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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Kolmogorov M, et al. Among authors: behera s. Nat Methods. 2023 Oct;20(10):1483-1492. doi: 10.1038/s41592-023-01993-x. Epub 2023 Sep 14. Nat Methods. 2023. PMID: 37710018
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.
Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AA, Mahmoud M, Paulin LF, Raza MS, Pfeifer SP, Agustinho DP, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LC, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DM, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRR, Kubica J, Lakra P, Lattimer D, Liew CS, Lo BW, Lo C, Lötter A, Majidian S, Mendem SK, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon CL, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, Busby B. Walker K, et al. Among authors: behera s. F1000Res. 2022 May 16;11:530. doi: 10.12688/f1000research.110194.1. eCollection 2022. F1000Res. 2022. PMID: 36262335 Free PMC article.
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PA, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P; North American Brain Expression Consortium (NABEC); Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Kolmogorov M, et al. Among authors: behera s. bioRxiv [Preprint]. 2023 Apr 5:2023.01.12.523790. doi: 10.1101/2023.01.12.523790. bioRxiv. 2023. PMID: 36711673 Free PMC article. Updated. Preprint.
FixItFelix: improving genomic analysis by fixing reference errors.
Behera S, LeFaive J, Orchard P, Mahmoud M, Paulin LF, Farek J, Soto DC, Parker SCJ, Smith AV, Dennis MY, Zook JM, Sedlazeck FJ. Behera S, et al. Genome Biol. 2023 Feb 21;24(1):31. doi: 10.1186/s13059-023-02863-7. Genome Biol. 2023. PMID: 36810122 Free PMC article.
Detection of mosaic and population-level structural variants with Sniffles2.
Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ. Smolka M, et al. Among authors: behera s. Nat Biotechnol. 2024 Jan 2. doi: 10.1038/s41587-023-02024-y. Online ahead of print. Nat Biotechnol. 2024. PMID: 38168980
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates.
Mc Cartney AM, Mahmoud M, Jochum M, Agustinho DP, Zorman B, Al Khleifat A, Dabbaghie F, K Kesharwani R, Smolka M, Dawood M, Albin D, Aliyev E, Almabrazi H, Arslan A, Balaji A, Behera S, Billingsley K, L Cameron D, Daw J, T Dawson E, De Coster W, Du H, Dunn C, Esteban R, Jolly A, Kalra D, Liao C, Liu Y, Lu TY, M Havrilla J, M Khayat M, Marin M, Monlong J, Price S, Rafael Gener A, Ren J, Sagayaradj S, Sapoval N, Sinner C, C Soto D, Soylev A, Subramaniyan A, Syed N, Tadimeti N, Tater P, Vats P, Vaughn J, Walker K, Wang G, Zeng Q, Zhang S, Zhao T, Kille B, Biederstedt E, Chaisson M, English A, Kronenberg Z, J Treangen T, Hefferon T, Chin CS, Busby B, J Sedlazeck F. Mc Cartney AM, et al. Among authors: behera s. F1000Res. 2021 Mar 26;10:246. doi: 10.12688/f1000research.51477.2. eCollection 2021. F1000Res. 2021. PMID: 34621504 Free PMC article.
Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk.
Behera S, Belyeu JR, Chen X, Paulin LF, Nguyen NQH, Newman E, Mahmoud M, Menon VK, Qi Q, Joshi P, Marcovina S, Rossi M, Roller E, Han J, Onuchic V, Avery CL, Ballantyne CM, Rodriguez CJ, Kaplan RC, Muzny DM, Metcalf GA, Gibbs R, Yu B, Boerwinkle E, Eberle MA, Sedlazeck FJ. Behera S, et al. bioRxiv [Preprint]. 2023 Apr 27:2023.04.24.538128. doi: 10.1101/2023.04.24.538128. bioRxiv. 2023. PMID: 37163057 Free PMC article. Preprint.
831 results