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Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity.
Published in:
Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-021-01114-3
By:
- Xiong, Yuguang;
- Liu, Tong;
- Chen, Tong;
- Hansen, Jens;
- Hu, Bin;
- Chen, Yibang;
- Jayaraman, Gomathi;
- Schürer, Stephan;
- Vidovic, Dusica;
- Goldfarb, Joseph;
- Sobie, Eric A.;
- Birtwistle, Marc R.;
- Iyengar, Ravi;
- Li, Hong;
- Azeloglu, Evren U.
Publication type:
Article
Predicting individual-specific cardiotoxicity responses induced by tyrosine kinase inhibitors.
Published in:
Frontiers in Pharmacology, 2023, v. 14, p. 1, doi. 10.3389/fphar.2023.1158222
By:
- Shim, Jaehee V.;
- Yuguang Xiong;
- Dhanan, Priyanka;
- Dariolli, Rafael;
- Azeloglu, Evren U.;
- Bin Hu;
- Jayaraman, Gomathi;
- Schaniel, Christoph;
- Birtwistle, Marc R.;
- Iyengar, Ravi;
- Dubois, Nicole C.;
- Sobie, Eric A.
Publication type:
Article
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31138-1
By:
- Erdem, Cemal;
- Mutsuddy, Arnab;
- Bensman, Ethan M.;
- Dodd, William B.;
- Saint-Antoine, Michael M.;
- Bouhaddou, Mehdi;
- Blake, Robert C.;
- Gross, Sean M.;
- Heiser, Laura M.;
- Feltus, F. Alex;
- Birtwistle, Marc R.
Publication type:
Article
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise.
Published in:
BMC Systems Biology, 2012, v. 6, n. 1, p. 109, doi. 10.1186/1752-0509-6-109
By:
- Birtwistle, Marc R.;
- Rauch, Jens;
- Kiyatkin, Anatoly;
- Aksamitiene, Edita;
- Dobrzyński, Maciej;
- Hoek, Jan B.;
- Kolch, Walter;
- Ogunnaike, Babatunde A.;
- Kholodenko, Boris N.
Publication type:
Article
Relating individual cell division events to single-cell ERK and Akt activity time courses.
Published in:
Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-23071-6
By:
- Stern, Alan D.;
- Smith, Gregory R.;
- Santos, Luis C.;
- Sarmah, Deepraj;
- Zhang, Xiang;
- Lu, Xiaoming;
- Iuricich, Federico;
- Pandey, Gaurav;
- Iyengar, Ravi;
- Birtwistle, Marc R.
Publication type:
Article
Silence on the relevant literature and errors in implementation.
Published in:
Nature Biotechnology, 2015, v. 33, n. 4, p. 336, doi. 10.1038/nbt.3185
By:
- Bastiaens, Philippe;
- Birtwistle, Marc R;
- Blüthgen, Nils;
- Bruggeman, Frank J;
- Cho, Kwang-Hyun;
- Cosentino, Carlo;
- de la Fuente, Alberto;
- Hoek, Jan B;
- Kiyatkin, Anatoly;
- Klamt, Steffen;
- Kolch, Walter;
- Legewie, Stefan;
- Mendes, Pedro;
- Naka, Takashi;
- Santra, Tapesh;
- Sontag, Eduardo;
- Westerhoff, Hans V;
- Kholodenko, Boris N
Publication type:
Article
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39729-2
By:
- Erdem, Cemal;
- Gross, Sean M.;
- Heiser, Laura M.;
- Birtwistle, Marc R.
Publication type:
Article
Evaluating Strategies to Normalise Biological Replicates of Western Blot Data.
Published in:
PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0087293
By:
- Degasperi, Andrea;
- Birtwistle, Marc R.;
- Volinsky, Natalia;
- Rauch, Jens;
- Kolch, Walter;
- Kholodenko, Boris N.
Publication type:
Article
Novel Somatic Mutations to PI3K Pathway Genes in Metastatic Melanoma.
Published in:
PLoS ONE, 2012, v. 7, n. 8, p. 1, doi. 10.1371/journal.pone.0043369
By:
- Shull, Austin Y.;
- Latham-Schwark, Alicia;
- Ramasamy, Poornema;
- Leskoske, Kristin;
- Oroian, Dora;
- Birtwistle, Marc R.;
- Buckhaults, Phillip J.;
- Chammas, Roger
Publication type:
Article
Linear Approaches to Intramolecular Förster Resonance Energy Transfer Probe Measurements for Quantitative Modeling.
Published in:
PLoS ONE, 2011, v. 6, n. 11, p. 1, doi. 10.1371/journal.pone.0027823
By:
- Birtwistle, Marc R.;
- Kriegsheim, Alexander von;
- Kida, Katarzyna;
- Schwarz, Juliane P.;
- Anderson, Kurt I.;
- Kolch, Walter
Publication type:
Article
Wilm's tumor 1 promotes memory flexibility.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-11781-x
By:
- Mariottini, Chiara;
- Munari, Leonardo;
- Gunzel, Ellen;
- Seco, Joseph M.;
- Tzavaras, Nikos;
- Hansen, Jens;
- Stern, Sarah A.;
- Gao, Virginia;
- Aleyasin, Hossein;
- Sharma, Ali;
- Azeloglu, Evren U.;
- Hodes, Georgia E.;
- Russo, Scott J.;
- Huff, Vicki;
- Birtwistle, Marc R.;
- Blitzer, Robert D.;
- Alberini, Cristina M.;
- Iyengar, Ravi
Publication type:
Article
Mitochondrial origins of fractional control in regulated cell death.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-09275-x
By:
- Santos, Luís C.;
- Vogel, Robert;
- Chipuk, Jerry E.;
- Birtwistle, Marc R.;
- Stolovitzky, Gustavo;
- Meyer, Pablo
Publication type:
Article
Cell size assays for mass cytometry.
Published in:
Cytometry. Part A, 2017, v. 91, n. 1, p. 14, doi. 10.1002/cyto.a.23000
By:
- Stern, Alan D.;
- Rahman, Adeeb H.;
- Birtwistle, Marc R.
Publication type:
Article
CNS Anticancer Drug Discovery and Development Conference White Paper.
Published in:
Neuro-Oncology, 2015, v. 17, p. vi1, doi. 10.1093/neuonc/nov169
By:
- Levin, Victor A.;
- Tonge, Peter J.;
- Gallo, James M.;
- Birtwistle, Marc R.;
- Dar, Arvin C.;
- Iavarone, Antonio;
- Paddison, Patrick J.;
- Heffron, Timothy P.;
- Elmquist, William F.;
- Lachowicz, Jean E.;
- Johnson, Ted W.;
- White, Forest M.;
- Joohee Sul;
- Smith, Quentin R.;
- Wang Shen;
- Sarkaria, Jann N.;
- Samala, Ramakrishna;
- Wen, Patrick Y.;
- Berry, Donald A.;
- Petter, Russell C.
Publication type:
Article
Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses.
Published in:
Molecular Systems Biology, 2007, v. 3, n. 1, p. 1, doi. 10.1038/msb4100188
By:
- Birtwistle, Marc R;
- Hatakeyama, Mariko;
- Yumoto, Noriko;
- Ogunnaike, Babatunde A;
- Hoek, Jan B;
- Kholodenko, Boris N
Publication type:
Article
A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data.
Published in:
PLoS ONE, 2016, v. 11, n. 6, p. 1, doi. 10.1371/journal.pone.0157828
By:
- Smith, Gregory R.;
- Birtwistle, Marc R.
Publication type:
Article
Predicting anti-cancer drug combination responses with a temporal cell state network model.
Published in:
PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011082
By:
- Sarmah, Deepraj;
- Meredith, Wesley O.;
- Weber, Ian K.;
- Price, Madison R.;
- Birtwistle, Marc R.
Publication type:
Article
Predicting In Vivo Efficacy from In Vitro Data: Quantitative Systems Pharmacology Modeling for an Epigenetic Modifier Drug in Cancer.
Published in:
CTS: Clinical & Translational Science, 2020, v. 13, n. 2, p. 419, doi. 10.1111/cts.12727
By:
- Bouhaddou, Mehdi;
- Yu, Li J.;
- Lunardi, Serena;
- Stamatelos, Spyros K.;
- Mack, Fiona;
- Gallo, James M.;
- Birtwistle, Marc R.;
- Walz, Antje‐Christine
Publication type:
Article
MEMMAL: A tool for expanding large-scale mechanistic models with machine learned associations and big datasets.
Published in:
Frontiers in Systems Biology, 2023, v. 3, p. 1, doi. 10.3389/fsysb.2023.1099413
By:
- Erdem, Cemal;
- Birtwistle, Marc R.
Publication type:
Article
Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.
Published in:
Bioinformatics Advances, 2023, v. 3, n. 1, p. 1, doi. 10.1093/bioadv/vbad039
By:
- Mutsuddy, Arnab;
- Erdem, Cemal;
- Huggins, Jonah R;
- Salim, Misha;
- Cook, Daniel;
- Hobbs, Nicole;
- Feltus, F Alex;
- Birtwistle, Marc R
Publication type:
Article
Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array.
Published in:
Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-29436-0
By:
- Koch, Rick J.;
- Barrette, Anne Marie;
- Stern, Alan D.;
- Hu, Bin;
- Bouhaddou, Mehdi;
- Azeloglu, Evren U.;
- Iyengar, Ravi;
- Birtwistle, Marc R.
Publication type:
Article
Anti-invasive efficacy and survival benefit of the YAP-TEAD inhibitor verteporfin in preclinical glioblastoma models.
Published in:
Neuro-Oncology, 2022, v. 24, n. 5, p. 694, doi. 10.1093/neuonc/noab244
By:
- Barrette, Anne Marie;
- Ronk, Halle;
- Joshi, Tanvi;
- Mussa, Zarmeen;
- Mehrotra, Meenakshi;
- Bouras, Alexandros;
- Nudelman, German;
- Raj, Joe Gerald Jesu;
- Bozec, Dominique;
- Lam, William;
- Houldsworth, Jane;
- Yong, Raymund;
- Zaslavsky, Elena;
- Hadjipanayis, Constantinos G;
- Birtwistle, Marc R;
- Tsankova, Nadejda M
Publication type:
Article
Multiscale mapping of transcriptomic signatures for cardiotoxic drugs.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52145-4
By:
- Hansen, Jens;
- Xiong, Yuguang;
- Siddiq, Mustafa M.;
- Dhanan, Priyanka;
- Hu, Bin;
- Shewale, Bhavana;
- Yadaw, Arjun S.;
- Jayaraman, Gomathi;
- Tolentino, Rosa E.;
- Chen, Yibang;
- Martinez, Pedro;
- Beaumont, Kristin G.;
- Sebra, Robert;
- Vidovic, Dusica;
- Schürer, Stephan C.;
- Goldfarb, Joseph;
- Gallo, James M.;
- Birtwistle, Marc R.;
- Sobie, Eric A.;
- Azeloglu, Evren U.
Publication type:
Article
Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events.
Published in:
NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00389-7
By:
- Bennett, Jamie J. R.;
- Stern, Alan D.;
- Zhang, Xiang;
- Birtwistle, Marc R.;
- Pandey, Gaurav
Publication type:
Article
Network inference from perturbation time course data.
Published in:
NPJ Systems Biology & Applications, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41540-022-00253-6
By:
- Sarmah, Deepraj;
- Smith, Gregory R.;
- Bouhaddou, Mehdi;
- Stern, Alan D.;
- Erskine, James;
- Birtwistle, Marc R.
Publication type:
Article
A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach.
Published in:
Biosensors (2079-6374), 2013, v. 3, n. 3, p. 238, doi. 10.3390/bios3030238
By:
- Wesolowski, Sergiusz;
- Birtwistle, Marc R.;
- Rempala, Grzegorz A.
Publication type:
Article
Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-18396-7
By:
- van Hasselt, J. G. Coen;
- Rahman, Rayees;
- Hansen, Jens;
- Stern, Alan;
- Shim, Jaehee V.;
- Xiong, Yuguang;
- Pickard, Amanda;
- Jayaraman, Gomathi;
- Hu, Bin;
- Mahajan, Milind;
- Gallo, James M.;
- Goldfarb, Joseph;
- Sobie, Eric A.;
- Birtwistle, Marc R.;
- Schlessinger, Avner;
- Azeloglu, Evren U.;
- Iyengar, Ravi
Publication type:
Article
Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics.
Published in:
Frontiers in Physiology, 2017, p. 1, doi. 10.3389/fphys.2017.00651
By:
- Shim, Jaehee V.;
- van Hasselt, Johan G. C.;
- Birtwistle, Marc R.;
- Sobie, Eric A.;
- Chun, Bryan;
- Saucerman, Jeffrey J.
Publication type:
Article
Analysis of copy number loss of the ErbB4 receptor tyrosine kinase in glioblastoma.
Published in:
PLoS ONE, 2018, v. 13, n. 1, p. 1, doi. 10.1371/journal.pone.0190664
By:
- Jones, DeAnalisa C.;
- Scanteianu, Adriana;
- DiStefano, Matthew;
- Bouhaddou, Mehdi;
- Birtwistle, Marc R.
Publication type:
Article
Endocytosis and signalling: A meeting with mathematics
Published in:
Molecular Oncology, 2009, v. 3, n. 4, p. 308, doi. 10.1016/j.molonc.2009.05.009
By:
- Birtwistle, Marc R.;
- Kholodenko, Boris N.
Publication type:
Article
A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens.
Published in:
PLoS Computational Biology, 2018, v. 14, n. 3, p. 1, doi. 10.1371/journal.pcbi.1005985
By:
- Bouhaddou, Mehdi;
- Barrette, Anne Marie;
- Stern, Alan D.;
- Koch, Rick J.;
- DiStefano, Matthew S.;
- Riesel, Eric A.;
- Santos, Luis C.;
- Tan, Annie L.;
- Mertz, Alex E.;
- Birtwistle, Marc R.
Publication type:
Article

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