Additional materials of the author at
CSHL Institutional Repository

Pinto, Brendan J, O'Connor, Brian, Schatz, Michael C, Zarate, Samantha , Wilson, Melissa A (2023) Concerning the eXclusion in human genomics: the choice of sex chromosome representation in the human genome drastically affects the number of identified variants. Hahn, M (Ed.). G3: Genes, Genomes, Genetics, 13(10) pp. jkad169.

Scheben, Armin, Mendivil Ramos, Olivia, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel J, Schatz, Michael C, Simmons, Nancy B, Siepel, Adam , McCombie, W Richard (2023) Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Pfeifer, Susanne (Ed.). Genome Biology and Evolution, 15(9)

Rhie, Arang, Nurk, Sergey, Cechova, Monika, Hoyt, Savannah J, Taylor, Dylan J, Altemose, Nicolas, Hook, Paul W, Koren, Sergey, Rautiainen, Mikko, Alexandrov, Ivan A, Allen, Jamie, Asri, Mobin, Bzikadze, Andrey V, Chen, Nae-Chyun, Chin, Chen-Shan, Diekhans, Mark, Flicek, Paul, Formenti, Giulio, Fungtammasan, Arkarachai, Garcia Giron, Carlos, Garrison, Erik, Gershman, Ariel, Gerton, Jennifer L, Grady, Patrick GS, Guarracino, Andrea, Haggerty, Leanne, Halabian, Reza, Hansen, Nancy F, Harris, Robert, Hartley, Gabrielle A, Harvey, William T, Haukness, Marina, Heinz, Jakob, Hourlier, Thibaut, Hubley, Robert M, Hunt, Sarah E, Hwang, Stephen, Jain, Miten, Kesharwani, Rupesh K, Lewis, Alexandra P, Li, Heng, Logsdon, Glennis A, Lucas, Julian K, Makalowski, Wojciech, Markovic, Christopher, Martin, Fergal J, Mc Cartney, Ann M, McCoy, Rajiv C, McDaniel, Jennifer, McNulty, Brandy M, Medvedev, Paul, Mikheenko, Alla, Munson, Katherine M, Murphy, Terence D, Olsen, Hugh E, Olson, Nathan D, Paulin, Luis F, Porubsky, David, Potapova, Tamara, Ryabov, Fedor, Salzberg, Steven L, Sauria, Michael EG, Sedlazeck, Fritz J, Shafin, Kishwar, Shepelev, Valery A, Shumate, Alaina, Storer, Jessica M, Surapaneni, Likhitha, Taravella Oill, Angela M, Thibaud-Nissen, Françoise, Timp, Winston, Tomaszkiewicz, Marta, Vollger, Mitchell R, Walenz, Brian P, Watwood, Allison C, Weissensteiner, Matthias H, Wenger, Aaron M, Wilson, Melissa A, Zarate, Samantha, Zhu, Yiming, Zook, Justin M, Eichler, Evan E, O'Neill, Rachel J, Schatz, Michael C, Miga, Karen H, Makova, Kateryna D , Phillippy, Adam M (2023) The complete sequence of a human Y chromosome. Nature, 621(7978) pp. 344-354.

Stevenson, Dennis Wm, Ramakrishnan, Srividya, Alves, Cristiane de Santis, Coelho, Laís Araujo, Kramer, Melissa, Goodwin, Sara, Ramos, Olivia Mendevil, Eshel, Gil, Sondervan, Veronica M, Frangos, Samantha, Zumajo-Cardona, Cecilia, Jenike, Katherine, Ou, Shujun, Wang, Xiaojin, Lee, Yin Peng, Loke, Stella, Rossetto, Maurizio, McPherson, Hannah, Nigris, Sebastiano, Moschin, Silvia, Little, Damon P, Katari, Manpreet S, Varala, Kranthi, Kolokotronis, Sergios-Orestis, Ambrose, Barbara, Croft, Larry J, Coruzzi, Gloria M, Schatz, Michael, McCombie, W Richard , Martienssen, Robert A (2023) The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. bioRxiv,

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 (2023) Characterization of large-scale genomic differences in the first complete human genome. Genome Biology, 24(1) pp. 157.

Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D, Rabbani, Keon, Balacco, Jennifer R, Chaisson, Mark, Cheng, Haoyu, Collins, Joanna, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, Jain, Nivesh, Johnson, Cassidy, Kim, Heebal, Lee, Chul, Marques-Bonet, Tomas, O'Toole, Brian, Rhie, Arang, Secomandi, Simona, Sozzoni, Marcella, Tilley, Tatiana, Uliano-Silva, Marcela, van den Beek, Marius, Waterhouse, Robert M, Phillippy, Adam M, Jarvis, Erich D, Schatz, Michael C, Nekrutenko, Anton , Formenti, Giulio (2023) Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.

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 (2023) Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. BMC Bioinformatics, 24(1) pp. 263.

Devos, Katrien M, Qi, Peng, Bahri, Bochra A, Gimode, Davis M, Jenike, Katharine, Manthi, Samuel J, Lule, Dagnachew, Lux, Thomas, Martinez-Bello, Liliam, Pendergast, Thomas H, Plott, Chris, Saha, Dipnarayan, Sidhu, Gurjot S, Sreedasyam, Avinash, Wang, Xuewen, Wang, Hao, Wright, Hallie, Zhao, Jianxin, Deshpande, Santosh, de Villiers, Santie, Dida, Mathews M, Grimwood, Jane, Jenkins, Jerry, Lovell, John, Mayer, Klaus FX, Mneney, Emmarold E, Ojulong, Henry F, Schatz, Michael C, Schmutz, Jeremy, Song, Bo, Tesfaye, Kassahun , Odeny, Damaris A (2023) Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nature Communications, 14(1) pp. 3694.

Hall, Jennifer L, Honeycutt, Sally, Gonzalez, Nicole, O'Donnell-Luria, Anne, Overby Taylor, Casey, Stevens, Laura, Philippakis, Anthony A , Schatz, Michael C (2023) National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space: Reaching out to Clinicians.. Circulation: Genomic and Precision Medicine, 16(3) pp. 275-276.

Simner, Patricia J, Bergman, Yehudit, Fan, Yunfan, Jacobs, Emily B, Ramakrishnan, Srividya, Lu, Jennifer, Lewis, Shawna, Hanlon, Ann, Tamma, Pranita D, Schatz, Michael C, Timp, Winston , Carroll, Karen C (2023) Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids. JAC-Antimicrobial Resistance, 5(3) pp. dlad061.

Xiang, Guanjue, He, Xi, Giardine, Belinda M, Weaver, Kathryn J, Taylor, Dylan J, McCoy, Rajiv C, Jansen, Camden, Keller, Cheryl A, Wixom, Alexander Q, Cockburn, April, Miller, Amber, Qi, Qian, He, Yanghua, Li, Yichao, Lichtenberg, Jens, Heuston, Elisabeth F, Anderson, Stacie M, Luan, Jing, Vermunt, Marit W, Yue, Feng, Sauria, Michael EG, Schatz, Michael C, Taylor, James, Göttgens, Berthold, Hughes, Jim R, Higgs, Douglas R, Weiss, Mitchell J, Cheng, Yong, Blobel, Gerd A, Bodine, David, Zhang, Yu, Li, Qunhua, Mahony, Shaun , Hardison, Ross C (2023) Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv,

Rozowsky, Joel, Gao, Jiahao, Borsari, Beatrice, Yang, Yucheng T, Galeev, Timur, Gürsoy, Gamze, Epstein, Charles B, Xiong, Kun, Xu, Jinrui, Li, Tianxiao, Liu, Jason, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Sun, Maxwell S, Wright, James, Chang, Justin, Cameron, Christopher JF, Shoresh, Noam, Gaskell, Elizabeth, Drenkow, Jorg, Adrian, Jessika, Aganezov, Sergey, Aguet, François, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo Barreto, Chee, Sora, Chhetri, Surya B, Cortez Martins, Gabriel Conte, Danyko, Cassidy, Davis, Carrie A, Farid, Daniel, Farrell, Nina P, Gabdank, Idan, Gofin, Yoel, Gorkin, David U, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin C, Issner, Robbyn, Jiang, Yunzhe, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita R, Li, Shantao, Li, Bian, Li, Xiqi, Lin, Khine Zin, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill E, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry E, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob M, Sedlazeck, Fritz J, See, Lei Hoon, Sherman, Rachel M, Shi, Xu, Shi, Minyi, Sloan, Cricket Alicia, Strattan, J Seth, Tan, Zhen, Tanaka, Forrest Y, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J Michael, Mendenhall, Eric M, Noble, William S, Weng, Zhiping, Levine, Morgan E, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard M, Snyder, Michael P, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael C, Bernstein, Bradley E, Guigó, Roderic, Gingeras, Thomas R , Gerstein, Mark (2023) The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell, 186(7) pp. 1493-1511.e40.

Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Battle, Alexis, Aganezov, Sergey , Schatz, Michael C (2023) Jasmine and Iris: population-scale structural variant comparison and analysis. Nature Methods, 20(3) pp. 408-417.

Pinto, Brendan J, O'Connor, Brian, Schatz, Michael C, Zarate, Samantha , Wilson, Melissa A (2023) Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants.

Kovaka, Sam, Ou, Shujun, Jenike, Katharine M , Schatz, Michael C (2023) Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing. Nature Methods, 20(1) pp. 12-16.

Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B, Schatz, Michael C , Soyk, Sebastian (2022) Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology, 23(1) pp. 258.

Jarvis, Erich D, Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R, Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A, Carnevali, Paolo, Chaisson, Mark JP, Chin, Chen-Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S, Fulton, Lucinda L, Garg, Shilpa, Gerton, Jennifer L, Ghurye, Jay, Granat, Anastasiya, Green, Richard E, Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B, Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O, Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W, McDaniel, Jennifer, Nie, Fan, Olsen, Hugh E, Olson, Nathan D, Pesout, Trevor, Potapova, Tamara, Puiu, Daniela, Regier, Allison, Ruan, Jue, Salzberg, Steven L, Sanders, Ashley D, Schatz, Michael C, Schmitt, Anthony, Schneider, Valerie A, Selvaraj, Siddarth, Shafin, Kishwar, Shumate, Alaina, Stitziel, Nathan O, Stober, Catherine, Torrance, James, Wagner, Justin, Wang, Jianxin, Wenger, Aaron, Xiao, Chuanle, Zimin, Aleksey V, Zhang, Guojie, Wang, Ting, Li, Heng, Garrison, Erik, Haussler, David, Hall, Ira, Zook, Justin M, Eichler, Evan E, Phillippy, Adam M, Paten, Benedict, Howe, Kerstin, Miga, Karen H , Human Pangenome Reference Consortium, (2022) Semi-automated assembly of high-quality diploid human reference genomes. Nature, 611(7936) pp. 519-531.

Das, Arun , Schatz, Michael C (2022) Sketching and sampling approaches for fast and accurate long read classification. BMC Bioinformatics, 23(1) pp. 452.

He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan T, Hendelman, Anat, Van Eck, Joyce, Schatz, Michael C , Lippman, Zachary B (2022) Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. The Plant Cell, 35(1) pp. 351-368.

Genomic Data Science Community Network, . (2022) Diversifying the genomic data science research community. Genome Research, 32(7) pp. 1231-1241.

Hunt, Martin, Letcher, Brice, Malone, Kerri M, Nguyen, Giang, Hall, Michael B, Colquhoun, Rachel M, Lima, Leandro, Schatz, Michael C, Ramakrishnan, Srividya, CRyPTIC consortium, , Iqbal, Zamin (2022) Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biology, 23(1) pp. 147.

Wagner, J, Olson, ND, Harris, L, Khan, Z, Farek, J, Mahmoud, M, Stankovic, A, Kovacevic, V, Yoo, B, Miller, N, Rosenfeld, JA, Ni, B, Zarate, S, Kirsche, M, Aganezov, S, Schatz, MC, Narzisi, G, Byrska-Bishop, M, Clarke, W, Evani, US, Markello, C, Shafin, K, Zhou, X, Sidow, A, Bansal, V, Ebert, P, Marschall, T, Lansdorp, P, Hanlon, V, Mattsson, CA, Barrio, AM, Fiddes, IT, Xiao, C, Fungtammasan, A, Chin, CS, Wenger, AM, Rowell, WJ, Sedlazeck, FJ, Carroll, A, Salit, M , Zook, JM (2022) Benchmarking challenging small variants with linked and long reads. Cell Genomics, 2(5) pp. 100128-100128.

Fields, Peter D, Waneka, Gus, Naish, Matthew, Schatz, Michael C, Henderson, Ian R , Sloan, Daniel B (2022) Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome. Slotte, Tanja (Ed.). Genome Biology and Evolution, 14(5) pp. evac059.

Galaxy Community, (2022) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.. Nucleic Acids Research,

Aganezov, Sergey, Yan, Stephanie M, Soto, Daniela C, Kirsche, Melanie, Zarate, Samantha, Avdeyev, Pavel, Taylor, Dylan J, Shafin, Kishwar, Shumate, Alaina, Xiao, Chunlin, Wagner, Justin, McDaniel, Jennifer, Olson, Nathan D, Sauria, Michael EG, Vollger, Mitchell R, Rhie, Arang, Meredith, Melissa, Martin, Skylar, Lee, Joyce, Koren, Sergey, Rosenfeld, Jeffrey A, Paten, Benedict, Layer, Ryan, Chin, Chen-Shan, Sedlazeck, Fritz J, Hansen, Nancy F, Miller, Danny E, Phillippy, Adam M, Miga, Karen H, McCoy, Rajiv C, Dennis, Megan Y, Zook, Justin M , Schatz, Michael C (2022) A complete reference genome improves analysis of human genetic variation. Science, 376(6588) pp. eabl3533.

Altemose, Nicolas, Logsdon, Glennis A, Bzikadze, Andrey V, Sidhwani, Pragya, Langley, Sasha A, Caldas, Gina V, Hoyt, Savannah J, Uralsky, Lev, Ryabov, Fedor D, Shew, Colin J, Sauria, Michael EG, Borchers, Matthew, Gershman, Ariel, Mikheenko, Alla, Shepelev, Valery A, Dvorkina, Tatiana, Kunyavskaya, Olga, Vollger, Mitchell R, Rhie, Arang, McCartney, Ann M, Asri, Mobin, Lorig-Roach, Ryan, Shafin, Kishwar, Lucas, Julian K, Aganezov, Sergey, Olson, Daniel, de Lima, Leonardo Gomes, Potapova, Tamara, Hartley, Gabrielle A, Haukness, Marina, Kerpedjiev, Peter, Gusev, Fedor, Tigyi, Kristof, Brooks, Shelise, Young, Alice, Nurk, Sergey, Koren, Sergey, Salama, Sofie R, Paten, Benedict, Rogaev, Evgeny I, Streets, Aaron, Karpen, Gary H, Dernburg, Abby F, Sullivan, Beth A, Straight, Aaron F, Wheeler, Travis J, Gerton, Jennifer L, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Dennis, Megan Y, O'Neill, Rachel J, Zook, Justin M, Schatz, Michael C, Pevzner, Pavel A, Diekhans, Mark, Langley, Charles H, Alexandrov, Ivan A , Miga, Karen H (2022) Complete genomic and epigenetic maps of human centromeres. Science, 376(6588) pp. eabl4178.

Hoyt, Savannah J, Storer, Jessica M, Hartley, Gabrielle A, Grady, Patrick GS, Gershman, Ariel, de Lima, Leonardo G, Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias, Altemose, Nicolas, Rhie, Arang, Core, Leighton J, Gerton, Jennifer L, Makalowski, Wojciech, Olson, Daniel, Rosen, Jeb, Smit, Arian FA, Straight, Aaron F, Vollger, Mitchell R, Wheeler, Travis J, Schatz, Michael C, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Miga, Karen H , O'Neill, Rachel J (2022) From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science, 376(6588) pp. eabk3112.

Nurk, Sergey, Koren, Sergey, Rhie, Arang, Rautiainen, Mikko, Bzikadze, Andrey V, Mikheenko, Alla, Vollger, Mitchell R, Altemose, Nicolas, Uralsky, Lev, Gershman, Ariel, Aganezov, Sergey, Hoyt, Savannah J, Diekhans, Mark, Logsdon, Glennis A, Alonge, Michael, Antonarakis, Stylianos E, Borchers, Matthew, Bouffard, Gerard G, Brooks, Shelise Y, Caldas, Gina V, Chen, Nae-Chyun, Cheng, Haoyu, Chin, Chen-Shan, Chow, William, de Lima, Leonardo G, Dishuck, Philip C, Durbin, Richard, Dvorkina, Tatiana, Fiddes, Ian T, Formenti, Giulio, Fulton, Robert S, Fungtammasan, Arkarachai, Garrison, Erik, Grady, Patrick GS, Graves-Lindsay, Tina A, Hall, Ira M, Hansen, Nancy F, Hartley, Gabrielle A, Haukness, Marina, Howe, Kerstin, Hunkapiller, Michael W, Jain, Chirag, Jain, Miten, Jarvis, Erich D, Kerpedjiev, Peter, Kirsche, Melanie, Kolmogorov, Mikhail, Korlach, Jonas, Kremitzki, Milinn, Li, Heng, Maduro, Valerie V, Marschall, Tobias, McCartney, Ann M, McDaniel, Jennifer, Miller, Danny E, Mullikin, James C, Myers, Eugene W, Olson, Nathan D, Paten, Benedict, Peluso, Paul, Pevzner, Pavel A, Porubsky, David, Potapova, Tamara, Rogaev, Evgeny I, Rosenfeld, Jeffrey A, Salzberg, Steven L, Schneider, Valerie A, Sedlazeck, Fritz J, Shafin, Kishwar, Shew, Colin J, Shumate, Alaina, Sims, Ying, Smit, Arian FA, Soto, Daniela C, Sović, Ivan, Storer, Jessica M, Streets, Aaron, Sullivan, Beth A, Thibaud-Nissen, Françoise, Torrance, James, Wagner, Justin, Walenz, Brian P, Wenger, Aaron, Wood, Jonathan MD, Xiao, Chunlin, Yan, Stephanie M, Young, Alice C, Zarate, Samantha, Surti, Urvashi, McCoy, Rajiv C, Dennis, Megan Y, Alexandrov, Ivan A, Gerton, Jennifer L, O'Neill, Rachel J, Timp, Winston, Zook, Justin M, Schatz, Michael C, Eichler, Evan E, Miga, Karen H , Phillippy, Adam M (2022) The complete sequence of a human genome. Science, 376(6588) pp. 44-53.

Gershman, Ariel, Sauria, Michael EG, Guitart, Xavi, Vollger, Mitchell R, Hook, Paul W, Hoyt, Savannah J, Jain, Miten, Shumate, Alaina, Razaghi, Roham, Koren, Sergey, Altemose, Nicolas, Caldas, Gina V, Logsdon, Glennis A, Rhie, Arang, Eichler, Evan E, Schatz, Michael C, O'Neill, Rachel J, Phillippy, Adam M, Miga, Karen H , Timp, Winston (2022) Epigenetic patterns in a complete human genome. Science, 376(6588) pp. eabj5089.

Gularte-Mérida, Rodrigo, Smith, Shaleigh, Bowman, Anita S, da Cruz Paula, Arnaud, Chatila, Walid, Bielski, Craig M, Vyas, Monika, Borsu, Laetitia, Zehir, Ahmet, Martelotto, Luciano G, Shia, Jinru, Yaeger, Rona, Fang, Fang, Gardner, Rui, Luo, Ruibang, Schatz, Michael C, Shen, Ronglai, Weigelt, Britta, Sánchez-Vega, Francisco, Reis-Filho, Jorge S , Hechtman, Jaclyn F (2022) Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer. JCO Precision Oncology, 6(6) pp. e2100365.

Fields, Peter D, Waneka, Gus, Naish, Matthew, Schatz, Michael C, Henderson, Ian R , Sloan, Daniel B (2022) Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome. bioRxiv,

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, WH Wilson (2022) Artificial Intelligence and Cardiovascular Genetics. Life, 12(2) pp. 279-279.

Network, The Genomic Data Science Community, Alcazar, Rosa, Alvarez, Maria, Arnold, Rachel, Ayalew, Mentewab, Best, Lyle G, Campbell, Michael C, Chowdhury, Kamal, Cox, Katherine EL, Daulton, Christina, Deng, Youping, Easter, Carla, Fuller, Karla, Hakim, Shazia Tabassum, Hoffman, Ava M, Kucher, Natalie, Lee, Andrew, Lee, Joslynn, Leek, Jeffrey T, Meller, Robert, Méndez, Loyda B, Méndez-González, Miguel P, Mosher, Stephen, Nishiguchi, Michele, Pratap, Siddharth, Rolle, Tiffany, Roy, Sourav, Saidi, Rachel, Schatz, Michael C, Sen, Shurjo, Sniezek, James, Martinez, Edu Suarez, Tan, Frederick, Vessio, Jennifer, Watson, Karriem, Westbroek, Wendy, Wilcox, Joseph , Xie, Xianfa (2022) Diversifying the Genomic Data Science Research Community.

Schatz, Michael C, Philippakis, Anthony A, Afgan, Enis, Banks, Eric, Carey, Vincent J, Carroll, Robert J, Culotti, Alessandro, Ellrott, Kyle, Goecks, Jeremy, Grossman, Robert L, Hall, Ira M, Hansen, Kasper D, Lawson, Jonathan, Leek, Jeffrey T, Luria, Anne O’Donnell, Mosher, Stephen, Morgan, Martin, Nekrutenko, Anton, O’Connor, Brian D, Osborn, Kevin, Paten, Benedict, Patterson, Candace, Tan, Frederick J, Taylor, Casey Overby, Vessio, Jennifer, Waldron, Levi, Wang, Ting, Wuichet, Kristin, Baumann, Alexander, Rula, Andrew, Kovalsy, Anton, Bernard, Clare, Caetano-Anollés, Derek, Van der Auwera, Geraldine A, Canas, Justin, Yuksel, Kaan, Herman, Kate, Taylor, M Morgan, Simeon, Marianie, Baumann, Michael, Wang, Qi, Title, Robert, Munshi, Ruchi, Chaluvadi, Sushma, Reeves, Valerie, Disman, William, Thomas, Salin, Hajian, Allie, Kiernan, Elizabeth, Gupta, Namrata, Vosburg, Trish, Geistlinger, Ludwig, Ramos, Marcel, Oh, Sehyun, Rogers, Dave, McDade, Frances, Hastie, Mim, Turaga, Nitesh, Ostrovsky, Alexander, Mahmoud, Alexandru, Baker, Dannon, Clements, Dave, Cox, Katherine EL, Suderman, Keith, Kucher, Nataliya, Golitsynskiy, Sergey, Zarate, Samantha, Wheelan, Sarah J, Kammers, Kai, Stevens, Ana, Hutter, Carolyn, Wellington, Christopher, Ghanaim, Elena M, Wiley, Ken L, Sen, Shurjo K, Di Francesco, Valentina, s Yuen, Deni, Walsh, Brian, Sargent, Luke, Jalili, Vahid, Chilton, John, Shepherd, Lori, Stubbs, BJ, O’Farrell, Ash, Vizzier, Benton A, Overbeck, Charles, Reid, Charles, Steinberg, David Charles, Sheets, Elizabeth A, Lucas, Julian, Blauvelt, Lon, Cabansay, Louise, Warren, Noah, Hannafious, Brian, Harris, Tim, Reddy, Radhika, Torstenson, Eric, Banasiewicz, M Katie, Abel, Haley J , Walker, Jason (2022) Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genomics, 2(1) pp. 100085-100085.

He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan, Hendelman, Anat, Eck, Joyce Van, Schatz, Michael , Lippman, Zachary (2022) Establishing Physalisas a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. bioRxiv,

Ou, Shujun, Collins, Tyler, Qiu, Yinjie, Seetharam, Arun, Menard, Claire, Manchanda, Nancy, Gent, Jonathan, Schatz, Michael, Anderson, Sarah, Hufford, Matthew , Hirsch, Candice (2022) Differences in activity and stability drive transposable element variation in tropical and temperate maize.

Razaghi, Roham, Hook, Paul, Ou, Shujun, Schatz, Michael, Hansen, Kasper, Jain, Miten , Timp, Winston (2022) Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering. bioRxiv,

Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary, Schatz, Michael , Soyk, Sebastian (2021) Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing. BioRxiv,

Naish, Matthew, Alonge, Michael, Wlodzimierz, Piotr, Tock, Andrew J, Abramson, Bradley W, Schmücker, Anna, Mandáková, Terezie, Jamge, Bhagyshree, Lambing, Christophe, Kuo, Pallas, Yelina, Natasha, Hartwick, Nolan, Colt, Kelly, Smith, Lisa M, Ton, Jurriaan, Kakutani, Tetsuji, Martienssen, Robert A, Schneeberger, Korbinian, Lysak, Martin A, Berger, Frédéric, Bousios, Alexandros, Michael, Todd P, Schatz, Michael C , Henderson, Ian R (2021) The genetic and epigenetic landscape of the Arabidopsis centromeres. Science, 374(6569) pp. eabi7489.

Das, Arun , Schatz, Michael (2021) Sketching and sampling approaches for fast and accurate long read classification. BioRxiv,

Kirsche, Melanie , Schatz, Michael C (2021) Democratizing long-read genome assembly.. Cell Systems, 12(10) pp. 945-947.

Baslan, Timour, Kovaka, Sam, Sedlazeck, Fritz J, Zhang, Yanming, Wappel, Robert, Tian, Sha, Lowe, Scott W, Goodwin, Sara , Schatz, Michael C (2021) High resolution copy number inference in cancer using short-molecule nanopore sequencing.. Nucleic Acids Research,

Yan, Stephanie M, Sherman, Rachel M, Taylor, Dylan J, Nair, Divya R, Bortvin, Andrew N, Schatz, Michael C , McCoy, Rajiv C (2021) Local adaptation and archaic introgression shape global diversity at human structural variant loci.. eLife, 10

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 (2021) An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids.. The Plant Genome, pp. e20101.

Pereira, L, Sapkota, M, Alonge, M, Zheng, Y, Zhang, Y, Razifard, H, Taitano, NK, Schatz, MC, Fernie, AR, Wang, Y, Fei, Z, Caicedo, AL, Tieman, DM , van der Knaap, E (2021) Natural Genetic Diversity in Tomato Flavor Genes. Frontiers in Plant Science, 12

Ahmed, Omar, Rossi, Massimiliano, Kovaka, Sam, Schatz, Michael C, Gagie, Travis, Boucher, Christina , Langmead, Ben (2021) Pan-genomic Matching Statistics for Targeted Nanopore Sequencing. iScience, pp. 102696-102696.

Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Aganezov, Sergey , Schatz, Michael (2021) Jasmine: Population-scale structural variant comparison and analysis. BioRxiv,

Kirsche, Melanie, Das, Arun , Schatz, Michael C (2021) Sapling: accelerating suffix array queries with learned data models.. Bioinformatics, 37(6) pp. 744-749.

Fouks, Bertrand, Brand, Philipp, Nguyen, Hung N, Herman, Jacob, Camara, Francisco, Ence, Daniel, Hagen, Darren E, Hoff, Katharina J, Nachweide, Stefanie, Romoth, Lars, Walden, Kimberly KO, Guigo, Roderic, Stanke, Mario, Narzisi, Giuseppe, Yandell, Mark, Robertson, Hugh M, Koeniger, Nikolaus, Chantawannakul, Panuwan, Schatz, Michael C, Worley, Kim C, Robinson, Gene E, Elsik, Christine G , Rueppell, Olav (2021) The genomic basis of evolutionary differentiation among honey bees.. Genome Research, 31(7) pp. 1203-1215.

Ranallo-Benavidez, T Rhyker, Lemmon, Zachary, Soyk, Sebastian, Aganezov, Sergey, Salerno, William J, McCoy, Rajiv C, Lippman, Zachary B, Schatz, Michael C , Sedlazeck, Fritz J (2021) Optimized sample selection for cost-efficient long-read population sequencing.. Genome Research, 31(5) pp. 910-918.

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 (2021) A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor.. PLoS Pathogens, 17(4) pp. e1009537.

Kovaka, Sam, Fan, Yunfan, Ni, Bohan, Timp, Winston , Schatz, Michael C (2021) Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.. Nature Biotechnology, 39(4) pp. 431-441.

Thielen, Peter M, Wohl, Shirlee, Mehoke, Thomas, Ramakrishnan, Srividya, Kirsche, Melanie, Falade-Nwulia, Oluwaseun, Trovão, Nídia S, Ernlund, Amanda, Howser, Craig, Sadowski, Norah, Morris, C Paul, Hopkins, Mark, Schwartz, Matthew, Fan, Yunfan, Gniazdowski, Victoria, Lessler, Justin, Sauer, Lauren, Schatz, Michael C, Evans, Jared D, Ray, Stuart C, Timp, Winston , Mostafa, Heba H (2021) Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area.. JCI Insight, 6(6)

Guerler, Aysam, Baker, Dannon, van den Beek, Marius, Gruening, Bjoern, Bouvier, Dave, Coraor, Nate, Shank, Stephen, Zehr, Jordan, Schatz, Michael , Nekrutenko, Anton (2021) Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy.. BioRxiv,

Xu, Zhuwei, Green, Brian, Benoit, Nicole, Sobel, Jack D, Schatz, Michael C, Wheelan, Sarah , Cormack, Brendan P (2021) Cell wall protein variation, break-induced replication, and subtelomere dynamics in Candida glabrata.. Molecular Microbiology,

Choi, Charlotte P, Tay, Rebecca J, Starostik, Margaret R, Feng, Suhua, Moresco, James J, Montgomery, Brooke E, Xu, Emily, Hammonds, Maya A, Schatz, Michael C, Montgomery, Taiowa A, Yates, John R, Jacobsen, Steven E , Kim, John K (2021) SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans.. eLife, 10 pp. 1-35.

Ostrovsky, A, Hillman-Jackson, J, Bouvier, D, Clements, D, Afgan, E, Blankenberg, D, Schatz, MC, Nekrutenko, A, Taylor, J, Team, TG , Lariviere, D (2021) Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update. Current Protocols, 1(2)

Mencia-Trinchant, Nuria, MacKay, Matthew J, Chin, Christopher, Afshinnekoo, Ebrahim, Foox, Jonathan, Meydan, Cem, Butler, Daniel, Mozsary, Christopher, Vernice, Nicholas A, Darby, Charlotte, Schatz, Michael C, Bailey, Susan M, Melnick, Ari M, Guzman, Monica L, Bolton, Kelly, Braunstein, Lior Z, Garrett-Bakelman, Francine, Levine, Ross L, Hassane, Duane C , Mason, Christopher E (2020) Clonal Hematopoiesis Before, During, and After Human Spaceflight.. Cell Reports, 33(10) pp. 108458.

Palatnick, A., Zhou, B., Ghedin, E. , Schatz, M. C. (2020) iGenomics: Comprehensive DNA sequence analysis on your Smartphone. Gigascience, 9(12)

Chin, C. S., Wagner, J., Zeng, Q., Garrison, E., Garg, S., Fungtammasan, A., Rautiainen, M., Aganezov, S., Kirsche, M., Zarate, S., Schatz, M. C., Xiao, C., Rowell, W. J., Markello, C., Farek, J., Sedlazeck, F. J., Bansal, V., Yoo, B., Miller, N., Zhou, X., Carroll, A., Barrio, A. M., Salit, M., Marschall, T., Dilthey, A. T. , Zook, J. M. (2020) A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nat Commun, 11(1) pp. 4794.

Scheben, Armin, Ramos, Olivia Mendivil, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel, Schatz, Michael, Simmons, Nancy, Siepel, Adam , McCombie, Richard (2020) Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus. BioRxiv,

Aganezov, S., Goodwin, S., Sherman, R. M., Sedlazeck, F. J., Arun, G., Bhatia, S., Lee, I., Kirsche, M., Wappel, R., Kramer, M., Kostroff, K., Spector, D. L., Timp, W., McCombie, W. R. , Schatz, M. C. (2020) Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Res, 30(9) pp. 1258-1273.

Nattestad, M., Aboukhalil, R., Chin, C. S. , Schatz, M. C. (2020) Ribbon: Intuitive visualization for complex genomic variation. Bioinformatics,

Chou, H. C., Bhalla, K., El Demerdash, O., Klingbeil, O., Hanington, Kaarina, Aganezov, S., Andrews, P., Alsudani, H., Chang, K., Vakoc, C. R., Schatz, M. C., McCombie, W. R. , Stillman, B. (2020) The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure. BioRxiv,

Ranallo-Benavidez, Rhyker, Lemmon, Zachary, Soyk, Sebastian, Aganezov, Sergey, Salerno, William, McCoy, Rajiv, Lippman, Zachary, Schatz, Michael , Sedlazeck, Fritz (2020) SVCollector: Optimized sample selection for cost-efficient long-read population sequencing. BioRxiv,

Tsai, Hung-Ji, Nelliat, Anjali R, Kucharavy, Andrei, Choudhury, Mohammad Ikbal, Sun, Sean X, Schatz, Michael C , Li, Rong (2020) On the Transcriptomic Signature and General Stress State Associated with Aneuploidy.

Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., Levy, Y., Harel, T. H., Shalev-Schlosser, G., Amsellem, Z., Razifard, H., Caicedo, A. L., Tieman, D. M., Klee, H., Kirsche, M., Aganezov, S., Ranallo-Benavidez, T. R., Lemmon, Z. H., Kim, J., Robitaille, G., Kramer, M., Goodwin, S., McCombie, W. R., Hutton, S., Van Eck, J., Gillis, J., Eshed, Y., Sedlazeck, F. J., van der Knaap, E., Schatz, M. C. , Lippman, Z. B. (2020) Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell, 182(1) pp. 145-161.e23.

Darby, C.A., Gaddipati, R., Schatz, M.C. , Langmead, B. (2020) Vargas: Heuristic-Free Alignment for Assessing Linear and Graph Read Aligners. Bioinformatics,

Wang, L., Lu, Z., Delabastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Xu, X., Ortiz-Ramirez, C., Marco, C.F., Goodwin, S., Dobin, A., Birnbaum, K. D., Jackson, D. P., Martienssen, R. A., McCombie, W. R., Micklos, D. A., Schatz, M. C., Ware, D. H. , Gingeras, T. R. (2020) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science, 11(289)

Ranallo-Benavidez, T.R., Jaron, K.S. , Schatz, M. C. (2020) GenomeScope 2.0 and Smudgeplot for Reference-Free Profiling of Polyploid Genomes. Nat Commun, 11(1432) pp. 1-10.

Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J. , Eberle, M. A. (2019) Paragraph: A graph-based structural variant genotyper for short-read sequence data. Genome Biology, 20(1) pp. Article 291.

Aganezov, S., Zban, I., Aksenov, V., Alexeev, N. , Schatz, M. C. (2019) Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics, 20(Suppl) pp. 641.

Souza, G. M., Van Sluys, M. A., Lembke, C. G., Lee, H., Margarido, G. R. A., Hotta, C. T., Gaiarsa, J. W., Diniz, A. L., Oliveira, M. M., Ferreira, S. S., Nishiyama, M. Y., Ten-Caten, F., Ragagnin, G. T., Andrade, P. M., de Souza, R. F., Nicastro, G. G., Pandya, R., Kim, C., Guo, H., Durham, A. M., Carneiro, M. S., Zhang, J., Zhang, X., Zhang, Q., Ming, R., Schatz, M. C., Davidson, B., Paterson, A. H. , Heckerman, D. (2019) Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience, 8(12) pp. giz129.

Wang, Liya, Lu, Zhenyuan, delaBastide, Melissa, Van Buren, Peter, Wang, Xiaofei, Ghiban, Cornel, Regulski, Michael, Drenkow, Jorg, Xu, Xiaosa, Ortiz-Ramirez, Carlos, Fernandez-Marco, Cristina, Goodwin, Sara, Dobin, Alexander, Birnbaum, Kenneth, Jackson, David, Martienssen, Robert, McCombie, William, Micklos, David, Schatz, Michael, Ware, Doreen , Gingeras, Thomas (2019) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. BioRxiv,

Alonge, M., Soyk, S., Ramakrishnan, S., Wang, X., Goodwin, S., Sedlazeck, F. J., Lippman, Z. B. , Schatz, M. C. (2019) RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol, 20(1) pp. 224.

Darby, C. A., Fitch, J. R., Brennan, P. J., Kelly, B. J., Bir, N., Magrini, V., Leonard, J., Cottrell, C. E., Gastier-Foster, J. M., Wilson, R. K., Mardis, E. R., White, P., Langmead, B. , Schatz, M. C. (2019) Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads. iScience, 18(Specia) pp. 1-10.

Alonge, M. , Schatz, M. C. (2019) A master regulator of regeneration. Science, 363(6432) pp. 1152-1153.

Dennenmoser, S., Sedlazeck, F. J., Schatz, M. C., Altmuller, J., Zytnicki, M. , Nolte, A. W. (2018) Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol, 28(6) pp. 1491-1505.

Kent, C. F., Dey, A., Patel, H., Tsvetkov, N., Tiwari, T., MacPhail, V. J., Gobeil, Y., Harpur, B. A., Gurtowski, J., Schatz, M. C., Colla, S. R. , Zayed, A. (2018) Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes. Front Genet, 9 pp. 316.

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, J., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., McPherson, J., Hicks, J., McCombie, W. R. , Schatz, M. C. (2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res, 28(8) pp. 1126-1135.

Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel MD, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae , Yu, Dantong (2018) KBase: The United States Department of Energy Systems Biology Knowledgebase.. Nature Biotechnology, 36(7) pp. 566-569.

Sedlazeck, F. J., Lee, H., Darby, C. A. , Schatz, M. C. (2018) Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet, 19(6) pp. 329-346.

Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A. , Schatz, M. C. (2018) Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods, 15(6) pp. 461-468.

Gomez-Romero, L., Palacios-Flores, K., Reyes, J., Garcia, D., Boege, M., Davila, G., Flores, M., Schatz, M. C. , Palacios, R. (2018) Precise detection of de novo single nucleotide variants in human genomes. Proc Natl Acad Sci U S A, 115(21) pp. 5516-5521.

Horvath, D. P., Patel, S., Doǧramaci, M., Chao, W. S., Anderson, J. V., Foley, M. E., Scheffler, B., Lazo, G., Dorn, K., Yan, C., Childers, A., Schatz, M. , Marcus, S. (2018) Gene Space and Transcriptome Assemblies of Leafy Spurge (Euphorbia esula) Identify Promoter Sequences, Repetitive Elements, High-Quality Markers, and a Full-Length Chloroplast Genome. Weed Science, 66(3) pp. 355-367.

Fang, Han, Huang, Yi-Fei, Radhakrishnan, Aditya, Siepel, Adam, Lyon, Gholson J. , Schatz, Michael C. (2018) Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Systems, 6(2) pp. 180-191.

Luo, Ruibang, Sedlazeck, Fritz J., Darby, Charlotte A., Kelly, Stephen M. , Schatz, Michael C. (2017) LRSim: A Linked-Reads Simulator generating insights for better genome partitioning. Computational and Structural Biotechnology Journal, 15 pp. 478-484.

Miller, J. R., Zhou, P., Mudge, J., Gurtowski, J., Lee, H., Ramaraj, T., Walenz, B. P., Liu, J., Stupar, R. M., Denny, R., Song, L., Singh, N., Maron, L. G., McCouch, S. R., McCombie, W. R., Schatz, M. C., Tiffin, P., Young, N. D. , Silverstein, K. A. T. (2017) Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics, 18(1) pp. 541.

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J. , Schatz, M. C. (2017) GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics, 33(14) pp. 2202-2204.

Feigin, M. E., Garvin, T., Bailey, P., Waddell, N., Chang, D. K., Kelley, D. R., Shuai, S., Gallinger, S., McPherson, J. D., Grimmond, S. M., Khurana, E., Stein, L. D., Biankin, A. V., Schatz, M. C. , Tuveson, D. A. (2017) Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nat Genet, 49(6) pp. 825-833.

Schatz, M. C. (2017) Nanopore sequencing meets epigenetics. Nat Methods, 14(4) pp. 347-348.

Heath, L. S., Bravo, H. C., Caccamo, M. , Schatz, M. (2017) Bioinformatics of DNA. Proceedings of the Ieee, 105(3) pp. 419-421.

Pal, D., Pertot, A., Shirole, N. H., Yao, Z., Anaparthy, N., Garvin, T., Cox, H., Chang, K., Rollins, F., Kendall, J., Edwards, L., Singh, V. A., Stone, G. C., Schatz, M. C., Hicks, J., Hannon, G. , Sordella, R. (2017) TGF-beta reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells. Elife, 6

Vij, S, Kuhl, H, Kuznetsova, IS, Komissarov, A, Yurchenko, AA, Van Heusden, P, Singh, S, Thevasagayam, NM, Sridatta Prakki, SR, Purushothaman, K, Saju, JM, Jiang, J, Mbandi, SK, Jonas, M, Tong, AHY, Mwangi, S, Lau, D, Ngoh, SY, Liew, WC, Shen, X, Hon, LS, Drake, JP, Boitano, M, Hall, R, Chin, CS, Lachumanan, R, Korlach, J, Trifonov, V, Kabilov, M, Tupikin, A, Green, D, Moxon, S, Garvin, T, Sedlazeck, FJ, Vurture, GW, Gopalapillai, G, Katneni, VK, Noble, TH, Scaria, V, Sivasubbu, S, Jerry, DR, O’Brien, SJ, Schatz, MC, Dalmay, T, Turner, SW, Lok, S, Christoffels, A , Orbán, L (2016) Erratum: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genetics, 12(12) pp. e1006500-e1006500.

Chin, C. S., Peluso, P., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., Cramer, G. R., Delledonne, M., Luo, C., Ecker, J. R., Cantu, D., Rank, D. R. , Schatz, M. C. (2016) Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods, 13(12) pp. 1050-1054.

Fang, H., Bergmann, E. A., Arora, K., Vacic, V., Zody, M. C., Iossifov, I., O'Rawe, J. A., Wu, Y., Jimenez Barron, L. T., Rosenbaum, J., Ronemus, M., Lee, Y. H., Wang, Z., Dikoglu, E., Jobanputra, V., Lyon, G. J., Wigler, M., Schatz, M. C. , Narzisi, G. (2016) Indel variant analysis of short-read sequencing data with Scalpel. Nat Protoc, 11(12) pp. 2529-2548.

Lemmon, Z. H., Park, S. J., Jiang, K., Van Eck, J., Schatz, M. C. , Lippman, Z. B. (2016) The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation. Genome Res, 26(12) pp. 1676-1686.

Nattestad, Maria, Chin, Chen-Shan , Schatz, Michael (2016) Ribbon: Visualizing complex genome alignments and structural variation. bioRxiv,

Nattestad, M. , Schatz, M. C. (2016) Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics, 32(19) pp. 3021-3023.

Amin, M. R., Skiena, S. , Schatz, M. C. (2016) NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads. 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), IEEE.

Vembar, S. S., Seetin, M., Lambert, C., Nattestad, M., Schatz, M. C., Baybayan, P., Scherf, A. , Smith, M. L. (2016) Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Res, 23(4) pp. 339-351.

Bombarely, A., Moser, M., Amrad, A., Bao, M., Bapaume, L., Barry, C. S., Bliek, M., Boersma, M. R., Borghi, L., Bruggmann, R., Bucher, M., D'Agostino, N., Davies, K., Druege, U., Dudareva, N., Egea-Cortines, M., Delledonne, M., Fernandez-Pozo, N., Franken, P., Grandont, L., Heslop-Harrison, J. S., Hintzsche, J., Johns, M., Koes, R., Lv, X., Lyons, E., Malla, D., Martinoia, E., Mattson, N. S., Morel, P., Mueller, L. A., Muhlemann, J., Nouri, E., Passeri, V., Pezzotti, M., Qi, Q., Reinhardt, D., Rich, M., Richert-Poggeler, K. R., Robbins, T. P., Schatz, M. C., Schranz, M. E., Schuurink, R. C., Schwarzacher, T., Spelt, K., Tang, H., Urbanus, S. L., Vandenbussche, M., Vijverberg, K., Villarino, G. H., Warner, R. M., Weiss, J., Yue, Z., Zethof, J., Quattrocchio, F., Sims, T. L. , Kuhlemeier, C. (2016) Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nat Plants, 2(6) pp. 16074.

Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. A., Van Heusden, P., Singh, S., Thevasagayam, N. M., Prakki, S. R., Purushothaman, K., Saju, J. M., Jiang, J., Mbandi, S. K., Jonas, M., Hin Yan Tong, A., Mwangi, S., Lau, D., Ngoh, S. Y., Liew, W. C., Shen, X., Hon, L. S., Drake, J. P., Boitano, M., Hall, R., Chin, C. S., Lachumanan, R., Korlach, J., Trifonov, V., Kabilov, M., Tupikin, A., Green, D., Moxon, S., Garvin, T., Sedlazeck, F. J., Vurture, G. W., Gopalapillai, G., Kumar Katneni, V., Noble, T. H., Scaria, V., Sivasubbu, S., Jerry, D. R., O'Brien, S. J., Schatz, M. C., Dalmay, T., Turner, S. W., Lok, S., Christoffels, A. , Orban, L. (2016) Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet, 12(4) pp. e1005954.

Rosenfeld, J. A., Reeves, D., Brugler, M. R., Narechania, A., Simon, S., Durrett, R., Foox, J., Shianna, K., Schatz, M. C., Gandara, J., Afshinnekoo, E., Lam, E. T., Hastie, A. R., Chan, S., Cao, H., Saghbini, M., Kentsis, A., Planet, P. J., Kholodovych, V., Tessler, M., Baker, R., DeSalle, R., Sorkin, L. N., Kolokotronis, S. O., Siddall, M. E., Amato, G. , Mason, C. E. (2016) Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nat Commun, 7 pp. 10164.

Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., Lyons, E., Wang, M. L., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H., Yim, W. C., Priest, H. D., Zheng, C., Woodhouse, M., Edger, P. P., Guyot, R., Guo, H. B., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F. J., Harkess, A., McKain, M. R., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L. Y., Shirley, N., Lin, Y. R., Liu, L. Y., Hernandez, A. G., Wright, C. L., Bulone, V., Tuskan, G. A., Heath, K., Zee, F., Moore, P. H., Sunkar, R., Leebens-Mack, J. H., Mockler, T., Bennetzen, J. L., Freeling, M., Sankoff, D., Paterson, A. H., Zhu, X., Yang, X., Smith, J. A., Cushman, J. C., Paull, R. E. , Yu, Q. (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet, 47 pp. 1435-1442.

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M. , Schatz, M. C. (2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12 pp. 1058-1060.

Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M. C. , McCombie, W. R. (2015) Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res, 25(11) pp. 1750-1756.

Zhou, X., Battistoni, G., El Demerdash, O., Gurtowski, J., Wunderer, J., Falciatori, I., Ladurner, P., Schatz, M. C., Hannon, G. J. , Wasik, K. A. (2015) Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano. RNA, 21(11) pp. 1885-1897.

Smolka, M., Rescheneder, P., Schatz, M. C., von Haeseler, A. , Sedlazeck, F. J. (2015) Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol, 16(1) pp. 235.

Schatz, M. C. (2015) Biological data sciences in genome research. Genome Res, 25(10) pp. 1417-22.

Wences, A. H. , Schatz, M. C. (2015) Metassembler: merging and optimizing de novo genome assemblies. Genome Biol, 16(1) pp. 207.

Wasik, K., Gurtowski, J., Zhou, X., Ramos, O. M., Delas, M. J., Battistoni, G., El Demerdash, O., Falciatori, I., Vizoso, D. B., Smith, A. D., Ladurner, P., Scharer, L., McCombie, W. R., Hannon, G. J. , Schatz, M. (2015) Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A, 112(40) pp. 12462-12467.

Stephens, Z. D., Lee, S. Y., Faghri, F., Campbell, R. H., Zhai, C., Efron, M. J., Iyer, R., Schatz, M. C., Sinha, S. , Robinson, G. E. (2015) Big Data: Astronomical or Genomical?. PLoS Biol, 13(7) pp. e1002195.

MacColl, Elisabeth, Therkelsen, Matthew D., Sherpa, Tshering, Ellerbrock, Hannah, Johnston, Lily A., Jariwala, Ravi, Chang, WeiShu, Gurtowski, James, Schatz, Michael C., Mozammal Hossain, M., Cassidy-Hanley, Donna M., Clark, Theodore G. , Chang, Wei-Jen (2015) Molecular Genetic Diversity and Characterization of Conjugation Genes in the Fish Parasite Ichthyophthirius multifiliis. Molecular Phylogenetics and Evolution, 86 pp. 1-7.

Church, D. M., Schneider, V. A., Steinberg, K. M., Schatz, M. C., Quinlan, A. R., Chin, C. S., Kitts, P. A., Aken, B., Marth, G. T., Hoffman, M. M., Herrero, J., Mendoza, M. L. Z., Durbin, R. , Flicek, P. (2015) Extending reference assembly models. Genome Biology, 16 pp. Article no. 13.

Garvin, Tyler, Aboukhalil, Robert, Kendall, Jude, Baslan, Timour, Atwal, Gurinder S, Hicks, James, Wigler, Michael , Schatz, Michael (2015) Interactive analysis and quality assessment of single-cell copy-number variations. Nature Methods, 12 pp. 1058-1060.

Narzisi, G. , Schatz, M. C. (2015) The challenge of small-scale repeats for indel discovery. Front Bioeng Biotechnol, 3 pp. 8.

Schatz, M. C., Maron, L. G., Stein, J. C., Hernandez Wences, A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright, M. H., Chia, J. M., Ware, D., McCouch, S. R. , McCombie, W. R. (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol, 15(11) pp. 506.

Iossifov, I., O'Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., Stessman, H. A., Witherspoon, K. T., Vives, L., Patterson, K. E., Smith, J. D., Paeper, B., Nickerson, D. A., Dea, J., Dong, S., Gonzalez, L. E., Mandell, J. D., Mane, S. M., Murtha, M. T., Sullivan, C. A., Walker, M. F., Waqar, Z., Wei, L., Willsey, A. J., Yamrom, B., Lee, Y. H., Grabowska, E., Dalkic, E., Wang, Z., Marks, S., Andrews, P., Leotta, A., Kendall, J., Hakker, I., Rosenbaum, J., Ma, B., Rodgers, L., Troge, J., Narzisi, G., Yoon, S., Schatz, M. C., Ye, K., McCombie, W. R., Shendure, J., Eichler, E. E., State, M. W. , Wigler, M. (2014) The contribution of de novo coding mutations to autism spectrum disorder. Nature, 515(7526) pp. 216-221.

Marcus, S., Lee, H. , Schatz, M. C. (2014) SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips. Bioinformatics, 30(24) pp. 3476-3483.

Narzisi, G., O'Rawe, Jason, Iossifov, I., Fang, Han, Lee, Y. H., Wang, Zihua, Wu, Yiyang, Lyon, Gholson J., Wigler, M. H. , Schatz, M. C. (2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature Methods, 11(10) pp. 1033-1036.

Blood, P. D., Marcus, S. , Schatz, M. C. (2014) Large-scale sequencing and assembly of cereal genomes using blacklight. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment, pp. Article number 20. Association for Computing Machinery.

Ganapathy, G., Howard, J. T., Ward, J. M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D. C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J. R., Koren, S., Warren, W. C., Zhang, G., Phillippy, A. M. , Jarvis, E. D. (2014) High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience, 3 pp. 11.

Titmus, M. A., Gurtowski, J. , Schatz, M. C. (2014) Answering the demands of digital genomics. Concurrency Computation Practice and Experience, 26(4) pp. 917-928.

Fang, Han, Wu, Yiyang, Narzisi, G., O'Rawe, Jason, Jimenez Barron, Laura, Rosenbaum, J., Ronemus, M., Iossifov, I., Schatz, M. C. , Lyon, Gholson J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med, 6(10) pp. 89.

Saw, J. H. W., Schatz, M., Brown, M. V., Kunkel, D. D., Foster, J. S., Shick, H., Christensen, S., Hou, S., Wan, X. , Donachie, S. P. (2013) Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i. PLoS ONE, 8(10)

Schatz, M. C. , Langmead, B. (2013) THE DNA DATA DELUGE FAST, EFFICIENT GENOME-SEQUENCING MACHINES ARE SPEWING OUT MORE DATA THAN GENETICISTS CAN ANALYZE. IEEE Spectrum, 50(7) pp. 28-33.

Schatz, M. C., Taylor, J. , Schelhorn, S. E. (2013) The DNA60IFX contest. Genome Biol, 14(6) pp. 124.

Doolittle, W. F., Fraser, P., Gerstein, M. B., Graveley, B. R., Henikoff, S., Huttenhower, C., Oshlack, A., Ponting, C. P., Rinn, J. L., Schatz, M. C., Ule, J., Weigel, D. , Weinstock, G. M. (2013) Sixty years of genome biology. Genome Biology, 14(4)

Maron, L. G., Guimaraes, C. T., Kirst, M., Albert, P. S., Birchler, J. A., Bradbury, P. J., Buckler, E. S., Coluccio, A. E., Danilova, T. V., Kudrna, D., Magalhaes, J. V., Pineros, M. A., Schatz, M. C., Wing, R. A. , Kochian, L. V. (2013) Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proceedings of the National Academy of Sciences of the United States of America, 110(13) pp. 5241-5246.

Schatz, M. C., Phillippy, A. M., Sommer, D. D., Delcher, A. L., Puiu, D., Narzisi, G., Salzberg, S. L. , Pop, M. (2013) Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics, 14(2) pp. 213-224.

Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, İnanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Fabbro, Cristian Del, Docking, T Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Vieira, Bruno Miguel, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J Graham, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo , Korf, Ian F (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience,

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J. A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W. C., Corbeil, J., Del Fabbro, C., Docking, T. R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N. A., Ganapathy, G., Gibbs, R. A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J. B., Ho, I. Y., Howard, J., Hunt, M., Jackman, S. D., Jaffe, D. B., Jarvis, E. D., Jiang, H., Kazakov, S., Kersey, P. J., Kitzman, J. O., Knight, J. R., Koren, S., Lam, T. W., Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., Maccallum, I., Macmanes, M. D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T. D., Paten, B., Paulo, O. S., Phillippy, A. M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F. J., Richards, S., Rokhsar, D. S., Ruby, J. G., Scalabrin, S., Schatz, M. C., Schwartz, D. C., Sergushichev, A., Sharpe, T., Shaw, T. I., Shendure, J., Shi, Y., Simpson, J. T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B. M., Wang, J., Worley, K. C., Yin, S., Yiu, S. M., Yuan, J., Zhang, G., Zhang, H., Zhou, S. , Korf, I. F. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2(1) pp. 10.

Ming, R., VanBuren, R., Liu, Y. L., Yang, M., Han, Y. P., Li, L. T., Zhang, Q., Kim, M. J., Schatz, M. C., Campbell, M., Li, J. P., Bowers, J. E., Tang, H. B., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., Jiao, Y. N., Der, J. P., Zeng, F. C., Han, J., Min, X. J., Hudson, K. A., Singh, R., Grennan, A. K., Karpowicz, S. J., Watling, J. R., Ito, K., Robinson, S. A., Hudson, M. E., Yu, Q. Y., Mockler, T. C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R. Z., Chen, N., Arro, J., Wai, C. M., Wafula, E., Spence, A., Han, Y. N., Xu, L. M., Zhang, J. S., Peery, R., Haus, M. J., Xiong, W. W., Walsh, J. A., Wu, J., Wang, M. L., Zhu, Y. J., Paull, R. E., Britt, A. B., Du, C. G., Downie, S. R., Schuler, M. A., Michael, T. P., Long, S. P., Ort, D. R., Schopf, J. W., Gang, D. R., Jiang, N., Yandell, M., dePamphilis, C. W., Merchant, S. S., Paterson, A. H., Buchanan, B. B., Li, S. H. , Shen-Miller, J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14(5)

Roberts, R. J., Carneiro, M. O. , Schatz, M. C. (2013) The advantages of SMRT sequencing. Genome Biology, 14(7) pp. 4.

Schatz, M. C. (2012) Computational thinking in the era of big data biology. Genome Biology, 13(11) pp. 177.

Gurtowski, J., Schatz, M. C. , Langmead, B. (2012) Genotyping in the cloud with crossbow. Current Protocols in Bioinformatics, pp. 15.3.

Lee, H. , Schatz, M. C. (2012) Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. Bioinformatics, 28(16) pp. 2097-2105.

Koren, S., Schatz, M. C., Walenz, B. P., Martin, J., Howard, J. T., Ganapathy, G., Wang, Z., Rasko, D. A., McCombie, W. R., Jarvis, E. D. , Phillippy, A. M. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30(7) pp. 693-700.

Schatz, M. C., Witkowski, J. , McCombie, W. R. (2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biology, 13(4) pp. 243.

Iossifov, I., Ronemus, M., Levy, D., Wang, Z. H., Hakker, I., Rosenbaum, J., Yamrom, B., Lee, Y. H., Narzisi, G., Leotta, A., Kendall, J., Grabowska, E., Ma, B. C., Marks, S., Rodgers, L., Stepansky, A., Troge, J., Andrews, P., Bekritsky, M., Pradhan, K., Ghiban, E., Kramer, M., Parla, J., Demeter, R., Fulton, L. L., Fulton, R. S., Magrini, V. J., Ye, K., Darnell, J. C., Darnell, R. B., Mardis, E. R., Wilson, R. K., Schatz, M. C., McCombie, W. R. , Wigler, M. (2012) De Novo Gene Disruptions in Children on the Autistic Spectrum. Neuron, 74(2) pp. 285-299.

Salzberg, S. L., Phillippy, A. M., Zimin, A., Puiu, D., Magoc, T., Koren, S., Treangen, T. J., Schatz, M. C., Delcher, A. L., Roberts, M., Marcais, G., Pop, M. , Yorke, J. A. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res, 22(3) pp. 557-67.

Park, S. J., Jiang, K., Schatz, M. C. , Lippman, Z. B. (2012) Rate of meristem maturation determines inflorescence architecture in tomato. Proceedings of the National Academy of Sciences of the United States of America, 109(2) pp. 639-44.

Bogdanove, A. J., Koebnik, R., Lu, H., Furutani, A., Angiuoli, S. V., Patil, P. B., Van Sluys, M. A., Ryan, R. P., Meyer, D. F., Han, S. W., Aparna, G., Rajaram, M., Delcher, A. L., Phillippy, A. M., Puiu, D., Schatz, M. C., Shumway, M., Sommer, D. D., Trapnell, C., Benahmed, F., Dimitrov, G., Madupu, R., Radune, D., Sullivan, S., Jha, G., Ishihara, H., Lee, S. W., Pandey, A., Sharma, V., Sriariyanun, M., Szurek, B., Vera-Cruz, C. M., Dorman, K. S., Ronald, P. C., Verdier, V., Dow, J. M., Sonti, R. V., Tsuge, S., Brendel, V. P., Rabinowicz, P. D., Leach, J. E., White, F. F. , Salzberg, S. L. (2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology, 193(19) pp. 5450-5464.

Donia, M. S., Fricke, W. F., Partensky, F., Cox, J., Elshahawi, S. I., White, J. R., Phillippy, A. M., Schatz, M. C., Piel, J., Haygood, M. G., Ravel, J. , Schmidt, E. W. (2011) Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proceedings of the National Academy of Sciences of the United States of America, 108(51) pp. E1423-E1432.

Earl, D., Bradnam, K., St. John, J., Darling, A., Lin, D., Fass, J., Yu, H. O. K., Buffalo, V., Zerbino, D. R., Diekhans, M., Nguyen, N., Ariyaratne, P. N., Sung, W. K., Ning, Z., Haimel, M., Simpson, J. T., Fonseca, N. A., Birol, I., Docking, T. R., Ho, I. Y., Rokhsar, D. S., Chikhi, R., Lavenier, D., Chapuis, G., Naquin, D., Maillet, N., Schatz, M. C., Kelley, D. R., Phillippy, A. M., Koren, S., Yang, S. P., Wu, W., Chou, W. C., Srivastava, A., Shaw, T. I., Ruby, J. G., Skewes-Cox, P., Betegon, M., Dimon, M. T., Solovyev, V., Seledtsov, I., Kosarev, P., Vorobyev, D., Ramirez-Gonzalez, R., Leggett, R., MacLean, D., Xia, F., Luo, R., Li, Z., Xie, Y., Liu, B., Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Sharpe, T., Hall, G., Kersey, P. J., Durbin, R., Jackman, S. D., Chapman, J. A., Huang, X., DeRisi, J. L., Caccamo, M., Li, Y., Jaffe, D. B., Green, R. E., Haussler, D., Korf, I. , Paten, B. (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21(12) pp. 2224-2241.

Menon, R. K., Bhat, G. P. , Schatz, M. C. (2011) Rapid parallel genome indexing with MapReduce. 2nd International Workshop on MapReduce and Its Applications, MapReduce'11, Co-located with 20th International ACM Symposium on High-Performance Parallel and Distributed Computing, HPDC 2011. MapReduce '11 Proceedings of the second international workshop on MapReduce and its applications , pp. 51-58. ACM.

Kelley, D. R., Schatz, M. C. , Salzberg, S. L. (2010) Quake: Quality-aware detection and correction of sequencing errors. Genome Biology, 11(11)

Schatz, M. C., Langmead, B. , Salzberg, S. L. (2010) Cloud computing and the DNA data race. Nature Biotechnology, 28(7) pp. 691-693.

Cornman, S. R., Schatz, M. C., Johnston, S. J., Chen, Y., Pettis, J., Hunt, G., Bourgeois, L., Elsik, C., Anderson, D., Grozinger, C. M. , Evans, J. D. (2010) Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. BMC Genomics, 11(1)

Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Blomberg, L. A., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., Cooper, K., Coulombe, R. A., De, S., Delany, M. E., Dodgson, J. B., Dong, J. J., Evans, C., Frederickson, K. M., Flicek, P., Florea, L., Folkerts, O., Groenen, M. A. M., Harkins, T. T., Herrero, J., Hoffmann, S., Megens, H. J., Jiang, A., de Jong, P., Kaiser, P., Kim, H., Kim, K. W., Kim, S., Langenberger, D., Lee, M. K., Lee, T., Mane, S., Marcais, G., Marz, M., McElroy, A. P., Modise, T., Nefedov, M., Notredame, C., Paton, I. R., Payne, W. S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Ruffier, M., Salzberg, S. L., Schatz, M. C., Scheuring, C., Schmidt, C. J., Schroeder, S., Searle, S. M. J., Smith, E. J., Smith, J., Sonstegard, T. S., Stadler, P. F., Tafer, H., Tu, Z., van Tassell, C. P., Vilella, A. J., Williams, K. P., Yorke, J. A., Zhang, L., Zhang, H. B., Zhang, X., Zhang, Y. , Reed, K. M. (2010) Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis. PLoS Biology, 8(9)

Kingsford, C., Schatz, M. C. , Pop, M. (2010) Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics, 11

Lin, J. , Schatz, M. C. (2010) Design patterns for efficient graph algorithms in MapReduce. 8th Workshop on Mining and Learning with Graphs, MLG'10. Proceedings of the Eighth Workshop on Mining and Learning with Graphs , pp. 78-85. MLG.

Schatz, M. C. (2010) The missing graphical user interface for genomics. Genome Biology, 11(8) pp. 128.

Schatz, M. C., Delcher, A. L. , Salzberg, S. L. (2010) Assembly of large genomes using second-generation sequencing. Genome Research, 20(9) pp. 1165-1173.

Schatz, M. C., Phillippy, A. M., Gajer, P., DeSantis, T. Z., Andersen, G. L. , Ravel, J. (2010) Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray. Applied and Environmental Microbiology, 76(16) pp. 5636-5638.

Suzuki, J. Y., Tripathi, S., Fermín, G. A., Jan, F. J., Hou, S., Saw, J. H., Ackerman, C. M., Yu, Q., Schatz, M. C., Pitz, K. Y., Yépes, M., Fitch, M. M. M., Manshardt, R. M., Slightom, J. L., Ferreira, S. A., Salzberg, S. L., Alam, M., Ming, R., Moore, P. H. , Gonsalves, D. (2010) Efforts to deregulate Rainbow papaya in Japan: Molecular characterization of transgene and vector inserts. Acta Horticulturae, 851 pp. 235-240.

Cornman, R. S., Chen, Y. P., Schatz, M. C., Street, C., Zhao, Y., Desany, B., Egholm, M., Hutchison, S., Pettis, J. S., Lipkin, W. I. , Evans, J. D. (2009) Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathogens, 5(6)

Langmead, B., Schatz, M. C., Lin, J., Pop, M. , Salzberg, S. L. (2009) Searching for SNPs with cloud computing. Genome Biology, 10(11)

Navlakha, S., Schatz, M. C. , Kingsford, C. (2009) Revealing biological modules via graph summarization. Journal of Computational Biology, 16(2) pp. 253-264.

Schatz, M. C. (2009) CloudBurst: Highly sensitive read mapping with MapReduce. Bioinformatics, 25(11) pp. 1363-1369.

Trapnell, C. , Schatz, M. C. (2009) Optimizing data intensive GPGPU computations for DNA sequence alignment. Parallel Computing, 35(8-9) pp. 429-440.

Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C. P., Sonstegard, T. S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J. A. , Salzberg, S. L. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology, 10(4)

Desjardins, C. A., Gundersen-Rindal, D. E., Hostetler, J. B., Tallon, L. J., Fadrosh, D. W., Fuester, R. W., Pedroni, M. J., Haas, B. J., Schatz, M. C., Jones, K. M., Crabtree, J., Forberger, H. , Nene, V. (2008) Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps. Genome Biology, 9(12)

Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J. H., Senin, P., Wang, W., Ly, B. V., Lewis, K. L. T., Salzberg, S. L., Feng, L., Jones, M. R., Skelton, R. L., Murray, J. E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., Tong, E., Tang, H., Lyons, E., Paull, R. E., Michael, T. P., Wall, K., Rice, D. W., Albert, H., Wang, M. L., Zhu, Y. J., Schatz, M., Nagarajan, N., Acob, R. A., Guan, P., Blas, A., Wai, C. M., Ackerman, C. M., Ren, Y., Liu, C., Wang, J., Na, J. K., Shakirov, E. V., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J. E., Gschwend, A. R., Delcher, A. L., Singh, R., Suzuki, J. Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Pérez, R., Torres, M. J., Feltus, F. A., Porter, B., Li, Y., Burroughs, A. M., Luo, M. C., Liu, L., Christopher, D. A., Mount, S. M., Moore, P. H., Sugimura, T., Jiang, J., Schuler, M. A., Friedman, V., Mitchell-Olds, T., Shippen, D. E., Depamphilis, C. W., Palmer, J. D., Freeling, M., Paterson, A. H., Gonsalves, D., Wang, L. , Alam, M. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 452(7190) pp. 991-996.

Phillippy, A. M., Schatz, M. C. , Pop, M. (2008) Genome assembly forensics: Finding the elusive mis-assembly. Genome Biology, 9(3)

Salzberg, S. L., Sommer, D. D., Schatz, M. C., Phillippy, A. M., Rabinowicz, P. D., Tsuge, S., Furutani, A., Ochiai, H., Delcher, A. L., Kelley, D., Madupu, R., Puiu, D., Radune, D., Shumway, M., Trapnell, C., Aparna, G., Jha, G., Pandey, A., Patil, P. B., Ishihara, H., Meyer, D. F., Szurek, B., Verdier, V., Koebnik, R., Maxwell, J. M., Ryan, R. P., Hirata, H., Tsuyumu, S., Won Lee, S., Ronald, P. C., Sonti, R. V., Van Sluys, M. A., Leach, J. E., White, F. F. , Bogdanove, A. J. (2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics, 9

Suzuki, Jon Y., Tripathi, Savarni, Fermín, Gustavo A., Jan, Fuh-Jyh, Hou, Shaobin, Saw, Jimmy H., Ackerman, Christine M., Yu, Qingyi, Schatz, Michael C., Pitz, Karen Y., Yépes, Marcela, Fitch, Maureen M. M., Manshardt, Richard M., Slightom, Jerry L., Ferreira, Stephen A., Salzberg, Steven L., Alam, Maqsudul, Ming, Ray, Moore, Paul H. , Gonsalves, Dennis (2008) Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop. Tropical Plant Biology, 1(3-4) pp. 293-309.

Carlton, J. M., Hirt, R. P., Silva, J. C., Delcher, A. L., Schatz, M., Zhao, Q., Wortman, J. R., Bidwell, S. L., Alsmark, U. C. M., Besteiro, S., Sicheritz-Ponten, T., Noel, C. J., Dacks, J. B., Foster, P. G., Simillion, C., Van De Peer, Y., Miranda-Saavedra, D., Barton, G. J., Westrop, G. D., Müller, S., Dessi, D., Fiori, P. L., Ren, Q., Paulsen, I., Zhang, H., Bastida-Corcuera, F. D., Simoes-Barbosa, A., Brown, M. T., Hayes, R. D., Mukherjee, M., Okumura, C. Y., Schneider, R., Smith, A. J., Vanacova, S., Villalvazo, M., Haas, B. J., Pertea, M., Feldblyum, T. V., Utterback, T. R., Shu, C. L., Osoegawa, K., De Jong, P. J., Hrdy, I., Horvathova, L., Zubacova, Z., Dolezal, P., Malik, S. B., Logsdon Jr, J. M., Henze, K., Gupta, A., Wang, C. C., Dunne, R. L., Upcroft, J. A., Upcroft, P., White, O., Salzberg, S. L., Tang, P., Chiu, C. H., Lee, Y. S., Embley, T. M., Coombs, G. H., Mottram, J. C., Tachezy, J., Fraser-Liggett, C. M. , Johnson, P. J. (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science, 315(5809) pp. 207-212.

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Desjardins, C. A., Gundersen-Rindal, D. E., Hostetler, J. B., Tallon, L. J., Fuester, R. W., Schatz, M. C., Pedroni, M. J., Fadrosh, D. W., Haas, B. J., Toms, B. S., Chen, D. , Nene, V. (2007) Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. BMC Microbiology, 7

Ghedin, E., Wang, S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J. E., Delcher, A. L., Guiliano, D. B., Miranda-Saavedra, D., Angiuoli, S. V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N. M., Wortman, J. R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S. L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G. J., Carlow, C. K. S., Crawford, M. J., Daub, J., Dimmic, M. W., Estes, C. F., Foster, J. M., Ganatra, M., Gregory, W. F., Johnson, N. M., Jin, M., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B. W., Li, W., Lindblom, T. H., Lustigman, S., Ma, D., Maina, C. V., Martin, D. M. A., McCarter, J. P., McReynolds, L., Mitreva, M., Nutman, T. B., Parkinson, J., Peregrín-Alvarez, J. M., Poole, C., Ren, Q., Saunders, L., Sluder, A. E., Smith, K., Stanke, M., Unnasch, T. R., Ware, J., Wei, A. D., Weil, G., Williams, D. J., Zhang, Y., Williams, S. A., Fraser-Liggett, C., Slatko, B., Blaxter, M. L. , Scott, A. L. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science, 317(5845) pp. 1756-1760.

Nene, V., Wortman, J. R., Lawson, D., Haas, B., Kodira, C., Tu, Z., Loftus, B., Xi, Z., Megy, K., Grabherr, M., Ren, Q., Zdobnov, E. M., Lobo, N. F., Campbell, K. S., Brown, S. E., Bonaldo, M. F., Zhu, J., Sinkins, S. P., Hogenkamp, D. G., Amedeo, P., Arensburger, P., Atkinson, P. W., Bidwell, S., Biedler, J., Birney, E., Bruggner, R. V., Costas, J., Coy, M. R., Crabtree, J., Crawford, M., DeBruyn, B., DeCaprio, D., Eiglmeier, K., Eisenstadt, E., El-Dorry, H., Gelbart, W. M., Gomes, S. L., Hammond, M., Hannick, L. I., Hogan, J. R., Holmes, M. H., Jaffe, D., Johnston, J. S., Kennedy, R. C., Koo, H., Kravitz, S., Kriventseva, E. V., Kulp, D., LaButti, K., Lee, E., Li, S., Lovin, D. D., Mao, C., Mauceli, E., Menck, C. F. M., Miller, J. R., Montgomery, P., Mori, A., Nascimento, A. L., Naveira, H. F., Nusbaum, C., O'Leary, S., Orvis, J., Pertea, M., Quesneville, H., Reidenbach, K. R., Rogers, Y. H., Roth, C. W., Schneider, J. R., Schatz, M., Shumway, M., Stanke, M., Stinson, E. O., Tubio, J. M. C., VanZee, J. P., Verjovski-Almeida, S., Werner, D., White, O., Wyder, S., Zeng, Q., Zhao, Q., Zhao, Y., Hill, C. A., Raikhel, A. S., Soares, M. B., Knudson, D. L., Lee, N. H., Galagan, J., Salzberg, S. L., Paulsen, I. T., Dimopoulos, G., Collins, F. H., Birren, B., Fraser-Liggett, C. M. , Severson, D. W. (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 316(5832) pp. 1718-1723.

Schatz, M. C., Phillippy, A. M., Shneiderman, B. , Salzberg, S. L. (2007) Hawkeye: An interactive visual analytics tool for genome assemblies. Genome Biology, 8(3)

Schatz, M. C., Trapnell, C., Delcher, A. L. , Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. Bmc Bioinformatics, 8

Fouts, D. E., Mongodin, E. F., Mandrell, R. E., Miller, W. G., Rasko, D. A., Ravel, J., Brinkac, L. M., Deboy, R. T., Parker, C. T., Daugherty, S. C., Dodson, R. J., Scott Durkin, A., Madupu, R., Sullivan, S. A., Shetty, J. U., Ayodeji, M. A., Shvartsbeyn, A., Schatz, M. C., Badger, J. H., Fraser, C. M. , Nelson, K. E. (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biology, 3(1)

Gajer, P., Schatz, M. , Salzberg, S. L. (2004) Automated correction of genome sequence errors. Nucleic Acids Research, 32(2) pp. 562-569.