Author

Afif Elghraoui

San Diego State UniversityORCID 0000-0002-6489-9444Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 5 Approach:experimental assay· 4 Organism:bacteria (other)· 3 Approach:statistical model· 3 Research Focus:variant calling· 3 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Research Focus:deconvolution· 1

Frequent Co-Authors

Faramarz ValafariD· 5 shared Deepika GunasekaraniD· 2 shared Alyssa M. ZlotnickiiD· 1 shared Anthony D. BaughniD· 1 shared Carmela K. Chan· 1 shared Cassidy RobinholdiD· 1 shared Emma Bishop· 1 shared Kellie J. KimiD· 1 shared

Activity by Year

2016-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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5 shared papersGenomics

Faramarz ValafarORCID

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Author profile →

5 papers

Recent·Most cited

Hybran: Hybrid Reference Transfer and ab initio Prokaryotic Genome Annotation

Afif Elghraoui, Deepika Gunasekaran, Sarah M. Radecke, Emma Bishop, Faramarz Valafar

Hybran combines reference-based and ab initio methods to annotate prokaryotic genomes, improving accuracy by leveraging conserved features and filling gaps with predictions.

bioRxiv · Nov 9, 2022 · PreprintBioinformatics

Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using Mycobacterium tuberculosis Isolates

Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar

The paper evaluates syntenic block detection methods and their impact on rearrangement phylogeny using Mycobacterium tuberculosis genomes, finding that method choice affects results, especially in low-support branches.

bioRxiv · Feb 18, 2022 · PreprintGenomics

Structure-aware M. tuberculosis functional annotation uncloaks resistance, metabolic, and virulence genes

Samuel J. Modlin, Afif Elghraoui, Deepika Gunasekaran, Alyssa M. Zlotnicki, Nicholas Allen Dillon, Nermeeta Dhillon, Norman Kuo, Cassidy Robinhold, Carmela K. Chan, Anthony D. Baughn, Faramarz Valafar

The paper updates functional annotations for Mycobacterium tuberculosis genes using literature curation and structural modeling, identifying resistance, metabolic, and virulence genes.

bioRxiv · Jun 30, 2021 · PreprintGenomics

PBHoover and CigarRoller: a method for confident haploid variant calling on Pacific Biosciences data and its application to heterogeneous population analysis

Sarah M. Ramirez-Busby, Afif Elghraoui, Yeon Bin Kim, Kellie J. Kim, Faramarz Valafar

PBHoover and CigarRoller improve haploid variant calling on Pacific Biosciences data, enabling sensitive detection of subpopulations in clinical isolates.

bioRxiv · Jul 2, 2018 · PreprintBioinformatics

SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis

Afif Elghraoui, Samuel J Modlin, Faramarz Valafar

The paper assembles a high-quality H37Ra genome using SMRT sequencing, revealing fewer variants than previously thought and challenging prior conclusions about virulence in Mycobacterium tuberculosis.

bioRxiv · Jul 21, 2016Genomics