Jana Ebler

Most-cited papers

1. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

   A. Wenger, P. Peluso, W. Rowell, Pi-Chuan Chang +24 more

   2019Nature Biotechnology1,596 citations Open access

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2. A draft human pangenome reference

   Wen-Wei Liao, Mobin Asri, Jana Ebler, D. Doerr +115 more

   2022bioRxiv983 citations Open access

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3. Haplotype-resolved diverse human genomes and integrated analysis of structural variation

   Peter Ebert, P. Audano, Qi-Hui Zhu, B. Rodriguez-Martin +61 more

   2021Science671 citations Open access

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4. Pangenome graph construction from genome alignments with Minigraph-Cactus

   G. Hickey, Jean Monlong, Jana Ebler, Adam M. Novak +6 more

   2023Nature Biotechnology295 citations Open access

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5. Pangenome graphs

   Jordan M. Eizenga, Adam M. Novak, J. Sibbesen, Simon Heumos +12 more

   2020Annual review of genomics and human genetics (Print)267 citations Open access

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6. Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

   Jana Ebler, Peter Ebert, Wayne E. Clarke, T. Rausch +8 more

   2022Nature Genetics234 citations Open access

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7. Fully phased human genome assembly without parental data using single-cell Strand-seq and long reads

   D. Porubsky, Peter Ebert, P. Audano, M. Vollger +17 more

   2020Nature Biotechnology162 citations Open access

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8. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

   D. Porubsky, Wolfram Höps, Hufsah Ashraf, Ping-Hsun Hsieh +21 more

   2022Cell149 citations Open access

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9. Recombination between heterologous human acrocentric chromosomes

   A. Guarracino, S. Buonaiuto, L. G. de Lima, Tamara A. Potapova +119 more

   2023bioRxiv112 citations Open access

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10. Complex genetic variation in nearly complete human genomes

    G. Logsdon, Peter Ebert, P. Audano, Mark Loftus +64 more

    2024bioRxiv106 citations Open access

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11. Structural variation in 1,019 diverse humans based on long-read sequencing

    Siegfried Schloissnig, Samarendra Pani, Jana Ebler, C. Hain +28 more

    2025Nature91 citations Open access

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12. Haplotype threading: accurate polyploid phasing from long reads

    Sven Schrinner, Rebecca Serra Mari, Jana Ebler, Mikko Rautiainen +5 more

    2020Genome Biology71 citations Open access

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13. Complex genetic variation in nearly complete human genomes

    G. Logsdon, Peter Ebert, P. Audano, Mark Loftus +64 more

    2025Nature65 citations Open access

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14. Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

    A. Wenger, P. Peluso, W. Rowell, Pi-Chuan Chang +24 more

    2019bioRxiv62 citations Open access

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15. Haplotype-aware diplotyping from noisy long reads

    Jana Ebler, Marina Haukness, Trevor Pesout, T. Marschall +1 more

    2019Genome Biology53 citations Open access

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16. A multi-platform reference for somatic structural variation detection

    J. E. Valle-Inclán, N. Besselink, E. de Bruijn, D. Cameron +15 more

    2020bioRxiv48 citations Open access

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17. Inversion polymorphism in a complete human genome assembly

    D. Porubsky, William T. Harvey, Allison N. Rozanski, Jana Ebler +8 more

    2022bioRxiv28 citations Open access

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18. Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall

    William T. Harvey, Peter Ebert, Jana Ebler, P. Audano +7 more

    2023bioRxiv25 citations Open access

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19. BubbleGun: enumerating bubbles and superbubbles in genome graphs

    Fawaz Dabbaghie, Jana Ebler, T. Marschall

    2020bioRxiv22 citations Open access

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20. Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project

    Siegfried Schloissnig, Samarendra Pani, B. Rodriguez-Martin, Jana Ebler +11 more

    2024bioRxiv21 citations Open access

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21. Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall

    William T. Harvey, Peter Ebert, Jana Ebler, P. Audano +7 more

    2023Genome Research21 citations Open access

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22. Pangenome-based genome inference

    Jana Ebler, Wayne E. Clarke, T. Rausch, P. Audano +6 more

    2020bioRxiv20 citations Open access

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23. Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia

    Danielle Brandes, Layal Yasin, K. Nebral, Jana Ebler +13 more

    2023HemaSphere18 citations Open access

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24. Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

    G. Hickey, Jean Monlong, Jana Ebler, Adam M. Novak +5 more

    2023bioRxiv16 citations Open access

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25. A strategy for building and using a human reference pangenome

    Bastien Llamas, Giuseppe Narzisi, Valerie A. Schneider, P. Audano +36 more

    2019F1000Research16 citations Open access

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26. SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads

    Neng Huang, Heng Li, A. A. Tayoun, D. Albracht +194 more

    2025bioRxiv15 citations

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27. Impact and characterization of serial structural variations across humans and great apes

    Wolfram Höps, T. Rausch, Michael Jendrusch, Hufsah Ashraf +50 more

    2023bioRxiv13 citations Open access

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28. Genotyping of Inversions and Tandem Duplications

    Jana Ebler, A. Schönhuth, T. Marschall

    2016bioRxiv13 citations Open access

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29. Haplotype-aware genotyping from noisy long reads

    Jana Ebler, Marina Haukness, Trevor Pesout, T. Marschall +1 more

    2018bioRxiv10 citations Open access

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30. HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

    Julian K. Lucas, Prajna Hebbar, Wen-Wei Liao, Juan F. Macias-Velasco +211 more

    2026bioRxiv9 citations Open access

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31. SVarp: pangenome-based structural variant discovery

    Arda Söylev, Jana Ebler, Samarendra Pani, T. Rausch +2 more

    2024bioRxiv9 citations Open access

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32. De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

    Peter Ebert, P. Audano, Qi-Hui Zhu, B. Rodriguez-Martin +59 more

    2020bioRxiv9 citations Open access

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33. Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders

    D. Porubsky, Wolfram Höps, Hufsah Ashraf, Ping-Hsun Hsieh +21 more

    2021bioRxiv8 citations Open access

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34. Building and applying pangenome references to capture genetic diversity.

    Hufsah Ashraf, Daniel Doerr, Jana Ebler, Tobias Marschall

    2026Nature reviews genetics2 citations

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35. Author Correction: Complex genetic variation in nearly complete human genomes

    G. Logsdon, Peter Ebert, P. Audano, Mark Loftus +64 more

    2025Nature2 citations Open access

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36. Structural and transduction patterns of human-specific polymorphic SVA insertions

    Ashley E. Kirby, Mark Loftus, Emily C. Golba, H. Abel +65 more

    2025Mobile DNA2 citations Open access

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37. Allele detection using k-mer-based sequencing error profiles

    Hufsah Ashraf, Jana Ebler, T. Marschall

    2023Bioinformatics Advances2 citations Open access

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38. Pangenome-based human genome analysis improves trait association and genomic prediction

    Shuang-Jia Lu, Wen-Wei Liao, Marianne K. DeGorter, Pagé C. Goddard +7 more

    2026bioRxiv1 citations Open access

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39. Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

    P. Hallast, A. Rhie, Mark Loftus, Mariateresa Mazzetto +43 more

    2026bioRxiv0 citations Open access

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40. Scalable and rare-variant aware genome inference across the 1kGP cohort

    Jana Ebler, Timofey Prodanov, Andrew P. Blair, Samuel K. Lee +3 more

    2026bioRxiv0 citations Open access

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