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Paper

Ou, Shujun, Scheben, Armin, Collins, Tyler, Qiu, Yinjie, Seetharam, Arun S, Menard, Claire C, Manchanda, Nancy, Gent, Jonathan I, Schatz, Michael C, Anderson, Sarah N, Hufford, Matthew B, Hirsch, Candice N (September 2024) Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research. ISSN 1088-9051

Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Grimanelli, Daniel, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert A (August 2024) Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature. ISSN 0028-0836 (Public Dataset)

Serio, Ryan N, Scheben, Armin, Lu, Billy, Gargiulo, Domenic V, Patruno, Lucrezia, Buckholtz, Caroline L, Chaffee, Ryan J, Jibilian, Megan C, Persaud, Steven G, Staklinski, Stephen J, Hassett, Rebecca, Brault, Lise M, Ramazzotti, Daniele, Barbieri, Christopher E, Siepel, Adam C, Nowak, Dawid G (July 2024) Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer. Cancer Discovery. ISSN 2159-8274

Zhai, Jingjing, Gokaslan, Aaron, Schiff, Yair, Berthel, Ana, Liu, Zong-Yan, Miller, Zachary R, Scheben, Armin, Stitzer, Michelle C, Romay, M Cinta, Buckler, Edward S, Kuleshov, Volodymyr (June 2024) Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model. bioRxiv. (Public Dataset) (Submitted)

Wang, Kejun, Hua, Guoying, Li, Jingyi, Yang, Yu, Zhang, Chenxi, Yang, Lan, Hu, Xiaoyu, Scheben, Armin, Wu, Yanan, Gong, Ping, Zhang, Shuangjie, Fan, Yanfeng, Zeng, Tao, Lu, Lizhi, Gong, Yanzhang, Jiang, Ruirui, Sun, Guirong, Tian, Yadong, Kang, Xiangtao, Hu, Haifei, Li, Wenting (December 2023) Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution. iMeta, 3 (1). e154. ISSN 2770-5986 (Public Dataset)

Hu, Haifei, Scheben, Armin, Wang, Jian, Li, Fangping, Li, Chengdao, Edwards, David, Zhao, Junliang (November 2023) Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. Plant Biotechnology Journal. ISSN 1467-7644

Staklinski, Stephen J, Scheben, Armin, Siepel, Adam, Kilberg, Michael S (November 2023) Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification. bioRxiv. (Submitted)

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 (September 2023) Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biology and Evolution, 15 (9). ISSN 1759-6653 (Public Dataset)

Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert A (August 2023) Teosinte Pollen Drive guides maize domestication and evolution by RNAi. bioRxiv. (Public Dataset) (Submitted)

Vranken, S, Scheben, A, Batley, J, Wernberg, T, Coleman, MA (October 2022) Genomic consequences and selection efficacy in sympatric sexual versus asexual kelps. Frontiers in Marine Science, 9. ISSN 2296-7745

Byrne, Dennis, Scheben, Armin, Scott, John K, Webber, Bruce L, Batchelor, Kathryn L, Severn-Ellis, Anita A, Gooden, Ben, Bell, Karen L (August 2022) Genomics reveals the history of a complex plant invasion and improves the management of a biological invasion from the South African-Australian biotic exchange. Ecology and Evolution, 12 (8). e9179. ISSN 2045-7758

Wu, Yaoyao, Johnson, Lynn, Song, Baoxing, Romay, Cinta, Stitzer, Michelle, Siepel, Adam, Buckler, Edward, Scheben, Armin (April 2022) A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants. The Plant Genome. e20204. ISSN 1940-3372

Xiang Neik, Ting, Ghanbarnia, Kaveh, Ollivier, Bénédicte, Scheben, Armin, Severn-Ellis, Anita, Larkan, Nicholas J, Haddadi, Parham, Fernando, Dilantha WG, Rouxel, Thierry, Batley, Jacqueline, Borhan, Hossein M, Balesdent, Marie-Hélène (March 2022) Two independent approaches converge to the cloning of a new Leptosphaeria maculans avirulence effector gene, AvrLmS-Lep2. Molecular Plant Pathology. ISSN 1464-6722

Yuan, Yuxuan, Scheben, Armin, Edwards, David, Chan, Ting-Fung (November 2021) Towards haplotype studies in polyploid plants to assist breeding. Molecular Plant. ISSN 1674-2052

Wolter, Felix, Schindele, Patrick, Beying, Natalja, Scheben, Armin, Puchta, Holger (August 2021) Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants. The Plant Cell. ISSN 1532-298X

Hu, Haifei, Scheben, Armin, Verpaalen, Brent, Tirnaz, Soodeh, Bayer, Philipp E, Hodel, Richard GJ, Batley, Jacqueline, Soltis, Douglas E, Soltis, Pamela S, Edwards, David (July 2021) Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. New Phytologist. ISSN 0028-646X

Wang, Kejun, Hu, Haifei, Tian, Yadong, Li, Jingyi, Scheben, Armin, Zhang, Chenxi, Li, Yiyi, Wu, Junfeng, Yang, Lan, Fan, Xuewei, Sun, Guirong, Li, Donghua, Zhang, Yanhua, Han, Ruili, Jiang, Ruirui, Huang, Hetian, Yan, Fengbin, Wang, Yanbin, Li, Zhuanjian, Li, Guoxi, Liu, Xiaojun, Li, Wenting, Edwards, David, Kang, Xiangtao (July 2021) The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Molecular Biology and Evolution. ISSN 0737-4038

Mehravi, Shaghayegh, Ranjbar, Gholam Ali, Mirzaghaderi, Ghader, Severn-Ellis, Anita Alice, Scheben, Armin, Edwards, David, Batley, Jacqueline (June 2021) De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing. Agronomy, 11 (7). p. 1342. ISSN 2073-4395

Wu, Yaoyao, Johnson, Lynn, Song, Baoxing, Romay, Cinta, Stitzer, Michelle, Siepel, Adam, Buckler, Edward, Scheben, Armin (June 2021) A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants. BioRxiv. (Unpublished)

Vranken, Sofie, Wernberg, Thomas, Scheben, Armin, Severn-Ellis, Anita, Batley, Jacqueline, Philipp, Bayer Emanuel, Edwards, David, Wheeler, David, Coleman, Melinda Ann (May 2021) Genotype-environment mismatch of kelp forests under climate change. Molecular Ecology. ISSN 0962-1083

Mo, Ziyi, Scheben, Armin, Steinberg, Joshua, Siepel, Adam, Martienssen, Robert (March 2021) Circadian immunity, sunrise time and the seasonality of respiratory infections. medRxiv. (Unpublished)

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

Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J., Edwards, D. (August 2020) Plant pan-genomes are the new reference. Nat Plants, 6 (8). pp. 914-920. ISSN 2055-0278