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BEAST 2: a software platform for Bayesian evolutionary analysis

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003537

2014

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Software for computing and annotating genomic ranges

PLoS computational biology, 2013-08, Vol.9 (8), p.e1003118-e1003118

2013

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ClonalFrameML: efficient inference of recombination in whole bacterial genomes

PLoS computational biology, 2015-02, Vol.11 (2), p.e1004041-e1004041

2015

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A toolbox for representational similarity analysis

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003553-e1003553

2014

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Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005665-e1005665

2017

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CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

PLoS computational biology, 2012-10, Vol.8 (10), p.e1002708

2012

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rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003571-e1003571

2014

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SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

PLoS computational biology, 2015-11, Vol.11 (11), p.e1004575-e1004575

2015

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SMOG 2: A Versatile Software Package for Generating Structure-Based Models

PLoS computational biology, 2016-03, Vol.12 (3), p.e1004794-e1004794

2016

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Chaste: an open source C++ library for computational physiology and biology

PLoS computational biology, 2013-03, Vol.9 (3), p.e1002970-e1002970

2013

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Getting more out of biomedical documents with GATE's full lifecycle open source text analytics

PLoS computational biology, 2013-02, Vol.9 (2), p.e1002854-e1002854

2013

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Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

PLoS computational biology, 2016-04, Vol.12 (4), p.e1004879-e1004879

2016

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VBA: a probabilistic treatment of nonlinear models for neurobiological and behavioural data

PLoS computational biology, 2014-01, Vol.10 (1), p.e1003441

2014

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OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis

PLoS computational biology, 2014-08, Vol.10 (8), p.e1003806

2014

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SeqRepo: A system for managing local collections of biological sequences

PloS one, 2020-12, Vol.15 (12), p.e0239883-e0239883

2020

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Ten simple rules for the open development of scientific software

PLoS computational biology, 2012-12, Vol.8 (12), p.e1002802-e1002802

2012

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Wham: Identifying Structural Variants of Biological Consequence

PLoS computational biology, 2015-12, Vol.11 (12), p.e1004572-e1004572

2015

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Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

PLoS computational biology, 2016-12, Vol.12 (12), p.e1005220-e1005220

2016

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Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology

PLoS computational biology, 2018-06, Vol.14 (6), p.e1006220-e1006220

2018

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CeleST: computer vision software for quantitative analysis of C. elegans swim behavior reveals novel features of locomotion

PLoS computational biology, 2014-07, Vol.10 (7), p.e1003702-e1003702

2014

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biochem4j: Integrated and extensible biochemical knowledge through graph databases

PloS one, 2017-07, Vol.12 (7), p.e0179130-e0179130

2017

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kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity

PLoS computational biology, 2017-09, Vol.13 (9), p.e1005727

2017

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Automated tracking of whiskers in videos of head fixed rodents

PLoS computational biology, 2012-07, Vol.8 (7), p.e1002591-e1002591

2012

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rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

PLoS computational biology, 2016-10, Vol.12 (10), p.e1005107-e1005107

2016

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Using biological pathway data with paxtools

PLoS computational biology, 2013-09, Vol.9 (9), p.e1003194-e1003194

2013

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BEAST 2: a software platform for Bayesian evolutionary analysis

Software for computing and annotating genomic ranges

ClonalFrameML: efficient inference of recombination in whole bacterial genomes

A toolbox for representational similarity analysis

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

SMOG 2: A Versatile Software Package for Generating Structure-Based Models

Chaste: an open source C++ library for computational physiology and biology

Getting more out of biomedical documents with GATE's full lifecycle open source text analytics

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

VBA: a probabilistic treatment of nonlinear models for neurobiological and behavioural data

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis

SeqRepo: A system for managing local collections of biological sequences

Ten simple rules for the open development of scientific software

Wham: Identifying Structural Variants of Biological Consequence

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology

CeleST: computer vision software for quantitative analysis of C. elegans swim behavior reveals novel features of locomotion

biochem4j: Integrated and extensible biochemical knowledge through graph databases

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity

Automated tracking of whiskers in videos of head fixed rodents

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

Using biological pathway data with paxtools

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