Faculty

Institution

Unit

Venue

Mohammed El-Kebir

Associate Professor

University of Illinois Urbana-Champaign

Affiliations

The Grainger College of Engineering

Siebel School of Computing and Data Science

Mohammed El-kebir is currently serving as a Siebel School Of Computing And Data Science Associate Professor at University of Illinois Urbana-Champaign.

Honors

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Experiences

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Education

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Mohammed El-Kebir

University of Illinois Urbana-Champaign

Associate Professor

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computational biology bioinformatics systems biology genome biology genetics biomedical informatics tumor heterogeneity genomics molecular informatics cancer discovery molecular diagnostics cancer research cancer genomics single cell sequencing molecular evolution next-generation sequencing biostatistics phylogenetics theoretical biology cancer cells computational genomics biological networks molecular biology tumor biology somatic variant high throughput sequencing virus research sequence analysis single-cell analysis evolutionary process computational complexity phylogenetic methods communicable diseases general virology systematics biological network visualization bioinformatics online discrete algorithms combinatorial optimization computational optimization pulmonary tuberculosis copy number aberrations mathematical optimization evolutionary applications dna sequencing cancer biology viral evolution phylogeny comparison phylogenomics infectious disease modelling protein bioinformatics deep reinforcement learning phylogenetic tree granulocyte system immunology molecular design evolution-based method interaction network liver cancer hepatocellular carcinoma network algorithms epidemiological dynamic interspecies transmission interactomics global network alignment cancer evolution same tumor reference genomes sequenced genomes computational pan-genomics tumor composition clonal trees mutational history mycobacterium tuberculosis infection critical role multiscale computational modeling bioinformatics database informatics translational bioinformatics

Video Presentations

Notable Scholarly Works

Notable Federal Grants

Collaborators

Bioinformatics. Bioinformatics 41(Supplement 1) (2025)

Mohammed El-Kebir

Bioinformatics 41(Supplement 1), 2025 I170–I179, 2025. Special Issue for Intelligent Systems for Molecular Biology/European Conference on Computational Biology (Ismb/Eccb) 2025. (2025)

Mohammed El-Kebir

biomedical informaticsbioinformatics 41bioinformaticscomputational genomicsspecial issueintelligent systemsgenomicsbiologycomputational biologymolecular informaticsprotein bioinformaticsgenome biologymolecular biologytranslational bioinformatics

Characterizing the Solution Space of Migration Histories of Metastatic Cancers With Mach2. Lecture notes in computer science (2025)

Mrinmoy S. RoddurVikram RamavarapuAbigail BunkumAriana HuebnerRoman MineyevNicholas McGranahanSimone ZaccariaMohammed El-Kebir

metastasiscancer lettertumor biologymigration historiescancer researchradiation oncologyoncologycancer biologycancer cellsoncogenescell migrationsystems biologymetastatic cancerssolution spacetumor heterogeneity

CNREIN: An Evolution-Aware Deep Reinforcement Learning Algorithm for Single-Cell Dna Copy Number Calling. Genome biology (2025)

Stefan IvanovicMohammed El-Kebir

biomedical informaticsdeep reinforcement learninggeneticscomputational intelligencesingle cell sequencingmachine learning researchbioinformaticsreinforcement learningcnrein infersmachine learningsystems biologybreast cancer patientcomputational biologymolecular informaticsgenome biologydeep learningtumor heterogeneity

Development of a Whole-Exome Sequencing Kit to Facilitate Porcine Biomedical Research. Genome biology (2025)

Vishwaarth VijayakumarTanvi JoshiLobna ElkhadragyLawrence B SchookRon C GabaMohammed El-KebirKyle M Schachtschneider

cancer genomicsmolecular diagnosticsgeneticsvariant interpretationporcine breedsanimal biotechnologyfunctional genomicsporcine modelsanimal geneticsgenomicsgenome biologyporcine biomedical researchcancer discoverycancer geneticsnext-generation sequencingpathology

DOLPHYIN: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer. WABI 2025, Workshop on Algorithms in Bioinformatics (2025)

Mohammed El-Kebir

molecular evolutiongeneticsbioinformaticsphylogeneticsgenomicsbiologycomputational biologygenome biologycombinatorial algorithmcancer discoverysystematicsphylogenetic methodsphylogenomics

Fast Tumor Phylogeny Regression via Tree-Structured Dual Dynamic Programming. Bioinformatics (2025)

Henri SchmidtYuanyuan QiBenjamin J RaphaelMohammed El-Kebir

biomedical informaticslarge-scale global optimizationbioinformaticsfastppm supportsfastppm enables analysislarge scale optimizationmachine learningbiostatisticssystems biologycomputational optimizationcomputational biologyimplementation fastppmphylogenetic methods

PHARMING: Joint Clonal Tree Reconstruction of Snv and Cna Evolution From Single-Cell Dna Sequencing of Tumors. Lecture notes in computer science (2025)

Leah L. WeberAnna HartIdoia OchoaMohammed El-Kebir

tumor heterogeneitytumor biologymolecular diagnosticssingle cell sequencingcancer researchsingle-cell dna sequencingdna sequencingsingle-cell analysiscell biologycancer cellssystems biologygenome biologycna evolutionpathology

A Novel Method for Inferring B Cell Clonal Lineages From Single-Cell Rna Sequencing Data. The Journal of Immunology (2024)

Leah WeberDerek ReimanMrinmoy RoddurYuanyuan QiMohammed El-KebirAly Khan

molecular evolutiongeneticssingle cell sequencingb cellsbioinformaticsaffinity maturationtranscriptomeevolutionary biologygenomicsmolecular ecologygenome biologyb cell receptornext-generation sequencing

Characterizing the Solution Space of Migration Histories of Metastatic Cancers With Mach2. bioRxiv (Cold Spring Harbor Laboratory) (2024)

Mrinmoy Saha RoddurVIkram RamavarapuAbigail BunkumAriana HuebnerRoman MinyevNicholas McGranahanSimone ZaccariaMohammed El-Kebir

metastasisbiomedical informaticscancer genomicscancer researchoncologymach2 solution spacescancer cellsbiostatisticssystems biologymolecular informaticsmigration historycancer discoverytumor heterogeneity

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Mohammed El-Kebir

Associate Professor

University of Illinois Urbana-Champaign

Affiliations

The Grainger College of Engineering

Siebel School of Computing and Data Science

Mohammed El-kebir is currently serving as a Siebel School Of Computing And Data Science Associate Professor at University of Illinois Urbana-Champaign.

Honors

Create free account to unlock more features

Experiences

Create free account to unlock more features

Education

Create free account to unlock more features

Mohammed El-Kebir

University of Illinois Urbana-Champaign

Associate Professor

You can click a keyword to filter the displayed items

Video Presentations

Notable Scholarly Works

Notable Federal Grants

Collaborators

Bioinformatics. Bioinformatics 41(Supplement 1) (2025)

Mohammed El-Kebir

Bioinformatics 41(Supplement 1), 2025 I170–I179, 2025. Special Issue for Intelligent Systems for Molecular Biology/European Conference on Computational Biology (Ismb/Eccb) 2025. (2025)

Mohammed El-Kebir

Characterizing the Solution Space of Migration Histories of Metastatic Cancers With Mach2. Lecture notes in computer science (2025)

Mrinmoy S. RoddurVikram RamavarapuAbigail BunkumAriana HuebnerRoman MineyevNicholas McGranahanSimone ZaccariaMohammed El-Kebir

CNREIN: An Evolution-Aware Deep Reinforcement Learning Algorithm for Single-Cell Dna Copy Number Calling. Genome biology (2025)

Stefan IvanovicMohammed El-Kebir

Development of a Whole-Exome Sequencing Kit to Facilitate Porcine Biomedical Research. Genome biology (2025)

Vishwaarth VijayakumarTanvi JoshiLobna ElkhadragyLawrence B SchookRon C GabaMohammed El-KebirKyle M Schachtschneider

DOLPHYIN: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer. WABI 2025, Workshop on Algorithms in Bioinformatics (2025)

Mohammed El-Kebir

molecular evolutiongeneticsbioinformaticsphylogeneticsgenomicsbiologycomputational biologygenome biologycombinatorial algorithmcancer discoverysystematicsphylogenetic methodsphylogenomics

Fast Tumor Phylogeny Regression via Tree-Structured Dual Dynamic Programming. Bioinformatics (2025)

Henri SchmidtYuanyuan QiBenjamin J RaphaelMohammed El-Kebir

PHARMING: Joint Clonal Tree Reconstruction of Snv and Cna Evolution From Single-Cell Dna Sequencing of Tumors. Lecture notes in computer science (2025)

Leah L. WeberAnna HartIdoia OchoaMohammed El-Kebir

A Novel Method for Inferring B Cell Clonal Lineages From Single-Cell Rna Sequencing Data. The Journal of Immunology (2024)

Leah WeberDerek ReimanMrinmoy RoddurYuanyuan QiMohammed El-KebirAly Khan

Characterizing the Solution Space of Migration Histories of Metastatic Cancers With Mach2. bioRxiv (Cold Spring Harbor Laboratory) (2024)

Mrinmoy Saha RoddurVIkram RamavarapuAbigail BunkumAriana HuebnerRoman MinyevNicholas McGranahanSimone ZaccariaMohammed El-Kebir

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