Farah Abdul-Rahman
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Postdoctoral AssociateDownloadHi-Res Photo
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Postdoctoral Associate
Appointments
Department of Ecology & Evolutionary Biology
Postdoctoral AssociatePrimary
Other Departments & Organizations
- Biological Sciences
- Department of Ecology & Evolutionary Biology
Research
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Overview
I am interested in understanding the ecological and evolutionary consequences of functional redundancy in microbial communities. Functional redundancy, where different species encode overlapping functions, is a widespread feature of many microbiomes, as revealed by metagenomic surveys. However, these surveys capture only potential function rather than realized activity. To overcome this limitation, I aim to use starch degradation as an ecologically relevant model system with a defined genetic basis, which allows the construction of synthetic consortia that can be directly manipulated to uncover the principles governing functional redundancy in microbial communities.
Public Health Interests
Bioinformatics; Evolution; Genetics, Genomics, Epigenetics; Microbial Ecology
ORCID
0000-0001-6854-570X- View Lab Website
Martina Dal Bello
Research at a Glance
Publications Timeline
A big-picture view of Farah Abdul-Rahman's research output by year.
12Publications
242Citations
Publications
2025
Template switching during DNA replication is a prevalent source of adaptive gene amplification
Chuong J, Nun N, Suresh I, Matthews J, De T, Avecilla G, Abdul-Rahman F, Brandt N, Ram Y, Gresham D. Template switching during DNA replication is a prevalent source of adaptive gene amplification. ELife 2025, 13: rp98934. PMID: 39899365, PMCID: PMC11790251, DOI: 10.7554/elife.98934.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsCopy number variantsLong terminal repeatTemplate switchingDNA replicationDynamics of copy number variantsCNV formationEffect of copy number variantsOrigin of DNA replicationSource of genetic variationFitness effectsLocal DNA featuresSaccharomyces cerevisiaeGene amplificationGenome architectureGenome evolutionGenomic elementsGenomic locationsDNA elementsAdaptive evolutionLagging strandEngineered strainGenetic variationHomologous recombinationFrequent amplificationRate of adaptationTemplate switching during DNA replication is a prevalent source of adaptive gene amplification
Chuong J, Ben Nun N, Suresh I, Matthews J, De T, Avecilla G, Abdul-Rahman F, Brandt N, Ram Y, Gresham D. Template switching during DNA replication is a prevalent source of adaptive gene amplification. ELife 2025, 13 DOI: 10.7554/elife.98934.3.Peer-Reviewed Original ResearchCitationsConceptsCopy number variantsGAP1 CNVsLong terminal repeatTemplate switchingDNA replicationDynamics of copy number variantsCNV formationEffect of copy number variantsOrigin of DNA replicationSource of genetic variationFitness effectsLocal DNA featuresGene amplificationGAP1 geneGenome architectureGenome evolutionGenomic elementsGenomic locationsDNA elementsSaccharomyces cerevisiaeAdaptive evolutionLagging strandEngineered strainGenetic variationHomologous recombination
2023
Carboxysomes, Structure and Function
Blanchard J, Abdul-Rahman F. Carboxysomes, Structure and Function. 2023, 486-488. DOI: 10.1007/978-3-662-65093-6_5185.Peer-Reviewed Original ResearchMechanisms of division of labor in mammalian tissue
Abdul-Rahman F. Mechanisms of division of labor in mammalian tissue. Cell Reports 2023, 42: 112366. PMID: 37083329, DOI: 10.1016/j.celrep.2023.112366.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and Concepts
2021
Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection
Abdul-Rahman F, Tranchina D, Gresham D. Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection. Molecular Biology And Evolution 2021, 38: 4362-4375. PMID: 34132791, PMCID: PMC8476146, DOI: 10.1093/molbev/msab173.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsDistribution of fitness effectsNeutral fitness effectsGenetic diversityFitness effectsFluctuating environmentsMaintenance of genetic diversityGene deletion collectionHigh-fitness genotypesTemporally fluctuating environmentsShort-term fitnessVariable selection effectDynamics of selectionDeletion collectionBarcode sequencesFit genotypesNutrient limitationUnique genotypesGenetic variationContinuous cultureEvolutionary biologyEnvironmental fluctuationsDiversityEnvironmental conditionsGenotypesPopulation diversity
2018
An incoherent feedforward loop facilitates adaptive tuning of gene expression
Hong J, Brandt N, Abdul-Rahman F, Yang A, Hughes T, Gresham D. An incoherent feedforward loop facilitates adaptive tuning of gene expression. ELife 2018, 7: e32323. PMID: 29620523, PMCID: PMC5903863, DOI: 10.7554/elife.32323.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsEvolution of gene expressionTuning of gene expressionDNA-binding domainI1-FFLGene expressionAdaptive evolution of gene expressionIncoherent type-1 feedforward loopLong-term experimental evolutionTranscription factor binding affinityAmmonium-limited chemostatsGene regulatory architectureAmmonium transporter genesNon-synonymous variationsSaccharomyces cerevisiaeIncoherent feedforward loopFeedforward loopAdaptive evolutionConsensus sequenceExperimental evolutionTranscriptional networksTranscriptional activityBinding domainRegulatory architectureControl expressionMissense mutations
2017
Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq)
Abdul-Rahman F, Gresham D. Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq). Methods In Molecular Biology 2017, 1720: 15-24. PMID: 29236248, DOI: 10.1007/978-1-4939-7540-2_2.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsNewly transcribed RNAPopulation of RNAsMRNA decay ratesRNA spike-insRNA degradation ratesStreptavidin magnetic beadsBiotinylated RNARNA speciesUnlabeled RNARNAseq librariesSynthesized RNASpike-insRNA approachBiotinylated moleculesRNAReactive thiol groupsCultures of cellsMagnetic beadsDegradation rateDegradation rate constantLabeled populationThiol groupsTranscriptionRNAseqMultiple time pointsThe Role of mRNA Degradation in Dynamic Nitrogen Environments in Saccharomyces cerevisiae
Rodriguez‐Tirado C, Gresham D, Abdul‐Rahman F. The Role of mRNA Degradation in Dynamic Nitrogen Environments in Saccharomyces cerevisiae. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.596.4.Peer-Reviewed Original ResearchConceptsNitrogen catabolite repressionReprogramming of gene expressionNitrogen-poor conditionsMRNA degradationUntranslated regionGene expressionAmino acid permeaseNitrogen-rich conditionsSaccharomyces cerevisiae cellsNitrogen-poor environmentsKnock-outAmino acid substratesNitrogen-rich environmentCatabolite repressionSaccharomyces cerevisiaeIdentified mutantsGrowth defectRegulates localizationGAP1MutantsStem cell differentiationAccelerated degradationGrowth rateAcid substratesPlasma membrane
2016
A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells
Velasco S, Ibrahim M, Kakumanu A, Garipler G, Aydin B, Al-Sayegh M, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni E. A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. Cell Stem Cell 2016, 20: 205-217.e8. PMID: 27939218, PMCID: PMC5291817, DOI: 10.1016/j.stem.2016.11.006.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAnimalsCellular ReprogrammingChromatinDNAEmbryonic Stem CellsEnhancer Elements, GeneticGenetic LociMiceModels, BiologicalMotor NeuronsNucleotide MotifsPromoter Regions, GeneticProtein BindingSequence Analysis, RNASingle-Cell AnalysisTime FactorsTranscription FactorsTranscription, GeneticConceptsTranscription factorsGene expressionOverexpression of transcription factorsControl cell fateCell fate programsOnecut transcription factorsNeuronal programTF bindingChromatin stateRegulatory regionsCell fateRegulatory stepTranscriptional modulationNeuronal enhancersEmbryonic stem cellsCell differentiationChromatinGenesCell programBindingNgn2ExpressionCellsOnecutStem cellsSteady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen
Airoldi E, Miller D, Athanasiadou R, Brandt N, Abdul-Rahman F, Neymotin B, Hashimoto T, Bahmani T, Gresham D. Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen. Molecular Biology Of The Cell 2016, 27: 1383-1396. PMID: 26941329, PMCID: PMC4831890, DOI: 10.1091/mbc.e14-05-1013.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsNitrogen catabolite repressionNitrogen-limited chemostatsPreferred nitrogen sourceGene expression programsCell growth rateNitrogen sourceEnvironmental nitrogenProtein translationExpression programsNitrogen-regulated gene expressionDynamic gene expression programsGlobal gene expression programsGene expressionNitrogen-limited cellsNitrogen-responsive genesAccelerated mRNA degradationDifferential gene expressionDose-dependent repressionGrowth rateCatabolite repressionSaccharomyces cerevisiaeNitrogen assimilationFast growth rateChemostat conditionsBatch culture
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