Sedlazeck Lab

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
GenomeScope	Estimate genomic properties from unassembled sequencing reads
LRSim	Linked Read Simulator
MuMmer SGE	Parallization script for MUMMer.
NGM	Short read mapper especially suitable for high SNP rates
NGM-LR	Fast 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
Sniffles	Detection of Structural Variations from Long Reads
SURVIVOR	Detection 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.
Teaser	Fast personalized benchmarks and optimization for NGS read mapping
Vulcan	Utilizing two scoring functions to improve long read mapping

Lab Members


	Fritz Sedlazeck, Ph.D. Associate Professor	Office: Alkek 1619 Phone: 713 798-4951 fritz.sedlazeck [at] bcm.edu Home page

	Medhat Mahmoud, Ph.D. PostDoc	Office: Alkek 1619 Phone: 713 798-3525 medhat.mahmoud [at] bcm.edu Home page


	Daniel Paiva Agustinho, Ph.D. Staff Scientist	daniel.agustinho [at] bcm.edu Home page


	Sairam Behera, Ph.D. PostDoc	Office: Alkek 1619 Phone: 713 798-4951 Sairam.Behera [at] bcm.edu Home page


	Luis Paulin, Ph.D. PostDoc	luis.paulin [at] bcm.edu Home page


	Moritz Smolka, B.Sc. Visiting Scientist	moritz.smolka [at] bcm.edu Home page


	Damaris Lattimer Internship Student	damaris.lattimer [at] bcm.edu Home page


	Philippe Sanio, M.Sc. Internship Student	philippe.sanio [at] bcm.edu GitHub


	Sina Majidian, Ph.D. Visiting PostDoc	Office: Genopode, UNIL Sina.Majidian [at] unil.ch Home page


	Michal Izydorczyk, PhD Postdoc	michal.izydorczyk [at] bcm.edu GitHub


	Xinchang Zheng, PhD Postdoc	Xinchang.Zheng [at] bcm.edu


	Farhang Jaryani, PhD Postdoc	Farhang.Jarynai [at] bcm.edu


	Yilei Fu, PhD Postdoc	Yilei.Fu [at] bcm.edu

Publications

Title	Cite	Year
Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations Y Ji, J Zhao, J Gong, FJ Sedlazeck, S Fan Molecular Genetics and Genomics 299 (1), 65 , 2024		2024
Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing P Alvarez Jerez, K Daida, FP Grenn, L Malik, A Miano-Burkhardt, ... npj Parkinson's Disease 10 (1), 136 , 2024		2024
Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci CM Grochowski, JD Bengtsson, H Du, M Gandhi, MY Lun, MG Mehaffey, ... Cell Genomics , 2024		2024
The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics SK Deb, D Kalra, J Kubica, E Stricker, VQ Truong, Q Zeng, CJ Fiscus, ... F1000Research 13, 708 , 2024		2024
Considerations for reporting variants in novel candidate genes identified during clinical genomic testing JX Chong, SI Berger, S Baxter, E Smith, C Xiao, DG Calame, MH Hawley, ... Genetics in Medicine, 101199 , 2024		2024
MethPhaser: methylation-based long-read haplotype phasing of human genomes Y Fu, S Aganezov, M Mahmoud, J Beaulaurier, S Juul, TJ Treangen, ... Nature Communications 15 (1), 5327 , 2024	3 *	2024
Profiling complex repeat expansions in RFC1 in Parkinson’s disease P Alvarez Jerez, K Daida, A Miano-Burkhardt, H Iwaki, L Malik, G Cogan, ... npj Parkinson's Disease 10 (1), 108 , 2024		2024
De Novo Genome Assembly for the Coppery Titi Monkey ( Plecturocebus cupreus ): An Emerging Nonhuman Primate Model for Behavioral Research SP Pfeifer, A Baxter, LE Savidge, FJ Sedlazeck, KL Bales Genome Biology and Evolution 16 (5), evae108 , 2024		2024
Unveiling microbial diversity: harnessing long-read sequencing technology DP Agustinho, Y Fu, VK Menon, GA Metcalf, TJ Treangen, FJ Sedlazeck Nature Methods, 1-13 , 2024	1	2024
Analysis and benchmarking of small and large genomic variants across tandem repeats AC English, E Dolzhenko, H Ziaei Jam, SK McKenzie, ND Olson, ... Nature Biotechnology, 1-12 , 2024	3	2024
Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes F Chen, Y Zhang, FJ Sedlazeck, CJ Creighton Cell Reports Medicine 5 (3) , 2024	1	2024
The benefit of a complete reference genome for cancer structural variant analysis LF Paulin, J Fan, K O’Neill, E Pleasance, VL Porter, SJM Jones, ... medRxiv , 2024	1	2024
Closing the gap: Solving complex medically relevant genes at scale M Mahmoud, J Harting, H Corbitt, X Chen, SN Jhangiani, H Doddapaneni, ... medRxiv , 2024	1	2024
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation JA Gustafson, SB Gibson, N Damaraju, MPG Zalusky, K Hoekzema, ... medRxiv , 2024	9	2024
Utility of long-read sequencing for All of Us M Mahmoud, Y Huang, K Garimella, PA Audano, W Wan, N Prasad, ... Nature communications 15 (1), 837 , 2024	24	2024
Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms S Behera, S Catreux, M Rossi, S Truong, Z Huang, M Ruehle, A Visvanath, ... bioRxiv , 2024		2024
Detection of mosaic and population-level structural variants with Sniffles2 M Smolka, LF Paulin, CM Grochowski, DW Horner, M Mahmoud, ... Nature biotechnology, 1-10 , 2024	122 *	2024
Characterization and visualization of tandem repeats at genome scale E Dolzhenko, A English, H Dashnow, G De Sena Brandine, T Mokveld, ... Nature Biotechnology, 1-9 , 2024	30 *	2024
Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions K Bilgrav Saethe, J Eisfeldt, J Bengtsson, MY Lun, CM Grochowski, ... medRxiv, 2024.04. 22.24305780 , 2024		2024
Long-read sequencing of 945 Han individuals identifies novel structural variants associated with phenotypic diversity and disease susceptibility J Gong, H Sun, K Wang, Y Zhao, Y Huang, Q Chen, H Qiao, Y Gao, ... medRxiv, 2024.03. 21.24304654 , 2024	1	2024
The benefit of a complete reference genome for cancer structural variant analysis F Sedlazeck, LF Paulin, K O Neill, J Fan, E Pleasance, SJM Jones, ... medRxiv, 2024.03. 15.24304369 , 2024		2024
Shining light on the dark genome: accurate quantification of tandem repeats for translational and basic research E Dolzhenko, A English, H Dashnow, W Rowell, Z Kronenberg, ... EUROPEAN JOURNAL OF HUMAN GENETICS 32, 27-27 , 2024		2024
Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes K O'Neill, E Pleasance, J Fan, V Akbari, G Chang, K Dixon, V Csizmok, ... medRxiv, 2024.02. 20.24302959 , 2024	2	2024
Inter and intra-host diversity of RSV in hematopoietic stem cell transplant adults with normal and delayed viral clearance V Avadhanula, DP Agustinho, VK Menon, RF Chemaly, DP Shah, X Qin, ... Virus Evolution 10 (1), vead086 , 2024	2	2024
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree D Dylus, A Altenhoff, S Majidian, FJ Sedlazeck, C Dessimoz Nature Biotechnology 42 (1), 139-147 , 2024	19	2024
Improved sequence mapping using a complete reference genome and lift-over NC Chen, LF Paulin, FJ Sedlazeck, S Koren, AM Phillippy, B Langmead Nature Methods 21 (1), 41-49 , 2024	10	2024
Association Analysis of Common Structural Variants in the Alzheimer’s Disease Sequencing Project S Lee, AC English, R Xia, GM Peloso, JC Bis, H Lin, SH Choi, ... Alzheimer's & Dementia 19, e078821 , 2023		2023
Small variant benchmark from a complete assembly of X and Y chromosomes J Wagner, ND Olson, J McDaniel, L Harris, BJ Pinto, D Jaspez, ... bioRxiv, 2023.10. 31.564997 , 2023		2023
VariantSurvival: a tool to identify genotype–treatment response T Krannich, MH Sarrias, H Ben Aribi, M Shokrof, A Iacoangeli, ... Frontiers in Bioinformatics 3, 1277923 , 2023		2023
Genomic variant benchmark: if you cannot measure it, you cannot improve it S Majidian, DP Agustinho, CS Chin, FJ Sedlazeck, M Mahmoud Genome Biology 24 (1), 221 , 2023	11	2023
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation M Kolmogorov, KJ Billingsley, M Mastoras, M Meredith, J Monlong, ... Nature Methods 20 (10), 1483-1492 , 2023	40	2023
The complete sequence of a human Y chromosome A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor, N Altemose, PW Hook, ... Nature 621 (7978), 344-354 , 2023	157	2023
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes E Kalef-Ezra, ZG Turan, D Perez-Rodriguez, I Bomann, S Behera, ... bioRxiv , 2023		2023
Beyond the exome: what’s next in diagnostic testing for Mendelian conditions MH Wojcik, CM Reuter, S Marwaha, M Mahmoud, MH Duyzend, ... The American Journal of Human Genetics 110 (8), 1229-1248 , 2023	32	2023
Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes CS Chin, S Behera, A Khalak, FJ Sedlazeck, PH Sudmant, J Wagner, ... Nature Methods 20 (8), 1213-1221 , 2023	17	2023
Variant calling and benchmarking in an era of complete human genome sequences ND Olson, J Wagner, N Dwarshuis, KH Miga, FJ Sedlazeck, M Salit, ... Nature Reviews Genetics 24 (7), 464-483 , 2023	38	2023
Genome‐wide analysis of structural variants in Parkinson disease KJ Billingsley, J Ding, PA Jerez, A Illarionova, K Levine, FP Grenn, ... Annals of neurology 93 (5), 1012-1022 , 2023	16	2023
Identification of allele-specific KIV-2 repeats and impact on Lp (a) measurements for cardiovascular disease risk S Behera, JR Belyeu, X Chen, LF Paulin, NQH Nguyen, E Newman, ... bioRxiv , 2023	5	2023
Intratumoral heterogeneity and clonal evolution induced by HPV integration K Akagi, DE Symer, M Mahmoud, B Jiang, S Goodwin, D Wangsa, Z Li, ... Cancer discovery 13 (4), 910-927 , 2023	30	2023
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models J Rozowsky, J Gao, B Borsari, YT Yang, T Galeev, G Gürsoy, CB Epstein, ... Cell 186 (7), 1493-1511. e40 , 2023	23	2023
Impact and characterization of serial structural variations across humans and great apes W Höps, T Rausch, P Ebert, ... bioRxiv, 2023.03. 09.531868 , 2023		2023
A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly M Dawood, G Akay, T Mitani, D Marafi, JM Fatih, A Gezdirici, H Najmabadi, ... American Journal of Medical Genetics Part A 191 (3), 794-804 , 2023		2023
FixItFelix: improving genomic analysis by fixing reference errors S Behera, J LeFaive, P Orchard, M Mahmoud, LF Paulin, J Farek, ... Genome biology 24 (1), 31 , 2023	11 *	2023
Structural variation across 138,134 samples in the TOPMed consortium G Jun, AC English, GA Metcalf, J Yang, MJP Chaisson, N Pankratz, ... bioRxiv , 2023	7	2023
StratoMod: Predicting sequencing and variant calling errors with interpretable machine learning N Dwarshuis, P Tonner, ND Olson, FJ Sedlazeck, J Wagner, JM Zook bioRxiv, 2023.01. 20.524401 , 2023	1	2023
SVhound: detection of regions that harbor yet undetected structural variation LF Paulin, M Raveendran, RA Harris, J Rogers, A von Haeseler, ... BMC bioinformatics 24 (1), 23 , 2023		2023
The GIAB genomic stratifications resource for human reference genomes N Dwarshuis, D Kalra, J McDaniel, P Sanio, P Alvarez Jerez, B Jadhav, ... BioRxiv, 2023.10. 27.563846 , 2023	1	2023
Benchmarking of small and large variants across tandem repeats A English, E Dolzhenko, H Ziaei-Jam, ND Olson, S Mckenzie, ... bioRxiv, 2023.10. 29.564632 , 2023	13	2023
Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures CM Grochowski, JD Bengtsson, H Du, M Gandhi, MY Lun, MG Mehaffey, ... bioRxiv, 2023.10. 02.560172 , 2023	1	2023
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments J Farek, D Hughes, W Salerno, Y Zhu, A Pisupati, A Mansfield, ... GigaScience 12, giac125 , 2023	33	2023
Truvari: refined structural variant comparison preserves allelic diversity AC English, VK Menon, RA Gibbs, GA Metcalf, FJ Sedlazeck Genome Biology 23 (1), 271 , 2022	84	2022
Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program MM Wheeler, AM Stilp, S Rao, BV Halldórsson, D Beyter, J Wen, ... Nature communications 13 (1), 7592 , 2022	4	2022
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, CM Grochowski, M Dawood, ... Human mutation 43 (12), 2033-2053 , 2022	7	2022
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, ... Genome biology 23, 1-26 , 2022	28	2022
Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation M Orantes-Bonilla, M Makhoul, HT Lee, HS Chawla, P Vollrath, ... Frontiers in Plant Science 13, 1057953 , 2022	5	2022
The multiple de novo copy number variant (M dn CNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation H Du, A Jolly, CM Grochowski, B Yuan, M Dawood, SN Jhangiani, H Li, ... Genome Medicine 14 (1), 122 , 2022	9	2022
Multiple genome alignment in the telomere-to-telomere assembly era B Kille, A Balaji, FJ Sedlazeck, M Nute, TJ Treangen Genome Biology 23 (1), 182 , 2022	21	2022
Genome-wide analysis of structural variants in Parkinson’s disease using short-read sequencing data KJ Billingsley, J Ding, PA Jerez, A Illarionova, FP Grenn, MB Makarious, ... bioRxiv, 2022.08. 22.504867 , 2022	3	2022
Characterizing the genetic polymorphisms in 370 challenging medically relevant genes using long-read sequencing data from 41 human individuals among 19 global populations Y Ji, J Gong, FJ Sedlazeck, S Fan bioRxiv, 2022.08. 03.502734 , 2022	5	2022
Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene M Toffoli, X Chen, FJ Sedlazeck, CY Lee, S Mullin, A Higgins, S Koletsi, ... Communications Biology 5 (1), 670 , 2022	19	2022
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing SD Goenka, JE Gorzynski, K Shafin, DG Fisk, T Pesout, TD Jensen, ... Nature Biotechnology 40 (7), 1035-1041 , 2022	55	2022
Frequent spontaneous structural rearrangements promote transgenerational genome diversification in Brassica napus M Orantes-Bonilla, M Makhoul, HT Lee, HS Chawla, P Vollrath, ... Biorxiv, 2022.06. 27.497715 , 2022	2	2022
A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA CS Chin, S Behera, GA Metcalf, RA Gibbs, E Boerwinkle, FJ Sedlazeck bioRxiv, 2022.06. 08.495395 , 2022	9	2022
TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data L Huang, JD Rosen, Q Sun, J Chen, MM Wheeler, Y Zhou, YI Min, ... The American Journal of Human Genetics 109 (6), 1175-1181 , 2022	38	2022
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions ND Olson, J Wagner, J McDaniel, SH Stephens, ST Westreich, ... Cell genomics 2 (5) , 2022	127	2022
Benchmarking challenging small variants with linked and long reads J Wagner, ND Olson, L Harris, Z Khan, J Farek, M Mahmoud, A Stankovic, ... Cell genomics 2 (5) , 2022	123	2022
Curated variation benchmarks for challenging medically relevant autosomal genes J Wagner, ND Olson, L Harris, J McDaniel, H Cheng, A Fungtammasan, ... Nature biotechnology 40 (5), 672-680 , 2022	136	2022
Searching thousands of genomes to classify somatic and novel structural variants using STIX M Chowdhury, BS Pedersen, FJ Sedlazeck, AR Quinlan, RM Layer Nature methods 19 (4), 445-448 , 2022	9 *	2022
Centers for Mendelian Genomics: A decade of facilitating gene discovery SM Baxter, JE Posey, NJ Lake, N Sobreira, JX Chong, S Buyske, EE Blue, ... Genetics in Medicine 24 (4), 784-797 , 2022	52	2022
Ultra-rapid nanopore whole genome genetic diagnosis of dilated cardiomyopathy in an adolescent with cardiogenic shock JE Gorzynski, SD Goenka, K Shafin, TD Jensen, DG Fisk, ME Grove, ... Circulation: Genomic and Precision Medicine 15 (2), e003591 , 2022	3	2022
A complete reference genome improves analysis of human genetic variation S Aganezov, SM Yan, DC Soto, M Kirsche, S Zarate, P Avdeyev, ... Science 376 (6588), eabl3533 , 2022	233	2022
The complete sequence of a human genome S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ... Science 376 (6588), 44-53 , 2022	2035	2022
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data Y Liu, J Kearney, M Mahmoud, B Kille, FJ Sedlazeck, TJ Treangen Nature communications 13 (1), 1321 , 2022	26	2022
Towards accurate and reliable resolution of structural variants for clinical diagnosis Z Liu, R Roberts, TR Mercer, J Xu, FJ Sedlazeck, W Tong Genome biology 23 (1), 68 , 2022	47	2022
Ultrarapid nanopore genome sequencing in a critical care setting JE Gorzynski, SD Goenka, K Shafin, TD Jensen, DG Fisk, ME Grove, ... New England Journal of Medicine 386 (7), 700-702 , 2022	157	2022
Accurate Detection of Structural Variations at Population Scale M Smolka, L Paulin, C Carvalho, C Proukakis, FJ Sedlazeck Plant and Animal Genome XXIX Conference (January 8-12, 2022) , 2022		2022
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, DC Soto, F Dabbaghie, ... F1000Research 11 , 2022	2	2022
Fully resolved assembly of Cryptosporidium parvum VK Menon, PC Okhuysen, CL Chappell, M Mahmoud, M Mahmoud, ... Gigascience 11, giac010 , 2022	7	2022
Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus RA Harris, M Raveendran, DT Lyfoung, FJ Sedlazeck, M Mahmoud, ... GigaScience 11, giac039 , 2022	4	2022
Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device CL Hall, RK Kesharwani, NR Phillips, JV Planz, FJ Sedlazeck, ... Forensic Science International: Genetics 56, 102629 , 2022	18	2022
Whole genome sequencing identifies common and rare structural variants contributing to hematologic traits in the NHLBI TOPMed program MM Wheeler, AM Stilp, S Rao, BV Halldórsson, D Beyter, J Wen, ... Medrxiv, 2021.12. 16.21267871 , 2021	4	2021
High resolution copy number inference in cancer using short-molecule nanopore sequencing T Baslan, S Kovaka, FJ Sedlazeck, Y Zhang, R Wappel, S Tian, SW Lowe, ... Nucleic acids research 49 (21), e124-e124 , 2021	20	2021
Hidden biases in germline structural variant detection MM Khayat, SME Sahraeian, S Zarate, A Carroll, H Hong, B Pan, L Shi, ... Genome biology 22, 1-15 , 2021	21	2021
PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation M Mahmoud, H Doddapaneni, W Timp, FJ Sedlazeck Genome biology 22, 1-17 , 2021	31	2021
Comprehensive analysis of GBA using a novel algorithm for Illumina whole-genome sequence data or targeted Nanopore sequencing M Toffoli, X Chen, FJ Sedlazeck, CY Lee, S Mullin, A Higgins, S Koletsi, ... medRxiv, 2021.11. 12.21266253 , 2021	3	2021
Investigation of product-derived lymphoma following infusion of piggyBac -modified CD19 chimeric antigen receptor T cells KP Micklethwaite, K Gowrishankar, BS Gloss, Z Li, JA Street, L Moezzi, ... Blood, The Journal of the American Society of Hematology 138 (16), 1391-1405 , 2021	134	2021
Benzyl isothiocyanate induces cardiomyocyte proliferation and heart regeneration A Sakaguchi, M Kawasaki, Y Saito, K Murata, H Masumoto, W Kimura bioRxiv, 2021.09. 08.459197 , 2021		2021
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study J Foox, SW Tighe, CM Nicolet, JM Zook, M Byrska-Bishop, WE Clarke, ... Nature biotechnology 39 (9), 1129-1140 , 2021	91	2021
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment Y Fu, M Mahmoud, VV Muraliraman, FJ Sedlazeck, TJ Treangen GigaScience 10 (9), giab063 , 2021	16	2021
Towards population-scale long-read sequencing W De Coster, MH Weissensteiner, FJ Sedlazeck Nature Reviews Genetics 22 (9), 572-587 , 2021	216	2021
Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals H Doddapaneni, SJ Cregeen, R Sucgang, Q Meng, X Qin, V Avadhanula, ... PLoS One 16 (8), e0244468 , 2021	35	2021
muCNV: genotyping structural variants for population-level sequencing G Jun, F Sedlazeck, Q Zhu, A English, G Metcalf, HM Kang, ... Bioinformatics 37 (14), 2055-2057 , 2021	7	2021
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, FJ Sedlazeck, ... Movement Disorders 36 (6), 1456-1460 , 2021	6	2021
Discovery and population genomics of structural variation in a songbird genus (vol 11, 3403, 2020) MH Weissensteiner, I Bunikis, A Catalan, KJ Francoijs, U Knief, W Heim, ... Nature Communications 12 (1) , 2021		2021
Optimized sample selection for cost-efficient long-read population sequencing TR Ranallo-Benavidez, Z Lemmon, S Soyk, S Aganezov, WJ Salerno, ... Genome research 31 (5), 910-918 , 2021	16 *	2021
Multi-tissue integrative analysis of personal epigenomes J Rozowsky, J Drenkow, Y Yang, G Gursoy, T Galeev, B Borsari, ... BioRxiv , 2021	7	2021
SVhound: Detection of future Structural Variation hotspots LF Paulin, M Raveendran, RA Harris, J Rogers, A von Haeseler, ... bioRxiv, 2021.04. 09.439237 , 2021		2021
Long-read sequencing for diagnosis in the Undiagnosed Diseases Network D Murdock, J Rosenfeld, F Xia, L Burrage, M Mahmoud, F Sedlazeck, ... Molecular Genetics and Metabolism 132, S253-S254 , 2021		2021
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission N Sapoval, M Mahmoud, MD Jochum, Y Liu, RAL Elworth, Q Wang, ... Genome research 31 (4), 635-644 , 2021	54 *	2021
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions D Butler, C Mozsary, C Meydan, J Foox, J Rosiene, A Shaiber, D Danko, ... Nature communications 12 (1), 1660 , 2021	229 *	2021
Chromosome-scale, haplotype-resolved assembly of human genomes S Garg, A Fungtammasan, A Carroll, M Chou, A Schmitt, X Zhou, S Mac, ... Nature Biotechnology 39 (3), 309-312 , 2021	162	2021
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, ... F1000Research 10 , 2021	5	2021
Parliament2: Accurate structural variant calling at scale S Zarate, A Carroll, M Mahmoud, O Krasheninina, G Jun, WJ Salerno, ... GigaScience 9 (12), giaa145 , 2020	84 *	2020
Complex mosaic structural variations in human fetal brains S Sekar, L Tomasini, C Proukakis, T Bae, L Manlove, Y Jang, S Scuderi, ... Genome research 30 (12), 1695-1704 , 2020	28	2020
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing I Lee, R Razaghi, T Gilpatrick, M Molnar, A Gershman, N Sadowski, ... Nature methods 17 (12), 1191-1199 , 2020	169	2020
A robust benchmark for detection of germline large deletions and insertions JM Zook, NF Hansen, ND Olson, L Chapman, JC Mullikin, C Xiao, ... Nature biotechnology 38 (11), 1347-1355 , 2020	342 *	2020
Cas9 Enrichment for Nanopore Sequencing T Gilpatrick, I Lee, JE Graham, E Raimondeau, R Bowen, A Heron, ...		2020
A diploid assembly-based benchmark for variants in the major histocompatibility complex CS Chin, J Wagner, Q Zeng, E Garrison, S Garg, A Fungtammasan, ... Nature communications 11 (1), 4794 , 2020	61	2020
Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine M Mahmoud, AR Gener, MM Khayat, AC English, A Balaji, A Zhou, ... F1000Research 9 (1141), 1141 , 2020		2020
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes K Shafin, T Pesout, R Lorig-Roach, M Haukness, HE Olsen, C Bosworth, ... Nature biotechnology 38 (9), 1044-1053 , 2020	439	2020
Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing S Aganezov, S Goodwin, RM Sherman, FJ Sedlazeck, G Arun, S Bhatia, ... Genome research 30 (9), 1258-1273 , 2020	95	2020
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, ... Cell 182 (1), 145-161. e23 , 2020	550	2020
Discovery and population genomics of structural variation in a songbird genus MH Weissensteiner, I Bunikis, A Catalán, KJ Francoijs, U Knief, W Heim, ... Nature communications 11 (1), 3403 , 2020	115	2020
PhaseME: Automatic rapid assessment of phasing quality and phasing improvement S Majidian, FJ Sedlazeck Gigascience 9 (7), giaa078 , 2020	10	2020
Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes FJ Sedlazeck, B Yu, AJ Mansfield, H Chen, O Krasheninina, A Tin, Q Qi, ... bioRxiv, 2020.05. 02.074096 , 2020	6	2020
Targeted nanopore sequencing with Cas9-guided adapter ligation T Gilpatrick, I Lee, JE Graham, E Raimondeau, R Bowen, A Heron, ... Nature biotechnology 38 (4), 433-438 , 2020	384	2020
Taking the bait: A PCR-free enrichment strategy for nanopore sequencing applications J Planz, F Sedlazeck, R Zascavage		2020
Potential applications of nanopore sequencing for forensic analysis CL Hall, RR Zascavage, FJ Sedlazeck, JV Planz Forensic science review 32 (1), 23-54 , 2020	21	2020
Structural variant calling: the long and the short of it M Mahmoud, N Gobet, DI Cruz-Dávalos, N Mounier, C Dessimoz, ... Genome biology 20, 1-14 , 2019	553	2019
Approaches to whole mitochondrial genome sequencing on the Oxford Nanopore MinION RR Zascavage, CL Hall, K Thorson, M Mahmoud, FJ Sedlazeck, JV Planz Current Protocols in Human Genetics 104 (1), e94 , 2019	18	2019
RaGOO: fast and accurate reference-guided scaffolding of draft genomes M Alonge, S Soyk, S Ramakrishnan, X Wang, S Goodwin, FJ Sedlazeck, ... Genome biology 20, 1-17 , 2019	562	2019
Paragraph: a graph-based structural variant genotyper for short-read sequence data S Chen, P Krusche, E Dolzhenko, RM Sherman, R Petrovski, ... Genome biology 20, 1-13 , 2019	140	2019
A genocentric approach to discovery of Mendelian disorders AW Hansen, M Murugan, H Li, MM Khayat, L Wang, J Rosenfeld, ... The American Journal of Human Genetics 105 (5), 974-986 , 2019	35	2019
Phasing of complex genomic rearrangements reveal involvement of both homologous chromosomes in pre-and post-zigotic events CM Carvalho, C Beck, Z Akdemir, F Sedlazeck, Q Meng, J Hu, ... EUROPEAN JOURNAL OF HUMAN GENETICS 27, 1137-1137 , 2019		2019
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome AM Wenger, P Peluso, WJ Rowell, PC Chang, RJ Hall, GT Concepcion, ... Nature biotechnology 37 (10), 1155-1162 , 2019	1371	2019
Evaluation of computational genotyping of structural variation for clinical diagnoses V Chander, RA Gibbs, FJ Sedlazeck GigaScience 8 (9), giz110 , 2019	40	2019
Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel T Chiang, X Liu, TJ Wu, J Hu, FJ Sedlazeck, S White, D Schaid, ... Genetics in Medicine 21 (9), 2135-2144 , 2019	22	2019
Ancestral admixture is the main determinant of global biodiversity in fission yeast S Tusso, BPS Nieuwenhuis, FJ Sedlazeck, JW Davey, DC Jeffares, ... Molecular biology and evolution 36 (9), 1975-1989 , 2019	57	2019
Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato (vol 5, pg 471, 2019) S Soyk, ZH Lemmon, FJ Sedlazeck, JM Jimenez-Gomez, M Alonge, ... NATURE PLANTS 5 (8), 903-903 , 2019		2019
Why So Pale and Wan: Comparative Genomics of a New Cavefish in Europe F Sedlazeck, M Mahmoud, Y Jia, J Behrmann, AW Nolte Plant and Animal Genome XXVII Conference (January 12-16, 2019) , 2019		2019
Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato S Soyk, ZH Lemmon, FJ Sedlazeck, JM Jiménez-Gómez, M Alonge, ... Nature plants 5 (5), 471-479 , 2019	76	2019
Megabase length hypermutation accompanies human structural variation at 17p11. 2 CR Beck, CMB Carvalho, ZC Akdemir, FJ Sedlazeck, X Song, Q Meng, ... Cell 176 (6), 1310-1324. e10 , 2019	65	2019
Sequencing Long Amplicon Microsatellite Loci Using the Oxford Nanopore Technologies MinION Device R Zascavage, F Sedlazeck, J Planz		2019
A multi-task convolutional deep neural network for variant calling in single molecule sequencing R Luo, FJ Sedlazeck, TW Lam, MC Schatz Nature communications 10 (1), 998 , 2019	176	2019
Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION M Leija‐Salazar, FJ Sedlazeck, M Toffoli, S Mullin, K Mokretar, ... Molecular genetics & genomic medicine 7 (3), e564 , 2019	83	2019
Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish S Dennenmoser, FJ Sedlazeck, MC Schatz, J Altmüller, M Zytnicki, ... Molecular Ecology 28 (6), 1491-1505 , 2019	15	2019
Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase S Schenk, SC Bannister, FJ Sedlazeck, D Anrather, BQ Minh, A Bileck, ... Elife 8, e41556 , 2019	51	2019
A strategy for building and using a human reference pangenome B Llamas, G Narzisi, V Schneider, PA Audano, E Biederstedt, L Blauvelt, ... F1000Research 8 , 2019	16	2019
Sequencing Long Amplicon Microsatellite Loci Using the Oxford Nanopore Technologies MinION [TM] Device CL Hall		2019
Fine-scale analysis of Structural Genomic Variation in Natural Populations MH Weissensteiner, I Bunikis, U Knief, V Peona, SD Pophaly, A Suh, ...		2019
Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line M Nattestad, S Goodwin, K Ng, T Baslan, FJ Sedlazeck, P Rescheneder, ... Genome research 28 (8), 1126-1135 , 2018	177	2018
Piercing the dark matter: bioinformatics of long-range sequencing and mapping FJ Sedlazeck, H Lee, CA Darby, MC Schatz Nature Reviews Genetics 19 (6), 329-346 , 2018	488	2018
Accurate detection of complex structural variations using single-molecule sequencing FJ Sedlazeck, P Rescheneder, M Smolka, H Fang, M Nattestad, ... Nature methods 15 (6), 461-468 , 2018	1321	2018
Copy number increases of transposable elements and protein‐coding genes in an invasive fish of hybrid origin S Dennenmoser, FJ Sedlazeck, E Iwaszkiewicz, XY Li, J Altmüller, ... Molecular Ecology 26 (18), 4712-4724 , 2017	33	2017
GenomeScope: fast reference-free genome profiling from short reads GW Vurture, FJ Sedlazeck, M Nattestad, CJ Underwood, H Fang, ... Bioinformatics 33 (14), 2202-2204 , 2017	1320	2017
regions [version 1; referees: 2 approved, 1 approved with I Dolgalev, F Sedlazeck, B Busby		2017
Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast DC Jeffares, C Jolly, M Hoti, D Speed, L Shaw, C Rallis, F Balloux, ... Nature communications 8 (1), 14061 , 2017	533	2017
Supplementary material for'Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast' DC Jeffares, C Jolly, M Hoti, D Speed, L Shaw, C Rallis, F Balloux, ... Nature Publishing Group , 2017		2017
Tools for annotation and comparison of structural variation FJ Sedlazeck, A Dhroso, DL Bodian, J Paschall, F Hermes, JM Zook F1000Research 6 , 2017	22	2017
DangerTrack: A scoring system to detect difficult-to-assess regions I Dolgalev, F Sedlazeck, B Busby F1000Research 6 , 2017	13	2017
LRSim: a linked-reads simulator generating insights for better genome partitioning R Luo, FJ Sedlazeck, CA Darby, SM Kelly, MC Schatz Computational and structural biotechnology journal 15, 478-484 , 2017	41	2017
Phased diploid genome assembly with single-molecule real-time sequencing CS Chin, P Peluso, FJ Sedlazeck, M Nattestad, GT Concepcion, A Clum, ... Nature methods 13 (12), 1050-1054 , 2016	1749	2016
The genomic basis of circadian and circalunar timing adaptations in a midge TS Kaiser, B Poehn, D Szkiba, M Preussner, FJ Sedlazeck, A Zrim, ... Nature 540 (7631), 69-73 , 2016	105	2016
SplitThreader: Exploration and analysis of rearrangements in cancer genomes M Nattestad, MC Alford, FJ Sedlazeck, MC Schatz BioRxiv, 087981 , 2016	12	2016
Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing M Nattestad, K Ng, S Goodwin, T Baslan, F Sedlazeck, J Gurtowski, ... Cancer Research 76 (14_Supplement), 850-850 , 2016		2016
Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding S Vij, H Kuhl, IS Kuznetsova, A Komissarov, AA Yurchenko, ... PLoS genetics 12 (4), e1005954 , 2016	157	2016
The pineapple genome and the evolution of CAM photosynthesis R Ming, R VanBuren, CM Wai, H Tang, MC Schatz, JE Bowers, E Lyons, ... Nature genetics 47 (12), 1435-1442 , 2015	524	2015
Teaser: Individualized benchmarking and optimization of read mapping results for NGS data M Smolka, P Rescheneder, MC Schatz, A von Haeseler, FJ Sedlazeck Genome biology 16, 1-10 , 2015	32	2015
Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study M Krunic, R Ertl, B Hagen, FJ Sedlazeck, R Hofmann-Lehmann, ... BMC veterinary research 11, 1-7 , 2015	23	2015
The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways M Tscherner, F Zwolanek, S Jenull, FJ Sedlazeck, A Petryshyn, IE Frohner, ... PLoS pathogens 11 (10), e1005218 , 2015	58	2015
Ectodysplasin signalling genes and phenotypic evolution in sculpins ( Cottus ) J Cheng, F Sedlazek, J Altmüller, AW Nolte Proceedings of the Royal Society B: Biological Sciences 282 (1815), 20150746 , 2015	12	2015
DetectionofStructuralVariants usingthirdgenerationsequencing FJ Sedlazeck, P Rescheneder, M Nattestad, MC Schatz	2	2015
Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study A von Haeseler, M Krunic, F Sedlazeck BioMed Central Ltd 11 (90) , 2015		2015
ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain C Vesely, S Tauber, FJ Sedlazeck, M Tajaddod, A Haeseler, MF Jantsch Nucleic acids research 42 (19), 12155-12168 , 2014	61	2014
ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain A von Haeseler, F Sedlazeck, S Tauber Oxford University Press on behalf of Nucleic Acids Research , 2014		2014
NextGenMap: fast and accurate read mapping in highly polymorphic genomes FJ Sedlazeck, P Rescheneder, A Von Haeseler Bioinformatics 29 (21), 2790-2791 , 2013	410	2013
Updating benchtop sequencing performance comparison S Jünemann, FJ Sedlazeck, K Prior, A Albersmeier, U John, J Kalinowski, ... Nature biotechnology 31 (4), 294-296 , 2013	490	2013
Benefit-of-doubt (BOD) scoring: A sequencing-based method for SNP candidate assessment from high to medium read number data sets FJ Sedlazeck, P Talloji, A von Haeseler, A Bachmair Genomics 101 (3), 204-209 , 2013	1	2013
Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs C Vesely, S Tauber, FJ Sedlazeck, A von Haeseler, MF Jantsch Genome research 22 (8), 1468-1476 , 2012	92	2012
Advanced Methylome Analysis after Bisulfite Deep Sequencing: An Example in Arabidopsis HQ Dinh, M Dubin, FJ Sedlazeck, N Lettner, O Mittelsten Scheid, ... PloS one 7 (7), e41528 , 2012	33	2012
Genome evolution following admixture in invasive sculpins L Xiang-Yi, F Sedlazek, K Konrad Max-Planck-Institute für Evolutionsbiologie Plön , 2012	2	2012
MASon: Million Alignments in Seconds-A Platform Independent Pairwise Sequence Alignment Library for next Generation Sequencing Data P Rescheneder, A von Haeseler, FJ Sedlazeck International Conference on Bioinformatics Models, Methods and Algorithms 2 … , 2012	4	2012
Benchtop sequencing on benchtop computers FJ Sedlazeck na , 2012		2012
Classification of Coverage Patterns S Tauber, F Sedlazeck, L Tierney, K Kuchler, A von Haeseler The R User Conference, useR! 2011 August 16-18 2011 University of Warwick … , 2011		2011
A strategy for building and using a human referenc e pangenome [version 1; peer review: 1 approved, 1 approved B Llamas, G Narzisi, V Schneider, PA Audano, E Biederstedt, L Blauvelt, ...
Supplementary Material of VariantSurvival: A tool to identify genotype-treatment response T Krannich, MH Sarrias, HB Aribi, M Shokrof, A Iacoangeli, A Al-Chalabi, ...
Better Data for Better Health S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ...
A strategy for building and using a human reference pangenome [version 1; peer review: awaiting peer review] B Llamas, G Narzisi, V Schneider, PA Audano, E Biederstedt, L Blauvelt, ...
Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing Supplemental Methods S Aganezov, S Goodwin, RM Sherman, FJ Sedlazeck, G Arun, S Bhatia, ...
Better Data for Better Health SD Goenka, JE Gorzynski, K Shafin, DG Fisk, T Pesout, TD Jensen, ...
Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Materials in the ABRF Next-Generation Sequencing Study J Foox, SW Tighe, CM Nicolet, JM Zook, M Byrska-Bishop, WE Clarke, ...	1 *
RaGOO: Fast Reference-Guided Ordering and Orienting of Genome Assembly Contigs M Alonge, S Soyk, S Goodwin, S Ramakrishnan, FJ Sedlazeck, ... Plant and Animal Genome XXVII Conference (January 12-16, 2019) , 0
Professional Review and Commentary M Case, CL Hall, RR Zascavage, FJ Sedlazeck, JV Planz, HGS Center
regions [version 1; referees: awaiting peer review] I Dolgalev, F Sedlazeck, B Busby

See more in Google Scholar.
The ones marked * may be different from the article in the profile.

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