COATi: Statistical Pairwise Alignment of Protein-Coding Sequences
García Mesa, Juan José, Zhu, Ziqi, Cartwright, Reed A
Published in Molecular biology and evolution (03.07.2024)
Published in Molecular biology and evolution (03.07.2024)
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Comparative population genomics of maize domestication and improvement
Hufford, Matthew B, Xu, Xun, van Heerwaarden, Joost, Pyhäjärvi, Tanja, Chia, Jer-Ming, Cartwright, Reed A, Elshire, Robert J, Glaubitz, Jeffrey C, Guill, Kate E, Kaeppler, Shawn M, Lai, Jinsheng, Morrell, Peter L, Shannon, Laura M, Song, Chi, Springer, Nathan M, Swanson-Wagner, Ruth A, Tiffin, Peter, Wang, Jun, Zhang, Gengyun, Doebley, John, McMullen, Michael D, Ware, Doreen, Buckler, Edward S, Yang, Shuang, Ross-Ibarra, Jeffrey
Published in Nature genetics (01.07.2012)
Published in Nature genetics (01.07.2012)
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A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions
Loewenthal, Gil, Rapoport, Dana, Avram, Oren, Moshe, Asher, Wygoda, Elya, Itzkovitch, Alon, Israeli, Omer, Azouri, Dana, Cartwright, Reed A, Mayrose, Itay, Pupko, Tal
Published in Molecular biology and evolution (09.12.2021)
Published in Molecular biology and evolution (09.12.2021)
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Journal Article
Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR
Sievert, Christian, Nieves, Lizbeth M., Panyon, Larry A., Loeffler, Taylor, Morris, Chandler, Cartwright, Reed A., Wang, Xuan
Published in Proceedings of the National Academy of Sciences - PNAS (11.07.2017)
Published in Proceedings of the National Academy of Sciences - PNAS (11.07.2017)
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Journal Article
A community-maintained standard library of population genetic models
Adrion, Jeffrey R, Cole, Christopher B, Dukler, Noah, Galloway, Jared G, Gladstein, Ariella L, Gower, Graham, Kyriazis, Christopher C, Ragsdale, Aaron P, Tsambos, Georgia, Baumdicker, Franz, Carlson, Jedidiah, Cartwright, Reed A, Durvasula, Arun, Gronau, Ilan, Kim, Bernard Y, McKenzie, Patrick, Messer, Philipp W, Noskova, Ekaterina, Ortega-Del Vecchyo, Diego, Racimo, Fernando, Struck, Travis J, Gravel, Simon, Gutenkunst, Ryan N, Lohmueller, Kirk E, Ralph, Peter L, Schrider, Daniel R, Siepel, Adam, Kelleher, Jerome, Kern, Andrew D
Published in eLife (23.06.2020)
Published in eLife (23.06.2020)
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DeNovoGear: de novo indel and point mutation discovery and phasing
Ramu, Avinash, Noordam, Michiel J, Schwartz, Rachel S, Wuster, Arthur, Hurles, Matthew E, Cartwright, Reed A, Conrad, Donald F
Published in Nature methods (01.10.2013)
Published in Nature methods (01.10.2013)
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Journal Article
The role of gene flow in rapid and repeated evolution of cave‐related traits in Mexican tetra, Astyanax mexicanus
Herman, Adam, Brandvain, Yaniv, Weagley, James, Jeffery, William R., Keene, Alex C., Kono, Thomas J. Y., Bilandžija, Helena, Borowsky, Richard, Espinasa, Luis, O'Quin, Kelly, Ornelas‐García, Claudia P., Yoshizawa, Masato, Carlson, Brian, Maldonado, Ernesto, Gross, Joshua B., Cartwright, Reed A., Rohner, Nicolas, Warren, Wesley C., McGaugh, Suzanne E.
Published in Molecular ecology (01.11.2018)
Published in Molecular ecology (01.11.2018)
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A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant
Orr, Adam J, Padovan, Amanda, Kainer, David, Külheim, Carsten, Bromham, Lindell, Bustos-Segura, Carlos, Foley, William, Haff, Tonya, Hsieh, Ji-Fan, Morales-Suarez, Alejandro, Cartwright, Reed A, Lanfear, Robert
Published in Proceedings of the Royal Society. B, Biological sciences (11.03.2020)
Published in Proceedings of the Royal Society. B, Biological sciences (11.03.2020)
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Journal Article
Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia
Winter, David J, Pacheco, M Andreína, Vallejo, Andres F, Schwartz, Rachel S, Arevalo-Herrera, Myriam, Herrera, Socrates, Cartwright, Reed A, Escalante, Ananias A
Published in PLoS neglected tropical diseases (01.12.2015)
Published in PLoS neglected tropical diseases (01.12.2015)
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Journal Article
Phylogenomic reconstruction supports supercontinent origins for Leishmania
Harkins, Kelly M., Schwartz, Rachel S., Cartwright, Reed A., Stone, Anne C.
Published in Infection, genetics and evolution (01.03.2016)
Published in Infection, genetics and evolution (01.03.2016)
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Journal Article
Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools
Malukiewicz, Joanna, D’arc, Mirela, Dias, Cecilia A., Cartwright, Reed A., Grativol, Adriana D., Moreira, Silvia Bahadian, Souza, Antonizete R., Tavares, Maria Clotilde Henriques, Pissinatti, Alcides, Ruiz-Miranda, Carlos R., Santos, André F. A.
Published in Scientific reports (21.09.2023)
Published in Scientific reports (21.09.2023)
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The gut microbiome of exudivorous marmosets in the wild and captivity
Malukiewicz, Joanna, Cartwright, Reed A., Dergam, Jorge A., Igayara, Claudia S., Kessler, Sharon E., Moreira, Silvia B., Nash, Leanne T., Nicola, Patricia A., Pereira, Luiz C. M., Pissinatti, Alcides, Ruiz-Miranda, Carlos R., Ozga, Andrew T., Quirino, Adriana A., Roos, Christian, Silva, Daniel L., Stone, Anne C., Grativol, Adriana D.
Published in Scientific reports (23.03.2022)
Published in Scientific reports (23.03.2022)
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Journal Article
Federated learning and Indigenous genomic data sovereignty
Boscarino, Nima, Cartwright, Reed A., Fox, Keolu, Tsosie, Krystal S.
Published in Nature machine intelligence (01.11.2022)
Published in Nature machine intelligence (01.11.2022)
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Journal Article
Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
Malukiewicz, Joanna, Cartwright, Reed A., Dergam, Jorge A., Igayara, Claudia S., Nicola, Patricia A., Pereira, Luiz M. C., Ruiz-Miranda, Carlos R., Stone, Anne C., Silva, Daniel L., Silva, Fernanda de Fatima Rodrigues da, Varsani, Arvind, Walter, Lutz, Wilson, Melissa A., Zinner, Dietmar, Roos, Christian
Published in Scientific reports (26.08.2021)
Published in Scientific reports (26.08.2021)
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Journal Article
The khmer software package: enabling efficient nucleotide sequence analysis [version 1; peer review: 2 approved, 1 approved with reservations]
Crusoe, Michael R, Alameldin, Hussien F, Awad, Sherine, Boucher, Elmar, Caldwell, Adam, Cartwright, Reed, Charbonneau, Amanda, Constantinides, Bede, Edvenson, Greg, Fay, Scott, Fenton, Jacob, Fenzl, Thomas, Fish, Jordan, Garcia-Gutierrez, Leonor, Garland, Phillip, Gluck, Jonathan, González, Iván, Guermond, Sarah, Guo, Jiarong, Gupta, Aditi, Herr, Joshua R, Howe, Adina, Hyer, Alex, Härpfer, Andreas, Irber, Luiz, Kidd, Rhys, Lin, David, Lippi, Justin, Mansour, Tamer, McA'Nulty, Pamela, McDonald, Eric, Mizzi, Jessica, Murray, Kevin D, Nahum, Joshua R, Nanlohy, Kaben, Nederbragt, Alexander Johan, Ortiz-Zuazaga, Humberto, Ory, Jeramia, Pell, Jason, Pepe-Ranney, Charles, Russ, Zachary N, Schwarz, Erich, Scott, Camille, Seaman, Josiah, Sievert, Scott, Simpson, Jared, Skennerton, Connor T, Spencer, James, Srinivasan, Ramakrishnan, Standage, Daniel, Stapleton, James A, Steinman, Susan R, Stein, Joe, Taylor, Benjamin, Trimble, Will, Wiencko, Heather L, Wright, Michael, Wyss, Brian, Zhang, Qingpeng, zyme, en, Brown, C. Titus
Published in F1000 research (2015)
Published in F1000 research (2015)
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The importance of selection in the evolution of blindness in cavefish
Cartwright, Reed A, Schwartz, Rachel S, Merry, Alexandra L, Howell, Megan M
Published in BMC evolutionary biology (07.02.2017)
Published in BMC evolutionary biology (07.02.2017)
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