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101 Reviews — EMBO Press — Systems Biology

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Genome-scale prediction of gene ontology from mass fingerprints reveals new metabolic gene functions
Vavricka, C., Mochizuki, M., Yuzawa, S., Murata, M., Yoshida, T., Watanabe, N., Nakatsui, M., Ishii, J., Hara, K., Alper, H. S., Hasunuma, T., Kondo, A., Araki, M.
10.1101/2024.11.27.625594 — Posted: 2024-12-02 — Discussion: 2025-10-01  EMBO Press
Transcriptional regulators ensuring specific gene expression and decision making at high TGFβ doses
Legewie, S., Hartmann, L., Kristofori, P., Lenhardt, S., Loewer, A., Hexemer, L., Becker, K., Bohn, S., Voss, B., Weiss, S., Li, C.
10.1101/2024.04.23.590740 — Posted: 2024-04-27 — Discussion: 2024-12-03  EMBO Press
A large-scale cancer-specific protein-DNA interaction network
Lu, Y., Berenson, A., Lane, R., Guelin, I., Li, Z., Chen, Y., Shah, S., Yin, M., Soto-Ugaldi, L. F., Fiszbein, A., Fuxman Bass, J. I.
10.1101/2024.01.24.577099 — Posted: 2024-01-29 — Discussion: 2024-07-30  EMBO Press
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
Ostaszewski, M., Niarakis, A., Mazein, A., Kuperstein, I., Phair, R., Orta-Resendiz, A., Singh, V., Aghamiri, S. S., Acencio, M. L., Glaab, E., Ruepp, A., Fobo, G., Montrone, C., Brauner, B., Frishman, G., Monraz Gomez, L. C., Somers, J., Hoch, M., Gupta, S. K., Scheel, J., Borlinghaus, H., Czauderna, T., Schreiber, F., Montagud, A., Ponce de Leon, M., Funahashi, A., Hiki, Y., Hiroi, N., Yamada, T. G., Drager, A., Renz, A., Naveez, M., Bocskei, Z., Messina, F., Bornigen, D., Fergusson, L., Conti, M., Rameil, M., Nakonecnij, V., Vanhoefer, J., Schmiester, L., Wang, M., Ackerman, E. E., Shoemake
10.1101/2020.10.26.356014 — Posted: 2020-10-28 — Discussion: 2024-05-29  EMBO Press
Suppression of Betacellulin expression is a key mechanism for omega-3 fatty acid mediated attenuation of nonalcoholic steatohepatitis
Padiadpu, J., Garcia-Jaramillo, M., Newman, N., Pederson, J., Rodrigues, R., Li, Z., Singh, S., Monnier, P., Trinchieri, G., Brown, K., Dzutsev, A. K., Shulzhenko, N., Jump, D. B., Morgun, A.
10.1101/2022.10.03.510635 — Posted: 2022-10-05 — Discussion: 2023-12-12  EMBO Press
Robust dimethyl-based multiplex-DIA workflow doubles single-cell proteome depth via a reference channel
Thielert, M., Itang, C. E. M., Ammar, C., Schober, F. A., Bludau, I., Skowronek, P., Wahle, M., Zeng, W.-F., Zhou, X.-X., Brunner, A.-D., Richter, S., Theis, F. J., Steger, M., Mann, M.
10.1101/2022.12.02.518917 — Posted: 2022-12-03 — Discussion: 2023-09-01  EMBO Press
N-terminal proteoforms may engage in different protein complexes
Bogaert, A., Fijalkowska, D., Staes, A., Van de Steene, T., Vuylsteke, M., Stadler, C., Eyckerman, S., Spirohn, K., Hao, T., Calderwood, M. A., Gevaert, K.
10.1101/2023.01.17.524352 — Posted: 2023-01-18 — Discussion: 2023-07-13  EMBO Press
Antibody reliability influences observed mRNA-protein correlations in tumour samples
Upadhya, S. R., Ryan, C. J.
10.1101/2022.12.23.521733 — Posted: 2022-12-23 — Discussion: 2023-07-13  EMBO Press
Missense variant interaction scanning reveals a critical role of the FERM-F3 domain for tumor suppressor protein NF2 conformation and function
Moesslacher, C. S., Woodsmith, J., Auernig, E., Feichtner, A., Jany-Luig, E., Jehle, S., Worseck, J. M., Stefan, E., Stelzl, U.
10.1101/2022.12.11.519953 — Posted: 2022-12-11 — Discussion: 2023-06-28  EMBO Press
Systems-level transcriptional regulation of Caenorhabditis elegans metabolism
Walhout, A. J., Nanda, S., Jacques, M.-A., Wang, W., Myers, C. L., Yilmaz, S.
10.1101/2022.11.08.515576 — Posted: 2022-11-09 — Discussion: 2023-06-02  EMBO Press

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