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Humboldt-Universität zu Berlin - IRI Life Sciences

Publications

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2018 - 2017 - 2016 2015 - 2014

 

2018

Publications Core Groups

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. 2018 Mar 2; 50(3)

 

2017

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. 2017 Jan 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. 2017 Mar 28;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. 2017 Apr 5. 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. 2017 May 3;13(5):928.

Hermey G, Blüthgen N, Kuhl D. Neuronal activity-regulated alternative mRNA splicing. Int J Biochem Cell Biol. 2017 Oct;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. 2017 Dec 19; 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. 2017 Jun 5;216(6):1567-1577.

Piechotta M, Wyler E, Ohler U, Landthaler M, Dieterich C. JACUSA: site-specific identification of RNA editing events from replicate sequencing data. BMC Bioinformatics. 2017 Jan 3;18(1):7.

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. 2017 Jun 8. 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. 2017 Jan 3;18(1):7.

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. 2017 Oct 31;18(1):209.

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. 2017 Oct 13:0.

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. 2017 Mar 15. pii: S1097-2765(17)30136-3.

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. 2017 Mar 15. pi

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.

 

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. 2017;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. 2017 Jun 2;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. 2017 Aug 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. 2017 Sep 19;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. 2017 Mar 13. pii: mcp.M116.065904.

 

2016

Publications Core Groups

Beckmann BM. RNA interactome capture in yeast. Methods. 2016 Dec 16. pii: S1046-2023(16)30490-X.

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

 

2015

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

Bauer M, Trupke J, Ringrose L (2016) The quest for mammalian Polycomb response elements: are we there yet? Chromosoma 125: 471-496

 

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

 

2014

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

Schulz EG, Meisig J, Nakamura T, Okamoto I, Sieber A, Picard C, Borensztein M, Saitou M, Blüthgen N, Heard E (2014) The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network. Cell stem cell 14: 203-216

 

Joint Publications 

Hilsch M, Goldenbogen B, Sieben C, Hofer CT, Rabe JP, Klipp E, Herrmann A, Chiantia S (2014) Influenza A matrix protein M1 multimerizes upon binding to lipid membranes. Biophysical journal 107: 912-923

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