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List of works by Julio Saez-Rodriguez

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.

scientific article

A Functional Landscape of CKD Entities From Public Transcriptomic Data

scientific article published on 13 November 2019

A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions

scientific article

A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

scientific article published on 18 January 2022

A community computational challenge to predict the activity of pairs of compounds

scientific article

A community effort to assess and improve drug sensitivity prediction algorithms.

scientific article

A comprehensive database for integrated analysis of omics data in autoimmune diseases

scientific article published on 24 June 2021

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.

scientific article

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks

scientific article

A functional landscape of chronic kidney disease entities from public transcriptomic data

A landscape of pharmacogenomic interactions in cancer.

scientific article published on 05 July 2016

A logical model provides insights into T cell receptor signaling

scientific article

A methodology for the structural and functional analysis of signaling and regulatory networks

scientific article published on 7 February 2006

A microfluidics platform for combinatorial drug screening on cancer biopsies.

scientific article published on 22 June 2018

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models

scientific article published on 23 July 2014

A multipathway phosphoproteomic signaling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes

scientific article published on January 2009

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology

scientific article

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells

scientific article

A single-cell model of PIP3 dynamics using chemical dimerization

scientific article published on 7 May 2015

A systematic atlas of chaperome deregulation topologies across the human cancer landscape

scientific article published on 2 January 2018

Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue

scientific article published in Nature Communications

Alternative models for sharing confidential biomedical data

article by Justin Guinney et al published 9 May 2018 in Nature Biotechnology

Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.

scientific article published on 14 May 2019

Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression

Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. ⬇️

scientific article published on 29 December 2015

Assessment of network module identification across complex diseases

scientific article published on 30 August 2019

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules

scientific article

Benchmark and integration of resources for the estimation of human transcription factor activities

Benchmark and integration of resources for the estimation of human transcription factor activities

scientific article published on 24 July 2019

Benchmarking substrate-based kinase activity inference using phosphoproteomic data

scientific article

Big Data Approaches in Heart Failure Research

scientific article published on 12 August 2020

Big science and big data in nephrology

scientific article published on 05 March 2019

BioServices: a common Python package to access biological Web Services programmatically

scientific article published on 23 September 2013

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

scientific article published on 25 March 2013

Bringing data from curated pathway resources to Cytoscape with OmniPath

scientific article published on 30 December 2019

CELLector: Genomics Guided Selection of Cancer in vitro Models

article

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms ⬇️

journal article from 'Molecular Systems Biology' published in 2021

Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network

scientific article

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses

scientific article published on 01 January 2021

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

scientific article

Cellular Regulatory Networks

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

scientific article published on 17 June 2019

Comparing signaling networks between normal and transformed hepatocytes using discrete logical models

scientific article

Computational discovery of dynamic cell line specific Boolean Networks from multiplex time-course data

scientific article published on 29 October 2018

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity

scientific article published on 11 April 2022

Consensus Transcriptional Landscape of Human End-Stage Heart Failure

publication published on 31 March 2021

Construction of cell type-specific logic models of signaling networks using CellNOpt

scientific article

Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2.

scientific article published on January 2010

Cooperative development of logical modelling standards and tools with CoLoMoTo

scientific article published on 25 January 2015

Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges.

scientific article published on 9 March 2010

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

scientific article (publication date: May 2012)

Crowdsourcing biomedical research: leveraging communities as innovation engines

scientific article (publication date: 15 July 2016)

Crowdsourcing network inference: the DREAM predictive signaling network challenge

scientific article

CySBGN: a Cytoscape plug-in to integrate SBGN maps

scientific article

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

scientific article published on 19 September 2013

DREAMTools: a Python package for scoring collaborative challenges.

scientific article

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models

scientific article

Decoding myofibroblast origins in human kidney fibrosis

scientific article published on 11 November 2020

Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signalling

scientific article published on 01 March 2022

Democratising Knowledge Representation with BioCypher

scientific article published on 27 December 2022

Democratizing knowledge representation with BioCypher

Designing Experiments to Discriminate Families of Logic Models

scientific article

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

scientific article

Dissecting the puzzle of life: modularization of signal transduction networks

article published in 2005

Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.

scientific article

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing

scientific article published in 2024

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.

scientific article

Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy

scientific article

Dynamics of proximal signaling events after TCR/CD8-mediated induction of proliferation or apoptosis in mature CD8+ T cells

scientific article published in May 2008

Dysregulated mesenchymal PDGFR-β drives kidney fibrosis

scientific article published on 14 January 2020

Efficient randomization of biological networks while preserving functional characterization of individual nodes

scientific article

Elastin imaging enables noninvasive staging and treatment monitoring of kidney fibrosis

scientific article published on 01 April 2019

Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data

scientific article published on 01 August 2019

Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury

article

Empirical inference of circuitry and plasticity in a kinase signaling network

scientific article published on 9 June 2015

Evaluation of methods for modeling transcription factor sequence specificity

scientific article published on 27 January 2013

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

scientific article

Experimental and computational technologies to dissect the kidney at the single-cell level

scientific article published on 17 December 2020

Explainable multiview framework for dissecting spatial relationships from highly multiplexed data

scientific article published in 2022

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.

scientific article

Fast randomization of large genomic datasets while preserving alteration counts

scientific article published on September 2014

Flexible informatics for linking experimental data to mathematical models via DataRail

scientific article

From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

scientific article published on 11 November 2019

Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition

scientific article published on 31 August 2016

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening

article

Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling

scientific article

GDSCTools for Mining Pharmacogenomic Interactions in Cancer

scientific article published on 24 November 2017

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations

scientific article published on 8 February 2017

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

scientific article published on August 2017

Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results

Gli1+ Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target.

scientific article published on 13 April 2017

High-Throughput Protein-Based Technologies and Computational Models for Drug Development, Efficacy, and Toxicity

article

How to find the right drug for each patient? Advances and challenges in pharmacogenomics

scientific article published on 01 August 2018

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury

scientific article

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data

scientific article

In silico prioritization of transporter-drug relationships from drug sensitivity screens

Inferring causal molecular networks: empirical assessment through a community-based effort

scientific article

Inferring clonal composition from multiple tumor biopsies

scientific article published on 25 August 2020

Influence of Liver Fibrosis on Lobular Zonation

scientific article published on 02 December 2019

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

scientific article published on 22 March 2021

Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells

scientific article published on 08 February 2016

Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks

scientific article published in 2022

Integrating literature-constrained and data-driven inference of signalling networks

scientific article

Integration of Structured Biological Data Sources using Biological Expression Language

BioRxiv scholarly article describing Bio2BEL

Integrative approaches for signalling and metabolic networks

Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer

Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer

scientific article published on 10 December 2019

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data

scientific article

Learning Boolean logic models of signaling networks with ASP

Linking drug target and pathway activation for effective therapy using multi-task learning.

scientific article published on 29 May 2018

Logic Modeling in Quantitative Systems Pharmacology

scientific article

Logic-based models for the analysis of cell signaling networks

scientific article published on April 2010

Logical Modeling and Dynamical Analysis of Cellular Networks

scientific article

Looking beyond the cancer cell for effective drug combinations

scientific article published on 25 November 2016

MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis

scientific article published on 19 April 2019

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

scientific article

MEK1/2 inhibitor withdrawal reverses acquired resistance driven by BRAF amplification whereas KRAS amplification promotes EMT-chemoresistance

scientific article published on 02 May 2019

Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties

scientific article

Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways

scientific article published on 02 May 2022

Mapping the human phosphatome on growth pathways

scientific article

Mechanism-based biomarker discovery

scientific article

Metabolic rewiring of the hypertensive kidney

scientific article published on 10 December 2019

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

scientific article published on 01 October 2019

Modeling Signaling Networks Using High-throughput Phospho-proteomics ⬇️

scientific article published on January 1, 2012

Modeling Signaling Networks to Advance New Cancer Therapies

scientific article published on 14 August 2015

Modeling signaling networks with different formalisms: a preview

scientific article published in January 2013

Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis

Molecular consequences of SARS-CoV-2 liver tropism

scientific article published on 28 March 2022

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

scientific article published on 18 February 2019

Multistability of signal transduction motifs

scientific article published in March 2008

NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction.

scientific article published in February 2018

Network based elucidation of drug response: from modulators to targets

scientific article

Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer

scientific article published on 08 July 2019

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

scientific article

Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes

scientific article

New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids

scientific article published on 20 June 2021

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways

scientific article

Norepinephrine promotes triglyceride storage in macrophages via beta2-adrenergic receptor activation

scientific article published on 01 February 2021

Novel plasma peptide markers involved in the pathology of CKD identified using mass spectrometric approach

scientific article published on 05 August 2019

OmniPath: guidelines and gateway for literature-curated signaling pathway resources.

scientific article

Only Hyperuricemia with Crystalluria, but not Asymptomatic Hyperuricemia, Drives Progression of Chronic Kidney Disease

scientific article published on 16 September 2020

Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases

PIP₃ induces the recycling of receptor tyrosine kinases

scientific article published on 14 January 2014

Path2Models: large-scale generation of computational models from biochemical pathway maps

scientific article

Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich

article

Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.

scientific article published on 30 April 2018

Patient-specific Boolean models of signalling networks guide personalised treatments

scientific article published in 2022

Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies

Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies

scientific article published on 01 February 2020

Personalized signaling models for personalized treatments

scientific article published on 01 January 2020

Perturbation-response genes reveal signaling footprints in cancer gene expression

scientific article published on 2 January 2018

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast

scientific article

Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors

scientific article

Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells

scientific article published in January 2018

Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.

scientific article published on 27 November 2017

Prediction of combination therapies based on topological modeling of the immune signaling network in Multiple Sclerosis

Prediction of human population responses to toxic compounds by a collaborative competition

scientific article

Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens

scientific article published on 10 April 2019

Prospective derivation of a living organoid biobank of colorectal cancer patients.

scientific article published on May 2015

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

scientific article published on 31 October 2019

Quantitative Systems Toxicology Modeling To Address Key Safety Questions in Drug Development: A Focus of the TransQST Consortium

scientific article published on 07 January 2020

Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics

Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells

Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling.

scientific article published in June 2004

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

scientific article published on 10 September 2019

Retroactivity as a Criterion to Define Modules in Signaling Networks

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

scientific article published on 8 December 2020

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

scientific article

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

scientific article published on 12 February 2020

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

scientific article

SREBP1-induced fatty acid synthesis depletes macrophages antioxidant defences to promote their alternative activation

scientific article published on 16 September 2021

Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

scientific article published on 21 April 2020

Setting the standards for signal transduction research

scientific article published on 15 February 2011

Signaling networks in MS: a systems-based approach to developing new pharmacological therapies

scientific article

Signatures of cell death and proliferation in perturbation transcriptomics data - from confounding factor to effective prediction:

Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction

scientific article published on 01 November 2019

Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics

scientific article published on 07 December 2023

State-time spectrum of signal transduction logic models

scientific article published on 07 August 2012

Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.

scientific article

Stratification and prediction of drug synergy based on target functional similarity

scientific article published on 02 June 2020

Structural and functional analysis of cellular networks with CellNetAnalyzer

scientific article

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

scientific article published on 12 December 2016

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast

scientific article

Systematic identification of genomic markers of drug sensitivity in cancer cells

scientific article (publication date: 28 March 2012)

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines

scientific article published on 24 November 2017

Systems biology--an engineering perspective.

scientific article published on 24 February 2007

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

scientific article published on 28 June 2020

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

scientific article published on 30 June 2020

The authors reply

The germline genetic component of drug sensitivity in cancer cell lines

scientific article published in Nature Communications

The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment

scientific article published on 09 October 2021

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data

scientific article

The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling

scientific article

The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury

scientific article published on 03 December 2018

The spatial transcriptomic landscape of the healing mouse intestine following damage

scientific article published on 11 February 2022

The tissue proteome in the multi-omic landscape of kidney disease

scientific article published on 07 October 2020

Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders

scientific article published on 31 October 2019

Towards a rigorous assessment of systems biology models: the DREAM3 challenges

scientific article

Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli

scientific article

Transcription Factor Activity Inference in Systemic Lupus Erythematosus

Transcription factor activities enhance markers of drug sensitivity in cancer.

scientific article published on 11 December 2017

Transcriptional data: a new gateway to drug repositioning?

scientific article

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents

scientific article published on 11 March 2016

Transfer of regulatory knowledge from human to mouse for functional genomics analysis

scientific article published on 13 September 2019

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

scientific article

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

scientific article published on 13 August 2018

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Using chemical reaction network theory to discard a kinetic mechanism hypothesis

scientific article published in December 2005

Visual setup of logical models of signaling and regulatory networks with ProMoT.

scientific article published on 17 November 2006

Whither systems medicine?

scientific article published on 2 March 2018

Why do pathway methods work better than they should?

scientific article published on 03 December 2020

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer

scientific article published on 9 October 2017

caspo: a toolbox for automated reasoning on the response of logical signaling networks families

scientific article

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