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Covasim: An agent-based model of COVID-19 dynamics and interventions

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009149

2021

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SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008686

2021

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MicrobeTrace: Retooling molecular epidemiology for rapid public health response

PLoS computational biology, 2021-09, Vol.17 (9), p.e1009300-e1009300

2021

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SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy

PLoS computational biology, 2020-02, Vol.16 (2), p.e1007604-e1007604

2020

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pyTFM: A tool for traction force and monolayer stress microscopy

PLoS computational biology, 2021-06, Vol.17 (6), p.e1008364-e1008364

2021

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MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics

PLoS computational biology, 2021-05, Vol.17 (5), p.e1009030

2021

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FastTrack: An open-source software for tracking varying numbers of deformable objects

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008697-e1008697

2021

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POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009148-e1009148

2021

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A fast machine-learning-guided primer design pipeline for selective whole genome amplification

PLoS computational biology, 2023-04, Vol.19 (4), p.e1010137-e1010137

2023

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MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009594-e1009594

2021

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SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks

PLoS computational biology, 2018-08, Vol.14 (8), p.e1006369-e1006369

2018

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Structure learning for gene regulatory networks

PLoS computational biology, 2023-05, Vol.19 (5), p.e1011118-e1011118

2023

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CytoPy: An autonomous cytometry analysis framework

PLoS computational biology, 2021-06, Vol.17 (6), p.e1009071-e1009071

2021

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CHOIRBM: An R package for exploratory data analysis and interactive visualization of pain patient body map data

PLoS computational biology, 2022-10, Vol.18 (10), p.e1010496-e1010496

2022

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Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

PLoS computational biology, 2022-05, Vol.18 (5), p.e1010138-e1010138

2022

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VGsim: Scalable viral genealogy simulator for global pandemic

PLoS computational biology, 2022-08, Vol.18 (8), p.e1010409-e1010409

2022

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Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases

PLoS computational biology, 2023-01, Vol.19 (1), p.e1010799-e1010799

2023

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Arioc: High-concurrency short-read alignment on multiple GPUs

PLoS computational biology, 2020-11, Vol.16 (11), p.e1008383-e1008383

2020

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Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics

PLoS computational biology, 2022-06, Vol.18 (6), p.e1009773-e1009773

2022

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ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008685-e1008685

2021

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linus: Conveniently explore, share, and present large-scale biological trajectory data in a web browser

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009503-e1009503

2021

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COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008769

2021

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IOCBIO Kinetics: An open-source software solution for analysis of data traces

PLoS computational biology, 2020-12, Vol.16 (12), p.e1008475-e1008475

2020

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Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations

PLoS computational biology, 2021-08, Vol.17 (8), p.e1009274-e1009274

2021

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DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP

PLoS computational biology, 2018-04, Vol.14 (4), p.e1006090-e1006090

2018

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Covasim: An agent-based model of COVID-19 dynamics and interventions

SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19

MicrobeTrace: Retooling molecular epidemiology for rapid public health response

SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy

pyTFM: A tool for traction force and monolayer stress microscopy

MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics

FastTrack: An open-source software for tracking varying numbers of deformable objects

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

A fast machine-learning-guided primer design pipeline for selective whole genome amplification

MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data

SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks

Structure learning for gene regulatory networks

CytoPy: An autonomous cytometry analysis framework

CHOIRBM: An R package for exploratory data analysis and interactive visualization of pain patient body map data

Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

VGsim: Scalable viral genealogy simulator for global pandemic

Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases

Arioc: High-concurrency short-read alignment on multiple GPUs

Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways

linus: Conveniently explore, share, and present large-scale biological trajectory data in a web browser

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data

IOCBIO Kinetics: An open-source software solution for analysis of data traces

Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP

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