Publications

Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B
The American Journal of Human Genetics, August 8, 2024
Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, O’Neal WK, Valdmanis PN, Marschall T, Bloom JD, Eichler EE
Panacus: fast and exact pangenome growth and core size estimation
bioRxiv, June 12, 2024
Parmigiani L, Garrison E, Stoye J, Marschall T, Doerr D
Locityper: targeted genotyping of complex polymorphic genes
bioRxiv, May 6, 2024
Prodanov T, Plender EG, Seebohm G, Meuth SG, Eichler EE, Marschall T
Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project
bioRxiv, April 20, 2024
Schloissnig S, Pani S, Rodriguez-Martin B, Ebler J, Hain C, Tsapalou V, Söylev A, Hüther P, Ashraf H, Prodanov T, Asparuhova M, Hunt S, Rausch T, Marschall T, Korbel J
SVarp: pangenome-based structural variant discovery
bioRxiv, February 18, 2024
Söylev A, Ebler J, Pani S, Rausch T, O. Korbel J, Marschall T
Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing
bioRxiv, February 16, 2024
Henglin M, Ghareghani M, Harvey W, Porubsky D, Koren S, Eichler E, Ebert P, Marschall T
Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
Genome Biology, January 19, 2024
Serra Mari R, Schrinner S, Finkers R, Ziegler FMR, Arens P, Schmidt MH, Usadel B, Klau GW, Marschall T
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
PanPA: generation and alignment of panproteome graphs
Bioinformatics Advances, November 24, 2023
Dabbaghie F, Sikakulam S K, Marschall T, Kallinina O K
Allele detection using k -mer-based sequencing error profiles
Bioinformatics Advances, October 20, 2023
Ashraf H, Ebler J, Marschall T
Constructing founder sets under allelic and non-allelic homologous recombination
Algorithms for Molecular Biology, September 29, 2023
Bonnet K, Marschall T†, Doerr D†
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
Cell Rep Methods, August 28, 2023
Lee H, Greer SU, Pavlichin DS, Zhou B, Urban AE, Weissman T, Human Pangenome Reference Consortium, Ji HP
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
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
Increased mutation and gene conversion within human segmental duplications
Nature, May 10, 2023
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Human Pangenome Reference Consortium, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE
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
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
Recombination between heterologous human acrocentric chromosomes
Nature, May 10, 2023
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Human Pangenome Reference Consortium, Gerton JL, Phillippy AM, Colonna V, Garrison E
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
Functional analysis of structural variants in single cells using Strand-seq
Nat Biotechnol, November 24, 2022
Jeong H*, Grimes K*, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO
Read-Based Phasing and Analysis of Phased Variants with WhatsHap
Methods Mol Biol, November 7, 2022
Martin M, Ebert P, Marschall T
Semi-automated assembly of high-quality diploid human reference genomes
Nature, October 19, 2022
Jarvis ED* … Ebert P … Marschall T … Human Pangenome Reference Consortium
SVision: a deep learning approach to resolve complex structural variants
Nat Methods, September 16, 2022
Lin J*, Wang S*, Audano PA, Meng D, Flores JI, Kosters W, Yang X, Jia P, Marschall T, Beck CR, Ye K
High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
Cell, September 1, 2022
Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Human Genome Structural Variation Consortium, Flicek P, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC
Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), August 26, 2022
Bonnet K, Marschall T†, Doerr D†
BubbleGun: Enumerating Bubbles and Superbubbles in Genome Graphs
Bioinformatics, July 7, 2022
Dabbaghie F, Ebler J, Marschall T
Genetic polyploid phasing from low-depth progeny samples
iScience, June 17, 2022
Schrinner S, Serra Mari R, Finkers R, Arens P, Usadel B†, Marschall T†, Klau GW†
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†
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
Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
bioRxiv, May 10, 2022
Serra Mari R, Schrinner S, Finkers R, Arens P, Schmidt MH, Usadel B†, Klau GW†, Marschall T†
The Human Pangenome Project: a global resource to map genomic diversity
Nature, April 20, 2022
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison NA, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D, Human Pangenome Reference Consortium
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
The complete sequence of a human genome
Science, March 31, 2022
Nurk S* … Rautiainen M* … Marschall T … Phillippy AM†
K2P18.1 translates T cell receptor signals into thymic regulatory T cell development
Cell Res, October 26, 2021
Ruck T*, Bock S*, Pfeuffer S, Schroeter CB, Cengiz D, Marciniak P, Lindner M, Herrmann A, Liebmann M, Kovac S, Gola L, Rolfes L, Pawlitzki M, Opel N, Hahn T, Dannlowski U, Pap T, Luessi F, Schreiber JA, Wünsch B, Kuhlmann T, Seebohm G, Tackenberg B, Seja P, Döring F, Wischmeyer E, Chasan AI, Roth J, Klotz L, Meyer zu Hörste G, Wiendl H, Marschall T, Floess S, Huehn J, Budde T, Bopp T, Bittner S, Meuth SG
ASHLEYS: automated quality control for single-cell Strand-seq data
Bioinformatics, October 1, 2021
Gros C, Sanders AD, Korbel JO, Marschall T, Ebert P
Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies
Am J Hum Genet, March 30, 2021
Zhao X, Collins RL, Lee W, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, Human Genome Structural Variation Consortium, Gerstein MB, Devine SE, Marschall T, Korbel JO, Eichler EE, Chaisson MJP, Lee C, Mills RE, Brand H, Talkowski ME
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†
MBG: Minimizer-based Sparse de Bruijn Graph Construction
Bioinformatics, January 21, 2021
Rautiainen M, Marschall T
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†
Chromosome-scale, haplotype-resolved assembly of human genomes
Nat Biotechnol, December 7, 2020
Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin C, Church GM, Li H
GraphAligner: rapid and versatile sequence-to-graph alignment
Genome Biol, September 24, 2020
Rautiainen M, Marschall T
A diploid assembly-based benchmark for variants in the major histocompatibility complex
Nat Commun, September 22, 2020
Chin C, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, Sedlazeck FJ, Bansal V, Yoo B, Miller N, Zhou X, Carroll A, Barrio AM, Salit M, Marschall T, Dilthey AT, Zook JM
Haplotype threading: accurate polyploid phasing from long reads
Genome Biol, September 21, 2020
Schrinner SD, Serra Mari R, Ebler J, Rautiainen M, Seillier L, Reimer JJ, Usadel B, Marschall T, Klau GW
A robust benchmark for detection of germline large deletions and insertions
Nat Biotechnol, June 15, 2020
Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, Hajirasouliha I, Ricketts C, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari N, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JA, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Chaisson MJP, Spies N, Sedlazeck FJ, Salit M
Recurrent inversion toggling and great ape genome evolution
Nat Genet, June 15, 2020
Porubsky D*, Sanders AD*, Höps W, Hsieh P, Sulovari A, Li R, Mercuri L, Sorensen M, Murali SC, Gordon D, Cantsilieris S, Pollen AA, Ventura M, Antonacci F, Marschall T, Korbel JO, Eichler EE
Pangenome Graphs
Annu Rev Genomics Hum Genet, May 26, 2020
Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Siren J, Garrison E
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Nat Biotechnol, May 4, 2020
Shafin K*, Pesout T*, Lorig-Roach R*, Haukness M*, Olsen HE*, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B
Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
Genome Biol, April 28, 2020
Köster J, Dijkstra LJ, Marschall T, Schönhuth A
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
J. Comput. Biol., March 11, 2020
Chakraborty S, Canzar S, Marschall T, Schulz MH
Eleven grand challenges in single-cell data science
Genome Biol, February 7, 2020
Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P , Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, de Barbanson B, Cappuccio A, CorleoneG , Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, de Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A
The effects of common structural variants on 3D chromatin structure
BMC Genomics, January 30, 2020
Shanta O, Noor A, Human Genome Structural Variation Consortium (HGSVC) , Sebat J
Single-cell analysis of structural variations and complex rearrangements with tri-channel processing
Nat Biotechnol, December 23, 2019
Sanders AD*, Meiers S*, Ghareghani M*, Porubsky D*, Jeong H, van Vliet MACC, Rausch T, Richter-Pechanska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin J, Marschall T, Korbel JO
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†
Fully-sensitive seed finding in sequence graphs using a hybrid index
Bioinformatics, July 5, 2019
Ghaffaari A, Marschall T
Haplotype-aware diplotyping from noisy long reads
Genome Biol, June 3, 2019
Ebler J*, Haukness M*, Pesout T*, Marschall T†, Paten B†
Multi-platform discovery of haplotype-resolved structural variation in human genomes
Nat Commun, April 16, 2019
Chaisson MJP* … Marschall T … Lee C
SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome
PLoS One, April 12, 2019
Neininger K, Marschall T, Helms V
Bit-parallel sequence-to-graph alignment
Bioinformatics, March 9, 2019
Rautiainen M, Mäkinen V, Marschall T
Strand-seq enables reliable separation of long reads by chromosome via expectation maximization
Bioinformatics, June 27, 2018
Ghareghani M, Porubsky D, Sanders DA, Meiers S, Eichler EE, Korbel JO, Marschall T
A graph-based approach to diploid genome assembly
Bioinformatics, June 27, 2018
Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T
Chromatyping: Reconstructing nucleosome profiles from NOMe sequencing data
Proceedings of the 22nd Annual International Conference on Research in Computational Molecular Biology (RECOMB), March 11, 2018
Chakraborty S, Canzar S, Marschall T†, H. Schulz M†
Genotyping Inversions and Tandem Duplications
Bioinformatics, December 15, 2017
Ebler J, Schönhuth A, Marschall T
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Nat Commun, November 6, 2017
Stancu MC*, Roosmalen MJ*, Renkens I, Nieboer MM, Middelkamp S, de Ligt J, Pregno G, Giachino D, Mandrile G, Valle-Inclan JE, Korzelius J, de Bruijn E, Cuppen E, Talkowski ME, Marschall T, de Ridder J, Kloosterman WP
Dense and accurate whole-chromosome haplotyping of individual genomes
Nat Commun, November 3, 2017
Porubsky D, Garg S, Sanders AD, Korbel JO, Guryev V, Lansdorp PM, Marschall T
A Guided Tour to Computational Haplotyping
Proceedings of Computability in Europe (CiE), May 12, 2017
Klau GW, Marschall T
Negative selection in humans and fruit flies involves synergistic epistasis
Science, May 5, 2017
Sohail M, Vakhrusheva OA, Sul JH, Pulit SL, Francioli LC, Genome of the Netherlands Consortium , Alzheimer's Disease Neuroimaging Initiative , van den Berg LH, Veldink JH, de Bakker PIW, Bazykin GA, Kondrashov AS, Sunyaev SR
WhatsHap: fast and accurate read-based phasing
bioRxiv, December 1, 2016
Martin M*, Patterson M*, Garg S, Fischer SO, Pisanti N, Klau GW, Schönhuth A, Marschall T
Computational pan-genomics: status, promises and challenges
Brief Bioinform, October 21, 2016
Marschall T, Marz M, Abeel T, Dijkstra L, Dutilh BE, Ghaffaari A, Kersey P, Kloosterman WP, Mäkinen V, Novak AM, Paten B, Porubsky D, Rivals E, Alkan C, Baaijens J, de Bakker PIW, Boeva V, Bonnal RJP, Chiaromonte F, Chikhi R, Ciccarelli FD, Cijvat R, Datema E, Van Duijn CM, Eichler EE, Ernst C, Eskin E, Garrison E, El-Kebir M, Klau GW, Korbel JO, Lameijer EW, Langmead B, Martin M, Medvedev P, Mu JC, Neerincx P, Ouwens K, Peterlongo P, Pisanti N, Rahmann S, Raphael B, Reinert K, de Ridder D, de Ridder J, Schlesner M, Schulz-Trieglaff O, Sanders A, Sheikhizadeh S, Shneider C, Smit S, Valenzuela D, Wang J, Wessels L, Zhang Y, Guryev V, Vandin F, Ye K, Schönhuth A
A high-quality human reference panel reveals the complexity and distribution of genomic structural variants
Nature Communications, October 6, 2016
Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, Ligt Jd, Lameijer E, Dijk Fv, Hormozdiari F, Uitterlinden AG, Duijn CMv, Eichler EE, Bakker PIWd, Swertz MA, Wijmenga C, Ommen GBv, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V
PWHATSHAP: efficient haplotyping for future generation sequencing
BMC Bioinformatics, September 22, 2016
Bracciali A, Aldinucci M, Patterson M, Marschall T, Pisanti N, Merelli I, Torquati M
Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries
Bioinformatics, August 29, 2016
Trappe K, Marschall T, Y. Renard B
Discovering and Genotyping Twilight Zone Deletions
Computational Methods for Next Generation Sequencing Data Analysis - Chapter 7, August 26, 2016
Marschall T, Schönhuth A
Representing Pattern Matching Algorithms by Polynomial-Size Automata
arXiv, July 1, 2016
Marschall T, Passing NE
Selecting Reads for Haplotype Assembly
bioRxiv, June 14, 2016
Fischer SO, Marschall T
Read-Based Phasing of Related Individuals
Bioinformatics, June 11, 2016
Garg S, Martin M, Marschall T
Eliminating Blind Spots in Genetic Variant Discovery
ERCIM News 104 January 2016 Special theme:Tackling Big Data in the Life Sciences, January 13, 2016
Schönhuth A, Marschall T
Genome sequence analysis with MonetDB: A case study on Ebola virus diversity
Datenbank-Spektrum, October 12, 2015
Cijvat R, Manegold S, Kersten M, Klau GW, Schönhuth A, Marschall T, Zhang Y
Next Generation Cluster Editing
PeerJ PrePrints, August 13, 2015
Bellitto T, Marschall T, Schönhuth, A, Klau GW
Population-specific genotype imputations using minimac or IMPUTE2
Nat Protoc, July 30, 2015
van Leeuwen EM, Kanterakis A, Deelen P, Kattenberg MV, The Genome of the Netherlands Consortium, Slagboom PE, de Bakker PIW, Wijmenga C, Swertz MA, Boomsma DI, van Duijn CM, Karssen LC, Hottenga JJ
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads
J Comput Biol, May 28, 2015
Patterson M*, Marschall T*, Pisanti N, van Iersel L, Stougie L, Klau GW†, Schönhuth A†
Genome-wide patterns and properties of de novo mutations in humans
Nature Genetics, May 18, 2015
Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I, Genome of the Netherlands Consortium , van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PIW, Sunyaev SR
Repeat- and Error-Aware Comparison of Deletions
Bioinformatics, May 15, 2015
Wittler R, Marschall T, Schönhuth A†, Mäkinen V†
Characteristics of de novo structural changes in the human genome
Genome Res., April 16, 2015
Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer E, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, Suchiman ED, Cuppen E, Thung DT, McVey M, Wendl MC, Geneome of the Netherlands Consortium; Uitterlinden A, van Duijn CM, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Eichler EE, de Bakker PIW, Ye K, Guryev V
Extending SeqAn with a BWT-based suffix array construction
Biological Sequence Analysis Using the Seqan C++ Library, March 30, 2015
Marschall T, Martin M, Rahmann S
SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines
BMC Genomics, March 25, 2015
Leung WY, Marschall T, Paudel Y, Falquet L, Mei H, Schönhuth A, Maoz (Moss) TY
Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels
Nat Commun, March 9, 2015
van Leeuwen EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, Kanterakis A, Trompet S, Postmus I, Verweij N, van Enckevort DJ, Huffman JE, White CC, Feitosa MF, Bartz TM, Manichaikul A, Joshi PK, Peloso GM, Deelen P, van Dijk F, Willemsen G, de Geus EJ, Milaneschi Y, Penninx BWJH, Francioli LC, Menelaou A, Pulit SL, Rivadeneira F, Hofman A, Oostra BA, Franco OH, Leach IM, Beekman M, de Craen AJM, Uh H, Trochet H, Hocking LJ, Porteous DJ, Sattar N, Packard CJ, Buckley BM, Brody JA, Bis JC, Rotter JI, Mychaleckyj JC, Campbell H, Duan Q, Lange LA, Wilson JF, Hayward C, Polasek O, Vitart V, Rudan I, Wright AF, Rich SS, Psaty BM, Borecki IB, Kearney PM, Stott DJ, Adrienne Cupples L, The Genome of the Netherlands Consortium , Jukema JW, van der Harst P, Sijbrands EJ, Hottenga J, Uitterlinden AG, Swertz MA, van Ommen GB, de Bakker PIW, Eline Slagboom P, Boomsma DI, Wijmenga C, van Duijn CM
High-Performance Haplotype Assembly
Proceedings of the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), February 5, 2015
Aldinucci M, Bracciali A, Marschall T, Patterson M, Pisanti N, Torquati M
Improved imputation quality of low-frequency and rare variants in European samples using the `Genome of The Netherlands'
Eur J Hum Genet, July 8, 2014
Deelen P, Menelaou A, van Leeuwen EM, Kanterakis A, van Dijk F, Medina-Gomez C, Francioli LC, Hottenga JJ, Karssen LC, Estrada K, Kreiner-Møller E, Rivadeneira F, van Setten J, Gutierrez-Achury J, Westra H, Franke L, van Enckevort D, Dijkstra M, Byelas H, van Duijn CM, Genome of the Netherlands Consortium , Bakker PIWd, Wijmenga C, Swertz MA
Whole-genome sequence variation, population structure and demographic history of the Dutch population
Nat Genet, June 29, 2014
Genome of the Netherlands Consortium
Discovering motifs that induce sequencing errors
BMC Bioinformatics (Proceedings of RECOMB-seq), June 27, 2014
Allhoff M, Schönhuth A, Martin M, Costa IG, Rahmann S, Marschall T
Viral Quasispecies Assembly via Maximal Clique Enumeration
PLoS Comput Biol, March 27, 2014
Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A†, Beerenwinkel N†
Mapping proteins in the presence of paralogs using units of coevolution
BMC Bioinformatics, October 15, 2013
El-Kebir M, Marschall T, Wohlers I, Patterson M, Heringa J, Schönhuth A, Klau GW
MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels
Bioinformatics, September 25, 2013
Marschall T, Hajirasouliha I, Schönhuth A
Sensitive Long-Indel-Aware Alignment of Sequencing Reads
arXiv, March 14, 2013
Marschall T, Schönhuth A
Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data
Methods, October 23, 2012
Rahmann S, Martin M, Schulte JH, Köster J, Marschall T, Schramm A
CLEVER: clique-enumerating variant finder
Bioinformatics, October 11, 2012
Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schönhuth A
Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome
Br J Cancer, October 9, 2012
Schramm A, Schowe B, Fielitz K, Heilmann M, Martin M, Marschall T, Köster J, Vandesompele J, Vermeulen J, de Preter K, Koster J, Versteeg R, Noguera R, Speleman F, Rahmann S, Eggert A, Morik K, Schulte JH
Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma
Int J Cancer, August 21, 2012
Schramm A, Köster J, Marschall T, Martin M, Schwermer M, Fielitz K, Büchel G, Barann M, Esser D, Rosenstiel P, Rahmann S, Eggert A, Schulte JH
Probabilistic Arithmetic Automata and Their Applications
IEEE/ACM Trans Comput Biol Bioinform, August 2, 2012
Marschall T, Herms I, Kaltenbach HM, Rahmann S
Solving the Minimum String Cover Problem
Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX), February 8, 2012
Canzar S, Marschall T, Rahmann S, Schwiegelshohn C
An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms
Algorithms, October 31, 2011
Marschall T, Rahmann S
Algorithms and statistical methods for exact motif discovery
Dissertation, May 23, 2011
Marschall T
Construction of minimal deterministic finite automata from biological motifs
Theoretical Computer Science, December 13, 2010
Marschall T
Construction of minimal DFAs from biological motifs
arXiv, December 9, 2010
Marschall T
Pattern Matching Statistics -- An Approach Based on Finite Automata
Masters Thesis, October 12, 2010
Marschall T
Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size
Algorithms in Bioinformatics. WABI 2010. Lecture Notes in Computer Science(), vol 6293. Springer, Berlin, Heidelberg, September 6, 2010
Marschall T, Rahmann S
Exact Analysis of Horspool's and Sunday's Pattern Matching Algorithms with Probabilistic Arithmetic Automata
Proceedings of the Fourth International Conference on Language and Automata Theory and Applications (LATA), September 3, 2010
Marschall T, Rahmann S
Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma
Nucleic Acids Res, May 13, 2010
Schulte JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, Schlierf S, Thor T, Vandesompele J, Eggert A, Schreiber S, Rahmann S, Schramm A
Modeling evolutionary fitness for DNA motif discovery
Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), July 8, 2009
Rahmann S, Marschall T, Behler F, Kramer O
Efficient exact motif discovery
Bioinformatics, May 27, 2009
Marschall T, Rahmann S
Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics
Combinatorial Pattern Matching. CPM 2008. Lecture Notes in Computer Science, vol 5029. Springer, Berlin, Heidelberg, June 18, 2008
Marschall T, Rahmann S
Automatic Detection of Song Changes in Music Mixes Using Stochastic Models
18th International Conference on Pattern Recognition (ICPR'06), September 18, 2006
Plötz T, Fink GA, Husemann P, Kanies S, Lienemann K, Marschall T, Martin M, Schillingmann L, Steinrücken M, Sudek H

Legend: * joint first author; † joint last author