VCF-kit: assorted utilities for the variant call format by Cook, Daniel E, Andersen, Erik C

Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans by Kim, Chuna, Kim, Jun, Kim, Sunghyun, Cook, Daniel E., Evans, Kathryn S., Andersen, Erik C., Lee, Junho

Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations by Crombie, Tim A, Zdraljevic, Stefan, Cook, Daniel E, Tanny, Robyn E, Brady, Shannon C, Wang, Ye, Evans, Kathryn S, Hahnel, Steffen, Lee, Daehan, Rodriguez, Briana C, Zhang, Gaotian, van der Zwagg, Joost, Kiontke, Karin, Andersen, Erik C

Natural variation in a single amino acid substitution underlies physiological responses to topoisomerase II poisons by Zdraljevic, Stefan, Strand, Christine, Seidel, Hannah S., Cook, Daniel E., Doench, John G., Andersen, Erik C.

Discovery of genomic intervals that underlie nematode responses to benzimidazoles by Zamanian, Mostafa, Cook, Daniel E., Zdraljevic, Stefan, Brady, Shannon C., Lee, Daehan, Lee, Junho, Andersen, Erik C.

Accurate human genome analysis with element avidity sequencing by 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

easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application by Di Bernardo, Matteo, Crombie, Timothy A., Cook, Daniel E., Andersen, Erik C.

CeNDR, the Caenorhabditis elegans natural diversity resource by Cook, Daniel E., Zdraljevic, Stefan, Roberts, Joshua P., Andersen, Erik C.

A draft human pangenome reference by Liao, Wen-Wei, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cook, Daniel E., Cook-Deegan, Robert M., Diekhans, Mark, Ebert, Peter, Fedrigo, Olivier, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A., Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Koenig, Barbara A., Korbel, Jan O., Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D., Popejoy, Alice B., Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M. D., Zimin, Aleksey V., Bourque, Guillaume, Chaisson, Mark J. P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Wang, Ting, Miga, Karen H., Garrison, Erik, Marschall, Tobias, Hall, Ira M., Li, Heng, Paten, Benedict

DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer by 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

Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance by Webster, Amy K, Hung, Anthony, Moore, Brad T, Guzman, Ryan, Jordan, James M, Kaplan, Rebecca E W, Hibshman, Jonathan D, Tanny, Robyn E, Cook, Daniel E, Andersen, Erik, Baugh, L Ryan

Increased mutation and gene conversion within human segmental duplications by Vollger, Mitchell R., Dishuck, Philip C., Harvey, William T., DeWitt, William S., Guitart, Xavi, Goldberg, Michael E., Rozanski, Allison N., Lucas, Julian, Asri, Mobin, Munson, Katherine M., Lewis, Alexandra P., Hoekzema, Kendra, Logsdon, Glennis A., Porubsky, David, Paten, Benedict, Harris, Kelley, Hsieh, PingHsun, Eichler, Evan E.

Glial expression of a steroidogenic enzyme underlies natural variation in hitchhiking behavior by Yang, Heeseung, Lee, Daehan, Kim, Heekyeong, Cook, Daniel E., Paik, Young-Ki, Andersen, Erik C., Lee, Junho

The complete sequence and comparative analysis of ape sex chromosomes by Makova, Kateryna D., Pickett, Brandon D., Harris, Robert S., Hartley, Gabrielle A., Cechova, Monika, Pal, Karol, Nurk, Sergey, Yoo, DongAhn, Li, Qiuhui, Hebbar, Prajna, McGrath, Barbara C., Antonacci, Francesca, Aubel, Margaux, Biddanda, Arjun, Borchers, Matthew, Bornberg-Bauer, Erich, Bouffard, Gerard G., Brooks, Shelise Y., Carbone, Lucia, Carrel, Laura, Carroll, Andrew, Chang, Pi-Chuan, Chin, Chen-Shan, Cook, Daniel E., Craig, Sarah J. C., de Gennaro, Luciana, Diekhans, Mark, Dutra, Amalia, Garcia, Gage H., Grady, Patrick G. S., Green, Richard E., Haddad, Diana, Hallast, Pille, Harvey, William T., Hickey, Glenn, Hillis, David A., Hoyt, Savannah J., Jeong, Hyeonsoo, Kamali, Kaivan, Pond, Sergei L. Kosakovsky, LaPolice, Troy M., Lee, Charles, Lewis, Alexandra P., Loh, Yong-Hwee E., Masterson, Patrick, McGarvey, Kelly M., McCoy, Rajiv C., Medvedev, Paul, Miga, Karen H., Munson, Katherine M., Pak, Evgenia, Paten, Benedict, Pinto, Brendan J., Potapova, Tamara, Rhie, Arang, Rocha, Joana L., Ryabov, Fedor, Ryder, Oliver A., Sacco, Samuel, Shafin, Kishwar, Shepelev, Valery A., Slon, Viviane, Solar, Steven J., Storer, Jessica M., Sudmant, Peter H., Sweetalana, Sweeten, Alex, Tassia, Michael G., Thibaud-Nissen, Françoise, Ventura, Mario, Wilson, Melissa A., Young, Alice C., Zeng, Huiqing, Zhang, Xinru, Szpiech, Zachary A., Huber, Christian D., Gerton, Jennifer L., Yi, Soojin V., Schatz, Michael C., Alexandrov, Ivan A., Koren, Sergey, O’Neill, Rachel J., Eichler, Evan E., Phillippy, Adam M.

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length by Cook, Daniel E, Zdraljevic, Stefan, Tanny, Robyn E, Seo, Beomseok, Riccardi, David D, Noble, Luke M, Rockman, Matthew V, Alkema, Mark J, Braendle, Christian, Kammenga, Jan E, Wang, John, Kruglyak, Leonid, Félix, Marie-Anne, Lee, Junho, Andersen, Erik C

A Novel Gene Underlies Bleomycin-Response Variation in Caenorhabditis elegans by Brady, Shannon C, Zdraljevic, Stefan, Bisaga, Karol W, Tanny, Robyn E, Cook, Daniel E, Lee, Daehan, Wang, Ye, Andersen, Erik C

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing by Keskus, Ayse G., Bryant, Asher, Ahmad, Tanveer, Yoo, Byunggil, Aganezov, Sergey, Goretsky, Anton, Donmez, Ataberk, Lansdon, Lisa A., Rodriguez, Isabel, Park, Jimin, Liu, Yuelin, Cui, Xiwen, Gardner, Joshua, McNulty, Brandy, Sacco, Samuel, Shetty, Jyoti, Zhao, Yongmei, Tran, Bao, Narzisi, Giuseppe, Helland, Adrienne, Cook, Daniel E., Chang, Pi-Chuan, Kolesnikov, Alexey, Carroll, Andrew, Molloy, Erin K., Bi, Chengpeng, Walter, Adam, Gibson, Margaret, Pushel, Irina, Guest, Erin, Pastinen, Tomi, Shafin, Kishwar, Miga, Karen H., Malikic, Salem, Day, Chi-Ping, Robine, Nicolas, Sahinalp, Cenk, Dean, Michael, Farooqi, Midhat S., Paten, Benedict, Kolmogorov, Mikhail

The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation by Gilbert, Kimberly J, Zdraljevic, Stefan, Cook, Daniel E, Cutter, Asher D, Andersen, Erik C, Baer, Charles F

Highly accurate assembly polishing with DeepPolisher by 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

Clonal driver neoantigen loss under EGFR TKI and immune selection pressures by Al Bakir, Maise, Reading, James L., Gamble, Samuel, Rosenthal, Rachel, Uddin, Imran, Rowan, Andrew, Przewrocka, Joanna, Rogers, Amber, Wong, Yien Ning Sophia, Bentzen, Amalie K., Veeriah, Selvaraju, Ward, Sophia, Garnett, Aaron T., Kalavakur, Paula, Martínez-Ruiz, Carlos, Puttick, Clare, Huebner, Ariana, Cook, Daniel E., Moore, David A., Abbosh, Chris, Hiley, Crispin T., Naceur-Lombardelli, Cristina, Watkins, Thomas B. K., Petkovic, Marina, Schwarz, Roland F., Gálvez-Cancino, Felipe, Litchfield, Kevin, Meldgaard, Peter, Sorensen, Boe Sandahl, Madsen, Line Bille, Jäger, Dirk, Forster, Martin D., Arkenau, Tobias, Domingo-Vila, Clara, Tree, Timothy I. M., Kadivar, Mohammad, Hadrup, Sine Reker, Chain, Benny, Quezada, Sergio A., McGranahan, Nicholas, Swanton, Charles