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BEATRICE: Bayesian fine-mapping from summary data using deep variational inference.
Published in:
Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae590
By:
- Ghosal, Sayan;
- Schatz, Michael C;
- Venkataraman, Archana
Publication type:
Article
SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.60681
By:
- Choi, Charlotte P.;
- Tay, Rebecca J.;
- Starostik, Margaret R.;
- Suhua Feng;
- Moresco, James J.;
- Montgomery, Brooke E.;
- Xu, Emily;
- Hammonds, Maya A.;
- Schatz, Michael C.;
- Montgomery, Taiowa A.;
- Yates III, John R.;
- Jacobsen, Steven E.;
- Kim, John K.
Publication type:
Article
The human origin recognition complex is essential for pre-RC assembly, mitosis, and maintenance of nuclear structure.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.61797
By:
- Hsiang-Chen Chou;
- Bhalla, Kuhulika;
- Demerdesh, Osama E. L.;
- Klingbeil, Olaf;
- Hanington, Kaarina;
- Aganezov, Sergey;
- Andrews, Peter;
- Alsudani, Habeeb;
- Chang, Kenneth;
- Vakoc, Christopher R.;
- Schatz, Michael C.;
- McCombie, W. Richard;
- Stillman, Bruce
Publication type:
Article
TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24− cancer cells.
Published in:
eLife, 2017, p. 1, doi. 10.7554/eLife.21615
By:
- Pal, Debjani;
- Pertot, Anja;
- Shirole, Nitin H.;
- Yao, Zhan;
- Anaparthy, Naishitha;
- Garvin, Tyler;
- Cox, Hilary;
- Chang, Kenneth;
- Rollins, Fred;
- Kendall, Jude;
- Edwards, Leyla;
- Singh, Vijay A;
- Stone, Gary C.;
- Schatz, Michael C.;
- Hicks, James;
- Hannon, Gregory J.;
- Sordella, Raffaella
Publication type:
Article
Artificial Intelligence and Cardiovascular Genetics.
Published in:
Life (2075-1729), 2022, v. 12, n. 2, p. N.PAG, doi. 10.3390/life12020279
By:
- Krittanawong, Chayakrit;
- Johnson, Kipp W.;
- Choi, Edward;
- Kaplin, Scott;
- Venner, Eric;
- Murugan, Mullai;
- Wang, Zhen;
- Glicksberg, Benjamin S.;
- Amos, Christopher I.;
- Schatz, Michael C.;
- Tang, W. H. Wilson
Publication type:
Article
Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud.
Published in:
Frontiers in Plant Science, 2020, p. 1, doi. 10.3389/fpls.2020.00289
By:
- Wang, Liya;
- Lu, Zhenyuan;
- delaBastide, Melissa;
- Van Buren, Peter;
- Wang, Xiaofei;
- Ghiban, Cornel;
- Regulski, Michael;
- Drenkow, Jorg;
- Xu, Xiaosa;
- Ortiz-Ramirez, Carlos;
- Marco, Cristina F.;
- Goodwin, Sara;
- Dobin, Alexander;
- Birnbaum, Kenneth D.;
- Jackson, David P.;
- Martienssen, Robert A.;
- McCombie, William R.;
- Micklos, David A.;
- Schatz, Michael C.;
- Ware, Doreen H.
Publication type:
Article
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.
Published in:
Nature Biotechnology, 2021, v. 39, n. 4, p. 431, doi. 10.1038/s41587-020-0731-9
By:
- Kovaka, Sam;
- Fan, Yunfan;
- Ni, Bohan;
- Timp, Winston;
- Schatz, Michael C.
Publication type:
Article
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Published in:
Nature Biotechnology, 2019, v. 37, n. 10, p. 1155, doi. 10.1038/s41587-019-0217-9
By:
- 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
Publication type:
Article
Hybrid error correction and de novo assembly of single-molecule sequencing reads.
Published in:
Nature Biotechnology, 2012, v. 30, n. 7, p. 693, doi. 10.1038/nbt.2280
By:
- Koren, Sergey;
- Schatz, Michael C;
- Walenz, Brian P;
- Martin, Jeffrey;
- Howard, Jason T;
- Ganapathy, Ganeshkumar;
- Wang, Zhong;
- Rasko, David A;
- McCombie, W Richard;
- Jarvis, Erich D;
- Phillippy, Adam M
Publication type:
Article
Cloud computing and the DNA data race.
Published in:
2010
By:
- Schatz, Michael C.;
- Langmead, Ben;
- Salzberg, Steven L.
Publication type:
Opinion
Interactive analysis and assessment of single-cell copy-number variations.
Published in:
Nature Methods, 2015, v. 12, n. 11, p. 1058, doi. 10.1038/nmeth.3578
By:
- Garvin, Tyler;
- Aboukhalil, Robert;
- Kendall, Jude;
- Baslan, Timour;
- Atwal, Gurinder S;
- Hicks, James;
- Wigler, Michael;
- Schatz, Michael C
Publication type:
Article
Accurate de novo and transmitted indel detection in exome-capture data using microassembly.
Published in:
Nature Methods, 2014, v. 11, n. 10, p. 1033, doi. 10.1038/nmeth.3069
By:
- Narzisi, Giuseppe;
- O'Rawe, Jason A;
- Iossifov, Ivan;
- Fang, Han;
- Lee, Yoon-ha;
- Wang, Zihua;
- Wu, Yiyang;
- Lyon, Gholson J;
- Wigler, Michael;
- Schatz, Michael C
Publication type:
Article
ModDotPlot—rapid and interactive visualization of tandem repeats.
Published in:
Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae493
By:
- Sweeten, Alexander P;
- Schatz, Michael C;
- Phillippy, Adam M
Publication type:
Article
Sapling: accelerating suffix array queries with learned data models.
Published in:
Bioinformatics, 2021, v. 37, n. 6, p. 744, doi. 10.1093/bioinformatics/btaa911
By:
- Kirsche, Melanie;
- Das, Arun;
- Schatz, Michael C
Publication type:
Article
Ribbon: intuitive visualization for complex genomic variation.
Published in:
Bioinformatics, 2021, v. 37, n. 3, p. 413, doi. 10.1093/bioinformatics/btaa680
By:
- Nattestad, Maria;
- Aboukhalil, Robert;
- Chin, Chen-Shan;
- Schatz, Michael C
Publication type:
Article
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.
Published in:
Briefings in Bioinformatics, 2013, v. 14, n. 2, p. 213, doi. 10.1093/bib/bbr074
By:
- Schatz, Michael C.;
- Phillippy, Adam M.;
- Sommer, Daniel D.;
- Delcher, Arthur L.;
- Puiu, Daniela;
- Narzisi, Giuseppe;
- Salzberg, Steven L.;
- Pop, Mihai
Publication type:
Article
Parliament2: Accurate structural variant calling at scale.
Published in:
GigaScience, 2020, v. 9, n. 12, p. 1, doi. 10.1093/gigascience/giaa145
By:
- Zarate, Samantha;
- Carroll, Andrew;
- Mahmoud, Medhat;
- Krasheninina, Olga;
- Jun, Goo;
- Salerno, William J;
- Schatz, Michael C;
- Boerwinkle, Eric;
- Gibbs, Richard A;
- Sedlazeck, Fritz J
Publication type:
Article
iGenomics: Comprehensive DNA sequence analysis on your Smartphone.
Published in:
GigaScience, 2020, v. 9, n. 12, p. 1, doi. 10.1093/gigascience/giaa138
By:
- Palatnick, Aspyn;
- Zhou, Bin;
- Ghedin, Elodie;
- Schatz, Michael C
Publication type:
Article
16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model.
Published in:
GigaScience, 2017, v. 6, n. 7, p. 1, doi. 10.1093/gigascience/gix045
By:
- Ruibang Luo;
- Schatz, Michael C.;
- Salzberg, Steven L.
Publication type:
Article
Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish.
Published in:
Molecular Ecology, 2019, v. 28, n. 6, p. 1491, doi. 10.1111/mec.14969
By:
- Dennenmoser, Stefan;
- Sedlazeck, Fritz J.;
- Schatz, Michael C.;
- Altmüller, Janine;
- Zytnicki, Matthias;
- Nolte, Arne W.
Publication type:
Article
An anchored chromosome‐scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids.
Published in:
Plant Genome, 2021, v. 14, n. 2, p. 1, doi. 10.1002/tpg2.20101
By:
- Hulse‐Kemp, Amanda M;
- Bostan, Hamed;
- Chen, Shiyu;
- Ashrafi, Hamid;
- Stoffel, Kevin;
- Sanseverino, Walter;
- Li, Linzhou;
- Cheng, Shifeng;
- Schatz, Michael C.;
- Garvin, Tyler;
- du Toit, Lindsey J.;
- Tseng, Elizabeth;
- Chin, Jason;
- Iorizzo, Massimo;
- Van Deynze, Allen
Publication type:
Article
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02714-x
By:
- Hunt, Martin;
- Letcher, Brice;
- Malone, Kerri M.;
- Nguyen, Giang;
- Hall, Michael B.;
- Colquhoun, Rachel M.;
- Lima, Leandro;
- Schatz, Michael C.;
- Ramakrishnan, Srividya;
- Iqbal, Zamin
Publication type:
Article
Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy.
Published in:
BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05389-8
By:
- Guerler, Aysam;
- Baker, Dannon;
- van den Beek, Marius;
- Gruening, Bjoern;
- Bouvier, Dave;
- Coraor, Nate;
- Shank, Stephen D.;
- Zehr, Jordan D.;
- Schatz, Michael C.;
- Nekrutenko, Anton
Publication type:
Article
A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor.
Published in:
PLoS Pathogens, 2021, v. 17, n. 4, p. 1, doi. 10.1371/journal.ppat.1009537
By:
- Vornhagen, Jay;
- Bassis, Christine M.;
- Ramakrishnan, Srividya;
- Hein, Robert;
- Mason, Sophia;
- Bergman, Yehudit;
- Sunshine, Nicole;
- Fan, Yunfan;
- Holmes, Caitlyn L.;
- Timp, Winston;
- Schatz, Michael C.;
- Young, Vincent B.;
- Simner, Patricia J.;
- Bachman, Michael A.
Publication type:
Article
Local adaptation and archaic introgression shape global diversity at human structural variant loci.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.67615
By:
- Yan, Stephanie M.;
- Sherman, Rachel M.;
- Taylor, Dylan J.;
- Nair, Divya R.;
- Bortvin, Andrew N.;
- Schatz, Michael C.;
- McCoy, Rajiv C.
Publication type:
Article
Natural Genetic Diversity in Tomato Flavor Genes.
Published in:
Frontiers in Plant Science, 2021, v. 12, p. 1, doi. 10.3389/fpls.2021.642828
By:
- Pereira, Lara;
- Sapkota, Manoj;
- Alonge, Michael;
- Zheng, Yi;
- Zhang, Youjun;
- Razifard, Hamid;
- Taitano, Nathan K.;
- Schatz, Michael C.;
- Fernie, Alisdair R.;
- Wang, Ying;
- Fei, Zhangjun;
- Caicedo, Ana L.;
- Tieman, Denise M.;
- van der Knaap, Esther
Publication type:
Article
Cell wall protein variation, break‐induced replication, and subtelomere dynamics in Candida glabrata.
Published in:
Molecular Microbiology, 2021, v. 116, n. 1, p. 260, doi. 10.1111/mmi.14707
By:
- Xu, Zhuwei;
- Green, Brian;
- Benoit, Nicole;
- Sobel, Jack D.;
- Schatz, Michael C.;
- Wheelan, Sarah;
- Cormack, Brendan P.
Publication type:
Article
A multi-task convolutional deep neural network for variant calling in single molecule sequencing.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-09025-z
By:
- Luo, Ruibang;
- Sedlazeck, Fritz J.;
- Lam, Tak-Wah;
- Schatz, Michael C.
Publication type:
Article
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99<sup>A</sup>.
Published in:
BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-204
By:
- Salzberg, Steven L.;
- Sommer, Daniel D.;
- Schatz, Michael C.;
- Phillippy, Adam M.;
- Rabinowicz, Pablo D.;
- Tsuge, Seiji;
- Furutani, Ayako;
- Ochiai, Hirokazu;
- Delcher, Arthur L.;
- Kelley, David;
- Madupu, Ramana;
- Puiu, Daniela;
- Radune, Diana;
- Shumway, Martin;
- Trapnell, Cole;
- Aparna, Gudlur;
- Jha, Gopaljee;
- Pandey, Alok;
- Patil, Prabhu B.;
- Ishihara, Hiromichi
Publication type:
Article
Assembly complexity of prokaryotic genomes using short reads.
Published in:
BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-21
By:
- Kingsford, Carl;
- Schatz, Michael C;
- Pop, Mihai
Publication type:
Article
High-throughput sequence alignment using Graphics Processing Units.
Published in:
BMC Bioinformatics, 2007, v. 8, p. 474, doi. 10.1186/1471-2105-8-474
By:
- Schatz, Michael C.;
- Trapnell, Cole;
- Delcher, Arthur L.;
- Varshney, Amitabh
Publication type:
Article
Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome.
Published in:
Plant Cell, 2023, v. 35, n. 1, p. 351, doi. 10.1093/plcell/koac305
By:
- He, Jia;
- Alonge, Michael;
- Ramakrishnan, Srividya;
- Benoit, Matthias;
- Soyk, Sebastian;
- Reem, Nathan T;
- Hendelman, Anat;
- Van Eck, Joyce;
- Schatz, Michael C;
- Lippman, Zachary B
Publication type:
Article
Concerning the eXclusion in human genomics: the choice of sex chromosome representation in the human genome drastically affects the number of identified variants.
Published in:
G3: Genes | Genomes | Genetics, 2023, v. 13, n. 10, p. 1, doi. 10.1093/g3journal/jkad169
By:
- Pinto, Brendan J.;
- O'Connor, Brian;
- Schatz, Michael C.;
- Zarate, Samantha;
- Wilson, Melissa A.
Publication type:
Article
Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats.
Published in:
Genome Biology & Evolution, 2023, v. 15, n. 9, p. 1, doi. 10.1093/gbe/evad148
By:
- Scheben, Armin;
- Ramos, Olivia Mendivil;
- Kramer, Melissa;
- Goodwin, Sara;
- Oppenheim, Sara;
- Becker, Daniel J;
- Schatz, Michael C;
- Simmons, Nancy B;
- Siepel, Adam;
- McCombie, W Richard
Publication type:
Article
Recovering rearranged cancer chromosomes from karyotype graphs.
Published in:
BMC Bioinformatics, 2019, v. 20, p. 1, doi. 10.1186/s12859-019-3208-4
By:
- Aganezov, Sergey;
- Zban, Ilya;
- Aksenov, Vitaly;
- Alexeev, Nikita;
- Schatz, Michael C.
Publication type:
Article
Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius.
Published in:
Nature Communications, 2016, v. 7, n. 2, p. 10164, doi. 10.1038/ncomms10164
By:
- Rosenfeld, Jeffrey A.;
- Reeves, Darryl;
- Brugler, Mercer R.;
- Narechania, Apurva;
- Simon, Sabrina;
- Durrett, Russell;
- Foox, Jonathan;
- Shianna, Kevin;
- Schatz, Michael C.;
- Gandara, Jorge;
- Afshinnekoo, Ebrahim;
- Lam, Ernest T.;
- Hastie, Alex R.;
- Chan, Saki;
- Cao, Han;
- Saghbini, Michael;
- Kentsis, Alex;
- Planet, Paul J.;
- Kholodovych, Vladyslav;
- Tessler, Michael
Publication type:
Article
Characterization of large-scale genomic differences in the first complete human genome.
Published in:
Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02995-w
By:
- Yang, Xiangyu;
- Wang, Xuankai;
- Zou, Yawen;
- Zhang, Shilong;
- Xia, Manying;
- Fu, Lianting;
- Vollger, Mitchell R.;
- Chen, Nae-Chyun;
- Taylor, Dylan J.;
- Harvey, William T.;
- Logsdon, Glennis A.;
- Meng, Dan;
- Shi, Junfeng;
- McCoy, Rajiv C.;
- Schatz, Michael C.;
- Li, Weidong;
- Eichler, Evan E.;
- Lu, Qing;
- Mao, Yafei
Publication type:
Article
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02823-7
By:
- Alonge, Michael;
- Lebeigle, Ludivine;
- Kirsche, Melanie;
- Jenike, Katie;
- Ou, Shujun;
- Aganezov, Sergey;
- Wang, Xingang;
- Lippman, Zachary B.;
- Schatz, Michael C.;
- Soyk, Sebastian
Publication type:
Article
Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.
Published in:
Genome Biology, 2015, v. 16, p. 1, doi. 10.1186/s13059-015-0803-1
By:
- Smolka, Moritz;
- Rescheneder, Philipp;
- Schatz, Michael C.;
- von Haeseler, Arndt;
- Sedlazeck, Fritz J.
Publication type:
Article
Metassembler: merging and optimizing de novo genome assemblies.
Published in:
Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0764-4
By:
- Wences, Alejandro Hernandez;
- Schatz, Michael C.
Publication type:
Article
Extending reference assembly models.
Published in:
Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0587-3
By:
- Church, Deanna M.;
- Schneider, Valerie A.;
- Steinberg, Karyn Meltz;
- Schatz, Michael C.;
- Quinlan, Aaron R.;
- Chen-Shan Chin;
- Kitts, Paul A.;
- Aken, Bronwen;
- Marth, Gabor T.;
- Hoffman, Michael M.;
- Herrero, Javier;
- Zepeda Mendoza, M. Lisandra;
- Durbin, Richard;
- Flicek, Paul
Publication type:
Article
Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.
Published in:
Genome Biology, 2014, v. 15, n. 11, p. 1, doi. 10.1186/s13059-014-0506-z
By:
- Schatz, Michael C.;
- Maron, Lyza G.;
- Stein, Joshua C.;
- Wences, Alejandro Hernandez;
- Gurtowski, James;
- Biggers, Eric;
- Lee, Hayan;
- Kramer, Melissa;
- Antoniou, Eric;
- Ghiban, Elena;
- Wright, Mark H.;
- Jer-ming Chia;
- Ware, Doreen;
- McCouch, Susan R.;
- McCombie, W. Richard
Publication type:
Article
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).
Published in:
Genome Biology, 2013, v. 14, n. 5, p. 1, doi. 10.1186/gb-2013-14-5-r41
By:
- Ray Ming;
- Van Buren, Robert;
- Yanling Liu;
- Mei Yang;
- Yuepeng Han;
- Lei-Ting Li;
- Qiong Zhang;
- Min-Jeong Kim;
- Schatz, Michael C.;
- Campbell, Michael;
- Jingping Li;
- Bowers, John E.;
- Haibao Tang;
- Lyons, Eric;
- Ferguson, Ann A.;
- Narzisi, Giuseppe;
- Nelson, David R.;
- Blaby-Haas, Crysten E.;
- Gschwend, Andrea R.;
- Yuannian Jiao
Publication type:
Article
The advantages of SMRT sequencing
Published in:
Genome Biology, 2013, v. 14, n. 7, p. 405, doi. 10.1186/gb-2013-14-6-405
By:
- Roberts, Richard J;
- Carneiro, Mauricio O;
- Schatz, Michael C
Publication type:
Article
The DNA60IFX contest.
Published in:
Genome Biology, 2013, v. 14, n. 6, p. 1, doi. 10.1186/gb-2013-14-6-124
By:
- Schatz, Michael C.;
- Taylor, James;
- Schelhorn, Sven-Eric
Publication type:
Article
Sixty years of genome biology.
Published in:
Genome Biology, 2013, v. 14, n. 4, p. 113, doi. 10.1186/gb-2013-14-4-113
By:
- Doolittle, W Ford;
- Fraser, Peter;
- Gerstein, Mark B;
- Graveley, Brenton R;
- Henikoff, Steven;
- Huttenhower, Curtis;
- Oshlack, Alicia;
- Ponting, Chris P;
- Rinn, John L;
- Schatz, Michael C;
- Ule, Jernej;
- Weigel, Detlef;
- Weinstock, George M
Publication type:
Article
The advantages of SMRT sequencing.
Published in:
2013
By:
- Roberts, Richard J;
- Carneiro, Mauricio O;
- Schatz, Michael C
Publication type:
Letter
Computational thinking in the era of big data biology.
Published in:
Genome Biology, 2012, v. 13, n. 11, p. 177, doi. 10.1186/gb-2012-13-11-177
By:
- Schatz, Michael C
Publication type:
Article
Current challenges in de novo plant genome sequencing and assembly.
Published in:
Genome Biology, 2012, v. 13, n. 4, p. 243, doi. 10.1186/gb-2012-13-4-243
By:
- Schatz, Michael C.;
- Witkowski, Jan;
- McCombie, W. Richard
Publication type:
Article
Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome.
Published in:
Genome Biology & Evolution, 2022, v. 14, n. 5, p. 1, doi. 10.1093/gbe/evac059
By:
- Fields, Peter D.;
- Waneka, Gus;
- Naish, Matthew;
- Schatz, Michael C.;
- Henderson, Ian R.;
- Sloan, Daniel B.
Publication type:
Article

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