Farren Isaacs, PhD
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About
Titles
Professor of Molecular, Cellular and Developmental Biology
Education & Training
- PhD
- Boston University, Bioinformatics (2003)
- BS
- University of Pennsylvania, Bioengineering
- MS
- Boston University, Biomedical Engineering
- Research Fellow
- Harvard Medical School
Research
Overview
Medical Subject Headings (MeSH)
Bioengineering; Gene Editing; Gene Regulatory Networks; Genetic Variation; Genetics; Genomics; Glioblastoma; Synthetic Biology; Systems Biology
ORCID
0000-0001-8615-8236
Research at a Glance
Publications Timeline
A big-picture view of Farren Isaacs's research output by year.
Research Interests
Research topics Farren Isaacs is interested in exploring.
7Publications
3,050Citations
Gene Editing
Genetic Variation
Publications
2024
Enhanced eMAGE applied to identify genetic factors of nuclear hormone receptor dysfunction via combinatorial gene editing
Ciaccia P, Liang Z, Schweitzer A, Metzner E, Isaacs F. Enhanced eMAGE applied to identify genetic factors of nuclear hormone receptor dysfunction via combinatorial gene editing. Nature Communications 2024, 15: 5218. PMID: 38890276, PMCID: PMC11189492, DOI: 10.1038/s41467-024-49365-z.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsGenome modificationEngineered nucleasesMultiplex genome engineeringEfficient multiplex editingLigand-binding domain of human estrogen receptor alphaMethods of genome editingCancer-associated mutationsHomology-directed repairMismatch repair systemLigand-binding domainSaccharomyces cerevisiaeYeast modelSynthetic genomesGenome engineeringPolygenic basisComplex phenotypesBackground mutationsGenomeGenome editingMultiplex editingEditing frequencyHuman estrogen receptor alphaDNA breaksEstrogen receptor alphaMMR inactivation
2023
Metagenomics harvested genus-specific single-stranded DNA-annealing proteins improve and expand recombineering in Pseudomonas species
Asin-Garcia E, Garcia-Morales L, Bartholet T, Liang Z, Isaacs F, dos Santos V. Metagenomics harvested genus-specific single-stranded DNA-annealing proteins improve and expand recombineering in Pseudomonas species. Nucleic Acids Research 2023, 51: 12522-12536. PMID: 37941137, PMCID: PMC10711431, DOI: 10.1093/nar/gkad1024.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPseudomonas genusMetabolic engineering effortsSynthetic biology applicationsGenetic engineering toolsGenome editing capabilitiesRelated speciesStress resistanceValuable hostBiology applicationsActive variantsEnvironmental biotechnologyDifferent PseudomonasRecombineeringPseudomonas speciesPseudomonas putidaPseudomonas fluorescensSpeciesGenusNGS analysisCharacteristics of toleranceRemarkable abilityProteinEngineering effortsPseudomonasValuable compounds
2011
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 2011, 333: 348-353. PMID: 21764749, PMCID: PMC5472332, DOI: 10.1126/science.1205822.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGenome engineeringSynonymous codon substitutionsGenome engineering technologiesSynthetic lethal effectMegabase scaleCodon replacementsTAA codonCodon substitutionsRecombination frequencyCodon modificationGenetic landscapeEscherichia coliGenomeChromosomesCodonPrecise changesLethal effectsPrecise manipulationEngineering technologyNucleotidesColiPhenotypeTagsModification
2009
Programming cells by multiplex genome engineering and accelerated evolution
Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460: 894-898. PMID: 19633652, PMCID: PMC4590770, DOI: 10.1038/nature08187.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and Concepts
2006
RNA synthetic biology
Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nature Biotechnology 2006, 24: 545-554. PMID: 16680139, DOI: 10.1038/nbt1208.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsRNA moleculesSynthetic biologyDiverse regulatory rolesRNA synthetic biologyNew biological functionsCellular control systemsSensors of intracellularMammalian systemsRNA componentBiological functionsGene expressionNatural versatilityCellular behaviorRegulatory roleRNA systemsEnvironmental stimuliBiological networksSmall moleculesBiologyNucleic acidsMoleculesYeastProteinBacteriaIntracellular
2004
Engineered riboregulators enable post-transcriptional control of gene expression
Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology 2004, 22: 841-847. PMID: 15208640, DOI: 10.1038/nbt986.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsStem-loop structureGene expressionPost-transcriptional controlPost-transcriptional regulation systemSmall noncoding RNAsTrans targetsCis-repressive sequenceRibosome bindingNoncoding RNAsEndogenous RNATarget genesCis sequencesRegulatory roleEscherichia coliRNABiological networksRiboregulatorsMechanistic actionGenesExpressionRecent studiesSequenceRegulation systemTranscriptionPromoter
2003
Prediction and measurement of an autoregulatory genetic module
Isaacs FJ, Hasty J, Cantor CR, Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings Of The National Academy Of Sciences Of The United States Of America 2003, 100: 7714-7719. PMID: 12808135, PMCID: PMC164653, DOI: 10.1073/pnas.1332628100.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGene regulatory networksGenetic modulesGene networksRegulatory networksComplex gene regulatory networksPhenotypic cellular responsesAutoregulatory gene networksStochastic versionCellular processesExpression statesProtein destabilizationCellular controlModel fluctuationsGene expressionSystems biologyCellular responsesProper quantitative descriptionQuantitative agreementSuch networksInternal noiseQuantitative descriptionQuantitative understandingKey propertiesPopulation distributionExperimental validation
Academic Achievements and Community Involvement
honor Beckman Young Investigator Award
National AwardArnold and Mabel Beckman FoundationDetails09/01/2012United Stateshonor Rising Young Stars of Science
UnknownGenome Technology MagazineDetails01/01/2008United States
Links & Media
News
- October 12, 2022
Yale Cancer Center Members Receive Faculty Innovation Awards
- April 04, 2022Source: YaleNews
Synthetic Key Unlocks a Hidden Biology Treasure Chest
- April 01, 2022
Synthetic Key Unlocks a Hidden Biology Treasure Chest
- July 01, 2020
COVID-related Pilot Projects Are Selected for Research Funding
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Locations
Science Hill
Academic Office
Kline Biology Tower
219 Prospect Street, Ste KBT 802
New Haven, CT 06511
Appointments
203.432.3783West Campus
Lab
100 West Campus Drive, Ste B-31, #209
Orange, CT 06477