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Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.
Bickhart DM, Kolmogorov M, Tseng E, Portik DM, Korobeynikov A, Tolstoganov I, Uritskiy G, Liachko I, Sullivan ST, Shin SB, Zorea A, Andreu VP, Panke-Buisse K, Medema MH, Mizrahi I, Pevzner PA, Smith TPL. Bickhart DM, et al. Among authors: tseng e. Nat Biotechnol. 2022 May;40(5):711-719. doi: 10.1038/s41587-021-01130-z. Epub 2022 Jan 3. Nat Biotechnol. 2022. PMID: 34980911
De novo assembly of the cattle reference genome with single-molecule sequencing.
Rosen BD, Bickhart DM, Schnabel RD, Koren S, Elsik CG, Tseng E, Rowan TN, Low WY, Zimin A, Couldrey C, Hall R, Li W, Rhie A, Ghurye J, McKay SD, Thibaud-Nissen F, Hoffman J, Murdoch BM, Snelling WM, McDaneld TG, Hammond JA, Schwartz JC, Nandolo W, Hagen DE, Dreischer C, Schultheiss SJ, Schroeder SG, Phillippy AM, Cole JB, Van Tassell CP, Liu G, Smith TPL, Medrano JF. Rosen BD, et al. Among authors: tseng e. Gigascience. 2020 Mar 1;9(3):giaa021. doi: 10.1093/gigascience/giaa021. Gigascience. 2020. PMID: 32191811 Free PMC article.
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AWC, Heaton MP, Phillippy AM, Hiendleder S, Smith TPL, Williams JL. Low WY, et al. Among authors: tseng e. Nat Commun. 2020 Apr 29;11(1):2071. doi: 10.1038/s41467-020-15848-y. Nat Commun. 2020. PMID: 32350247 Free PMC article.
An improved pig reference genome sequence to enable pig genetics and genomics research.
Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. Warr A, et al. Among authors: tseng e. Gigascience. 2020 Jun 1;9(6):giaa051. doi: 10.1093/gigascience/giaa051. Gigascience. 2020. PMID: 32543654 Free PMC article.
SpaRC: scalable sequence clustering using Apache Spark.
Shi L, Meng X, Tseng E, Mascagni M, Wang Z. Shi L, et al. Among authors: tseng e. Bioinformatics. 2019 Mar 1;35(5):760-768. doi: 10.1093/bioinformatics/bty733. Bioinformatics. 2019. PMID: 30816928
351 results