Evolution of SARS-CoV-2 in the Rhine-Neckar/Heidelberg Region 01/2021 - 07/2023.

Bundschuh C, Weidner N, Klein J, Rausch T, Azevedo N, Telzerow A, Mallm JP, Kim H, Steiger S, Seufert I, Börner K, Bauer K, Hübschmann D, Jost KL, Parthé S, Schnitzler P, Boutros M, Rippe K, Müller B, Bartenschlager R, Kräusslich HG, Benes V

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2024

doi:10.1016/j.meegid.2024.105577.

Assembly of 43 human Y chromosomes reveals extensive complexity and variation.

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

Nature, 2023

doi:10.1038/s41586-023-06425-6.

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.

Rausch T, Snajder R, Leger A, Simovic M, Giurgiu M, Villacorta L, Henssen AG, Fröhling S, Stegle O, Birney E, Bonder MJ, Ernst A, Korbel JO

Cell genomics, 2023

doi:10.1016/j.xgen.2023.100281.

Author correction: the NSL complex maintains nuclear architecture stability via lamin A/C acetylation.

Karoutas A, Szymanski W, Rausch T, Guhathakurta S, Rog-Zielinska EA, Peyronnet R, Seyfferth J, Chen HR, de Leeuw R, Herquel B, Kimura H, Mittler G, Kohl P, Medalia O, Korbel JO, Akhtar A

Nature cell biology, 2023

doi:10.1038/s41556-023-01106-y.

Functional analysis of structural variants in single cells using Strand-seq.

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

Nature biotechnology, 2022

doi:10.1038/s41587-022-01551-4.

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.

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, Paul Flicek, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC

Cell, 2022

doi:10.1016/j.cell.2022.08.004.

Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution.

Richter-Pechańska P, Kunz JB, Rausch T, Erarslan-Uysal B, Bornhauser B, Frismantas V, Assenov Y, Zimmermann M, Happich M, von Knebel-Doeberitz C, von Neuhoff N, Köhler R, Stanulla M, Schrappe M, Cario G, Escherich G, Kirschner-Schwabe R, Eckert C, Avigad S, Pfister SM, Muckenthaler MU, Bourquin JP, Korbel JO, Kulozik AE

Leukemia, 2022

doi:10.1038/s41375-022-01587-0.

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

Ebler J, Ebert P, Clarke WE, Rausch T, Audano PA, Houwaart T, Mao Y, Korbel JO, Eichler EE, Zody MC, Dilthey AT, Marschall T

Nature genetics, 2022

doi:10.1038/s41588-022-01043-w.

Neutralizing antibody response against the B.1.617.2 (delta) and the B.1.1.529 (omicron) variant after a third mRNA SARS-CoV-2 vaccine dose in kidney transplant recipients.

Benning L, Morath C, Bartenschlager M, Kim H, Reineke M, Beimler J, Buylaert M, Nusshag C, Kälble F, Reichel P, Töllner M, Schaier M, Klein K, Benes V, Rausch T, Rieger S, Stich M, Tönshoff B, Weidner N, Schnitzler P, Zeier M, Süsal C, Tran TH, Bartenschlager R, Speer C

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 2022

doi:10.1111/ajt.17054.

Evidence for the Association between the Intronic Haplotypes of Ionotropic Glutamate Receptors and First-Episode Schizophrenia.

Hirschfeldova K, Cerny J, Bozikova P, Kuchtiak V, Rausch T, Benes V, Spaniel F, Gregus D, Horacek J, Vyklicky L, Balik A

Journal of personalized medicine, 2021

doi:10.3390/jpm11121250.

Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors.

Marongiu L, Landry JJM, Rausch T, Abba ML, Delecluse S, Delecluse HJ, Allgayer H

Molecular oncology, 2021

doi:10.1002/1878-0261.13070.

Genomic insights into the pathogenesis of Epstein-Barr virus-associated diffuse large B-cell lymphoma by whole-genome and targeted amplicon sequencing.

Gebauer N, Künstner A, Ketzer J, Witte HM, Rausch T, Benes V, Zimmermann J, Gebauer J, Merz H, Bernard V, Harder L, Ratjen K, Gesk S, Peter W, Busch Y, Trojok P, von Bubnoff N, Biersack H, Busch H, Feller AC

Blood cancer journal, 2021

doi:10.1038/s41408-021-00493-5.

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

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

Science (New York, N.Y.), 2021

doi:10.1126/science.abf7117.

TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data.

Bolognini D, Magi A, Benes V, Korbel JO, Rausch T

GigaScience, 2020

doi:10.1093/gigascience/giaa101.

Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors.

Erarslan-Uysal B, Kunz JB, Rausch T, Richter-Pechańska P, van Belzen IA, Frismantas V, Bornhauser B, Ordoñez-Rueada D, Paulsen M, Benes V, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Loukanov T, Gorenflo M, Waszak SM, Bourquin JP, Muckenthaler MU, Korbel JO, Kulozik AE

EMBO molecular medicine, 2020

doi:10.15252/emmm.202012104.

Germline Elongator mutations in Sonic Hedgehog medulloblastoma.

Waszak SM, Robinson GW, Gudenas BL, Smith KS, Forget A, Kojic M, Garcia-Lopez J, Hadley J, Hamilton KV, Indersie E, Buchhalter I, Kerssemakers J, Jäger N, Sharma T, Rausch T, Kool M, Sturm D, Jones DTW, Vasilyeva A, Tatevossian RG, Neale G, Lombard B, Loew D, Nakitandwe J, Rusch M, Bowers DC, Bendel A, Partap S, Chintagumpala M, Crawford J, Gottardo NG, Smith A, Dufour C, Rutkowski S, Eggen T, Wesenberg F, Kjaerheim K, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Remke M, Puget S, Pajtler KW, Milde T, Witt O, Ryzhova M, Korshunov A, Orr BA, Ellison DW, Brugieres L, Lichter P, Nichols KE, Gajjar A, Wainwright BJ, Ayrault O, Korbel JO, Northcott PA, Pfister SM

Nature, 2020

doi:10.1038/s41586-020-2164-5.

Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files.

Rausch T, Fritz MH, Untergasser A, Benes V

BMC genomics, 2020

doi:10.1186/s12864-020-6635-8.

The effects of common structural variants on 3D chromatin structure.

Shanta O, Noor A, Sebat J, Chaisson MJP, Sanders AD, Zhao XF, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong XM, Hormozdiari F, Lee DL, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen XT, Chin CS, Chong ZC, Chuang NST, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeey T, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee JC, Lee WP, Lee SP, Li ST, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Rosanio G, Ryan M, Stutz A, Spierings DCJ, Ward A, Welch AME, Xiao M, Xu W, Zhang CS, Zhu QH, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Shi XH, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee CL

BMC GENOMICS, 2020

doi:10.1186/s12864-020-6516-1.

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.

Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Schrappe M, Benes V, Kulozik AE, Mardin BR, Bourquin JP, Bornhauser B, Korbel JO, Marschall T

Nature biotechnology, 2019

doi:10.1038/s41587-019-0366-x.

The molecular landscape of ETMR at diagnosis and relapse.

Lambo S, Gröbner SN, Rausch T, Waszak SM, Schmidt C, Gorthi A, Romero JC, Mauermann M, Brabetz S, Krausert S, Buchhalter I, Koster J, Zwijnenburg DA, Sill M, Hübner JM, Schwalm B, Mack N, Hovestadt V, Ryzhova M, Chan JA, Papillon-Cavanagh S, Ho B, Landgraf P, Witt O, Milde T, Sahm F, Ecker J, Ellison DW, Sumerauer D, Darabi A, Orr BA, Wesseling P, Schittenhelm J, Haberler C, Figarella-Branger D, Gil-da-Costa MJ, Łastowska M, Remke M, Taylor MD, Hauser P, Pietsch T, Grajkowska W, Hasselblatt M, Masliah-Planchon J, Rigau V, Uro-Coste E, Bourdeaut F, Schüller U, Li XN, Wolf S, Alexandrescu S, Jabado N, Giangaspero F, Karajannis MA, Snuderl M, von Hoff K, Korbel JO, Jones DTW, von Deimling A, Pfister SM, Bishop AJR, Huang A, Lichter P, Korshunov A, Kool M

Nature, 2019

doi:10.1038/s41586-019-1815-x.

A highly soluble Sleeping Beauty transposase improves control of gene insertion.

Querques I, Mades A, Zuliani C, Miskey C, Alb M, Grueso E, Machwirth M, Rausch T, Einsele H, Ivics Z, Hudecek M, Barabas O

Nature biotechnology, 2019

doi:10.1038/s41587-019-0291-z.

The NSL complex maintains nuclear architecture stability via lamin A/C acetylation.

Karoutas A, Szymanski W, Rausch T, Guhathakurta S, Rog-Zielinska EA, Peyronnet R, Seyfferth J, Chen HR, de Leeuw R, Herquel B, Kimura H, Mittler G, Kohl P, Medalia O, Korbel JO, Akhtar A

Nature cell biology, 2019

doi:10.1038/s41556-019-0397-z.

VISOR: a versatile haplotype-aware structural variant simulator for short and long read sequencing.

Bolognini D, Sanders A, Korbel JO, Magi A, Benes V, Rausch T

Bioinformatics (Oxford, England), 2019

doi:10.1093/bioinformatics/btz719.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Hormozdiari F, Kong X, Wenger AM, Lee D, Antaki D, Hastie AR, Audano PA, Anantharaman T, Cantsilieris S, Brand H, Cerveira E, Cao H, Chen X, Chen C, Chong Z, Chin CS, Church DM, Clarke L, Chuang NT, Lambert CC, Galeev T, Gorkin DU, Farrell A, Flores J, Heaton WH, Korlach J, Gujral M, Guryev V, Lam ET, Lee JE, Kumar S, Kwon JY, Li S, Lee SP, Lee WP, Lee J, Munson KM, Meiers S, Viaud-Martinez K, Marks P, Noor A, Nodzak C, Nelson BJ, Navarro FCP, Rosanio G, Qiu Y, Pang AWC, Kyriazopoulou-Panagiotopoulou S, Welch AE, Xiao M, Xu W, Zhang C, Ryan M, Stütz A, Spierings DCJ, Ward A, McCarroll S, Jun G, Ding L, Koh CL, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, Lansdorp PM, Kwok PY, Sebat J, Marth GT, Flicek P, Ren B, Gerstein MB, Chen K, Mills RE, Talkowski ME, Korbel JO, Marschall T, Bashir A, Shi X, Devine SE, Ye K, Eichler EE, Lee C

Nature communications, 2019

doi:10.1038/s41467-018-08148-z.

JUNB, DUSP2, SGK1, SOCS1 and CREBBP are frequently mutated in T-cell/histiocyte rich large B-cell lymphoma.

Schuhmacher B, Bein J, Rausch T, Benes V, Tousseyn T, Vornanen M, Ponzoni M, Thurner L, Gascoyne R, Steidl C, Küppers R, Hansmann ML, Hartmann S

Haematologica, 2018

doi:10.3324/haematol.2018.203224.

Missense variants in NOX1 and p22phox in a case of very-early-onset inflammatory bowel disease are functionally linked to NOD2.

Lipinski S, Petersen BS, Barann M, Piecyk A, Tran F, Mayr G, Jentzsch M, Aden K, Stengel ST, Klostermeier UC, Sheth V, Ellinghaus D, Rausch T, Korbel JO, Nothnagel M, Gilissen C, Krawczak M, Forster M, Veltman JA, Lee CC, Forster P, Schreiber S, Fritscher-Ravens A, Rosenstiel P, Franke A

Cold Spring Harbor molecular case studies, 2019

doi:10.1101/mcs.a002428.

PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia.

Richter-Pechańska P, Kunz JB, Bornhauser B, von Knebel Doeberitz C, Rausch T, Erarslan-Uysal B, Assenov Y, Frismantas V, Marovca B, Waszak SM, Zimmermann M, Seemann J, Happich M, Stanulla M, Schrappe M, Escherich G, Cario G, Kirschner-Schwabe R, Bakharevich K, Muckenthaler MU, Eckert C, Bourquin JP, Korbel JO, Kulozik AE

EMBO molecular medicine, 2018

doi:10.15252/emmm.201809443.

Alfred: Interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.

Rausch T, Fritz MH, Korbel JO, Benes V

Bioinformatics (Oxford, England), 2018

doi:10.1093/bioinformatics/bty1007.

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.

Waszak SM, Northcott PA, Buchhalter I, Robinson GW, Sutter C, Groebner S, Grund KB, Brugières L, Jones DTW, Pajtler KW, Morrissy AS, Kool M, Sturm D, Chavez L, Ernst A, Brabetz S, Hain M, Zichner T, Segura-Wang M, Weischenfeldt J, Rausch T, Mardin BR, Zhou X, Baciu C, Lawerenz C, Chan JA, Varlet P, Guerrini-Rousseau L, Fults DW, Grajkowska W, Hauser P, Jabado N, Ra YS, Zitterbart K, Shringarpure SS, De La Vega FM, Bustamante CD, Ng HK, Perry A, MacDonald TJ, Hernáiz Driever P, Bendel AE, Bowers DC, McCowage G, Chintagumpala MM, Cohn R, Hassall T, Fleischhack G, Eggen T, Wesenberg F, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Kjaerheim K, Monoranu CM, Archer TC, Duke E, Pomeroy SL, Shelagh R, Frank S, Sumerauer D, Scheurlen W, Ryzhova MV, Milde T, Kratz CP, Samuel D, Zhang J, Solomon DA, Marra M, Eils R, Bartram CR, von Hoff K, Rutkowski S, Ramaswamy V, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Malkin D, Gajjar A, Korbel JO, Pfister SM

The Lancet. Oncology, 2018

doi:10.1016/S1470-2045(18)30242-0.

ToTem: a tool for variant calling pipeline optimization.

Tom N, Tom O, Malcikova J, Pavlova S, Kubesova B, Rausch T, Kolarik M, Benes V, Bystry V, Pospisilova S

BMC bioinformatics, 2018

doi:10.1186/s12859-018-2227-x.

Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers.

Kikulska A, Rausch T, Krzywinska E, Pawlak M, Wilczynski B, Benes V, Rutkowski P, Wilanowski T

BMC cancer, 2018

doi:10.1186/s12885-017-3943-8.

Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy.

Haas J, Mester S, Lai A, Frese KS, Sedaghat-Hamedani F, Kayvanpour E, Rausch T, Nietsch R, Boeckel JN, Carstensen A, Völkers M, Dietrich C, Pils D, Amr A, Holzer DB, Martins Bordalo D, Oehler D, Weis T, Mereles D, Buss S, Riechert E, Wirsz E, Wuerstle M, Korbel JO, Keller A, Katus HA, Posch AE, Meder B

EMBO molecular medicine, 2017

doi:10.15252/emmm.201707838.

Potential Protective Role of Grainyhead-like Genes in the Development of Clear Cell Renal Cell Carcinoma.

Pawlak M, Kikulska A, Wrzesinski T, Rausch T, Kwias Z, Wilczynski B, Benes V, Wesoly J, Wilanowski T

Molecular carcinogenesis, 2017

doi:10.1002/mc.22682.

Characterization of Two Historic Smallpox Specimens from a Czech Museum.

Pajer P, Dresler J, Kabíckova H, Písa L, Aganov P, Fucik K, Elleder D, Hron T, Kuzelka V, Velemínsky P, Klimentova J, Fucikova A, Pejchal J, Hrabakova R, Benes V, Rausch T, Dundr P, Pilin A, Cabala R, Hubalek M, Stríbrny J, Antwerpen MH, Meyer H

Viruses, 2017

doi:10.3390/v9080200.

Identification of novel follicular dendritic cell sarcoma markers, FDCSP and SRGN, by whole transcriptome sequencing.

Lorenzi L, Döring C, Rausch T, Benes V, Lonardi S, Bugatti M, Campo E, Cabeçadas J, Simonitsch-Klupp I, Borges A, Mehta J, Agostinelli C, Pileri SA, Facchetti F, Hansmann ML, Hartmann S

Oncotarget, 2017

doi:10.18632/oncotarget.14864.

Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia.

Richter-Pechańska P, Kunz JB, Hof J, Zimmermann M, Rausch T, Bandapalli OR, Orlova E, Scapinello G, Sagi JC, Stanulla M, Schrappe M, Cario G, Kirschner-Schwabe R, Eckert C, Benes V, Korbel JO, Muckenthaler MU, Kulozik AE

Blood Cancer Journal, 2017

doi:10.1038/bcj.2017.3.

Highly recurrent mutations of SGK1, DUSP2 and JUNB in nodular lymphocyte predominant Hodgkin lymphoma.

Hartmann S, Schuhmacher B, Rausch T, Fuller L, Döring C, Weniger M, Lollies A, Weiser C, Thurner L, Rengstl B, Brunnberg U, Vornanen M, Pfreundschuh M, Benes V, Küppers R, Newrzela S, Hansmann ML

Leukemia, 2016

doi:10.1038/leu.2015.328.

MCM3AP and POMP Mutations Cause a DNA-Repair and DNA-Damage-Signaling Defect in an Immunodeficient Child.

Gatz SA, Salles D, Jacobsen EM, Dörk T, Rausch T, Aydin S, Surowy H, Volcic M, Vogel W, Debatin KM, Stütz AM, Schwarz K, Pannicke U, Hess T, Korbel JO, Schulz AS, Schumacher J, Wiesmüller L

Human mutation, 2015

doi:10.1002/humu.22939.

A novel autosomal recessive TERT T1129P mutation in a dyskeratosis congenita family leads to cellular senescence and loss of CD34+ hematopoietic stem cells not reversible by mTOR-inhibition.

Stockklausner C, Raffel S, Klermund J, Bandapalli OR, Beier F, Brümmendorf TH, Bürger F, Sauer SW, Hoffmann GF, Lorenz H, Tagliaferri L, Nowak D, Hofmann WK, Buergermeister R, Kerber C, Rausch T, Korbel JO, Luke B, Trumpp A, Kulozik AE

Aging, 2015

doi:10.18632/aging.100835.

A global reference for human genetic variation.

1000 Genomes Project Consortium

Nature, 2015

doi:10.1038/nature15393.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO

Nature, 2015

doi:10.1038/nature15394.

Pediatric T-lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation.

Kunz JB, Rausch T, Bandapalli OR, Eilers J, Pechanska P, Schuessele S, Assenov Y, Stütz AM, Kirschner-Schwabe R, Hof J, Eckert C, von Stackelberg A, Schrappe M, Stanulla M, Koehler R, Avigad S, Elitzur S, Handgretinger R, Benes V, Weischenfeldt J, Korbel JO, Muckenthaler MU, Kulozik AE

Haematologica, 2015

doi:10.3324/haematol.2015.129692.

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A

Nature methods, 2015

doi:10.1038/nmeth.3454.

Identification of cytokine-induced modulation of microRNA expression and secretion as measured by a novel microRNA specific qPCR assay.

Benes V, Collier P, Kordes C, Stolte J, Rausch T, Muckentaler MU, Häussinger D, Castoldi M

Scientific reports, 2015

doi:10.1038/srep11590.

The landscape of human STR variation.

Willems T, Gymrek M, Highnam G, 1000 Genomes Project Consortium, Mittelman D, Erlich Y

Genome research, 2014

doi:10.1101/gr.177774.114.

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

Delaneau O, Marchini J, 1000 Genomes Project Consortium

Nature communications, 2014

doi:10.1038/ncomms4934.

The activating STAT5B N642H mutation is a common abnormality in pediatric T-cell acute lymphoblastic leukemia and confers a higher risk of relapse

Bandapalli OR, Schuessele S, Kunz JB, Rausch T, Stütz AM, Tal N, Geron I, Gershman N, Izraeli S, Eilers J, Vaezipour N, Kirschner-Schwabe R, Hof J, von Stackelberg A, Schrappe M, Stanulla M, Zimmermann M, Koehler R, Avigad S, Handgretinger R, Frismantas V, Bourquin JP, Bornhauser B, Korbel JO, Muckenthaler MU, Kulozik AE

Haematologica, 2014

doi:10.3324/haematol.2014.104992.

Identification of novel sequence variations in microRNAs in chronic lymphocytic leukemia.

Kminkova J, Mraz M, Zaprazna K, Navrkalova V, Tichy B, Plevova K, Malcikova J, Cerna K, Rausch T, Benes V, Brychtova Y, Doubek M, Mayer J, Pospisilova S

Carcinogenesis, 2014

doi:10.1093/carcin/bgt396.

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, ICGC PedBrain Tumor Project

Cancer cell, 2014

doi:10.1016/j.ccr.2014.02.004.

The genomic and transcriptomic landscape of a HeLa cell line

Landry JJ, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, Steinmetz LM

G3 (Bethesda, Md.), 2013

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Whole-exome sequencing links caspase recruitment domain 11 (CARD11) inactivation to severe combined immunodeficiency

Greil J, Rausch T, Giese T, Bandapalli OR, Daniel V, Bekeredjian-Ding I, Stütz AM, Drees C, Roth S, Ruland J, Korbel JO, Kulozik AE

The Journal of allergy and clinical immunology, 2013

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Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

Zichner T, Garfield DA, Rausch T, Stütz AM, Cannavó E, Braun M, Furlong EE, Korbel JO

Genome research, 2013

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Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

Weischenfeldt J, Simon R, Feuerbach L, Schlangen K, Weichenhan D, Minner S, Wuttig D, Warnatz HJ, Stehr H, Rausch T, Jäger N, Gu L, Bogatyrova O, Stütz AM, Claus R, Eils J, Eils R, Gerhäuser C, Huang PH, Hutter B, Kabbe R, Lawerenz C, Radomski S, Bartholomae CC, Fälth M, Gade S, Schmidt M, Amschler N, Haß T, Galal R, Gjoni J, Kuner R, Baer C, Masser S, von Kalle C, Zichner T, Benes V, Raeder B, Mader M, Amstislavskiy V, Avci M, Lehrach H, Parkhomchuk D, Sultan M, Burkhardt L, Graefen M, Huland H, Kluth M, Krohn A, Sirma H, Stumm L, Steurer S, Grupp K, Sültmann H, Sauter G, Plass C, Brors B, Yaspo ML, Korbel JO, Schlomm T

Cancer cell, 2013

doi:10.1016/j.ccr.2013.01.002.

Identification of a Ninein (NIN) mutation in a family with spondyloepimetaphyseal dysplasia with joint laxity (leptodactylic type)-like phenotype

Grosch M, Grüner B, Spranger S, Stütz AM, Rausch T, Korbel JO, Seelow D, Nürnberg P, Sticht H, Lausch E, Zabel B, Winterpacht A, Tagariello A

Matrix biology : journal of the International Society for Matrix Biology, 2013

doi:10.1016/j.matbio.2013.05.001.

Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing

Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J, Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RA, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PF, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B, Siebert R, ICGC MMML-Seq Project

Nature genetics, 2012

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An integrated map of genetic variation from 1,092 human genomes

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA

Nature, 2012

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DELLY: structural variant discovery by integrated paired-end and split-read analysis

Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO

Bioinformatics (Oxford, England), 2012

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Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma (vol 482, pg 226, 2012)

Schwartzentruber J, Korshunov A, Liu XY, Jones DTW, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DAK, Tonjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jager N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Fruhwald MC, Roggendorf W, Kramm C, Durken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong ZF, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N

NATURE, 2012

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Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DA, Tönjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jäger N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Frühwald MC, Roggendorf W, Kramm C, Dürken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N

Nature, 2012

doi:10.1038/nature10833.

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

Rausch T, Jones DT, Zapatka M, Stütz AM, Zichner T, Weischenfeldt J, Jäger N, Remke M, Shih D, Northcott PA, Pfaff E, Tica J, Wang Q, Massimi L, Witt H, Bender S, Pleier S, Cin H, Hawkins C, Beck C, von Deimling A, Hans V, Brors B, Eils R, Scheurlen W, Blake J, Benes V, Kulozik AE, Witt O, Martin D, Zhang C, Porat R, Merino DM, Wasserman J, Jabado N, Fontebasso A, Bullinger L, Rücker FG, Döhner K, Döhner H, Koster J, Molenaar JJ, Versteeg R, Kool M, Tabori U, Malkin D, Korshunov A, Taylor MD, Lichter P, Pfister SM, Korbel JO

Cell, 2012

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Mapping copy number variation by population-scale genome sequencing

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project

Nature, 2011

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