Hoffmann Research Group
Publications at FLI
2020
- Pan-cancer analysis of whole genomes.
Campbell PJ, Getz G, Korbel Jea, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
Nature 2020, 578(7793), 82-93 - Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.
Cortés-Ciriano I, Lee JJK, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, PCAWG Structural Variation Working Group, Park PJ, PCAWG Consortium
Nat Genet 2020, 52(3), 331 - The evolutionary history of 2,658 cancers.
Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium
Nature 2020, 578(7793), 122-8 - Dichotomous Impact of Myc on rRNA Gene Activation and Silencing in B Cell Lymphomagenesis.
Joshi* G, Eberhardt* AO, Lange L, Winkler R, Hoffmann S, Kosan C, Bierhoff H
Cancers (Basel) 2020, 12(10), E3009. doi: 10.3390/cancers12103 * equal contribution - Bashing irreproducibility with shournal
Kirchner T, Riege K, Hoffmann S
bioRxiv 2020, https://doi.org/10.1101/2020.08. - Patterns of somatic structural variation in human cancer genomes.
Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ, PCAWG Consortium
Nature 2020, 578(7793), 112-21 - ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom
Moore M, Wesemann C, Gossmann N, Sahm A, Krüger J, Sczyrba A, Dietz KJ
BMC Bioinformatics 2020, 21(1), 490 - Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Consortium
Nature 2020, 578(7793), 129-36 - Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G, PCAWG Consortium
Nature 2020, 578(7793), 102-11 - Dissecting the DNA binding landscape and gene regulatory network of p63 and p53.
Riege K, Kretzmer H, Sahm A, McDade SS, Hoffmann S, Fischer M
Elife 2020, 9, e63266