Jana Ebler, Dr. rer. nat

PostDoc

HHU
UKD
eblerhhu.de

Jana received her BSc and MSc in Bioinformatics from Saarland University, Saarbrücken. In 2018, she started her PhD in Tobias Marschall's group at the Max Planck Institute for Informatics, Saarbrücken, and moved to Universitätsklinikum Düsseldorf in April 2020. She completed her PhD in July 2023. Jana's research interests include Genotyping, Phasing and PanGenomics.

Software

PanGenie

A short-read genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph.
Publications
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
Genome Research, December 7, 2023
Harvey WT, Ebert P, Ebler J, Audano PA, Munson KM, Hoekzema K, Porubsky D, Beck CR, Marschall T, Garimella K, Eichler EE
Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia
Hemasphere, July 17, 2023
Brandes D, Yasin L, Nebral K, Ebler J, Schinnerl D, Picard D, Bergmann AK, Alam J, Köhrer S, Haas OA, Attarbaschi A, Marschall T, Stanulla M, Borkhardt A, Brozou T, Fischer U, Wagener R
A Draft Human Pangenome Reference
Nature, May 10, 2023
Liao W*, Asri M*, Ebler J*, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Tomlinson C, Villani F, Vollger MR, Human Pangenome Reference Consortium, Bourque G, Chaisson MJ, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Jarvis ED, Miga KH, Wang T, Garrison E†, Marschall T†, Hall I†, Li H†, Paten B†
Pangenome graph construction from genome alignments with Minigraph-Cactus
Nat Biotechnol, May 10, 2023
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B
Inversion polymorphism in a complete human genome assembly
Genome Biol, April 30, 2023
Porubsky D, Harvey WT, Rozanski AN, Ebler J, Höps W, Ashraf H, Hasenfeld P, Human Pangenome Reference Consortium (HPRC), Human Genome Structural Variation Consortium (HGSVC), Paten B, Sanders AD, Marschall T, Korbel JO, Eichler EE
A multi-platform reference for somatic structural variation detection
Cell Genom, June 8, 2022
Espejo Valle-Inclan J, Besselink NJM, de Bruijn E, Cameron DL, Ebler J, Kutzera J, van Lieshout S, Marschall T, Nelen M, Priestley P, Renkens I, Roemer MGM, van Roosmalen MJ, Wenger AM, Ylstra B, Fijneman RJA, Kloosterman WP, Cuppen E
Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders
Cell, May 26, 2022
Porubsky D*, Höps W*, Ashraf H*, Hsieh P, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maria MFA, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q, Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T†, Eichler EE†, Korbel JO†
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
Nature Genet, April 11, 2022
Ebler J, Ebert P, Clarke WE, Rausch T, Audano PA, Houwaart T, Mao Y, Korbel JO, Eichler EE, Zody MC, Dilthey AT, Marschall T
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Science, February 25, 2021
Ebert P*, Audano PA*, Zhu Q*, Rodriguez-Martin B*, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C†, Korbel JO†, Marschall T†, Eichler EE†
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
Nat Biotechnol, December 7, 2020
Porubsky D*, Ebert P*, Audano PA, Vollger MR, Harvey WT, Marijon P, Ebler J, Munson KM, Sorensen M, Sulovari A, Haukness M, Ghareghani M, Lansdorp PM, Paten B, Devine SE, Sanders AD, Lee C, Chaisson MJP, Korbel JO, Eichler EE†, Marschall T†
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
Nat Biotechnol, August 12, 2019
Wenger AM*, Peluso P*, Rowell WJ, Chang P, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin C, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR†, Hunkapiller MW†
Genotyping Inversions and Tandem Duplications
Bioinformatics, December 15, 2017
Ebler J, Schönhuth A, Marschall T

Legend: * joint first author; † joint last author