Fluorescence Multiplexing with Spectral Imaging and Combinatorics
Hadassa Y. Holzapfel, Alan D. Stern, Mehdi Bouhaddou, Caitlin M. Anglin, Danielle Putur, Sarah Comer and Marc R. Birtwistle
ACS Combinatorial Science, DOI: 10.1021/acscombsci.8b00101 (19 October 2018)
Supplementary Methods
Tables S1 and S2
Supplementary Code

Gene-Specific Predictability of Protein Levels from mRNA Data in Humans
Alief Moulana, Adriana Scanteianu, DeAnalisa Jones, Alan D Stern, Mehdi Bouhaddou, Marc Birtwistle bioRxiv Pre-Print, August 2018

Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array
Rick J Koch, Anne Marie Barrette, Alan D Stern, Bin Hu, Evren U Azeloglu, Ravi Iyengar, Marc R Birtwistle
Scientific Reports 8, Article number:11329 (27 July 2018)

Network Reconstruction from Perturbation Time Course Data
Gregory R. Smith, Mehdi Bouhaddou, Alan D. Stern, Caitlin M. Anglin, Orrod M Zadeh, Jake Erskin, Marc R. Birtwistle
bioRxiv Pre-Print, June 2018
Supplementary Code

A Mechanistic Pan-Cancer Pathway Model Informed by Multi-Omics Data Interprets Stochastic Cell Fate Responses to Drugs and Mitogens
Mehdi Bouhaddou, Anne Marie Barrette, Alan D. Stern, Rick J. Koch, Matthew S. DiStefano, Eric A. Riesel, Luis C. Santos, Annie L. Tan, Alex E. Mertz, Marc R. Birtwistle
PLoS Comp Bio. March 2018; 14(3):e1005985

Analysis of Copy Number Loss of the ErbB4 Receptor Tyrosine Kinase in Glioblastoma
DeAnalisa C. Jones, Adriana Scanteianu, Matthew DiStefano, Mehdi Bouhaddou, Marc R. Birtwistle
PLoS One. January 2018; 13(1):e0190664


The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations
Alexandra B. Keenan, LINCS Consortium
Cell Systems (29 November 2017)

A Multi-Center Study on Factors Influencing the Reproducibility of in Vitro Drug-Response Studies
Mario Niepel, Marc Hafner, Elizabeth Hope Williams, Mirra Chung, Anne Marie Barrette, Alan D. Stern, Bin Hu, LINCS Consortium, Joe W. Gray, Marc R. Birtwistle, Laura M. Heiser, Peter K. Sorger
bioRxiv preprint (November 2017)

A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries
Yuguang Xiong , Magali Soumillon, Jie Wu, Jens Hansen, Bin Hu, Johan G.C. van Hasselt, Gomathi Jayaraman, Ryan Lim, Mehdi Bouhaddou, Loren Ornelas, Jim Bochicchio, Lindsay Lenaeus, Jennifer Stocksdale, Jaehee Shim, Emilda Gomez, Dhruv Sareen, Clive Svendsen, Leslie M. Thompson, Milind Mahajan, Ravi Iyengar, Eric A. Sobie, Evren U. Azeloglu, Marc R. Birtwistle
Scientific Reports 7, Article number: 14626 (07 November 2017)

Origins of Fractional Control in Regulated Cell Death
Luis C. Santos, Robert Vogel, Jerry E. Chipuk, Marc R. Birtwistle, Gustavo Stolovitzky, Pablo Meyer
bioRxiv preprint (October 2017)

Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials
Anne Marie Barrette, Mehdi Bouhaddou, Marc R. Birtwistle
ACS Chem. Neuroscience 2017

Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics
Jaehee V. Shim, Bryan Chun, Johan G. C. van Hasselt, Marc R. Birtwistle, Jeffrey J. Saucerman and Eric A. Sobie
Front. Physiol. 2017


Kinetic Models of Biochemical Signaling Networks
Mehdi Bouhaddou, Marc R. Birtwistle
Systems Pharmacology and Pharmacodynamics, Chapter 6 (02 December 2016)

Systems Pharmacology: An Overview
Marc R. Birtwistle, Jens Hansen, James M. Gallo, Sreeharish, Muppirisetty, Peter Man-Un Ung, Ravi Iyengar, Avner Schlessinger
Systems Pharmacology and Pharmacodynamics, Chapter 4 (02 December 2016)

Drug response consistency in CCLE and CGP
Mehdi Bouhaddou, Matthew S. DiStefano, Eric A. Riesel, Emilce Carrasco, Hadassa Y. Holzapfel, DeAnalisa C. Jones, Gregory R. Smith, Alan D. Stern, Sulaiman S. Somani, T. Victoria Thompson, Marc R. Birtwistle
Nature 540, E9–E10, (01 December 2016)

Cell Size Assays for Mass Cytometry
Alan D. Stern, Adeeb H. Rahman, Marc R. Birtwistle
Cytometry A. 2016 Oct 21. doic 10.1002/cyto.a.23000

A Temporal Logic Inference Approach for Model Discrimination
Zhe Xu, Marc Birtwistle, Calin Belta, Agung Julius
IEEE Life Sciences Letters, Volume 2 Issue 3 (September 2016)

A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data
Gregory R. Smith, Marc R. Birtwistle
PLoS One. June 2016; 11(6): e0157828
Supplementary Data 1
Supplementary Data 2

Creating Complex Fluorophore Spectra on Antibodies Through Combinatorial Labeling
Hadassa Y. Holzapfel, Marc R. Birtwistle
Translational Science. March 2016; pii: e03

Current Proteomic Methods to Investigate the Dynamics of Histone Turnover in the Central Nervous System
L.A. Farrelly, B.D. Dill, H. Molina, M.R. Birtwistle, I. Maze
Methods in Enzymology. February 2016; Volume 574, Pages 331-354

Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches
Kate M. Byrne, Naser Monsefi, John C. Dawson, Andrea Degasperi, Jimi-Carlo Bukowski-Wills, Natalia Volinsky, Maciej Dobrzyński, Marc R. Birtwistle, Mikhail A. Tsyganov, Anatoly Kiyatkin, Katarzyna Kida, Andrew Finch, Neil Carragher, Walter Kolch, Lan K. Nguyen, Alex von Kriegsheim, Boris N. Kholodenko
Cell Systems. January 2016; Volume 2 Issue 1, Pages 38-48
Supplementary Data 1 
Supplementary Data 2 
Supplementary Data 3

Clinically-weighted transcriptomic signatures for protein kinase inhibitor associated cardiotoxicity
Johan G.C. van Hasselt, Jens Hansen, Yuguang Xiong, JaeHee Shim, Amanda Pickard, Gomathi Jayaraman, B Hu, Milind Mahajan, James Gallo, Eric A Sobie, Marc R Birtwistle, Evren U Azeloglu, Ravi Iyengar
BioRxiv, January 2016, 075754


In silico model-based inference: an emerging approach for inverse problems in engineering better medicines
David J Klinke II, Marc R Birtwistle
Current Opinion in Chemical Engineering Volume 10, November 2015, Pages 14–24

CNS Anticancer Drug Discovery and Development Conference White Paper
Vic tor A. Levin, Peter J. Tonge, James M. Gallo , Marc R. Bir twistle, Arvin C. Dar, Antonio Iavarone, Patrick J. Paddison, Timothy P. Heffron, William F. Elmquist, Jean E. Lachowicz, Ted W. Johnson, Forest M. White, Joohee Sul, Quentin R. Smith, Wang Shen, Jann N. Sarkaria, Ramakrishna Samala, Patrick Y. Wen, Donald A. Berry, and Russell C. Petter
Neuro Oncol. 2015 Nov;17(suppl 6):vi1-vi26

Analytical reduction of combinatorial complexity arising from multiple protein modification sites.
Marc R. Birtwistle
J. R. Soc. Interface 12: 20141215
Supplementary Data

Silence on the relevant literature and errors in implementation.
Philippe Bastiaens, Marc R Birtwistle, Nils Blüthgen, Frank J Bruggeman, Kwang-Hyun Cho, Carlo Cosentino, Alberto de la Fuente, Jan B Hoek, Anatoly Kiyatkin, Steffen Klamt, Walter Kolch, Stefan Legewie, Pedro Mendes, Takashi Naka, Tapesh Santra, Eduardo Sontag, Hans V Westerhoff & Boris N Kholodenko
Nature Biotechnology 33, 336–339 (2015)
Supplementary Data

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity.
Ian Maze, Wendy Wenderski, Kyung-Min Noh, Rosemary C. Bagot, Nikos Tzavaras, Immanuel Purushothaman,
Simon J. Elsasser, Yin Guo, Carolina Ionete, Yasmin L. Hurd, Carol A. Tamminga, Tobias Halene, Lorna Farrelly,
Alexey A. Soshnev, Duancheng Wen, Shahin Rafii, Marc R. Birtwistle, Schahram Akbarian, Bruce A. Buchholz,
Robert D. Blitzer, Eric J. Nestler, Zuo-Fei Yuan, Benjamin A. Garcia, Li Shen, Henrik Molina,
and C. David Allis
Neuron Volume 87, Issue 1, 1 July 2015, Pages 77–94
Supplementary Data 1 
Supplementary Data 2

Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation
Malgorzata Milewska, David Romano, Ana Herrero, Maria Luisa Guerriero, Marc Birtwistle, Franz Quehenberger, Stefan Hatzl, Boris N. Kholodenko, Oreste Segatto, Walter Kolch, and Armin Zebisch
PLoS One. 2015; 10(6): e0129859
Supplementary Data

Network pharmacodynamic models for customized cancer therapy
Gallo JM, Birtwistle MR.
Wiley Interdiscip Rev Syst Biol Med. 2015 Jul-Aug;7(4):243-51


Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses. 
Dobrzyński M, Nguyen LK, Birtwistle MR, von Kriegsheim A, Blanco Fernandez A, Cheong A, Kolch W, Kholodenko BN.
Journal of the Royal Society Interface. 2014 Sep 6;11(98). pii: 20140383.
Supplementary Data

Transcriptomes and shRNA Suppressors in a TP53 Allele-Specific Model of Early-Onset Colon Cancer in African Americans. 
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, Banister CE, Buckhaults PJ.
Molecular Cancer Research. 2014 Jul;12(7):1029-41.
Supplementary Data

Dimerization-based control of cooperativity. 
Bouhaddou M, Birtwistle MR.
Molecular BioSystems 2014 Jun 3;10(7):1824-32
Supplementary Data

Evaluating Strategies to Normalise Biological Replicates of Western Blot Data
Andrea Degrasperi, Marc R Birtwistle, Natalia Volinsky, Jens Rauch, Walter Kolch, Boris N Kholodenko
PloS one, January 2014 9 (1), e87293

A general network pharmacodynamic model-based design pipeline for customized cancer therapy applied to the VEGFR pathway. 
Zhang XY, Birtwistle MR, Gallo JM.
CPT Pharmacometrics & Systems Pharmacology. 2014 Jan 15;3:e92
Supplementary Data


Extracellular signal-regulated kinase regulates RhoA activation and tumor cell plasticity by inhibiting guanine exchange factor H1 activity
Anne von Thun, Christian Preisinger, Oliver Rath, Juliane P Schwarz, Chris Ward, Naser Monsefi, Javier Rodriguez, Amaya Garcia-Munoz, Marc Birtwistle, Willy Bienvenut, Kurt I Anderson, Walter Kolch, Alex von Kriegsheim
Molecular And Cellular Biology. September 2013, Vol 33 No 22 4526-4537

Mechanistic vs. empirical network models of drug action. 
Birtwistle MR, Mager DE, Gallo JM.
CPT Pharmacometrics & Systems Pharmacology. 2013 Sep 6;2:e72

Bayesian multivariate Poisson abundance models for T-cell receptor data
Joshua Greene, Marc R Birtwistle, Leszek Ignatowicz, Grzegorz A Rempala
Journal of Theoretical Biology. June 2013; Volume 326 Pages 1-10


Mammalian protein expression noise: scaling principles and the implications for knockdown experiments. 
Birtwistle MR, Kriegsheim Av, Dobrzyński M, Kholodenko BN, Kolch W.
Molecular BioSystems. 2012 Oct 2;8(11):3068-76

Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. 
Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzy 324 Ski M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN.
BMC Systems Biology. 2012 Aug 24;6(1):109
Supplementary Data

Novel somatic mutations to PI3K pathway genes in metastatic melanoma. 
Shull AY, Latham-Schwark A, Ramasamy P, Leskoske K Oroian D, Birtwistle MR, Buckhaults PJ.
PLoS One. 7(8) 2012 Aug 17
Supplementary Data

ERK2 drives tumour cell migration in three-dimensional microenvironments by suppressing expression of Rab17 and liprin-β2. 
von Thun A, Birtwistle M, Kalna G, Grindlay J, Strachan D, Kolch W, von Kriegsheim A, Norman JC.
Journal of Cell Science. 2012 Mar 15;125(Pt 6):1465-77.
Supplementary Data


Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modeling. 
Birtwistle MR, von Kriegsheim A, Kida K, Schwarz JP, Anderson KI, Kolch W.
PLoS One. 2011;6(11):e27823.

Raf family kinases: old dogs have learned new tricks. 
Matallanas D, Birtwistle M, Romano D, Zebisch A, Rauch J, von Kriegsheim A, Kolch W.
Genes Cancer. 2011 Mar;2(3):232-60.

Biology using engineering tools: the negative feedback amplifier. 
Birtwistle MR, Kolch W.
Cell Cycle. 2011 Jul 1;10(13):2069-76.


The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. 
Sturm O, Orton R, Grindlay J, Birtwistle M, Vyshemirsky V, Gilbert D, Calder M, Pitt A, Kholodenko B, Kolch W.
Science Signaling. 2010 Dec 21;3(153):ra90
Supplementary Data

Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. 
Nakakuki T, Birtwistle MR, Saeki Y, Yumoto N, Ide K, Nagashima T, Brusch L, Ogunnaike BA, Okada-Hatakeyama M, Kholodenko BN.
Cell. 2010 May 28;141(5):884-96
Supplementary Data


Four-dimensional dynamics of MAPK information processing systems. 
Kholodenko BN, Birtwistle MR.
Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2009 Jul-Aug;1(1):28-44.

Cell fate decisions are specified by the dynamic ERK interactome. 
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.
Nature Cell Biology. 2009 Dec;11(12):1458-64
Supplementary Data

Endocytosis and signalling: a meeting with mathematics. 
Birtwistle MR, Kholodenko BN.
Molecular Oncology. 2009 Aug;3(4):308-20


Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. 
Birtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN.
Molecular Systems Biology. 2007;3:144
Supplementary Data