Farren Isaacs, PhD
Professor of Molecular, Cellular and Developmental BiologyDownloadHi-Res Photo
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Professor of Molecular, Cellular and Developmental Biology
Departments & Organizations
- Biochemistry, Quantitative Biology, Biophysics and Structural Biology (BQBS)
- Center for RNA Science and Medicine
- Genomics, Genetics, and Epigenetics
- Microbiology
- Molecular Cell Biology, Genetics and Development
- Plant Molecular Biology
- Yale Cancer Center
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
- Yale Ventures
Education & Training
- PhD
- Boston University, Bioinformatics (2003)
- BS
- University of Pennsylvania, Bioengineering
- MS
- Boston University, Biomedical Engineering
- Research Fellow
- Harvard Medical School
Research
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Overview
Medical Research Interests
Bioengineering; Gene Editing; Gene Regulatory Networks; Genetic Variation; Genetics; Genomics; Glioblastoma; Synthetic Biology; Systems Biology
ORCID
0000-0001-8615-8236- View Lab Website
Isaacs Lab
Research at a Glance
Yale Co-Authors
Frequent collaborators of Farren Isaacs's published research.
Publications Timeline
A big-picture view of Farren Isaacs's research output by year.
Research Interests
Research topics Farren Isaacs is interested in exploring.
Jesse Rinehart, PhD
Monkol Lek, PhD
Ruslan Medzhitov, PhD
Svetlana Rogulina
13Publications
3,306Citations
Gene Editing
Genetic Variation
Publications
2025
Building Decision Points Into Research’s Slipperiest Slopes
Evans J, Callender C, Devaraj N, Isaacs F, Kaebnick G. Building Decision Points Into Research’s Slipperiest Slopes. Issues In Science And Technology 2025, 41: 78-82. DOI: 10.58875/nlse3159.Peer-Reviewed Original ResearchConceptsPrecision multiplexed base editing in human cells using Cas12a-derived base editors
Schweitzer A, Adams E, Nguyen M, Lek M, Isaacs F. Precision multiplexed base editing in human cells using Cas12a-derived base editors. Nature Communications 2025, 16: 5061. PMID: 40449999, PMCID: PMC12126522, DOI: 10.1038/s41467-025-59653-x.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsMultiplex base editingBase editingBase editorsBase editor variantsMammalian genome engineeringBase editing technologyGenome engineering technologiesDNA double strand breaksBase editing systemMammalian genomesDouble strand breaksMultiple lociPolygenic phenotypesHuman cell linesHuman genomeGenome engineeringTarget nucleotideEditing outcomesMutation rateMultiplex editingMultiple gRNAsHuman cellsExpression cassetteEditing technologyGenomeSynthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16
Nakamura A, Fulk E, Johnson C, Isaacs F. Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16. ACS Synthetic Biology 2025, 14: 943-953. PMID: 40048245, PMCID: PMC11934965, DOI: 10.1021/acssynbio.4c00869.Peer-Reviewed Original ResearchCitationsMeSH Keywords and ConceptsConceptsSynthetic genetic elementsExpression of heterologous pathwaysUptake systemCupriavidus necator H16Genome engineering technologiesHeterologous pathwaysHeterotrophic conditionsGenetic elementsChromosomal expressionTunable expressionInducible promoterGenetic engineering technologyModel microbesCarbon sourceGene expressionFacultative chemolithotrophsUptake pathwayH16PathwayLanding padExpressionGenomeGenesMicrobesChemolithotrophsEngineering a genomically recoded organism with one stop codon
Grome M, Nguyen M, Moonan D, Mohler K, Gurara K, Wang S, Hemez C, Stenton B, Cao Y, Radford F, Kornaj M, Patel J, Prome M, Rogulina S, Sozanski D, Tordoff J, Rinehart J, Isaacs F. Engineering a genomically recoded organism with one stop codon. Nature 2025, 639: 512-521. PMID: 39910296, PMCID: PMC11903333, DOI: 10.1038/s41586-024-08501-x.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and Concepts
2024
Confronting risks of mirror life
Adamala K, Agashe D, Belkaid Y, Bittencourt D, Cai Y, Chang M, Chen I, Church G, Cooper V, Davis M, Devaraj N, Endy D, Esvelt K, Glass J, Hand T, Inglesby T, Isaacs F, James W, Jones J, Kay M, Lenski R, Liu C, Medzhitov R, Nicotra M, Oehm S, Pannu J, Relman D, Schwille P, Smith J, Suga H, Szostak J, Talbot N, Tiedje J, Venter J, Winter G, Zhang W, Zhu X, Zuber M. Confronting risks of mirror life. Science 2024, 386: 1351-1353. PMID: 39666824, DOI: 10.1126/science.ads9158.Peer-Reviewed Original ResearchCitationsAltmetricEnabling equitable and affordable access to novel therapeutics for pandemic preparedness and response via creative intellectual property agreements
Griffen E, Boulet P, Albrecht R, Akbar A, Amick I, Aschenbrenner J, Balcomb B, Barr H, Battu H, Benjamin J, Bloom J, Boby M, Bogyo M, Bolon D, Boulet P, Clerkin A, Cadagan R, Capkin E, Castellanos M, Chandran A, Chen S, Chodera J, Cole D, Cousins D, Cuadrado S, de Godoy A, Dhalech A, Diaz R, DiPoto M, Doherty J, Dotson D, Duggan S, Evans M, Fairhead M, Fate G, Fearon D, Federov O, Ferla M, Ferreira L, Fieseler K, Filep M, Flores D, Flynn J, Fraisse L, Ronen G, Gad B, Garcia-Sastre A, Gathecha C, Gayvert J, Giroud C, Parejo C, Goldberger E, Golding M, Gordon M, Griffen E, Hannon W, Hassan H, Henry M, Hertzman R, Horton J, Huang F, Huang Q, Iacovella C, Isaacs F, James D, Jameson M, Kaminow B, Kenney I, Kenton N, Kirkegaard K, Koekemoer L, Kurtyilmaz N, La V, Lahav N, Lambert M, Lavie M, Lee A, Lefker B, Lemons K, Lindenbach B, Lithgo R, Livnah E, London N, Lynch N, MacDermott H, MacLean E, Marples P, Marsden B, McGovern B, Minh D, Mugeni M, Nadir A, Luong N, Ni X, Nitz S, Ookhin H, Orlov A, Payne A, Pearl R, Pedowitz N, Peng S, Perry B, Pulido I, Rawal D, Reid L, Retchin M, Richardson R, Ripka E, Robinson M, Robinson R, Rodriguez M, Roper G, Rosales R, Salim M, Scheen J, Schiffer C, Shamir Y, Shaqra A, Shaw C, Shertzer O, Singh S, Sjo P, Slater J, Souffront A, Stacey J, Gordon H, Starr T, Stewart H, Szommer T, Tanner W, Thomas V, Thompson W, Tierney J, Tivon B, Tomlinson C, Vargo T, Villalo F, von Delft A, von Delft F, Walsh M, Sije W, Wang S, Wang Y, Waring M, White K, Wild C, Wilen C, Williams E, Williams M, Winokan M, Wright N, Xavier M, Yap J, Zhang I, Zhu J, Zwaka T, Robinson M, London N, Resnick E, Zaidmann D, Gehrtz P, Reddi R, Gabizon R, Barr H, Duberstein S, Zidane H, Shurrush K, Cohen G, Solmesky L, Lee A, Jajack A, Cvitkovic M, Pan J, Pai R, Ripka E, Nguyen L, Shafeev M, Matviiuk T, Michurin O, Chernyshenko E, Bilenko V, Kinakh S, Logvinenko I, Melnykov K, Huliak V, Tsurupa I, Gorichko M, Shaikh A, Pinjari J, Swamy V, Pingle M, BVNBS S, Aimon A, von Delft F, Fearon D, Tomlinson C, Balcomb B, Lithgo R, Aschenbrenner J, Dunnett L, Douangamath A, Dias A, Powell A, Neto J, Skyner R, Thompson W, Gorrie-Stone T, Walsh M, Owen C, Lukacik P, Strain-Damerell C, Mikolajek H, Horrell S, Marples P, Koekemoer L, Krojer T, Fairhead M, MacLean E, Thompson A, Wild C, Smilova M, Wright N, von Delft A, Gileadi C, Rangel V, Schofield C, Salah E, Malla T, Tumber A, John T, Vakonakis I, Kantsadi A, Zitzmann N, Brun J, Kiappes J, Hill M, Witt K, Alonzi D, Makower L, Varghese F, Overheul G, Miesen P, van Rij R, Jansen J, Smeets B, Tomásio S, Weatherall C, Vaschetto M, Macdonald H, Chodera J, Rufa D, Wittmann M, Boby M, Henry M, Glass W, Eastman P, Coffland J, Dotson D, Griffen E, McCorkindale W, Morris A, Glen R, Cole J, Foster R, Foster H, Calmiano M, Tennant R, Heer J, Shi J, Jnoff E, Hurley M, Lefker B, Robinson R, Giroud C, Bennett J, Fedorov O, Reid P, Morwitzer M, Cox L, Morris G, Ferla M, Moustakas D, Dudgeon T, Pšenák V, Kovar B, Voelz V, Carbery A, Contini A, Clyde A, Ben-Shmuel A, Sittner A, Politi B, Vitner E, David E, Tamir H, Achdout H, Levy H, Glinert I, Paran N, Erez N, Puni R, Melamed S, Weiss S, Israely T, Yahalom-Ronen Y, Smalley A, Oleinikovas V, Spencer J, Kenny P, Ward W, Cattermole E, Ferrins L, Eyermann C, Milne B, Godoy A, Noske G, Oliva G, Fernandes R, Nakamura A, Gawriljuk V, White K, McGovern B, Rosales R, García-Sastre A, Carney D, Chang E, Saikatendu K, Vangeel L, Neyts J, Donckers K, Jochmans D, De Jonghe S, Bowman G, Borden B, Singh S, Volkamer A, Rodriguez-Guerra J, Fate G, Hart S, Saar K, Perry B, Fraisse L, Sjö P, Boulet P, Laghnimi-Hahn S, Mowbray C, Reid L, Rees P, Huang Q, Zvornicanin S, Shaqra A, Yilmaz N, Schiffer C, Zhang I, Pulido I, Taylor J, Croll T, Brewitz L, Kang L, La V, Haneef A, Minh D, Filep M, Scheen J, Kaminow B, Arbon R, Payne A, Schaller D. Enabling equitable and affordable access to novel therapeutics for pandemic preparedness and response via creative intellectual property agreements. Wellcome Open Research 2024, 9: 374. PMID: 39184131, PMCID: PMC11342024, DOI: 10.12688/wellcomeopenres.22645.1.Peer-Reviewed Original ResearchCitationsAltmetricConceptsIntellectual propertyContractual agreementsIntellectual property agreementsGlobal intellectual propertyEquitable accessIP policyPatent protectionIP frameworkEffective global responsePandemic preparednessGlobal frameworkMarket forcesCOVID-19 pandemicAgreementGlobal responseObligationsRightsOpen science approachOpen scienceNegotiationProtectionScience approachCOVID-19AccessPandemicEnhanced 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 ResearchCitationsAltmetricMeSH 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
Academic Achievements & Community Involvement
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Honors
honor Beckman Young Investigator Award
09/01/2012National AwardArnold and Mabel Beckman FoundationDetailsUnited Stateshonor Rising Young Stars of Science
01/01/2008UnknownGenome Technology MagazineDetailsUnited States
News & Links
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News
- June 09, 2025Source: Yale News
Yale Genome Engineers Expand the Reach and Precision of Human Gene Editing
- February 06, 2025Source: Yale News
Yale Scientists Recode the Genome for Programmable Synthetic Proteins
- February 05, 2025Source: Nature
Engineering a genomically recoded organism with one stop codon
- October 12, 2022
Yale Cancer Center Members Receive Faculty Innovation Awards
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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