopher E, additional

Published
2014
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7. Sequencing by avidity enables high accuracy with low reagent consumption.

Author

Arslan S, Garcia FJ, Guo M, Kellinger MW, Kruglyak S, LeVieux JA, Mah AH, Wang H, Zhao J, Zhou C, Altomare A, Bailey J, Byrne MB, Chang C, Chen SX, Cho B, Dennler CN, Dien VT, Fuller D, Kelley R, Khandan O, Klein MG, Kim M, Lajoie BR, Lin B, Liu Y, Lopez T, Mains PT, Price AD, Robertson SR, Taylor-Weiner H, Tippana R, Tomaney AB, Zhang S, Abtahi M, Ambroso MR, Bajari R, Bellizzi AM, Benitez CB, Berard DR, Berti L, Blease KN, Blum AP, Boddicker AM, Bondar L, Brown C, Bui CA, Calleja-Aguirre J, Cappa K, Chan J, Chang VW, Charov K, Chen X, Constandse RM, Damron W, Dawood M, DeBuono N, Dimalanta JD, Edoli L, Elango K, Faustino N, Feng C, Ferrari M, Frankie K, Fries A, Galloway A, Gavrila V, Gemmen GJ, Ghadiali J, Ghorbani A, Goddard LA, Guetter AR, Hendricks GL, Hentschel J, Honigfort DJ, Hsieh YT, Hwang Fu YH, Im SK, Jin C, Kabu S, Kincade DE, Levy S, Li Y, Liang VK, Light WH, Lipsher JB, Liu TL, Long G, Ma R, Mailloux JM, Mandla KA, Martinez AR, Mass M, McKean DT, Meron M, Miller EA, Moh CS, Moore RK, Moreno J, Neysmith JM, Niman CS, Nunez JM, Ojeda MT, Ortiz SE, Owens J, Piland G, Proctor DJ, Purba JB, Ray M, Rong D, Saade VM, Saha S, Tomas GS, Scheidler N, Sirajudeen LH, Snow S, Stengel G, Stinson R, Stone MJ, Sundseth KJ, Thai E, Thompson CJ, Tjioe M, Trejo CL, Trieger G, Truong DN, Tse B, Voiles B, Vuong H, Wong JC, Wu CT, Yu H, Yu Y, Yu M, Zhang X, Zhao D, Zheng G, He M, and Previte M

Subjects
DNA Replication, Base Pairing, Polymers, Nucleotides genetics, Nucleotides chemistry, DNA genetics, DNA chemistry
Abstract

We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of stepping along a DNA template and that of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase-polymer-nucleotide complexes bound to clonal copies of DNA targets. These polymer-nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar and yield negligible dissociation rates. Avidity sequencing achieves high accuracy, with 96.2% and 85.4% of base calls having an average of one error per 1,000 and 10,000 base pairs, respectively. We show that the average error rate of avidity sequencing remained stable following a long homopolymer., (© 2023. The Author(s).)

Published
2024
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8. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Author

Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, and Slikker W Jr

Subjects
Equipment Design, Equipment Failure Analysis, Gene Expression Profiling methods, Quality Control, Reproducibility of Results, Sensitivity and Specificity, United States, Gene Expression Profiling instrumentation, Oligonucleotide Array Sequence Analysis instrumentation, Quality Assurance, Health Care methods
Abstract

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.

Published
2006
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