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Article

Dissecting the spatiotemporal diversity of adult neural stem cells.
Mitic, N., Neuschulz, A., Spanjaard, B., Schneider, J., Fresmann, N., Novoselc, K.T., Strunk, T., Münster, L., Olivares-Chauvet, P., 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., Secker, C., Olivet, J., Blavier, J., Kostova, S., Maseko, S.B., Minia, I., Silva Ramos, E., Cassonnet, P., Golusik, S., Zenkner, M., Beetz, S., Liebich, M.J., Scharek, N., Schutz, A., Sperling, M., Lisurek, M., Wang, Y., Spirohn, K., Hao, T., Calderwood, M.A., Hill, D.E., Landthaler, M., Choi, S.G., Twizere, J.C., 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., Arsiè, R., Schwabe, D., Schilling, M., Minia, I., Alles, J., Boltengagen, A., Kocks, C., Falcke, M., Friedman, N., 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., Alves, R., Zimmermann-Kogadeeva, M., Nishijima, S., Blasche, S., Driessen, M., Geyer, P.E, Hercog, R., Kartal, E., Maier, L., Müller, J.B., Garcia Santamarina, S., Schmidt, T.S.B., Sevin, D.C., Telzerow, A., Treit, P.V., Wenzel, T., Typas, A., Patil, K.R, Mann, M., 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., Arnold, C., Claringbould, A., Moussa, R., Servaas, N.H., Kholmatov, M., Daga, N., Nogina, D., Mueller-Dott, S., Reyes-Palomares, A., Palla, G., Sigalova, O., Bunina, D., 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., Bakina, O., Badillo Lisakowski, V., Olivares-Chauvet, P., Conrad, T., Gotthardt, M., 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., Friedmann, K., Postmus, D., Emanuel, J., Fischer, C., Jansen, J., Richter, A., Bosquillon de Jarcy, L., Schüler, C., Sohn, M., Sauer, S., Drosten, C., Saliba, A.E., Sander, L.E., Müller, M.A., 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., Thielert, M., Vasilopoulou, C., Ammar, C., Coscia, F., Mund, A., Hoerning, O.B., Bache, N., Apalategui, A., Lubeck, M., Richter, S., Fischer, D.S., Raether, O., Park, M.A., Meier, F., 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., Josipovic, N., Nikolic, M., Kargapolova, Y., Übelmesser, N., Varamogianni-Mamatsi, V., Zirkel, A., Papadionysiou, I., Loughran, G., Keane, J., Michel, A., Gusmao, E.G., Becker, C., Altmüller, J., Georgomanolis, T., 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., Formichetti, S., Junker, J.P., 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., Geyer, P.E., Müller, J.B., Strauss, M.T., Koch, M., Leypoldt, F., Koertvelyessy, P., Bittner, D., Schipke, C.G., Incesoy, E.I., Peters, O., Deigendesch, N., Simons, M., Jensen, M.K., 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., Friedel, L., Finzel, A., Herrmann, A., 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., Kruse, S., Kostova, S., Hoffmann, S., Buntru, A., Tempelmeier, A., Secker, C., Diez, L., Schulz, A., Klockmeier, K., Zenkner, M., Golusik, S., Rau, K., Schnoegl, S., 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., Beck, M., 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., Sarma, U., Jentsch, M., Bohn, S., Sheng, C., Horbelt, D., Knaus, P., Legewie, S. and Loewer, A.
Molecular Systems Biology 14 (1): e7733. 25 January 2018

Subspecies in the global human gut microbiome.
Costea, P.I., Coelho, L.P., Sunagawa, S., Munch, R., Huerta-Cepas, J., Forslund, K., Hildebrand, F., Kushugulova, A., 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., Torlai Triglia, E., Risner-Janiczek, J.R., Rito, T., Rackham, O.J.L., De Santiago, I., Kukalev, A., Nicodemi, M., Akalin, A., Li, M., 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., Sieber, A., Wyler, E., Fritsche-Guenther, R., Meisig, J., Landthaler, M., 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., Zhang, B., Li, Y.S., Gao, Q., 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., Hou, J., 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., Teo, G., Krueger, S., Rock, T.M., Koh, H.W.L., 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., Ferrai, C., Chiariello, A.M., Schueler, M., Rito, T., Laudanno, G., Barbieri, M., Moore, B.L., Kraemer, D.C.A., Aitken, S., Xie, S.Q., Morris, K.J., Itoh, M., Kawaji, H., Jaeger, I., Hayashizaki, Y., Carninci, P., Forrest, A.R.R., Semple, C.A., Dostie, J., Pombo, A. and Nicodemi, M.
Molecular Systems Biology 11 (12): 852. 23 December 2015

Extensive allele-specific translational regulation in hybrid mice.
Hou, J., Wang, X., McShane, E., Zauber, H., Sun, W., 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., Sun, W., Ballegeer, M., 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., Delgado, J., Chen, W.-H., Llorens-Rico, V., O'Reilly, F.J., Wodke, J.A.H., Unal, E.B., Yus, E., Martinez, S., Nichols, R.J., Ferrar, T., Vivancos, A., Schmeisky, A., Stuelke, J., van Noort, V., Gavin, A.-C., 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., Tap, J., Voigt, A.Y., Sunagawa, S., Kultima, J.R., Costea, P.I., Amiot, A., Boehm, J., Brunetti, F., Habermann, N., Hercog, R., Koch, M., Luciani, A., Mende, D.R., Schneider, M.A., Schrotz-King, P., Tournigand, C., Tran Van Nhieu, J., Yamada, T., Zimmermann, J., Benes, V., Kloor, M., Ulrich, C.M., von Knebel Doeberitz, M., 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., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K.H., Runz, H., Gavin, A.C., Pepperkok, R., van Noort, V. and Bork, P.
Molecular Systems Biology 9 : 662. 2013

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

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

Novel biomarkers for pre-diabetes identified by metabolomics.
Wang-Sattler, R., Yu, Z., Herder, C., Messias, A.C., Floegel, A., He, Y., Heim, K., Campillos, M., Holzapfel, C., Thorand, B., Grallert, H., Xu, T., Bader, E., Huth, C., Mittelstrass, K., Doering, A., Meisinger, C., Gieger, C., Prehn, C., Roemisch-Margl, W., Carstensen, M., Xie, L., Yamanaka-Okumura, H., Xing, G., Ceglarek, U., Thiery, J., Giani, G., Lickert, H., Lin, X., Li, Y., Boeing, H., Joost, H.G., de Angelis, M.H., Rathmann, W., Suhre, K., Prokisch, H., Peters, A., Meitinger, T., Roden, M., Wichmann, H.E., Pischon, T., 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., Parca, L., Diella, F., Mende, D.R., Kumar, R., Helmer-Citterich, M., Gavin, A.C., 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., Waller, A.S., Raes, J., Zelezniak, A., Perchat, N., Perret, A., Salanoubat, M., Patil, K.R., Weissenbach, J. and Bork, P.
Molecular Systems Biology 8 : 581. 8 May 2012

Stimulus-dependent dynamics of p53 in single cells.
Batchelor, E., Loewer, A., 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., Letunic, I., Yamada, T., 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., Zhang, L., Megraw, M., Martinez, N.J., Jiang, E., Yi, C.S., Liu, W., Zeng, A., Taylor-Teeples, M., Kim, D., Ahnert, S., Ohler, U., Ware, D., 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., Campillos, M., Letunic, I., 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., Raes, J., Harris, J.K., Spear, J.R., Walker, J.J., Ivanova, N., von Mering, C., Bebout, B.M., Pace, N.R., 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., Boue, S., Krause, R., Jensen, L.J., Mason, C.E., Ghanim, M., White, K.P., 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., Bork, P., Krogan, N.J. and van Noort, V.
Molecular Systems Biology 9 : 714. 22 December 2013

Editorial

The rise of proteome-wide biophysics.
Mateus, A., 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., Karsenti, E., 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