- Chemophoresis engine: A general mechanism of ATPase-driven cargo transport
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Research Article | published 25 Jul 2022 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1010324
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- A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications
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Research Article | published 23 May 2022 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1010106
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- Model-based identification of conditionally-essential genes from transposon-insertion sequencing data
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Research Article | published 07 Mar 2022 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1009273
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- Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages
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Research Article | published 04 Dec 2020 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1008482
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- Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
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Research Article | published 17 Aug 2020 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1008137
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- AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments
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Research Article | published 17 Jul 2020 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1007980
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- SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures
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Research Article | published 17 Mar 2020 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1007737
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- Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
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Research Article | published 30 Sep 2019 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1006453
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- TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements
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Research Article | published 19 Aug 2019 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1007293
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- Evolutionary model for the unequal segregation of high copy plasmids
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Research Article | published 05 Mar 2019 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1006724
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- A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome
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Research Article | published 26 Dec 2018 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1006673
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- A machine learning based framework to identify and classify long terminal repeat retrotransposons
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Research Article | published 23 Apr 2018 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1006097
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- Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse
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Research Article | published 20 Apr 2018 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1006091
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- The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes
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Research Article | published 31 Mar 2017 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1005471
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- Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer
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Research Article | published 23 Jun 2016 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1004985
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