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Sparse and compositionally robust inference of microbial ecological networks

PLoS computational biology, 2015-05, Vol.11 (5), p.e1004226

2015

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Helminth infection promotes colonization resistance via type 2 immunity

Science (American Association for the Advancement of Science), 2016-04, Vol.352 (6285), p.608-612

2016

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Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

PLoS computational biology, 2021-01, Vol.17 (1), p.e1008569-e1008569

2021

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Why are there hotspot mutations in the TP53 gene in human cancers?

Cell death and differentiation, 2018-01, Vol.25 (1), p.154-160

2018

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Modeling the temporal dynamics of the gut microbial community in adults and infants

PLoS computational biology, 2019-06, Vol.15 (6), p.e1006960-e1006960

2019

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Computational translation of genomic responses from experimental model systems to humans

PLoS computational biology, 2019-01, Vol.15 (1), p.e1006286-e1006286

2019

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Structural host-microbiota interaction networks

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005579

2017

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PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions

PLoS computational biology, 2012-12, Vol.8 (12), p.e1002838-e1002838

2012

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Diversity and plasticity of Th cell types predicted from regulatory network modelling

PLoS computational biology, 2010-09, Vol.6 (9), p.e1000912-e1000912

2010

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Improving breast cancer survival analysis through competition-based multidimensional modeling

PLoS computational biology, 2013-05, Vol.9 (5), p.e1003047-e1003047

2013

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Differential expression analysis for pathways

PLoS computational biology, 2013-03, Vol.9 (3), p.e1002967-e1002967

2013

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Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptor-mediated apoptosis

PLoS computational biology, 2012-04, Vol.8 (4), p.e1002482-e1002482

2012

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Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet

Genome medicine, 2016-04, Vol.8 (1), p.48-48, Article 48

2016

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Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs

The Journal of immunology (1950), 2020-08, Vol.205 (4), p.1070-1083

2020

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Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs

PLoS computational biology, 2013-09, Vol.9 (9), p.e1003204-e1003204

2013

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Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice

Cell host & microbe, 2021-08, Vol.29 (8), p.1249-1265.e9

2021

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Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model

PLoS computational biology, 2011-01, Vol.7 (1), p.e1001046-e1001046

2011

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Accurate quantification of functional analogy among close homologs

PLoS computational biology, 2011-02, Vol.7 (2), p.e1001074-e1001074

2011

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Interspecies translation of disease networks increases robustness and predictive accuracy

PLoS computational biology, 2011-11, Vol.7 (11), p.e1002258-e1002258

2011

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Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation

PLoS computational biology, 2010-12, Vol.6 (12), p.e1001032-e1001032

2010

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A scalable approach for discovering conserved active subnetworks across species

PLoS computational biology, 2010-12, Vol.6 (12), p.e1001028-e1001028

2010

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Correction: Differential Expression Analysis for Pathways

PLoS computational biology, 2013-04, Vol.9 (4)

2013

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Integrating quantitative knowledge into a qualitative gene regulatory network

PLoS computational biology, 2011-09, Vol.7 (9), p.e1002157-e1002157

2011

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Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells

Inflammatory bowel diseases, 2017-09, Vol.23 (9), p.1544-1554

2017

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Sparse and compositionally robust inference of microbial ecological networks

Helminth infection promotes colonization resistance via type 2 immunity

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2

Why are there hotspot mutations in the TP53 gene in human cancers?

Modeling the temporal dynamics of the gut microbial community in adults and infants

Computational translation of genomic responses from experimental model systems to humans

Structural host-microbiota interaction networks

PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions

Diversity and plasticity of Th cell types predicted from regulatory network modelling

Improving breast cancer survival analysis through competition-based multidimensional modeling

Differential expression analysis for pathways

Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptor-mediated apoptosis

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet

Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs

Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs

Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice

Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model

Accurate quantification of functional analogy among close homologs

Interspecies translation of disease networks increases robustness and predictive accuracy

Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation

A scalable approach for discovering conserved active subnetworks across species

Correction: Differential Expression Analysis for Pathways

Integrating quantitative knowledge into a qualitative gene regulatory network

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells

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