GHOFRAN OTHOUM
Edmond,OK
Summary
I specialize in analyzing high-throughput data and developing integrative approaches to explore molecular mechanisms in disease. My work spans sequencing data processing, comparative multi-omics studies, and the identification of previously uncharacterized biomarkers.
Overview
7
7
years of professional experience
Work History
Senior Research Scientist
Washington University in St. Louis
07.2023 - 10.2025
- Translated multi-omics research findings into clinical insights through close collaboration with surgical oncology teams
- Supported precision medicine efforts by integrating genomic and proteomic features into tumor board decision-making
- Developed analytical workflows that identified emerging biomarkers with potential clinical utility in aggressive cancers
- Provided expert bioinformatics support for patient-centered studies, improving sample-to-insight turnaround
Postdoctoral Associate
Maher Lab, Washington University in St. Louis
07.2018 - 06.2023
- Designed and executed large-scale proteogenomic workflows integrating CPTAC and TCGA datasets to uncover cryptic protein expression in cancer
- Discovered novel peptide products from long noncoding and circular RNAs, advancing targeted biomarker discovery
- Developed and maintained pipelines for MS/MS and RNA-seq analysis, enabling reproducible and scalable research outputs
- Mentored graduate students and visiting scholars in bioinformatics methods and data interpretation
- Supported collaborative studies with experimental and clinical teams, facilitating translational research progress
Education
PhD - Chemical and Biological Engineering
King Abdullah University of Science and Technology (KAUST)
Thuwal, KSA01.2018
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Oxford University
Oxford, UK01.2013
M.Sc. - Bioscience
King Abdullah University of Science and Technology (KAUST)
Thuwal, KSA01.2013
B.Sc. - Computer Science
Effat University
Jeddah, KSA01.2011
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Sussex University
London, United Kingdom01.2009
Skills
- Bioinformatics & Genomics: NGS processing, proteogenomics, variant calling, RNA-seq, long-read sequencing, differential expression/splicing
- Programming: Python, R, Bash; workflow automation
- Tools & Platforms: STAR, Salmon, BWA, DESeq2, GATK, MaxQuant, Proteome Discoverer
- Data Integration: Multi-omics analysis (genomics, transcriptomics, proteomics)
- Infrastructure: HPC, cloud environments, version control (Git)
- Visualization & Annotation: scanpy, Seurat, Bioconductor, Enrichr
Awards And Recognitions
Recipient of the L’Oréal-UNESCO For Women in Science fellowship for outstanding research, 2018., Regional final for the 2015 HULT prize.
Publications
- Frye CC, Tennant L, Yeager A, Azimzadeh P, Bhardwaj P, Xu Y, Liu J, Othoum G, Maher CA, Chernock R, Goedegebuure SP. Overexpression of human DNA polymerase theta is a biomarker of aggressive and DNA repair-deficient papillary thyroid cancers. Surgery. 2024 Jun 18.
- Zhao S, Ly A, Mudd J, Rozycki EB, Webster J, Coonrod E, Othoum G, Luo J, Dang HX, Fields RC, Maher CA, Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis, Nucleic acids research cancer, 2023.
- Othoum G and Maher CA, CrypticProteinDB: an integrated database of proteome and immunopeptidome derived non-canonical cancer proteins, Nucleic acids research cancer, 2023.
- Nickless, A., Zhang, J., Othoum, G., Webster, J., Inkman, M. J., Coonrod, E., Fontes, S., Rozycki, E. B., Maher, C. A., & White, N. M. Pan-Cancer Analysis Reveals Recurrent BCAR4 Gene Fusions across Solid Tumors. Molecular cancer research. 2022; 20(10), 1481–1488.
- Othoum G, Coonrod E, Zhao S, Dang HX, Maher CA. Pan-cancer proteogenomic analysis reveals long and circular noncoding RNAs encoding peptides. Nucleic acids research cancer. 2020 Sep;2(3):zcaa015.
- Othoum G, Prigent S, Derouiche A, Shi L, Bokhari A, Alamoudi S, Bougouffa S, Gao X, Hoehndorf R, Arold ST, Gojobori T. Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs). Scientific Reports. 2019 Dec 17;9(1):1-3.
- Othoum G, Bougouffa S, Bokhari A, Lafi FF, Gojobori T, Hirt H, Mijakovic I, Bajic VB, Essack M. Mining biosynthetic gene clusters in Virgibacillus genomes. BMC genomics. 2019 Dec 1;20(1):696.
- Othoum G, Bougouffa S, Razali R, Bokhari A, Alamoudi S, Antunes A, Gao X, Hoehndorf R, Arold ST, Gojobori T, Hirt H. In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters. BMC genomics. 2018 Dec;19(1):382.
- Salhi A, Essack M, Radovanovic A, Marchand B, Bougouffa S, Antunes A, Simoes MF, Lafi FF, Motwalli OA, Bokhari A, Othoum G, ...Bajic VB, DESM: portal for microbial knowledge exploration systems. Nucleic acids research. 2015 Nov 5;44(D1): D624-33.
- Paper (#156) titled “Genome mining of Bacillus paralicheniformis strains from the Red Sea with focus on the biosynthesis of antimicrobial products”, International conference on systems biology, VirginiaTech, Blacksburg, Virginia, USA, 2017.
- Ho YS, Adroub SA, Aleisa F, Mahmood H, Othoum G, Rashid F, Zaher M, Ali S, Bitter W, Pain A, Abdallah AM. Complete genome sequence of Mycobacterium fortuitum subsp. fortuitum type strain DSM46621. Journal of bacteriology. 2012 Nov 15;194(22):6337-8.
Languages
Arabic
Native or Bilingual
English
Full Professional
French
Elementary
Timeline
Senior Research Scientist
Washington University in St. Louis
07.2023 - 10.2025
Postdoctoral Associate
Maher Lab, Washington University in St. Louis
07.2018 - 06.2023
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Oxford University
M.Sc. - Bioscience
King Abdullah University of Science and Technology (KAUST)
B.Sc. - Computer Science
Effat University
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Sussex University
PhD - Chemical and Biological Engineering
King Abdullah University of Science and Technology (KAUST)