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A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

Genome research, 2012-11, Vol.22 (11), p.2302-2314

2012

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Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance

Molecular ecology, 2021-09, Vol.30 (18), p.4466-4480

2021

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Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

Nature communications, 2023-09, Vol.14 (1), p.5682-13, Article 5682

2023

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Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

BMC bioinformatics, 2006-06, Vol.7 (1), p.280-280, Article 280

2006

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

Genome research, 2003-11, Vol.13 (11), p.2498-2504

2003

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Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana

Proceedings of the National Academy of Sciences - PNAS, 2013-04, Vol.110 (18), p.7518-7523

2013

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CTCF physically links cohesin to chromatin

Proceedings of the National Academy of Sciences - PNAS, 2008-06, Vol.105 (24), p.8309-8314

2008

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Origin of biogeographically distinct ecotypes during laboratory evolution

Nature communications, 2024-08, Vol.15 (1), p.7451-14, Article 7451

2024

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History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications

Frontiers in physiology, 2021-03, Vol.12, p.637999-637999

2021

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Ocean acidification conditions increase resilience of marine diatoms

Nature communications, 2018-06, Vol.9 (1), p.2328-10, Article 2328

2018

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Path‐seq identifies an essential mycolate remodeling program for mycobacterial host adaptation

Molecular systems biology, 2019-03, Vol.15 (3), p.e8584-n/a

2019

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Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics

PloS one, 2021-02, Vol.16 (2), p.e0247534-e0247534

2021

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Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance

Frontiers in microbiology, 2021-09, Vol.12, p.712631

2021

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cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

Nucleic acids research, 2015-07, Vol.43 (13), p.e87

2015

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Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Cell reports (Cambridge), 2020-04, Vol.31 (4), p.107577-107577, Article 107577

2020

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Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005489-e1005489

2017

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Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages

Scientific reports, 2024-05, Vol.14 (1), p.11898-11898, Article 11898

2024

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A systems-level gene regulatory network model for Plasmodium falciparum

Nucleic acids research, 2021-05, Vol.49 (9), p.4891-4906

2021

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A role for programmed cell death in the microbial loop

PloS one, 2013-05, Vol.8 (5), p.e62595-e62595

2013

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Use and abuse of correlation analyses in microbial ecology

The ISME Journal, 2019-11, Vol.13 (11), p.2647-2655

2019

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Catabolite Control Protein A (CcpA) Contributes to Virulence and Regulation of Sugar Metabolism in Streptococcus pneumoniae

Journal of Bacteriology, 2005-12, Vol.187 (24), p.8340-8349

2005

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MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance

Cell reports (Cambridge), 2023-08, Vol.42 (8), p.112875-112875, Article 112875

2023

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A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

Nucleic acids research, 2014-10, Vol.42 (18), p.11291-11303

2014

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Global analysis of mRNA stability in Mycobacterium tuberculosis

Nucleic acids research, 2013-01, Vol.41 (1), p.509-517

2013

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The Gaggle: an open-source software system for integrating bioinformatics software and data sources

BMC bioinformatics, 2006-03, Vol.7 (1), p.176-176, Article 176

2006

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A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

Cytoscape: a software environment for integrated models of biomolecular interaction networks

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana

CTCF physically links cohesin to chromatin

Origin of biogeographically distinct ecotypes during laboratory evolution

History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications

Ocean acidification conditions increase resilience of marine diatoms

Path‐seq identifies an essential mycolate remodeling program for mycobacterial host adaptation

Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics

Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages

A systems-level gene regulatory network model for Plasmodium falciparum

A role for programmed cell death in the microbial loop

Use and abuse of correlation analyses in microbial ecology

Catabolite Control Protein A (CcpA) Contributes to Virulence and Regulation of Sugar Metabolism in Streptococcus pneumoniae

MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

Global analysis of mRNA stability in Mycobacterium tuberculosis

The Gaggle: an open-source software system for integrating bioinformatics software and data sources

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