@article{UBHD-69155046,
  author={Alexandrov, Theodore and Sáez Rodríguez, Julio and Saka, Sinem},
  title={Enablers and challenges of spatial omics, a melting pot of technologies},
  year={2023},
  pages={1-16},
  language={eng},
  issn={1744-4292},
  volume={19},
  note={Online ver{\"o}ffentlicht: 16. Oktober 2023 ; Gesehen am 20.12.2023},
  journal={Molecular systems biology},
  doi={10.15252/msb.202110571},
}
@article{UBHD-68447424,
  author={Arnol, Damien and Sáez Rodríguez, Julio and Stegle, Oliver},
  title={Modeling cell-cell interactions from spatial molecular data with spatial variance component analysis},
  year={2019},
  pages={202-211.e6},
  language={eng},
  issn={2211-1247},
  volume={29},
  number={1},
  note={Gesehen am 29.10.2019},
  journal={Cell reports},
  doi={10.1016/j.celrep.2019.08.077},
}
@article{UBHD-69216044,
  author={Badia-i-Mompel, Pau and Wessels, Lorna and M{\"u}ller-Dott, Sophia and Trimbour, Rémi and Ramirez Flores, Ricardo O. and Argelaguet, Ricard and Sáez Rodríguez, Julio},
  title={Gene regulatory network inference in the era of single-cell multi-omics},
  year={2023},
  pages={739-754},
  language={eng},
  issn={1471-0064},
  volume={24},
  number={11 vom: Nov.},
  note={Online ver{\"o}ffentlicht: 26. Juni 2023 ; Gesehen am 21.05.2024},
  journal={Nature reviews},
  doi={10.1038/s41576-023-00618-5},
}
@article{UBHD-68988274,
  author={Barsi, Szilvia and Papp, Henrietta and Valdeolivas, Alberto and Tóth, Dániel J. and Kuczmog, Anett and Madai, Mónika and Hunyady, László and Várnai, Péter and Sáez Rodríguez, Julio and Jakab, Ferenc and Szalai, Bence},
  title={Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity},
  year={2022},
  pages={1-20},
  language={eng},
  issn={1553-7358},
  volume={18},
  note={Gesehen am 07.11.2023},
  journal={PLoS Computational Biology},
  doi={10.1371/journal.pcbi.1010021},
}
@article{UBHD-68432636,
  author={Behan, Fiona M. and Iorio, Francesco and Picco, Gabriele and Gonçalves, Emanuel and Beaver, Charlotte M. and Migliardi, Giorgia and Santos, Rita and Rao, Yanhua and Sassi, Francesco and Pinnelli, Marika and Ansari, Rizwan and Harper, Sarah and Jackson, David Adam and McRae, Rebecca and Pooley, Rachel and Wilkinson, Piers and Meer, Dieudonne van der and Dow, David and Buser-Doepner, Carolyn and Bertotti, Andrea and Trusolino, Livio and Stronach, Euan A. and Sáez Rodríguez, Julio and Yusa, Kosuke and Garnett, Mathew J.},
  title={Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens},
  year={2019},
  pages={511-516},
  language={eng},
  issn={1476-4687},
  volume={568},
  number={7753},
  note={Gesehen am 24.09.2019},
  journal={Nature},
  doi={10.1038/s41586-019-1103-9},
}
@article{UBHD-68794482,
  author={Bernardo Faura, Martí and Rinas, Melanie and Wirbel, Jakob and Pertsovskaya, Inna and Pliaka, Vicky and Messinis, Dimitris E. and Vila, Gemma and Sakellaropoulos, Theodore and Faigle, Wolfgang and Stridh, Pernilla and Behrens, Janina R. and Olsson, Tomas and Martin, Roland and Paul, Friedemann and Alexopoulos, Leonidas G. and Villoslada, Pablo and Sáez Rodríguez, Julio},
  title={Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis},
  year={2021},
  pages={1-16},
  language={eng},
  issn={1756-994X},
  volume={13},
  number={Artikel-ID 117},
  note={Gesehen am 28.10.2021},
  journal={Genome medicine},
  doi={10.1186/s13073-021-00925-8},
  url={https://doi.org/10.1186/s13073-021-00925-8},
  library={UB},
}
@article{UBHD-69308393,
  author={Billing, Anja M. and Kim, Young Chul and Gullaksen, Søren and Schrage, Benedikt and Raabe, Janice and Hutzfeldt, Arvid and Demir, Fatih and Kovalenko, Elina and Lassé, Moritz and Dugourd, Aurelien and Fallegger, Robin and Klampe, Birgit and Jaegers, Johannes and Li, Qing and Kravtsova, Olha and Crespo-Masip, Maria and Palermo, Amelia and Fenton, Robert A. and Hoxha, Elion and Blankenberg, Stefan and Kirchhof, Paulus and Huber, Tobias B. and Laugesen, Esben and Zeller, Tanja and Chrysopoulou, Maria and Sáez Rodríguez, Julio and Magnussen, Christina and Eschenhagen, Thomas and Staruschenko, Alexander and Siuzdak, Gary and Poulsen, Per L. and Schwab, Clarissa and Cuello, Friederike and Vallon, Volker and Rinschen, Markus M.},
  title={Metabolic communication by SGLT2 inhibition},
  year={2024},
  pages={860-884},
  language={eng},
  issn={1524-4539},
  volume={149},
  number={11 vom: M{\"a}rz},
  note={Online ver{\"o}ffentlicht 23. Dezember 2023 ; Gesehen am 25.02.2025},
  journal={Circulation},
  doi={10.1161/CIRCULATIONAHA.123.065517},
}
@article{UBHD-68654305,
  author={Buhl, Eva Miriam and Djudjaj, Sonja and Klinkhammer, Barbara M. and Ermert, Katja and Puelles, Victor G. and Lindenmeyer, Maja T. and Cohen, Clemens David and He, Chaoyong and Borkham-Kamphorst, Erawan and Weiskirchen, Ralf and Denecke, Bernd and Trairatphisan, Panuwat and Sáez Rodríguez, Julio and Huber, Tobias B. and Olson, Lorin E. and Floege, J{\"u}rgen and Boor, Peter},
  title={Dysregulated mesenchymal PDGFR-β drives kidney fibrosis},
  year={2020},
  language={eng},
  issn={1757-4684},
  volume={12(2020},
  note={Gesehen am 27.10.2020},
  journal={EMBO molecular medicine},
  doi={10.15252/emmm.201911021},
}
@article{UBHD-68874281,
  author={Callegaro, Giulia and Kunnen, Steven J. and Trairatphisan, Panuwat and Grosdidier, Solène and Niemeijer, Marije and den Hollander, Wouter and Guney, Emre and Piñero Gonzalez, Janet and Furlong, Laura and Webster, Yue W. and Sáez Rodríguez, Julio and Sutherland, Jeffrey J. and Mollon, Jennifer and Stevens, James L. and van de Water, Bob},
  title={The human hepatocyte TXG-MAPr},
  subtitle={gene co-expression network modules to support mechanism-based risk assessment},
  year={2021},
  pages={3745-3775},
  language={eng},
  issn={1432-0738},
  volume={95},
  number={12},
  note={Gesehen am 04.02.2022},
  journal={Archives of toxicology},
  doi={10.1007/s00204-021-03141-w},
}
@article{UBHD-68721206,
  author={Cappelletti, Valentina and Hauser, Thomas and Piazza, Ilaria and Pepelnjak, Monika and Malinovska, Liliana and Fuhrer, Tobias and Li, Yaozong and D{\"o}rig, Christian and Boersema, Paul and Gillet, Ludovic and Grossbach, Jan and Dugourd, Aurélien and Sáez Rodríguez, Julio and Beyer, Andreas and Zamboni, Nicola and Caflisch, Amedeo and de Souza, Natalie and Picotti, Paola},
  title={Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ},
  year={2021},
  pages={545-559},
  language={eng},
  issn={1097-4172},
  volume={184},
  number={2},
  note={Das PDF enth{\"a}lt zus{\"a}tzlich einen Anhang von 13 Seiten ; Available online 23 December 2020 ; Gesehen am 08.09.2021},
  journal={Cell},
  doi={10.1016/j.cell.2020.12.021},
}
@article{UBHD-68563921,
  author={Ceccarelli, Francesco and Turei, Denes and Gabor, Attila and Sáez Rodríguez, Julio},
  title={Bringing data from curated pathway resources to cytoscape with OmniPath},
  year={2020},
  pages={2632-2633},
  language={eng},
  issn={1367-4811},
  volume={36},
  number={8},
  note={Advance access publication date: 30 December 2019 ; Gesehen am 25.03.2021},
  journal={Bioinformatics},
  doi={10.1093/bioinformatics/btz968},
}
@article{UBHD-68563960,
  author={Choobdar, Sarvenaz and Ahsen, Mehmet Eren and Crawford, Jake and Tomasoni, Mattia and Fang, Tao and Lamparter, David and Lin, Junyuan and Hescott, Benjamin and Hu, Xiaozhe and Mercer, Johnathan and Natoli, Ted and Narayan, Rajiv and Subramanian, Aravind and Zhang, Jitao D. and Stolovitzky, Gustavo and Kutalik, Zoltán and Lage, Kasper and Slonim, Donna K. and Sáez Rodríguez, Julio and Cowen, Lenore J. and Bergmann, Sven and Marbach, Daniel},
  title={Assessment of network module identification across complex diseases},
  year={2019},
  pages={843-852},
  language={eng},
  issn={1548-7105},
  volume={16},
  number={9},
  note={Gesehen am 14.04.2020},
  journal={Nature methods},
  doi={10.1038/s41592-019-0509-5},
}
@article{UBHD-68957274,
  author={Dimitrov, Daniel and T{\"u}rei, Dénes and Garrido-Rodriguez, Martin and Burmedi, Paul L. and Nagai, James S. and Boys, Charlotte and Ramirez Flores, Ricardo O. and Kim, Hyojin and Szalai, Bence and Costa, Ivan G. and Valdeolivas, Alberto and Dugourd, Aurélien and Sáez Rodríguez, Julio},
  title={Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data},
  year={2022},
  pages={1-13},
  language={eng},
  issn={2041-1723},
  volume={13},
  number={Artikel-ID 3224},
  note={Gesehen am 25.08.2022},
  journal={Nature Communications},
  doi={10.1038/s41467-022-30755-0},
  url={https://doi.org/10.1038/s41467-022-30755-0},
  library={UB},
}
@article{UBHD-69260053,
  author={Dimitrov, Daniel and Sch{\"a}fer, Philipp and Farr, Elias and Rodriguez Mier, Pablo and Lobentanzer, Sebastian and Badia-i-Mompel, Pau and Dugourd, Aurélien and Tanevski, Jovan and Ramirez Flores, Ricardo O. and Sáez Rodríguez, Julio},
  title={LIANA+ provides an all-in-one framework for cell-cell communication inference},
  year={2024},
  pages={1613-1622},
  language={eng},
  issn={1476-4679},
  volume={26},
  number={9},
  note={Gesehen am 07.10.2024},
  journal={Nature cell biology},
  doi={10.1038/s41556-024-01469-w},
}
@article{UBHD-68999776,
  author={Douglass, Eugene F. and Allaway, Robert J. and Szalai, Bence and Wang, Wenyu and Tian, Tingzhong and Fernández-Torras, Adrià and Realubit, Ron and Karan, Charles and Zheng, Shuyu and Pessia, Alberto and Tanoli, Ziaurrehman and Jafari, Mohieddin and Wan, Fangping and Li, Shuya and Xiong, Yuanpeng and Duran-Frigola, Miquel and Bertoni, Martino and Badia-i-Mompel, Pau and Mateo, Lídia and Guitart-Pla, Oriol and Chung, Verena and Tang, Jing and Zeng, Jianyang and Aloy, Patrick and Sáez Rodríguez, Julio and Guinney, Justin and Gerhard, Daniela S. and Califano, Andrea},
  title={A community challenge for a pancancer drug mechanism of action inference from perturbational profile data},
  year={2022},
  pages={20 S.},
  language={eng},
  issn={2666-3791},
  volume={3},
  note={Gesehen am 20.12.2022},
  journal={Cell reports},
  doi={10.1016/j.xcrm.2021.100492},
}
@article{UBHD-68867739,
  author={Dr{\"a}ger, Andreas and Helikar, Tomáš and Barberis, Matteo and Birtwistle, Marc and Calzone, Laurence and Chaouiya, Claudine and Hasenauer, Jan and Karr, Jonathan R. and Niarakis, Anna and Rodríguez Martínez, María and Sáez Rodríguez, Julio and Thakar, Juilee},
  title={SysMod},
  subtitle={the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems},
  year={2021},
  pages={3702-3706},
  language={eng},
  issn={1367-4811},
  volume={37},
  number={11},
  note={Gesehen am 19.01.2022},
  journal={Bioinformatics},
  doi={10.1093/bioinformatics/btab229},
}
@article{UBHD-68707532,
  author={Dugourd, Aurélien and Gjerga, Enio and Gabor, Attila and Sáez Rodríguez, Julio and Kuppe, Christoph and Sciacovelli, Marco and Emdal, Kristina B. and Vieira, Vitor and Bekker-Jensen, Dorte B. and Kranz, Jennifer and Bindels, Eric M. J. and Costa, Ana S. H. and Sousa, Abel and Beltrao, Pedro and Rocha, Miguel and Olsen, Jesper V. and Frezza, Christian and Kramann, Rafael},
  title={Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses},
  year={2021},
  pages={1-17},
  language={eng},
  issn={1744-4292},
  volume={17},
  note={Gesehen am 05.05.2022},
  journal={Molecular systems biology},
  doi={10.15252/msb.20209730},
  url={https://doi.org/10.15252/msb.20209730},
  library={UB},
}
@article{UBHD-68410900,
  author={Eduati, Federica and Longerich, Thomas and Sáez Rodríguez, Julio},
  title={A microfluidics platform for combinatorial drug screening on cancer biopsies},
  year={2018},
  pages={13 S.},
  language={eng},
  issn={2041-1723},
  volume={9(2018) Article number: 2434},
  number={13 Seiten},
  note={Gesehen am 22.07.2019},
  journal={Nature Communications},
  doi={10.1038/s41467-018-04919-w},
}
@article{UBHD-68653906,
  author={Eduati, Federica and Jaaks, Patricia and Wappler, Jessica and Cramer, Thorsten and Merten, Christoph and Garnett, Mathew J and Sáez Rodríguez, Julio},
  title={Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies},
  year={2020},
  pages={13 S.},
  language={eng},
  issn={1744-4292},
  volume={16(2020},
  note={Gesehen am 26.10.2020},
  journal={Molecular systems biology},
  doi={10.15252/msb.20188664},
}
@article{UBHD-68435831,
  author={Ellrott, Kyle and Sáez Rodríguez, Julio},
  title={Reproducible biomedical benchmarking in the cloud},
  subtitle={lessons from crowd-sourced data challenges},
  year={2019},
  pages={9 S.},
  language={eng},
  issn={1474-760X},
  volume={20(2019) Artikel-Nummer 195},
  number={9 Seiten},
  note={Gesehen am 07.10.2019},
  journal={Genome biology},
  doi={10.1186/s13059-019-1794-0},
}
@article{UBHD-69010928,
  author={Emdal, Kristina B. and Palacio-Escat, Nicolàs and Wigerup, Caroline and Eguchi, Akihiro and Nilsson, Helén and Bekker-Jensen, Dorte B. and R{\"o}nnstrand, Lars and Kazi, Julhash U. and Puissant, Alexandre and Itzykson, Raphaël and Sáez Rodríguez, Julio and Masson, Kristina and Blume-Jensen, Peter and Olsen, Jesper V.},
  title={Phosphoproteomics of primary AML patient samples reveals rationale for AKT combination therapy and p53 context to overcome selinexor resistance},
  year={2022},
  pages={24 S.},
  language={eng},
  issn={2211-1247},
  volume={40},
  note={Gesehen am 27.01.2023},
  journal={Cell reports},
  doi={10.1016/j.celrep.2022.111177},
}
@article{UBHD-69224172,
  author={Engblom, Camilla and Thrane, Kim and Lin, Qirong and Andersson, Alma and Toosi, Hosein and Chen, Xinsong and Steiner, Embla and Lu, Chang and Mantovani, Giulia and Hagemann-Jensen, Michael and Saarenp{\"a}{\"a}, Sami and Jangard, Mattias and Sáez Rodríguez, Julio and Michaëlsson, Jakob and Hartman, Johan and Lagergren, Jens and Mold, Jeff E. and Lundeberg, Joakim and Frisén, Jonas},
  title={Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics},
  year={2023},
  pages={1-17},
  language={eng},
  issn={1095-9203},
  volume={382},
  note={Gesehen am 18.06.2024},
  journal={Science},
  doi={10.1126/science.adf8486},
}
@article{UBHD-69339848,
  author={Farr, Elias and Dimitrov, Daniel and Schmidt, Christina and T{\"u}rei, Dénes and Lobentanzer, Sebastian and Dugourd, Aurélien and Sáez Rodríguez, Julio},
  title={MetalinksDB},
  subtitle={a flexible and contextualizable resource of metabolite-protein interactions},
  year={2024},
  pages={bbae347$p1-12},
  language={eng},
  issn={1477-4054},
  volume={25},
  number={4 vom: Juli},
  note={Ver{\"o}ffentlicht: 22. Juli 2024 ; Gesehen am 28.04.2025},
  journal={Briefings in bioinformatics},
  doi={10.1093/bib/bbae347},
}
@article{UBHD-69055996,
  author={Frede, Annika and Czarnewski, Paulo and Monasterio, Gustavo and Tripathi, Kumar P. and Bejarano, David A. and Ramirez Flores, Ricardo O. and Sorini, Chiara and Larsson, Ludvig and Luo, Xinxin and Geerlings, Laura and Novella-Rausell, Claudio and Zagami, Chiara and Kuiper, Raoul and Morales, Rodrigo A. and Castillo, Francisca and Hunt, Matthew and Mariano, Livia Lacerda and Hu, Yue O. O. and Engblom, Camilla and Lennon-Duménil, Ana-Maria and Mittenzwei, Romy and Westendorf, Astrid M. and H{\"o}velmeyer, Nadine and Lundeberg, Joakim and Sáez Rodríguez, Julio and Schlitzer, Andreas and Das, Srustidhar and Villablanca, Eduardo J.},
  title={B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing},
  year={2022},
  pages={28 S.},
  language={eng},
  issn={1097-4180},
  volume={55},
  note={Online ver{\"o}ffentlicht am 2. Dezember 2022, Artikelversion vom 13. Dezember 2022 ; Gesehen am 28.11.2023},
  journal={Immunity},
  doi={10.1016/j.immuni.2022.11.002},
}
@article{UBHD-69240989,
  author={Fuchs, Stijn and Stalmann, Ursula S. A. and Snoeren, Inge A. M. and Bindels, Eric and Schmitz, Stephani and Banjanin, Bella and Hoogenboezem, Remco M. and van Herk, Stanley and Saad, Mohamed and Walter, Wencke and Haferlach, Torsten and Seillier, Lancelot and Sáez Rodríguez, Julio and Dugourd, Aurélien and Lehmann, Kjong-Van and Ben-Neriah, Yinon and Gleitz, Hélène F. E. and Schneider, Rebekka K.},
  title={Collaborative effect of Csnk1a1 haploinsufficiency and mutant p53 in Myc induction can promote leukemic transformation},
  year={2024},
  pages={766-779},
  language={eng},
  issn={2473-9537},
  volume={8},
  number={3},
  note={Gesehen am 06.08.2024},
  journal={Blood advances},
  doi={10.1182/bloodadvances.2022008926},
}
@article{UBHD-68870863,
  author={Gabor, Attila and Tognetti, Marco and Driessen, Alice and Tanevski, Jovan and Guo, Baosen and Cao, Wencai and Shen, He and Yu, Thomas and Chung, Verena and Bodenmiller, Bernd and Sáez Rodríguez, Julio},
  title={Cell-to-cell and type-to-type heterogeneity of signaling networks},
  subtitle={insights from the crowd},
  year={2021},
  pages={1-16},
  language={eng},
  issn={1744-4292},
  volume={17},
  note={Gesehen am 26.01.2022},
  journal={Molecular systems biology},
  doi={10.15252/msb.202110402},
}
@article{UBHD-68441507,
  author={Gajjala, Prathibha Reddy and Sáez Rodríguez, Julio},
  title={Novel plasma peptide markers involved in the pathology of CKD identified using mass spectrometric approach},
  year={2019},
  pages={1451-1463},
  language={eng},
  issn={1432-1440},
  volume={97},
  number={10},
  note={Gesehen am 17.10.2019},
  journal={Journal of molecular medicine},
  doi={10.1007/s00109-019-01823-8},
}
@article{UBHD-68478911,
  author={Garcia-Alonso, Luz and Holland, Christian H. and Sáez Rodríguez, Julio},
  title={Benchmark and integration of resources for the estimation of human transcription factor activities},
  year={2019},
  pages={1363-1375},
  language={eng},
  issn={1549-5469},
  volume={29},
  number={8},
  note={Gesehen am 21.01.2020},
  journal={Genome research},
  doi={10.1101/gr.240663.118},
}
@article{UBHD-68957357,
  author={Garrido-Rodriguez, Martin and Zirngibl, Katharina and Ivanova, Olga A. and Lobentanzer, Sebastian and Sáez Rodríguez, Julio},
  title={Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks},
  year={2022},
  pages={1-15},
  language={eng},
  issn={1744-4292},
  volume={18},
  note={Gesehen am 25.08.2022},
  journal={Molecular systems biology},
  doi={10.15252/msb.202211036},
}
@article{UBHD-69006758,
  author={Gegner, Hagen M. and Naake, Thomas and Dugourd, Aurélien and M{\"u}ller, Torsten and Czernilofsky, Felix and Kliewer, Georg and J{\"a}ger, Evelyn and Helm, Barbara and Kunze-Rohrbach, Nina and Klingm{\"u}ller, Ursula and Hopf, Carsten and M{\"u}ller-Tidow, Carsten and Dietrich, Sascha and Sáez Rodríguez, Julio and Huber, Wolfgang and Hell, R{\"u}diger and Poschet, Gernot and Krijgsveld, Jeroen},
  title={Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis},
  year={2022},
  pages={1-13},
  language={eng},
  issn={2296-889X},
  volume={9},
  number={Artikel-ID 961448},
  note={Gesehen am 16.01.2023},
  journal={Frontiers in molecular biosciences},
  doi={10.3389/fmolb.2022.961448},
  url={https://doi.org/10.3389/fmolb.2022.961448},
  library={UB},
}
@article{UBHD-69289211,
  author={Gegner, Hagen M. and Naake, Thomas and Aljakouch, Karim and Dugourd, Aurélien and Kliewer, Georg and M{\"u}ller, Torsten and Schilling, Dustin and Schneider, Marc and Kunze-Rohrbach, Nina and Gr{\"u}newald, Thomas G. P. and Hell, R{\"u}diger and Sáez Rodríguez, Julio and Huber, Wolfgang and Poschet, Gernot and Krijgsveld, Jeroen},
  title={A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens},
  year={2024},
  pages={1-17},
  language={eng},
  issn={1559-0275},
  volume={21},
  number={Artikel-ID 49},
  note={Gesehen am 10.01.2025},
  journal={Clinical proteomics},
  doi={10.1186/s12014-024-09501-9},
}
@article{UBHD-68491143,
  author={Ghallab, Ahmed and Holland, Christian H. and Sáez Rodríguez, Julio},
  title={Influence of liver fibrosis on lobular zonation},
  year={2019},
  pages={21 S.},
  language={eng},
  issn={2073-4409},
  volume={8(2019},
  note={Gesehen am 19.02.2020},
  journal={Cells},
  doi={10.3390/cells8121556},
}
@article{UBHD-69181568,
  author={Ghasemi, David R. and Okonechnikov, Konstantin and Rademacher, Anne and Tirier, Stephan Marius and Maaß, Kendra K. and Schumacher, Hanna and Joshi, Piyush and Gold, Maxwell P. and Sundheimer, Julia and Statz, Britta and Rifaioglu, Ahmet and Bauer, Katharina and Schumacher, Sabrina and Bortolomeazzi, Michele and Giangaspero, Felice and Ernst, Kati and Clifford, Steven C. and Sáez Rodríguez, Julio and Jones, David T. W. and Kawauchi, Daisuke and Fraenkel, Ernest and Mallm, Jan-Philipp and Rippe, Karsten and Korshunov, Andrey and Pfister, Stefan and Pajtler, Kristian Wilfried},
  title={Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage},
  year={2024},
  pages={1-20},
  language={eng},
  issn={2041-1723},
  volume={15},
  number={Artikel-ID 269},
  note={Gesehen am 13.02.2024},
  journal={Nature Communications},
  doi={10.1038/s41467-023-44117-x},
}
@article{UBHD-68697186,
  author={Gjerga, Enio and Trairatphisan, Panuwat and Gabor, Attila and Koch, Hermann and Chevalier, Celine and Ceccarelli, Franceco and Dugourd, Aurélien and Mitsos, Alexander and Sáez Rodríguez, Julio},
  title={Converting networks to predictive logic models from perturbation signalling data with CellNOpt},
  year={2020},
  pages={4523-4524},
  language={eng},
  issn={1367-4811},
  volume={36},
  number={16},
  note={Gesehen am 09.02.2021},
  journal={Bioinformatics},
  doi={10.1093/bioinformatics/btaa561},
}
@article{UBHD-68740248,
  author={Gjerga, Enio and Dugourd, Aurélien and Tobalina, Luis and Sousa, Abel and Sáez Rodríguez, Julio},
  title={PHONEMeS},
  subtitle={efficient modeling of signaling networks derived from large-scale mass spectrometry data},
  year={2021},
  pages={2138-2144},
  language={eng},
  issn={1535-3907},
  volume={20},
  number={4},
  note={Gesehen am 21.05.2021},
  journal={Journal of proteome research},
  doi={10.1021/acs.jproteome.0c00958},
}
@article{UBHD-68665956,
  author={Gleitz, Hélène and Dugourd, Aurélien and Sáez Rodríguez, Julio},
  title={Increased CXCL4 expression in hematopoietic cells links inflammation and progression of bone marrow fibrosis in MPN},
  year={2020},
  pages={2051-2064},
  language={eng},
  issn={1528-0020},
  volume={136},
  number={18},
  note={Gesehen am 26.11.2020},
  journal={Blood},
  doi={10.1182/blood.2019004095},
}
@article{UBHD-68422279,
  author={Gonzalez, Patricia and Arg{\"u}eso-Alejandro, Pablo and Penas, David R. and Pardo, Xoan C. and Sáez Rodríguez, Julio and Banga, Julio R. and Doallo, Ramón},
  title={Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology},
  year={2019},
  pages={3471-3498},
  language={eng},
  issn={1573-0484},
  volume={75},
  number={7},
  note={Gesehen am 20.08.2019},
  journal={The journal of supercomputing},
  doi={10.1007/s11227-019-02871-0},
}
@article{UBHD-69007058,
  author={Gonzalez, Patricia and Prado-Rodriguez, Roberto and Gabor, Attila and Sáez Rodríguez, Julio and Banga, Julio R. and Doallo, Ramón},
  title={Parallel ant colony optimization for the training of cell signaling networks},
  year={2022},
  pages={1-16},
  language={eng},
  volume={208(2022) vom: Dez.},
  number={Artikel-ID 118199},
  note={Gesehen am 08.11.2023},
  journal={Expert systems with applications},
  doi={10.1016/j.eswa.2022.118199},
}
@article{UBHD-68560567,
  author={Holland, Christian H. and Tanevski, Jovan and Perales-Patón, Javier and Gleixner, Jan and Kumar, Manu P. and Mereu, Elisabetta and Joughin, Brian A. and Stegle, Oliver and Lauffenburger, Douglas A. and Heyn, Holger and Szalai, Bence and Sáez Rodríguez, Julio},
  title={Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data},
  year={2020},
  pages={19 S.},
  language={eng},
  issn={1474-760X},
  volume={21(2020) Artikel-Nummer 36},
  note={Gesehen am 02.04.2020},
  journal={Genome biology},
  doi={10.1186/s13059-020-1949-z},
}
@article{UBHD-68583943,
  author={Holland, Christian H. and Szalai, Bence and Sáez Rodríguez, Julio},
  title={Transfer of regulatory knowledge from human to mouse for functional genomics analysis},
  year={2020},
  pages={8 S.},
  language={eng},
  issn={1876-4320},
  volume={1863(2020},
  note={Available online: 13 September 2019 ; Gesehen am 04.06.2020},
  journal={Biochimica et biophysica acta},
  doi={10.1016/j.bbagrm.2019.194431},
}
@book{UBHD-68328258,
  author={Iorio, Francesco and Sáez Rodríguez, Julio},
  title={Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting},
  publisher={BioMed Central ; Springer},
  address={London ; Berlin ; Heidelberg},
  year={2018},
  pages={1 Online-Ressource (16 Seiten)},
  language={eng},
  note={Aus: BMC Genomics, 19 (2018), Nr. 604. pp. 1-16. ISSN 1471-2164},
  doi={10.1186/s12864-018-4989-y},
  url={https://nbn-resolving.org/urn:nbn:de:bsz:16-heidok-254444},
  library={UB},
}
@article{UBHD-68957343,
  author={Kay, Emily J. and Paterson, Karla and Riera-Domingo, Carla and Sumpton, David and D{\"a}britz, J. Henry M. and Tardito, Saverio and Boldrini, Claudia and Hernandez-Fernaud, Juan R. and Athineos, Dimitris and Dhayade, Sandeep and Stepanova, Ekaterina and Gjerga, Enio and Neilson, Lisa J. and Lilla, Sergio and Hedley, Ann and Koulouras, Grigorios and McGregor, Grace and Jamieson, Craig and Johnson, Radia Marie and Park, Morag and Kirschner, Kristina and Miller, Crispin and Kamphorst, Jurre J. and Loayza-Puch, Fabricio and Sáez Rodríguez, Julio and Mazzone, Massimiliano and Blyth, Karen and Zagnoni, Michele and Zanivan, Sara},
  title={Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix},
  year={2022},
  pages={693-710},
  language={eng},
  issn={2522-5812},
  volume={4},
  number={6},
  note={Gesehen am 25.08.2022 ; Correction to: Nature Metabolism https://doi.org/10.1038/s42255-022-00582-0, published online 27 June 2022: In the version of this article initially published, the surname of the third author, Carla Riera-Domingo, was misspelled as Riero-Domingo. The error has been corrected in the HTML and PDF versions of the article},
  journal={Nature metabolism},
  doi={10.1038/s42255-022-00582-0},
}
@article{UBHD-69245504,
  author={Kennedy, Keith Endres and Rosbo, Nicole Kerlero de and Uccelli, Antonio and Cellerino, Maria and Ivaldi, Federico and Contini, Paola and Palma, Raffaele De and Harbo, Hanne F. and Berge, Tone and Bos, Steffan D. and Høgestøl, Einar A. and Brune-Ingebretsen, Synne and Benavent, Sigrid A. de Rodez and Paul, Friedemann and Brandt, Alexander U. and B{\"a}cker-Koduah, Priscilla and Behrens, Janina and Kuchling, Joseph and Asseyer, Susanna and Scheel, Michael and Chien, Claudia and Zimmermann, Hanna and Motamedi, Seyedamirhosein and Kauer-Bonin, Josef and Sáez Rodríguez, Julio and Rinas, Melanie and Alexopoulos, Leonidas G. and Andorra, Magi and Llufriu, Sara and Saiz, Albert and Blanco, Yolanda and Martinez-Heras, Eloy and Solana, Elisabeth and Pulido-Valdeolivas, Irene and Martinez-Lapiscina, Elena H. and Garcia-Ojalvo, Jordi and Villoslada, Pablo},
  title={Multiscale networks in multiple sclerosis},
  year={2024},
  pages={1-35},
  language={eng},
  issn={1553-7358},
  volume={20},
  note={Gesehen am 20.08.2024},
  journal={PLoS Computational Biology},
  doi={10.1371/journal.pcbi.1010980},
}
@article{UBHD-68489593,
  author={Kotelnikova, Ekaterina and Sáez Rodríguez, Julio},
  title={MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis},
  year={2019},
  pages={9671-9676},
  language={eng},
  issn={1091-6490},
  volume={116},
  number={19},
  note={Gesehen am 17.02.2020},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  doi={10.1073/pnas.1818347116},
}
@article{UBHD-69210244,
  author={Kuppe, Christoph and Ibrahim, Mahmoud M. and Kranz, Jennifer and Zhang, Xiaoting and Ziegler, Susanne and Perales-Patón, Javier and Jansen, Jitske and Reimer, Katharina C. and Smith, James R. and Dobie, Ross and Wilson-Kanamori, John R. and Halder, Maurice and Xu, Yaoxian and Kabgani, Nazanin and Kaesler, Nadine and Klaus, Martin and Gernhold, Lukas and Puelles, Victor G. and Huber, Tobias and Boor, Peter and Menzel, Sylvia and Hoogenboezem, Remco M. and Bindels, Eric M. J. and Steffens, Joachim and Fl{\"o}ge, J{\"u}rgen and Schneider, Rebekka K. and Sáez Rodríguez, Julio and Henderson, Neil C. and Kramann, Rafael},
  title={Decoding myofibroblast origins in human kidney fibrosis},
  year={2021},
  pages={281-286},
  language={eng},
  issn={1476-4687},
  volume={589(2021) vom: Jan.},
  note={Gesehen am 02.05.2024 ; Online ver{\"o}ffentlicht: 11 November 2020},
  journal={Nature},
  doi={10.1038/s41586-020-2941-1},
}
@article{UBHD-68995866,
  author={Kuppe, Christoph and Perales-Patón, Javier and Sáez Rodríguez, Julio and Kramann, Rafael},
  title={Experimental and computational technologies to dissect the kidney at the single-cell level},
  year={2022},
  pages={628-637},
  language={eng},
  issn={1460-2385},
  volume={37},
  number={4},
  note={Online ver{\"o}ffentlicht am 17. Dezember 2020 ; Gesehen am 12.12.2022},
  journal={Nephrology, dialysis, transplantation},
  doi={10.1093/ndt/gfaa233},
}
@article{UBHD-68805330,
  author={Lanzer, Jan David and Leuschner, Florian and Kramann, Rafael and Levinson, Rebecca T. and Sáez Rodríguez, Julio},
  title={Big data approaches in heart failure research},
  year={2020},
  pages={213-224},
  language={eng},
  issn={1546-9549},
  volume={17},
  number={5},
  note={Gesehen am 25.11.2021},
  journal={Current heart failure reports},
  doi={10.1007/s11897-020-00469-9},
  url={https://doi.org/10.1007/s11897-020-00469-9},
  library={UB},
}
@article{UBHD-69125903,
  author={Lanzer, Jan David and Valdeolivas, Alberto and Pepin, Mark and Hund, Hauke and Backs, Johannes and Frey, Norbert and Friederich, Hans-Christoph and Schultz, Jobst-Hendrik and Sáez Rodríguez, Julio and Levinson, Rebecca T.},
  title={A network medicine approach to study comorbidities in heart failure with preserved ejection fraction},
  year={2023},
  pages={1-21},
  language={eng},
  issn={1741-7015},
  volume={21},
  number={Artikel-ID 267},
  note={Ver{\"o}ffentlicht: 24. Juli 2023 ; Gesehen am 02.10.2023},
  journal={BMC medicine},
  doi={10.1186/s12916-023-02922-7},
}
@article{UBHD-69320560,
  author={Lanzer, Jan David and Wienecke, Laura Marie and Ramirez Flores, Ricardo O. and Zylla, Maura Magdalena and Kley, Celina and Hartmann, Niklas and Sicklinger, Florian and Schultz, Jobst-Hendrik and Frey, Norbert and Sáez Rodríguez, Julio and Leuschner, Florian},
  title={Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction},
  year={2024},
  pages={1001-1028},
  language={eng},
  issn={1435-1803},
  volume={119},
  number={6},
  note={Gesehen am 20.03.2025},
  journal={Basic research in cardiology},
  doi={10.1007/s00395-024-01074-w},
}
@article{UBHD-68798824,
  author={Lanzer, Peter and Hannan, Fadil M. and Lanzer, Jan David and Janzen, Jan and Raggi, Paolo and Furniss, Dominic and Schuchardt, Mirjam and Thakker, Rajesh and Fok, Pak-Wing and Sáez Rodríguez, Julio and Millan, Angel and Sato, Yu and Ferraresi, Roberto and Virmani, Renu and St. Hilaire, Cynthia},
  title={Medial arterial calcification},
  subtitle={JACC state-of-the-art review},
  year={2021},
  pages={1145-1165},
  language={eng},
  issn={1558-3597},
  volume={78},
  number={11 vom: 14. Sept.},
  note={Gesehen am 10.11.2021},
  journal={Journal of the American College of Cardiology},
  doi={10.1016/j.jacc.2021.06.049},
}
@article{UBHD-69277318,
  author={Laury, Anna and Zheng, Shuyu and Aho, Niina and Fallegger, Robin and H{\"a}nninen, Satu and Sáez Rodríguez, Julio and Tanevski, Jovan and Youssef, Omar and Tang, Jing and Carpén, Olli Mikael},
  title={Opening the black box},
  subtitle={spatial transcriptomics and the relevance of artificial intelligence-detected prognostic regions in high-grade serous carcinoma},
  year={2024},
  pages={1-12},
  language={eng},
  issn={1530-0285},
  volume={37},
  note={Online verf{\"u}gbar: 3. Mai 2024, Artikelversion: 29. Mai 2024 ; Gesehen am 27.11.2024},
  journal={Modern pathology},
  doi={10.1016/j.modpat.2024.100508},
}
@article{UBHD-69331015,
  author={Lerma Martin, Celia and Badia-i-Mompel, Pau and Ramirez Flores, Ricardo O. and Sekol, Patricia and Sch{\"a}fer, Philipp and Riedl, Christian J. and Hofmann, Annika and Th{\"a}wel, Thomas and W{\"u}nnemann, Florian and Ibarra-Arellano, Miguel A. and Trobisch, Tim and Eisele, Philipp and Schapiro, Denis and Haeussler, Maximilian and Hametner, Simon and Sáez Rodríguez, Julio and Schirmer, Lucas},
  title={Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions},
  year={2024},
  pages={2354-2365},
  language={eng},
  issn={1546-1726},
  volume={27},
  number={12 vom: Dez.},
  note={Online ver{\"o}ffentlicht: 5. November 2024 ; Gesehen am 14.04.2025},
  journal={Nature neuroscience},
  doi={10.1038/s41593-024-01796-z},
}
@article{UBHD-68559252,
  author={Liu, Anika and Trairatphisan, Panuwat and Gjerga, Enio and Sáez Rodríguez, Julio},
  title={From expression footprints to causal pathways},
  subtitle={contextualizing large signaling networks with CARNIVAL},
  year={2019},
  pages={10 S.},
  language={eng},
  issn={2056-7189},
  volume={5(2019},
  note={Gesehen am 30.03.2020 ; Anika Liu, Panuwat Trairatphisan and Enio Gjerga contributed equally},
  journal={npj Systems biology and applications},
  doi={10.1038/s41540-019-0118-z},
}
@article{UBHD-68373849,
  author={Liu, Yansheng and Sáez Rodríguez, Julio},
  title={Multi-omic measurements of heterogeneity in HeLa cells across laboratories},
  year={2019},
  pages={314-322},
  language={eng},
  issn={1546-1696},
  volume={37},
  number={3},
  note={Gesehen am 28.03.2019},
  journal={Nature biotechnology},
  doi={10.1038/s41587-019-0037-y},
}
@article{UBHD-69274819,
  author={Lobentanzer, Sebastian and Rodriguez Mier, Pablo and Bauer, Stefan and Sáez Rodríguez, Julio},
  title={Molecular causality in the advent of foundation models},
  year={2024},
  pages={848-858},
  language={eng},
  issn={1744-4292},
  volume={20},
  number={8 vom: Aug.},
  note={Online ver{\"o}ffentlicht: 18. Juni 2024 ; Gesehen am 19.11.2024},
  journal={Molecular systems biology},
  doi={10.1038/s44320-024-00041-w},
}
@article{UBHD-68874258,
  author={Lone, Anna Mari and Giansanti, Piero and Jørgensen, Marthe Jøntvedt and Gjerga, Enio and Dugourd, Aurélien and Scholten, Arjen and Sáez Rodríguez, Julio and Heck, Albert J. R. and Taskén, Kjetil},
  title={Systems approach reveals distinct and shared signaling networks of the four PGE2 receptors in T cells},
  year={2021},
  pages={1-19},
  language={eng},
  issn={1937-9145},
  volume={14},
  note={Im Titel ist "2" tiefgestellt ; Gesehen am 04.02.2022},
  journal={Science signaling},
  doi={10.1126/scisignal.abc8579},
}
@article{UBHD-68747814,
  author={Lopez-Dominguez, Raul and Toro-Dominguez, Daniel and Martorell-Marugan, Jordi and Garcia-Moreno, Adrian and Holland, Christian H. and Sáez Rodríguez, Julio and Goldman, Daniel and Petri, Michelle A. and Alarcón-Riquelme, Marta E. and Carmona-Saez, Pedro},
  title={Transcription factor activity inference in Systemic Lupus Erythematosus},
  year={2021},
  pages={1-12},
  language={eng},
  issn={2075-1729},
  volume={11},
  note={Gesehen am 14.06.2021},
  journal={Life},
  doi={10.3390/life11040299},
}
@article{UBHD-68421206,
  author={Lun, Xiaokang and Sáez Rodríguez, Julio},
  title={Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling},
  year={2019},
  pages={23 S.},
  language={eng},
  issn={1097-4164},
  volume={74},
  note={Gesehen am 15.08.2019},
  journal={Molecular cell},
  doi={10.1016/j.molcel.2019.04.021},
}
@article{UBHD-69316094,
  author={Lussana, Alessandro and M{\"u}ller-Dott, Sophia and Sáez Rodríguez, Julio and Petsalaki, Evangelia},
  title={PhosX},
  subtitle={data-driven kinase activity inference from phosphoproteomics experiments},
  year={2024},
  pages={1-5},
  language={eng},
  issn={1367-4811},
  volume={40},
  note={Ver{\"o}ffentlicht: 19. November 2024 ; Gesehen am 07.03.2025},
  journal={Bioinformatics},
  doi={10.1093/bioinformatics/btae697},
}
@article{UBHD-69281598,
  author={Maier, Andreas and Hartung, Michael and Abovsky, Mark and Adamowicz, Klaudia and Bader, Gary D and Baier, Sylvie and Blumenthal, David B and Chen, Jing and Elkjaer, Maria L and Garcia-Hernandez, Carlos and Helmy, Mohamed and Hoffmann, Markus and Jurisica, Igor and Kotlyar, Max and Lazareva, Olga and Levi, Hagai and List, Markus and Lobentanzer, Sebastian and Loscalzo, Joseph and Malod-Dognin, Noel and Manz, Quirin and Matschinske, Julian and Mee, Miles and Oubounyt, Mhaned and Pastrello, Chiara and Pico, Alexander R and Pillich, Rudolf T and Poschenrieder, Julian M and Pratt, Dexter and Pržulj, Nataša and Sadegh, Sepideh and Sáez Rodríguez, Julio and Sarkar, Suryadipto and Shaked, Gideon and Shamir, Ron and Trummer, Nico and Turhan, Ugur and Wang, Rui-Sheng and Zolotareva, Olga and Baumbach, Jan},
  title={Drugst},
  subtitle={One - a plug-and-play solution for online systems medicine and network-based drug repurposing},
  year={2024},
  pages={W481-W488},
  language={eng},
  issn={1362-4962},
  volume={52(2024},
  number={W1)},
  note={Ver{\"o}ffentlicht: 23 May 2024 ; Gesehen am 09.12.2024},
  journal={Nucleic acids research},
  doi={10.1093/nar/gkae388},
}
@article{UBHD-68678642,
  author={Maier-Hein, Lena and Reinke, Annika and Kozubek, Michal and Martel, Anne L. and Arbel, Tal and Eisenmann, Matthias and Hanbury, Allan and Jannin, Pierre and M{\"u}ller, Henning and Onogur, Sinan and Sáez Rodríguez, Julio and van Ginneken, Bram and Kopp-Schneider, Annette and Landman, Bennett A.},
  title={BIAS},
  subtitle={transparent reporting of biomedical image analysis challenges},
  year={2020},
  pages={7 S.},
  language={eng},
  issn={1361-8423},
  volume={66(2020) Artikel-Nummer 101796},
  number={7 Seiten},
  note={Gesehen am 11.01.2021},
  journal={Medical image analysis},
  doi={10.1016/j.media.2020.101796},
}
@article{UBHD-69187799,
  author={Maier-Hein, Lena and Reinke, Annika and Godau, Patrick and Tizabi, Minu and Christodoulou, Evangelia and Isensee, Fabian and Wiesenfarth, Manuel and Kavur, A. Emre and Baumgartner, Michael and Eisenmann, Matthias and Heckmann-N{\"o}tzel, Doreen and R{\"a}dsch, Tim and Kopp-Schneider, Annette and Kreshuk, Anna and Maier-Hein, Klaus H. and Sáez Rodríguez, Julio and J{\"a}ger, Paul F.},
  title={Metrics reloaded},
  subtitle={recommendations for image analysis validation},
  year={2024},
  pages={195-212},
  language={eng},
  issn={1548-7105},
  volume={21},
  number={2},
  note={Gesehen am 04.03.2024},
  journal={Nature methods},
  doi={10.1038/s41592-023-02151-z},
}
@article{UBHD-68640393,
  author={Manica, Matteo and Kim, Hyunjae Ryan and Mathis, Roland and Chouvarine, Philippe and Rutishauser, Dorothea and De Vargas Roditi, Laura and Szalai, Bence and Wagner, Ulrich and Oehl, Kathrin and Saba, Karim and Pati, Arati and Sáez Rodríguez, Julio and Roy, Angshumoy and Parsons, Donald W. and Wild, Peter J. and Martínez, María Rodríguez and Sumazin, Pavel},
  title={Inferring clonal composition from multiple tumor biopsies},
  year={2020},
  pages={1-13},
  language={eng},
  issn={2056-7189},
  volume={6},
  number={1},
  note={Gesehen am 25.09.2020},
  journal={npj Systems biology and applications},
  doi={10.1038/s41540-020-00147-5},
}
@article{UBHD-68477723,
  author={Manica, Matteo and Oskooei, Ali and Born, Jannis and Subramanian, Vigneshwari and Sáez Rodríguez, Julio and Rodríguez Martínez, María},
  title={Toward explainable anticancer compound sensitivity prediction via multimodal attention-based convolutional encoders},
  year={2019},
  pages={4797-4806},
  language={eng},
  issn={1543-8392},
  volume={16},
  number={12},
  note={Gesehen am 17.01.2020},
  journal={Molecular pharmaceutics},
  doi={10.1021/acs.molpharmaceut.9b00520},
}
@article{UBHD-68782291,
  author={Martorell-Marugán, Jordi and López-Domínguez, Raúl and García-Moreno, Adrián and Toro-Domínguez, Daniel and Villatoro-García, Juan Antonio and Barturen, Guillermo and Martín-Gómez, Adoración and Troule, Kevin and Gómez-López, Gonzalo and Al-Shahrour, Fátima and González-Rumayor, Víctor and Peña-Chilet, María and Dopazo, Joaquín and Sáez Rodríguez, Julio and Alarcón-Riquelme, Marta E. and Carmona-Sáez, Pedro},
  title={A comprehensive database for integrated analysis of omics data in autoimmune diseases},
  year={2021},
  pages={1-14},
  language={eng},
  issn={1471-2105},
  volume={22},
  number={Artikel-ID 343},
  note={Gesehen am 22.09.2021},
  journal={BMC bioinformatics},
  doi={10.1186/s12859-021-04268-4},
}
@article{UBHD-69304134,
  author={Masarapu, Yuvarani and Cekanaviciute, Egle and Andrusivova, Zaneta and Westholm, Jakub O. and Bj{\"o}rklund, Åsa and Fallegger, Robin and Badia-i-Mompel, Pau and Boyko, Valery and Vasisht, Shubha and Saravia-Butler, Amanda and Gebre, Samrawit and Lázár, Enikő and Graziano, Marta and Frapard, Solène and Hinshaw, Robert G. and Bergmann, Olaf Ingmar and Taylor, Deanne M. and Wallace, Douglas C. and Sylvén, Christer and Meletis, Konstantinos and Sáez Rodríguez, Julio and Galazka, Jonathan M. and Costes, Sylvain V. and Giacomello, Stefania},
  title={Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice},
  year={2024},
  pages={1-14},
  language={eng},
  issn={2041-1723},
  volume={15},
  number={Artikel-ID 4778},
  note={Gesehen am 13.02.2025},
  journal={Nature Communications},
  doi={10.1038/s41467-024-48916-8},
}
@article{UBHD-68963716,
  author={Mathur, Lukas and Szalai, B. and Du, N. H. and Utharala, Ramesh and Ballinger, Martine and Landry, Jonathan and Ryckelynck, M. and Benes, Vladimir and Sáez Rodríguez, Julio and Merten, Christoph A.},
  title={Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets},
  year={2022},
  pages={1-15},
  language={eng},
  issn={2041-1723},
  volume={13},
  number={Artikel-ID 4450},
  note={Gesehen am 09.09.2022},
  journal={Nature Communications},
  doi={10.1038/s41467-022-32197-0},
}
@article{UBHD-68819295,
  author={Mazein, Alexander and Rougny, Adrien and Karr, Jonathan R and Sáez Rodríguez, Julio and Ostaszewski, Marek and Schneider, Reinhard},
  title={Reusability and composability in process description maps},
  subtitle={RAS-RAF-MEK-ERK signalling},
  year={2021},
  pages={1-8},
  language={eng},
  issn={1477-4054},
  volume={22},
  note={Gesehen am 13.12.2021},
  journal={Briefings in bioinformatics},
  doi={10.1093/bib/bbab103},
}
@article{UBHD-68478940,
  author={Menden, Michael and Wang, Dennis and Mason, Mike J. and Szalai, Bence and Bulusu, Krishna C. and Guan, Yuanfang and Yu, Thomas and Kang, Jaewoo and Jeon, Minji and Wolfinger, Russ and Nguyen, Tin and Zaslavskiy, Mikhail and Jang, In Sock and Ghazoui, Zara and Ahsen, Mehmet Eren and Vogel, Robert and Neto, Elias Chaibub and Norman, Thea and Tang, Eric K. Y. and Garnett, Mathew J. and Veroli, Giovanni Y. Di and Fawell, Stephen and Stolovitzky, Gustavo and Guinney, Justin and Dry, Jonathan R. and Sáez Rodríguez, Julio},
  title={Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen},
  year={2019},
  pages={17 S.},
  language={eng},
  issn={2041-1723},
  volume={10(2019) Artikel-Nummer 2674},
  number={17 Seiten},
  note={Published online 2019 Jun 17 ; Gesehen am 21.01.2020},
  journal={Nature Communications},
  doi={10.1038/s41467-019-09799-2},
}
@article{UBHD-68559263,
  author={Menden, Michael and Casale, Francesco Paolo and Stephan, Johannes and Bignell, Graham R. and Iorio, Francesco and McDermott, Ultan and Garnett, Mathew J. and Sáez Rodríguez, Julio and Stegle, Oliver},
  title={The germline genetic component of drug sensitivity in cancer cell lines},
  year={2018},
  pages={8 S.},
  language={eng},
  issn={2041-1723},
  volume={9(2018) Artikel-Nummer 3385},
  number={8 Seiten},
  note={Gesehen am 30.03.2020},
  journal={Nature Communications},
  doi={10.1038/s41467-018-05811-3},
}
@article{UBHD-68760826,
  author={Meyer, Pablo and Sáez Rodríguez, Julio},
  title={Advances in systems biology modeling},
  subtitle={10 years of crowdsourcing DREAM challenges},
  year={2021},
  pages={636-653},
  language={eng},
  issn={2405-4720},
  volume={12},
  number={6},
  note={Gesehen am 16.07.2021},
  journal={Cell systems},
  doi={10.1016/j.cels.2021.05.015},
}
@article{UBHD-68721671,
  author={Mohs, Antje and Otto, Tobias and Schneider, Kai Markus and Peltzer, Mona and Boekschoten, Mark and Holland, Christian H. and Hudert, Christian A. and Kalveram, Laura and Wiegand, Susanna and Sáez Rodríguez, Julio and Longerich, Thomas and Hengstler, Jan G. and Trautwein, Christian},
  title={Hepatocyte-specific NRF2 activation controls fibrogenesis and carcinogenesis in steatohepatitis},
  year={2021},
  pages={638-648},
  language={eng},
  issn={1600-0641},
  volume={74},
  number={3},
  note={Available online 24 October 2020 ; Gesehen am 02.09.2021},
  journal={Journal of hepatology},
  doi={10.1016/j.jhep.2020.09.037},
}
@article{UBHD-68934807,
  author={Montagud, Arnau and Béal, Jonas and Tobalina, Luis and Traynard, Pauline and Subramanian, Vigneshwari and Szalai, Bence and Alf{\"o}ldi, Róbert and Puskás, László and Valencia, Alfonso and Barillot, Emmanuel and Sáez Rodríguez, Julio and Calzone, Laurence},
  title={Patient-specific Boolean models of signalling networks guide personalised treatments},
  year={2022},
  pages={1-81},
  language={eng},
  issn={2050-084X},
  volume={11},
  number={Artikel-ID e72626},
  note={Gesehen am 27.06.2022},
  journal={eLife},
  doi={10.7554/eLife.72626},
}
@article{UBHD-68732010,
  author={Moreno-Indias, Isabel and Lahti, Leo and Nedyalkova, Miroslava and Elbere, Ilze and Roshchupkin, Gennady and Adilovic, Muhamed and Aydemir, Onder and Bakir-Gungor, Burcu and Santa Pau, Enrique Carrillo-de and D’Elia, Domenica and Desai, Mahesh S. and Falquet, Laurent and Gundogdu, Aycan and Hron, Karel and Klammsteiner, Thomas and Lopes, Marta B. and Marcos-Zambrano, Laura Judith and Marques, Cláudia and Mason, Michael and May, Patrick and Pašić, Lejla and Pio, Gianvito and Pongor, Sándor and Promponas, Vasilis J. and Przymus, Piotr and Sáez Rodríguez, Julio and Sampri, Alexia and Shigdel, Rajesh and Stres, Blaz and Suharoschi, Ramona and Truu, Jaak and Truică, Ciprian-Octavian and Vilne, Baiba and Vlachakis, Dimitrios and Yilmaz, Ercument and Zeller, Georg F. and Zomer, Aldert L. and Gómez-Cabrero, David and Claesson, Marcus J.},
  title={Statistical and machine learning techniques in human microbiome studies},
  subtitle={contemporary challenges and solutions},
  year={2021},
  pages={1-9},
  language={eng},
  issn={1664-302X},
  volume={12},
  number={Artikel-ID 635781},
  note={Gesehen am 04.05.2021},
  journal={Frontiers in microbiology},
  doi={10.3389/fmicb.2021.635781},
}
@article{UBHD-69149565,
  author={M{\"u}ller-Dott, Sophia and Tsirvouli, Eirini and Vazquez, Miguel and Ramirez Flores, Ricardo O. and Badia-i-Mompel, Pau and Fallegger, Robin and T{\"u}rei, Dénes and Lægreid, Astrid and Sáez Rodríguez, Julio},
  title={Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities},
  year={2023},
  pages={10934-10949},
  language={eng},
  issn={1362-4962},
  volume={51},
  number={20},
  note={Online verf{\"u}gbar: 16. Oktober 2023 ; Gesehen am 05.12.2023},
  journal={Nucleic acids research},
  doi={10.1093/nar/gkad841},
}
@article{UBHD-68627363,
  author={Najgebauer, Hanna and Sáez Rodríguez, Julio},
  title={CELLector},
  subtitle={genomics-guided selection of cancer in vitro models},
  year={2020},
  pages={424-432.e6},
  language={eng},
  issn={2405-4720},
  volume={10},
  number={5},
  note={Gesehen am 13.08.2020},
  journal={Cell systems},
  doi={10.1016/j.cels.2020.04.007},
}
@article{UBHD-69241241,
  author={Niarakis, Anna and Ostaszewski, Marek and Mazein, Alexander and Kuperstein, Inna and Kutmon, Martina and Gillespie, Marc E. and Funahashi, Akira and Acencio, Marcio Luis and Hemedan, Ahmed and Aichem, Michael and Klein, Karsten and Czauderna, Tobias and Burtscher, Felicia and Yamada, Takahiro G. and Hiki, Yusuke and Hiroi, Noriko F. and Hu, Finterly and Pham, Nhung and Ehrhart, Friederike and Willighagen, Egon L. and Valdeolivas, Alberto and Dugourd, Aurélien and Messina, Francesco and Esteban-Medina, Marina and Peña-Chilet, Maria and Rian, Kinza and Soliman, Sylvain and Aghamiri, Sara Sadat and Puniya, Bhanwar Lal and Naldi, Aurélien and Helikar, Tomáš and Singh, Vidisha and Fernández, Marco Fariñas and Bermudez, Viviam and Tsirvouli, Eirini and Montagud, Arnau and Noël, Vincent and Ponce-de-Leon, Miguel and Maier, Dieter and Bauch, Angela and Gyori, Benjamin M. and Bachman, John A. and Luna, Augustin and Piñero, Janet and Furlong, Laura I. and Balaur, Irina and Rougny, Adrien and Jarosz, Yohan and Overall, Rupert W. and Phair, Robert and Perfetto, Livia and Matthews, Lisa and Rex, Devasahayam Arokia Balaya and Orlic-Milacic, Marija and Gomez, Luis Cristobal Monraz and De Meulder, Bertrand and Ravel, Jean Marie and Jassal, Bijay and Satagopam, Venkata and Wu, Guanming and Golebiewski, Martin and Gawron, Piotr and Calzone, Laurence and Beckmann, Jacques S. and Evelo, Chris T. and D’Eustachio, Peter and Schreiber, Falk and Sáez Rodríguez, Julio and Dopazo, Joaquin and Kuiper, Martin and Valencia, Alfonso and Wolkenhauer, Olaf and Kitano, Hiroaki and Barillot, Emmanuel and Auffray, Charles and Balling, Rudi and Schneider, Reinhard},
  title={Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches},
  year={2023},
  pages={1-24},
  language={eng},
  issn={1664-3224},
  volume={14},
  number={Artikel-ID 1282859},
  note={Gesehen am 07.08.2024},
  journal={Frontiers in immunology},
  doi={10.3389/fimmu.2023.1282859},
}
@article{UBHD-68774098,
  author={Niarakis, Anna and Kuiper, Martin and Ostaszewski, Marek and Malik Sheriff, Rahuman S and Casals-Casas, Cristina and Thieffry, Denis and Freeman, Tom C and Thomas, Paul and Touré, Vasundra and Noël, Vincent and Stoll, Gautier and Sáez Rodríguez, Julio and Naldi, Aurélien and Oshurko, Eugenia and Xenarios, Ioannis and Soliman, Sylvain and Chaouiya, Claudine and Helikar, Tomáš and Calzone, Laurence},
  title={Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod workshop},
  year={2021},
  pages={1848-1859},
  language={eng},
  issn={1477-4054},
  volume={22},
  number={2 vom: M{\"a}rz},
  note={Gesehen am 26.08.2021 ; First published:  21 April 2020},
  journal={Briefings in bioinformatics},
  doi={10.1093/bib/bbaa046},
}
@article{UBHD-68878946,
  author={Ostaszewski, Marek and T{\"u}rei, Dénes and Valdeolivas, Alberto and Dugourd, Aurélien and Sáez Rodríguez, Julio and Dopazo, Joaquin and Valencia, Alfonso and Kitano, Hiroaki and Barillot, Emmanuel and Auffray, Charles and Balling, Rudolf and Schneider, Reinhard},
  title={COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms},
  year={2021},
  pages={1-22},
  language={eng},
  issn={1744-4292},
  volume={17},
  note={Gesehen am 16.02.2022},
  journal={Molecular systems biology},
  doi={10.15252/msb.202110387},
}
@article{UBHD-68915700,
  author={Parigi, Sara M. and Larsson, Ludvig and Das, Srustidhar and Ramirez Flores, Ricardo O. and Frede, Annika and Tripathi, Kumar P. and Diaz, Oscar E. and Selin, Katja and Morales, Rodrigo A. and Luo, Xinxin and Monasterio, Gustavo and Engblom, Camilla and Gagliani, Nicola and Sáez Rodríguez, Julio and Lundeberg, Joakim and Villablanca, Eduardo J.},
  title={The spatial transcriptomic landscape of the healing mouse intestine following damage},
  year={2022},
  pages={1-16},
  language={eng},
  issn={2041-1723},
  volume={13},
  number={Artikel-ID 828},
  note={Gesehen am 06.05.2022},
  journal={Nature Communications},
  doi={10.1038/s41467-022-28497-0},
}
@article{UBHD-69284021,
  author={Paton, Victor and Ramirez Flores, Ricardo O. and Gabor, Attila and Badia-i-Mompel, Pau and Tanevski, Jovan and Garrido-Rodriguez, Martin and Sáez Rodríguez, Julio},
  title={Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results},
  year={2024},
  pages={8100-8111},
  language={eng},
  issn={1362-4962},
  volume={52},
  number={14 vom: Aug.},
  note={Ver{\"o}ffentlicht: 29 June 2024 ; Gesehen am 16.12.2024},
  journal={Nucleic acids research},
  doi={10.1093/nar/gkae552},
}
@article{UBHD-68938739,
  author={Pérez-Martí, Albert and Ramakrishnan, Suresh Krishna and Li, Jiayi and Dugourd, Aurélien and Molenaar, Martijn R and De La Motte, Luigi R and Grand, Kelli and Mansouri, Anis and Parisot, Mélanie and Lienkamp, Soeren S and Sáez Rodríguez, Julio and Simons, Matias},
  title={Reducing lipid bilayer stress by monounsaturated fatty acids protects renal proximal tubules in diabetes},
  year={2022},
  pages={1-31},
  language={eng},
  issn={2050-084X},
  volume={11},
  number={Artikel-ID e74391},
  note={Gesehen am 06.07.2022},
  journal={eLife},
  doi={10.7554/eLife.74391},
}
@article{UBHD-68754270,
  author={Petkevicius, Kasparas and Bidault, Guillaume and Virtue, Sam and Jenkins, Benjamin and Dierendonck, Xanthe A. M. H. van and Dugourd, Aurélien and Sáez Rodríguez, Julio and Stienstra, Rinke and Koulman, Albert and Vidal-Puig, Antonio},
  title={Norepinephrine promotes triglyceride storage in macrophages via beta2-adrenergic receptor activation},
  year={2021},
  pages={1-18},
  language={eng},
  issn={1530-6860},
  volume={35},
  note={Gesehen am 30.06.2021},
  journal={The FASEB journal},
  doi={10.1096/fj.202001101R},
}
@article{UBHD-68402021,
  author={Picco, Gabriele and Chen, Elisabeth D. and Sáez Rodríguez, Julio},
  title={Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening},
  year={2019},
  pages={12 S.},
  language={eng},
  issn={2041-1723},
  volume={10(2019) Artikel-Nummer 2198},
  number={12 Seiten},
  note={Gabriele Picco and Elisabeth D. Chen contributed equally ; Gesehen am 26.06.2019},
  journal={Nature Communications},
  doi={10.1038/s41467-019-09940-1},
}
@article{UBHD-68924097,
  author={Poletti, Martina and Treveil, Agatha and Csabai, Luca and Gul, Leila and Modos, Dezso and Madgwick, Matthew and Olbei, Marton and Bohar, Balazs and Valdeolivas, Alberto and Turei, Denes and Verstockt, Bram and Triana, Sergio and Alexandrov, Theodore and Sáez Rodríguez, Julio and Stanifer, Megan and Boulant, Steeve and Korcsmaros, Tamas},
  title={Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways},
  year={2022},
  pages={1-19},
  language={eng},
  issn={2056-7189},
  volume={8},
  note={Gesehen am 31.05.2022},
  journal={npj Systems biology and applications},
  doi={10.1038/s41540-022-00224-x},
}
@article{UBHD-69292487,
  author={Rahimi, Arezou and Vale Silva, Luis A. and F{\"a}lth Savitski, Maria and Tanevski, Jovan and Sáez Rodríguez, Julio},
  title={DOT},
  subtitle={a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics},
  year={2024},
  pages={1-15},
  language={eng},
  issn={2041-1723},
  volume={15},
  number={Artikel-ID 4994},
  note={Gesehen am 20.01.2025},
  journal={Nature Communications},
  doi={10.1038/s41467-024-48868-z},
}
@article{UBHD-68740486,
  author={Ramirez Flores, Ricardo O. and Lanzer, Jan David and Holland, Christian H. and Leuschner, Florian and Most, Patrick and Schultz, Jobst-Hendrik and Levinson, Rebecca T. and Sáez Rodríguez, Julio},
  title={Consensus Transcriptional Landscape of Human End‐Stage Heart Failure},
  year={2021},
  pages={1-40},
  language={eng},
  issn={2047-9980},
  volume={10},
  note={Gesehen am 25.05.2021},
  journal={Journal of the American Heart Association},
  doi={10.1161/JAHA.120.019667},
  url={https://doi.org/10.1161/JAHA.120.019667},
  library={UB},
}
@article{UBHD-69221231,
  author={Ramirez Flores, Ricardo O. and Lanzer, Jan David and Dimitrov, Daniel and Velten, Britta and Sáez Rodríguez, Julio},
  title={Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease},
  year={2023},
  pages={1-27},
  language={eng},
  issn={2050-084X},
  volume={12},
  number={Artikel-ID e93161},
  note={Gesehen am 06.06.2024},
  journal={eLife},
  doi={10.7554/eLife.93161},
}
@article{UBHD-69272346,
  author={Reinke, Annika and Tizabi, Minu and Baumgartner, Michael and Eisenmann, Matthias and Heckmann, Doreen and Kavur, A. Emre and R{\"a}dsch, Tim and Sudre, Carole H. and Acion, Laura and Antonelli, Michela and Arbel, Tal and Bakas, Spyridon and Benis, Arriel and Buettner, Florian and Cardoso, M. Jorge and Cheplygina, Veronika and Chen, Jianxu and Christodoulou, Evangelia and Cimini, Beth A. and Farahani, Keyvan and Ferrer, Luciana and Galdran, Adrian and van Ginneken, Bram and Glocker, Ben and Godau, Patrick and Hashimoto, Daniel A. and Hoffman, Michael M. and Huisman, Merel and Isensee, Fabian and Jannin, Pierre and Kahn, Charles E. and Kainmueller, Dagmar and Kainz, Bernhard and Karargyris, Alexandros and Kleesiek, Jens Philipp and Kofler, Florian and Kooi, Thijs and Kopp-Schneider, Annette and Kozubek, Michal and Kreshuk, Anna and Kurc, Tahsin and Landman, Bennett A. and Litjens, Geert and Madani, Amin and Maier-Hein, Klaus H. and Martel, Anne L. and Meijering, Erik and Menze, Bjoern and Moons, Karel G. M. and M{\"u}ller, Henning and Nichyporuk, Brennan and Nickel, Felix and Petersen, Jens and Rafelski, Susanne M. and Rajpoot, Nasir and Reyes, Mauricio and Riegler, Michael A. and Rieke, Nicola and Sáez Rodríguez, Julio and Sánchez, Clara I. and Shetty, Shravya and Summers, Ronald M. and Taha, Abdel A. and Tiulpin, Aleksei and Tsaftaris, Sotirios A. and Van Calster, Ben and Varoquaux, Gaël and Yaniv, Ziv R. and Jaeger, Paul F. and Maier-Hein, Lena},
  title={Understanding metric-related pitfalls in image analysis validation},
  year={2024},
  pages={182-194},
  language={eng},
  issn={1548-7105},
  volume={21},
  number={2},
  note={Gesehen am 11.11.2024},
  journal={Nature methods},
  doi={10.1038/s41592-023-02150-0},
}
@article{UBHD-68882381,
  author={Reusch, Bj{\"o}rn and Bartram, Malte P. and Dafinger, Claudia and Palacio-Escat, Nicolàs and Wenzel, Andrea and Fenton, Robert A. and Sáez Rodríguez, Julio and Schermer, Bernhard and Benzing, Thomas and Altm{\"u}ller, Janine and Beck, Bodo B. and Rinschen, Markus M.},
  title={MAGED2 controls vasopressin-induced aquaporin-2 expression in collecting duct cells},
  year={2022},
  pages={1-9},
  language={eng},
  issn={1876-7737},
  volume={252},
  note={Available online 12 November 2021 ; Gesehen am 09.03.2022},
  journal={Journal of proteomics},
  doi={10.1016/j.jprot.2021.104424},
}
@article{UBHD-68492891,
  author={Rinschen, Markus Matthias and Palygin, Oleg and Guijas, Carlos and Palermo, Amelia and Palacio-Escat, Nicolàs and Domingo-Almenara, Xavier and Montenegro-Burke, Rafael and Sáez Rodríguez, Julio and Staruschenko, Alexander and Siuzdak, Gary},
  title={Metabolic rewiring of the hypertensive kidney},
  year={2019},
  pages={?},
  language={eng},
  issn={1937-9145},
  volume={12(2019},
  number={611) Artikel-Nummer eaax9760},
  note={Gesehen am 25.02.2020},
  journal={Science signaling},
  doi={10.1126/scisignal.aax9760},
}
@article{UBHD-69307530,
  author={Rinschen, Markus Matthias and Sáez Rodríguez, Julio},
  title={The tissue proteome in the multi-omic landscape of kidney disease},
  year={2021},
  pages={205-219},
  language={eng},
  issn={1759-507X},
  volume={17},
  number={3 vom: M{\"a}rz},
  note={Zuerst online ver{\"o}ffentlicht: 07 October 2020 ; Gesehen am 24.02.2025},
  journal={Nature reviews},
  doi={10.1038/s41581-020-00348-5},
}
@article{UBHD-68920484,
  author={Robrahn, Laura Marie and Dupont, Aline and Jumpertz, Sandra and Zhang, Kaiyi and Holland, Christian H. and Guillaume, Joël and Rappold, Sabrina and Roth, Johanna and Cerovic, Vuk and Sáez Rodríguez, Julio and Hornef, Mathias W. and Cramer, Thorsten},
  title={Stabilization but no functional influence of HIF-1α expression in the intestinal epithelium during salmonella typhimurium infection},
  year={2022},
  language={eng},
  issn={1098-5522},
  volume={90},
  note={Gesehen am 19.05.2022},
  journal={Infection and immunity},
  doi={10.1128/iai.00222-21},
}
@article{UBHD-68491157,
  author={Sáez Rodríguez, Julio and Rinschen, Markus Matthias and Fl{\"o}ge, J{\"u}rgen and Kramann, Rafael},
  title={The authors reply [Big data: creating the right balance]},
  subtitle={letter to the editor},
  year={2019},
  pages={1422-1423},
  language={eng},
  issn={1523-1755},
  volume={96},
  number={6},
  note={Gesehen am 19.02.2020},
  journal={Kidney international},
}
@article{UBHD-68488567,
  author={Sáez Rodríguez, Julio and Rinschen, Markus M. and Floege, J{\"u}rgen and Kramann, Rafael},
  title={Big science and big data in nephrology},
  year={2019},
  pages={1326-1337},
  language={eng},
  issn={1523-1755},
  volume={95},
  number={6},
  note={Gesehen am 13.02.2020},
  journal={Kidney international},
  doi={10.1016/j.kint.2018.11.048},
}
@book{UBHD-69331900,
  author={Sáez Rodríguez, Julio and Zeller, Georg F.},
  organization={Universit{\"a}tsklinikum Heidelberg / Institute for Computational Biomedicine and European Molecular Biology Laboratory},
  title={LAMarCK - Longitudinal multiomics characterization of disease using prior knowledge},
  subtitle={Schlussbericht : LAMarCK - Verbundprojekt: Teilprojekt: AG Saez-Rodriguez : Laufzeit: 1. April 2019-31. M{\"a}rz 2023},
  publisher={Heidelberg University, Faculty of Medicine, Institut f{\"u}r Computational Biomedicine},
  address={Heidelberg},
  year={2023},
  pages={1 Online-Ressource (12 Seiten, 157,52 KB)},
  language={ger},
  doi={10.2314/KXP:1920112715},
  keywords={Krankengeschichte / Omics-Technologie / Physiologische Chemie / Biomedizin / Biomathematik},
}
@article{UBHD-68575746,
  author={Sáez Rodríguez, Julio and Bl{\"u}thgen, Nils},
  title={Personalized signaling models for personalized treatments},
  year={2020},
  pages={3 S.},
  language={eng},
  issn={1744-4292},
  volume={16(2020},
  note={Gesehen am 12.05.2020},
  journal={Molecular systems biology},
  doi={10.15252/msb.20199042},
}
@article{UBHD-69058599,
  author={Salovska, Barbora and Gao, Erli and M{\"u}ller-Dott, Sophia and Li, Wenxue and Cordon, Carlos Chacon and Wang, Shisheng and Dugourd, Aurélien and Rosenberger, George and Sáez Rodríguez, Julio and Liu, Yansheng},
  title={Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities},
  year={2023},
  pages={1-25},
  language={eng},
  issn={2001-1326},
  volume={13},
  note={Gesehen am 31.03.2023},
  journal={Clinical and translational medicine},
  doi={10.1002/ctm2.1179},
}
@article{UBHD-68442676,
  author={Sch{\"a}fer, Alexander and Sáez Rodríguez, Julio},
  title={Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data},
  year={2019},
  pages={19 S.},
  language={eng},
  issn={1744-4292},
  volume={15(2019},
  note={Gesehen am 21.10.2019},
  journal={Molecular systems biology},
  doi={10.15252/msb.20198828},
}
@article{UBHD-69043881,
  author={Schneider, Kai Markus and Mohs, Antje and Gui, Wenfang and Galvez, Eric J. C. and Candels, Lena Susanna and Hoenicke, Lisa and Muthukumarasamy, Uthayakumar and Holland, Christian H. and Elfers, Carsten and Kilic, Konrad and Schneider, Carolin Victoria and Schierwagen, Robert and Strnad, Pavel and Wirtz, Theresa H. and Marschall, Hanns-Ulrich and Latz, Eicke and Lelouvier, Benjamin and Sáez Rodríguez, Julio and de Vos, Willem and Strowig, Till and Trebicka, Jonel and Trautwein, Christian},
  title={Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment},
  year={2022},
  pages={1-19},
  language={eng},
  issn={2041-1723},
  volume={13(2022) vom: Juli},
  number={Artikel-ID 3964},
  note={Gesehen am 21.02.2023},
  journal={Nature Communications},
  doi={10.1038/s41467-022-31312-5},
}
@article{UBHD-69043728,
  author={Schreibing, Felix and Hannani, Monica T. and Kim, Hyojin and Nagai, James S. and Ticconi, Fabio and Fewings, Eleanor and Bleckwehl, Tore and Begemann, Matthias and Torow, Natalia and Kuppe, Christoph and Kurth, Ingo and Kranz, Jennifer and Frank, Dario and Anslinger, Teresa M. and Ziegler, Patrick and Kraus, Thomas and Enczmann, J{\"u}rgen and Balz, Vera and Windhofer, Frank and Balfanz, Paul and Kurts, Christian and Marx, Gernot and Marx, Nikolaus and Dreher, Michael and Schneider, Rebekka K. and Sáez Rodríguez, Julio and Costa, Ivan and Hayat, Sikander and Kramann, Rafael},
  title={Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling},
  year={2022},
  pages={1-23},
  language={eng},
  issn={1664-3224},
  volume={13},
  number={Artikel-ID 1066176},
  note={Gesehen am 21.02.2023},
  journal={Frontiers in immunology},
  doi={10.3389/fimmu.2022.1066176},
}
@article{UBHD-68792407,
  author={Schwabenland, Marius and Salié, Henrike and Tanevski, Jovan and Killmer, Saskia and Lago, Marilyn Salvat and Schlaak, Alexandra Emilia and Mayer, Lena and Matschke, Jakob and P{\"u}schel, Klaus and Fitzek, Antonia and Ondruschka, Benjamin and Mei, Henrik E. and Boettler, Tobias and Neumann-Haefelin, Christoph and Hofmann, Maike and Breithaupt, Angele and Genc, Nafiye and Stadelmann, Christine and Sáez Rodríguez, Julio and Bronsert, Peter and Knobeloch, Klaus-Peter and Blank, Thomas and Thimme, Robert and Glatzel, Markus and Prinz, Marco and Bengsch, Bertram},
  title={Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions},
  year={2021},
  pages={28 S.},
  language={eng},
  issn={1097-4180},
  volume={54},
  note={Gesehen am 21.10.2021},
  journal={Immunity},
  doi={10.1016/j.immuni.2021.06.002},
}
@article{UBHD-69062819,
  author={Sciacovelli, Marco and Dugourd, Aurélien and Jimenez, Lorea Valcarcel and Yang, Ming and Nikitopoulou, Efterpi and Costa, Ana S. H. and Tronci, Laura and Caraffini, Veronica and Rodrigues, Paulo and Schmidt, Christina and Ryan, Dylan Gerard and Young, Timothy and Zecchini, Vincent R. and Rossi, Sabrina H. and Massie, Charlie and Lohoff, Caroline and Masid, Maria and Hatzimanikatis, Vassily and Kuppe, Christoph and Von Kriegsheim, Alex and Kramann, Rafael and Gnanapragasam, Vincent and Warren, Anne Y. and Stewart, Grant D. and Erez, Ayelet and Vanharanta, Sakari and Sáez Rodríguez, Julio and Frezza, Christian},
  title={Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression},
  year={2022},
  pages={1-20},
  language={eng},
  issn={2041-1723},
  volume={13(2022) vom: Dez.},
  number={Artikel-ID 7830},
  note={Gesehen am 05.04.2023},
  journal={Nature Communications},
  doi={10.1038/s41467-022-35036-4},
}
@article{UBHD-68684187,
  author={Sellmayr, Markus and Petzsche, Moritz Roman Hernandez and Ma, Qiuyue and Kr{\"u}ger, Nils and Liapis, Helen and Brink, Andreas and Lenz, Barbara and Angelotti, Maria Lucia and Gnemmi, Viviane and Kuppe, Christoph and Kim, Hyojin and Bindels, Eric Moniqué Johannes and Tajti, Ferenc and Sáez Rodríguez, Julio and Lech, Maciej and Kramann, Rafael and Romagnani, Paola and Anders, Hans-Joachim and Steiger, Stefanie},
  title={Only hyperuricemia with crystalluria, but not asymptomatic hyperuricemia, drives progression of chronic kidney disease},
  year={2020},
  pages={2773-2792},
  language={eng},
  issn={1533-3450},
  volume={31},
  number={12},
  note={Gesehen am 27.01.2021},
  journal={Journal of the American Society of Nephrology},
  doi={10.1681/ASN.2020040523},
}
@book{UBHD-69050176,
  author={Song, Chen and Roller, Jonas and Ponce Bobadilla, Ana Victoria and Palacio-Escat, Nicolàs and Sáez Rodríguez, Julio and Heuveline, Vincent},
  title={Spatial effect on separatrix of two-cell system and parameter sensitivity analysis},
  publisher={Univ.-Bibliothek},
  address={Heidelberg},
  year={2021},
  pages={1 Online-Ressource (15 Seiten)},
  language={eng},
  number={ARRAY(0x55c509864130)},
  series={Preprint series of the Engineering Mathematics and Computing Lab (EMCL)},
  note={Gesehen am 09.03.2023},
  doi={10.11588/emclpp.2021.01.81012},
  url={https://doi.org/10.11588/emclpp.2021.01.81012},
  library={UB},
}
@article{UBHD-68560092,
  author={Souza, Terezinha and Trairatphisan, Panuwat and Piñero, Janet and Furlong, Laura I. and Sáez Rodríguez, Julio and Kleinjans, Jos and Jennen, Danyel},
  title={Embracing the dark side},
  subtitle={computational approaches to unveil the functionality of genes lacking biological annotation in drug-induced liver injury},
  year={2018},
  pages={12 S.},
  language={eng},
  issn={1664-8021},
  volume={9(2018) Artikel-Nummer 527},
  number={12 Seiten},
  note={Gesehen am 01.04.2020},
  journal={Frontiers in genetics},
  doi={10.3389/fgene.2018.00527},
}
@article{UBHD-68378340,
  author={Sp{\"a}th, Martin Richard and Sáez Rodríguez, Julio},
  title={The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury},
  year={2019},
  pages={333-349},
  language={eng},
  issn={1523-1755},
  volume={95},
  number={2},
  note={published online 3 December 2018 ; Gesehen am 03.04.2019},
  journal={Kidney international},
  doi={10.1016/j.kint.2018.08.037},
}
@article{UBHD-68423929,
  author={Sun, Qinxue and Baues, Maike and Klinkhammer, Barbara M. and Ehling, Josef and Djudjaj, Sonja and Drude, Natascha I. and Daniel, Christoph and Amann, Kerstin and Kramann, Rafael and Kim, Hyojin and Sáez Rodríguez, Julio and Weiskirchen, Ralf and Onthank, David C. and Botnar, Rene M. and Kiessling, Fabian and Floege, J{\"u}rgen and Lammers, Twan and Boor, Peter},
  title={Elastin imaging enables noninvasive staging and treatment monitoring of kidney fibrosis},
  year={2019},
  pages={14 S.},
  language={eng},
  issn={1946-6242},
  volume={11(2019},
  note={Gesehen am 26.08.2019},
  journal={Science translational medicine},
  doi={10.1126/scitranslmed.aat4865},
}
@article{UBHD-69255363,
  author={Sun, Rui and Ge, Weigang and Zhu, Yi and Sayad, Azin and Luna, Augustin and Lyu, Mengge and Liang, Shuang and Tobalina, Luis and Rajapakse, Vinodh N. and Yu, Chenhuan and Zhang, Huanhuan and Fang, Jie and Wu, Fang and Xie, Hui and Sáez Rodríguez, Julio and Ying, Huazhong and Reinhold, William C. and Sander, Chris and Pommier, Yves and Neel, Benjamin G. and Aebersold, Ruedi and Guo, Tiannan},
  title={Proteomic dynamics of breast cancer cell lines identifies potential therapeutic protein targets},
  year={2023},
  pages={1-15},
  language={eng},
  issn={1535-9484},
  volume={22},
  note={Gesehen am 23.09.2024},
  journal={Molecular & cellular proteomics},
  doi={10.1016/j.mcpro.2023.100602},
}
@article{UBHD-68484474,
  author={Szalai, Bence and Sáez Rodríguez, Julio and Holland, Christian H.},
  title={Signatures of cell death and proliferation in perturbation transcriptomics data},
  subtitle={from confounding factor to effective prediction},
  year={2019},
  pages={10010-10026},
  language={eng},
  issn={1362-4962},
  volume={47},
  number={19},
  note={Gesehen am 04.02.2020},
  journal={Nucleic acids research},
  doi={10.1093/nar/gkz805},
}
@article{UBHD-68781159,
  author={Szalai, Bence and Sáez Rodríguez, Julio},
  title={Why do pathway methods work better than they should?},
  year={2020},
  pages={4189-4200},
  language={eng},
  issn={1873-3468},
  volume={594},
  number={24 vom: 14. Dez.},
  note={Gesehen am 18.09.2021},
  journal={FEBS letters},
  doi={10.1002/1873-3468.14011},
  url={https://doi.org/10.1002/1873-3468.14011},
  library={UB},
}
@article{UBHD-68498563,
  author={Tajti, Ferenc and Kuppe, Christoph and Antoranz, Asier and Ibrahim, Mahmoud M. and Kim, Hyojin and Ceccarelli, Francesco and Holland, Christian H. and Olauson, Hannes and Floege, J{\"u}rgen and Alexopoulos, Leonidas G. and Kramann, Rafael and Sáez Rodríguez, Julio},
  title={A functional landscape of CKD entities from public transcriptomic data},
  year={2020},
  pages={211-224},
  language={eng},
  issn={2468-0249},
  volume={5},
  number={2},
  note={Published online 13 November 2019 ; Gesehen am 10.03.2020},
  journal={Kidney international},
  doi={10.1016/j.ekir.2019.11.005},
}
@article{UBHD-68919453,
  author={Tanevski, Jovan and Ramirez Flores, Ricardo O. and Gabor, Attila and Schapiro, Denis and Sáez Rodríguez, Julio},
  title={Explainable multiview framework for dissecting spatial relationships from highly multiplexed data},
  year={2022},
  pages={1-31},
  language={eng},
  issn={1474-760X},
  volume={23},
  number={Artikel-ID 97},
  note={Gesehen am 17.05.2022},
  journal={Genome biology},
  doi={10.1186/s13059-022-02663-5},
  url={https://doi.org/10.1186/s13059-022-02663-5},
  library={UB},
}
@article{UBHD-68705429,
  author={Tanevski, Jovan and Nguyen, Thin and Truong, Buu and Karaiskos, Nikos and Ahsen, Mehmet Eren and Zhang, Xinyu and Shu, Chang and Xu, Ke and Liang, Xiaoyu and Hu, Ying and Pham, Hoang VV and Xiaomei, Li and Le, Thuc D. and Tarca, Adi L. and Bhatti, Gaurav and Romero, Roberto and Karathanasis, Nestoras and Loher, Phillipe and Chen, Yang and Ouyang, Zhengqing and Mao, Disheng and Zhang, Yuping and Zand, Maryam and Ruan, Jianhua and Hafemeister, Christoph and Qiu, Peng and Tran, Duc and Nguyen, Tin and Gabor, Attila and Yu, Thomas and Guinney, Justin and Glaab, Enrico and Krause, Roland and Banda, Peter and Consortium, Dream Sctc and Stolovitzky, Gustavo and Rajewsky, Nikolaus and Sáez Rodríguez, Julio and Meyer, Pablo},
  title={Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data},
  year={2020},
  pages={13 S.},
  language={eng},
  issn={2575-1077},
  volume={3(2020},
  note={Gesehen am 01.03.2020},
  journal={Life science alliance},
  doi={10.26508/lsa.202000867},
}
@article{UBHD-68464256,
  author={Tang, Jing and Gautam, Prson and Gupta, Abhishekh and He, Liye and Timonen, Sanna and Akimov, Yevhen and Wang, Wenyu and Szwajda, Agnieszka and Jaiswal, Alok and Turei, Denes and Yadav, Bhagwan and Kankainen, Matti and Saarela, Jani and Sáez Rodríguez, Julio and Wennerberg, Krister and Aittokallio, Tero},
  title={Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer},
  year={2019},
  pages={1-11},
  language={eng},
  issn={2056-7189},
  volume={5},
  number={1},
  note={Gesehen am 05.12.2019},
  journal={npj Systems biology and applications},
  doi={10.1038/s41540-019-0098-z},
}
@article{UBHD-68795010,
  author={Tillie, Renée J. H. A. and De Bruijn, Jenny and Perales-Patón, Javier and Temmerman, Lieve and Ghosheh, Yanal and Van Kuijk, Kim and Gijbels, Marion J. and Carmeliet, Peter and Ley, Klaus and Sáez Rodríguez, Julio and Sluimer, Judith C.},
  title={Partial inhibition of the 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3) enzyme in myeloid cells does not affect atherosclerosis},
  year={2021},
  pages={1-11},
  language={eng},
  issn={2296-634X},
  volume={9},
  number={Artikel-ID 695684},
  note={Gesehen am 29.10.2021},
  journal={Frontiers in cell and developmental biology},
  doi={10.3389/fcell.2021.695684},
}
@article{UBHD-68881378,
  author={Tognetti, Marco and Gabor, Attila and Yang, Mi and Cappelletti, Valentina and Windhager, Jonas and Rueda, Oscar M. and Charmpi, Konstantina and Esmaeilishirazifard, Elham and Bruna, Alejandra and de Souza, Natalie and Caldas, Carlos and Beyer, Andreas and Picotti, Paola and Sáez Rodríguez, Julio and Bodenmiller, Bernd},
  title={Deciphering the signaling network of breast cancer improves drug sensitivity prediction},
  year={2021},
  pages={30 S.},
  language={eng},
  issn={2405-4720},
  volume={12},
  note={Gesehen am 22.02.2022},
  journal={Cell systems},
  doi={10.1016/j.cels.2021.04.002},
}
@article{UBHD-68759963,
  author={Touré, Vasundra and Vercruysse, Steven and Acencio, Marcio Luis and Lovering, Ruth C and Orchard, Sandra and Bradley, Glyn and Casals-Casas, Cristina and Chaouiya, Claudine and del-Toro, Noemi and Flobak, Åsmund and Gaudet, Pascale and Hermjakob, Henning and Hoyt, Charles Tapley and Licata, Luana and Lægreid, Astrid and Mungall, Christopher J and Niknejad, Anne and Panni, Simona and Perfetto, Livia and Porras, Pablo and Pratt, Dexter and Sáez Rodríguez, Julio and Thieffry, Denis and Thomas, Paul D and T{\"u}rei, Dénes and Kuiper, Martin},
  title={The minimum information about a molecular interaction causal statement (MI2CAST)},
  year={2020},
  pages={5712-5718},
  language={eng},
  issn={1367-4811},
  volume={36},
  number={24 vom: 15. Dez.},
  note={Gesehen am 14.07.2021},
  journal={Bioinformatics},
  doi={10.1093/bioinformatics/btaa622},
}
@article{UBHD-68788377,
  author={Trairatphisan, Panuwat and de Souza, Terezinha Maria and Kleinjans, Jos and Jennen, Danyel and Sáez Rodríguez, Julio},
  title={Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury},
  year={2021},
  pages={40-51},
  language={eng},
  issn={1879-3169},
  volume={350},
  note={Gesehen am 11.10.2021},
  journal={Toxicology letters},
  doi={10.1016/j.toxlet.2021.06.020},
}
@article{UBHD-69275898,
  author={Triantafyllidis, Charalampos P. and Barberis, Alessandro and Hartley, Fiona and Cuervo, Ana Miar and Gjerga, Enio and Charlton, Philip and van Bijsterveldt, Linda and Sáez Rodríguez, Julio and Buffa, Francesca M.},
  title={A machine learning and directed network optimization approach to uncover TP53 regulatory patterns},
  year={2023},
  pages={1-19},
  language={eng},
  issn={2589-0042},
  volume={26},
  note={Online verf{\"u}gbar: 26. Oktober 2022, Artikelversion: 17. November 2023 ; Gesehen am 22.11.2024},
  journal={iScience},
  doi={10.1016/j.isci.2023.108291},
}
@article{UBHD-69006984,
  author={Trobisch, Tim and Zulji, Amel and Stevens, Nikolas and Schwarz, Sophia and Wischnewski, Sven and {\"O}zt{\"u}rk, Mikail and Perales-Patón, Javier and Haeussler, Maximilian and Sáez Rodríguez, Julio and Velmeshev, Dmitry and Schirmer, Lucas},
  title={Cross-regional homeostatic and reactive glial signatures in multiple sclerosis},
  year={2022},
  pages={987-1003},
  language={eng},
  issn={1432-0533},
  volume={144},
  number={5},
  note={Gesehen am 17.01.2023},
  journal={Acta neuropathologica},
  doi={10.1007/s00401-022-02497-2},
  url={https://doi.org/10.1007/s00401-022-02497-2},
  library={UB},
}
@article{UBHD-68747895,
  author={T{\"u}rei, Dénes and Valdeolivas, Alberto and Gul, Lejla and Palacio-Escat, Nicolàs and Klein, Michal and Ivanova, Olga A. and {\"O}lbei, Márton and Gabor, Attila and Theis, Fabian and Módos, Dezső and Korcsmáros, Tamás and Sáez Rodríguez, Julio},
  title={Integrated intra- and intercellular signaling knowledge for multicellular omics analysis},
  year={2021},
  pages={1-16},
  language={eng},
  issn={1744-4292},
  volume={17},
  note={Gesehen am 14.06.2021},
  journal={Molecular systems biology},
  doi={10.15252/msb.20209923},
  url={https://doi.org/10.15252/msb.20209923},
  library={UB},
}
@article{UBHD-69276336,
  author={Unger Avila, Paula and Padvitski, Tsimafei and Leote, Ana Carolina and Chen, He and Sáez Rodríguez, Julio and Kann, Martin and Beyer, Andreas},
  title={Gene regulatory networks in disease and ageing},
  year={2024},
  pages={616-633},
  language={eng},
  issn={1759-507X},
  volume={20},
  number={9},
  note={Gesehen am 25.11.2024},
  journal={Nature reviews},
  doi={10.1038/s41581-024-00849-7},
}
@article{UBHD-69191624,
  author={Valdeolivas, Alberto and Amberger, Bettina Theresia and Giroud, Nicolas and Richardson, Marion and Gálvez, Eric J. C. and Badillo, Solveig and Julien-Laferrière, Alice and Túrós, Demeter and Voith von Voithenberg, Lena and Wells, Isabelle and Pesti, Benedek and Lo, Amy A. and Yáng{\"u}ez, Emilio and Das Thakur, Meghna and Bscheider, Michael and Sultan, Marc and Kumpesa, Nadine and Jacobsen, Bj{\"o}rn and Bergauer, Tobias and Sáez Rodríguez, Julio and Rottenberg, Sven and Schwalie, Petra C. and Hahn, Kerstin},
  title={Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics},
  year={2024},
  pages={1-16},
  language={eng},
  issn={2397-768X},
  volume={8},
  note={Gesehen am 13.03.2024},
  journal={npj precision oncology},
  doi={10.1038/s41698-023-00488-4},
}
@article{UBHD-68702663,
  author={Wang, Dennis and Hensman, James and Kutkaite, Ginte and Toh, Tzen S. and Galhoz, Ana and Dry, Jonathan R. and Sáez Rodríguez, Julio and Garnett, Mathew J. and Menden, Michael and Dondelinger, Frank},
  title={A statistical framework for assessing pharmacological responses and biomarkers using uncertainty estimates},
  year={2020},
  pages={21 S.},
  language={eng},
  issn={2050-084X},
  volume={9(2020) Artikel-Nummer e60352},
  number={21 Seiten},
  note={Gesehen am 23.02.2021},
  journal={eLife},
  doi={10.7554/eLife.60352},
}
@article{UBHD-68936791,
  author={Wanner, Nicola and Andrieux, Geoffroy and Badia-i-Mompel, Pau and Edler, Carolin and Pfefferle, Susanne and Lindenmeyer, Maja T. and Schmidt-Lauber, Christian and Czogalla, Jan and Wong, Milagros N. and Okabayashi, Yusuke and Braun, Fabian and L{\"u}tgehetmann, Marc and Meister, Elisabeth and Lu, Shun and Noriega, Maria L. M. and G{\"u}nther, Thomas and Grundhoff, Adam and Fischer, Nicole and Br{\"a}uninger, Hanna and Lindner, Diana and Westermann, Dirk and Haas, Fabian and Roedl, Kevin and Kluge, Stefan and Addo, Marylyn M. and Huber, Samuel and Lohse, Ansgar W. and Reiser, Jochen and Ondruschka, Benjamin and Sperhake, Jan P. and Sáez Rodríguez, Julio and B{\"o}rries, Melanie and Hayek, Salim S. and Aepfelbacher, Martin and Scaturro, Pietro and Puelles, Victor G. and Huber, Tobias},
  title={Molecular consequences of SARS-CoV-2 liver tropism},
  year={2022},
  pages={310-319},
  language={eng},
  issn={2522-5812},
  volume={4},
  number={3 vom: M{\"a}rz},
  note={Gesehen am 02.07.2022},
  journal={Nature metabolism},
  doi={10.1038/s42255-022-00552-6},
}
@article{UBHD-69318508,
  author={White, Brian S. and de Reyniès, Aurélien and Newman, Aaron M. and Waterfall, Joshua J. and Lamb, Andrew and Petitprez, Florent and Lin, Yating and Yu, Rongshan and Guerrero-Gimenez, Martin E. and Domanskyi, Sergii and Monaco, Gianni and Chung, Verena and Banerjee, Jineta and Derrick, Daniel and Valdeolivas, Alberto and Li, Haojun and Xiao, Xu and Wang, Shun and Zheng, Frank and Yang, Wenxian and Catania, Carlos A. and Lang, Benjamin J. and Bertus, Thomas J. and Piermarocchi, Carlo and Caruso, Francesca P. and Ceccarelli, Michele and Yu, Thomas and Guo, Xindi and Bletz, Julie and Coller, John and Maecker, Holden and Duault, Caroline and Shokoohi, Vida and Patel, Shailja and Liliental, Joanna E. and Simon, Stockard and Sáez Rodríguez, Julio and Heiser, Laura M. and Guinney, Justin and Gentles, Andrew J.},
  title={Community assessment of methods to deconvolve cellular composition from bulk gene expression},
  year={2024},
  pages={1-22},
  language={eng},
  issn={2041-1723},
  volume={15},
  number={Artikel-ID 7362},
  note={Gesehen am 14.03.2025},
  journal={Nature Communications},
  doi={10.1038/s41467-024-50618-0},
}
@article{UBHD-68792319,
  author={Wijaya, Lukas Surya and Trairatphisan, Panuwat and Gabor, Attila and Niemeijer, Marije and Keet, Jason and Alcalà Morera, Ariadna and Snijders, Kirsten E. and Wink, Steven and Yang, Huan and Schildknecht, Stefan and Stevens, James L. and Bouwman, Peter and Kamp, Hennike and Hengstler, Jan and Beltman, Joost and Leist, Marcel and Le Dévédec, Sylvia and Sáez Rodríguez, Julio and van de Water, Bob},
  title={Integration of temporal single cell cellular stress response activity with logic-ODE modeling reveals activation of ATF4-CHOP axis as a critical predictor of drug-induced liver injury},
  year={2021},
  pages={1-17},
  language={eng},
  issn={1873-2968},
  volume={190(2021) vom: Aug.},
  number={Artikel-ID 114591},
  note={Gesehen am 21.10.2021},
  journal={Biochemical pharmacology},
  doi={10.1016/j.bcp.2021.114591},
}
@article{UBHD-69237120,
  author={Wijaya, Lukas Surya and Gabor, Attila and Pot, Iris E and van de Have, Luca and Sáez Rodríguez, Julio and Stevens, James L and Le Dévédec, Sylvia E and Callegaro, Giulia and van de Water, Bob},
  title={A network-based transcriptomic landscape of HepG2 cells uncovering causal gene-cytotoxicity interactions underlying drug-induced liver injury},
  year={2024},
  pages={14-30},
  language={eng},
  issn={1096-0929},
  volume={198},
  number={1 vom: M{\"a}rz},
  note={Ver{\"o}ffentlicht: 28. November 2023 ; Gesehen am 24.07.2024},
  journal={Toxicological sciences},
  doi={10.1093/toxsci/kfad121},
}
@incollection{UBHD-68560080,
  author={Wirbel, Jakob and Cutillas, Pedro and Sáez Rodríguez, Julio},
  title={Phosphoproteomics-based profiling of kinase activities in cancer cells},
  year={2018},
  pages={103-132},
  language={eng},
  isbn={978-1-4939-7493-1},
  note={Gesehen am 01.04.2020},
  booktitle={Cancer Systems Biology},
  editor={Stechow, Louise von},
  doi={10.1007/978-1-4939-7493-1_6},
}
@article{UBHD-69127844,
  author={Wolf, Stephanie and Ehlting, Christian and M{\"u}ller-Dott, Sophia and Poschmann, Gereon and Petzsch, Patrick and Lautwein, Tobias and Wang, Sai and Helm, Barbara and Schilling, Marcel and Sáez Rodríguez, Julio and Vucur, Mihael and St{\"u}hler, Kai and K{\"o}hrer, Karl and Tacke, Frank and Dooley, Steven and Klingm{\"u}ller, Ursula and Luedde, Tom and Bode, Johannes G.},
  title={Hepatocytes reprogram liver macrophages involving control of TGF-β activation, influencing liver regeneration and injury},
  year={2023},
  pages={1-17},
  language={eng},
  issn={2471-254X},
  volume={7},
  note={Gesehen am 09.10.2023},
  journal={Hepatology communications},
  doi={10.1097/HC9.0000000000000208},
}
@article{UBHD-68735138,
  author={Yang, Mi and Jaaks, Patricia and Dry, Jonathan and Garnett, Mathew and Menden, Michael P. and Sáez Rodríguez, Julio},
  title={Stratification and prediction of drug synergy based on target functional similarity},
  year={2020},
  pages={1-10},
  language={eng},
  issn={2056-7189},
  volume={6},
  number={Artikel-ID 16},
  note={Gesehen am 07.05.2021},
  journal={npj Systems biology and applications},
  doi={10.1038/s41540-020-0136-x},
}
@article{UBHD-68641196,
  author={Yang, Mi and Sáez Rodríguez, Julio},
  title={Community assessment of the predictability of cancer protein and phosphoprotein levels from genomics and transcriptomics},
  year={2020},
  pages={19 S.},
  language={eng},
  issn={2405-4720},
  volume={11(2020},
  note={The members of the NCI-CPTAC-DREAM Consortium are Tunde Aderinwale, Ebrahim Afyounian, Piyush Agrawal, Mehreen Ali, Alicia Amadoz, Francisco Azuaje, John Bachman, Seohui Bae, Sherry Bhalla, José Carbonell-Caballero, Priyanka Chakraborty, Kumardeep Chaudhary, Yonghwa Choi, Yoonjung Choi, Cankut Çubuk, Sandeep Kumar Dhanda, Joaquín Dopazo, Laura L. Elo, Ábel Fóthi, Olivier Gevaert, Kirsi Granberg, Russell Greiner, Eunji Heo, Marta R. Hidalgo, Vivek Jayaswal, Hwisang Jeon, Minji Jeon, Sunil V. Kalmady, Yasuhiro Kambara, Jaewoo Kang, Keunsoo Kang, Tony Kaoma, Harpreet Kaur, Hilal Kazan, Devishi Kesar, Juha Kesseli, Daehan Kim, Keonwoo Kim, Sang-Yoon Kim, Sunkyu Kim, Sajal Kumar, Bora Lee, Heewon Lee, Yunpeng Liu, Roland Luethy, Swapnil Mahajan, Mehrad Mahmoudian, Arnaud Muller, Petr V. Nazarov, Hien Nguyen, Matti Nykter, Shujiro Okuda, Sungsoo Park, Gajendra Pal Singh Raghava, Jagath C. Rajapakse, Tommi Rantapero, Hobin Ryu, Francisco Salavert, Sohrab Saraei, Ruby Sharma, Ari Siitonen, Artem Sokolov, Kartik Subramanian, Veronika Suni, Tomi Suomi, Léon-Charles Tranchevent, Salman Sadullah Usmani, Tommi V{\"a}likangas, Roberto Vega, and Hua Zhong ; Gesehen am 29.09.2020},
  journal={Cell systems},
  doi={10.1016/j.cels.2020.06.013},
}