Publications | BCM-HGSC

Export 30 results:

Filters: Author is Mahmoud, Medhat [Clear All Filters]

2023

Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: what's next in diagnostic testing for Mendelian conditions. ArXiv. 2023 ;.

Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet. 2023 ;110(8):1229-1248.

Behera S, LeFaive J, Orchard P, Mahmoud M, Paulin LF, Farek J, Soto DC, Parker SCJ, Smith AV, Dennis MY, Zook JM, Sedlazeck FJ. FixItFelix: improving genomic analysis by fixing reference errors. Genome Biol. 2023 ;24(1):31.

Billingsley KJ, Ding J, Jerez PAlvarez, Illarionova A, Levine K, Grenn FP, Makarious MB, Moore A, Vitale D, Reed X, Hernandez D, Torkamani A, Ryten M, Hardy J, Chia R, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach TG, Serrano GE, Quinn JP, Bubb VJ, Collins RL, Zhao X, Walker M, Pierce-Hoffman E, Brand H, Talkowski ME, Casey B, Cookson MR, Markham A, Nalls MA, Mahmoud M, Sedlazeck FJ, Blauwendraat C, J Gibbs R, Singleton AB. Genome-Wide Analysis of Structural Variants in Parkinson Disease. Ann Neurol. 2023 ;93(5):1012-1022.

Majidian S, Agustinho DPaiva, Chin C-S, Sedlazeck FJ, Mahmoud M. Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biol. 2023 ;24(1):221.

Akagi K, Symer DE, Mahmoud M, Jiang B, Goodwin S, Wangsa D, Li Z, Xiao W, Dunn JDan, Ried T, Coombes KR, Sedlazeck FJ, Gillison ML. Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration. Cancer Discov. 2023 ;13(4):910-927.

2022

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 C-A, Barrio AMartinez, Fiddes IT, Xiao C, Fungtammasan A, Chin C-S, Wenger AM, Rowell WJ, Sedlazeck FJ, Carroll A, Salit M, Zook JM. Benchmarking challenging small variants with linked and long reads. Cell Genom. 2022 ;2(5).

Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny DM, Wiseman RW, O'Connor DH, Rogers J. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience. 2022 ;11.

Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang Y-C, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, Xiao C, Yoo B, Sahraeian SMohammad E, Miller DE, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Narzisi G, Evani UShanker, Clarke WE, Lee J, Mason CE, Lincoln SE, Miga KH, Ebbert MTW, Shumate A, Li H, Chin C-S, Zook JM, Sedlazeck FJ. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol. 2022 ;40(5):672-680.

Menon V, Okhuysen PC, Chappell CL, Mahmoud M, Mahmoud M, Meng Q, Doddapaneni H, Vee V, Han Y, Salvi S, Bhamidipati S, Kottapalli K, Weissenberger G, Shen H, Ross MC, Hoffman KL, Cregeen SJavornik, Muzny DM, Metcalf GA, Gibbs RA, Petrosino JF, Sedlazeck FJ. Fully resolved assembly of Cryptosporidium parvum. Gigascience. 2022 ;11.

Menon V, Okhuysen PC, Chappell CL, Mahmoud M, Mahmoud M, Meng Q, Doddapaneni H, Vee V, Han Y, Salvi S, Bhamidipati S, Kottapalli K, Weissenberger G, Shen H, Ross MC, Hoffman KL, Cregeen SJavornik, Muzny DM, Metcalf GA, Gibbs RA, Petrosino JF, Sedlazeck FJ. Fully resolved assembly of Cryptosporidium parvum. Gigascience. 2022 ;11.

Chander V, Mahmoud M, Hu J, Dardas Z, Grochowski CM, Dawood M, Khayat MM, Li H, Li S, Jhangiani S, Korchina V, Shen H, Weissenberger G, Meng Q, Gingras M-C, Muzny DM, Doddapaneni H, Posey JE, Lupski JR, Sabo A, Murdock DR, Sedlazeck FJ, Gibbs RA. Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism. Hum Mutat. 2022 ;43(12):2033-2053.

Liu Y, Kearney J, Mahmoud M, Kille B, Sedlazeck FJ, Treangen TJ. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data. Nat Commun. 2022 ;13(1):1321.

Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AAl, Mahmoud M, Paulin LF, Raza MSohail, Pfeifer SP, Agustinho DPaiva, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LChuin, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DMorgan, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRohit Raj, Kubica J, Lakra P, Lattimer D, Liew C-S, Lo B-W, Lo C, Lötter A, Majidian S, Mendem SKumar, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon C-L, 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. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res. 2022 ;11:530.

2021

Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol. 2021 ;39(11):1466.

Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin C-S, Church GM, Li H. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol. 2021 ;39(3):309-312.

Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol. 2021 ;39(9):1129-1140.

Mahmoud M, Doddapaneni H, Timp W, Sedlazeck FJ. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol. 2021 ;22(1):268.

Liu Y, Kearney J, Mahmoud M, Kille B, Sedlazeck FJ, Treangen TJ. Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data. bioRxiv. 2021 ;.

Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RALeo, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Berry IMaljkovic, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021 ;31(4):635-644.

Fu Y, Mahmoud M, Muraliraman VVaibhav, Sedlazeck FJ, Treangen TJ. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. Gigascience. 2021 ;10(9).

1
2
next
last