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Environments that induce synthetic microbial ecosystems

PLoS computational biology, 2010-11, Vol.6 (11), p.e1001002-e1001002

2010

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Tipping the balance: robustness of tip cell selection, migration and fusion in angiogenesis

PLoS computational biology, 2009-10, Vol.5 (10), p.e1000549-e1000549

2009

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Topography of extracellular matrix mediates vascular morphogenesis and migration speeds in angiogenesis

PLoS computational biology, 2009-07, Vol.5 (7), p.e1000445-e1000445

2009

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mixOmics: An R package for 'omics feature selection and multiple data integration

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005752-e1005752

2017

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A primer on metagenomics

PLoS computational biology, 2010-02, Vol.6 (2), p.e1000667-e1000667

2010

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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005659-e1005659

2017

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Ten years of pathway analysis: current approaches and outstanding challenges

PLoS computational biology, 2012-02, Vol.8 (2), p.e1002375-e1002375

2012

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006650-e1006650

2019

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Protein-protein interactions essentials: key concepts to building and analyzing interactome networks

PLoS computational biology, 2010-06, Vol.6 (6), p.e1000807-e1000807

2010

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Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

PLoS computational biology, 2018-01, Vol.14 (1), p.e1005929

2018

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MUMmer4: A fast and versatile genome alignment system

PLoS computational biology, 2018-01, Vol.14 (1), p.e1005944-e1005944

2018

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MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis

BMC bioinformatics, 2019-11, Vol.20 (1), p.545-10, Article 545

2019

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Hypergraphs and cellular networks

PLoS computational biology, 2009-05, Vol.5 (5), p.e1000385-e1000385

2009

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Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005134-e1005134

2017

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Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation

PLoS computational biology, 2010-06, Vol.6 (6), p.e1000822-e1000822

2010

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Efficient counting of k-mers in DNA sequences using a bloom filter

BMC bioinformatics, 2011-08, Vol.12 (1), p.333-333, Article 333

2011

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Comparing families of dynamic causal models

PLoS computational biology, 2010-03, Vol.6 (3), p.e1000709-e1000709

2010

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Detailed simulations of cell biology with Smoldyn 2.1

PLoS computational biology, 2010-03, Vol.6 (3), p.e1000705-e1000705

2010

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Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis

PLoS computational biology, 2009-07, Vol.5 (7), p.e1000423-e1000423

2009

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Geometric interpretation of gene coexpression network analysis

PLoS computational biology, 2008-08, Vol.4 (8), p.e1000117-e1000117

2008

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Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

PLoS computational biology, 2009-03, Vol.5 (3), p.e1000312-e1000312

2009

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Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors

PLoS computational biology, 2009-03, Vol.5 (3), p.e1000303-e1000303

2009

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Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems

BMC bioinformatics, 2024-04, Vol.25 (1), p.166-166, Article 166

2024

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Systems biology informed deep learning for inferring parameters and hidden dynamics

PLoS computational biology, 2020-11, Vol.16 (11), p.e1007575-e1007575

2020

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CD-HIT: accelerated for clustering the next-generation sequencing data

Bioinformatics, 2012-12, Vol.28 (23), p.3150-3152

2012

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Environments that induce synthetic microbial ecosystems

Tipping the balance: robustness of tip cell selection, migration and fusion in angiogenesis

Topography of extracellular matrix mediates vascular morphogenesis and migration speeds in angiogenesis

mixOmics: An R package for 'omics feature selection and multiple data integration

A primer on metagenomics

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Ten years of pathway analysis: current approaches and outstanding challenges

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Protein-protein interactions essentials: key concepts to building and analyzing interactome networks

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

MUMmer4: A fast and versatile genome alignment system

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis

Hypergraphs and cellular networks

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology

Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation

Efficient counting of k-mers in DNA sequences using a bloom filter

Comparing families of dynamic causal models

Detailed simulations of cell biology with Smoldyn 2.1

Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis

Geometric interpretation of gene coexpression network analysis

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors

Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems

Systems biology informed deep learning for inferring parameters and hidden dynamics

CD-HIT: accelerated for clustering the next-generation sequencing data

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