Tobias Neumann

Tobias Neumann

Bioinformatician / Data Analyst / Space exploration enthusiast

Articles • Talks • Posters
Articles
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Transcriptomics

  • • Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL & Rescheneder P: Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. BMC Bioinformatics, 2019. 20(1), 258.
  • • Muhar M, Ebert A, Neumann T, Umkehrer C, Jude J, Wieshofer C, Rescheneder P, Lipp JJ, Herzog VA, Reichholf B, Cisneros DA, Hoffmann T, Schlapansky MF, Bhat P, von Haeseler A, Köcher T, Obenauf AC, Popow J, Ameres SL† & Zuber J†: SLAM-seq defines direct gene regulatory functions of the BRD4-MYC axis. Science, 2018. 360(6390), 800–805.
  • • Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J & Ameres SL: Thiol-linked alkylation of RNA to assess expression dynamics. Nature Methods, 2017. 14(12), 1198–1204.
  • • Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Stefan L Ameres SL & Miska EA: Sequencing cell type-specific transcriptomes with SLAM-ITseq. Nature Protocols, 2019. 87(13), 166.
  • • Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Stefan L Ameres SL & Miska EA: SLAM-ITseq: Sequencing cell type-specific transcriptomes without cell sorting. Development, 2018. 145(13).
  • • Fitz J, Neumann T, Steininger M, Wiedemann EM, Cantoran Garcia A, Athanasiadis A, Schoeberl UE & Pavri R: Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Nature Genetics, 2020. 52(5), 505–515.
  • • Fitz J, Neumann T & Pavri R: Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation. EMBO J, 2018. 37(8), e97965.

CRISPR technology development

  • • Michlits G*, Jude J*, Hinterndorfer M, de Almeida M, Vainorius G, Hubmann M, Neumann T, Schleiffer A, Burkard T, Fellner M, Gijsbertsen M, Traunbauer A, Zuber J† & Elling U†: Multilayered VBC-score predicts sgRNAs that efficiently generate loss-of-function alleles. Nature Methods, 2020. 17(7), 708–716.
  • • de Almeida M*, Hinterndorfer M*, Brunner H, Grishkovskaya I, Singh K, Schleiffer A, Jude J, Deswal S, Kalis R, Vunjak M, Lendl T, Imre R, Roitinger E, Neumann T, Kandolf S, Schutzbier M, Mechtler K, Versteeg G, Haselbach D† & Zuber J†: AKIRIN2 controls the nuclear import of proteasomes in vertebrates. Nature, 2021. 599, 491–496.
  • • Umkehrer C, Holstein F, Formenti L, Jude J, Froussios K, Neumann T, Cronin SM, Haas L, Lipp JJ, Burkard TR, Fellner M, Wiesner T, Zuber J & Obenauf AC: Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters. Nature Biotechnology, 2020. 39, 174–178.

Genomics

  • • Peycheva M, Neumann T, Malzl D, Nazarova M, Schoeberl UE & Pavri R: DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations. Science, 2022. 377(6612), 1277.
  • • Malzl D*, Peycheva M*, Rahjouei A, Gnan S, Klein K, Nazarova M, Schoeberl UE, Gilbert DM, Buonomo S, Di Virgilio M, Neumann T† & Pavri R†: RIF1 regulates early replication timing in murine B cells. Nature Communications, 2023. 14(8049).
  • • Kaiser T, Poehn P, Szkiba D, Preussner M, Sedlazeck F, Zrim A, Neumann T, Nguyen LT, Betancourt A, Hummel T, Vogel H, Dorner S, Heyd F, Arndt von Haeseler A & Tessmar-Raible K: The genomic basis of circadian and circalunar timing adaptations in a midge. Nature, 2016. 540(7631), 69–73.
  • • Thiecke MJ, Wutz G, Muhar M, Tang W, Bevan S, Malysheva V, Stocsits R, Neumann T, Zuber J, Fraser P, Schoenfelder S, Peters J-M, & Spivakov M.: Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers. Cell Reports, 2020. 32(3), 107929.
  • • Chipman AD, Ferrier DEK, Brena C, Qu J, Hughes DST [...], Neumann T et al.: The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biology, 2014. 12(11), e1002005.

Cancer

  • • Leiendecker L, Neumann T, Jung PS, Cronin SM, Steinacker TL, Schleiffer A, Schutzbier M, Mechtler K, Kervarrec T, Laurent E, Bachiri K, Coyaud E, Murali R, Busam KJ, Itzinger-Monshi B, Kirnbauer R, Cerroni L, Calonje E, Rutten A, Stubenrauch F, Griewank KG, Wiesner T† & Obenauf AC†: Human papillomavirus 42 drives digital papillary adenocarcinoma and elicits a germ-cell like program conserved in HPV-positive cancers. Cancer Discovery, 2023. 13(1):70-84.
  • • Rathert P*, Roth M*, Neumann T, Muerdter F, Roe J-S, Muhar M, Deswal S, Cerny-Reiterer S, Peter B, Jude J, Hoffmann T, Boryn LM, Axelsson E, Schweifer N, Tontsch-Grunt U, Dow LE, Gianni D, Pearson M, Valent P, Stark A, Kraut N, Vakoc CR & Zuber J: Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature, 2015. 525(7570), 543–547.
  • • Haas L, Elewaut A, Gerard CL, Umkehrer C, Leiendecker L, Pedersen M, Krecioch I, Hoffmann D, Novatchkova M, Kuttke M, Neumann T, de Silva IP, Witthock H, Cuendet MA, Carotta S, Harrington KJ, Zuber J, Scolyer RA, Long GV, Wilmott JS, Michielin O, Vanharanta S, Wiesner T & Obenauf AC: Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma. Nature Cancer, 2021. 2, 693–708.
  • • Leiendecker L*, Jung PS*, Krecioch I, Neumann T, Schleiffer A, Mechtler K, Wiesner T & Obenauf AC: LSD1 inhibition induces differentiation and cell death in Merkel cell carcinoma. EMBO Mol. Med., 2020. 17, e12525.
  • • Schmoellerl J*, Barbosa IAM*, Minnich M, Andersch F, Smeenk L, Havermans M, Eder T, Neumann T, Jude J, Fellner M, Ebert A, Steininger M, Delwel R, Grebien F† & Zuber J†: EVI1 drives leukemogenesis through aberrant ERG activation. Blood, 2023. 141, 5.

SARS-CoV-2 (part of the VCDI team)

  • • Yelagandula R, Bykov A, Vogt A, Heinen R, Özkan E, Strobl MM, Baar JC, Uzunova K, Hajdusits B, Kordic D, Suljic E, Kurtovic-Kozaric A, Izetbegovic S, Schaeffer J, Hufnagl P, Zoufaly A, Seitz T, VCDI, Födinger M, Allerberger F, Stark A, Cochella L† & Elling U†: Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq. Nature Communications, 2021. 12, 3132.
  • • Kellner MJ*†, Ross JJ*, Schnabl J*, Dekens MPS, Matl M, Heinen R, Grishkovskaya I, Bauer B, Stadlmann J, Menéndez-Arias L, Straw AD, Fritsche-Polanz R, Traugott M, Seitz T, Zoufaly A, Födinger M, Wenisch C, Zuber J, VCDI, Pauli A†, & Brennecke J†: A Rapid, Highly Sensitive and Open-Access SARS-CoV-2 Detection Assay for Laboratory and Home Testing. Frontiers in Molecular Biosciences, 2021. 9.
  • • Kellner MJ, Matl M, Ross JJ, Schnabl J, Handler D, Heinen R, Schaeffer J, Hufnagl P, Indra A, Dekens MPS, Fritsche-Polanz R, Födinger M, Zuber J, VCDI, Allerberger F, Pauli A & Brennecke J: Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RT-qPCR on extracted RNA for rapid SARS-CoV-2 diagnostics. medRxiv, 2021.
Talks
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  • • Neumann T: SLAMdunk – a pipeline for analyzing SLAMseq data in established and emerging applications, Orlando, USA, 2018. AGBT 2018
Posters
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  • • Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL & Rescheneder P: Quantifying experimentally induced nucleotide-conversions in high-throughput sequencing, Orlando, USA, 2018. AGBT 2018