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Your search keyword '"Cook, Daniel E."' showing total 21 results
Start Over Author "Cook, Daniel E." Publisher cold spring harbor laboratory
21 results on '"Cook, Daniel E."'

1. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Author

Keskus, Ayse, primary, Bryant, Asher, additional, Ahmad, Tanveer, additional, Yoo, Byunggil, additional, Aganezov, Sergey, additional, Goretsky, Anton, additional, Donmez, Ataberk, additional, Lansdon, Lisa A., additional, Rodriguez, Isabel, additional, Park, Jimin, additional, Liu, Yuelin, additional, Cui, Xiwen, additional, Gardner, Joshua, additional, McNulty, Brandy, additional, Sacco, Samuel, additional, Shetty, Jyoti, additional, Zhao, Yongmei, additional, Tran, Bao, additional, Narzisi, Giuseppe, additional, Helland, Adrienne, additional, Cook, Daniel E., additional, Chang, Pi-Chuan, additional, Kolesnikov, Alexey, additional, Carroll, Andrew, additional, Molloy, Erin K., additional, Pushel, Irina, additional, Guest, Erin, additional, Pastinen, Tomi, additional, Shafin, Kishwar, additional, Miga, Karen H., additional, Malikic, Salem, additional, Day, Chi-Ping, additional, Robine, Nicolas, additional, Sahinalp, Cenk, additional, Dean, Michael, additional, Farooqi, Midhat S., additional, Paten, Benedict, additional, and Kolmogorov, Mikhail, additional

Published
2024
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2. Local read haplotagging enables accurate long-read small variant calling

Author

Kolesnikov, Alexey, primary, Cook, Daniel E., additional, Nattestad, Maria, additional, Ashley, Euan A., additional, Gorzynski, John, additional, Goenka, Sneha D., additional, Jain, Miten, additional, McNulty, Brandy, additional, Miga, Karen H., additional, Paten, Benedict, additional, Chang, Pi-Chuan, additional, Carroll, Andrew, additional, and Shafin, Kishwar, additional

Published
2023
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3. Accurate human genome analysis with Element Avidity sequencing

Author

Carroll, Andrew, primary, Kolesnikov, Alexey, additional, Cook, Daniel E., additional, Brambrink, Lucas, additional, Wiseman, Kelly N., additional, Billings, Sophie M., additional, Kruglyak, Semyon, additional, Lajoie, Bryan R., additional, Zhao, June, additional, Levy, Shawn E, additional, McLean, Cory Y, additional, Shafin, Kishwar, additional, Nattestad, Maria, additional, and Chang, Pi-Chuan, additional

Published
2023
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6. Two sides to every coin: complementary introgression line populations in Caenorhabditis elegans

Author

Sterken, Mark G., primary, van Sluijs, Lisa van, additional, van Creij, Jelle W., additional, Cook, Daniel E., additional, Riksen, Joost A.G., additional, Jovic, Katharina, additional, Schouten, Jasmijn, additional, Steeghs, Maarten, additional, Wang, Yiru A., additional, Stastna, Jana J., additional, Snoek, L. Basten, additional, Harvey, Simon C., additional, and Kammenga, Jan E., additional

Published
2022
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8. Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands

Author

Crombie, Timothy A, primary, Battlay, Paul, additional, Tanny, Robyn E, additional, Evans, Kathryn S, additional, Buchanan, Claire M, additional, Cook, Daniel E, additional, Dilks, Clayton M, additional, Stinson, Loraina A, additional, Zdraljevic, Stefan, additional, Zhang, Gaotian, additional, Roberto, Nicole M, additional, Lee, Daehan, additional, Ailion, Michael, additional, Hodgins, Kathryn A, additional, and Andersen, Erik C, additional

Published
2021
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9. DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction

Author

Baid, Gunjan, primary, Cook, Daniel E., additional, Shafin, Kishwar, additional, Yun, Taedong, additional, Llinares-López, Felipe, additional, Berthet, Quentin, additional, Wenger, Aaron M., additional, Rowell, William J., additional, Nattestad, Maria, additional, Yang, Howard, additional, Kolesnikov, Alexey, additional, Töpfer, Armin, additional, Ammar, Waleed, additional, Vert, Jean-Philippe, additional, Vaswani, Ashish, additional, McLean, Cory Y., additional, Chang, Pi-Chuan, additional, and Carroll, Andrew, additional

Published
2021
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12. Balancing selection maintains hyper-divergent haplotypes inC. elegans

Author

Lee, Daehan, primary, Zdraljevic, Stefan, additional, Stevens, Lewis, additional, Wang, Ye, additional, Tanny, Robyn E., additional, Crombie, Timothy A., additional, Cook, Daniel E., additional, Webster, Amy K., additional, Chirakar, Rojin, additional, Baugh, L. Ryan, additional, Sterken, Mark G., additional, Braendle, Christian, additional, Félix, Marie-Anne, additional, Rockman, Matthew V., additional, and Andersen, Erik C., additional

Published
2020
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13. Deep sampling of HawaiianCaenorhabditis elegansreveals high genetic diversity and admixture with global populations

Author

Crombie, Timothy A., primary, Zdraljevic, Stefan, additional, Cook, Daniel E., additional, Tanny, Robyn E., additional, Brady, Shannon C., additional, Wang, Ye, additional, Evans, Kathryn S., additional, Hahnel, Steffen, additional, Lee, Daehan, additional, Rodriguez, Briana C., additional, Zhang, Gaotian, additional, van der Zwaag, Joost, additional, Kiontke, Karin C., additional, and Andersen, Erik C., additional

Published
2019
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15. Population selection and sequencing ofC. eleganswild isolates identifies a region on chromosome III affecting starvation resistance

Author

Webster, Amy K., primary, Hung, Anthony, additional, Moore, Brad T., additional, Guzman, Ryan, additional, Jordan, James M., additional, Kaplan, Rebecca E. W., additional, Hibshman, Jonathan D., additional, Tanny, Robyn E., additional, Cook, Daniel E., additional, Andersen, Erik, additional, and Ryan Baugh, L., additional

Published
2019
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16. Selection and gene flow shape niche-associated copy-number variation of pheromone receptor genes

Author

Lee, Daehan, primary, Zdraljevic, Stefan, additional, Cook, Daniel E., additional, Frézal, Lise, additional, Hsu, Jung-Chen, additional, Sterken, Mark G., additional, Riksen, Joost A.G., additional, Wang, John, additional, Kammenga, Jan E., additional, Braendle, Christian, additional, Félix, Marie-Anne, additional, Schroeder, Frank C., additional, and Andersen, Erik C., additional

Published
2019
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18. Natural variation in a single amino acid underlies cellular responses to topoisomerase II poisons

Author

Zdraljevic, Stefan, Strand, Christine, Seidel, Hannah S., Cook, Daniel E., Doench, John G., and Andersen, Erik C.

Subjects
Genetics, Genome instability, medicine.medical_specialty, Methionine, biology, ved/biology, Topoisomerase, ved/biology.organism_classification_rank.species, biology.organism_classification, Glutamine, chemistry.chemical_compound, Biochemistry, chemistry, Molecular genetics, biology.protein, medicine, Model organism, Etoposide, Caenorhabditis elegans, medicine.drug
Abstract

Many medications, including chemotherapeutics, are differentially effective from one patient to the next. Understanding the causes of these population-wide differences is a critical step towards the development of personalized treatments and improvements to existing medications. Here, we investigate natural differences in sensitivity to anti-neoplastic drugs that target topoisomerase II, using the model organismCaenorhabditis elegans. We show that wild isolates ofC. elegansvary in their sensitivity to these drugs, and we use an unbiased statistical and molecular genetics approach to demonstrate that this variation is explained by a methionine-to-glutamine substitution in topoisomerase II (TOP-2). The presence of a non-polar methionine at this residue increases hydrophobic interactions between TOP-2 and the poison etoposide, as compared to a polar glutamine. We hypothesize that this stabilizing interaction results in increased genomic instability in strains that contain a methionine residue. The residue affected by this substitution is conserved from yeast to humans and is one of the few differences between the two human topoisomerase II isoforms (methionine in hTOPIIα and glutamine in hTOPIIβ). We go on to show that this substitution influences binding and cytotoxicity of etoposide and two additional topoisomerase II poisons in human cell lines. These results explain why hTOPIIα and hTOPIIβ are differentially affected by various poisons and demonstrate the utility ofC. elegansin understanding the genetics of drug responses.

Published
2017

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