Author

Alan R. Pacheco

Boston UniversityORCID 0000-0002-1128-3232Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Bioinformatics· 2 Microbiology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:bacteria (other)· 2 Research Focus:benchmarking· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Research Focus:drug response / drug discovery· 1 Assay:imaging· 1 Approach:machine learning (classical)· 1 Assay:metabolomics· 1

Frequent Co-Authors

Daniel SegrèiD· 3 shared Anthony Convers· 1 shared Bouke Bentvelsen· 1 shared David B. BernsteiniD· 1 shared Devlin C. MoyeriD· 1 shared Giovanni Stefano UgoliniiD· 1 shared Helena TodoroviD· 1 shared Jan Roelof van der MeeriD· 1 shared

Activity by Year

2019-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Daniel SegrèORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Dimalis: A complete standalone pipeline to analyse prokaryotic cell growth from time-lapse imaging

Helena Todorov, Bouke Bentvelsen, Giovanni Stefano Ugolini, Alan R. Pacheco, Anthony Convers, Tania Miguel Trabajo, Jan Roelof van der Meer

Dimalis automates the analysis of bacterial cell growth from time-lapse imaging, providing standardized outputs for downstream processing.

bioRxiv · Apr 23, 2024 · PreprintMicrobiology

An evolutionary algorithm for designing microbial communities via environmental modification

Alan R. Pacheco, Daniel Segrè

This paper introduces an evolutionary algorithm combining machine learning and dynamic flux balance analysis to design microbial communities by optimizing environmental conditions for target phenotypes.

Journal of The Royal Society Interface · Jun 1, 2021Peer-reviewedBioinformatics

Stoichiometric Modelling of String Chemistries

Devlin C. Moyer, Alan R. Pacheco, David B. Bernstein, Daniel Segrè

This paper develops a Python tool for studying string chemistries and introduces a network-pruning algorithm to generate minimal metabolic networks.

bioRxiv · Sep 16, 2020 · PreprintBioinformatics

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

Alan R. Pacheco, Mauricio Moel, Daniel Segrè

The paper uses genome-scale metabolic models to show that costless metabolite exchange can drive stable microbial interactions and synthetic consortia.

Nature Communications · Jan 3, 2019Peer-reviewedSystems Biology