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Model-based analysis of competing-endogenous pathways (MACPath) in human cancers

PLoS computational biology, 2018-03, Vol.14 (3), p.e1006074-e1006074

2018

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Evaluating a large language model’s ability to solve programming exercises from an introductory bioinformatics course

PLoS computational biology, 2023-09, Vol.19 (9), p.e1011511-e1011511

2023

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Programming cell growth into different cluster shapes using diffusible signals

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009576-e1009576

2021

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Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

PLoS computational biology, 2017-01, Vol.13 (1), p.e1005331-e1005331

2017

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Evaluation of residue-residue contact prediction methods: From retrospective to prospective

PLoS computational biology, 2021-05, Vol.17 (5), p.e1009027-e1009027

2021

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Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009234-e1009234

2021

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The genetic basis for adaptation of model-designed syntrophic co-cultures

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006213-e1006213

2019

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Scalable nonlinear programming framework for parameter estimation in dynamic biological system models

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006828-e1006828

2019

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Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data

PLoS computational biology, 2009-12, Vol.5 (12), p.e1000591-e1000591

2009

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Ten quick tips for teaching programming

PLoS computational biology, 2018-04, Vol.14 (4), p.e1006023-e1006023

2018

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SteadyCom: Predicting microbial abundances while ensuring community stability

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005539-e1005539

2017

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An Introduction to Programming for Bioscientists: A Python-Based Primer

PLoS computational biology, 2016-06, Vol.12 (6), p.e1004867-e1004867

2016

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Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming

PLoS computational biology, 2016-04, Vol.12 (4), p.e1004838-e1004838

2016

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BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005544-e1005544

2017

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Ten simple rules for quick and dirty scientific programming

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008549-e1008549

2021

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Computational Modeling, Formal Analysis, and Tools for Systems Biology

PLoS computational biology, 2016-01, Vol.12 (1), p.e1004591-e1004591

2016

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Ten quick tips for delivering programming lessons

PLoS computational biology, 2019-10, Vol.15 (10), p.e1007433-e1007433

2019

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Deep reinforcement learning for optimal experimental design in biology

PLoS computational biology, 2022-11, Vol.18 (11), p.e1010695-e1010695

2022

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TRANSIT--A Software Tool for Himar1 TnSeq Analysis

PLoS computational biology, 2015-10, Vol.11 (10), p.e1004401-e1004401

2015

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kCSD-python, reliable current source density estimation with quality control

PLoS computational biology, 2024-03, Vol.20 (3), p.e1011941-e1011941

2024

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Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006867-e1006867

2019

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A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

PLoS computational biology, 2018-02, Vol.14 (2), p.e1005958-e1005958

2018

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Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

PLoS computational biology, 2016-03, Vol.12 (3), p.e1004808-e1004808

2016

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From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

PLoS computational biology, 2017-04, Vol.13 (4), p.e1005409-e1005409

2017

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Model-based analysis of competing-endogenous pathways (MACPath) in human cancers

Evaluating a large language model’s ability to solve programming exercises from an introductory bioinformatics course

Programming cell growth into different cluster shapes using diffusible signals

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

Evaluation of residue-residue contact prediction methods: From retrospective to prospective

Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations

The genetic basis for adaptation of model-designed syntrophic co-cultures

Scalable nonlinear programming framework for parameter estimation in dynamic biological system models

Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data

Ten quick tips for teaching programming

SteadyCom: Predicting microbial abundances while ensuring community stability

An Introduction to Programming for Bioscientists: A Python-Based Primer

Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Ten simple rules for quick and dirty scientific programming

Computational Modeling, Formal Analysis, and Tools for Systems Biology

Ten quick tips for delivering programming lessons

Deep reinforcement learning for optimal experimental design in biology

TRANSIT--A Software Tool for Himar1 TnSeq Analysis

kCSD-python, reliable current source density estimation with quality control

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

The experience of teaching introductory programming skills to bioscientists in Brazil

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