Vyzkoušejte nový nástroj s podporou AI
Summon Research Assistant
BETA
Accurate, scalable cohort variant calls using DeepVariant and GLnexus
Yun, Taedong, Li, Helen, Chang, Pi-Chuan, Lin, Michael F, Carroll, Andrew, McLean, Cory Y
Published in Bioinformatics (05.04.2021)
Published in Bioinformatics (05.04.2021)
Get full text
Journal Article
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads
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
Published in Nature methods (01.11.2021)
Published in Nature methods (01.11.2021)
Get full text
Journal Article
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
Wenger, Aaron M., Peluso, Paul, Rowell, William J., Chang, Pi-Chuan, Hall, Richard J., Concepcion, Gregory T., Ebler, Jana, Fungtammasan, Arkarachai, Kolesnikov, Alexey, Olson, Nathan D., Töpfer, Armin, Alonge, Michael, Mahmoud, Medhat, Qian, Yufeng, Chin, Chen-Shan, Phillippy, Adam M., Schatz, Michael C., Myers, Gene, DePristo, Mark A., Ruan, Jue, Marschall, Tobias, Sedlazeck, Fritz J., Zook, Justin M., Li, Heng, Koren, Sergey, Carroll, Andrew, Rank, David R., Hunkapiller, Michael W.
Published in Nature biotechnology (01.10.2019)
Published in Nature biotechnology (01.10.2019)
Get full text
Journal Article
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
Sirén, Jouni, Monlong, Jean, Chang, Xian, Novak, Adam M., Eizenga, Jordan M., Markello, Charles, Sibbesen, Jonas A., Hickey, Glenn, Chang, Pi-Chuan, Carroll, Andrew, Gupta, Namrata, Gabriel, Stacey, Blackwell, Thomas W., Ratan, Aakrosh, Taylor, Kent D., Rich, Stephen S., Rotter, Jerome I., Haussler, David, Garrison, Erik, Paten, Benedict
Published in Science (American Association for the Advancement of Science) (17.12.2021)
Published in Science (American Association for the Advancement of Science) (17.12.2021)
Get full text
Journal Article
Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting
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
Published in The New England journal of medicine (17.02.2022)
Published in The New England journal of medicine (17.02.2022)
Get full text
Journal Article
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing
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.
Published in Nature biotechnology (01.07.2022)
Published in Nature biotechnology (01.07.2022)
Get full text
Journal Article
Comparison of GATK and DeepVariant by trio sequencing
Lin, Yi-Lin, Chang, Pi-Chuan, Hsu, Ching, Hung, Miao-Zi, Chien, Yin-Hsiu, Hwu, Wuh-Liang, Lai, FeiPei, Lee, Ni-Chung
Published in Scientific reports (02.02.2022)
Published in Scientific reports (02.02.2022)
Get full text
Journal Article
Improving variant calling using population data and deep learning
Chen, Nae-Chyun, Kolesnikov, Alexey, Goel, Sidharth, Yun, Taedong, Chang, Pi-Chuan, Carroll, Andrew
Published in BMC bioinformatics (12.05.2023)
Published in BMC bioinformatics (12.05.2023)
Get full text
Journal Article
Local read haplotagging enables accurate long-read small variant calling
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
Published in Nature communications (13.07.2024)
Published in Nature communications (13.07.2024)
Get full text
Journal Article
Accurate human genome analysis with element avidity sequencing
Carroll, Andrew, Kolesnikov, Alexey, Cook, Daniel E., Brambrink, Lucas, Wiseman, Kelly N., Billings, Sophie M., Kruglyak, Semyon, Lajoie, Bryan R., Zhao, Junhua, Levy, Shawn E., McLean, Cory Y., Shafin, Kishwar, Nattestad, Maria, Chang, Pi-Chuan
Published in BMC bioinformatics (25.07.2025)
Published in BMC bioinformatics (25.07.2025)
Get full text
Journal Article
A universal SNP and small-indel variant caller using deep neural networks
Poplin, Ryan, Chang, Pi-Chuan, Alexander, David, Schwartz, Scott, Colthurst, Thomas, Ku, Alexander, Newburger, Dan, Dijamco, Jojo, Nguyen, Nam, Afshar, Pegah T, Gross, Sam S, Dorfman, Lizzie, McLean, Cory Y, DePristo, Mark A
Published in Nature biotechnology (01.11.2018)
Published in Nature biotechnology (01.11.2018)
Get full text
Journal Article
Deep learning of genomic variation and regulatory network data
Telenti, Amalio, Lippert, Christoph, Chang, Pi-Chuan, DePristo, Mark
Published in Human molecular genetics (01.05.2018)
Published in Human molecular genetics (01.05.2018)
Get full text
Journal Article
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
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
Published in Nature biotechnology (01.02.2023)
Published in Nature biotechnology (01.02.2023)
Get full text
Journal Article
Personalized pangenome references
Sirén, Jouni, Eskandar, Parsa, Ungaro, Matteo Tommaso, Hickey, Glenn, Eizenga, Jordan M., Novak, Adam M., Chang, Xian, Chang, Pi-Chuan, Kolmogorov, Mikhail, Carroll, Andrew, Monlong, Jean, Paten, Benedict
Published in Nature methods (01.11.2024)
Published in Nature methods (01.11.2024)
Get full text
Journal Article
A complete pedigree-based graph workflow for rare candidate variant analysis
Markello, Charles, Huang, Charles, Rodriguez, Alex, Carroll, Andrew, Chang, Pi-Chuan, Eizenga, Jordan, Markello, Thomas, Haussler, David, Paten, Benedict
Published in Genome research (01.05.2022)
Published in Genome research (01.05.2022)
Get full text
Journal Article
Highly accurate assembly polishing with DeepPolisher
Mastoras, Mira, Asri, Mobin, Brambrink, Lucas, Hebbar, Prajna, Kolesnikov, Alexey, Cook, Daniel E., Nattestad, Maria, Lucas, Julian, Won, Taylor S., Chang, Pi-Chuan, Carroll, Andrew, Paten, Benedict, Shafin, Kishwar
Published in Genome research (01.07.2025)
Published in Genome research (01.07.2025)
Get full text
Journal Article
The Platinum Pedigree: a long-read benchmark for genetic variants
Kronenberg, Zev, Nolan, Cillian, Porubsky, David, Mokveld, Tom, Rowell, William J., Lee, Sangjin, Dolzhenko, Egor, Chang, Pi-Chuan, Holt, James M., Saunders, Christopher T., Olson, Nathan D., Steely, Cody J., McGee, Sean, Guarracino, Andrea, Koundinya, Nidhi, Harvey, William T., Watkins, W. Scott, Munson, Katherine M., Hoekzema, Kendra, Chua, Khi Pin, Chen, Xiao, Fanslow, Cairbre, Lambert, Christine, Dashnow, Harriet, Garrison, Erik, Smith, Joshua D., Lansdorp, Peter M., Zook, Justin M., Carroll, Andrew, Jorde, Lynn B., Neklason, Deborah W., Quinlan, Aaron R., Eichler, Evan E., Eberle, Michael A.
Published in Nature methods (01.08.2025)
Published in Nature methods (01.08.2025)
Get full text
Journal Article
Enteral Access Potentially Endangers Esophageal Carcinoma Patients Under Multi-modality Therapy: A Population-based Study
HUANG, CHUN-HOU, HSIEH, TSUNG-CHENG, CHANG, BEE-SONG, WANG, TSO-FU, WU, JUNG-LUN, CHANG, PI-CHUAN, PENG, TAI-CHU
Published in Anticancer research (01.04.2019)
Published in Anticancer research (01.04.2019)
Get full text
Journal Article