Publications

publications by categories in reversed chronological order.

2024

  1. Improved sequence mapping using a complete reference genome and lift-over
    Nae-Chyun Chen, Luis F Paulin, Fritz J Sedlazeck, and 3 more authors
    Nature Methods, 2024
  2. StratoMod: predicting sequencing and variant calling errors with interpretable machine learning
    Nathan Dwarshuis, Peter Tonner, Nathan D Olson, and 3 more authors
    Communications Biology, 2024
  3. Utility of long-read sequencing for All of Us
    Medhat Mahmoud, Yongqing Huang, Kiran Garimella, and 8 more authors
    Nature communications, 2024
  4. Impact and characterization of serial structural variations across humans and great apes
    Wolfram Höps, Tobias Rausch, Michael Jendrusch, and 2 more authors
    Nature Communications, 2024
  5. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
    David Dylus, Adrian Altenhoff, Sina Majidian, and 2 more authors
    Nature Biotechnology, 2024
  6. Identification of allele-specific KIV-2 repeats and impact on Lp (a) measurements for cardiovascular disease risk
    Sairam Behera, Jonathan R Belyeu, Xiao Chen, and 8 more authors
    BMC Medical Genomics, 2024
  7. Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
    Ester Kalef-Ezra, Zeliha Gozde Turan, Diego Perez-Rodriguez, and 8 more authors
    Communications Biology, 2024
  8. The GIAB genomic stratifications resource for human reference genomes
    Nathan Dwarshuis, Divya Kalra, Jennifer McDaniel, and 8 more authors
    Nature Communications, 2024
  9. Inter and intra-host diversity of RSV in hematopoietic stem cell transplant adults with normal and delayed viral clearance
    Vasanthi Avadhanula, Daniel Paiva Agustinho, Vipin Kumar Menon, and 8 more authors
    Virus Evolution, 2024
  10. Characterization and visualization of tandem repeats at genome scale
    Egor Dolzhenko, Adam English, Harriet Dashnow, and 8 more authors
    Nature Biotechnology, 2024
  11. Detection of mosaic and population-level structural variants with Sniffles2
    Moritz Smolka, Luis F Paulin, Christopher M Grochowski, and 8 more authors
    Nature biotechnology, 2024
  12. Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes
    Kieran O’Neill, Erin Pleasance, Jeremy Fan, and 8 more authors
    Cell Genomics, 2024
  13. Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes
    Fengju Chen, Yiqun Zhang, Fritz J Sedlazeck, and 1 more author
    Cell Reports Medicine, 2024
  14. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation
    Jonas A Gustafson, Sophia B Gibson, Nikhita Damaraju, and 8 more authors
    medRxiv, 2024
  15. Shining light on the dark genome: accurate quantification of tandem repeats for translational and basic research
    Egor Dolzhenko, Adam English, Harriet Dashnow, and 8 more authors
    In EUROPEAN JOURNAL OF HUMAN GENETICS, 2024
  16. Closing the gap: Solving complex medically relevant genes at scale
    Medhat Mahmoud, John Harting, Holly Corbitt, and 8 more authors
    medRxiv, 2024
  17. Long-read sequencing of 945 Han individuals identifies novel structural variants associated with phenotypic diversity and disease susceptibility
    Jiao Gong, Huiru Sun, Kaiyuan Wang, and 8 more authors
    medRxiv, 2024
  18. The benefit of a complete reference genome for cancer structural variant analysis
    Luis F Paulin, Jeremy Fan, Kieran O’Neill, and 4 more authors
    medRxiv, 2024
  19. Analysis and benchmarking of small and large genomic variants across tandem repeats
    Adam C English, Egor Dolzhenko, Helyaneh Ziaei Jam, and 8 more authors
    Nature Biotechnology, 2024
  20. Unveiling microbial diversity: harnessing long-read sequencing technology
    Daniel P Agustinho, Yilei Fu, Vipin K Menon, and 3 more authors
    Nature Methods, 2024
  21. Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions
    Kristine Bilgrav Saethe, Jesper Eisfeldt, Jesse Bengtsson, and 8 more authors
    medRxiv, 2024
  22. De Novo Genome Assembly for the Coppery Titi Monkey (Plecturocebus cupreus): An Emerging Nonhuman Primate Model for Behavioral Research
    Susanne P Pfeifer, Alexander Baxter, Logan E Savidge, and 2 more authors
    Genome Biology and Evolution, 2024
  23. Profiling complex repeat expansions in RFC1 in Parkinson’s disease
    Pilar Alvarez Jerez, Kensuke Daida, Abigail Miano-Burkhardt, and 8 more authors
    npj Parkinson’s Disease, 2024
  24. Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci
    Christopher M Grochowski, Jesse D Bengtsson, Haowei Du, and 8 more authors
    Cell Genomics, 2024
  25. MethPhaser: methylation-based long-read haplotype phasing of human genomes
    Yilei Fu, Sergey Aganezov, Medhat Mahmoud, and 4 more authors
    Nature Communications, 2024
  26. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing
    Jessica X Chong, Seth I Berger, Samantha Baxter, and 8 more authors
    Genetics in Medicine, 2024
  27. The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
    Sontosh K Deb, Divya Kalra, Jędrzej Kubica, and 8 more authors
    F1000Research, 2024
  28. Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations
    Yanfeng Ji, Junfan Zhao, Jiao Gong, and 2 more authors
    Molecular Genetics and Genomics, 2024
  29. Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing
    Pilar Alvarez Jerez, Kensuke Daida, Francis P Grenn, and 8 more authors
    npj Parkinson’s Disease, 2024
  30. Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment
    Sravya V Bhamidipati, Anil Surathu, Hsu Chao, and 8 more authors
    bioRxiv, 2024
  31. Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks
    Jennifer H McDaniel, Vaidehi Patel, Nathan D Olson, and 8 more authors
    2024
  32. High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    Jonas A Gustafson, Sophia B Gibson, Nikhita Damaraju, and 8 more authors
    Genome Research, 2024
  33. STIX: Long-reads based Accurate Structural Variation Annotation at Population Scale
    Xinchang Zheng, Murad Chowdhury, Behzod Mirpochoev, and 3 more authors
    bioRxiv, 2024
  34. Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases
    Ben Weisburd, Egor Dolzhenko, Mark F Bennett, and 8 more authors
    bioRxiv, 2024
  35. When less is more: sketching with minimizers in genomics
    Malick Ndiaye, Silvia Prieto-Baños, Lucy M Fitzgerald, and 6 more authors
    Genome Biology, 2024
  36. Extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair towards development of somatic benchmarks
    Jennifer H McDaniel, Vaidehi Patel, Nathan D Olson, and 8 more authors
    bioRxiv, 2024
  37. Comprehensive genome analysis and variant detection at scale using DRAGEN
    Sairam Behera, Severine Catreux, Massimiliano Rossi, and 8 more authors
    Nature Biotechnology, 2024
  38. K-mer analysis of long-read alignment pileups for structural variant genotyping
    Adam C English, Fabio Cunial, Ginger A Metcalf, and 2 more authors
    bioRxiv, 2024
  39. Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
    Kristine Bilgrav Saether, Jesper Eisfeldt, Jesse D Bengtsson, and 8 more authors
    Genome Research, 2024
  40. Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
    Judith Arres, Santosh Elavalli, Shalini Behl, and 8 more authors
    medRxiv, 2024
  41. Single cell long read whole genome sequencing reveals somatic transposon activity in human brain
    Michal B Izydorczyk, Ester Kalef-Ezra, Dominic Horner, and 8 more authors
    medRxiv, 2024
  42. Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data
    Zhenxian Zheng, Xian Yu, Lei Chen, and 7 more authors
    bioRxiv, 2024

2023

  1. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments
    Jesse Farek, Daniel Hughes, William Salerno, and 8 more authors
    GigaScience, 2023
  2. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes
    Chen-Shan Chin, Sairam Behera, Asif Khalak, and 4 more authors
    Nature Methods, 2023
  3. Intratumoral heterogeneity and clonal evolution induced by HPV integration
    Keiko Akagi, David E Symer, Medhat Mahmoud, and 8 more authors
    Cancer discovery, 2023
  4. The complete sequence of a human Y chromosome
    Arang Rhie, Sergey Nurk, Monika Cechova, and 8 more authors
    Nature, 2023
  5. A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly
    Moez Dawood, Gulsen Akay, Tadahiro Mitani, and 8 more authors
    American Journal of Medical Genetics Part A, 2023
  6. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
    Mikhail Kolmogorov, Kimberley J Billingsley, Mira Mastoras, and 8 more authors
    Nature Methods, 2023
  7. Beyond the exome: what’s next in diagnostic testing for Mendelian conditions
    Monica H Wojcik, Chloe M Reuter, Shruti Marwaha, and 8 more authors
    The American Journal of Human Genetics, 2023
  8. SVhound: detection of regions that harbor yet undetected structural variation
    Luis F Paulin, Muthuswamy Raveendran, R Alan Harris, and 3 more authors
    BMC bioinformatics, 2023
  9. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
    Joel Rozowsky, Jiahao Gao, Beatrice Borsari, and 8 more authors
    Cell, 2023
  10. Genome-wide analysis of structural variants in Parkinson disease
    Kimberley J Billingsley, Jinhui Ding, Pilar Alvarez Jerez, and 8 more authors
    Annals of neurology, 2023
  11. Structural variation across 138,134 samples in the TOPMed consortium
    Goo Jun, Adam C English, Ginger A Metcalf, and 8 more authors
    bioRxiv, 2023
  12. FixItFelix: improving genomic analysis by fixing reference errors
    Sairam Behera, Jonathon LeFaive, Peter Orchard, and 8 more authors
    Genome biology, 2023
  13. Variant calling and benchmarking in an era of complete human genome sequences
    Nathan D Olson, Justin Wagner, Nathan Dwarshuis, and 4 more authors
    Nature Reviews Genetics, 2023
  14. Association Analysis of Common Structural Variants in the Alzheimer’s Disease Sequencing Project
    Songmi Lee, Adam C English, Rui Xia, and 8 more authors
    Alzheimer’s & Dementia, 2023
  15. VariantSurvival: a tool to identify genotype–treatment response
    Thomas Krannich, Marina Herrera Sarrias, Hiba Ben Aribi, and 6 more authors
    Frontiers in Bioinformatics, 2023
  16. Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures
    Christopher M Grochowski, Jesse D Bengtsson, Haowei Du, and 8 more authors
    bioRxiv, 2023
  17. Genomic variant benchmark: if you cannot measure it, you cannot improve it
    Sina Majidian, Daniel Paiva Agustinho, Chen-Shan Chin, and 2 more authors
    Genome Biology, 2023
  18. Benchmarking of small and large variants across tandem repeats
    Adam English, Egor Dolzhenko, Helyaneh Ziaei Jam, and 8 more authors
    BioRxiv, 2023
  19. Small variant benchmark from a complete assembly of X and Y chromosomes
    Justin Wagner, Nathan D Olson, Jennifer McDaniel, and 8 more authors
    bioRxiv, 2023

2022

  1. Benchmarking challenging small variants with linked and long reads
    Justin Wagner, Nathan D Olson, Lindsay Harris, and 8 more authors
    Cell genomics, 2022
  2. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
    Nathan D Olson, Justin Wagner, Jennifer McDaniel, and 8 more authors
    Cell genomics, 2022
  3. The complete sequence of a human genome
    Sergey Nurk, Sergey Koren, Arang Rhie, and 8 more authors
    Science, 2022
  4. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device
    Courtney L Hall, Rupesh K Kesharwani, Nicole R Phillips, and 3 more authors
    Forensic Science International: Genetics, 2022
  5. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus
    R Alan Harris, Muthuswamy Raveendran, Dustin T Lyfoung, and 8 more authors
    GigaScience, 2022
  6. Fully resolved assembly of Cryptosporidium parvum
    Vipin K Menon, Pablo C Okhuysen, Cynthia L Chappell, and 8 more authors
    Gigascience, 2022
  7. A complete reference genome improves analysis of human genetic variation
    Sergey Aganezov, Stephanie M Yan, Daniela C Soto, and 8 more authors
    Science, 2022
  8. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data
    Yunxi Liu, Joshua Kearney, Medhat Mahmoud, and 3 more authors
    Nature communications, 2022
  9. Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
    Bohu Pan, Luyao Ren, Vitor Onuchic, and 8 more authors
    Genome biology, 2022
  10. Ultrarapid nanopore genome sequencing in a critical care setting
    John E Gorzynski, Sneha D Goenka, Kishwar Shafin, and 8 more authors
    New England Journal of Medicine, 2022
  11. Curated variation benchmarks for challenging medically relevant autosomal genes
    Justin Wagner, Nathan D Olson, Lindsay Harris, and 8 more authors
    Nature biotechnology, 2022
  12. Ultra-rapid nanopore whole genome genetic diagnosis of dilated cardiomyopathy in an adolescent with cardiogenic shock
    John E Gorzynski, Sneha D Goenka, Kishwar Shafin, and 8 more authors
    Circulation: Genomic and Precision Medicine, 2022
  13. Centers for Mendelian Genomics: A decade of facilitating gene discovery
    Samantha M Baxter, Jennifer E Posey, Nicole J Lake, and 8 more authors
    Genetics in Medicine, 2022
  14. Truvari: refined structural variant comparison preserves allelic diversity
    Adam C English, Vipin K Menon, Richard A Gibbs, and 2 more authors
    Genome Biology, 2022
  15. Towards accurate and reliable resolution of structural variants for clinical diagnosis
    Zhichao Liu, Ruth Roberts, Timothy R Mercer, and 3 more authors
    Genome biology, 2022
  16. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing
    Sneha D Goenka, John E Gorzynski, Kishwar Shafin, and 8 more authors
    Nature Biotechnology, 2022
  17. Searching thousands of genomes to classify somatic and novel structural variants using STIX
    Murad Chowdhury, Brent S Pedersen, Fritz J Sedlazeck, and 2 more authors
    Nature methods, 2022
  18. TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data
    Le Huang , Jonathan D Rosen, Quan Sun, and 8 more authors
    The American Journal of Human Genetics, 2022
  19. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms
    Kimberly Walker, Divya Kalra, Rebecca Lowdon, and 8 more authors
    F1000Research, 2022
  20. A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA
    Chen-Shan Chin, Sairam Behera, Ginger A Metcalf, and 3 more authors
    bioRxiv, 2022
  21. Frequent spontaneous structural rearrangements promote transgenerational genome diversification in Brassica napus
    Mauricio Orantes-Bonilla, Manar Makhoul, HueyTyng Lee, and 6 more authors
    Biorxiv, 2022
  22. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene
    Marco Toffoli, Xiao Chen, Fritz J Sedlazeck, and 8 more authors
    Communications Biology, 2022
  23. Accurate Detection of Structural Variations at Population Scale
    Moritz Smolka, Luis Paulin, Claudia Carvalho, and 2 more authors
    In Plant and Animal Genome XXIX Conference (January 8-12, 2022), 2022
  24. Characterizing the genetic polymorphisms in 370 challenging medically relevant genes using long-read sequencing data from 41 human individuals among 19 global populations
    Yanfeng Ji, Jiao Gong, Fritz J Sedlazeck, and 1 more author
    bioRxiv, 2022
  25. Genome-wide analysis of structural variants in Parkinson’s disease using short-read sequencing data
    Kimberley J Billingsley, Jinhui Ding, Pilar Alvarez Jerez, and 8 more authors
    bioRxiv, 2022
  26. Multiple genome alignment in the telomere-to-telomere assembly era
    Bryce Kille, Advait Balaji, Fritz J Sedlazeck, and 2 more authors
    Genome Biology, 2022
  27. Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism
    Varuna Chander, Medhat Mahmoud, Jianhong Hu, and 8 more authors
    Human mutation, 2022
  28. The multiple de novo copy number variant (M dn CNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation
    Haowei Du, Angad Jolly, Christopher M Grochowski, and 8 more authors
    Genome Medicine, 2022
  29. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program
    Marsha M Wheeler, Adrienne M Stilp, Shuquan Rao, and 8 more authors
    Nature communications, 2022
  30. Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation
    Mauricio Orantes-Bonilla, Manar Makhoul, HueyTyng Lee, and 6 more authors
    Frontiers in Plant Science, 2022
  31. Additional file 14 of Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
    Bohu Pan, Luyao Ren, Vitor Onuchic, and 8 more authors
    2022

2021

  1. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals
    Harsha Doddapaneni, Sara Javornik Cregeen, Richard Sucgang, and 8 more authors
    PLoS One, 2021
  2. High resolution copy number inference in cancer using short-molecule nanopore sequencing
    Timour Baslan, Sam Kovaka, Fritz J Sedlazeck, and 6 more authors
    Nucleic acids research, 2021
  3. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
    Daniel Butler, Christopher Mozsary, Cem Meydan, and 8 more authors
    Nature communications, 2021
  4. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
    Nicolae Sapoval, Medhat Mahmoud, Michael D Jochum, and 8 more authors
    Genome research, 2021
  5. muCNV: genotyping structural variants for population-level sequencing
    Goo Jun, Fritz Sedlazeck, Qihui Zhu, and 7 more authors
    Bioinformatics, 2021
  6. Chromosome-scale, haplotype-resolved assembly of human genomes
    Shilpa Garg, Arkarachai Fungtammasan, Andrew Carroll, and 8 more authors
    Nature Biotechnology, 2021
  7. Optimized sample selection for cost-efficient long-read population sequencing
    T Rhyker Ranallo-Benavidez, Zachary Lemmon, Sebastian Soyk, and 6 more authors
    Genome research, 2021
  8. SVhound: Detection of future Structural Variation hotspots
    Luis F Paulin, Muthuswamy Raveendran, R Alan Harris, and 3 more authors
    bioRxiv, 2021
  9. Long-read sequencing for diagnosis in the Undiagnosed Diseases Network
    David Murdock, Jill Rosenfeld, Fan Xia, and 8 more authors
    Molecular Genetics and Metabolism, 2021
  10. Multi-tissue integrative analysis of personal epigenomes
    Joel Rozowsky, Jorg Drenkow, Yucheng Yang, and 8 more authors
    BioRxiv, 2021
  11. Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells
    Kenneth P Micklethwaite, Kavitha Gowrishankar, Brian S Gloss, and 8 more authors
    Blood, The Journal of the American Society of Hematology, 2021
  12. Intronic Haplotypes in the GBA Gene Do Not Predict Age at Diagnosis of Parkinson’s Disease
    Marco Toffoli, Abigail Higgins, Chiao Lee, and 7 more authors
    Movement Disorders, 2021
  13. Towards population-scale long-read sequencing
    Wouter De Coster, Matthias H Weissensteiner, and Fritz J Sedlazeck
    Nature Reviews Genetics, 2021
  14. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment
    Yilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, and 2 more authors
    GigaScience, 2021
  15. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
    Jonathan Foox, Scott W Tighe, Charles M Nicolet, and 8 more authors
    Nature biotechnology, 2021
  16. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation
    Medhat Mahmoud, Harshavardhan Doddapaneni, Winston Timp, and 1 more author
    Genome biology, 2021
  17. Comprehensive analysis of GBA using a novel algorithm for Illumina whole-genome sequence data or targeted Nanopore sequencing
    Marco Toffoli, Xiao Chen, Fritz J Sedlazeck, and 8 more authors
    medRxiv, 2021
  18. Hidden biases in germline structural variant detection
    Michael M Khayat, Sayed Mohammad Ebrahim Sahraeian, Samantha Zarate, and 8 more authors
    Genome biology, 2021
  19. Whole genome sequencing identifies common and rare structural variants contributing to hematologic traits in the NHLBI TOPMed program
    Marsha M Wheeler, Adrienne M Stilp, Shuquan Rao, and 8 more authors
    Medrxiv, 2021
  20. Benzyl isothiocyanate induces cardiomyocyte proliferation and heart regeneration
    Akane Sakaguchi, Miwa Kawasaki, Yuichi Saito, and 3 more authors
    bioRxiv, 2021
  21. Discovery and population genomics of structural variation in a songbird genus (vol 11, 3403, 2020)
    Matthias H Weissensteiner, Ignas Bunikis, Ana Catalan, and 8 more authors
    Nature Communications, 2021
  22. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
    Ann M Mc Cartney, Medhat Mahmoud, Michael Jochum, and 8 more authors
    F1000Research, 2021

2020

  1. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
    Isac Lee, Roham Razaghi, Timothy Gilpatrick, and 7 more authors
    Nature methods, 2020
  2. Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
    Sergey Aganezov, Sara Goodwin, Rachel M Sherman, and 8 more authors
    Genome research, 2020
  3. Potential applications of nanopore sequencing for forensic analysis
    Courtney L Hall, Roxanne R Zascavage, FJ Sedlazeck, and 1 more author
    Forensic science review, 2020
  4. Targeted nanopore sequencing with Cas9-guided adapter ligation
    Timothy Gilpatrick, Isac Lee, James E Graham, and 7 more authors
    Nature biotechnology, 2020
  5. Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes
    Fritz J Sedlazeck, Bing Yu, Adam J Mansfield, and 8 more authors
    bioRxiv, 2020
  6. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
    Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, and 8 more authors
    Nature biotechnology, 2020
  7. A robust benchmark for detection of germline large deletions and insertions
    Justin M Zook, Nancy F Hansen, Nathan D Olson, and 8 more authors
    Nature biotechnology, 2020
  8. Major impacts of widespread structural variation on gene expression and crop improvement in tomato
    Michael Alonge, Xingang Wang, Matthias Benoit, and 8 more authors
    Cell, 2020
  9. Discovery and population genomics of structural variation in a songbird genus
    Matthias H Weissensteiner, Ignas Bunikis, Ana Catalán, and 8 more authors
    Nature communications, 2020
  10. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement
    Sina Majidian, and Fritz J Sedlazeck
    Gigascience, 2020
  11. Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine
    Medhat Mahmoud, Alejandro Rafael Gener, Michael M Khayat, and 8 more authors
    F1000Research, 2020
  12. A diploid assembly-based benchmark for variants in the major histocompatibility complex
    Chen-Shan Chin, Justin Wagner, Qiandong Zeng, and 8 more authors
    Nature communications, 2020
  13. Complex mosaic structural variations in human fetal brains
    Shobana Sekar, Livia Tomasini, Christos Proukakis, and 8 more authors
    Genome research, 2020
  14. Taking the bait: A PCR-free enrichment strategy for nanopore sequencing applications
    John Planz, Fritz Sedlazeck, and Roxanne Zascavage
    2020
  15. Parliament2: Accurate structural variant calling at scale
    Samantha Zarate, Andrew Carroll, Medhat Mahmoud, and 7 more authors
    GigaScience, 2020
  16. Cas9 Enrichment for Nanopore Sequencing
    Timothy Gilpatrick, Isac Lee, James E Graham, and 5 more authors
    2020
  17. A robust benchmark for detection of germline large deletions and insertions (Jun, 10.1038/s41587-020-0538-8, 2020)
    Justin M Zook, Nancy F Hansen, Nathan D Olson, and 8 more authors
    NATURE BIOTECHNOLOGY, 2020

2019

  1. Ancestral admixture is the main determinant of global biodiversity in fission yeast
    Sergio Tusso, Bart PS Nieuwenhuis, Fritz J Sedlazeck, and 3 more authors
    Molecular biology and evolution, 2019
  2. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel
    Theodore Chiang, Xiuping Liu, Tsung-Jung Wu, and 8 more authors
    Genetics in Medicine, 2019
  3. Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish
    Stefan Dennenmoser, Fritz J Sedlazeck, Michael C Schatz, and 3 more authors
    Molecular Ecology, 2019
  4. Fine-scale analysis of Structural Genomic Variation in Natural Populations
    Matthias H Weissensteiner, Ignas Bunikis, Ulrich Knief, and 6 more authors
    2019
  5. Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION
    Melissa Leija-Salazar, Fritz J Sedlazeck, Marco Toffoli, and 8 more authors
    Molecular genetics & genomic medicine, 2019
  6. Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase
    Sven Schenk, Stephanie C Bannister, Fritz J Sedlazeck, and 8 more authors
    Elife, 2019
  7. Evaluation of computational genotyping of structural variation for clinical diagnoses
    Varuna Chander, Richard A Gibbs, and Fritz J Sedlazeck
    GigaScience, 2019
  8. Megabase length hypermutation accompanies human structural variation at 17p11. 2
    Christine R Beck, Claudia MB Carvalho, Zeynep C Akdemir, and 8 more authors
    Cell, 2019
  9. A multi-task convolutional deep neural network for variant calling in single molecule sequencing
    Ruibang Luo, Fritz J Sedlazeck, Tak-Wah Lam, and 1 more author
    Nature communications, 2019
  10. Sequencing Long Amplicon Microsatellite Loci Using the Oxford Nanopore Technologies MinION [TM] Device
    Courtney L Hall
    2019
  11. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
    Sebastian Soyk, Zachary H Lemmon, Fritz J Sedlazeck, and 6 more authors
    Nature plants, 2019
  12. Paragraph: a graph-based structural variant genotyper for short-read sequence data
    Sai Chen, Peter Krusche, Egor Dolzhenko, and 8 more authors
    Genome biology, 2019
  13. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
    Aaron M Wenger, Paul Peluso, William J Rowell, and 8 more authors
    Nature biotechnology, 2019
  14. Sequencing Long Amplicon Microsatellite Loci Using the Oxford Nanopore Technologies MinION Device
    Roxanne Zascavage, Fritz Sedlazeck, and John Planz
    2019
  15. A strategy for building and using a human reference pangenome
    Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, and 8 more authors
    F1000Research, 2019
  16. A genocentric approach to discovery of Mendelian disorders
    Adam W Hansen, Mullai Murugan, He Li, and 8 more authors
    The American Journal of Human Genetics, 2019
  17. RaGOO: fast and accurate reference-guided scaffolding of draft genomes
    Michael Alonge, Sebastian Soyk, Srividya Ramakrishnan, and 5 more authors
    Genome biology, 2019
  18. Phasing of complex genomic rearrangements reveal involvement of both homologous chromosomes in pre-and post-zigotic events
    CM Carvalho, C Beck, Z Akdemir, and 8 more authors
    In EUROPEAN JOURNAL OF HUMAN GENETICS, 2019
  19. Approaches to whole mitochondrial genome sequencing on the Oxford Nanopore MinION
    Roxanne R Zascavage, Courtney L Hall, Kelcie Thorson, and 3 more authors
    Current Protocols in Human Genetics, 2019
  20. Structural variant calling: the long and the short of it
    Medhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, and 3 more authors
    Genome biology, 2019
  21. Why So Pale and Wan: Comparative Genomics of a New Cavefish in Europe
    Fritz Sedlazeck, Medhat Mahmoud, Yue Jia, and 2 more authors
    In Plant and Animal Genome XXVII Conference (January 12-16, 2019), 2019

2018

  1. Accurate detection of complex structural variations using single-molecule sequencing
    Fritz J Sedlazeck, Philipp Rescheneder, Moritz Smolka, and 4 more authors
    Nature methods, 2018
  2. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
    Maria Nattestad, Sara Goodwin, Karen Ng, and 8 more authors
    Genome research, 2018
  3. Piercing the dark matter: bioinformatics of long-range sequencing and mapping
    Fritz J Sedlazeck, Hayan Lee, Charlotte A Darby, and 1 more author
    Nature Reviews Genetics, 2018

2017

  1. GenomeScope: fast reference-free genome profiling from short reads
    Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, and 4 more authors
    Bioinformatics, 2017
  2. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
    Daniel C Jeffares, Clemency Jolly, Mimoza Hoti, and 7 more authors
    Nature communications, 2017
  3. LRSim: a linked-reads simulator generating insights for better genome partitioning
    Ruibang Luo, Fritz J Sedlazeck, Charlotte A Darby, and 2 more authors
    Computational and structural biotechnology journal, 2017
  4. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin
    Stefan Dennenmoser, Fritz J Sedlazeck, Elzbieta Iwaszkiewicz, and 3 more authors
    Molecular Ecology, 2017
  5. DangerTrack: A scoring system to detect difficult-to-assess regions
    Igor Dolgalev, Fritz Sedlazeck, and Ben Busby
    F1000Research, 2017
  6. Tools for annotation and comparison of structural variation
    Fritz J Sedlazeck, Andi Dhroso, Dale L Bodian, and 3 more authors
    F1000Research, 2017
  7. regions [version 1; referees: 2 approved, 1 approved with
    Igor Dolgalev, Fritz Sedlazeck, and Ben Busby
    2017
  8. Supplementary material for’Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast’
    Daniel C Jeffares, Clemency Jolly, Mimoza Hoti, and 7 more authors
    2017

2016

  1. Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding
    Shubha Vij, Heiner Kuhl, Inna S Kuznetsova, and 8 more authors
    PLoS genetics, 2016
  2. Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing
    Maria Nattestad, Karen Ng, Sara Goodwin, and 8 more authors
    Cancer Research, 2016
  3. SplitThreader: Exploration and analysis of rearrangements in cancer genomes
    Maria Nattestad, Marley C Alford, Fritz J Sedlazeck, and 1 more author
    BioRxiv, 2016
  4. The genomic basis of circadian and circalunar timing adaptations in a midge
    Tobias S Kaiser, Birgit Poehn, David Szkiba, and 8 more authors
    Nature, 2016
  5. Phased diploid genome assembly with single-molecule real-time sequencing
    Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, and 8 more authors
    Nature methods, 2016

2015

  1. Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study
    Milica Krunic, Reinhard Ertl, Benedikt Hagen, and 4 more authors
    BMC veterinary research, 2015
  2. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data
    Moritz Smolka, Philipp Rescheneder, Michael C Schatz, and 2 more authors
    Genome biology, 2015
  3. The Candida albicans histone acetyltransferase Hat1 regulates stress resistance and virulence via distinct chromatin assembly pathways
    Michael Tscherner, Florian Zwolanek, Sabrina Jenull, and 7 more authors
    PLoS pathogens, 2015
  4. The pineapple genome and the evolution of CAM photosynthesis
    Ray Ming, Robert VanBuren, Ching Man Wai, and 8 more authors
    Nature genetics, 2015
  5. Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus)
    Jie Cheng, Fritz Sedlazek, Janine Altmüller, and 1 more author
    Proceedings of the Royal Society B: Biological Sciences, 2015
  6. Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study
    Arndt Haeseler, Milica Krunic, and Fritz Sedlazeck
    2015
  7. DetectionofStructuralVariants usingthirdgenerationsequencing
    Fritz J Sedlazeck, Philipp Rescheneder, Maria Nattestad, and 1 more author
    2015

2014

  1. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain
    Cornelia Vesely, Stefanie Tauber, Fritz J Sedlazeck, and 3 more authors
    Nucleic acids research, 2014
  2. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain
    Arndt Haeseler, Fritz Sedlazeck, and Stefanie Tauber
    2014

2013

  1. Updating benchtop sequencing performance comparison
    Sebastian Jünemann, Fritz Joachim Sedlazeck, Karola Prior, and 8 more authors
    Nature biotechnology, 2013
  2. NextGenMap: fast and accurate read mapping in highly polymorphic genomes
    Fritz J Sedlazeck, Philipp Rescheneder, and Arndt Von Haeseler
    Bioinformatics, 2013
  3. Benefit-of-doubt (BOD) scoring: A sequencing-based method for SNP candidate assessment from high to medium read number data sets
    Fritz Joachim Sedlazeck, Prabhavathi Talloji, Arndt Haeseler, and 1 more author
    Genomics, 2013

2012

  1. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs
    Cornelia Vesely, Stefanie Tauber, Fritz J Sedlazeck, and 2 more authors
    Genome research, 2012
  2. Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis
    Huy Q Dinh, Manu Dubin, Fritz J Sedlazeck, and 3 more authors
    PloS one, 2012
  3. MASon: Million Alignments in Seconds-A Platform Independent Pairwise Sequence Alignment Library for next Generation Sequencing Data
    Philipp Rescheneder, Arndt Haeseler, and Fritz J Sedlazeck
    In International Conference on Bioinformatics Models, Methods and Algorithms, 2012
  4. Benchtop sequencing on benchtop computers
    Fritz Joachim Sedlazeck
    2012
  5. Genome evolution following admixture in invasive sculpins
    Li Xiang-Yi, F Sedlazek, and K Konrad
    Max-Planck-Institute für Evolutionsbiologie Plön, 2012

2011

  1. Classification of Coverage Patterns
    Stefanie Tauber, Fritz Sedlazeck, Lanay Tierney, and 2 more authors
    In The R User Conference, useR! 2011 August 16-18 2011 University of Warwick, Coventry, UK, 2011