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Marc R. Birtwistle, Ph.D. - Publications

Affiliations: 
2008 Department of Chemical Engineering University of Delaware, Newark, DE, United States 
Area:
Chemical Engineering, Biochemistry, Molecular Biology
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49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Sarmah D, Smith GR, Bouhaddou M, Stern AD, Erskine J, Birtwistle MR. Network inference from perturbation time course data. Npj Systems Biology and Applications. 8: 42. PMID 36316338 DOI: 10.1038/s41540-022-00253-6  0.632
2022 Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR. A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nature Communications. 13: 3555. PMID 35729113 DOI: 10.1038/s41467-022-31138-1  0.69
2022 Walz AC, Van De Vyver AJ, Yu L, Birtwistle MR, Krogan NJ, Bouhaddou M. Leveraging modeling and simulation to optimize the therapeutic window for epigenetic modifier drugs. Pharmacology & Therapeutics. 235: 108162. PMID 35189161 DOI: 10.1016/j.pharmthera.2022.108162  0.701
2019 Bouhaddou M, Yu LJ, Lunardi S, Stamatelos SK, Mack F, Gallo JM, Birtwistle MR, Walz AC. Predicting In Vivo Efficacy from In Vitro Data: Quantitative Systems Pharmacology Modeling for an Epigenetic Modifier Drug in Cancer. Clinical and Translational Science. PMID 31729169 DOI: 10.1111/Cts.12727  0.684
2019 Niepel M, Hafner M, Mills CE, Subramanian K, Williams EH, Chung M, Gaudio B, Barrette AM, Stern AD, Hu B, Korkola JE, Gray JW, Birtwistle MR, Heiser LM, et al. A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines. Cell Systems. PMID 31302153 DOI: 10.1016/J.Cels.2019.06.005  0.38
2019 Santos LC, Vogel R, Chipuk JE, Birtwistle MR, Stolovitzky G, Meyer P. Mitochondrial origins of fractional control in regulated cell death. Nature Communications. 10: 1313. PMID 30899020 DOI: 10.1038/S41467-019-09275-X  0.353
2018 Holzapfel HY, Stern AD, Bouhaddou M, Anglin C, Putur D, Comer S, Birtwistle M. Fluorescence Multiplexing with Spectral Imaging and Combinatorics. Acs Combinatorial Science. PMID 30339749 DOI: 10.1021/Acscombsci.8B00101  0.625
2018 Koch RJ, Barrette AM, Stern AD, Hu B, Bouhaddou M, Azeloglu EU, Iyengar R, Birtwistle MR. Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array. Scientific Reports. 8: 11329. PMID 30054510 DOI: 10.1038/S41598-018-29436-0  0.625
2018 Bouhaddou M, Barrette AM, Stern AD, Koch RJ, DiStefano MS, Riesel EA, Santos LC, Tan AL, Mertz AE, Birtwistle MR. A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens. Plos Computational Biology. 14: e1005985. PMID 29579036 DOI: 10.1371/Journal.Pcbi.1005985  0.721
2018 Jones DC, Scanteianu A, DiStefano M, Bouhaddou M, Birtwistle MR. Analysis of copy number loss of the ErbB4 receptor tyrosine kinase in glioblastoma. Plos One. 13: e0190664. PMID 29342193 DOI: 10.1371/Journal.Pone.0190664  0.679
2018 Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, ... ... Birtwistle MR, et al. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems. 6: 13-24. PMID 29199020 DOI: 10.1016/J.Cels.2017.11.001  0.333
2017 Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, ... ... Birtwistle MR, et al. A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries. Scientific Reports. 7: 14626. PMID 29116112 DOI: 10.1038/S41598-017-14892-X  0.649
2017 Shim JV, Chun B, van Hasselt JGC, Birtwistle MR, Saucerman JJ, Sobie EA. Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics. Frontiers in Physiology. 8: 651. PMID 28951721 DOI: 10.3389/Fphys.2017.00651  0.412
2017 Barrette AM, Bouhaddou M, Birtwistle MR. Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials. Acs Chemical Neuroscience. PMID 28950062 DOI: 10.1021/Acschemneuro.7B00197  0.7
2017 Bouhaddou M, Barrette AM, Koch RJ, Birtwistle MR. Abstract 1568: Predicting stochastic proliferation and death in response to drugs with mechanistic models tailored to genomic, transcriptomic, and proteomic data Cancer Research. 77: 1568-1568. DOI: 10.1158/1538-7445.Am2017-1568  0.719
2016 Bouhaddou M, DiStefano MS, Riesel EA, Carrasco E, Holzapfel HY, Jones DC, Smith GR, Stern AD, Somani SS, Thompson TV, Birtwistle MR. Drug response consistency in CCLE and CGP. Nature. 540: E9-E10. PMID 27905419 DOI: 10.1038/Nature20580  0.646
2016 Byrne KM, Monsefi N, Dawson JC, Degasperi A, Bukowski-Wills JC, Volinsky N, Dobrzyński M, Birtwistle MR, Tsyganov MA, Kiyatkin A, Kida K, Finch AJ, Carragher NO, Kolch W, Nguyen LK, et al. Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches. Cell Systems. 2: 38-48. PMID 27136688 DOI: 10.1016/J.Cels.2016.01.003  0.591
2016 Byrne KM, Monsefi N, Dawson JC, Degasperi A, Bukowski-Wills JC, Volinsky N, Dobrzyński M, Birtwistle MR, Tsyganov MA, Kiyatkin A, Kida K, Finch AJ, Carragher NO, Kolch W, Nguyen LK, et al. Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches Cell Systems. 2: 38-48. DOI: 10.1016/j.cels.2016.01.003  0.502
2016 Shim JV, Birtwistle MR, Iyengar R, Sobie EA. Integrated Analysis for Quantitative Predictions of Drug Induced Cardiotoxicity Biophysical Journal. 110: 476a-477a. DOI: 10.1016/J.Bpj.2015.11.2549  0.423
2015 Milewska M, Romano D, Herrero A, Guerriero ML, Birtwistle M, Quehenberger F, Hatzl S, Kholodenko BN, Segatto O, Kolch W, Zebisch A. Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation. Plos One. 10: e0129859. PMID 26065894 DOI: 10.1371/Journal.Pone.0129859  0.575
2015 Gallo JM, Birtwistle MR. Network pharmacodynamic models for customized cancer therapy. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 7: 243-51. PMID 25914386 DOI: 10.1002/Wsbm.1300  0.346
2015 Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, et al. Silence on the relevant literature and errors in implementation. Nature Biotechnology. 33: 336-9. PMID 25850052 DOI: 10.1038/Nbt.3185  0.451
2015 Birtwistle MR. Analytical reduction of combinatorial complexity arising from multiple protein modification sites. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 25519995 DOI: 10.1098/Rsif.2014.1215  0.312
2014 DobrzyÅ„ski M, Nguyen LK, Birtwistle MR, von Kriegsheim A, Blanco Fernández A, Cheong A, Kolch W, Kholodenko BN. Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses. Journal of the Royal Society, Interface / the Royal Society. 11: 20140383. PMID 24966234 DOI: 10.1098/Rsif.2014.0383  0.57
2014 Weige CC, Birtwistle MR, Mallick H, Yi N, Berrong Z, Cloessner E, Duff K, Tidwell J, Clendenning M, Wilkerson B, Farrell C, Bunz F, Ji H, Shtutman M, Creek KE, et al. Transcriptomes and shRNA suppressors in a TP53 allele-specific model of early-onset colon cancer in African Americans. Molecular Cancer Research : McR. 12: 1029-41. PMID 24743655 DOI: 10.1158/1541-7786.Mcr-13-0286-T  0.312
2014 Bouhaddou M, Birtwistle MR. Dimerization-based control of cooperativity. Molecular Biosystems. 10: 1824-32. PMID 24736836 DOI: 10.1039/C4Mb00022F  0.65
2014 Degasperi A, Birtwistle MR, Volinsky N, Rauch J, Kolch W, Kholodenko BN. Evaluating strategies to normalise biological replicates of Western blot data. Plos One. 9: e87293. PMID 24475266 DOI: 10.1371/Journal.Pone.0087293  0.503
2014 Sutera C, Duran-Paez MA, Haughney E, Gucwa A, Birtwistle MR, Fink MY. Regulatory Feedback Programs in the Apoptotic Decision-Making of Her2-Positive Breast Cancer Cells in Response to HER2 Inhibition Biophysical Journal. 106: 593a. DOI: 10.1016/J.Bpj.2013.11.3285  0.39
2013 von Thun A, Preisinger C, Rath O, Schwarz JP, Ward C, Monsefi N, Rodríguez J, Garcia-Munoz A, Birtwistle M, Bienvenut W, Anderson KI, Kolch W, von Kriegsheim A. Extracellular signal-regulated kinase regulates RhoA activation and tumor cell plasticity by inhibiting guanine exchange factor H1 activity. Molecular and Cellular Biology. 33: 4526-37. PMID 24043311 DOI: 10.1128/Mcb.00585-13  0.352
2013 Greene J, Birtwistle MR, Ignatowicz L, Rempala GA. Bayesian multivariate Poisson abundance models for T-cell receptor data. Journal of Theoretical Biology. 326: 1-10. PMID 23467198 DOI: 10.1016/J.Jtbi.2013.02.009  0.31
2012 Birtwistle MR, von Kriegsheim A, Dobrzyński M, Kholodenko BN, Kolch W. Mammalian protein expression noise: scaling principles and the implications for knockdown experiments. Molecular Biosystems. 8: 3068-76. PMID 22990612 DOI: 10.1039/C2Mb25168J  0.546
2012 Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzyński M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN. Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. Bmc Systems Biology. 6: 109. PMID 22920937 DOI: 10.1186/1752-0509-6-109  0.697
2012 von Thun A, Birtwistle M, Kalna G, Grindlay J, Strachan D, Kolch W, von Kriegsheim A, Norman JC. ERK2 drives tumour cell migration in three-dimensional microenvironments by suppressing expression of Rab17 and liprin-β2. Journal of Cell Science. 125: 1465-77. PMID 22328529 DOI: 10.1242/Jcs.092916  0.36
2012 Bruning U, Fitzpatrick SF, Frank T, Birtwistle M, Taylor CT, Cheong A. NFκB and HIF display synergistic behaviour during hypoxic inflammation. Cellular and Molecular Life Sciences : Cmls. 69: 1319-29. PMID 22068612 DOI: 10.1007/S00018-011-0876-2  0.305
2011 Birtwistle MR, von Kriegsheim A, Kida K, Schwarz JP, Anderson KI, Kolch W. Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modeling. Plos One. 6: e27823. PMID 22114702 DOI: 10.1371/Journal.Pone.0027823  0.315
2011 Matallanas D, Birtwistle M, Romano D, Zebisch A, Rauch J, von Kriegsheim A, Kolch W. Raf family kinases: old dogs have learned new tricks. Genes & Cancer. 2: 232-60. PMID 21779496 DOI: 10.1177/1947601911407323  0.385
2011 Birtwistle MR, Kolch W. Biology using engineering tools: the negative feedback amplifier. Cell Cycle (Georgetown, Tex.). 10: 2069-76. PMID 21572255 DOI: 10.4161/Cc.10.13.16245  0.303
2010 Sturm OE, Orton R, Grindlay J, Birtwistle M, Vyshemirsky V, Gilbert D, Calder M, Pitt A, Kholodenko B, Kolch W. The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. Science Signaling. 3: ra90. PMID 21177493 DOI: 10.1126/Scisignal.2001212  0.577
2010 Nakakuki T, Birtwistle MR, Saeki Y, Yumoto N, Ide K, Nagashima T, Brusch L, Ogunnaike BA, Okada-Hatakeyama M, Kholodenko BN. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell. 141: 884-96. PMID 20493519 DOI: 10.1016/J.Cell.2010.03.054  0.666
2010 Kolch W, Birtwistle M, Kholodenko B, Grindlay J, Sturm O, Orton R, Gilbert D, von Kriegsheim A. 11 From benchside to byteside: what we can learn from computational modelling European Journal of Cancer Supplements. 8: 3. DOI: 10.1016/S1359-6349(10)70820-X  0.572
2009 Kholodenko BN, Birtwistle MR. Four-dimensional dynamics of MAPK information processing systems. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 1: 28-44. PMID 20182652 DOI: 10.1002/Wsbm.16  0.578
2009 von Kriegsheim A, Baiocchi D, Birtwistle M, Sumpton D, Bienvenut W, Morrice N, Yamada K, Lamond A, Kalna G, Orton R, Gilbert D, Kolch W. Cell fate decisions are specified by the dynamic ERK interactome. Nature Cell Biology. 11: 1458-64. PMID 19935650 DOI: 10.1038/Ncb1994  0.387
2009 Birtwistle MR, Kholodenko BN. Endocytosis and signalling: a meeting with mathematics. Molecular Oncology. 3: 308-20. PMID 19596615 DOI: 10.1016/J.Molonc.2009.05.009  0.561
2008 Birtwistle MR, Millili PG, Ogunnaike BA. A first-principles model for eukaryotic DNA synthesis dynamics and the implications for cell cycle analysis Aiche Annual Meeting, Conference Proceedings.  0.489
2008 Birtwistle MR, Ogunnaike BA. Development and analysis of models for cell-to-cell variability in protein expression Aiche Annual Meeting, Conference Proceedings.  0.52
2007 Birtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN. Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. Molecular Systems Biology. 3: 144. PMID 18004277 DOI: 10.1038/Msb4100188  0.694
2007 Birtwistle MR, Kholodenko BN, Kiyatkin A, Hoek JB, Ogunnaike BA. Experimental investigation and probabilistic modeling of switch-like signal transduction systems Aiche Annual Meeting, Conference Proceedings.  0.626
2006 Birtwistle MR, Hatakeyama M, Yumoto N, Hoek JB, Kholodenko BN, Ogunnaike BA. Modeling the ErbB signaling network in MCF-7 breast cancer cells and analysis of ligand-dependent responses Aiche Annual Meeting, Conference Proceedings.  0.672
2004 Birtwistle MR, Ogunnaike BA, Lombardo T. Analysis and optimization of cell-cycle specific cancer chemotherapy Aiche Annual Meeting, Conference Proceedings. 8771-8773.  0.493
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