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Article

Dissecting the spatiotemporal diversity of adult neural stem cells.
Mitic, N. and Neuschulz, A. and Spanjaard, B. and Schneider, J. and Fresmann, N. and Novoselc, K.T. and Strunk, T. and Münster, L. and Olivares-Chauvet, P. and Ninkovic, J. and Junker, J.P.
Molecular Systems Biology 20 (4): 321-337. 2 April 2024

AI-guided pipeline for protein-protein interaction drug discovery identifies an SARS-CoV-2 inhibitor.
Trepte, P. and Secker, C. and Olivet, J. and Blavier, J. and Kostova, S. and Maseko, S.B. and Minia, I. and Silva Ramos, E. and Cassonnet, P. and Golusik, S. and Zenkner, M. and Beetz, S. and Liebich, M.J. and Scharek, N. and Schutz, A. and Sperling, M. and Lisurek, M. and Wang, Y. and Spirohn, K. and Hao, T. and Calderwood, M.A. and Hill, D.E. and Landthaler, M. and Choi, S.G. and Twizere, J.C. and Vidal, M. and Wanker, E.E.
Molecular Systems Biology 20 (4): 428-457. 2 April 2024

SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.
Liu, H. and Arsiè, R. and Schwabe, D. and Schilling, M. and Minia, I. and Alles, J. and Boltengagen, A. and Kocks, C. and Falcke, M. and Friedman, N. and Landthaler, M. and Rajewsky, N.
Molecular Systems Biology 19 (10): e11427. 12 October 2023

Consistency across multi-omics layers in a drug-perturbed gut microbial community.
Wuyts, S. and Alves, R. and Zimmermann-Kogadeeva, M. and Nishijima, S. and Blasche, S. and Driessen, M. and Geyer, P.E and Hercog, R. and Kartal, E. and Maier, L. and Müller, J.B. and Garcia Santamarina, S. and Schmidt, T.S.B. and Sevin, D.C. and Telzerow, A. and Treit, P.V. and Wenzel, T. and Typas, A. and Patil, K.R and Mann, M. and Kuhn, M. and Bork, P.
Molecular Systems Biology 19 (9): e11525. 12 September 2023

GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks.
Kamal, A. and Arnold, C. and Claringbould, A. and Moussa, R. and Servaas, N.H. and Kholmatov, M. and Daga, N. and Nogina, D. and Mueller-Dott, S. and Reyes-Palomares, A. and Palla, G. and Sigalova, O. and Bunina, D. and Pabst, C. and Zaugg, J.B.
Molecular Systems Biology 19 (6): e11627. 12 June 2023

A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
Neuschulz, A. and Bakina, O. and Badillo Lisakowski, V. and Olivares-Chauvet, P. and Conrad, T. and Gotthardt, M. and Kettenmann, H. and Junker, J.P.
Molecular Systems Biology 19 (2): e11147. 10 February 2023

Nonproductive exposure of PBMCs to SARS‐CoV ‐2 induces cell‐intrinsic innate immune responses.
Kazmierski, J. and Friedmann, K. and Postmus, D. and Emanuel, J. and Fischer, C. and Jansen, J. and Richter, A. and Bosquillon de Jarcy, L. and Schüler, C. and Sohn, M. and Sauer, S. and Drosten, C. and Saliba, A.E. and Sander, L.E. and Müller, M.A. and Niemeyer, D. and Goffinet, C.
Molecular Systems Biology 18 (8): e10961. 1 August 2022

Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation.
Brunner, A.D. and Thielert, M. and Vasilopoulou, C. and Ammar, C. and Coscia, F. and Mund, A. and Hoerning, O.B. and Bache, N. and Apalategui, A. and Lubeck, M. and Richter, S. and Fischer, D.S. and Raether, O. and Park, M.A. and Meier, F. and Theis, F.J. and Mann, M.
Molecular Systems Biology 18 (3): e10798. 1 March 2022

HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence.
Sofiadis, K. and Josipovic, N. and Nikolic, M. and Kargapolova, Y. and Übelmesser, N. and Varamogianni-Mamatsi, V. and Zirkel, A. and Papadionysiou, I. and Loughran, G. and Keane, J. and Michel, A. and Gusmao, E.G. and Becker, C. and Altmüller, J. and Georgomanolis, T. and Mizi, A. and Papantonis, A.
Molecular Systems Biology 17 (6): e9760. 1 June 2021

The transcriptome dynamics of single cells during the cell cycle.
Schwabe, D. and Formichetti, S. and Junker, J.P. and Falcke, M. and Rajewsky, N.
Molecular Systems Biology 16 (11): e9946. 1 November 2020

Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease.
Bader, J.M. and Geyer, P.E. and Müller, J.B. and Strauss, M.T. and Koch, M. and Leypoldt, F. and Koertvelyessy, P. and Bittner, D. and Schipke, C.G. and Incesoy, E.I. and Peters, O. and Deigendesch, N. and Simons, M. and Jensen, M.K. and Zetterberg, H. and Mann, M.
Molecular Systems Biology 16 (6): e9356. 1 June 2020

Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency.
Friedrich, D. and Friedel, L. and Finzel, A. and Herrmann, A. and Preibisch, S. and Loewer, A.
Molecular Systems Biology 15 (12): e9068. 1 December 2019

LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells.
Trepte, P. and Kruse, S. and Kostova, S. and Hoffmann, S. and Buntru, A. and Tempelmeier, A. and Secker, C. and Diez, L. and Schulz, A. and Klockmeier, K. and Zenkner, M. and Golusik, S. and Rau, K. and Schnoegl, S. and Garner, C.C. and Wanker, E.E.
Molecular Systems Biology 14 (7): e8071. 11 July 2018

Quantifying compartment-associated variations of protein abundance in proteomics data.
Parca, L. and Beck, M. and Bork, P. and Ori, A.
Molecular Systems Biology 14 (7): e8131. 2 July 2018

Cell-specific responses to the cytokine TGFβ are determined by variability in protein levels.
Strasen, J. and Sarma, U. and Jentsch, M. and Bohn, S. and Sheng, C. and Horbelt, D. and Knaus, P. and Legewie, S. and Loewer, A.
Molecular Systems Biology 14 (1): e7733. 25 January 2018

Subspecies in the global human gut microbiome.
Costea, P.I. and Coelho, L.P. and Sunagawa, S. and Munch, R. and Huerta-Cepas, J. and Forslund, K. and Hildebrand, F. and Kushugulova, A. and Zeller, G. and Bork, P.
Molecular Systems Biology 13 (12): 960. 14 December 2017

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.
Ferrai, C. and Torlai Triglia, E. and Risner-Janiczek, J.R. and Rito, T. and Rackham, O.J.L. and De Santiago, I. and Kukalev, A. and Nicodemi, M. and Akalin, A. and Li, M. and Ungless, M.A. and Pombo, A.
Molecular Systems Biology 13 (10): 946. 16 October 2017

An immediate-late gene expression module decodes ERK signal duration.
Uhlitz, F. and Sieber, A. and Wyler, E. and Fritsche-Guenther, R. and Meisig, J. and Landthaler, M. and Klinger, B. and Blüthgen, N.
Molecular Systems Biology 13 (5): 928. 3 May 2017

Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation.
Xiao, M.S. and Zhang, B. and Li, Y.S. and Gao, Q. and Sun, W. and Chen, W.
Molecular Systems Biology 12 (12): 890. 8 December 2016

Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals.
Wang, X. and Hou, J. and Quedenau, C. and Chen, W.
Molecular Systems Biology 12 (7): 875. 18 July 2016

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.
Cheng, Z. and Teo, G. and Krueger, S. and Rock, T.M. and Koh, H.W.L. and Choi, H. and Vogel, C.
Molecular Systems Biology 12 (1): 855. 20 January 2016

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.
Fraser, J. and Ferrai, C. and Chiariello, A.M. and Schueler, M. and Rito, T. and Laudanno, G. and Barbieri, M. and Moore, B.L. and Kraemer, D.C.A. and Aitken, S. and Xie, S.Q. and Morris, K.J. and Itoh, M. and Kawaji, H. and Jaeger, I. and Hayashizaki, Y. and Carninci, P. and Forrest, A.R.R. and Semple, C.A. and Dostie, J. and Pombo, A. and Nicodemi, M.
Molecular Systems Biology 11 (12): 852. 23 December 2015

Extensive allele-specific translational regulation in hybrid mice.
Hou, J. and Wang, X. and McShane, E. and Zauber, H. and Sun, W. and Selbach, M. and Chen, W.
Molecular Systems Biology 11 (8): 825. 7 August 2015

Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing.
Gao, Q. and Sun, W. and Ballegeer, M. and Libert, C. and Chen, W.
Molecular Systems Biology 11 (7): 816. 1 July 2015

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
Lluch-Senar, M. and Delgado, J. and Chen, W.-H. and Llorens-Rico, V. and O'Reilly, F.J. and Wodke, J.A.H. and Unal, E.B. and Yus, E. and Martinez, S. and Nichols, R.J. and Ferrar, T. and Vivancos, A. and Schmeisky, A. and Stuelke, J. and van Noort, V. and Gavin, A.-C. and Bork, P. and Serrano, L.
Molecular Systems Biology 11 (1): 780. 21 January 2015

Potential of fecal microbiota for early-stage detection of colorectal cancer.
Zeller, G. and Tap, J. and Voigt, A.Y. and Sunagawa, S. and Kultima, J.R. and Costea, P.I. and Amiot, A. and Boehm, J. and Brunetti, F. and Habermann, N. and Hercog, R. and Koch, M. and Luciani, A. and Mende, D.R. and Schneider, M.A. and Schrotz-King, P. and Tournigand, C. and Tran Van Nhieu, J. and Yamada, T. and Zimmermann, J. and Benes, V. and Kloor, M. and Ulrich, C.M. and von Knebel Doeberitz, M. and Sobhani, I. and Bork, P.
Molecular Systems Biology 10 (11): 766. 28 November 2014

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.
Iskar, M. and Zeller, G. and Blattmann, P. and Campillos, M. and Kuhn, M. and Kaminska, K.H. and Runz, H. and Gavin, A.C. and Pepperkok, R. and van Noort, V. and Bork, P.
Molecular Systems Biology 9 : 662. 2013

Systematic identification of proteins that elicit drug side effects.
Kuhn, M. and Al Banchaabouchi, M. and Campillos, M. and Jensen, L.J. and Gross, C. and Gavin, A.C. and Bork, P.
Molecular Systems Biology 9 : 663. 2013

Widespread splicing changes in human brain development and aging.
Mazin, P. and Xiong, J. and Liu, X. and Yan, Z. and Zhang, X. and Li, M. and He, L. and Somel, M. and Yuan, Y. and Chen, Y.P.P. and Li, N. and Hu, Y. and Fu, N. and Ning, Z. and Zeng, R. and Yang, H. and Chen, W. and Gelfand, M. and Khaitovich, P.
Molecular Systems Biology 9 : 633. 2013

Novel biomarkers for pre-diabetes identified by metabolomics.
Wang-Sattler, R. and Yu, Z. and Herder, C. and Messias, A.C. and Floegel, A. and He, Y. and Heim, K. and Campillos, M. and Holzapfel, C. and Thorand, B. and Grallert, H. and Xu, T. and Bader, E. and Huth, C. and Mittelstrass, K. and Doering, A. and Meisinger, C. and Gieger, C. and Prehn, C. and Roemisch-Margl, W. and Carstensen, M. and Xie, L. and Yamanaka-Okumura, H. and Xing, G. and Ceglarek, U. and Thiery, J. and Giani, G. and Lickert, H. and Lin, X. and Li, Y. and Boeing, H. and Joost, H.G. and de Angelis, M.H. and Rathmann, W. and Suhre, K. and Prokisch, H. and Peters, A. and Meitinger, T. and Roden, M. and Wichmann, H.E. and Pischon, T. and Adamski, J. and Illig, T.
Molecular Systems Biology 8 : 615. 25 September 2012

Deciphering a global network of functionally associated post-translational modifications.
Minguez, P. and Parca, L. and Diella, F. and Mende, D.R. and Kumar, R. and Helmer-Citterich, M. and Gavin, A.C. and van Noort, V. and Bork, P.
Molecular Systems Biology 8 : 599. 17 July 2012

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.
Yamada, T. and Waller, A.S. and Raes, J. and Zelezniak, A. and Perchat, N. and Perret, A. and Salanoubat, M. and Patil, K.R. and Weissenbach, J. and Bork, P.
Molecular Systems Biology 8 : 581. 8 May 2012

Stimulus-dependent dynamics of p53 in single cells.
Batchelor, E. and Loewer, A. and Mock, C. and Lahav, G.
Molecular Systems Biology 7 : 488. 10 May 2011

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
Raes, J. and Letunic, I. and Yamada, T. and Jensen, L.J. and Bork, P.
Molecular Systems Biology 7 : 473. 15 March 2011

A stele-enriched gene regulatory network in the Arabidopsis root.
Brady, S.M. and Zhang, L. and Megraw, M. and Martinez, N.J. and Jiang, E. and Yi, C.S. and Liu, W. and Zeng, A. and Taylor-Teeples, M. and Kim, D. and Ahnert, S. and Ohler, U. and Ware, D. and Walhout, A.J.M. and Benfey, P.N.
Molecular Systems Biology 7 : 459. 18 January 2011

A side effect resource to capture phenotypic effects of drugs.
Kuhn, M. and Campillos, M. and Letunic, I. and Jensen, L.J. and Bork, P.
Molecular Systems Biology 6 : 343. 2010

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
Kunin, V. and Raes, J. and Harris, J.K. and Spear, J.R. and Walker, J.J. and Ivanova, N. and von Mering, C. and Bebout, B.M. and Pace, N.R. and Bork, P. and Hugenholtz, P.
Molecular Systems Biology 4 : 198. 2008

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
Hooper, S.D. and Boue, S. and Krause, R. and Jensen, L.J. and Mason, C.E. and Ghanim, M. and White, K.P. and Furlong, E.E. and Bork, P.
Molecular Systems Biology 3 : 72. January 2007

Review

Evolution and functional cross-talk of protein post-translational modifications.
Beltrao, P. and Bork, P. and Krogan, N.J. and van Noort, V.
Molecular Systems Biology 9 : 714. 22 December 2013

Editorial

The rise of proteome-wide biophysics.
Mateus, A. and Savitski, M.M. and Piazza, I.
Molecular Systems Biology 17 (7): e10442. July 2021

Computational eco-systems biology in Tara Oceans: translating data into knowledge.
Sunagawa, S. and Karsenti, E. and Bowler, C. and Bork, P.
Molecular Systems Biology 11 (5): 809. 21 May 2015

Is there biological research beyond Systems Biology? A comparative analysis of terms.
Bork, P.
Molecular Systems Biology 1 : 2005.0012 (Article Number). 1 January 2005