2019

Highly Multiplexed, Quantitative Tissue Imaging at Cellular Resolution
McCarthy, ME, Birtwistle MR.
Curr. Pathobiol. Opin. 2019

Mitochondrial origins of fractional control in regulated cell death
Santos LC, Vogel R, Chipuk JE, Birtwistle MR, Stolovitzky G, Meyer P.
Nat. Commun. 2019
Supplementary Information

A Multi-Center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines
Niepel M, Hafner M, Mills CE, Subramanian K, Williams EH, Chung M, Gaudio B, Barrette AM, Stern AD, Hu B, Korkola JE, LINCS Consortium, Gray JW, Birtwistle MR, Heiser LM, Sorger PK.
Cell Syst. 2019

Wilm’s tumor 1 promotes memory flexibility
Mariottini C, Munari L, Gunzel E, Seco JM, Tzavaras N, Hansen J, Stern SA, Gao V, Aleyasin H, Sharma A, Azeloglu EU, Hodes G, Russo SJ, Huff V, Birtwistle MR, Blitzer RD, Alberini CM, Iyengar R
Nat. Commun. 2019

2018

Fluorescence Multiplexing with Spectral Imaging and Combinatorics
Holzapfel HY, Stern AD, Bouhaddou M, Anglin CM, Putur D, Comer S, Birtwistle MR.
ACS Comb. Sci. 2018
Supplementary Methods
Tables S1 and S2
Supplementary Code

Gene-Specific Predictability of Protein Levels from mRNA Data in Humans
Moulana A, Scanteianu A, Jones D, Stern AD, Bouhaddou M, Birtwistle M.
bioRxiv. 2018

Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array
Koch RJ, Barrette AM, Stern AD, Hu B, Bouhaddou M, Azeloglu EU, Iyengar R, Birtwistle MR.
Sci. Rep. 2018

Network Reconstruction from Perturbation Time Course Data
Smith GR, Bouhaddou M, Stern AD, Anglin CM, Zadeh OM, Erskine J, Birtwistle MR.
bioRxiv. 2018
Supplementary Code

A Mechanistic Pan-Cancer Pathway Model Informed by Multi-Omics Data Interprets Stochastic Cell Fate Responses to Drugs and Mitogens
Bouhaddou M, Barrette AM, Stern AD, Koch RJ, DiStefano MS, Riesel EA, Santos LC, Tan AL, Mertz AE, Birtwistle MR.
PLoS Comput. Biol. 2018
Supplementary Materials and Code

Analysis of Copy Number Loss of the ErbB4 Receptor Tyrosine Kinase in Glioblastoma
Jones DC, Scanteianu A, DiStefano M, Bouhaddou M, Birtwistle MR.
PLoS One. 2018

2017

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations
Keenan AB, LINCS Consortium
Cell Syst. 2017

A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries
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, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR. Sci. Rep. 2017

Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials
Barrette AM, Bouhaddou M, Birtwistle MR.
ACS Chem. Neurosci. 2017

Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics
Shim JV, Chun B, van Hasselt JGC, Birtwistle MR, Saucerman JJ, Sobie EA.
Front. Physiol. 2017

2016

Kinetic Models of Biochemical Signaling Networks
Bouhaddou M, Birtwistle MR.
Syst. Pharmacol. Pharmacodyn. 2016

Systems Pharmacology: An Overview
Birtwistle MR, Hansen J, Gallo JM, Muppirisetty S, Ung PM, Iyengar R, Schlessinger A.
Syst. Pharmacol. Pharmacodyn. 2016

Drug response consistency in CCLE and CGP
Bouhaddou M, DiStefano MS, Riesel EA, Carrasco E, Holzapfel HY, Jones DC, Smith GR, Stern AD, Somani SS, Thompson TV, Birtwistle MR.
Nature. 2016

Cell Size Assays for Mass Cytometry
Stern AD, Rahman AH, Birtwistle MR.
Cytometry A. 2016

A Temporal Logic Inference Approach for Model Discrimination
Xu Z, Birtwistle M, Belta C, Julius A.
IEEE Life Sci. Lett. 2016

A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data
Smith GR, Birtwistle MR.
PLoS One. 2016
Supplementary Data 1
Supplementary Data 2

Creating Complex Fluorophore Spectra on Antibodies Through Combinatorial Labeling
Holzapfel HY, Birtwistle MR.
Transl. Sci. 2016

Current Proteomic Methods to Investigate the Dynamics of Histone Turnover in the Central Nervous System
Farrelly LA, Dill BD, Molina H, Birtwistle MR, Maze I.
Methods Enzymol. 2016

Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches
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, von Kriegsheim A, Kholodenko BN.
Cell Syst. 2016
Supplementary Data 1 
Supplementary Data 2 
Supplementary Data 3

Clinically-weighted transcriptomic signatures for protein kinase inhibitor associated cardiotoxicity
van Hasselt JGC, Hansen J, Xiong Y, Shim J, Pickard A, Jayaraman G, Hu B, Mahajan M, Gallo J, Sobie EA, Birtwistle MR, Azeloglu EU, Iyengar R.
bioRxiv. 2016

2015

In silico model-based inference: an emerging approach for inverse problems in engineering better medicines
Klinke DJ 2nd, Birtwistle MR.
Curr. Opin. Chem. Eng. 2015

CNS Anticancer Drug Discovery and Development Conference White Paper
Levin VA, Tonge PJ, Gallo JM, Birtwistle MR, Dar AC, Iavarone A, Paddison PJ, Heffron TP, Elmquist WF, Lachowicz JE, Johnson TW, White FM, Sul J, Smith QR, Shen W, Sarkaria JN, Samala R, Wen PY, Berry DA1, Petter RC.
Neuro. Oncol. 2015

Analytical reduction of combinatorial complexity arising from multiple protein modification sites.
Birtwistle MR.
J. R. Soc. Interface. 2015
Supplementary Data

Silence on the relevant literature and errors in implementation.
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, Sontag E, Westerhoff HV, Kholodenko BN.
Nat. Biotechnol. 2015
Supplementary Data

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity.
Maze I, Wenderski W, Noh KM, Bagot RC, Tzavaras N, Purushothaman I, Elsässer SJ, Guo Y, Ionete C, Hurd YL, Tamminga CA, Halene T, Farrelly L, Soshnev AA, Wen D, Rafii S, Birtwistle MR, Akbarian S, Buchholz BA, Blitzer RD, Nestler EJ, Yuan ZF, Garcia BA, Shen L, Molina H, Allis CD.
Neuron. 2015
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
Milewska M, Romano D, Herrero A, Guerriero ML, Birtwistle M, Quehenberger F, Hatzl S, Kholodenko BN, Segatto O, Kolch W, Zebisch A.
PLoS One. 2015
Supplementary Data

Network pharmacodynamic models for customized cancer therapy
Gallo JM, Birtwistle MR.
Wiley Interdiscip. Rev.: Syst. Biol. Med. 2015

2014

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.
J. R. Soc. Interface. 2014
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.
Mol. Cancer Res. 2014
Supplementary Data

Dimerization-based control of cooperativity. 
Bouhaddou M, Birtwistle MR.
Mol. BioSyst. 2014
Supplementary Data

Evaluating Strategies to Normalise Biological Replicates of Western Blot Data
Degasperi A, Birtwistle MR, Volinsky N, Rauch J, Kolch W, Kholodenko BN.
PloS One, 2014

A general network pharmacodynamic model-based design pipeline for customized cancer therapy applied to the VEGFR pathway. 
Zhang XY, Birtwistle MR, Gallo JM.
CPT: Pharmacomet. Syst. Pharmacol. 2014
Supplementary Data

2013

Extracellular signal-regulated kinase regulates RhoA activation and tumor cell plasticity by inhibiting guanine exchange factor H1 activity
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.
Mol. Cell. Biol. 2013

Mechanistic vs. empirical network models of drug action. 
Birtwistle MR, Mager DE, Gallo JM.
CPT: Pharmacomet. Syst. Pharmacol. 2013

Bayesian multivariate Poisson abundance models for T-cell receptor data
Greene J, Birtwistle MR, Ignatowicz L, Rempala GA.
J. Theor. Biol. 013

2012

Mammalian protein expression noise: scaling principles and the implications for knockdown experiments. 
Birtwistle MR, Kriegsheim Av, Dobrzyński M, Kholodenko BN, Kolch W.
Mol. BioSyst. 2012

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 Syst. Biol. 2012
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. 2012
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.
J. Cell Sci. 2012
Supplementary Data

2011

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

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

Biology using engineering tools: the negative feedback amplifier. 
Birtwistle MR, Kolch W.
Cell Cycle. 2011

2010

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.
Sci. Signal. 2010
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
Supplementary Data

2009

Four-dimensional dynamics of MAPK information processing systems. 
Kholodenko BN, Birtwistle MR.
Wiley Interdiscip. Rev.: Syst. Biol. Med. 2009

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.
Nat. Cell Biol. 2009
Supplementary Data

Endocytosis and signalling: a meeting with mathematics. 
Birtwistle MR, Kholodenko BN.
Mol. Oncol. 2009

2007

Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. 
Birtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN.
Mol. Syst. Biol. 2007
Supplementary Data