2024
Increasing Signal Intensity of Fluorescent Oligo-Labeled Antibodies to Enable Combination Multiplexing
McCarthy ME, Lu X, Ogunleye O, Latham DR, Abravanel M, Pritko D, Huggins JR, Haskell CV, Patel ND, Pittman ZA, Sanabria H, Birtwistle MR
Bioconjugate Chem 2024
(Pre-Print) A 96-Well Polyacrylamide Gel for Electrophoresis and Western Blotting
Birtwistle MR, Huggins JR, Zadeh CO, Sarmah D, Srikanth S, Jones BK, Cascio LN, Dean D
bioRxiv 2024
Bumbaca B, Birtwistle MR, Gallo JM
bioRxiv 2024
Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events
Bennett JJR, Stern AD, Zhang X, Birtwistle MR, Pandey G
NPJ Syst. Biol. Appl. 2024
2023
Predicting Anti-Cancer Drug Combination Responses with a Temporal Cell State Network Model
Sarmah D, Meredith WO, Weber IK, Price MR, Birtwistle MR
PLoS Comput. Biol. 2023
Computational Speed-up of Large-Scale, Single-Cell, Model Simulations via a Fully Integrated SBML-Based Format
Mutsuddy A, Erdem C, Huggins JR, Salim M, Cook D, Hobbs N, Feltus FA, Birtwistle MR
Bioinf. Adv. 2023
MEMMAL: A Tool for Expanding Large-scale Mechanistic Models with Machine Learned Associations and Big Datasets
Erdem C, Birtwistle MR
Front. Syst. Biol. 2023
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms
Erdem C, Gross, SM, Heiser LM, Birtwistle MR
Nat. Commun., 2023
A Theory for High-Throughput Genetic Interaction Screening
McCarthy ME, Dodd WB, Lu X, Patel ND, Haskell CV, Sanabria H, Blenner MA, Birtwistle MR
ACS Synthetic Biology 2023
2022
Modeling the Dynamics of Eukaryotic DNA Synthesis in Remembrance of Tunde Ogunnaike
Birtwistle MR
Ind. Eng. Chem. Res. 2022
Network Inference From Perturbation Time Course Data
Sarmah D, Smith GR, Bouhaddou M, Stern AD, Erskine J, Birtwistle MR
NPJ Syst. Biol. Appl. 2022
Relating Individual Cell Division Events to Single-Cell ERK and Akt Activity Time Courses
Stern AD, Smith GR, Santos LC, Sarmah D, Zhang X, Lu X, Iuricich F, Pandey G, Iyengar R, Birtwistle MR
Sci. Rep. 2022
A Multi-Omic Analysis of MCF10A Cells Provides a Resource for Integrative Assessment of Ligand-Mediated Molecular and Phenotypic Responses
Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramaninan K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Killburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma'ayan, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM
Commun. Biol. 2022
Computational Modelling in Health and Disease: Highlights of the 6th Annual SysMod Meeting
Niarakis A, Thakar J, Barberis M, Martínez MR, Helikar T, Birtwistle MR, Chaouiya C, Calzone L, Dräger A
Bioinformatics, 2022
Proteomic Cellular Signatures of Kinase Inhibitor-Induced Cardiotoxicity
Xiong Y, Liu T, Chen T, Hansen J, Hu B, Chen Y, Jayaraman G, Schürer S, Vidovic D, Goldfarb J, Sobie EA, Birtwistle MR, Iyengar R, Li H, Azeloglu EU
Sci. Data 2022
Leveraging Modeling and Simulation to Optimize the Therapeutic Window for Epigenetic Modifier Drugs
Walz AC, Van De Vyver AJ, Yu L, Birtwistle MR, Krogan NJ, Bouhaddou M
Pharmacol. Ther. 2022
A Scalable, Open-source Implementation of a Large-scale Mechanistic Model for Single Cell Proliferation and Death Signaling
Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR
Nat. Commun. 2022
CellTrackVis: Analyzing the Performance of Cell Tracking Algorithms
Li W, Zhang X, Stern A, Birtwistle MR, Iuricich F
EuroVis 2022
Method for Improved Fluorescence Corrections for Molar Mass Characterization by Multiangle Light Scattering
Pittman ZA, McCarthy ME, Birtwistle MR, Kitchens CL
Biomacromolecules 2022
Mesowestern Blot: Simultaneous Analysis of Hundreds of Submicroliter Lysates
Zadeh CO, Huggins JR, Sarmah D, Westbury BC, Interiano WR, Jordan MC, Phillips SA, Dodd WB, Meredith WO, Harold NJ, Erdem C, Birtwistle MR
ACS Omega 2022
2021
SysMod: the ISCB Community for Data-Driven Computational Modelling and Multi-Scale Analysis of Biological Systems
Dräger A, Helikar T, Barberis M, Birtwistle MR, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Martínez MR, Saez-Rodriguez J, Thakar J
Bioinformatics 2021
A Library of Induced Pluripotent Stem Cells from Clinically Well-Characterized, Diverse Healthy Human Individuals
Schaniel C, Dhanan P, Hu B, Xiong Y, Raghunandan T, Gonzalez D, Dariolli R, D'Souza SL, Yadaw AS, Hansen J, Jayaraman G, Mathew B, Machado M, Berger SI, Tripodig J, Najfeld V, Garg J, Miller M, Surlyn CS, Michelis KC, Tangirala NC, Weerahandi H, Thomas DC, Beaumont KG, Sebra R, Mahajan M, Schadat E, Vidovic D, Schurer SC, Goldfarb J, Azeloglu EU, Birtwistle MR, Sobie EA, Kovacic JC, Dubois NC, Iyengar R
Stem Cell Rep. 2021
Anti-Invasive Efficacy and Survival Benefit of the YAP-TEAD Inhibitor Verteporfin in Preclinical Glioblastoma Models
Barrette AM, Ronk H, Joshi T, Mussa Z, Mehrotra M, Bouras A, Nudelman G, Raj JGJ, Bozec D, Lam W, Houldsworth J, Young R, Zaslavsky E, Hadjipanayis CG, Birtwistle MR, Tsankova NM
Neuro-Oncol. 2021
Protocol for Creating Antibodies with Complex Fluorescence Spectra
McCarthy ME, Anglin CM, Peer HA, Boleman SA, Klaubert SR, Birtwistle MR
ACS Bioconjugate Chem. 2021
Protein Structure-Based Gene Expression Signatures
Rahman R, Zatorski N, Hansen J, Xiong Y, van Hasselt JGC, Sobie EA, Birtwistle MR, Azeloglu EU, Iyengar R, Schlessinger A
Proc. Natl. Acad. Sci. U.S.A. 2021
2020
Predicting In Vivo Efficacy from In Vitro Data: Quantitative Systems Pharmacology Modeling for an Epigenetic Modifier Drug in Cancer
Bouhaddou M, Yu LJ, Lunardi S, Stamatelos SK, Mack F, Gallo JM, Birtwistle MR, Walz AC
Clin. Transl. Sci. 2020
Transcriptomic Profiling of Human Cardiac Cells Predicts Protein Kinase Inhibitor-Associated Cardiotoxicity
Hasselt JGC, Rahman R, Hansen J, Stern A, Shim JV, Xiong Y, Pickard A, Jayaraman G, Hu B, Mahajan M, Gallo JM, Goldfarb J, Sobie EA, Birtwistle MR, Schlessinger A, Azeloglu EU, Iyengar R
Nat. Commun. 2020
2019
Highly Multiplexed, Quantitative Tissue Imaging at Cellular Resolution
McCarthy ME, Birtwistle MR.
Current Pathobiology Reports 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
A Multi-Center Study on the Reproducibility of Drug-Reponse 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 GE, 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
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
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