Welcome

Our research focuses on the detection and understanding of the mechanisms of origin of genomic Structural Variation (SV), to advance comparative genomics, biomedical research and ultimately, clinical care. SVs are an understudied form of genomic variation that includes deletions, duplications, insertions, inversions, and translocations. They represent an important class of variation, as in aggregate, they impact more of the human genome than does single nucleotide variation. The core strength of the Sedlazeck lab is to develop new methods and algorithms to obtain a deeper understanding of the underlying molecular biology. We are doing this with a focus on large scale genomics (hundreds of thousands of samples) and the application of novel technologies (e.g. long reads such as PacBio or Oxford Nanopore). Utilizing this we uncovered novel complexity accross human evolution, diseases (e.g. neurological, mendelian, cardiovascular), cancer (e.g. breast or viral associated), but also non-human based. The latter either to improve our understanding of human variations (e.g. rhesus macaque) or to improve certain phenotypes (e.g. tomato, yeast)

Going forward, the Sedlazeck lab utilizes novel biotechnology and develops algorithms to improve our understand of human diseases with a special focus on adult diseases. To achieve this, we have experience in phasing, methylation calling and variant calling in complex regions of the human genome. We also leverage both mapping and assembly approaches to obtain a comprehensive insight at the sample at hand. In addition to comprehensive genomics, we apply these approaches at scale to improve heritability and association of certain diseases. This is only possible with a dedication of scalable algorithms, cloud infrastructure and the application of machine learning techniques together with high filtering and quality control standards. As such our lab contributes to Topmed, CCDG, ADSP and other consortia to push innovation across genomics and genetics to address questions of evolution, diseases and development.




Fritz J Sedlazeck

Associate Professor

Human Genome Sequencing Center
Baylor College of Medicine
Houston, TX US

Cell: (713) 798-4951
E-mail: Fritz.Sedlazeck <at> bcm.edu
Twitter: @sedlazeck
ORCID: 0000-0001-6040-2691
Publons: E-4548-2018

Research Interests

1. The impact of SVs on gene expression / phenotypes

We led studies to identify the role of SV across multiple organisms. For example in yeast, we showed the transient behavior of rapid appearing and disappearing SV along almost identical genomes, leading to gene expression changes. These transient SV occurred much faster than SNV and improved the heritability of certain traits. Over the last two years, the Sedlazeck lab played a key role in identifying the impact of SV in tomatoes. Here we identified SV impacting: fruit growth, number of fruits, weakening the stem of the fruit and other highly important traits to improve the harvest and fruit quality. In addition, CRISPR-Cas9 was used to induce these alleles in sister clades to observe the reassembling of these traits as predicted. More recently, the Sedlazeck lab co-led the detection of SV across 19,652 human genomes from mixed ethnicities together with 4,000 protein measurements across 4,000 individuals. Here we associated SV with direct or indirect impact on proteins important for cardiovascular diseases.

2. SV in human diseases and diagnostics

Structural variation play a central role in polymorphic variation, pathogenic conditions as well as cancer; yet the robust detection of these events in human diseases remains challenging. We led several analysis efforts to identify SV and their pathogenicity or importance across breast cancer, neurological diseases and mendelian diseases. Sedlazeck lab was key to two breast cancer studies where he identified SV surrounding the Her2 oncogene amplifications and innovated the comparison across different sequencing technologies. Here we and the team showed how SV are connected and lead to large copy number changes with underlying molecular structure, which lead to new key insights in Her2+ breast cancer. We further pursued a more cost efficient strategy with collaborators to use CRISPR-Cas9 to target genes in cancer samples to identify haplotype resolved SNV, SV and methylation. In Parkinson and MSA diseases, Sedlazeck lab co-developed a cost efficient and high accurate assay to target the gene GBA. The team is now able to sequence ~160 samples per day and haplotype resolve all the SNV and SV. This approach is now being adopted in multiple hospitals. Lastly in Mendelian diseases, we collaborated with the Dr. James Lupski’s lab to help identify and phase pathogenic CNV and de-novo variation to assess their impact. The Sedlazeck lab now leads analysis efforts over 11,000 long read genomes to obtain novel insights in multiple diseases.

3. The role of SVs in evolution, through studies in Comparative Genomics

We have led and been involved in collaborations to identify SV and their role over multiple model and non model organisms (fungi, plants and animals). As an example, we studied the transposon activity and impact in the Crow and Fish population and identified their role for diversity and evolution. Sedlazeck lab further identified an important duplication explaining the compensation of modern Tomatoes for a splicing deficiency due to other SV impacting MADS-box gene that initially lead to a harmful phenotype. Most recently, we were able to identify small SVs also in SARS-CoV-2 samples from the NYC and Houston metro area. These SV mainly targeted NSP11 and NSP12 with common SV co occurring in SPIKE and other important genes. To improve the quality of reference genomes and thus the detection of SV, we also contributed to the development of Falcon-Unzip and Shasta de-novo assembler that are one of the few assemblers to produce high quality haplotype resolved assemblies.

4. Development of novel methods for Structural Variant Detection

Structural Variation (SV) remain hard to identify, but play an essential role in evolution and disease. We have spearheaded the detection of SV and the utilization of long reads in genomics and transitioning into medical research. The Sedlazeck lab has developed highly cited innovative methods that enabled a more comprehensive analysis such as NGM and NGMLR for alignments of short and long reads to reference genomes. We are the lead developer of multiple methods including Sniffles, the state of the art long read based SV caller. Sniffles has been cited over 344 times in 2 years and significantly advances the field of SV detection and interpretation and is utilized in hundreds to thousands of projects. Sedlazeck lab further led the development of SV calling methods for short reads such as Parliament2 to enable accurate SV calling at scale. This is needed to obtain accurate allele frequencies and we have used it across 200,000 human genomes (Topmed, CCDG). The Sedlazeck lab led the development of methods to accurately genotype SV in a population and others to compare SV. These methods are paving the way to include SV in comparative and medical research.

5. Benchmarks and standards in Genomics

We contributed to detailed analysis of sequencing biases including technology specific consensus errors that can be mistaken as SNPs, sequencing errors and nucleotide biases (e.g. GC). Sedlazeck lab also played a key role in establishing genomic benchmarks sets for SNV and SV in GIAB (NIST) and SEQC2 (FDA). In addition, we developed methods to facilitate the comparison between NGS mapping methods to enable key insights in their individual advantages and disadvantages across multiple parameters for non-expert users. This reflects our detailed knowledge of biases across different sequencing technologies and their implications on variation calling and establishing high quality call sets. These call sets are key to enable new biology and medical findings to study mechanism and occurrences of complex variations.

Software

BioBricks Software to simulate recombination to assess ancestry blocks
FALCON Phased Diploid Genome Assembly with PacBio sequencing reads
GenomeScopeEstimate genomic properties from unassembled sequencing reads
LRSim Linked Read Simulator
MuMmer SGE Parallization script for MUMMer.
NGMShort read mapper especially suitable for high SNP rates
NGM-LRFast and Accurate Mapping of Long Reads
Paragraph Genome graph based SV genotyping
PhaseME Phasing QC and utilization of linkage data
Princess Software for haplotype resolved detection of SNV, SV and methylation
Read2Tree Software for mapping reads directly onto orthology groups
SnifflesDetection of Structural Variations from Long Reads
SURVIVORDetection and Analysis of Structural Variations
SVCollector Method to optimally select samples for validation and resequencing based on a multi sample VCF.
SVHound Statistical software to predict SV in a cohort that have not been found yet.
TeaserFast personalized benchmarks and optimization for NGS read mapping
Vulcan Utilizing two scoring functions to improve long read mapping

Lab Members

 
headshot Fritz Sedlazeck, Ph.D.
Associate Professor
Office: Alkek 1619
Phone: 713 798-4951
fritz.sedlazeck [at] bcm.edu
Home page
GitHub Twitter Google-Scholar Linkedin
 
headshot Medhat Mahmoud,
Ph.D.
PostDoc
Office: Alkek 1619
Phone: 713 798-3525
medhat.mahmoud [at] bcm.edu
Home page
GitHub Twitter Google-Scholar Linkedin
 
 
headshot Daniel Paiva Agustinho, Ph.D.
Staff Scientist
daniel.agustinho [at] bcm.edu
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headshot Sairam Behera, Ph.D.
PostDoc
Office: Alkek 1619
Phone: 713 798-4951
Sairam.Behera [at] bcm.edu
Home page
GitHub Twitter Google-Scholar Linkedin
 
 
headshot Luis Paulin, Ph.D.
PostDoc

luis.paulin [at] bcm.edu
Home page
 
 
headshot Moritz Smolka, B.Sc.
Visiting Scientist

moritz.smolka [at] bcm.edu
Home page
 
 
headshot Damaris Lattimer
Internship Student

damaris.lattimer [at] bcm.edu
Home page
 
 
headshot Philippe Sanio, M.Sc.
Internship Student

philippe.sanio [at] bcm.edu
GitHub
 
 
headshot Sina Majidian, Ph.D.
Visiting PostDoc
Office: Genopode, UNIL
Sina.Majidian [at] unil.ch
Home page
GitHub Twitter Linkedin
 
 
headshot Michal Izydorczyk, PhD
Postdoc

michal.izydorczyk [at] bcm.edu
GitHub Twitter
 
 
headshot Xinchang Zheng, PhD
Postdoc

Xinchang.Zheng [at] bcm.edu
GitHub
 
 
headshot Farhang Jaryani, PhD
Postdoc

Farhang.Jarynai [at] bcm.edu

 

Publications

Preprints

P10. A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA
C. Chin, S. Behera, GA. Metcalf, RA. Gibbs, E. Boerwinkle, F.J. Sedlazeck(2022) bioRxiv doi: https://doi.org/10.1101/2022.06.08.495395
P9. Characterizing the genetic polymorphisms in 370 challenging medically relevant genes using long-read sequencing data from 41 human individuals among 19 global populations
C. Ji, J. Gong, F.J. Sedlazeck*, S. Fan*(2022) bioRxiv doi: https://doi.org/10.1101/2022.08.03.502734
P8. Frequent spontaneous structural rearrangements promote transgenerational genome diversification in Brassica napus
M. Orantes-Bonilla, M. Makhoul, H. Lee, H. Singh Chawla, P. Vollrath, A. Langstroff, F.J. Sedlazeck, J. Zou, RJ. Snowdon(2022) bioRxiv doi: https://doi.org/10.1101/2022.06.27.497715
P7. Multiscale Analysis of Pangenome Enables Improved Representation of Genomic Diversity For Repetitive And Clinically Relevant Genes
C. Chin, S. Behera, A.Khalak, F.J. Sedlazeck, J. Wagner, JM. Zook(2022) bioRxiv doi: https://doi.org/10.1101/2022.08.05.502980
P6. Improved sequence mapping using a complete reference genome and lift-over
N.C. Chen, L.F. Paulin, F.J. Sedlazeck, S. Koren, A.M. Phillippy, B. Langmead(2022) bioRxiv doi: https://doi.org/10.1101/2022.04.27.489683
P5. Read2Tree: scalable and accurate phylogenetic trees from raw reads
D. Dylus, AM. Altenhoff, S. Majidian, F.J. Sedlazeck* , C. Dessimoz* (2022) bioRxiv doi: https://doi.org/10.1101/2022.04.18.488678
P4. Comprehensive Structural Variant Detection: From Mosaic to Population-Level
M. Smolka, L.F. Paulin, C.M. Grochowski, M. Mahmoud, S. Behera, M. Gandhi, K. Hong, D. Pehlivan, S.W. Scholz, C.M.B. Carvalho, C. Proukakis, F.J. Sedlazeck (2022) bioRxiv doi: https://doi.org/10.1101/2022.04.04.487055
P3. Multi-tissue integrative analysis of personal epigenomes
J. Rozowsky, J. Drenkow, YT. Yang, G. Gursoy, T. Galeev, B. Borsari, C.B Epstein, K. Xiong, J. Xu, J. Gao, K. Yu, A. Berthel, Z. Chen, F. Navarro, J. Liu, MS. Sun, J. Wright, J. Chang, CJF. Cameron, N. Shoresh, E. Gaskell, J. Adrian, S. Aganezov, G. Balderrama-Gutierrez, S. Banskota, GB. Corona, S. Chee, SB. Chhetri, GCC. Martins, C. Danyko, CA. Davis, D. Farid, NP. Farrell, I. Gabdank, Y. Gofin, DU. Gorkin, M. Gu, V. Hecht, BC. Hitz, R. Issner, M. Kirsche, X. Kong, B.R Lam, S. Li, B. Li, T. Li, X. Li, KZ. Lin, R. Luo, M. Mackiewicz, J.E Moore, J. Mudge, N. Nelson, C. Nusbaum, I. Popov, HE. Pratt, Y. Qiu, S. Ramakrishnan, J. Raymond, L. Salichos, A. Scavelli, JM. Schreiber, F.J. Sedlazeck, LH. See, RM. Sherman, X. Shi, M. Shi, CA. Sloan, JS. Strattan, Z. Tan, FY. Tanaka, A.VJ. Wang, J. Werner, B. Williams, M. Xu, C. Yan, Lu Yu, C. Zaleski, J. Zhang, JM. Cherry, EM. Mendenhall, WS. Noble, Z. Weng, ME. Levine, A. Dobin, B. Wold, A. Mortazavi, B. Ren, J. Gillis, RM. Myers, MP. Snyder, J. Choudhary, A. Milosavljevic, MC. Schatz, R. Guigó, BE Bernstein, TR. Gingeras, M. Gerstein (2021) bioRxiv doi: https://doi.org/10.1101/2021.04.26.441442
P2. Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus
R.A. Harris, M. Raveendran, D.T. Lyfoung, F.J. Sedlazeck, M. Mahmoud, T.M. Prall, J.A. Karl, H. Doddapaneni, Q. Meng, Y. Han, D. Muzny, R.W. Wiseman, D.H. O’Connor, J. Rogers (2021) bioRxiv doi: https://doi.org/10.1101/2021.07.05.451071
P1. Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes
F.J. Sedlazeck, B. Yu, A.J. Mansfield, H. Chen, O. Krasheninina, A. Tin, Q. Qi, S. Zarate, J.L. Traynelis, V. Menon, BCM HGSC Sequencing Lab, J. Hu, H. Doddapaneni, G. A. Metcalf, J. Coresh, R. C. Kaplan, D.M. Muzny, G. Jun, R.A. Gibbs, W.J. Salerno, E. Boerwinkle (2021) bioRxiv doi: https://doi.org/10.1101/2020.05.02.074096

2023

98. FixItFelix: improving genomic analysis by fixing reference errors.
S. Behera, J. LeFaive, P. Orchard, M. Mahmoud, L. F. Paulin, J. Farek, D. C. Soto, S.C.J. Parker, A. V. Smith, M. Y. Dennis, J. M. Zook, F.J. Sedlazeck(2023) Genome Biology doi:https://doi.org/10.1186/s13059-023-02863-7
97. Intratumoral heterogeneity and clonal evolution induced by HPV integration
K. Akagi, DE. Symer, M. Mahmoud, B. Jiang, S. Goodwin, D. Wangsa, Z. Li, W. Xiao, JD. Dunn, R. McCombie, T. Ried, KR. Coombes, F.J. Sedlazeck, ML. Gillison(2023) Cancer Discovery doi:https://doi.org/10.1158/2159-8290.CD-22-0900
96. xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments
J. Farek, D. Hughes, W. Salerno, Y. Zhu, A. Pisupati, A. Mansfield, O. Krasheninina, A.C. English, G. Metcalf, E. Boerwinkle, D.M Muzny, R.A. Gibbs, Z. Khan, F.J. Sedlazeck (2023) Gigascience doi:https://doi.org/10.1093/gigascience/giac125
95. SVhound: Detection of future Structural Variation hotspots
L.F. Paulin, M. Raveendran, R.A. Harris, J. Rogers, A.v. Haeseler, F.J. Sedlazeck (2023) BCM Bioinformatics doi:https://doi.org/10.1186/s12859-022-05046-6
94. Genome-wide analysis of Structural Variants in Parkinson's Disease
K.J. Billingsley, J. Ding, P.A. Jerez, A. Illarionova, K. Levine, F.P. Grenn, M.B. Makarious, A. Moore, D. Vitale, X. Reed, D. Hernandez, A. Torkamani, M. Ryten, J. Hardy, UK Brain Expression Consortium (UKBEC), R. Chia, S.W. Scholz, B.J. Traynor, C.L. Dalgard, D.J. Ehrlich, T. Tanaka, L. Ferrucci, T.G. Beach, G.E. Serrano, J.P. Quinn, V.J. Bubb, R.L. Collins, X. Zhao, M. Walker, E. Pierce-Hoffman, H. Brand, M.E. Talkowski, B. Casey, M.R. Cookson, A. Markham, M.A. Nalls, M. Mahmoud, F.J. Sedlazeck , C. Blauwendraat, J. R. Gibbs, A.B. Singleton (2023) Annals of Neurology doi:https://doi.org/10.1002/ana.26608
93. Genome-wide analysis of Structural Variants in Parkinson's Disease
M. Dawood, G. Akay, T. Mitani, D. Marafi, J.M. Fatih, A. Gezdirici, H. Najmabadi, K. Kahrizi, J. Punetha, C.M. Grochowski, H. Du, A. Jolly, H. Li, Z. Coban‐Akdemir, F.J. Sedlazeck, J.V. Hunter, S.N. Jhangiani, D. Muzny, D. Pehlivan, J.E. Posey, C.MB. Carvalho, R.A. Gibbs, J.R. Lupski(2023) American Journal of Medical Genetics doi:https://doi.org/10.1002/ajmg.a.63080

2022

92. Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity
A.C. English, V.K. Menon, R. Gibbs, G.A. Metcalf, F.J. Sedlazeck (2022) Genome Biology doi: https://doi.org/10.1186/s13059-022-02840-6
91. Long read sequencing and expression studies of AHDC1 deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism
V. Chander, M. Mahmoud, J. Hu, Z. Dardas, C. M. Grochowski, M. Dawood, M.M. Khayat, H. Li, S. Li, S. Jhangiani, V. Korchina, H. Shen, G. Weissenberger, Q. Meng, M. Gingras, D.M. Muzny, H. Doddapaneni, J.E. Posey, J.R. Lupski, A. Sabo, D.R. Murdock, F.J. Sedlazeck, RA. Gibbsn (2022) Human Mutation doi: https://doi.org/10.1002/humu.24461
90. Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation
M. Orantes-Bonilla, M. Makhoul, H. Lee, H.S. Chawla, P. Vollrath, A. Langstroff, F.J. Sedlazeck, J. Zou, R.J. Snowdon (2022) Frontiers in Plant Science doi: https://doi.org/10.3389/fpls.2022.1057953
89. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms
K. Walker, D. Kalra, R. Lowdon, G. Chen, D. Molik, D.C. Soto, F. Dabbaghie, A.A. Khleifat, M. Mahmoud, L.F. Paulin, M.S. Raza, S.P. Pfeifer, D.P. Agustinho, E. Aliyev, P. Avdeyev, E.R. Barrozo, S. Behera, K. Billingsley, L.C. Chong, D. Choubey, W.D. Coster, Y. Fu, A.R. Gener, T. Hefferon, D.M. Henke, W. Höps, A. Illarionova, M.D. Jochum, M. Jose, R.K. Kesharwani, S. Kolora, J. Kubica, P. Lakra, D. Lattimer, C. Liew, B. Lo, C. Lo, A. Lötter, S. Majidian, S.K. Mendem, R. Mondal, H. Ohmiya, N. Parvin, C. Peralta, C. Poon, R. Prabhakaran, M. Saitou, A. Sammi, P. Sanio, N. Sapoval, N. Syed, T. Treangen, G. Wang, T. Xu, J. Yang, S. Zhang, W. Zhou, F.J. Sedlazeck, B. Busby (2022) F1000 doi:https://doi.org/10.12688/f1000research.110194.1
88. Multiple genome alignment in the telomere-to-telomere assembly era
Bryce Kille, Advait Balaji, F.J. Sedlazeck, Michael Nute, Todd J Treangen (2022) Genome biology doi: https://doi.org/10.1186/s13059-022-02735-6
87. The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation
H. Du, A. Jolly, C.M. Grochowski, B. Yuan, M. Dawood, S.N. Jhangiani, H. Li, D. Muzny, J.M. Fatih, Z. Coban-Akdemir, M.E. Carlin, A.E. Scheuerle, K. Witzl, JE. Posey, M. Pendleton, E. Harrington, S. Juul, PJ. Hastings, W. Bi, RA. Gibbs, F.J. Sedlazeck, JR. Lupski, C. Carvalho, P. Liu (2022) Genome Medicine doi: https://doi.org/10.1186/s13073-022-01123-w
86. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene
M. Toffoli, X. Chen, F.J. Sedlazeck, C. Lee, S. Mullin, A. Higgins, S. Koletsi, ME. Garcia-Segura, E. Sammler, SW. Scholz, AHV. Schapira, MA. Eberle, C. Proukakis(2022) Communications Biology volume doi: https://doi.org/10.1038/s42003-022-03610-7
85. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus
RA. Harris, M. Raveendran, DT. Lyfoung, F.J. Sedlazeck, M. Mahmoud, TM. Prall, JA. Karl, H. Doddapaneni, Q. Meng, Y. Han, D. Muzny, RW. Wiseman, DH. O'Connor, J. Rogers(2022) Gigascience doi: https://doi.org/10.1093/gigascience/giac039
84. TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data
L. Huang, J.D. Rosen, Q. Sun, J. Chen, M.M. Wheeler, Y. Zhou, Y. Min, C. Kooperberg, M.P. Conomos, A.M. Stilp, S.S. Rich, J.I. Rotter, A. Manichaikul, R.J.F. Loos, E.E. Kenny, T.W. Blackwell, A.V. Smith, G. Jun, F.J. Sedlazeck, G. Metcalf, E. Boerwinkle, LM. Raffield, A.P. Reiner, P.L. Auer, Y. Li (2022) The American Journal of Human Genetics doi: https://doi.org/10.1016/j.ajhg.2022.04.006
83. precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
N.D. Olson, J. Wagner, J. McDaniel, S.H. Stephens, S.T. Westreich, A.G. Prasanna, E. Johanson, E. Boja, E.J. Maier, O. Serang, D.Jáspez, J.M. Lorenzo-Salazar, A. Muñoz-Barrera, L.A. Rubio-Rodríguez, C. Flores, K. Kyriakidis, A. Malousi, K. Shafin, T. Pesout, M. Jain, B. Paten, P. Chang, A. Kolesnikov, M. Nattestad, G. Baid, S. Goel, H. Yang, A. Carroll, R. Eveleigh, M. Bourgey, G. Bourque, G. Li, M. ChouXian, L. Tang, D. YuanPing, S. Zhang, J. Morata, R. Tonda, G. Parra, J. Trotta, C. Brueffer, S. Demirkaya-Budak, D. Kabakci-Zorlu, D. Turgut, Ö. Kalay, G. Budak, K. Narcı, E. Arslan, R. Brown, I.J. Johnson, A. Dolgoborodov, V. Semenyuk, A. Jain, H.S. Tetikol, V. Jain, M. Ruehle, B. Lajoie, C. Roddey, S. Catreux, R. Mehio, M.U. Ahsan, Q. Liu, K. Wang, S.M.E. Sahraeian, L.T. Fang, M. Mohiyuddin, C. Hung, C. Jain, H. Feng, Z. Li, L. Chen, F.J. Sedlazeck, J.M. Zook (2022) Cell Genomics doi: https://doi.org/10.1016/j.xgen.2022.100129
82. Benchmarking challenging small variants with linked and long reads
J. Wagner, N.D. Olson, L. Harris, Z. Khan, J. Farek, M. Mahmoud, A. Stankovic, V. Kovacevic, A.M. Wenger, W.J. Rowell, C. Xiao, B. Yoo, N. Miller, J.A. Rosenfeld, B. Ni, S. Zarate, M. Kirsche, S. Aganezov, M.C. Schatz, G. Narzisi, M. Byrska-Bishop, W. Clarke, U.S. Evani, C. Markello, K. Shafin, X. Zhou, A. Sidow, V. Bansal, P. Ebert, T. Marschall, P. Lansdorp, V. Hanlon, C. Mattsson, A.M. Barrio, I.T. Fiddes, A. Fungtammasan, C. Chin, F.J. Sedlazeck, A. Carroll, M. Salit, J.M. Zook, Genome in a Bottle Consortium(2022) Cell Genomics doi: https://doi.org/10.1016/j.xgen.2022.100128
81. Searching thousands of genomes to classify somatic and novel structural variants using STIX
M. Chowdhury, B.S. Pedersen, F.J. Sedlazeck, A.R. Quinlan, R.M. Layer (2022) Nature Methods doi: https://doi.org/10.1038/s41592-022-01423-4
80. The complete sequence of a human genome
S. Nurk, S. Koren, A. Rhie, M. Rautiainen, AV. Bzikadze, A. Mikheenko, MR. Vollger, N. Altemose, L. Uralsky, A. Gershman, S. Aganezov, SJ. Hoyt, M. Diekhans, GA. Logsdon, M. Alonge, SE. Antonarakis, M. Borchers, GG. Bouffard, SY. Brooks, GV. Caldas, H. Cheng, C. Chin, W. Chow, LG. de Lima, PC. Dishuck, R. Durbin, T. Dvorkina, IT. Fiddes, G. Formenti, RS. Fulton, A. Fungtammasan, E. Garrison, PGS. Grady, TA. Graves-Lindsay, IM. Hall, NF. Hansen, GA. Hartley, M. Haukness, K. Howe, MW. Hunkapiller, C. Jain, M. Jain, ED. Jarvis, P. Kerpedjiev, M. Kirsche, M. Kolmogorov, J. Korlach, M. Kremitzki, H. Li, VV. Maduro, T. Marschall, AM. McCartney, J. McDaniel, DE. Miller, JC. Mullikin, EW. Myers, ND. Olson, B. Paten, P. Peluso, PA. Pevzner, D. Porubsky, T. Potapova, EI. Rogaev, JA. Rosenfeld, SL. Salzberg, VA. Schneider, F.J. Sedlazeck, K. Shafin, CJ. Shew, A. Shumate, Y. Sims, AFA. Smit, DC. Soto, I. Sović, JM. Storer, A.Streets, BA. Sullivan, F. Thibaud-Nissen, J. Torrance, J. Wagner, BP. Walenz, A. Wenger, JMD. Wood, C. Xiao, SM. Yan, AC. Young, S. Zarate, U.Surti, RC. McCoy, MY. Dennis, IA. Alexandrov, JL. Gerton, RJ. O’Neill, W. Timp, JM. Zook, MC. Schatz, EE. Eichler, KH. Miga, AM. Phillippy (2022) Science doi: https://doi.org/10.1126/science.abj6987
79. A complete reference genome improves analysis of human genetic variation
S. Aganezov, SM. Yan, DC. Soto, M. Kirsche, S. Zarate, P. Avdeyev, DJ. Taylor, K. Shafin, A. Shumate, C. Xiao, J. Wagner, J. McDaniel, ND. Olson, MEG. Sauria, MR. Vollger, A. Rhie, M. Meredith, S. Martin, J. Lee, S. Koren, J. Rosenfeld, B. Paten, R. Layer, C. Chin, F.J. Sedlazeck, NF. Hansen, DE. Miller, AM. Phillippy, KH. Miga, RC. McCoy*, MY. Dennis*, JM. Zook*, MC. Schatz* (2022) Science doi: https://doi.org/10.1126/science.abl3533
78. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing
SD. Goenka,JE. Gorzynski, K. Shafin, DG. Fisk, T. Pesout, TD. Jensen,J. Monlong, P. Chang, G. Baid, JA. Bernstein, JW. Christle, KP. Dalton, DR. Garalde, ME. Grove, J. Guillory, A. Kolesnikov, M. Nattestad, M.R.Z. Ruzhnikov, M. Samadi, A. Sethia, E. Spiteri, C.J. Wright, K. Xiong, T. Zhu, M. Jain, F.J. Sedlazeck, A. Carroll, B. Paten & E.A. Ashley (2022) Nature Biotechnology doi: https://doi.org/10.1038/s41587-022-01221-5
77. Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data
Y. Liu, J. Kearney, M. Mahmoud, B. Kille, F.J. Sedlazeck, T.J. Treangen (2022) Nature Communications doi: https://doi.org/10.1038/s41467-022-28852-1
76. Towards accurate and reliable resolution of structural variants for clinical diagnosis
Z. Liu,R. Roberts, TR. Mercer, J. Xu, F.J. Sedlazeck*, W. Tong* (2022) Genome Biology doi: https://doi.org/10.1186/s13059-022-02636-8
75. Fully resolved assembly of Cryptosporidium parvum
V.K. Menon, P.C. Okhuysen, C. Chappell, M. Mahmoud, Q. Meng, H. Doddapaneni, V. Vee, Y. Han, S. Salvi, S. Bhamidipati, K. Kottapalli, G. Weissenberger, H. Shen, M.C. Ross, K.L. Hoffman, S.J. Cregeen, D.M. Muzny, G.A. Metcalf, R.A. Gibbs, J.F. Petrosino, F.J. Sedlazeck (2022) GigaScience doi: https://doi.org/10.1093/gigascience/giac010
74. Centers for Mendelian Genomics: A decade of facilitating gene discovery
S.M. Baxter, J.E. Posey, N.J. Lake, N. Sobreira, J.X. Chong, S. Buyske, E.E. Blue, L.H. Chadwick, Z.H. Coban-Akdemir, K.F. Doheny, C.P. Davis, M. Lek,C. Wellington, S.N. Jhangiani, M. Gerstein, R.A. Gibbs, R.P. Lifton, D.G. MacArthur,T.C. Matise, J.R. Lupski, D. Valle, M. J.Bamshad, A. Hamosh, S. Mane, D.A.Nickerson, Centers for Mendelian Genomics Consortium ,H.L.Rehm, A. O’Donnell-Luria(2022) GigaScience doi: https://doi.org/10.1016/j.gim.2021.12.005
73. Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock
JE. Gorzynski, K. Shafin,TD. Jensen, DG. Fisk,E. Spiteri, T. Pesout, G. Baid, JA. Bernstein, P. Chang, JW. Christle, K. Dunn, DR. Garalde, JW. Knowles, A. Kolesnikov, M. Ma, T.Moscarello, M. Nattestad, M. Perez, M. Samadi, C. Wright, CJ. Wusthoff, T. Zhu, M. Jain, F.J. Sedlazeck, A. Carroll, B. Paten, EA. Ashley (2022) Circulation: Genomic and Precision Medicine doi: https://doi.org/10.1161/CIRCGEN.121.003591
72. Curated variation benchmarks for challenging medically relevant autosomal genes
J. Wagner, ND. Olson, L. Harris, J. McDaniel, H. Cheng, A. Fungtammasan, Y. Hwang, R. Gupta, AM. Wenger, WJ. Rowell, ZM. Khan, J. Farek, Y. Zhu, A. Pisupati, M. Mahmoud, C. Xiao, B. Yoo, SME. Sahraeian, DE. Miller, D. Jaspez, JM. Lorenzo-Salazar, A. Munoz-Barrera, LA. Rubio-Rodriguez, C. Flores, G. Narzisi, US. Evani, WE. Clarke, J. Lee, CE. Mason, SE. Lincoln, KH. Miga, MTW. Ebbert, A. Shumate, H. Li, C. Chin*, JM. Zook*, F.J. Sedlazeck* (2022) Nature Biotechnology doi: https://doi.org/10.1038/s41587-021-01158-1
71. Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting
JE. Gorzynski, K. Shafin,TD. Jensen, DG. Fisk,E. Spiteri, T. Pesout, G. Baid, JA. Bernstein, P. Chang, JW. Christle, K. Dunn, DR. Garalde, JW. Knowles, A. Kolesnikov, M. Ma, T.Moscarello, M. Nattestad, M. Perez, M. Samadi, C. Wright, CJ. Wusthoff, T. Zhu, M. Jain, F.J. Sedlazeck, A. Carroll, B. Paten, EA. Ashley (2022) New England Journal of Medicine doi: https://doi.org/10.1056/NEJMc2112090
70. Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
B. Pan, L. Ren, V. Onuchic, M. Guan, R. Kusko, S. Bruinsma, L. Trigg, A. Scherer, B. Ning, C. Zhang, C. Glidewell-Kenney, C. Xiao, E. Donaldson, F.J. Sedlazeck, G. Schroth, G. Yavas, H. Grunenwald, H. Chen, H. Meinholz, J. Meehan, J. Wang, J. Yang, J. Foox, J. Shang, K. Miclaus, L. Dong, L. Shi, M. Mohiyuddin, M. Pirooznia, P. Gong, R. Golshani, R. Wolfinger, S. Lababidi, S.M.E. Sahraeian, S. Sherry, T. Han, T. Chen, T. Shi, W. Hou, W. Ge, W. Zou, W. Guo, W. Bao, W. Xiao, X. Fan, Y. Gondo, Y. Yu, Y. Zhao, Z. Su, Z. Liu, W. Tong, W. Xiao, J.M. Zook, Y. Zheng, H. Hong(2022) Genome Biology doi: https://doi.org/10.1186/s13059-021-02569-8
69. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device
C.L. Hall, R.K. Kesharwani, N.R. Phillips, J.V. Planz, F.J. Sedlazeck, R.R. Zascavage (2022) Forensic Science International: Genetics doi: https://doi.org/10.1016/j.fsigen.2021.102629

2021

68. Hidden biases in germline structural variant detection
M.M. Khayat, S. Mohammad, E. Sahraeian, S. Zarate, A. Carroll, H. Hong, B. Pan, L. Shi, R.A. Gibbs, M. Mohiyuddin, Y. Zheng, F.J. Sedlazeck(2021) Genome Biology doi: https://doi.org/10.1186/s13059-021-02558-x
67. High resolution copy number inference in cancer using short-molecule nanopore sequencing
T. Baslan, S. Kovaka, F.J. Sedlazeck, Y. Zhang, R. Wappel, S.W. Lowe, S. Goodwin, M.C. Schatz(2021) Nucleic Acids Research doi: https://doi.org/10.1093/nar/gkab812
66. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation
M. Mahmoud, H. Doddapaneni, W. Timp, F.J. Sedlazeck (2021) Genome Biology doi: https://doi.org/10.1186/s13059-021-02486-w
65. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
J. Foox , S. Tighe , C. Nicolet , J. Zook , M. Byrska-Bishop , W. Clarke , M. Khayat , M. Mahmoud , P. Laaguiby , Z. Herbert , D. Warner , G. Grills , J. Jen , S. Levy , J. Xiang , A. Alonso , X. Zhao , W. Zhang , F. Teng , Y. Zhao , H. Lu , G. Schroth , G. Narzisi , W. Farmerie , F.J. Sedlazeck*, D. Baldwin*, C. Mason* (2021) Nature Biotechnology doi: https://doi.org/10.1038/s41587-021-01049-5
64. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals
H. Doddapaneni, S.J. Cregeen, R. Sucgang, Q. Meng, X. Qin, V. Avadhanula, H. Chao, V. Menon, E. Nicholson, D. Henke, F. Piedra, A. Rajan, Z. Momin, K. Kottapalli, K.L. Hoffman, F.J. Sedlazeck, G. Metcalf, P.A. Piedra, D.M. Muzny, J.F. Petrosino, R.A. Gibbs (2021) Plos One doi: https://doi.org/10.1371/journal.pone.0244468
63. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment
Y. Fu, M. Mahmoud, VV. Muraliraman, F.J. Sedlazeck*, TJ. Treangen* (2021) Gigascience doi: https://doi.org/10.1093/gigascience/giab063
62. Towards population-scale long-read sequencing
W.De Coster, M.H. Weissensteiner, F.J. Sedlazeck (2021) Nature Reviews Genetics doi: https://doi.org/10.1038/s41576-021-00367-3
61. Intronic Haplotypes in the GBA Gene Do Not Predict Age at Diagnosis of Parkinson's Disease
M. Toffoli, A. Higgins, C. Lee, S. Koletsi, X. Chen, M. Eberle, F.J. Sedlazeck, S. Mullin, C. Proukakis, A.H.V. Schapira (2021) Movement Disorders doi: https://doi.org/10.1002/mds.28616
60. Investigation of product derived lymphoma following infusion of piggyBac modified CD19 chimeric antigen receptor T-cells
K.P. Micklethwaite, K. Gowrishankar, B.S. Gloss, Z. Li, J.A. Street, L. Moezzi, M.A. Mach, G. Sutrave, L.E. Clancy, D.C. Bishop, R.H.Y. Louie, C. Cai, J. Foox, M. Mackay, F.J. Sedlazeck, P. Blombery, C.E. Mason, F. Luciani, D.J. Gottlieb, E. Blyth (2021) Blood doi: https://doi.org/10.1182/blood.2021010858
59. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
AM. Mc Cartney, M. Mahmoud, M. Jochum, DP. Agustinho, B.Zorman, AA. Khleifat, F. Dabbaghie, RK. Kesharwani, M. Smolka, M. Dawood, D. Albin, E. Aliyev, H. Almabrazi, A. Arslan, A. Balaji, S. Behera, K. Billingsley, DL. Cameron, J. Daw, ET. Dawson, W. De Coster, H. Du, C. Dunn, R. Esteban, A. Jolly, D. Kalra, C. Liao, Y. Liu, T. Lu, JM. Havrilla, MM. Khayat, M. Marin, J. Monlong, S. Price, A.R. Gener, J. Ren, S. Sagayaradj, N. Sapoval, C. Sinner, DC. Soto, A. Soylev, A. Subramaniyan, N. Syed, N. Tadimeti, P. Tater, P. Vats, J. Vaughn, K. Walker, G. Wang, Q. Zeng, S. Zhang, T. Zhao, B. Kille, E. Biederstedt, M. Chaisson, A. English, Z. Kronenberg, TJ. Treangen, T. Hefferon, C. Chin, B. Busby, F.J. Sedlazeck(2021) F1000Research doi: https://doi.org/10.12688/f1000research.51477.1
58. Optimized sample selection for cost-efficient long-read population sequencing
T.R. Ranallo-Benavidez, Z. Lemmon, S. Soyk, S. Aganezov, WJ. Salerno, RC. McCoy, ZB. Lippman, MC. Schatz, F.J. Sedlazeck(2021) Genome Research doi: https://doi.org/10.1101/gr.264879.120
57. Long-read sequencing for diagnosis in the Undiagnosed Diseases Network
D. Murdock, J. Rosenfeld, F. Xia, L. Burrage, M. Mahmoud, F.J. Sedlazeck, J. Nguyen, M. Guzman, J. Xu, S. Wu, P. Rosillo, C. Martinez J. Campbell, S. Nicholas, E. Hanson, C. Poli, T. Vogel, B. Lee (2021) Molecular Genetics and Metabolism doi: https://doi.org/10.1016/S1096-7192(21)00471-6
56. muCNV: Genotyping Structural Variants for Population-level Sequencing
G. Jun, F.J. Sedlazeck, Q. Zhu, A. English, G. Metcalf, H.M. Kang, C. Lee, R. Gibbs, E. Boerwinkle (2021) Oxford Bioinformatics doi: https://doi.org/10.1093/bioinformatics/btab199
55. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
N. Sapoval*, M. Mahmoud*, M.D. Jochum, Y. Liu, R.A.L. Elworth, Q. Wang, D. Albin, H. Ogilvie, M.D. Lee, S. Villapol, K.M. Hernandez, I.M. Berry, J. Foox, A. Beheshti, K. Ternus, K.M. Aagaard, D. Posada, C.E. Mason, F.J. Sedlazeck*, T.J. Treangen* (2021) Genome Research doi: https://doi.org/10.1101/gr.268961.120
54. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions
D. J. Butler, C. Mozsary, C. Meydan, D. Danko, J. Foox, J. Rosiene, A. Shaiber, E. Afshinnekoo, M. MacKay, F.J. Sedlazeck, N.A. Ivanov, M. Sierra, D. Pohle, M.Zietz, U. Gisladottir, V. Ramlall, C. D. Westover, K. Ryon, B. Young, C. Bhattacharya, P. Ruggiero, B.W. Langhorst, N. Tanner, J. Gawrys, D. Meleshko, D. Xu, P.A. D. Steel, A.J. Shemesh, J. Xiang, J. Thierry-Mieg, D. Thierry-Mieg, R.E. Schwartz, A. Iftner, D. Bezdan, J. Sipley, L. Cong, A. Craney, P. Velu, A. M. Melnick, I. Hajirasouliha, S. M. Horner, T. Iftner, M. Salvatore, M. Loda, L.F. Westblade, M. Cushing, S. Levy, S. Wu, N. Tatonetti, M. Imielinski, H. Rennert, C.E. Mason (2021) Nature Communications doi: https://doi.org/10.1038/s41467-021-21361-7
53. Chromosome-scale, haplotype-resolved assembly of human genomes
S. Garg, A. Fungtammasan, A. Carroll, M. Chou, A. Schmitt, X.Zhou, S. Mac, P. Peluso, E. Hatas, J. Ghurye, J. Maguire, M. Mahmoud, H. Cheng, D. Heller, J.M. Zook, T. Moemke, T. Marschall, F.J. Sedlazeck, J.Aach, Chen-S. Chin, G.M. Church, H. Li (2021) Nature Biotechnology doi: https://doi.org/10.1038/s41587-020-0711-0

2020

52. Parliament2: Fast Structural Variant Calling Using Optimized Combinations of Callers
S. Zarate, A. Carroll, M. Mahmoud, O. Krashenina, G. Jun, W. Salerno, MC. Schatz, E. Boerwinkle, R. Gibbs, F.J. Sedlazeck(2020) GigaScience doi: https://doi.org/10.1093/gigascience/giaa145
51. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
I. Lee, R. Razaghi, T. Gilpatrick, M. Molnar, N. Sadowski, J. T. Simpson, F.J. Sedlazeck, W. Timp (2020) Nature Methods doi: https://doi.org/10.1038/s41592-020-01000-7
50. Complex mosaic structural variations in human fetal brains
S. Sekar, L. Tomasini, C. Proukakis, T. Bae, L. Manlove, Y. Jang, S. Scuderi, B. Zhou, M. Kalyva, A. Amiri, J. Mariani, F.J. Sedlazeck, A.E. Urban, F.M. Vaccarino*, A. Abyzov*(2020) Genome Research doi: https://doi.org/10.1101/gr.262667.120
49. A diploid assembly-based benchmark for variants in the major histocompatibility complex
C. Chin, J. Wagner, Q. Zeng, E. Garrison, S. Garg, A. Fungtammasan, M. Rautiainen, S. Aganezov, M. Kirsche, S. Zarate, MC. Schatz, Chunlin X., WJ. Rowell, C. Markello, J. Farek, F.J. Sedlazeck, V. Bansal, B. Yoo, N. Miller, X. Zhou, A. Carroll, A.M. Barrio, M. Salit, T. Marschall, A.T. Dilthey, J.M. Zook(2020) Nature Communications doi: https://doi.org/10.1038/s41467-020-18564-9
48. Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
S. Aganezov, S. Goodwin, R.M. Sherman, F.J. Sedlazeck, G. Arun, S. Bhatia, I. Lee, M. Kirsche, R. Wappel, M. Kramer, K. Kostroff, D.L. Spector, W. Timp, W.R. McCombie, M.C. Schatz(2020) Genome Research doi: https://doi.org/10.1101/gr.260497.119
47. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement
S. Majidian, F.J. Sedlazeck(2020) Giga Science doi: https://doi.org/10.1093/gigascience/giaa078
46. Discovery and population genomics of structural variation in a songbird genus
M. H. Weissensteiner, I. Bunikis, A. Catalán, K.J. Francoijs, U. Knief, W. Heim, V. Peona, S. D. Pophaly, F.J. Sedlazeck, A. Suh, V. M. Warmuth, J. B.W. Wolf (2020) Nature Communications doi: https://doi.org/10.1038/s41467-020-17195-4
45. Major impacts of widespread structural variation on gene expression and crop improvement in tomato
M. Alonge, X. Wang, M. Benoit, S. Soyk, L. Pereira, L. Zhang, H. Suresh, S. Ramakrishnan, F. Maumus, D. Ciren, Y. Levy, T. H. Harel, G. Shalev-Schlosser, Z. Amsellem, H. Razifard, A.L. Caicedo, D. M. Tieman, H. Klee, M. Kirsche, S. Aganezov, T. R. Ranallo-Benavidez, Z. H. Lemmon, J. Kim, G. Robitaille, M. Kramer, S. Goodwin, W. R. McCombie, S. Hutton, J. Van Eck, J. Gillis, Y. Eshed, F.J. Sedlazeck, E. van der Knaap, M.C. Schatz*,Z. B. Lippman* (2020) CELL doi: https://doi.org/10.1016/j.cell.2020.05.021
44. A robust benchmark for germline structural variant detection
M. Zook, N. F. Hansen, N. D. Olson, L. M. Chapman, J. C. Mullikin, C. Xiao, S. Sherry, S. Koren, A. M. Phillippy, P. C. Boutros, S. Mohammad, E. Sahraeian, V. Huang, A. Rouette, N. Alexander, C. E. Mason, I. Hajirasouliha, C. Ricketts, J. Lee, R. Tearle, I. T. Fiddes, A. M. Barrio, J. Wala, A. Carroll, N. Ghaffari, O. L. Rodriguez, A. Bashir, S. Jackman, J. J. Farrell, A. M. Wenger, C. Alkan, A. Soylev, M. C. Schatz, S. Garg, G. Church, T. Marschall, K. Chen, X. Fan, A. C. English, J. A. Rosenfeld, W. Zhou, R. E. Mills, J. M. Sage, J. R. Davis, M. D. Kaiser, J. S. Oliver, A. P. Catalano, M.JP Chaisson, N. Spies, F.J. Sedlazeck, M. Salit (2020) Nature Biotechnology doi: https://doi.org/10.1038/s41587-020-0538-8
43. Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit
K. Shafin, T. Pesout, R. Lorig-Roach, M. Haukness, H. E. Olsen, C. Bosworth, J. Armstrong, K. Tigyi, N. Maurer, S. Koren, F.J. Sedlazeck, T. Marschall, S. Mayes, V. Costa, J. M. Zook, K. J. Liu, D. Kilburn, M. Sorensen, K. M. Munson, M. R. Vollger, E. E. Eichler, S. Salama, D. Haussler, R. E. Green, M. Akeson, A. Phillippy, K. H. Miga, P. Carnevali, M. Jain, B.Paten (2020) Nature Biotechnology doi: https://doi.org/10.1038/s41587-020-0503-6
42. Targeted Targeted nanopore sequencing with Cas9-guided adapter ligation
T. Gilpatrick, I. Lee, J.E. Graham, E. Raimondeau, R. Bowen, A. Heron, F.J. Sedlazeck, W. Timp (2020) Nature Biotechnology doi: https://doi.org/10.1038/s41587-020-0407-5
41. Potential applications of nanopore sequencing for forensic analysis
CL. Hall, R.R. Zascavage, F.J. Sedlazeck, J.V. Planz (2020) Forensic Sci Rev doi: https://doi.org/10.1038/s41587-020-0407-5

2019

40. Paragraph: A graph-based structural variant genotyper for short-read sequence data
S. Chen, P. Krusche, E. Dolzhenko, R.M. Sherman, R. Petrovski, F. Schlesinger, M. Kirsche, D.R. Bentley, M. C. Schatz, F.J. Sedlazeck*, M.A. Eberle* (2019) Genome Biology doi: https://doi.org/10.1186/s13059-019-1909-7
39. Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION
R. R. Zascavage, C. L. Hall, K. Thorson, M. Mahmoud, F.J. Sedlazeck, J. V. Planz (2019) Current Protocols in Human Genetics doi: https://doi.org/10.1002/cphg.94
38. Structural variant calling: the long and the short of it
M. Mahmoud, N. Gobet, D. I. Cruz-Dávalos, N. Mounier, C. Dessimoz*, F.J. Sedlazeck* (2019) Genome Biology doi: https://doi.org/10.1186/s13059-019-1828-7
37. A Genocentric Approach to Discovery of Mendelian Disorders
A. W. Hansen, M. Murugan, H. Li, M. M. Khayat, L. Wang, J. Rosenfeld, B. K. Andrews, S. N. Jhangiani, Z. H. Coban Akdemir, F.J. Sedlazeck, A. E. Ashley-Koch, P. Liu, D. M. Muzny, E. E. Davis, N. Katsanis, A. Sabo, J. E. Posey, Y. Yang, M. F. Wangler, C. M. Eng, V. Reid Sutton, J. R. Lupski, E. Boerwinkle, R. A. Gibbs (2019) The American Journal of Human Genetics doi: https://doi.org/10.1016/j.ajhg.2019.09.027
36. RaGOO: fast and accurate reference-guided scaffolding of draft genomes
M. Alonge, S. Soyk, S. Ramakrishnan, X. Wang, S. Goodwin, F.J. Sedlazeck, Z. B. Lippman, M. C. Schatz (2019) Genome Biology doi: https://doi.org/10.1186/s13059-019-1829-6
35. A strategy for building and using a human reference pangenome
B. Llamas*, G. Narzisi*, V. Schneider*, P.A. Audano, E. Bieder- stedt, L. Blauvelt, P. Bradbury, X. Chang, C. Chin, A. Fungtammasan, W.E. Clarke, A. Cleary, J.Ebler, J. Eizenga, J. A. Sibbesen, C.J. Markello, E. Garrison, S. Garg, G. Hickey, G. R. Lazo, M. F. Lin, M. Mahmoud, T. Marschall, I. Minkin, J. Monlong, R. L. Musunuri, S. Sagayaradj, A.M. Novak, M.Rautiainen, A. Regier F.J. Sedlazeck, J. Siren, Y. Souilmi J. Wagner, T. Wrightsman, T. T. Yokoyama, Q. Zeng, J.M. Zook, B. Paten, B. Busby(2019) F1000 doi: https://doi.org/10.12688/f1000research.19630.1
34. Evaluation of computational genotyping of Structural Variations for clinical diagnoses
V. Chander, R.A. Gibbs, F.J. Sedlazeck(2019) GigaScience doi: https://doi.org/10.1093/gigascience/giz110
33. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
A.M. Wenger, P. Peluso, W.J. Rowell, P. Chang, R.J. Hall, G.T. Concepcion, J. Ebler, A. Fungtammasan, A. Kolesnikov, N.D. Olson, A. Toepfer, C. Chin, M. Alonge, M. Mahmoud, Y. Qian, A.M. Phillippy, M.C. Schatz, G. Myers, M.A. DePristo, J. Ruan, T. Marschall, F.J. Sedlazeck, J.M. Zook, H. Li, S. Koren, A. Carroll, D.R. Rank, M.W. Hunkapiller (2019) Nature Biotechnology doi: https://doi.org/10.1038/s41587-019-0217-9
32. Ancestral admixture is the main determinant of global biodiversity in fission yeast
S. Tusso, B.P.S. Nieuwenhuis, F.J. Sedlazeck, J.W. Davey, D.C. Jeffares, J.B.W. Wolf (2019) Molecular Biology and Evolution doi: https://doi.org/10.1093/molbev/msz126
31. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
S. Soyk, Z.H. Lemmon, F.J. Sedlazeck, J.M. Jimenez-Gomez, M. Alonge, S.F. Hutton, J. Van Eck, M.C. Schatz, Z.B. Lippman (2019) Nature Plants doi: https://doi.org/10.1038/s41477-019-0422-z
30. Atlas- CNV: a validated approach to call Single-Exon CNVs in the eMERGESeq gene panel
T. Chiang, X. Liu, T. Wu, J. Hu, F.J. Sedlazeck, S. White, D. Schaid, M. Andrade, G.P. Jarvik, D. Crosslin, I. Stanaway, D.S. Carrell, J.J. Connolly, H. Hakonarson, E.E. Groopman, A.G. Gharavi, A. Fedotov, W. Bi, M. S Leduc, D.R. Murdock, Y. Jiang, L. Meng, C.M. Eng, S. Wen, Y. Yang, D.M. Muzny, E. Boerwinkle, W. Salerno, E. Venner, R.A. Gibbs (2019) Genetics in Medicine doi: https://doi.org/10.1038/s41436-019-0475-4
29. A multi-task convolutional deep neural network for variant calling in single molecule sequencing
R. Luo, F.J. Sedlazeck, TW. Lam, M.C. Schatz (2019) Nature Communication doi: https://doi.org/10.1038/s41467-019-09025-z
28. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2
C.R. Beck, C.M.B. CarvalhoZ.C. Akdemir, F.J. Sedlazeck, X.Song, Q. Meng, J. Hu, H. Doddapaneni, Z. Chong, E.S. Chen, P.C. Thornton, P. Liu, B. Yuan, M. Withers, S.N. Jhangiani, D. Kalra, K. Walker, A.C. English, Y. Han, K. Chen, D.M. Muzny, G. Ira, C.A. Shaw, R.A. Gibbs, P.J. Hastings, J.R. Lupski (2019) CELL doi: https://doi.org/10.1016/j.cell.2019.01.045
27. Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase
S. Schenk, S. Bannister, F.J. Sedlazeck, D. Anrather, B.Q. Minh, A. Bileck, M. Hartl, A. von Haeseler, C. Gerner, F. Raible, and K. Tessmar Raible (2019) eLIFE doi: https://doi.org/10.7554/eLife.41556
26. Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION
M. Leija Salazar, F.J. Sedlazeck, K. Mokretar, S. Mullin, M. Toffoli, M. Athanasopoulou, A. Donald, R. Sharma, D. Hughes, AH. Schapira, C. Proukakis (2019) Molecular Genetics & Genomic Medicine doi: https://doi.org/10.1002/mgg3.564

2018

25. Genome wide patterns of transposon proliferation in an evolutionary young hybrid fish
S. Dennemoser, F.J. Sedlazeck, Michael C. Schatz, A.W. Nolte (2018) Molecular Ecology doi: https://doi.org/10.1111/mec.14969
24. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
M. Nattestad, K. Ng, S. Goodwin, T. Baslan, F.J. Sedlazeck, J. Gurtowski, E. Hutton, M. Alford, E. Tseng,J. Chin, T. Beck, Y. Sundaravadanam, M. Kramer, E. Antoniou, J. McPherson, J. Hicks, M.C. Schatz, W.R. McCombie (2018) Genome Research doi: https://doi.org/10.1101/gr.231100.117
23. Accurate detection of complex structural variations using single-molecule sequencing
F.J. Sedlazeck*, P. Rescheneder*, M. Smolka, H. Fang, M. Nattestad, A. Haeseler, M.C. Schatz (2018) Nature Methods doi: https://doi.org/10.1038/s41592-018-0001-7
22. Piercing the dark matter: bioinformatics of long-range sequencing and mapping
F.J. Sedlazeck, L. Hayan, CA. Darby, M.C. Schatz (2018) Nature Reviews Genetics doi: https://doi.org/10.1038/s41576-018-0003-4

2017

21. LRSim: a Linked Reads Simulator generating insights for better genome partitioning
R.Luo, F.J. Sedlazeck, C.A. Darby,S. Kelly, M.C. Schatz (2017) Comput Struct Biotechnol. doi: https://doi.org/10.1016/j.csbj.2017.10.002
20. Tools for annotation and comparison of structural variation
F.J. Sedlazeck, A. Dhroso, D.L. Bodian, J. Paschall, F. Hermes, J. M. Zook(2017) F1000Research doi: https://doi.org/10.12688/f1000research.12516.1
19. DangerTrack: A scoring system to detect difficult-to-assess regions
I. Dolgalev*, F.J. Sedlazeck*, Ben Busby(2017) F1000Research doi: https://doi.org/10.12688/f1000research.11254.1
18. Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin
S. Dennenmoser, F.J. Sedlazeck, E. Iwaszkiewicz, X. Li, J. Altmuller, A.W. Nolte(2017) Molecular Ecology doi: https://doi.org/10.1111/mec.14134
17. GenomeScope: Fast genome-wide heterozygosity analysis from unassembled short reads
G. Vurture*, F.J. Sedlazeck*, M. Nattestad, C. Underwood, H. Fang, J. Gurtowski, M.C. Schatz (2017) Bioinformatics doi: https://doi.org/10.1093/bioinformatics/btx153
16. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
D.C. Jeffares, C. Jolly, M. Hoti, D. Speed, L. Shaw, C. Rallis, F. Balloux, C. Dessimoz*, J. Bahler*, F.J. Sedlazeck* (2017) Nature Communication doi: https://doi.org/10.1038/NCOMMS14061

2016

15. The genomic basis of circadian and circalunar timing adaptations in a midge
T.S. Kaiser, B. Poehn, D. Szkiba, M. Preussner, F.J. Sedlazeck, A. Zrim, T. Neumann, L. Nguyen, A.J. Betancourt, T. Hummel, H. Vogel, S. Dorner, F. Heyd, A. von Haeseler, K. Tessmar-Raible (2016) Nature doi: https://doi.org/10.1038/nature20151
14. Phased diploid genome assembly with single-molecule real-time sequencing
C.S. Chin, P. Peluso, F.J. Sedlazeck, M. Nattestad, G.T. Concepcion, A. Clum, C. Dunn, R.O. Malley, R. Figueroa-Balderas, A. Morales-Cruz, G.R. Cramer, M. Delledonne, C. Luo, J.R. Ecker, D. Cantu, D.R. Rank, M.C. Schatz (2016) Nature Methods doi: https://doi.org/10.1038/nmeth.4035
13. Chromosomal- Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multilayered Scaffolding
S. Vij, H. Kuh, I. S. Kuznetsova, A. Komissarov, A. A.Yurchenko, P. V. Heusden, S. Singh, N. M. Thevasagayam, P.S.R. Sridatta, K. Purushothaman, J.M. Saju1, J. Jiang, S.K. Mbandi, M. Jonas, A.H.Y. Tong, S. Mwangi, D. Lau, S.Y. Ngoh, W.C. Liew, X. Shen, L.S. Hon, J.P. Drake, M. Boitano, R. Hall, J. Chin, R. Lachumanan, J. Korlach, V. Trifonov, M. Kabilov, A. Tupikin, D. Green, S. Moxon, T. Garvin, F.J. Sedlazeck, G.W. Vurture, G. Gopikrishna, V.K. K, T.H. Noble, V. Scaria, S. Sivasubbu, D.R. Jerry, S.J. O’Brien, M.C. Schatz, T. Dalmay, S. Turner, S. Lok, A. Christoffels, L. Orban (2016) PLOS Genetics doi: https://doi.org/10.1371/journal.pgen.1005954

2015

12. The pineapple genome and the evolution of CAM photosynthesis
R. Ming, R. VanBuren, C.M. Wai, H. Tang, M.C. Schatz, J.E. Bowers, E. Lyons, M. Wang, J. Chen, E. Biggers, J. Zhang, L. Huang, L. Zhang, W. Miao, J. Zhang, Z. Ye, C. Miao, Z. Lin, H. Wang, H. Zhou, W.C. Yim, H.D. Priest, C. Zheng, M. Woodhouse, P.P. Edger, R. Guyot, H. Guo, H. Guo, G. Zheng, R. Singh, A. Sharma, X. Min, Y. Zheng, H. Lee, J. Gurtowski, F.J. Sedlazeck, A. Harkess, M.R. McKain, Z. Liao, J. Fang, J. Liu, X. Zhang, Q. Zhang, W. Hu, Y. Qin, K. Wang, L. Chen, N. Shirley, Y. Lin, L. Liu, A.G. Hernandez, C.L. Wright, V. Bulone, G.A. Tuskan, K. Heath, F. Zee, P.H. Moore, R. Sunkar, J. H. Leebens-Mack, T. Mockler, J.L. Bennetzen, M. Freeling, D. Sankoff, A.H. Paterson, X. Zhu, X. Yang, J.A.C. Smith, J.C. Cushman, R.E. Paull, Q. Yu (2015) Nature Genetics doi: https://doi.org/10.1038/ng.3435
11. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data
M. Smolka, P. Rescheneder, M.C. Schatz, A. von Haeseler, F.J. Sedlazeck(2015) Genome Biology doi: https://doi.org/10.1186/s13059-015-0803-1
10. The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
M. Tscherner, F. Zwolanek, S. Jenull, F.J. Sedlazeck, I.E. Frohner, N. Chauhan, A. von Haeseler and K. Kuchler (2015) PLOS Pathogen doi: https://doi.org/10.1371/journal.ppat.1005218
9. Ectodysplasin signaling genes and phenotypic evolution in sculpins (Cottus)
J. Cheng, F.J. Sedlazeck, J. Altmuller, A.W. Nolte (2015) Proceedings B doi: https://doi.org/10.1098/rspb.2015.0746
8. Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study
M. Krunic, R. Ertle, B. Hagen, F.J. Sedlazeck, R. Hofmann- Lehmann, A. von Haeseler and D. Klein (2015) BMC Veterinary Research doi: https://doi.org/10.1186/s12917-015-0378-9

2014

7. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain
C. Vesely, S. Tauber, F.J. Sedlazeck, M. Tajaddod,A. von Haeseler, M.F. Jantsch (2014) Nucleic Acids Research doi: https://doi.org/10.1093/nar/gku844

2013

6. NextGenMap: fast and accurate read mapping in highly polymorphic genomes
F.J. Sedlazeck∗, P. Rescheneder∗, and A. von Haeseler (2013) Bioinformatics doi: https://doi.org/10.1093/bioinformatics/btt468
5. Update on “Performance comparison of benchtop high-throughput sequencing platforms“
S. Jünemann, F.J. Sedlazeck, K. Prior, A. Albersmeier, U. John, J. Kalinowski, A. Mellmann, A. Goesmann, A. von Haeseler, J. Stoye, and D. Harmsen (2013) Nature Biotechnology doi: https://doi.org/10.1038/nbt.2522
4. Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets
F.J. Sedlazeck, P. Talloji, A. von Haeseler, and A. Bachmair(2013) Genomics doi: https://doi.org/10.1016/j.ygeno.2012.12.001

2012

3. Advanced Methylome Analysis after Bisulfite Deep Sequencing: an Example in Arabidopsis
H.Q. Dinh, M. Dubin∗ F.J. Sedlazeck∗ N. Lettner, O. Mittelsten Scheid, and A. von Haeseler (2012) PLoS ONE doi: https://doi.org/10.1371/journal.pone.0041528
2. MASon: Million Alignments In Seconds - A Platform Independent Pairwise Sequence Alignment Library for Next Generation Sequencing Data
P. Rescheneder, A. von Haeseler, and F.J. Sedlazeck(2012) Proceedings of the International Conference on Bioinformatics Models,Methods and Algorithms (BIOINFORMATICS 2012) doi: https://doi.org/10.5220/0003775701950201
1. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs
C. Vesely∗, S. Tauber∗, F.J. Sedlazeck, A. von Haeseler, and M.F. Jantsch (2012) Genome Research doi: https://doi.org/10.1101/gr.133025.111


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Applying to our lab

Computational Post-Doctoral Researchers
Applications are invited for a computational postdoctoral research position in my lab at Human Genomes Sequencing Center at Baylor College of Medicine (Houston, Texas). The researcher will develop novel methods for large scale DNA-seq, RNA-Seq and other omics data related to human, but also other organisms. Potential projects include SVs detection, SVs impact estimation and population scale research.

Ideal applicant will have:
  • A Ph.D. degree in Computer Science, Applied Mathematics, or related fields with a dissertation related to Computational Biology.
  • Strong programming and analytical skills, including experience with next-generation sequencing data.
  • Published at least two first author papers in English and demonstrated written communication skills in English.
To apply, please email me a letter of interest and current CV at fritz.sedlazeck @ bcm.edu