From Discrete to Continuous Modeling of Lymphocyte Development and Plasticity in Chronic Diseases

Mixed phenotype acute leukemia contains heterogeneous genetic mutations by next-generation sequencing

(2018) Andrés E. Quesada et al.   Oncotarget

Mast Cells and Innate Lymphoid Cells: Underappreciated Players in CNS Autoimmune Demyelinating Disease

(2018) Melissa A. Brown et al.   Frontiers in Immunology

Progression from the Common Lymphoid Progenitor to B/Myeloid PreproB and ProB Precursors during B Lymphopoiesis Requires C/EBPα

(2018) Hong Guo et al.   JOURNAL OF IMMUNOLOGY

A Mechanistic Computational Model Reveals That Plasticity of CD4+ T Cell Differentiation Is a Function of Cytokine Composition and Dosage

(2018) Bhanwar Lal Puniya et al.   Frontiers in Physiology

Dynamical Analysis of the Regulatory Network Controlling Natural Killer Cells Differentiation

(2018) Adhemar J. Liquitaya-Montiel et al.   Frontiers in Physiology

Role of Cytokine Combinations on CD4+ T Cell Differentiation, Partial Polarization, and Plasticity: Continuous Network Modeling Approach

(2018) Mariana E. Martinez-Sanchez et al.   Frontiers in Physiology

TCR Signal Strength Regulates Akt Substrate Specificity To Induce Alternate Murine Th and T Regulatory Cell Differentiation Programs

(2017) William F. Hawse et al.   JOURNAL OF IMMUNOLOGY

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation

(2017) Samuel Collombet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Th2/1 Hybrid Cells Occurring in Murine and Human Strongyloidiasis Share Effector Functions of Th1 Cells

(2017) Cristin N. Bock et al.   Frontiers in Cellular and Infection Microbiology

Role of T Lymphocytes in Type 2 Diabetes and Diabetes-Associated Inflammation

(2017) Chang Xia et al.   Journal of Diabetes Research

Innate Lymphoid Cells in Intestinal Inflammation

(2017) Alessandra Geremia et al.   Frontiers in Immunology

CD19 CAR immune pressure induces B-precursor acute lymphoblastic leukaemia lineage switch exposing inherent leukaemic plasticity

(2016) Elad Jacoby et al.   Nature Communications

Common-Lymphoid-Progenitor-Independent Pathways of Innate and T Lymphocyte Development

(2016) Maryam Ghaedi et al.   Cell Reports

A Network Model to Describe the Terminal Differentiation of B Cells

(2016) Akram Méndez et al.   PLoS Computational Biology

NF-κB oscillations translate into functionally related patterns of gene expression

(2016) Samuel Zambrano et al.   eLife

Modeling the Pro-inflammatory Tumor Microenvironment in Acute Lymphoblastic Leukemia Predicts a Breakdown of Hematopoietic-Mesenchymal Communication Networks

(2016) Jennifer Enciso et al.   Frontiers in Physiology

T-bet and Eomesodermin in NK Cell Development, Maturation, and Function

(2016) Federico Simonetta et al.   Frontiers in Immunology

A dynamical model of the regulatory network controlling lymphopoiesis

(2015) Luis Mendoza et al.   BIOSYSTEMS

Transcriptional Regulatory Network for the Development of Innate Lymphoid Cells

(2015) Chao Zhong et al.   MEDIATORS OF INFLAMMATION

A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle

(2015) Elizabeth Ortiz-Gutiérrez et al.   PLoS Computational Biology

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

(2015) David P. A. Cohen et al.   PLoS Computational Biology

A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity

(2015) Mariana Esther Martinez-Sanchez et al.   PLoS Computational Biology

Computational Modeling of a Transcriptional Switch Underlying B-Lymphocyte Lineage Commitment of Hematopoietic Multipotent Cells

(2015) Luca Salerno et al.   PLoS One

A logical model of HIV-1 interactions with the T-cell activation signalling pathway

(2014) Oyebode J. Oyeyemi et al.   BIOINFORMATICS

A committed precursor to innate lymphoid cells

(2014) Michael G. Constantinides et al.   NATURE

Commensal microbes drive intestinal inflammation by IL-17-producing CD4+ T cells through ICOSL and OX40L costimulation in the absence of B7-1 and B7-2

(2014) L. Xin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composition and abstraction of logical regulatory modules: application to multicellular systems

(2013) Nuno D. Mendes et al.   BIOINFORMATICS

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

(2013) Nicola Bonzanni et al.   BIOINFORMATICS

The regulatory network that controls the differentiation of T lymphocytes

(2013) Pablo Martínez-Sosa et al.   BIOSYSTEMS

A Virtual Culture of CD4+ T Lymphocytes

(2013) Luis Mendoza   BULLETIN OF MATHEMATICAL BIOLOGY

Dynamical modeling and analysis of large cellular regulatory networks

(2013) D. Bérenguier et al.   CHAOS

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning

(2013) Hernan G. Garcia et al.   CURRENT BIOLOGY

Th17-cell plasticity in Helicobacter hepaticus–induced intestinal inflammation

(2013) P J Morrison et al.   Mucosal Immunology

Boolean Network Model for Cancer Pathways: Predicting Carcinogenesis and Targeted Therapy Outcomes

(2013) Herman F. Fumiã et al.   PLoS One

The Duration of T Cell Stimulation Is a Critical Determinant of Cell Fate and Plasticity

(2013) N. Miskov-Zivanov et al.   Science Signaling

A Reduction Method for Boolean Network Models Proven to Conserve Attractors

(2013) Assieh Saadatpour et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS

Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity

(2013) Adria Carbo et al.   PLoS Computational Biology

In search of noise-induced bimodality

(2012) Kyung Kim et al.   BMC BIOLOGY

Ikaros represses and activates PU.1 cell-type-specifically through the multifunctional Sfpi1 URE and a myeloid specific enhancer

(2012) M A Zarnegar et al.   ONCOGENE

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

General Theory of Genotype to Phenotype Mapping: Derivation of Epigenetic Landscapes from N-Node Complex Gene Regulatory Networks

(2012) Carlos Villarreal et al.   PHYSICAL REVIEW LETTERS

Hematopoietic progenitor migration to the adult thymus

(2011) Daniel A. Zlotoff et al.   Annals of the New York Academy of Sciences

Identification of the earliest natural killer cell-committed progenitor in murine bone marrow

(2011) J. W. Fathman et al.   BLOOD

Predicting Pancreas Cell Fate Decisions and Reprogramming with a Hierarchical Multi-Attractor Model

(2011) Joseph Xu Zhou et al.   PLoS One

A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells

(2011) Tian Hong et al.   PLoS Computational Biology

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

(2011) Melody K. Morris et al.   PLoS Computational Biology

The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Natural killer-cell differentiation by myeloid progenitors

(2010) B. Grzywacz et al.   BLOOD

Dynamically consistent reduction of logical regulatory graphs

(2010) Aurélien Naldi et al.   THEORETICAL COMPUTER SCIENCE

A Bistable Switch Underlying B-Cell Differentiation and Its Disruption by the Environmental Contaminant 2,3,7,8-Tetrachlorodibenzo-p-dioxin

(2010) Sudin Bhattacharya et al.   TOXICOLOGICAL SCIENCES

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

(2010) Laurence Calzone et al.   PLoS Computational Biology

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling

(2010) Aurélien Naldi et al.   PLoS Computational Biology

Modeling lymphocyte homing and encounters in lymph nodes

(2009) Valentina Baldazzi et al.   BMC BIOINFORMATICS

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

(2009) Dominik M Wittmann et al.   BMC Systems Biology

Immune-Induced Epithelial to Mesenchymal Transition In vivo Generates Breast Cancer Stem Cells

(2009) M. Santisteban et al.   CANCER RESEARCH

Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells

(2009) Jayajit Das et al.   CELL

Inhibition of Th17 Cells Regulates Autoimmune Diabetes in NOD Mice

(2009) J. A. Emamaullee et al.   DIABETES

Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development

(2009) M. A. Inlay et al.   GENES & DEVELOPMENT

A Recurrent Network Involving the Transcription Factors PU.1 and Gfi1 Orchestrates Innate and Adaptive Immune Cell Fates

(2009) Chauncey J. Spooner et al.   IMMUNITY

Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective

(2009) Sui Huang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Lymphoid precursors are directed to produce dendritic cells as a result of TLR9 ligation during herpes infection

(2008) R. S. Welner et al.   BLOOD

Reductive isolation from bone marrow and blood implicates common lymphoid progenitors as the major source of thymopoiesis

(2008) T. Serwold et al.   BLOOD

Flk2+ common lymphoid progenitors possess equivalent differentiation potential for the B and T lineages

(2008) H. Karsunky et al.   BLOOD

Generation of highly suppressive adaptive CD8+CD25+FOXP3+ regulatory T cells by continuous antigen stimulation

(2008) Milada Mahic et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

The AKT–mTOR axis regulates de novo differentiation of CD4+Foxp3+cells

(2008) Sokol Haxhinasto et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast

(2008) Maria I. Davidich et al.   PLoS One

B Cell Antigen Presentation Promotes Th2 Responses and Immunopathology during Chronic Allergic Lung Disease

(2008) Dennis M. Lindell et al.   PLoS One

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network model of survival signaling in large granular lymphocyte leukemia

(2008) R. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

T cell receptor signaling controls Foxp3 expression via PI3K, Akt, and mTOR

(2008) S. Sauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variability and Robustness in T Cell Activation from Regulated Heterogeneity in Protein Levels

(2008) O. Feinerman et al.   SCIENCE