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Publications

Our members and group leaders have published in multiple scholarly journals spanning a wide range of topics and subject matter.

Publications Core Groups

2021 – 2014

  • Kletter T, Reusch S, Dempewolf N, Tischer C, Reber S. Volumetric morphometry reveals spindle width as the best predictor of mammalian spindle scaling. JCB 01-03-2022 issue, vol. 221 no. 1. doi: 10.1083/jcb.202106170.
  • Bischoff, P., Trinks, A., Obermayer, B., Pett, J. P., Wiederspahn, J., Uhlitz, F., Liang, X., Lehmann, A., Jurmeister, P., Elsner, A., Dziodzio, T., Rückert, J-C., Neudecker, J., Falk, C., Beule, D., Sers, C., Morkel, M., Horst, D., Blüthgen, N., Klauschen, F. Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma. Oncogene (2021). doi: 10.1038/s41388-021-02054-3.
  • Kusumaatmaja H, May AI, Feeney M, McKenna JF, Mizushima N, Frigerio L, Knorr RL. Wetting of phase-separated droplets on plant vacuole membranes leads to a competition between tonoplast budding and nanotube formation. Proc Natl Acad Sci U S A. 2021 Sep 7; 118(36) e2024109118; doi: 10.1073/pnas.2024109118.
  • Kusumaatmaja H, May AI, Knorr RL. Intracellular wetting mediates contacts between liquid compartments and membrane-bound organelles. J Cell Biol. 2021 Oct 4;220(10):e202103175. doi: 10.1083/jcb.202103175. Epub 2021 Aug 24. PMID: 34427635
  • Uhlitz F, Bischoff P, Peidli S, Sieber A, Trinks A, Lüthen M, Obermayer B, Blanc E, Ruchiy Y, Sell T, Mamlouk S, Arsie R, Wei TT, Klotz-Noack K, Schwarz RF, Sawitzki B, Kamphues C, Beule D, Landthaler M, Sers C, Horst D, Blüthgen N, Morkel M. Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. EMBO Mol Med. 2021 Aug 19:e14123. doi: 10.15252/emmm.202114123. Epub ahead of print. PMID: 34409732.
  • Gassen NC, Papies J, Bajaj T, Emanuel J, Dethloff F, Chua RL, Trimpert J, Heinemann N, Niemeyer C, Weege F, Hönzke K, Aschman T, Heinz DE, Weckmann K, Ebert T, Zellner A, Lennarz M, Wyler E, Schroeder S, Richter A, Niemeyer D, Hoffmann K, Meyer TF, Heppner FL, Corman VM, Landthaler M, Hocke AC, Morkel M, Osterrieder N, Conrad C, Eils R, Radbruch H, Giavalisco P, Drosten C, Müller MA. SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals. Nat Commun. 2021 Jun 21;12(1):3818. doi: 10.1038/s41467-021-24007-w.
  • Holler K, Neuschulz A, Drewe-Boß P, Mintcheva J, Spanjaard B, Arsiè R, Ohler U, Landthaler M, Junker JP. Spatio-temporal mRNA tracking in the early zebrafish embryo. Nat Commun. 2021 Jun 7;12(1):3358. doi: 10.1038/s41467-021-23834-1.
  • Calviello L, Venkataramanan S, Rogowski KJ, Wyler E, Wilkins K, Tejura M, Thai B, Krol J, Filipowicz W, Landthaler M, Floor SN. DDX3 depletion represses translation of mRNAs with complex 5' UTRs. Nucleic Acids Res. 2021 May 21;49(9):5336-5350. doi: 10.1093/nar/gkab287.
  • Gonzalez-Perez AC, Stempel M, Wyler E, Urban C, Piras A, Hennig T, Ganskih S, Wei Y, Heim A, Landthaler M, Pichlmair A, Dölken L, Munschauer M, Erhard F, Brinkmann MM. The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4/UL5 Transcripts. mBio. 2021 May 4;12(3):e02683-20. doi: 10.1128/mBio.02683-20.
  • Biswas A, Kim K, Cojoc G, Guck J, Reber S. The Xenopus spindle is as dense as the surrounding cytoplasm. Developmental Cell, Volume 56, Issue 7, 5 April 2021, Pages 967-975.e5. doi: 10.1016/j.devcel.2021.03.013
  • Kassuhn W, Klein O, Darb-Esfahani S, Lammert H, Handzik S, Taube ET, Schmitt WD, Keunecke C, Horst D, Dreher F, George J, Bowtell DD, Dorigo O, Hummel M, Sehouli J, Blüthgen N, Kulbe H, Braicu EI. Cancers (Basel). Classification of Molecular Subtypes of High-Grade Serous Ovarian Cancer by MALDI-Imaging. 2021 Mar 25;13(7):1512. doi: 10.3390/cancers13071512.
  • Emanuel W, Kirstin M, Vedran F, Asija D, Theresa GL, Roberto A, Filippos K, David K, Katja H, Salah A, Christopher B, Karen H, Anja R, Ivano L, Andranik I, Tommaso M, Simone DG, Jan P, Samantha P, Meyer Thomas F, Alexander MM, Daniela N, Andreas H, Matthias S, Altuna A, Nikolaus R, Christian D, Markus L.Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy. iScience. 2021 Feb 6:102151. doi: 10.1016/j.isci.2021.102151. Epub ahead of print. PMID: 33585804; PMCID: PMC7866843
  • Kraushar ML, Krupp F, Harnett D, Turko P, Ambrozkiewicz MC, Sprink T, Imami K, Günnigmann M, Zinnall U, Vieira-Vieira CH, Schaub T, Münster-Wandowski A, Bürger J, Borisova E, Yamamoto H, Rasin MR, Ohler U, Beule D, Mielke T, Tarabykin V, Landthaler M, Kramer G, Vida I, Selbach M, Spahn CMT. Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. Mol Cell. 2021 Jan 21;81(2):304-322.e16. doi: 10.1016/j.molcel.2020.11.037. Epub 2020 Dec 22. PMID: 33357414
  • Xiao H, Wyler E, Milek M, Grewe B, Kirchner P, Ekici A, Silva ABOV, Jungnickl D, Full F, Thomas M, Landthaler M, Ensser A, Überla K. CRNKL1 Is a Highly Selective Regulator of Intron-Retaining HIV-1 and Cellular mRNAs. mBio. 2021 Jan 19;12(1):e02525-20. doi: 10.1128/mBio.02525-20. PMID: 33468685

Publications Core Groups

  • Kuhn N, Klinger B, Uhlitz F, Sieber A, Rivera M, Klotz-Noack K, Fichtner I, Hoffmann J, Blüthgen N, Falk C, Sers C, Schäfer R. Mutation-specific effects of NRAS oncogenes in colorectal cancer cells. Adv Biol Regul. 2020 Dec 31:100778. doi: 10.1016/j.jbior.2020.100778. Online ahead of print. PMID: 33431353
  • Meisig J, Dreser N, Kapitza M, Henry M, Rotshteyn T, Rahnenführer J, Hengstler JG, Sachinidis A, Waldmann T, Leist M, Blüthgen N. Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation. Nucleic Acids Res. 2020 Dec 16;48(22):12577-12592. doi: 10.1093/nar/gkaa1089. PMID: 33245762
  • Denkena J, Zaisser A, Merz B, Klinger B, Kuhl D, Blüthgen N, Hermey G. Mol Brain. Neuronal activity regulates alternative exon usage. 2020 Nov 10;13(1):148. doi: 10.1186/s13041-020-00685-3. PMID: 33172478
  • Hirst WG, Kiefer C, Schaeffer E, and Reber S (2020). In vitro Reconstitution and Imaging of Microtubule Dynamics by TIRF and IR Microscopy. STAR Protocols 1, 100177.
  • Reusch S, Biswas A, and Reber S (2020). Affinity-Purification of Label-free Tubulins from Xenopus Egg Extracts. STAR Protocols 1, 100151.
  • Weber R, Chung MY, Keskeny C, Zinnall U, Landthaler M, Valkov E, Izaurralde E, Igreja C. Mediate Translation-Coupled Messenger RNA Decay .Cell Rep. 2020 Oct 13;33(2):108262.
  • Reinig J, Ruge F, Howard M, Ringrose L. A theoretical model of Polycomb/Trithorax action unites stable epigenetic memory and dynamic regulation. Nat Commun. 2020 Sep 22;11(1):4782
  • Klotz-Noack K, Klinger B, Rivera M, Bublitz N, Uhlitz F, Riemer P, Lüthen M, Sell T, Kasack K, Gastl B, Ispasanie SSS, Simon T, Janssen N, Schwab M, Zuber J, Horst D, Blüthgen N, Schäfer R, Morkel M, Sers C. SFPQ Depletion Is Synthetically Lethal with BRAF V600E in Colorectal Cancer Cells. Cell Rep.2020 Sep 22;32(12):108184
  • L.K. Scheffer C.S. Xu M. Januszewski Z. Lu S.Y. Takemura K.J. Hayworth G.B. Huang K. Shinomiya J. Maitlin-Shepard S. Berg J. Clements P.M. Hubbard W.T. Katz L. Umayam T. Zhao D. Ackerman T. Blakely J. Bogovic T. Dolafi D. Kainmueller T. Kawase K.A. Khairy L. Leavitt P.H. Li L. Lindsey N. Neubarth D.J. Olbris H. Otsuna E.T. Trautman M. Ito A.S. Bates J. Goldammer T. Wolff R. Svirskas P. Schlegel E.R. Neace C.J. Knecht C.X. Alvarado D.A. Bailey S. Ballinger J.A. Borycz B.S. Canino N. Cheatham M. Cook M. Dreher O. Duclos B. Eubanks K. Fairbanks S. Finley N. Forknall A. Francis G.P. Hopkins E.M. Joyce S.J. Kim N.A. Kirk J. Kovalyak S.A. Lauchie A. Lohff C. Maldonado E.A. Manley S. McLin C. Mooney M. Ndama O. Ogundeyi N. Okeoma C. Ordish N. Padilla C. Patrick T. Paterson E.E. Phillips E.M. Phillips N. Rampally C. Ribeiro M.K. Robertson J.T. Rymer S.M. Ryan M. Sammons A.K. Scott A.L. Scott A. Shinomiya C. Smith K. Smith N.L. Smith M.A. Sobeski A. Suleiman J. Swift S. Takemura I. Talebi D. Tarnogorska E. Tenshaw T. Tokhi J.J. Walsh T. Yang J.A. Horne F. Li R. Parekh P.K. Rivlin V. Jayaraman M. Costa G.S.X.E. Jefferis K. Ito S. Saalfeld R. George I.A. Meinertzhagen G.M. Rubin H.F. Hess V. Jain S.M. Plaza. A connectome and analysis of the adult Drosophila central brain. eLife 2020;9:e57443, doi: 10.7554/eLife.57443
  • Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk HD, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE; Deutsche COVID-19 OMICS Initiative (DeCOI). Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell. 2020 Aug 5:S0092-8674(20)30992-2.
  • Gross T, Blüthgen N. Identifiability and experimental design in perturbation studies. Bioinformatics. 2020 Jul 1;36(Supplement_1):i482-i489
  • Lécrivain AL, Beckmann BM. Bacterial RNA in Extracellular Vesicles: A New Regulator of Host-Pathogen Interactions? Biochim Biophys Acta Gene Regul Mech. 2020 Jul;1863(7):194519. Review
  • Gastl B, Klotz-Noack K, Klinger B, Ispasanie S, Salib KHF, Zuber J, Mamlouk S, Bublitz N, Blüthgen N, Horst D, Morkel M, Schäfer R, Sers C. Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe. Cell Death Dis 2020 Jul 1;11(7):499.
  • Rydenfelt M, Klinger B, Klünemann M, Blüthgen N. SPEED2: inferring upstream pathway activity from differential gene expression. Nucleic Acids Res. 2020 Jul 2;48(W1):W307-W312.
  • Urdaneta EC, Beckmann BM. Fast and unbiased purification of RNA-protein complexes after UV cross-linking. Methods. 2020 Jun 1;178:72-82.
  • Hirst WG, Biswas A, Mahalingan KK, Reber S. Differences in Intrinsic Tubulin Dynamic Properties Contribute to Spindle Length Control in Xenopus Species. Curr Biol. 2020 Jun 8;30(11):2184-2190.e5.
  • Babaian A, Rothe K, Girodat D, Minia I, Djondovic S, Milek M, Spencer Miko SE, Wieden HJ, Landthaler M, Morin GB, Mager DL. Loss of M 1 Acp 3 Ψ Ribosomal RNA Modification Is a Major Feature of Cancer. Mechanism of Virus Attenuation by Codon Pair Deoptimization. Cell Rep. 2020 May 5;31(5):107611.
  • Groenke N, Trimpert J, Merz S, Conradie AM, Wyler E, Zhang H, Hazapis OG, Rausch S, Landthaler M, Osterrieder N, Kunec D. Mechanism of Virus Attenuation by Codon Pair Deoptimization. Cell Rep. 2020 Apr 28;31(4):107586.
  • Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, Göbel M, Döring K, Menegatti J, Antrobus R, Matheson NJ, Künzig FWH, Mastrobuoni G, Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R, Landthaler M, Grässer F, Lehner PJ, Friedel CC, Erhard F, Dölken L. Integrative functional genomics decodes herpes simplex virus 1. Nat Commun. 2020 Apr 27;11(1):2038.
  • Benary M, Bohn S, Lüthen M, Nolis IK, Blüthgen N, Loewer A. Disentangling Pro-mitotic Signaling during Cell Cycle Progression using Time-Resolved Single-Cell. Cell Rep. 2020 Apr 14;31(2):107514.
  • Smith T, Villanueva E, RML Queiroz, Dawson CS, Elzek M, Urdaneta EC, Willis AE, Beckmann BM, Krijgsveld J, Lilley KS. Organic phase separation opens up new opportunities to intterrogate the RNA-binding proteome. Curr Opin Chem Biol. 2020 Feb;54:70-75. Review
  • Granada AE, Jiménez A, Stewart-Ornstein J, Blüthgen N, Reber S, Jambhekar A, Lahav G.  The effects of proliferation status and cell cycle phase on the response of single cells to chemotherapy. Mol Biol Cell. 2020 Feb 12:mbcE19090515
  • Silla, T, Schmid M, Dou Y, Garland W, Milek M, Imami K, Johnson D, Polak P, Andersen JS, Selbach M, Landthaler M, Jensen TH. The human ZC3G3 and RBN26/27 proteins are critical for PAXT-mediated nuclear RNA decay. Bucleic Acids Res. 2020 Jan 17. pii:gkz1238
  • Saez-Rodriguez J, Blüthgen N. Personalized signaling models for personalized treatments. Mol Syst Biol 2020 Jan; 16(1):e9042.
  • Dreser N, Madjar K, Holzer AK, Kapitza M, Scholz C, Kranaster P, Gutbier S, Klima S, Kolb D, Dietz C, Trefzer T, Meisig J, van Thriel C, Henry M, Berthold MR, Blüthgen N, Sachinidis A, Rahnenführer J, Hengstler JG, Waldmann T, Leist M. Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances. Arch Toxicol. 2020 Jan;94(1):151-171.


Joint Publications

  • Lenzen B, Rühle T, Lehniger MK, Okuzaki A, Labs M, Muino JM, Ohler U, Leister D, Schmitz-Linneweber C. The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation. Int J Mol Sci. 2020 Aug 6;21(16):E5633.

Publications Core Groups

  • Labi V, Peng S, Klironomos F, Munschauer M, Kastelic N, Chakraborty T, Schoeler K, Derudder E, Martella M, Mastrobuoni G, Hernandez-Miranda LR, Lahmann I, Kocks C, Birchmeier C, Kempa S, Quintanilla-Martinez de Fend L, Landthaler M, Rajewsky N, Rajewsky K. Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat. Genes Dev. 2019 Nov 7.
  • Wyler E, Franke V, Menegatti J, Kocks C, Boltengagen A, Praktiknjo S, Walch-Rückheim B, Bosse J, Rajewsky N, Grässer F, Akalin A, Landthaler M. Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program. Nat Commun. 2019 Oct 25;10(1):4878.
  • Beckmann BM, Granneman S. Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges. Methods Mol Biol. 2019;2049:213-231.
  • Urdaneta EC, Beckmann BM. Fast and unbiased purification of RNA-protein complexes after UV cross-linking. Methods. 2019 Oct 3. pii: S1046-2023(18)30486-9.
  • Hia F, Yang SF, Shichino Y, Yoshinaga M, Murakawa Y, Vandenbon A, Fukao A, Fujiwara T, Landthaler M, Natsume T, Adachi S, Iwasaki S, Takeuchi O. Codon bias confers stability to human mRNAs. MBO Rep. 2019 Sep 3:e48220.
  • Gross T, Wongchenko M, Yan Y and Blüthgen N. Robust network inference using response logic. Bioinformatics. 2019 Jul 15;35(14):i634-i642.
  • Brandt R, Sell T, Lüthen M, Uhlitz F, Klinger B, Riemer P, Giesecke-Thiel C, Schulze S, El-Shimy IA, Kunkel D, Fauler B, Mielke T, Mages N, Herrmann BG, Sers C, Blüthgen N, Morkel M. Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium. Nat Commun. 2019 Jul 2;10(1):2919.
  • Rydenfelt M, Wongchenko M, Klinger B, Yan Y, Blüthgen N. The cancer cell proteome and transcriptome predicts sensitivity to targeted and cytotoxic drugs. Life Sci Alliance. 2019 Jun 28;2(4). pii: e201900445.
  • De Santis R, Alfano V, de Turris V, Colantoni A, Santini L, Garone MG, Antonacci G, Peruzzi G, Sudria-Lopez E, Wyler E, Anink JJ, Aronica E, Landthaler M, Pasterkamp RJ, Bozzoni I, Rosa A. Mutant FUS and ELAVL4 (HuD) Aberrant Crosstalk in Amyotrophic Lateral Sclerosis. Cell Rep. 2019 Jun 25;27(13):3818-3831.e5.
  • Wrackmeyer U, Kaldrack J, Jüttner R, Pannasch U, Gimber N, Freiberg F, Purfürst B, Kainmueller D, Schmitz D, Haucke V, Rathjen FG, Gotthardt M. The cell adhesion protein CAR is a negative regulator of synaptic transmission. Sci Rep. 2019 May 1;9(1):6768.
  • van Heesch S, Witte F, Schneider-Lunitz V, Schulz JF, Adami E, Faber AB, Kirchner M, Maatz H, Blachut S, Sandmann CL, Kanda M, Worth CL, Schafer S, Calviello L, Merriott R, Patone G, Hummel O, Wyler E, Obermayer B, Mücke MB, Lindberg EL, Trnka F, Memczak S, Schilling M, Felkin LE, Barton PJR, Quaife NM, Vanezis K, Diecke S, Mukai M, Mah N, Oh SJ, Kurtz A, Schramm C, Schwinge D, Sebode M, Harakalova M, Asselbergs FW, Vink A, de Weger RA, Viswanathan S, Widjaja AA, Gärtner-Rommel A, Milting H, Dos Remedios C, Knosalla C, Mertins P, Landthaler M, Vingron M, Linke WA, Seidman JG, Seidman CE, Rajewsky N, Ohler U, Cook SA, Hubner N. The Translational Landscape of the Human Heart. Cell. 2019 May 29. pii: S0092-8674(19)30508-2
  • Peng PC, Khoueiry P, Girardot C, Reddington JP, Garfield DA, Furlong EEM, Sinha S. The role of chromatin accessibility in cis-regulatory evolution. Genome Biol Evol. 2019 May 22. pii: evz103.
  • Sneppen K, Ringrose, L. Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent. Nat Commun. 2019 May 13;10(1):2133.
  • Hood FE, Klinger B, Newlaczyl AU, Sieber A, Dorel M, Oliver SP, Coulson JM, Blüthgen N, Prior IA. Isoform-specific Ras signaling is growth factor dependent. Mol Biol Cell. 2019 Apr 15;30(9):1108-1117.
  • Bressin A, Schulte-Sasse R, Figini D, Urdaneta EC, Beckmann BM*, Marsico A*. TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs. Nucleic Acids Res. 2019 Mar 29. pii: gkz203
  • Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J,  Ohler U, Granneman S, Selbach M & Beckmann BM. Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nat Commun. 2019 Mar 1;10(1):990.
  • Kappor V, Hirst WG, Hentschel C, Preibisch S, Reber S. MTrack: Automated Detection, Tracking, and Analysis of Dynamic Microtubules. Sci Rep. 2019 Mar 7;9(1):3749.
  • Camargo Ortega G, Falk S, Johansson PA, Peyre E, Broix L, Sanjeeb, Sahu K,  Hirst W, Schlichthaerle T, Romero CJ, Draganova K, Vinopal S, Chinnappa K, Gavranovic A, Karakaya T, Steininger T, Merl-Pham J, Feederle R, Shao W, Shi SH, Hauck SM, Jungmann R,  Bradke F, Borrell V, Geerlof A, Reber S, Tiwari VK, Huttner WB, Wilsch-Bräuninger M, Nguyen L and Götz M. The centrosome protein AKNA regulates neurogenesis via microtubule organization. Nature. 2019 Mar;567(7746):113-117.
  • Funke J., Mais L., Champion A., Dye N., Kainmueller D. (2019) A Benchmark for Epithelial Cell Tracking. In: Leal-Taixé L., Roth S. (eds) Computer Vision – ECCV 2018 Workshops. ECCV 2018. Lecture Notes in Computer Science, vol 11134. Springer, Cham. doi.org/10.1007/978-3-030-11024-6_33
  • P. Swoboda, D. Kainmüller, A. Mokarian, C. Theobalt and F. Bernard, "A Convex Relaxation for Multi-Graph Matching," 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), Long Beach, CA, USA, 2019, pp. 11148-11157, doi: 10.1109/CVPR.2019.01141.


Joint Publications

  • Teufel L, Tummler K, Flöttmann M, Herrmann A, Barkai N, Klipp E. A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell. Sci Rep. 2019 Mar 4;9(1):3343.

Publications Core Groups

  • Bosdriesz E, Prahallad A, Klinger B, Sieber A, Bosma A, Bernards R, Blüthgen N, Wessels LFA. Comparative Network Reconstruction using mixed integer programming. Bioinformatics. 34(17):i997-i1004.
  • Klinger B, Blüthgen N. Reverse engineering gene regulatory networks by modular response analysis - a benchmark. Essays Biochem. 62(4):535-547.Review
  • Witzel F, Blüthgen N. When More Is Less: Dual Phosphorylation Protects Signaling Off State against Overexpression. Biophys J. 115(7):1383-1392
  • Besray Unal E, Kiel C, Benisty H, Campbell A, Pickering K, Blüthgen N, Sansom OJ, Serrano L. Systems level expression correlation of Ras GTPase regulators. Cell Commun Signal. 16(1):46.
  • Dorel M, Klinger B, Gross T, Sieber A, Prahallad A, Bosdriesz E, Wessels LFA, Blüthgen N. Modelling signalling networks from perturbation data. Bioinformatics. 34(23):4079-4086.
  • Meisig J, Blüthgen N. The gene regulatory network of mESC differentiation: a benchmark for reverse engineering methods. Philos Trans R Soc Lond B Biol Sci. 373(1750).
  • Godoy P, Schmidt-Heck W, Hellwig B, Nell P, Feuerborn D, Rahnenführer J, Kattler K, Walter J, Blüthgen N, Hengstler JG. Assessment of stem cell differentiation based on genome-wide expression profiles. Philos Trans R Soc Lond B Biol Sci. 373(1750). pii: 20170221. Review.
  • Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nat Commun. 2018 Jan 2;9(1):20
  • Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfert L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O. Whither systems medicine? Exp Mol Med. 50(3)
  • Cusanovich DA, Reddington JP, Garfield DA*, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature. 555(7697):538-542.
  • Rendleman J, Cheng Z, Maity S, Kastelic N, Munschauer M, Allgoewer K, Teo G, Zhang YBM, Lei A, Parker B, Landthaler M, Freeberg L, Kuersten S, Choi H, Vogel C. New insights into the cellular temporal response to proteostatic stress. Elife. 7. pii: e39054.
  • Imami K, Milek M, Bogdanow B, Yasuda T, Kastelic N, Zauber H, Ishihama Y, Landthaler M, Selbach M. Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis. Mol Cell. 72(1):84-98.e9. .
  • Milek M, Landthaler M. Systematic Detection of Poly(A)(+) RNA-Interacting Proteins and Their Differential Binding. Methods Mol Biol. 1649:405-417.
  • Hinze F, Drewe-Boss P, Milek M, Ohler U, Landthaler M, Gotthardt M. Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP. RNA Biol. 15(3):359-368.
     

Joint Publications

  • Qu Y, Legen J, Arndt J, Henkel S, Hoppe G, Thieme C, Ranzini G, Muino JM, Weihe A, Ohler U, Weber G, Ostersetzer O, Schmitz-Linneweber C. Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation. Front Plant Sci. 9:1453.
  • Hillebrand A, Matz JM, Almendinger M, Müller K, Matuschewski K, Schmitz-Linneweber C. Identification of clustered organellar short (cos) RNAs and of a conserved family of organellar RNA-binding proteins, the heptatricopeptide repeat proteins, in the malaria parasite. Nucleic Acids Res. 46(19):10417-10431.
  • Fritsche-Guenther R, Zasada C, Mastrobuoni G, Royla N, Rainer R, Roßner F, Pietzke M, Klipp E, Sers C, Kempa S. Alterations of mTOR signaling impact metabolic stress resistance in colorectal carcinomas with BRAF and KRAS mutations. Sci Rep. 8(1):9204.
  • Amoussouvi A, Teufel L, Reis M, Seeger M, Schlichting JK, Schreiber G, Herrmann A, Klipp E. Transcriptional timing and noise of yeast cell cycle regulators-a single cell and single molecule approach. NPJ Syst Biol Appl. 4:17.

Publications Core Groups

  • Zhan Y, Mariani L, Barozzi I, Schulz EG, Bluthgen N, Stadler M, Tiana G, Giorgetti L. Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes. Genome Res. 5. pii: gr.212803.116.
  • Blüthgen N, van Bentum M, Merz B, Kuhl D, Hermey G. Profiling the MAPK/ERK dependent and independent activity regulated transcriptional programs in the murine hippocampus in vivo. Sci Rep. 7:45101.
  • Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N*, Saez-Rodriguez J. Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models. Cancer Res.pii: canres.0078.2017.
  • Uhlitz F, Sieber A, Wyler E, Fritsche-Guenther R, Meisig J, Landthaler M, Klinger B, Blüthgen N. An immediate-late gene expression module decodes ERK signal duration. Mol Syst Biol. 13(5):928.
  • Hermey G, Blüthgen N, Kuhl D. Neuronal activity-regulated alternative mRNA splicing. Int J Biochem Cell Biol. 91(Pt B):184-193.
  • Ünal EB, Uhlitz F, Blüthgen N. A Compendium of ERK Targets. FEBS Lett. 2017 Jul 4
  • Cantini L, Calzone L, Martignetti L, Rydenfelt M, Blüthgen N, Barillot E, Zinovyev A. Classification of gene signatures for their information value and functional redundancy. NPJ Syst Biol Appl. 4:2
  • Riemer P, Rydenfelt M, Marks M, van Eunen K, Thedieck K, Herrmann BG, Blüthgen N, Sers C, Morkel M. Oncogenic β-catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids. J Cell Biol. 216(6):1567-1577.
  • Milek M, Imami K, Mukherjee N, De Bortoli F, Zinnall U, Hazapis O, Trahan C, Oeffinger M, Heyd F, Ohler U, Selbach M, Landthaler M. DDX54 regulates transcriptome dynamics during DNA damage response. Genome Res. pii: gr.218438.116.
  • Piechotta M, Wyler E, Ohler U, Landthaler M, Dieterich C. JACUSA: site-specific identification of RNA editing events from replicate sequencing data. BMC Bioinformatics. 18(1):7.
  • Maatz H. Kolonski M, Hubner N, Landthaler M. Transcriptome-wide Identification of RNA-binding Protein Binding Sites Using Photoactivatable-Ribonucleoside-Enhanced Crosslinking Immunoprecipitation (PAR-CLIP). Curr Protoc Mol Biol. 2017 Apr 3;118:27.6.1-27.6.19.
  • Wyler E, van Heesch S, Adami E, Hubner N, Landthaler M. Rattus norvegicus BN/SHR liver and heart left ventricle ribosomal RNA depleted directional RNA sequencing. BMC Res Notes 2017 Aug 11;10(1):395.
  • Wyler E, Menegatti J, Franke V, Kocks C, Boltengagen A, Hennig T, Theil K, Rutkowski A, Ferrai C, Baer L, Kermas L, Friedel C, Rajewsky N, Akalin A, Dölken L, Grässer F, Landthaler M. Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection. Genome Biol. 18(1):209.
  • Kastelic N, Landthaler M. mRNA interactome capture in mammalian cells. Methods. 2017 Aug 15;126:38-43
  • Pamudurti NR, Bartok O, Jens M, Ashwal-Fluss R, Stottmeister C, Ruhe L, Hanan M, Wyler E, Perez-Hernandez D, Ramberger E, Shenzis S, Samson M, Dittmar G, Landthaler M, Chekulaeva M, Rajewsky N, Kadener S. Translation of CircRNAs. Mol Cell. pii: S1097-2765(17)30136-3.
  • Ringrose L, Howard M. Dissecting chromatin-mediated gene regulation and epigenetic memory through mathematical modelling. Current Opinion in Systems Biology 3:7-14
  • Ringrose L. Noncoding RNAs in Polycomb and Trithorax Regulation: A Quantitative Perspective. Annu Rev Genet. 2017 Sep 15. doi: 10.1146/annurev-genet-120116-023402.
  • Beckmann BM. RNA interactome capture in yeast. Methods. 2017 Apr 15;118-119:82-92.


Joint Publications

  • Del Rio G, Klipp E, Herrmann A. Using Confocal Microscopy and Computational Modeling to Investigate the Cell-Penetrating Properties of Antimicrobial Peptides. Methods Mol Biol. 1548:191-199.
  • Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A. RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. Nucleic Acids Res. 45(10):e91.
  • Piwecka M, Glažar P, Hernandez-Miranda LR, Memczak S, Wolf SA, Rybak-Wolf A, Filipchyk A, Klironomos F, Cerda Jara CA, Fenske P, Trimbuch T, Zywitza V, Plass M, Schreyer L, Ayoub S, Kocks C, Kühn R, Rosenmund C, Birchmeier C, Rajewsky N. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science. 10 pii: eaam8526.
  • Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M. RNA localization is a key determinant of neurite-enriched proteome. Nat Commun. 8(1):583.
  • Sadewasser A, Paki K, Eichelbaum K, Bogdanow B, Saenger S, Budt M, Lesch M, Hinz KP, Herrmann A, Meyer TF, Karlas A, Selbach M, Wolff T. Quantitative proteomic approach identifies Vpr binding protein as novel host factor supporting influenza A virus infections in human cells. Mol Cell Proteomics.13. pii: mcp.M116.065904.

Publications Core Groups

  • Beckmann BM, Castello A, Medenbach J (2016). The expanding universe of ribonucleo-proteins: of novel RNA-binding proteins and unconventional interactions. Pflugers Arch 468: 1029-1040
  • Shinde V, Perumal Srinivasan S, Henry M, Rotshteyn T, Hescheler J, Rahnenführer J, Grinberg M, Meisig J, Blüthgen N, Waldmann T, Leist M, Hengstler JG, Sachinidis A. Comparison of a teratogenic transcriptome-based predictive test based on human embryonic versus inducible pluripotent stem cells. Stem Cell Res Ther. 2016 Dec 30;7(1):190.
  • Michna A, Braselmann H, Selmansberger M, Dietz A, Hess J, Gomolka M, Hornhardt S, Blüthgen N, Zitzelsberger H, Unger K. Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data. 2016 Aug 9.PLoS One 11: e0160791.
  • Fritsche-Guenther R, Witzel F, Kempa S, Brummer T, Sers C, Blüthgen N (2016) Effects of RAF inhibitors on PI3K/AKT signalling depend on mutational status of the RAS/RAF signalling axis. Oncotarget 7: 7960-7969
  • Godoy P, Widera A, Schmidt-Heck W, Campos G, Meyer C, Cadenas C, Reif R, Stober R, Hammad S, Putter L, Gianmoena K, Marchan R, Ghallab A, Edlund K, Nussler A, Thasler WE, Damm G, Seehofer D, Weiss TS, Dirsch O, Dahmen U, Gebhardt R, Chaudhari U, Meganathan K, Sachinidis A, Kelm J, Hofmann U, Zahedi RP, Guthke R, Blüthgen N, Dooley S, Hengstler JG (2016) Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue. Archives of toxicology 90: 2513-2529
  • Hoelting L, Klima S, Karreman C, Grinberg M, Meisig J, Henry M, Rotshteyn T, Rahnenfuhrer J, Blüthgen N, Sachinidis A, Waldmann T, Leist M (2016) Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants. Stem cells translational medicine 5: 476-487
  • Rohwer N, Bindel F, Grimm C, Lin SJ, Wappler J, Klinger B, Blüthgen N, Du Bois I, Schmeck B, Lehrach H, de Graauw M, Goncalves E, Saez-Rodriguez J, Tan P, Grabsch HI, Prigione A, Kempa S, Cramer T (2016) Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. Oncotarget 7: 6693-6710
  • Asaoka T, Almagro J, Ehrhardt C, Tsai I, Schleiffer A, Deszcz L, Junttila S, Ringrose L, Mechtler K, Kavirayani A, Gyenesei A, Hofmann K, Duchek P, Rittinger K, Ikeda F. Linear ubiquitination by LUBEL has a role in Drosophila heat stress response. EMBO Rep. 2016 Nov;17(11):1624-1640.
  • Bauer M, Trupke J, Ringrose L. The quest for mammalian Polycomb response elements: are we there yet? Chromosoma. 2016 Jun;125(3):471-96.


Joint Publications

  • Schelker M, Mair CM, Jolmes F, Welke RW, Klipp E, Herrmann A, Flöttmann M, Sieben C. Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency. PLoS Comput Biol. 2016 Oct 25;12(10):e1005075.
  • Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U (2016) Detecting actively translated open reading frames in ribosome profiling data. Nature methods 13: 165-170
  • Wessels HH, Imami K, Baltz AG, Kolinski M, Beldovskaya A, Selbach M, Small S, Ohler U, Landthaler M (2016) The mRNA-bound proteome of the early fly embryo. Genome research 26: 1000-1009

Publications Core Groups

  • Beckmann BM, Horos R, Fischer B, Castello A, Eichelbaum K, Alleaume AM, Schwarzl T, Curk T, Foehr S, Huber W, Krijgsveld J, Hentze MW (2015) The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. Nature communications 6: 10127
  • Amos M, Axmann IM, Blüthgen N, de la Cruz F, Jaramillo A, Rodriguez-Paton A, Simmel F (2015) Bacterial computing with engineered populations. Philosophical transactions Series A, Mathematical, physical, and engineering sciences 373
  • Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN (2015) Silence on the relevant literature and errors in implementation. Nat Biotechnol 33: 336-339
  • Blüthgen N (2015) Signaling output: it‘s all about timing and feedbacks. Molecular systems biology 11: 843
  • Dreser N, Zimmer B, Dietz C, Sugis E, Pallocca G, Nyffeler J, Meisig J, Blüthgen N, Berthold MR, Waldmann T, Leist M (2015) Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling. Neurotoxicology 50: 56-70
  • Murakawa Y, Hinz M, Mothes J, Schuetz A, Uhl M, Wyler E, Yasuda T, Mastrobuoni G, Friedel CC, Dolken L, Kempa S, Schmidt-Supprian M, Blüthgen N, Backofen R, Heinemann U, Wolf J, Scheidereit C, Landthaler M (2015) RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappaB pathway. Nature communications 6: 7367
  • Rempel E, Hoelting L, Waldmann T, Balmer NV, Schildknecht S, Grinberg M, Das Gaspar JA, Shinde V, Stober R, Marchan R, van Thriel C, Liebing J, Meisig J, Blüthgen N, Sachinidis A, Rahnenfuhrer J, Hengstler JG, Leist M (2015) A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors. Archives of toxicology 89: 1599-1618
  • Schmiedel JM, Klemm SL, Zheng Y, Sahay A, Blüthgen N*, Marks DS, van Oudenaarden A (2015) Gene expression. MicroRNA control of protein expression noise. Science 348: 128-132
  • Schulthess P, Loffler A, Vetter S, Kreft L, Schwarz M, Braeuning A, Blüthgen N* (2015) Signal integration by the CYP1A1 promoter-a quantitative study. Nucleic Acids Res 43: 5318-5330
  • Staudacher JJ, Naarmann-de Vries IS, Ujvari SJ, Klinger B, Kasim M, Benko E, Ostareck-Lederer A, Ostareck DH, Bondke Persson A, Lorenzen S, Meier JC, Blüthgen N, Persson PB, Henrion-Caude A, Mrowka R, Fahling M (2015) Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum. Nucleic Acids Res 43: 3219-3236
  • Thomas P, Durek P, Solt I, Klinger B, Witzel F, Schulthess P, Mayer Y, Tikk D, Blüthgen N*, Leser U (2015) Computer-assisted curation of a human regulatory core network from the biological literature. Bioinformatics (Oxford, England) 31: 1258-1266
  • Witzel F, Fritsche-Guenther R, Lehmann N, Sieber A, Blüthgen N (2015) Analysis of impedance-based cellular growth assays. Bioinformatics (Oxford, England) 31: 2705-2712
  • Reber S, Goehring NW (2015) Intracellular Scaling Mechanisms. Cold Spring Harbor perspectives in biology 7
  • Reber S, Hyman AA (2015) Emergent Properties of the Metaphase Spindle. Cold Spring Harbor perspectives in biology 7: a015784
  • Clevers H, Firestein S, Ringrose L, Bernards R, Darwin KH, Vance RE (2015) Radical Sabbaticals. Cell 163: 788-789
  • Ringrose L. (2015) Reconciling randomness and precision. Nature reviews Molecular cell biology 16: 642


Joint Publications

  • Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B (2015) Extensive identification and analysis of conserved small ORFs in animals. Genome biology 16: 179

Publications Core Groups

  • Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon KL, Hentze MW, Kohlbacher O, Urlaub H (2014) Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nature methods 11: 1064-1070
  • Lechner M, Nickel AI, Wehner S, Riege K, Wieseke N, Beckmann BM, Hartmann RK, Marz M (2014) Genomewide comparison and novel ncRNAs of Aquificales. BMC genomics 15: 522
  • Killig M, Friedrichs B, Meisig J, Gentilini C, Blüthgen N, Loddenkemper C, Labopin M, Basara N, Pfrepper C, Niederwieser DW, Uharek L, Romagnani C (2014) Tracking in vivo dynamics of NK cells transferred in patients undergoing stem cell transplantation. European journal of immunology 44: 2822-2834
  • Klinger B, Blüthgen N (2014) Consequences of feedback in signal transduction for targeted therapies. Biochem Soc Trans 42: 770-775
  • Kummer S, Flottmann M, Schwanhausser B, Sieben C, Veit M, Selbach M, Klipp E, Herrmann A (2014) Alteration of protein levels during influenza virus H1N1 infection in host cells: a proteomic survey of host and virus reveals differential dynamics. PLoS One 9: e94257
  • Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G (2014) Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. J Biol Chem 289: 14448-14457
  • Grun D, Kirchner M, Thierfelder N, Stoeckius M, Selbach M, Rajewsky N (2014) Conservation of mRNA and protein expression during development of C. elegans. Cell Rep 6: 565-577

* = joint first or joint last author