Nature Search

Drug response consistency in CCLE and CGP

Mehdi Bouhaddou
Matthew S. DiStefano
Marc R. Birtwistle
Research30 Nov 2016
Nature

Volume: 540, P: E9-E10
Multiscale mapping of transcriptomic signatures for cardiotoxic drugs

Using a new computational pipeline for identification of drug-selective transcriptomic responses and FAERS data, the authors identified potential pathways and genomic variants indicative of cancer drug cardiotoxicity in iPSC-derived cardiomyocytes.

Jens Hansen
Yuguang Xiong
Ravi Iyengar
ResearchOpen Access11 Sept 2024
Nature Communications

Volume: 15, P: 1-17
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling

Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. Here the authors develop a scalable, open-source pipeline for constructing and simulating large-scale, single-cell mechanistic models, an important building block for clinically-predictive mechanistic models and interpretable big data integration.

Cemal Erdem
Arnab Mutsuddy
Marc R. Birtwistle
ResearchOpen Access21 Jun 2022
Nature Communications

Volume: 13, P: 1-18
Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity

Cardiotoxic adverse events associated with kinase inhibitors are a growing concern in clinical oncology. Here the authors use cellular transcriptomic responses of human cardiomyocytes treated with protein kinase inhibitors and the associated drug structural signatures to determine an integrated predictive signature of cardiotoxicity.

J. G. Coen van Hasselt
Rayees Rahman
Ravi Iyengar
ResearchOpen Access23 Sept 2020
Nature Communications

Volume: 11, P: 1-12
Mitochondrial origins of fractional control in regulated cell death

Phenotypic cell-to-cell variability contributes to fractional killing, but the mechanisms are incompletely understood. Here the authors show that mitochondrial density correlates with cell survival in response to TRAIL, and that variable effective concentrations of Bax/Bak contribute to the effect.

Luís C. Santos
Robert Vogel
Pablo Meyer
ResearchOpen Access21 Mar 2019
Nature Communications

Volume: 10, P: 1-10
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms

A problem in network biology is identification of context-specific networks. Here the authors report Multi-Omics Binary Integration via Lasso Ensembles (MOBILE) to nominate molecular features associated with cellular phenotypes and pathways, and use this to assess interferon-γ regulated PD-L1 expression.

Cemal Erdem
Sean M. Gross
Marc R. Birtwistle
ResearchOpen Access06 Jul 2023
Nature Communications

Volume: 14, P: 1-16
Wilm’s tumor 1 promotes memory flexibility

Impairments in memory flexibility are associated with neuropsychiatric disorders such as PTSD and autism. Here, the authors report that the transcriptional repressor Wilm's Tumor 1 regulates synaptic plasticity leading to weakening of memory strength and enabling memory flexibility.

Chiara Mariottini
Leonardo Munari
Ravi Iyengar
ResearchOpen Access21 Aug 2019
Nature Communications

Volume: 10, P: 1-18
Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array

Rick J. Koch
Anne Marie Barrette
Marc R. Birtwistle
ResearchOpen Access27 Jul 2018
Scientific Reports

Volume: 8, P: 1-10
Relating individual cell division events to single-cell ERK and Akt activity time courses

Alan D. Stern
Gregory R. Smith
Marc R. Birtwistle
ResearchOpen Access27 Oct 2022
Scientific Reports

Volume: 12, P: 1-13
Cell fate decisions are specified by the dynamic ERK interactome

In differentiating cells, ERK activation shifts from transient to sustained. Quantitative proteomics reveals that, during differentiation, dynamic changes in ERK-interacting proteins regulate the pathway at several levels and by different mechanisms, suggesting a distributed control mechanism for the ERK pathway.

Alex von Kriegsheim
Daniela Baiocchi
Walter Kolch
Research22 Nov 2009
Nature Cell Biology

Volume: 11, P: 1458-1464
A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries

Yuguang Xiong
Magali Soumillon
Marc R. Birtwistle
ResearchOpen Access07 Nov 2017
Scientific Reports

Volume: 7, P: 1-12
Silence on the relevant literature and errors in implementation

Philippe Bastiaens
Marc R Birtwistle
Boris N Kholodenko
Correspondence07 Apr 2015
Nature Biotechnology

Volume: 33, P: 336-339
Network analyses of brain tumor multiomic data reveal pharmacological opportunities to alter cell state transitions

Brandon Bumbaca
Jonah R. Huggins
James M. Gallo
ResearchOpen Access01 Feb 2025
npj Systems Biology and Applications

Volume: 11, P: 1-12
A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses

Comprehensive profiling of ligand-induced perturbation responses of the MCF10A mammary epithelial cell line provides an exhaustive resource for identification of the molecular basis of cellular phenotypes.

Sean M. Gross
Mark A. Dane
Laura M. Heiser
ResearchOpen Access07 Oct 2022
Communications Biology

Volume: 5, P: 1-20
Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events

Jamie J. R. Bennett
Alan D. Stern
Gaurav Pandey
ResearchOpen Access04 Jun 2024
npj Systems Biology and Applications

Volume: 10, P: 1-10
Network inference from perturbation time course data

Deepraj Sarmah
Gregory R. Smith
Marc R. Birtwistle
ResearchOpen Access01 Nov 2022
npj Systems Biology and Applications

Volume: 8, P: 1-18
Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity

Yuguang Xiong
Tong Liu
Evren U. Azeloglu
ResearchOpen Access20 Jan 2022
Scientific Data

Volume: 9, P: 1-11

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