Search Results - Chunlin Xiao

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  1. 1
    Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms

    Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms by Thérese Sørlie, Yulei Wang, Chunlin Xiao, Hilde Johnsen, Bjørn Naume, Raymond R. Samaha, Anne‐Lise Børresen‐Dale

    Published 2006
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  2. 2
    The 1000 Genomes Project: data management and community access

    The 1000 Genomes Project: data management and community access by Laura Clarke, Xiangqun Zheng-Bradley, Richard Smith, Eugene Kulesha, Chunlin Xiao, Iliana Toneva, Brendan Vaughan, Don Preuss, Rasko Leinonen, Martin Shumway, Stephen T. Sherry, Paul Flicek

    Published 2012
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  3. 3
    Similarities and differences between variants called with human reference genome HG19 or HG38

    Similarities and differences between variants called with human reference genome HG19 or HG38 by Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong

    Published 2019
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  4. 4
    Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials

    Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials by Justin M. Zook, Jennifer McDaniel, Hemang Parikh, Haynes Heaton, Sean A. Irvine, Len Trigg, Rebecca Truty, Cory Y. McLean, Francisco M. De La Vega, Chunlin Xiao, Stephen T. Sherry, Marc Salit

    Published 2018
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  5. 5
    An open resource for accurately benchmarking small variant and reference calls

    An open resource for accurately benchmarking small variant and reference calls by Justin M. Zook, Jennifer McDaniel, Nathan D. Olson, Justin Wagner, Hemang Parikh, Haynes Heaton, Sean A. Irvine, Len Trigg, Rebecca Truty, Cory Y. McLean, Francisco M. De La Vega, Chunlin Xiao, Stephen T. Sherry, Marc Salit

    Published 2019
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  6. 6
    A diploid assembly-based benchmark for variants in the major histocompatibility complex

    A diploid assembly-based benchmark for variants in the major histocompatibility complex by Chen-Shan Chin, Justin Wagner, Qiandong Zeng, Erik Garrison, Shilpa Garg, Arkarachai Fungtammasan, Mikko Rautiainen, Sergey Aganezov, Melanie Kirsche, Samantha Zarate, Michael C. Schatz, Chunlin Xiao, William J. Rowell, Charles Markello, Jesse Farek, Fritz J. Sedlazeck, Vikas Bansal, Byunggil Yoo, Neil Miller, Xin Zhou, Andrew Carroll, Álvaro Martínez Barrio, Marc Salit, Tobias Marschall, Alexander Dilthey, Justin M. Zook

    Published 2020
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  7. 7
    Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome

    Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome by Daniall Masood, Luyao Ren, Cu Nguyen, Francesco Brundu, Lily Zheng, Yongmei Zhao, Erich Jaeger, Yong Li, Seong Won, Aaron R. Halpern, Sean Truong, Michael J. Virata, Chunhua Yan, Qingrong Chen, Andy Wing Chun Pang, R. Alberto, Chunlin Xiao, Zhaowei Yang, Wanqiu Chen, Charles Wang, F Richardson Cross, Severine Catreux, Leming Shi, Julia A. Beaver, Wenming Xiao, Daoud Meerzaman

    Published 2024
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  8. 8
    Small variant benchmark from a complete assembly of X and Y chromosomes

    Small variant benchmark from a complete assembly of X and Y chromosomes by Justin Wagner, Nathan D. Olson, Jennifer McDaniel, Lindsay Harris, Brendan J. Pinto, David Jáspez, Adrián Muñoz‐Barrera, Luis A. Rubio‐Rodríguez, José M. Lorenzo-Salazar, Carlos Flores, Sayed Mohammad Ebrahim Sahraeian, Giuseppe Narzisi, Marta Byrska-Bishop, Uday S. Evani, Chunlin Xiao, Juniper A. Lake, Peter Fontana, Craig S. Greenberg, Donald Freed, Mohammed Faizal Eeman Mootor, Paul C. Boutros, Lisa Murray, Kishwar Shafin, Andrew Carroll, Fritz J. Sedlazeck, Melissa A. Wilson, Justin M. Zook

    Published 2025
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  9. 9
    A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures

    A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures by Andrew J. Sharp, Heather C. Mefford, Kelly Li, Carl Baker, Cindy Skinner, Roger E. Stevenson, Richard J. Schroer, Francesca Novara, Manuela De Gregori, Roberto Ciccone, Adam Broomer, Iris Casuga, Yu Wang, Chunlin Xiao, Cátálin Bárbácioru, Giorgio Gimelli, Bernardo Dalla Bernardina, Claudia Torniero, Roberto Giorda, Regina Regan, Victoria Murday, Sahar Mansour, Marco Fichera, Lucia Castiglia, Pinella Failla, Mario Ventura, Zhaoshi Jiang, Gregory M. Cooper, Samantha J.L. Knight, Corrado Romano, Orsetta Zuffardi, Caifu Chen, Charles E. Schwartz, Evan E. Eichler

    Published 2008
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  10. 10
    Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study

    Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study by Yongmei Zhao, Li Tai Fang, Tsai-Wei Shen, Sulbha Choudhari, Keyur Talsania, Xiongfong Chen, Jyoti Shetty, Yuliya Kriga, Bao Tran, Bin Zhu, Zhong Chen, Wanqiu Chen, Charles Wang, Erich Jaeger, Daoud Meerzaman, Charles Lu, Kenneth B. Idler, Luyao Ren, Yuanting Zheng, Leming Shi, Virginie Petitjean, Marc Sultan, Tiffany Hung, Eric Peters, Jir̆ı́ Drábek, Petr Vojta, Roberta Maestro, Daniela Gasparotto, Sulev Kõks, Ene Reimann, Andreas Scherer, Jessica Nordlund, Ulrika Liljedahl, Jonathan Foox, Christopher E. Mason, Chunlin Xiao, Huixiao Hong, Wenming Xiao

    Published 2021
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  11. 11
    A complete reference genome improves analysis of human genetic variation

    A complete reference genome improves analysis of human genetic variation by Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D. Olson, Michael Sauria, Mitchell R. Vollger, Arang Rhie, Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey Rosenfeld, Benedict Paten, Ryan M. Layer, Chen-Shan Chin, Fritz J. Sedlazeck, Nancy F. Hansen, Danny E. Miller, Adam M. Phillippy, Karen H. Miga, Rajiv C. McCoy, Megan Y. Dennis, Justin M. Zook, Michael C. Schatz

    Published 2021
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  12. 12
    A complete reference genome improves analysis of human genetic variation

    A complete reference genome improves analysis of human genetic variation by Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D. Olson, Michael Sauria, Mitchell R. Vollger, Arang Rhie, Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey Rosenfeld, Benedict Paten, Ryan M. Layer, Chen-Shan Chin, Fritz J. Sedlazeck, Nancy F. Hansen, Danny E. Miller, Adam M. Phillippy, Karen H. Miga, Rajiv C. McCoy, Megan Y. Dennis, Justin M. Zook, Michael C. Schatz

    Published 2022
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  13. 13
    Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

    Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies by Keyur Talsania, Tsai-Wei Shen, Xiongfong Chen, Erich Jaeger, Zhipan Li, Zhong Chen, Wanqiu Chen, Bao Tran, Rebecca Kusko, Limin Wang, Andy Wing Chun Pang, Zhaowei Yang, Sulbha Choudhari, Michael Colgan, Li Tai Fang, Andrew Carroll, Jyoti Shetty, Yuliya Kriga, Oksana German, Tatyana I. Smirnova, Tiantain Liu, Jing Li, Ben Kellman, Karl Hong, Alex Hastie, Aparna Natarajan, Ali Moshrefi, Anastasiya Granat, Tiffany Truong, Robin G. Bombardi, Veronnica Mankinen, Daoud Meerzaman, Christopher E. Mason, Jack Collins, Eric Stahlberg, Chunlin Xiao, Charles Wang, Wenming Xiao, Yongmei Zhao

    Published 2022
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  14. 14
    Curated variation benchmarks for challenging medically relevant autosomal genes

    Curated variation benchmarks for challenging medically relevant autosomal genes by Justin Wagner, Nathan D. Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M. Wenger, William J. Rowell, Ziad Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E. Miller, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz‐Barrera, Luis A. Rubio‐Rodríguez, Carlos Flores, Giuseppe Narzisi, Uday S. Evani, Wayne E. Clarke, Joyce Lee, Christopher E. Mason, Stephen E. Lincoln, Karen H. Miga, Mark Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M. Zook, Fritz J. Sedlazeck

    Published 2022
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  15. 15
    Benchmarking challenging small variants with linked and long reads

    Benchmarking challenging small variants with linked and long reads by Justin Wagner, Nathan D. Olson, Lindsay Harris, Ziad Khan, Jesse Farek, Medhat Mahmoud, Ana Stanković, Vladimir Kovačević, Byunggil Yoo, Neil Miller, Jeffrey Rosenfeld, Bohan Ni, Samantha Zarate, Melanie Kirsche, Sergey Aganezov, Michael C. Schatz, Giuseppe Narzisi, Marta Byrska-Bishop, Wayne E. Clarke, Uday S. Evani, Charles Markello, Kishwar Shafin, Xin Zhou, Arend Sidow, Vikas Bansal, Peter Ebert, Tobias Marschall, Peter M. Lansdorp, Vincent C. T. Hanlon, Carl-Adam Mattsson, Álvaro Martínez Barrio, Ian T. Fiddes, Chunlin Xiao, Arkarachai Fungtammasan, Chen-Shan Chin, Aaron M. Wenger, William J. Rowell, Fritz J. Sedlazeck, Andrew Carroll, Marc Salit, Justin M. Zook

    Published 2022
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  16. 16
    High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

    High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios by Marta Byrska-Bishop, Uday S. Evani, Xuefang Zhao, Anna O. Basile, Haley Abel, Allison Regier, André Corvelo, Wayne E. Clarke, Rajeeva Musunuri, Kshithija Nagulapalli, Susan Fairley, Alexi Runnels, Lara Winterkorn, Ernesto Lowy, Paul Flicek, Søren Germer, Harrison Brand, Ira M. Hall, Michael E. Talkowski, Giuseppe Narzisi, Michael C. Zody, Evan E. Eichler, Jan O. Korbel, Charles Lee, Tobias Marschall, Scott E. Devine, William T. Harvey, Weichen Zhou, Ryan E. Mills, Tobias Rausch, Sushant Kumar, Can Alkan, Fereydoun Hormozdiari, Zechen Chong, Yu Chen, Xiaofei Yang, Jiadong Lin, Mark Gerstein, Kai Ye, Qihui Zhu, Feyza Yilmaz, Chunlin Xiao

    Published 2022
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  17. 17
    Benchmarking challenging small variants with linked and long reads

    Benchmarking challenging small variants with linked and long reads by Justin Wagner, Nathan D. Olson, Lindsay Harris, Jennifer McDaniel, Ziad Khan, Jesse Farek, Medhat Mahmoud, Ana Stanković, Vladimir Kovačević, Byunggil Yoo, Neil Miller, Jeffrey Rosenfeld, Bohan Ni, Samantha Zarate, Melanie Kirsche, Sergey Aganezov, Michael C. Schatz, Giuseppe Narzisi, Marta Byrska-Bishop, Wayne E. Clarke, Uday S. Evani, Charles Markello, Kishwar Shafin, Xin Zhou, Arend Sidow, Vikas Bansal, Peter Ebert, Tobias Marschall, Peter M. Lansdorp, Vincent C. T. Hanlon, Carl-Adam Mattsson, Álvaro Martínez Barrio, Ian T. Fiddes, Chunlin Xiao, Arkarachai Fungtammasan, Chen-Shan Chin, Aaron M. Wenger, William J. Rowell, Fritz J. Sedlazeck, Andrew Carroll, Marc Salit, Justin M. Zook

    Published 2020
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  18. 18
    Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

    Assessing reproducibility of inherited variants detected with short-read whole genome sequencing by Bohu Pan, Luyao Ren, Vitor Onuchic, Meijian Guan, Rebecca Kusko, Steve Bruinsma, Len Trigg, Andreas Scherer, Baitang Ning, Chaoyang Zhang, Christine Glidewell-Kenney, Chunlin Xiao, Eric Donaldson, Fritz J. Sedlazeck, Gary P. Schroth, Gökhan Yavaş, Haiying Grunenwald, Haodong Chen, Heather Meinholz, Joe Meehan, Jing Wang, Jingcheng Yang, Jonathan Foox, Jun Shang, Kelci Miclaus, Lianhua Dong, Leming Shi, Marghoob Mohiyuddin, Mehdi Pirooznia, Ping Gong, Rooz Golshani, Russ Wolfinger, Samir Lababidi, Sayed Mohammad Ebrahim Sahraeian, Stephen T. Sherry, Tao Han, Tao Chen, Tieliu Shi, Wanwan Hou, Weigong Ge, Wen Zou, Wenjing Guo, Wenjun Bao, Wenzhong Xiao, Xiaohui Fan, Yoichi Gondo, Ying Yu, Yongmei Zhao, Zhenqiang Su, Zhichao Liu, Weida Tong, Wenming Xiao, Justin M. Zook, Yuanting Zheng, Huixiao Hong

    Published 2022
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  19. 19
    A robust benchmark for germline structural variant detection

    A robust benchmark for germline structural variant detection by Justin M. Zook, Nancy F. Hansen, Nathan D. Olson, Lesley M. Chapman, James C. Mullikin, Chunlin Xiao, Stephen T. Sherry, Sergey Koren, Adam M. Phillippy, Paul C. Boutros, Sayed Mohammad Ebrahim Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E. Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T. Fiddes, Álvaro Martínez Barrio, Jeremiah A. Wala, Andrew Carroll, Noushin Ghaffari, Oscar L. Rodriguez, Ali Bashir, Shaun D. Jackman, John J. Farrell, Aaron M. Wenger, Can Alkan, Arda Söylev, Michael C. Schatz, Shilpa Garg, George M. Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C. English, Jeffrey Rosenfeld, Weichen Zhou, Ryan E. Mills, Jay M. Sage, Jennifer R. Davis, Michael D. Kaiser, John S. Oliver, Anthony P. Catalano, Mark Chaisson, Noah Spies, Fritz J. Sedlazeck, Marc Salit

    Published 2019
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  20. 20
    Extensive sequencing of seven human genomes to characterize benchmark reference materials

    Extensive sequencing of seven human genomes to characterize benchmark reference materials by Justin M. Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E. Mason, Noah Alexander, Elizabeth Hénaff, Alexa B. R. McIntyre, Dhruva Chandramohan, Feng Chen, Erich Jaeger, Ali Moshrefi, Khoa Pham, William Stedman, Tiffany Y Liang, Michael Saghbini, Željko Džakula, Alex Hastie, Han Cao, Gintaras Deikus, Eric E. Schadt, Robert Sebra, Ali Bashir, Rebecca Truty, Christopher Chang, Natali Gulbahce, Keyan Zhao, Srinka Ghosh, Fiona Hyland, Yutao Fu, Mark Chaisson, Chunlin Xiao, Jonathan Trow, Stephen T. Sherry, Alexander Wait Zaranek, Mad Price Ball, Jason Bobe, Preston W. Estep, George M. Church, Patrick Marks, Sofia Kyriazopoulou-Panagiotopoulou, Grace Zheng, Michael Schnall-Levin, Heather Ordonez, Patrice A. Mudivarti, Kristina Giorda, Ying Sheng, Karoline Bjarnesdatter Rypdal, Marc Salit

    Published 2016
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