Publications | BCM-HGSC

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Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin C-S, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019 ;37(10):1155-1162.

Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018 ;15(6):461-468.

Hall CL, Kesharwani RK, Phillips NR, Planz JV, Sedlazeck FJ, Zascavage RR. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device. Forensic Sci Int Genet. 2022 ;56:102629.

Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A, Jantsch MF. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res. 2014 ;42(19):12155-68.

Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A, Jantsch MF. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res. 2012 ;22(8):1468-76.

Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Scheid OMittelsten, von Haeseler A. Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS One. 2012 ;7(7):e41528.

English AC, Dolzhenko E, Jam HZiaei, McKenzie SK, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. Analysis and benchmarking of small and large genomic variants across tandem repeats. Nat Biotechnol. 2024 ;.

Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast. Mol Biol Evol. 2019 ;36(9):1975-1989.

Zascavage RR, Hall CL, Thorson K, Mahmoud M, Sedlazeck FJ, Planz JV. Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION. Curr Protoc Hum Genet. 2019 ;104(1):e94.

Pan B, Ren L, Onuchic V, Guan M, Kusko R, Bruinsma S, Trigg L, Scherer A, Ning B, Zhang C, Glidewell-Kenney C, Xiao C, Donaldson E, Sedlazeck FJ, Schroth G, Yavas G, Grunenwald H, Chen H, Meinholz H, Meehan J, Wang J, Yang J, Foox J, Shang J, Miclaus K, Dong L, Shi L, Mohiyuddin M, Pirooznia M, Gong P, Golshani R, Wolfinger R, Lababidi S, Sahraeian SMohammad E, Sherry S, Han T, Chen T, Shi T, Hou W, Ge W, Zou W, Guo W, Bao W, Xiao W, Fan X, Gondo Y, Yu Y, Zhao Y, Su Z, Liu Z, Tong W, Xiao W, Zook JM, Zheng Y, Hong H. Assessing reproducibility of inherited variants detected with short-read whole genome sequencing. Genome Biol. 2022 ;23(1):2.

Chiang T, Liu X, Wu T-J, Hu J, Sedlazeck FJ, White S, Schaid D, de Andrade M, Jarvik GP, Crosslin D, Stanaway I, Carrell DS, Connolly JJ, Hakonarson H, Groopman EE, Gharavi AG, Fedotov A, Bi W, Leduc MS, Murdock DR, Jiang Y, Meng L, Eng CM, Wen S, Yang Y, Muzny DM, Boerwinkle E, Salerno W, Venner E, Gibbs RA. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel. Genet Med. 2019 ;21(9):2135-2144.

Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SMohammad E, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AMartinez, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 ;38(11):1357.

Weissensteiner MH, Bunikis I, Catalán A, Francoijs K-J, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Author Correction: Discovery and population genomics of structural variation in a songbird genus. Nat Commun. 2021 ;12(1):3163.

Soyk S, Lemmon ZH, Sedlazeck FJ, Jiménez-Gómez JM, Alonge M, Hutton SF, Van Eck J, Schatz MC, Lippman ZB. Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants. 2019 ;5(8):903.

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.

Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM. Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nat Methods. 2022 ;19(6):770.

Liu Z, Roberts R, Mercer TR, Xu J, Sedlazeck FJ, Tong W. Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis. Genome Biol. 2022 ;23(1):198.

B

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).

Paulin LF, Fan J, O'Neill K, Pleasance E, Porter VL, Jones SJM, Sedlazeck FJ. The benefit of a complete reference genome for cancer structural variant analysis. medRxiv. 2024 ;.

Sedlazeck FJ, Talloji P, von Haeseler A, Bachmair A. Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets. Genomics. 2013 ;101(3):204-9.

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.

Dawood M, Akay G, Mitani T, Marafi D, Fatih JM, Gezdirici A, Najmabadi H, Kahrizi K, Punetha J, Grochowski CM, Du H, Jolly A, Li H, Coban-Akdemir Z, Sedlazeck FJ, Hunter JV, Jhangiani SN, Muzny DM, Pehlivan D, Posey JE, Carvalho CMB, Gibbs RA, Lupski JR. A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly. Am J Med Genet A. 2023 ;191(3):794-804.

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