Author

Chris Chandler

Simons FoundationORCID 0000-0002-5026-7702Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Research Focus:database / resource· 2 Approach:deep learning· 2 Organism:human· 2 Assay:protein structure· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Research Focus:chromatin & epigenetic regulation· 1 Approach:comparative / phylogenetic analysis· 1

Frequent Co-Authors

Richard BonneauiD· 4 shared Daniel BerenbergiD· 3 shared Ramnik J. XavieriD· 3 shared Tomasz KościółekiD· 3 shared Tommi VataneniD· 3 shared Vladimir GligorijevićiD· 3 shared Bryn C. TayloriD· 2 shared I. FiskiD· 2 shared

Activity by Year

2021-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersBioinformatics

Richard BonneauORCID

Mutual co-authors in cluster

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4 papers

Recent·Most cited

Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

Steven A. Sullivan, Jordan C. Orosco, Francisco Callejas‐Hernández, Frances Blow, Hayan Lee, T. Rhyker Ranallo-Benavidez, Andrew Peters, Shane Robert Raidal, Yvette A. Girard, Christine Kreuder Johnson, Krysta H. Rogers, Richard W. Gerhold, Hayley Mangelson, Ivan Liachko, Harsh Srivastava, , Jane M. Carlton

This study compares the genomics of seven Trichomonas species, revealing convergent genome size expansions in human-infecting lineages and genes involved in host-switching from birds to humans.

Nature Communications · Jul 24, 2025Peer-reviewedMicrobiology

Comprehensive function annotation of metagenomes and microbial genomes using a deep learning-based method

Mary Maranga, Paweł Szczerbiak, Valentyn Bezshapkin, Vladimir Gligorijević, Chris Chandler, Richard Bonneau, Ramnik J. Xavier, Tomasz Kościółek, Tommi Vatanen

The paper develops a metagenome analysis workflow combining de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotation, showing improved coverage over existing methods.

mSystems · Apr 3, 2023Peer-reviewedBioinformatics

Sequence-structure-function relationships in the microbial protein universe

Julia Koehler Leman, Paweł Szczerbiak, P. Douglas Renfrew, Vladimir Gligorijević, Daniel Berenberg, Tommi Vatanen, Bryn C. Taylor, Chris Chandler, Stefan Janssen, Andras Pataki, Nick Carriero, I. Fisk, Ramnik J. Xavier, Rob D. Knight, Richard Bonneau, Tomasz Kościółek

The paper predicts structures and annotates functions for diverse microbial protein sequences, identifying novel folds and highlighting the saturation of structural space.

bioRxiv · Mar 18, 2022 · PreprintBioinformatics

Structure-Based Function Prediction using Graph Convolutional Networks

Vladimir Gligorijević, P. Douglas Renfrew, Tomasz Kościółek, Julia Koehler Leman, Daniel Berenberg, Tommi Vatanen, Chris Chandler, Bryn C. Taylor, I. Fisk, Hera C. Vlamakis, Ramnik J. Xavier, Rob D. Knight, Kyunghyun Cho, Richard Bonneau

This paper introduces a Graph Convolutional Network for predicting protein function and identifying important residues, showing improved accuracy over sequence-based methods.

Nature Communications · May 26, 2021Peer-reviewedBioinformatics