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FRITZ SEDLAZECK

TitleAssociate Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
AddressOne Baylor Plaza
Houston, TX 77030
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    Other Positions
    TitleAssociate Professor
    InstitutionBaylor College of Medicine
    DepartmentHuman Genome Sequencing Center
    DivisionHuman Genome Sequencing Center


    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Ji Y, Zhao J, Gong J, Sedlazeck FJ, Fan S. Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations. Mol Genet Genomics. 2024 Jul 07; 299(1):65. PMID: 38972030.
      Citations:    Fields:    Translation:Humans
    2. Fu Y, Aganezov S, Mahmoud M, Beaulaurier J, Juul S, Treangen TJ, Sedlazeck FJ. MethPhaser: methylation-based long-read haplotype phasing of human genomes. Nat Commun. 2024 Jun 22; 15(1):5327. PMID: 38909018; PMCID: PMC11193733.
      Citations:    Fields:    Translation:HumansCells
    3. Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, H?ps W, Benito E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Hwang JP, Bhamidipati SV, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci. Cell Genom. 2024 Jul 10; 4(7):100590. PMID: 38908378.
      Citations:    Fields:    Translation:Humans
    4. Alvarez Jerez P, Daida K, Miano-Burkhardt A, Iwaki H, Malik L, Cogan G, Makarious MB, Sullivan R, Vandrovcova J, Ding J, Gibbs JR, Markham A, Nalls MA, Kesharwani RK, Sedlazeck FJ, Casey B, Hardy J, Houlden H, Blauwendraat C, Singleton AB, Billingsley KJ. Profiling complex repeat expansions in RFC1 in Parkinson's disease. NPJ Parkinsons Dis. 2024 May 24; 10(1):108. PMID: 38789445; PMCID: PMC11126591.
      Citations:    
    5. Pfeifer SP, Baxter A, Savidge LE, Sedlazeck FJ, Bales KL. De Novo Genome Assembly for the Coppery Titi Monkey (Plecturocebus cupreus): An Emerging Nonhuman Primate Model for Behavioral Research. Genome Biol Evol. 2024 05 02; 16(5). PMID: 38758096; PMCID: PMC11140417.
      Citations:    Fields:    Translation:Animals
    6. Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods. 2024 Jun; 21(6):954-966. PMID: 38689099.
      Citations: 1     Fields:    Translation:Humans
    7. English AC, Dolzhenko E, Ziaei Jam H, 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 Apr 26. PMID: 38671154.
      Citations: 4     Fields:    
    8. Bilgrav Saether K, Eisfeldt J, Bengtsson J, Lun MY, Grochowski CM, Mahmoud M, Chao HT, Rosenfeld JA, Liu P, Schuy J, Ameur A, Undiagnosed Diseases Network, Hwang JP, Sedlazeck FJ, Bi W, Marom R, Nordgren A, Carvalho CMB, Lindstrand A. Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions. medRxiv. 2024 Apr 24. PMID: 38712270; PMCID: PMC11071548.
      Citations:    
    9. Mahmoud M, Harting J, Corbitt H, Chen X, Jhangiani SN, Doddapaneni H, Meng Q, Han T, Lambert C, Zhang S, Baybayan P, Henno G, Shen H, Hu J, Han Y, Riegler C, Metcalf G, Chinn IK, Eberle MA, Kingan S, Farinholt T, Carvalho CMB, Gibbs RA, Kronenberg Z, Muzny D, Sedlazeck FJ. Closing the gap: Solving complex medically relevant genes at scale. medRxiv. 2024 Mar 18. PMID: 38562723; PMCID: PMC10984040.
      Citations:    
    10. 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 Mar 18. PMID: 38562786; PMCID: PMC10984048.
      Citations:    
    11. Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SH, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, 1000 Genomes ONT Sequencing Consortium, University of Washington Center for Rare Disease Research (UW-CRDR), Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. medRxiv. 2024 Mar 07. PMID: 38496498; PMCID: PMC10942501.
      Citations:    
    12. Chen F, Zhang Y, Sedlazeck FJ, Creighton CJ. Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes. Cell Rep Med. 2024 Mar 19; 5(3):101446. PMID: 38442712; PMCID: PMC10983041.
      Citations:    Fields:    Translation:HumansCells
    13. 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. Publisher Correction: Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol. 2024 Jan 22. PMID: 38253882.
      Citations:    Fields:    
    14. Behera S, Catreux S, Rossi M, Truong S, Huang Z, Ruehle M, Visvanath A, Parnaby G, Roddey C, Onuchic V, Cameron DL, English A, Mehtalia S, Han J, Mehio R, Sedlazeck FJ. Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms. bioRxiv. 2024 Jan 06. PMID: 38260545; PMCID: PMC10802302.
      Citations:    
    15. 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. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol. 2024 Jan 02. PMID: 38168980; PMCID: PMC11217151.
      Citations: 6     Fields:    
    16. Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Mart?nez-Cerde?o V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol. 2024 Jan 02. PMID: 38168995.
      Citations: 2     Fields:    
    17. Avadhanula V, Agustinho DP, Menon VK, Chemaly RF, Shah DP, Qin X, Surathu A, Doddapaneni H, Muzny DM, Metcalf GA, Cregeen SJ, Gibbs RA, Petrosino JF, Sedlazeck FJ, Piedra PA. Inter and intra-host diversity of RSV in hematopoietic stem cell transplant adults with normal and delayed viral clearance. Virus Evol. 2024; 10(1):vead086. PMID: 38361816; PMCID: PMC10868550.
      Citations:    
    18. Chen NC, Paulin LF, Sedlazeck FJ, Koren S, Phillippy AM, Langmead B. Improved sequence mapping using a complete reference genome and lift-over. Nat Methods. 2024 Jan; 21(1):41-49. PMID: 38036856.
      Citations: 2     Fields:    
    19. Kalef-Ezra E, Turan ZG, Perez-Rodriguez D, Bomann I, Behera S, Morley C, Scholz SW, Jaunmuktane Z, Demeulemeester J, Sedlazeck FJ, Proukakis C. Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. bioRxiv. 2023 Nov 21. PMID: 37609320; PMCID: PMC10441336.
      Citations:    
    20. English A, Dolzhenko E, Jam HZ, Mckenzie S, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. Benchmarking of small and large variants across tandem repeats. bioRxiv. 2023 Nov 01. PMID: 37961319; PMCID: PMC10634962.
      Citations:    
    21. Krannich T, Sarrias MH, Ben Aribi H, Shokrof M, Iacoangeli A, Al-Chalabi A, Sedlazeck FJ, Busby B, Al Khleifat A. VariantSurvival: a tool to identify genotype-treatment response. Front Bioinform. 2023; 3:1277923. PMID: 37885757; PMCID: PMC10598652.
      Citations:    
    22. Majidian S, Agustinho DP, Chin CS, Sedlazeck FJ, Mahmoud M. Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biol. 2023 10 05; 24(1):221. PMID: 37798733; PMCID: PMC10552390.
      Citations: 1     Fields:    
    23. Grochowski CM, Bengtsson JD, Du H, Gandhi M, Lun MY, Mehaffey MG, Park K, H?ps W, Benito-Garagorri E, Hasenfeld P, Korbel JO, Mahmoud M, Paulin LF, Jhangiani SN, Muzny DM, Fatih JM, Gibbs RA, Pendleton M, Harrington E, Juul S, Lindstrand A, Sedlazeck FJ, Pehlivan D, Lupski JR, Carvalho CMB. Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures. bioRxiv. 2023 Oct 03. PMID: 37873367; PMCID: PMC10592851.
      Citations:    
    24. 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. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nat Methods. 2023 10; 20(10):1483-1492. PMID: 37710018; PMCID: PMC11222905.
      Citations: 14     Fields:    Translation:HumansCells
    25. Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. The complete sequence of a human Y chromosome. Nature. 2023 Sep; 621(7978):344-354. PMID: 37612512; PMCID: PMC10752217.
      Citations: 23     Fields:    Translation:HumansCells
    26. Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, D?lot EC, Jain D, Sanchis-Juan A, Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, 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 08 03; 110(8):1229-1248. PMID: 37541186; PMCID: PMC10432150.
      Citations: 10     Fields:    Translation:Humans
    27. Chin CS, Behera S, Khalak A, Sedlazeck FJ, Sudmant PH, Wagner J, Zook JM. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nat Methods. 2023 08; 20(8):1213-1221. PMID: 37365340; PMCID: PMC10406601.
      Citations: 4     Fields:    Translation:Humans
    28. Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol. 2024 Jan; 42(1):139-147. PMID: 37081138; PMCID: PMC10791578.
      Citations:    Fields:    
    29. Olson ND, Wagner J, Dwarshuis N, Miga KH, Sedlazeck FJ, Salit M, Zook JM. Variant calling and benchmarking in an era of complete human genome sequences. Nat Rev Genet. 2023 Jul; 24(7):464-483. PMID: 37059810.
      Citations: 4     Fields:    Translation:Humans
    30. North American Brain Expression Consortium (NABEC), 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, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. bioRxiv. 2023 Apr 05. PMID: 36711673; PMCID: PMC9882142.
      Citations:    
    31. Akagi K, Symer DE, Mahmoud M, Jiang B, Goodwin S, Wangsa D, Li Z, Xiao W, Ried T, Coombes KR, Sedlazeck FJ, Gillison ML, Dunn JD. Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration. Cancer Discov. 2023 04 03; 13(4):910-927. PMID: 36715691; PMCID: PMC10070172.
      Citations: 2     Fields:    Translation:HumansCells
    32. Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, G?rsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guig? R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes?& variant-impact models. Cell. 2023 03 30; 186(7):1493-1511.e40. PMID: 37001506; PMCID: PMC10074325.
      Citations: 2     Fields:    
    33. 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 02 21; 24(1):31. PMID: 36810122; PMCID: PMC9942314.
      Citations: 2     Fields:    Translation:Humans
    34. Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJF, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. Res Sq. 2023 Feb 03. PMID: 36778386; PMCID: PMC9915771.
      Citations:    
    35. Illarionova A, Levine K, Ryten M, Hardy J, UK Brain Expression Consortium (UKBEC), Markham A, Billingsley KJ, Ding J, Jerez PA, Grenn FP, Makarious MB, Moore A, Vitale D, Reed X, Hernandez D, Torkamani A, 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, Nalls MA, Mahmoud M, Sedlazeck FJ, Blauwendraat C, Gibbs JR, Singleton AB. Genome-Wide Analysis of Structural Variants in Parkinson Disease. Ann Neurol. 2023 05; 93(5):1012-1022. PMID: 36695634; PMCID: PMC10192042.
      Citations: 3     Fields:    Translation:Humans
    36. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJF, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. bioRxiv. 2023 Jan 25. PMID: 36747810; PMCID: PMC9900832.
      Citations:    
    37. Paulin LF, Raveendran M, Harris RA, Rogers J, von Haeseler A, Sedlazeck FJ. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics. 2023 Jan 20; 24(1):23. PMID: 36670361; PMCID: PMC9854228.
      Citations:    Fields:    Translation:HumansAnimals
    38. Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, D?lot EC, Jain D, Sanchis-Juan A, Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, 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 Jan 18. PMID: 36713248; PMCID: PMC9882576.
      Citations:    
    39. 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 D, 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 03; 191(3):794-804. PMID: 36598158; PMCID: PMC9928800.
      Citations:    Fields:    Translation:Humans
    40. Farek J, Hughes D, Salerno W, Zhu Y, Pisupati A, Mansfield A, Krasheninina O, English AC, Metcalf G, Boerwinkle E, Muzny DM, Gibbs R, Khan Z, Sedlazeck FJ. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments. Gigascience. 2022 12 28; 12. PMID: 36644891; PMCID: PMC9841152.
      Citations: 6     Fields:    
    41. English AC, Menon VK, Gibbs RA, Metcalf GA, Sedlazeck FJ. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol. 2022 12 27; 23(1):271. PMID: 36575487; PMCID: PMC9793516.
      Citations: 22     Fields:    Translation:Humans
    42. Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Read2Tree: scalable and accurate phylogenetic trees from raw reads. bioRxiv. 2022 Dec 13. PMID: 36561179; PMCID: PMC9774205.
      Citations:    
    43. Wheeler MM, Stilp AM, Rao S, Halld?rsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, ?orsteinsd?ttir U, Magn?sson MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun. 2022 12 08; 13(1):7592. PMID: 36481753; PMCID: PMC9732337.
      Citations: 5     Fields:    Translation:HumansCells
    44. Orantes-Bonilla M, Makhoul M, Lee H, Chawla HS, Vollrath P, Langstroff A, Sedlazeck FJ, Zou J, Snowdon RJ. Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation. Front Plant Sci. 2022; 13:1057953. PMID: 36466276; PMCID: PMC9716091.
      Citations: 2     
    45. Du H, Jolly A, Grochowski CM, Yuan B, Dawood M, Jhangiani SN, Li H, Muzny D, Fatih JM, Coban-Akdemir Z, Carlin ME, Scheuerle AE, Witzl K, Posey JE, Pendleton M, Harrington E, Juul S, Hastings PJ, Bi W, Gibbs RA, Sedlazeck FJ, Lupski JR, Carvalho CMB, Liu P. The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation. Genome Med. 2022 10 27; 14(1):122. PMID: 36303224; PMCID: PMC9609164.
      Citations: 4     Fields:    Translation:Humans
    46. 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 MC, 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 12; 43(12):2033-2053. PMID: 36054313; PMCID: PMC10167679.
      Citations:    
    47. 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 Sep 20; 23(1):198. PMID: 36127716; PMCID: PMC9490989.
      Citations:    
    48. Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biol. 2022 08 29; 23(1):182. PMID: 36038949; PMCID: PMC9421119.
      Citations:    
    49. Toffoli M, Chen X, Sedlazeck FJ, Lee CY, Mullin S, Higgins A, Koletsi S, Garcia-Segura ME, Sammler E, Scholz SW, Schapira AHV, Eberle MA, Proukakis C. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson's disease-associated GBA gene. Commun Biol. 2022 07 06; 5(1):670. PMID: 35794204; PMCID: PMC9259685.
      Citations:    Translation:Humans
    50. 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 Jun; 19(6):770. PMID: 35618956; PMCID: PMC9184272.
      Citations:    Fields:    
    51. Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny D, 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 05 28; 11. PMID: 35640223; PMCID: PMC9155146.
      Citations: 2     Fields:    Translation:AnimalsCells
    52. 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, H?ps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRR, Kubica J, Lakra P, Lattimer D, Liew CS, Lo BW, Lo C, L?tter 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. 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. PMID: 36262335; PMCID: PMC9557141.
      Citations:    Fields:    Translation:HumansCells
    53. Huang L, Rosen JD, Sun Q, Chen J, Wheeler MM, Zhou Y, Min YI, Kooperberg C, Conomos MP, Stilp AM, Rich SS, Rotter JI, Manichaikul A, Loos RJF, Kenny EE, Blackwell TW, Smith AV, Jun G, Sedlazeck FJ, Metcalf G, Boerwinkle E, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Raffield LM, Reiner AP, Auer PL, Li Y. TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data. Am J Hum Genet. 2022 06 02; 109(6):1175-1181. PMID: 35504290; PMCID: PMC9247832.
      Citations:    Fields:    Translation:Humans
    54. 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 CA, Barrio AM, Fiddes IT, Xiao C, Fungtammasan A, Chin CS, Wenger AM, Rowell WJ, Sedlazeck FJ, Carroll A, Salit M, Zook JM. Benchmarking challenging small variants with linked and long reads. Cell Genom. 2022 May; 2(5). PMID: 36452119; PMCID: PMC9706577.
      Citations: 23     
    55. Olson ND, Wagner J, McDaniel J, Stephens SH, Westreich ST, Prasanna AG, Johanson E, Boja E, Maier EJ, Serang O, Kyriakidis K, Malousi A, Shafin K, Pesout T, Jain M, Paten B, Chang PC, Kolesnikov A, Nattestad M, Baid G, Goel S, Yang H, Carroll A, Li G, Ma C, Tang L, Du Y, Zhang S, Morata J, Brueffer C, Demirkaya-Budak S, Kabakci-Zorlu D, Turgut D, Budak G, Arslan E, Brown R, Johnson IJ, Dolgoborodov A, Semenyuk V, Jain A, Tetikol HS, Jain V, Ruehle M, Lajoie B, Roddey C, Catreux S, Mehio R, Ahsan MU, Liu Q, Wang K, Sahraeian SME, Fang LT, Mohiyuddin M, Hung C, Jain C, Feng H, Li Z, Chen L, Sedlazeck FJ, Zook JM, J?spez D, Lorenzo-Salazar JM, Mu?oz-Barrera A, Rubio-Rodr?guez LA, Flores C, Eveleigh R, Bourgey M, Bourque G, Tonda R, Parra G, Trotta JR, Kalay ?, Narci K. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions. Cell Genom. 2022 05 11; 2(5). PMID: 35720974; PMCID: PMC9205427.
      Citations: 3     
    56. Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM. Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nat Methods. 2022 04; 19(4):445-448. PMID: 35396485; PMCID: PMC9007735.
      Citations: 1     Fields:    Translation:Humans
    57. Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC. A complete reference genome improves analysis of human genetic variation. Science. 2022 04; 376(6588):eabl3533. PMID: 35357935; PMCID: PMC9336181.
      Citations: 10     Fields:    Translation:Humans
    58. Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sovic I, Storer JM, Streets A, Sullivan BA, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM, Marschall T, Thibaud-Nissen F. The complete sequence of a human genome. Science. 2022 04; 376(6588):44-53. PMID: 35357919; PMCID: PMC9186530.
      Citations: 53     Fields:    Translation:HumansCells
    59. Goenka SD, Gorzynski JE, Shafin K, Fisk DG, Pesout T, Jensen TD, Monlong J, Chang PC, Baid G, Bernstein JA, Christle JW, Dalton KP, Garalde DR, Grove ME, Guillory J, Kolesnikov A, Nattestad M, Ruzhnikov MRZ, Samadi M, Sethia A, Spiteri E, Wright CJ, Xiong K, Zhu T, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nat Biotechnol. 2022 07; 40(7):1035-1041. PMID: 35347328; PMCID: PMC9287171.
      Citations:    Fields:    Translation:Humans
    60. 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 03 14; 13(1):1321. PMID: 35288552; PMCID: PMC8921239.
      Citations: 5     Fields:    Translation:HumansCells
    61. Liu Z, Roberts R, Mercer TR, Xu J, Sedlazeck FJ, Tong W. Towards accurate and reliable resolution of structural variants for clinical diagnosis. Genome Biol. 2022 03 03; 23(1):68. PMID: 35241127; PMCID: PMC8892125.
      Citations: 2     Fields:    
    62. Menon VK, 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 SJ, Muzny DM, Metcalf GA, Gibbs RA, Petrosino JF, Sedlazeck FJ. Fully resolved assembly of Cryptosporidium parvum. Gigascience. 2022 02 15; 11. PMID: 35166336; PMCID: PMC8848321.
      Citations:    Fields:    Translation:HumansAnimals
    63. Gorzynski JE, Goenka SD, Shafin K, Jensen TD, Fisk DG, Grove ME, Spiteri E, Pesout T, Monlong J, Bernstein JA, Ceresnak S, Chang PC, Christle JW, Chubb H, Dunn K, Garalde DR, Guillory J, Ruzhnikov MRZ, Wright C, Wusthoff CJ, Xiong K, Hollander SA, Berry GJ, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA. Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock. Circ Genom Precis Med. 2022 04; 15(2):e003591. PMID: 35133172.
      Citations:    Fields:    Translation:Humans
    64. Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang YC, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, Xiao C, Yoo B, Sahraeian SME, Miller DE, Narzisi G, Evani US, Clarke WE, Lee J, Mason CE, Lincoln SE, Miga KH, Ebbert MTW, Shumate A, Li H, Chin CS, Zook JM, Sedlazeck FJ, J?spez D, Lorenzo-Salazar JM, Mu?oz-Barrera A, Rubio-Rodr?guez LA, Flores C. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol. 2022 05; 40(5):672-680. PMID: 35132260; PMCID: PMC9117392.
      Citations: 6     Fields:    Translation:Humans
    65. Gorzynski JE, Goenka SD, Shafin K, Jensen TD, Fisk DG, Grove ME, Spiteri E, Pesout T, Monlong J, Baid G, Bernstein JA, Ceresnak S, Chang PC, Christle JW, Chubb H, Dalton KP, Dunn K, Garalde DR, Guillory J, Knowles JW, Kolesnikov A, Ma M, Moscarello T, Nattestad M, Perez M, Ruzhnikov MRZ, Samadi M, Setia A, Wright C, Wusthoff CJ, Xiong K, Zhu T, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA. Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. N Engl J Med. 2022 02 17; 386(7):700-702. PMID: 35020984.
      Citations: 8     Fields:    Translation:Humans
    66. 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 SME, 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 01 03; 23(1):2. PMID: 34980216; PMCID: PMC8722114.
      Citations: 1     Fields:    Translation:Humans
    67. Khayat MM, Sahraeian SME, Zarate S, Carroll A, Hong H, Pan B, Shi L, Gibbs RA, Mohiyuddin M, Zheng Y, Sedlazeck FJ. Hidden biases in germline structural variant detection. Genome Biol. 2021 12 20; 22(1):347. PMID: 34930391; PMCID: PMC8686633.
      Citations: 2     Fields:    Translation:Cells
    68. Baslan T, Kovaka S, Sedlazeck FJ, Zhang Y, Wappel R, Tian S, Lowe SW, Goodwin S, Schatz MC. High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Res. 2021 12 02; 49(21):e124. PMID: 34551429; PMCID: PMC8643650.
      Citations: 1     Fields:    Translation:HumansCells
    69. 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 01; 56:102629. PMID: 34837788.
      Citations:    Fields:    Translation:HumansCells
    70. 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 Nov; 39(11):1466. PMID: 34635840.
      Citations:    Fields:    
    71. Micklethwaite KP, Gowrishankar K, Gloss BS, Li Z, Street JA, Moezzi L, Mach MA, Sutrave G, Clancy LE, Bishop DC, Louie RHY, Cai C, Foox J, MacKay M, Sedlazeck FJ, Blombery P, Mason CE, Luciani F, Gottlieb DJ, Blyth E. Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells. Blood. 2021 10 21; 138(16):1391-1405. PMID: 33974080; PMCID: PMC8532197.
      Citations: 22     Fields:    Translation:HumansCellsCTClinical Trials
    72. Fu Y, Mahmoud M, Muraliraman VV, Sedlazeck FJ, Treangen TJ. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. Gigascience. 2021 09 24; 10(9). PMID: 34561697; PMCID: PMC8463296.
      Citations: 2     Fields:    Translation:Humans
    73. Mahmoud M, Doddapaneni H, Timp W, Sedlazeck FJ. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol. 2021 09 14; 22(1):268. PMID: 34521442; PMCID: PMC8442460.
      Citations: 3     Fields:    Translation:HumansCells
    74. 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 09; 39(9):1129-1140. PMID: 34504351; PMCID: PMC8985210.
      Citations: 12     Fields:    Translation:Humans
    75. 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 Sep 06. PMID: 34518837; PMCID: PMC8437309.
      Citations:    
    76. Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One. 2021; 16(8):e0244468. PMID: 34432798; PMCID: PMC8386831.
      Citations: 8     Fields:    Translation:HumansCells
    77. De Coster W, Weissensteiner MH, Sedlazeck FJ. Towards population-scale long-read sequencing. Nat Rev Genet. 2021 09; 22(9):572-587. PMID: 34050336; PMCID: PMC8161719.
      Citations: 20     Fields:    Translation:Humans
    78. Weissensteiner MH, Bunikis I, Francoijs KJ, Knief U, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW, Catal?n A, Heim W. Author Correction: Discovery and population genomics of structural variation in a songbird genus. Nat Commun. 2021 May 20; 12(1):3163. PMID: 34017009; PMCID: PMC8138003.
      Citations:    Fields:    
    79. Toffoli M, Higgins A, Lee C, Koletsi S, Chen X, Eberle M, Sedlazeck FJ, Mullin S, Proukakis C, Schapira AHV. Intronic Haplotypes in the GBA Gene Do Not Predict Age at Diagnosis of Parkinson's Disease. Mov Disord. 2021 06; 36(6):1456-1460. PMID: 34008887; PMCID: PMC8436748.
      Citations: 2     Fields:    Translation:Humans
    80. Ranallo-Benavidez TR, Lemmon Z, Soyk S, Aganezov S, Salerno WJ, McCoy RC, Lippman ZB, Schatz MC, Sedlazeck FJ. Optimized sample selection for cost-efficient long-read population sequencing. Genome Res. 2021 05; 31(5):910-918. PMID: 33811084; PMCID: PMC8092009.
      Citations: 2     Fields:    Translation:Humans
    81. Jun G, Sedlazeck F, Zhu Q, English A, Metcalf G, Kang HM, Human Genome Structural Variation Consortium (HGSVC), Lee C, Gibbs R, Boerwinkle E. muCNV: Genotyping Structural Variants for Population-level Sequencing. Bioinformatics. 2021 Mar 24. PMID: 33760063; PMCID: PMC8496513.
      Citations: 1     Fields:    
    82. Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun. 2021 03 12; 12(1):1660. PMID: 33712587; PMCID: PMC7954844.
      Citations: 57     Fields:    Translation:HumansCellsPHPublic Health
    83. Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Maljkovic Berry I, 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 04; 31(4):635-644. PMID: 33602693; PMCID: PMC8015855.
      Citations: 22     Fields:    Translation:HumansCells
    84. Zarate S, Carroll A, Mahmoud M, Krasheninina O, Jun G, Salerno WJ, Schatz MC, Boerwinkle E, Gibbs RA, Sedlazeck FJ. Parliament2: Accurate structural variant calling at scale. Gigascience. 2020 12 21; 9(12). PMID: 33347570; PMCID: PMC7751401.
      Citations: 11     Fields:    Translation:Humans
    85. Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals. bioRxiv. 2020 Dec 11. PMID: 33330863; PMCID: PMC7743067.
      Citations:    
    86. 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, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H, Moemke T, Marschall T. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol. 2021 03; 39(3):309-312. PMID: 33288905; PMCID: PMC7954703.
      Citations: 25     Fields:    Translation:HumansCells
    87. Lee I, Razaghi R, Gilpatrick T, Molnar M, Gershman A, Sadowski N, Sedlazeck FJ, Hansen KD, Simpson JT, Timp W. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat Methods. 2020 12; 17(12):1191-1199. PMID: 33230324; PMCID: PMC7704922.
      Citations: 28     Fields:    Translation:HumansCells
    88. Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, 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, 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, Fiddes IT, Barrio AM, Marschall T. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 Nov; 38(11):1357. PMID: 32699374.
      Citations: 2     Fields:    
    89. Sekar S, Tomasini L, Proukakis C, Bae T, Manlove L, Jang Y, Scuderi S, Zhou B, Kalyva M, Amiri A, Mariani J, Sedlazeck FJ, Urban AE, Vaccarino FM, Abyzov A. Complex mosaic structural variations in human fetal brains. Genome Res. 2020 12; 30(12):1695-1704. PMID: 33122304; PMCID: PMC7706730.
      Citations: 3     Fields:    Translation:HumansCells
    90. Chin CS, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, Sedlazeck FJ, Bansal V, Yoo B, Miller N, Zhou X, Carroll A, Barrio AM, Salit M, Zook JM, Rautiainen M, Marschall T, Dilthey AT. A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nat Commun. 2020 09 22; 11(1):4794. PMID: 32963235; PMCID: PMC7508831.
      Citations: 13     Fields:    Translation:HumansCells
    91. Aganezov S, Goodwin S, Sherman RM, Sedlazeck FJ, Arun G, Bhatia S, Lee I, Kirsche M, Wappel R, Kramer M, Kostroff K, Spector DL, Timp W, McCombie WR, Schatz MC. Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Res. 2020 09; 30(9):1258-1273. PMID: 32887686; PMCID: PMC7545150.
      Citations: 22     Fields:    Translation:HumansCells
    92. Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. bioRxiv. 2020 Jul 27. PMID: 32766579; PMCID: PMC7402036.
      Citations:    
    93. Weissensteiner MH, Bunikis I, Francoijs KJ, Knief U, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW, Catal?n A, Heim W. Discovery and population genomics of structural variation in a songbird genus. Nat Commun. 2020 07 07; 11(1):3403. PMID: 32636372; PMCID: PMC7341801.
      Citations: 17     Fields:    Translation:AnimalsCells
    94. Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez KM, Berry IM, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck F, Treangen TJ. Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission. bioRxiv. 2020 Jul 02. PMID: 32637955; PMCID: PMC7337385.
      Citations: 2     
    95. Majidian S, Sedlazeck FJ. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement. Gigascience. 2020 07 01; 9(7). PMID: 32706368; PMCID: PMC7379178.
      Citations: 2     Fields:    Translation:Humans
    96. Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, Ranallo-Benavidez TR, Lemmon ZH, Kim J, Robitaille G, Kramer M, Goodwin S, McCombie WR, Hutton S, Van Eck J, Gillis J, Eshed Y, Sedlazeck FJ, van der Knaap E, Schatz MC, Lippman ZB, Maumus F. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. 2020 07 09; 182(1):145-161.e23. PMID: 32553272; PMCID: PMC7354227.
      Citations: 106     Fields:    Translation:Animals
    97. Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, 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, 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, Fiddes IT, Barrio AM, Marschall T. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 11; 38(11):1347-1355. PMID: 32541955; PMCID: PMC8454654.
      Citations: 63     Fields:    Translation:Humans
    98. Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B, Marschall T. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol. 2020 09; 38(9):1044-1053. PMID: 32686750; PMCID: PMC7483855.
      Citations: 90     Fields:    Translation:HumansCells
    99. Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, Mason CE. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions. bioRxiv. 2020 May 01. PMID: 32511352; PMCID: PMC7255793.
      Citations: 3     
    100. Gilpatrick T, Lee I, Graham JE, Raimondeau E, Bowen R, Heron A, Downs B, Sukumar S, Sedlazeck FJ, Timp W. Targeted nanopore sequencing with Cas9-guided adapter ligation. Nat Biotechnol. 2020 04; 38(4):433-438. PMID: 32042167; PMCID: PMC7145730.
      Citations: 77     Fields:    Translation:HumansAnimalsCells
    101. Chen S, Krusche P, Dolzhenko E, Sherman RM, Petrovski R, Schlesinger F, Kirsche M, Bentley DR, Schatz MC, Sedlazeck FJ, Eberle MA. Paragraph: a graph-based structural variant genotyper for short-read sequence data. Genome Biol. 2019 12 19; 20(1):291. PMID: 31856913; PMCID: PMC6921448.
      Citations: 40     Fields:    Translation:Humans
    102. 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 12; 104(1):e94. PMID: 31743587.
      Citations: 5     Fields:    Translation:Humans
    103. Mahmoud M, Gobet N, Mounier N, Dessimoz C, Sedlazeck FJ, Cruz-D?valos DI. Structural variant calling: the long and the short of it. Genome Biol. 2019 11 20; 20(1):246. PMID: 31747936; PMCID: PMC6868818.
      Citations: 99     Fields:    Translation:HumansAnimals
    104. Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019 10 28; 20(1):224. PMID: 31661016; PMCID: PMC6816165.
      Citations: 143     Fields:    Translation:Animals
    105. Hansen AW, Murugan M, Li H, Khayat MM, Wang L, Rosenfeld J, Andrews BK, Jhangiani SN, Coban Akdemir ZH, Sedlazeck FJ, Ashley-Koch AE, Liu P, Muzny DM, Task Force for Neonatal Genomics, Davis EE, Katsanis N, Sabo A, Posey JE, Yang Y, Wangler MF, Eng CM, Sutton VR, Lupski JR, Boerwinkle E, Gibbs RA. A Genocentric Approach to Discovery of Mendelian Disorders. Am J Hum Genet. 2019 11 07; 105(5):974-986. PMID: 31668702; PMCID: PMC6849092.
      Citations: 13     Fields:    Translation:Humans
    106. Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Regier A, Sedlazeck FJ, Siren J, Souilmi Y, Wagner J, Wrightsman T, Yokoyama TT, Zeng Q, Zook JM, Paten B, Busby B, Ebler J, Marschall T, Rautiainen M. A strategy for building and using a human reference pangenome. F1000Res. 2019; 8:1751. PMID: 34386196; PMCID: PMC8350888.
      Citations: 3     Fields:    
    107. Chander V, Gibbs RA, Sedlazeck FJ. Evaluation of computational genotyping of structural variation for clinical diagnoses. Gigascience. 2019 09 01; 8(9). PMID: 31494671; PMCID: PMC6732172.
      Citations: 17     Fields:    Translation:Humans
    108. 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 09 01; 36(9):1975-1989. PMID: 31225876; PMCID: PMC6736153.
      Citations: 22     Fields:    Translation:Animals
    109. Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Fungtammasan A, Kolesnikov A, Olson ND, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW, Ebler J, T?pfer A, Marschall T. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019 10; 37(10):1155-1162. PMID: 31406327; PMCID: PMC6776680.
      Citations: 294     Fields:    Translation:HumansCells
    110. Soyk S, Lemmon ZH, Sedlazeck FJ, Alonge M, Hutton SF, Van Eck J, Schatz MC, Lippman ZB, Jim?nez-G?mez JM. Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants. 2019 Aug; 5(8):903. PMID: 31292536.
      Citations: 1     Fields:    
    111. Soyk S, Lemmon ZH, Sedlazeck FJ, Alonge M, Hutton SF, Van Eck J, Schatz MC, Lippman ZB, Jim?nez-G?mez JM. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat Plants. 2019 05; 5(5):471-479. PMID: 31061537.
      Citations: 17     Fields:    Translation:Animals
    112. Chiang T, Liu X, Wu TJ, Hu J, Sedlazeck FJ, White S, Schaid D, 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 09; 21(9):2135-2144. PMID: 30890783; PMCID: PMC6752313.
      Citations: 7     Fields:    Translation:Humans
    113. Luo R, Sedlazeck FJ, Lam TW, Schatz MC. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nat Commun. 2019 03 01; 10(1):998. PMID: 30824707; PMCID: PMC6397153.
      Citations: 35     Fields:    Translation:HumansCells
    114. Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell. 2019 03 07; 176(6):1310-1324.e10. PMID: 30827684; PMCID: PMC6438178.
      Citations: 29     Fields:    Translation:HumansCells
    115. Schenk S, Bannister SC, Sedlazeck FJ, Anrather D, Minh BQ, Bileck A, Hartl M, von Haeseler A, Gerner C, Raible F, Tessmar-Raible K. Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase. Elife. 2019 02 15; 8. PMID: 30767890; PMCID: PMC6377233.
      Citations: 16     Fields:    Translation:AnimalsCells
    116. Dennenmoser S, Sedlazeck FJ, Schatz MC, Zytnicki M, Nolte AW, Altm?ller J. Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol. 2019 03; 28(6):1491-1505. PMID: 30520198.
      Citations: 5     Fields:    Translation:AnimalsCells
    117. Leija-Salazar M, Sedlazeck FJ, Toffoli M, Mullin S, Mokretar K, Athanasopoulou M, Donald A, Sharma R, Hughes D, Schapira AHV, Proukakis C. Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION. Mol Genet Genomic Med. 2019 03; 7(3):e564. PMID: 30637984; PMCID: PMC6418358.
      Citations: 30     Fields:    Translation:Humans
    118. Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin CS, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, McCombie WR, Schatz MC. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res. 2018 08; 28(8):1126-1135. PMID: 29954844; PMCID: PMC6071638.
      Citations: 49     Fields:    Translation:HumansCells
    119. Sedlazeck FJ, Lee H, Darby CA, Schatz MC. Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet. 2018 06; 19(6):329-346. PMID: 29599501.
      Citations: 142     Fields:    Translation:HumansAnimalsCells
    120. 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 06; 15(6):461-468. PMID: 29713083; PMCID: PMC5990442.
      Citations: 375     Fields:    Translation:Humans
    121. Luo R, Sedlazeck FJ, Darby CA, Kelly SM, Schatz MC. LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning. Comput Struct Biotechnol J. 2017; 15:478-484. PMID: 29213995; PMCID: PMC5711661.
      Citations: 14     
    122. Sedlazeck FJ, Dhroso A, Bodian DL, Paschall J, Hermes F, Zook JM. Tools for annotation and comparison of structural variation. F1000Res. 2017; 6:1795. PMID: 29123647; PMCID: PMC5668921.
      Citations: 6     Fields:    
    123. Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017 Jul 15; 33(14):2202-2204. PMID: 28369201; PMCID: PMC5870704.
      Citations: 389     Fields:    Translation:Animals
    124. Sedlazeck FJ, Li XY, Dennenmoser S, Iwaszkiewicz E, Altm?ller J, Nolte AW. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. Mol Ecol. 2017 Sep; 26(18):4712-4724. PMID: 28390096; PMCID: PMC5638112.
      Citations: 10     Fields:    Translation:AnimalsCells
    125. Dolgalev I, Sedlazeck F, Busby B. DangerTrack: A scoring system to detect difficult-to-assess regions. F1000Res. 2017; 6:443. PMID: 28503299; PMCID: PMC5405793.
      Citations: 3     Fields:    
    126. Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Sedlazeck FJ, B?hler J. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun. 2017 01 24; 8:14061. PMID: 28117401; PMCID: PMC5286201.
      Citations: 140     Fields:    Translation:AnimalsCells
    127. Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Katneni VK, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Turner SW, Lok S, Christoffels A, Dalmay T, Orb?n L. Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet. 2016 Dec; 12(12):e1006500. PMID: 27935956; PMCID: PMC5147801.
      Citations: 8     Fields:    
    128. Kaiser TS, Poehn B, Szkiba D, Preussner M, Sedlazeck FJ, Zrim A, Neumann T, Nguyen LT, Betancourt AJ, Hummel T, Dorner S, Heyd F, von Haeseler A, Tessmar-Raible K, Vogel H. The genomic basis of circadian and circalunar timing adaptations in a midge. Nature. 2016 12 01; 540(7631):69-73. PMID: 27871090; PMCID: PMC5133387.
      Citations: 31     Fields:    Translation:AnimalsCells
    129. Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016 Dec; 13(12):1050-1054. PMID: 27749838; PMCID: PMC5503144.
      Citations: 621     Fields:    Translation:HumansAnimals
    130. Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Turner SW, Lok S, Christoffels A, Dalmay T, Orb?n L. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet. 2016 Apr; 12(4):e1005954. PMID: 27082250; PMCID: PMC4833346.
      Citations: 59     Fields:    Translation:Animals
    131. Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JA, Cushman JC, Paull RE, Yu Q, Guyot R. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015 Dec; 47(12):1435-42. PMID: 26523774; PMCID: PMC4867222.
      Citations: 160     Fields:    Translation:AnimalsCells
    132. Smolka M, Rescheneder P, Schatz MC, von Haeseler A, Sedlazeck FJ. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol. 2015 Oct 22; 16:235. PMID: 26494581; PMCID: PMC4618857.
      Citations: 12     Fields:    Translation:Animals
    133. Tscherner M, Zwolanek F, Jenull S, Sedlazeck FJ, Petryshyn A, Frohner IE, Mavrianos J, Chauhan N, von Haeseler A, Kuchler K. The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways. PLoS Pathog. 2015 Oct; 11(10):e1005218. PMID: 26473952; PMCID: PMC4608838.
      Citations: 24     Fields:    Translation:Animals
    134. Krunic M, Ertl R, Hagen B, Sedlazeck FJ, Hofmann-Lehmann R, von Haeseler A, Klein D. Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study. BMC Vet Res. 2015 Apr 10; 11:90. PMID: 25879730; PMCID: PMC4424575.
      Citations: 1     Fields:    Translation:AnimalsCells
    135. Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, Jantsch MF, von Haeseler A. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res. 2014 Oct 29; 42(19):12155-68. PMID: 25260591; PMCID: PMC4231736.
      Citations: 22     Fields:    Translation:HumansAnimalsCells
    136. Sedlazeck FJ, Rescheneder P, von Haeseler A. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics. 2013 Nov 01; 29(21):2790-1. PMID: 23975764.
      Citations: 171     Fields:    
    137. Sedlazeck FJ, Prior K, Albersmeier A, John U, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D, J?nemann S, Kalinowski J. Updating benchtop sequencing performance comparison. Nat Biotechnol. 2013 Apr; 31(4):294-6. PMID: 23563421.
      Citations: 165     Fields:    Translation:Humans
    138. 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 Mar; 101(3):204-9. PMID: 23246509; PMCID: PMC3580289.
      Citations:    Fields:    Translation:HumansAnimalsCells
    139. Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Mittelsten Scheid O, von Haeseler A. Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS One. 2012; 7(7):e41528. PMID: 22911809; PMCID: PMC3401099.
      Citations: 9     Fields:    Translation:AnimalsCells
    140. 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 Aug; 22(8):1468-76. PMID: 22310477; PMCID: PMC3409260.
      Citations: 48     Fields:    Translation:AnimalsCells
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