Peter Ebert, Dr. rer. nat.

PostDoc / Bioinformatics Software Engineer

HHU
UKD
peter.ebertiscb.org

Peter Ebert studied Bioinformatics at Saarland University. After his graduation, he joined the group "Computational Biology and Applied Algorithmics" headed by Prof. Dr. Thomas Lengauer at the Max Planck Institute for Informatics as PhD student. During his PhD, Peter worked in the domain of computational epigenetics with an emphasis on studying histone modifications within and across species. In 2018, Peter started his postdoc in Tobias Marschall's group "Algorithms for Computational Genomics", switching from epi- to genomics, and later following Tobias to the Heinrich Heine University. Peter is now working mostly on problems in diploid genome assembly and on single cell analysis. Peter received the Ulrich-Hadding-Research-Award in 2021 for his work in the context of the Human Genome Structural Variation Consortium. A constant throughout the years has been Peter's interest in reproducible research and in research software engineering.

Publications
Assembly of 43 human Y chromosomes reveals extensive complexity and variation
Nature, August 23, 2023
Hallast P*, Ebert P*, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K, Li C, Hoyt SJ, Dishuck PC, Porubsky D, Tsetsos F, Kwon JY, Zhu Q, Munson KM, Hasenfeld P, Harvey WT, Lewis AP, Kordosky J, Hoekzema K, Human Genome Structural Variation Consortium (HGSVC), O'Neill RJ, Korbel JO, Tyler-Smith C, Eichler EE, Shi X, Beck CR, Marschall T, Konkel MK, Lee C
Gaps and complex structurally variant loci in phased genome assemblies
Genome Res, May 10, 2023
Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C, Human Pangenome Reference Consortium, Korbel JO, Paten B, Marschall T, Eichler EE
Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall
bioRxiv, May 4, 2023
Harvey WT, Ebert P, Ebler J, Audano PA, Munson KM, Hoekzema K, Porubsky D, Beck CR, Marschall T, Garimella K, Eichler EE
Semi-automated assembly of high-quality diploid human reference genomes
Nature, October 19, 2022
Jarvis ED* … Ebert P … Marschall T … Human Pangenome Reference Consortium
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†
Benchmarking challenging small variants with linked and long reads
Cell Genomics, May 11, 2022
Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, Schatz MC, Narzisi G, Byrska-Bishop M, Clarke W, Evani US, Markello C, Shafin K, Zhou X, Sidow A, Bansal V, Ebert P, Marschall T, Lansdorp P, Hanlon V, Mattsson C, Barrio AM, Fiddes IT, Xiao C, Fungtammasan A, Chin C, Wenger AM, Rowell WJ, Sedlazeck FJ, Carroll A, Salit M, Zook JM
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†

Legend: * joint first author; † joint last author