Publications

2024

GGTyper: genotyping complex structural variants using short-read sequencing data.
Mirus T, Lohmayer R, Döhring C, Halldórsson BV, Kehr B.
Bioinformatics 2024, 40(Supplement 2):ii11–ii19. To be presented at ECCB on Sept 18, 2024.

How do users design scientific workflows? The Case of Snakemake and Nextflow.
Pohl S, Elfaramawy N, Miling A, Cao K, Kehr B, Weidlich M.
In: Proceedings of the 36th International Conference on Scientific and Statistical Database Management (SSDBM 2024).

Restricting datasets to classifiable samples augments discovery of immune disease markers.
Glehr G, Riquelme P, Kronenberg K, Lohmayer R, Lopez-Madrona V, Kapinsky M, Schlitt H, Geissler E, Spang R, Haferkamp S, Hutchinson J.
Nature Communications 2024, 15:5417.

SpaCeNet: Spatial Cellular Networks from omics data.
Lück N, Lohmayer R, Solbrig S, Schrod S, Wipfler T, Shutta KH, Guebila MB, Schäfer A, Beißbarth T, Zacharias HU, Oefner PJ, Quackenbush J, Altenbuchinger M.
In: Research in Computational Molecular Biology (RECOMB 2024). LNCS, 14758:344-347.

2023

From Program Chains to Exploratory Workflows: PopinSnake for Genomic Insertion Detection.
Cao K, Elfaramawy N, Weidlich M, Kehr B.
In: Proceedings of the IEEE 19th International Conference on e-Science (e-Science 2023).

2022

Bcmap: fast alignment-free barcode mapping for linked-read sequencing data.
Lüpken R, Krannich T, Kehr B.
Preprint on bioRxiv.

Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs.
Krannich T, White WTJ, Niehus S, Holley G, Halldórsson BV, Kehr B.
Bioinformatics 2022, 38(3):604-611.

A comprehensive benchmarking of WGS-based deletion structural variant callers.
Sarwal V, Niehus S, Ayyala R, Kim M, Sakar A, Chang S, Lu A, Rajkumar N, Darci-Maher N, Littman R, Chhugani K, Soylev A, Comarova Z, Wesel E, Castellanos J, Chikka R, Distler MG, Eskin E, Flint J, Mangul S.
Briefings in Bioinformatics 2022, 23(4):bbac221.

BITES: Balanced Individual Treatment Effect for Survival data.
Schrod S, Schäfer A, Solbrig S, Lohmayer R, Gronwald W, Oefner PJ, Beißbarth T, Spang R, Zacharias HU, Altenbuchinger M.
Bioinformatics 2022, 38:i60-i67.

T cell-mediated elimination of cancer cells by blocking CEACAM6–CEACAM1 interaction.
Pinkert J, Boehm HH, Trautwein M, Doecke WD, Wessel F, Ge Y, Gutierrez EM, Carretero R, Freiberg C, Gritzan U, Luetke-Eversloh M, Golfier S, Von Ahsen O, Volpin V, Sorrentino A, Rathinasamy A, Xydia M, Lohmayer R, Sax J, Nur-Menevse A, Hussein A, Stamova S, Beckmann G, Glueck JM, Schoenfeld D, Weiske J, Zopf D, Offringa R, Kreft B, Beckhove P, Willuda J.
OncoImmunology 2022, 11(1):2008110.

2021

Strukturvarianten im Erbgut auf der Spur.
Niehus S, Kehr B.
GIT Labor-Fachzeitschrift 2021.

The collaborative research center FONDA.
Leser U, Hilbrich M, Draxl C, Eisert P, Grunske L, Hostert P, Kainmüller D, Kao O, Kehr B, Kehrer T, Koch C, Markl V, Meyerhenke H, Rabl T, Reinefeld A, Reinert K, Ritter K, Scheuermann B, Schintke F, Schweikardt N, Weidlich M
Datenbank-Spektrum 2021, 21:255-260.

Novel sequencing technologies and bioinformatic tools for deciphering the non-coding genome.
Schwarz JM, Luepken R, Seelow D, Kehr B.
Medizinische Genetik 2021, 33(2):133-145.

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Markowski J, Kempfer R, Kukalev A, Irastorza-Azcarate I, Loof G, Kehr B, Pombo A, Rahmann S, Schwarz RF.
Bioinformatics 2021, 37(19):3128-3135.

Lifelong reduction in LDL (low-density lipoprotein) cholesterol due to a gain-of-function mutation in LDLR.
Bjornsson E, Gunnarsdottir K, Halldorsson GH, Sigurdsson A, Arnadottir GA, Jonsson H, Olafsdottir EF, Niehus S, Kehr B, Sveinbjörnsson G, Gudmundsdottir S, Helgadottir A, Andersen K, Thorleifsson G, Eyjolfsson GI, Olafsson I, Sigurdardottir O, Saemundsdottir J, Jonsdottir I, Magnusson OTh, Masson G, Stefansson H, Gudbjartsson DF, Thorgeirsson G, Holm H, Halldorsson BV, Melsted P, Norddahl GL, Sulem P, Thorsteinsdottir U, Stefansson K.
Circulation: Genomic and Precision Medicine 2021, 14(1):e003029.

PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes.
Niehus S, Jónsson H, Schönberger J, Björnsson E, Beyter D, Eggertsson HP, Sulem P, Stefánsson K, Halldórsson BV, Kehr B.
Nature Communications 2021, 12:730.

2019

Sequence variants associating with urinary biomarkers.
Benonisdottir S, Kristjansson RP, Oddsson A, Steinthorsdottir V, Mikaelsdottir E, Kehr B, Jensson BO, Arnadottir GA, Sulem G, Sveinbjornsson G, Kristmundsdottir S, Ivarsdottir EV, Vogel LK, Vinicius T, Gunnarsson B, Runolfsdottir HL, Arthur JG, Deaton AM, Eyjolfsson GI, Davidsson OB, Asselbergs FW, Hreidarsson AB, Rafnar T, Thorleifsson G, Edvardsson V, Sigurdsson G, Helgadottir A, Halldorsson BV, Masson G, Holm H, Onundarson PT, Indridason OS, Benediktsson R, Palsson R, Gudbjartsson DF, Olafsson I, Thorsteinsdottir U, Sulem P, Stefansson K.
Human Molecular Genetics 2019, 28(7):1199-1211.

2018

Multiple transmissions of de novo mutations in families.
Jonsson H, Sulem P, Arnadottir GA, Palsson G, Eggertsson HP, Kristmundsdottir S, Zink F, Kehr B, Hjorleifsson KE, Jensson BO, Jonsdottir I, Marelsson SE, Gudjonsson SA, Gylfason A, Jonasdottir A, Jonasdottir A, Stacey SN, Magnusson OTh, Thorsteinsdottir U, Masson G, Kong A, Halldorsson BV, Helgason A, Gudbjartsson DF, Stefansson K.
Nature Genetics 2018, 50:1674–1680.

2017

Diversity in non-repetitive human sequences not found in the reference genome.
Kehr B, Helgadottir A, Melsted P, Jonsson H, Helgason H, Jonasdottir Ad, Jonasdottir As, Sigurdsson A, Gylfason A, Halldorsson GH, Kristmundsdottir S, Thorgeirsson G, Olafsson I, Holm H, Thorsteinsdottir U, Sulem P, Helgason A, Gudbjartsson DF, Halldorsson BV, Stefansson K.
Nature Genetics 2017, 49(4):588-593 [author link].

Graphtyper: Population-scale genotyping using pangenome graphs.
Eggertsson HP, Jonsson H, Kristmundsdottir S, Hjartarson E, Kehr B, Masson G, Zink F, Jonasdottir As, Jonasdottir Ad, Jonsdottir I, Gudbjartsson DF, Melsted P, Stefansson K, Halldorsson BV.
Nature Genetics 2017, 49:1654-1660.

Parental influence on human germline de novo mutations in 1,548 trios from Iceland.
Jonsson H, Sulem P, Kehr B, Kristmundsdottir S, Zink F, Hjartarson E, Hardarson MT, Hjorleifsson KE, Eggertsson HP, Gudjonsson SAA, Ward LD, Arnadottir GA, Helgason EA, Helgason H, Gylfason A, Jonasdottir As, Jonasdottir Ad, Rafnar Th, Frigge M, Stacey SN, Magnusson OTh, Thorsteinsdottir U, Masson G, Kong A, Halldorsson BV, Helgason A, Gudbjartsson DF, Stefansson K.
Nature 2017, 549(7673):519-522.

Whole genome characterization of sequence diversity of 15,220 Icelanders.
Jonsson H, Sulem P, Kehr B, Kristmundsdottir S, Zink F, Hjartarson E, Hardarson MT, Hjorleifsson KE, Eggertsson HP, Gudjonsson SAA, Ward LD, Arnadottir GA, Helgason EA, Helgason H, Gylfason A, Jonasdottir As, Jonasdottir Ad, Rafnar Th, Besenbacher S, Frigge M, Stacey SN, Magnusson OTh, Thorsteinsdottir U, Masson G, Kong A, Halldorsson BV, Helgason A, Gudbjartsson DF, Stefansson K.
Scientific Data 2017, 4:170115.

popSTR: population-scale detection of STR variants.
Kristmundsdottir S, Sigurpalsdottir BD, Kehr B, Halldorsson BV.
Bioinformatics 2017, 33(24):4041-4048.

A rare splice donor mutation in the haptoglobin gene associates with blood lipid levels and coronary artery disease.
Bjornsson E, Helgason H, Halldorsson G, Helgadottir A, Gylfason A, Kehr B, Jonasdottir Ad, Jonasdottir As, Sigurdsson A, Oddsson A, Thorleifsson G, Magnusson OTh, Gretarsdottir S, Zink F, Kristjansson RP, Asgeirsdottir M, Swinkels DW, Kiemeney LA, Eyjolfsson GI, Sigurdardottir O, Masson G, Olafsson I, Thorgeirsson G, Holm H, Thorsteinsdottir U, Gudbjartsson DF, Sulem P, Stefansson K.
Human Molecular Genetics 2017, 26(12):2364-2376.

Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2.
Haraldsdottir S, Rafnar Th, Frankel WL, Einarsdottir S, Sigurdsson A, Hampel H, Snaebjornsson P, Masson G, Weng D, Arngrimsson R, Kehr B, Yilmaz A, Haraldsson S, Sulem P, Stefansson T, Shields PG, Sigurdsson F, Bekaii-Saab T, Moller PH, Steinarsdottir M, Alexiusdottir K, Hitchins M, Pritchard CC, de la Chapelle A, Jonasson JG, Goldberg RM, Stefansson K.
Nature Communications 2017, 8:14755.

2016

PopIns: population-scale detection of novel sequence insertions.
Kehr B, Melsted P, Halldorsson BV.
Bioinformatics 2016, 32(7):961-967.

A sequence variant associating with educational attainment also affects childhood cognition.
Gunnarsson B, Jonsdottir GA, Bjornsdottir G, Konte B, Sulem P, Kristmundsdottir S, Kehr B, Gustafsson O, Helgason H, Iordache PD, Olafsson S, Frigge ML, Thorleifsson G, Arnarsdottir S, Stefansdottir B, Giegling I, Djurovic S, Sundet KS, Espeseth T, Melle I, Hartmann AM, Thorsteinsdottir U, Kong A, Gudbjartsson DF, Ettinger U, Andreassen OA, Rujescu D, Halldorsson JG, Stefansson H, Halldórsson BV, Stefansson K.
Scientific Reports 2016, 6:36189.

The rate of meiotic gene conversion varies by sex and age.
Halldorsson BV, Hardarson MT, Kehr B, Styrkarsdottir U, Gylfason A, Thorleifsson G, Zink F, Jonasdottir A, Jonasdottir A, Sulem P, Masson G, Thorsteinsdottir U, Helgason A, Kong A, Gudbjartsson DF, Stefansson K.
Nature Genetics 2016, 48:1377-1384.

chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts.
Kehr B, Melsted P.
Bioinformatics 2016, 32(14):2202-2204.

Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer.
Stacey SN, Kehr B, Gudmundsson J, Zink F, Jonasdottir A, Gudjonsson SA, Sigurdsson A, Halldorsson BV, Agnarsson BA, Benediktsdottir KR, Aben KK, Vermeulen SH, Cremers RG, Panadero A, Helfand BT, Cooper PR, Donovan JL, Hamdy FC, Jinga V, Okamoto I, Jonasson JG, Tryggvadottir L, Johannsdottir H, Kristinsdottir AM, Masson G, Magnusson OT, Iordache PD, Helgason A, Helgason H, Sulem P, Gudbjartsson DF, Kong A, Jonsson E, Barkardottir RB, Einarsson GV, Rafnar T, Thorsteinsdottir U, Mates IN, Neal DE, Catalona WJ, Mayordomo JI, Kiemeney LA, Thorleifsson G, Stefansson K (2016).
Human Molecular Genetics 2016, 25(5):1008-18.

2015

PopAlu: population-scale detection of Alu polymorphisms.
Qian Y, Kehr B, Halldorsson BV.
PeerJ 2015, 3:e1269.

New basal cell carcinoma susceptibility loci.
Stacey SN, Helgason H, Gudjonsson SA, Thorleifsson G, Zink F, Sigurdsson A, Kehr B, Gudmundsson J, Sulem P, Sigurgeirsson B, Benediktsdottir KR, Thorisdottir K, Ragnarsson R, Fuentelsaz V, Corredera C, Gilaberte Y, Grasa M, Planelles D, Sanmartin O, Rudnai P, Gurzau E, Koppova K, Nexo BA, Tjonneland A, Overvad K, Jonasson JG, Tryggvadottir L, Johannsdottir H, Kristinsdottir AM, Stefansson H, Masson G, Magnusson OT, Halldorsson BV, Kong A, Rafnar T, Thorsteinsdottir U, Vogel U, Kumar R, Nagore E, Mayordomo JI, Gudbjartsson DF, Olafsson JH, Stefansson K.
Nature Communications 2015, 6:6825.

2014

Genome alignment with graph data structures: a comparison.
Kehr B, Trappe K, Holtgrewe M, Reinert K.
BMC Bioinformatics 2014, 15:99.

Contributions to computing and modeling multiple whole-genome alignments.
Kehr B.
PhD Thesis, Freie Universität Berlin.

NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.
Hu J, Kehr B, Reinert K.
Bioinformatics 2014, 30(4):540-548.

2012

Hidden breakpoints in genome alignments.
Kehr B, Reinert K, Darling AE.
International Workshop on Algorithms in Bioinformatics (WABI) LNCS 2012, 7534:391-403.

2011

STELLAR: fast and exact local alignments.
Kehr B, Weese D, Reinert K.
BMC Bioinformatics 2011, 12(Suppl 9):S15.

Determination of glycan structure from tandem mass spectra.
Bocker S, Kehr B, Rasche F.
Transactions on Computational Biology and Bioinformatics 2011, 8(4):976-986.