Luke Gilbert, PhD
Associate Professor
Urology
School of Medicine

Grants and Projects

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• Spatial multiomic mapping of gene function with CRISPRoff, NIH, 2022-2027
• Editing CG and non-CG DNA methylation to identify genomic elements that regulate gene expression, NIH, 2021-2025
• A Genetic Interaction Map of the Human Nucleus, NIH, 2018-2023
• Drug target identification using CRISPRi/a screening, NIH, 2020-2021
• A functional genomics approach to determine the mechanism of cellular response to new anti-cancer, NIH, 2017-2020
• A functional genomics approach to determine the mechanism of cellular response to new anti-cancer drugs, NIH, 2016-2017

Publications (114)

Top publication keywords:
Genetic TechniquesCRISPR-Associated ProteinsMechanistic Target of Rapamycin Complex 1DNA RepairLipoproteins, HDLClustered Regularly Interspaced Short Palindromic RepeatsEndodeoxyribonucleasesCRISPR-Cas SystemsScavenger Receptors, Class BSynthetic Lethal MutationsFanconi AnemiaGene EditingGene Regulatory NetworksExocytosisParacrine Communication

• Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation.
  eLife 2016 Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS
• A protein-tagging system for signal amplification in gene expression and fluorescence imaging.
  Cell 2014 Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD
• Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.
  Cell 2014 Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS
• CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
  Cell 2013 Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS
• DNA damage-mediated induction of a chemoresistant niche.
  Cell 2010 Gilbert LA, Hemann MT

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• A multi-subunit autophagic capture complex facilitates degradation of ER-stalled MHC class I in pancreatic cancer.
  Molecular cell 2026 Berquez M, Li AL, Luy MA, Venida AC, McDowall S, O'Loughlin T, Rademaker G, Barpanda A, Hu J, Yano J, Wiita AP, Gilbert LA, Bruno PM, Perera RM
• mTORC1 activity suppresses ferroptosis through a SCARB1-dependent HDL-tocopherol uptake pathway.
  Molecular cell 2026 O'Loughlin TA, Stiles JS, Acharya P, Arab A, Goudy L, Dai R, Borah AA, Weiss WA, Medoh UN, Gilbert LA
• A Dimeric Rocaglate Promotes Multivalent eIF4A-RNA Assembly.
  bioRxiv : the preprint server for biology 2026 Liu J, Moore MK, Lou K, Wassarman DR, Arab A, Ojeda S, Karakyriakou B, Koglin AS, Ott CJ, Gilbert LA, Shokat KM
• Large-scale mapping of environmental-genetic interactions illustrates the dynamic nature of cell-cycle and DNA repair regulation.
  Molecular cell 2026 Herken BW, Wong GT, Mäkiniemi A, Lundberg E, Norman TM, Gilbert LA
• EcDNA-borne structural variants drive oncogenic fusion transcript amplification.
  Cell 2026 Yi H, Zhang S, Swinderman J, Wang Y, Kanakaveti V, Hung KL, Tsz-Lo Wong I, Srinivasan S, Curtis EJ, Bhargava-Shah A, Li R, Jones MG, Luebeck J, Bailey C, Zhao Y, Belk JA, Kraft K, Shi Q, Yan X, …
• FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry.
  Immunity 2025 Umhoefer JM, Arce MM, Kasinathan S, Whalen S, Dajani R, Subramanya S, Goudy L, Belk JA, Zhou R, Pham MTN, Zhang W, Hernandez R, Tran C, Kirthivasan N, Freimer JW, Mowery CT, Nguyen V, Ota M, Gowen BG,…
• Site-specific DNA insertion into the human genome with engineered recombinases.
  Nature biotechnology 2025 Fanton A, Bartie LJ, Martins JQ, Tran VQ, Goudy L, Kernick C, Durrant MG, Wei J, Armour-Garb Z, Pawluk A, Konermann S, Marson A, Gilbert LA, Roth TL, Hsu PD
• Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer.
  Nature genetics 2025 Li H, Melnyk JE, Fu BXH, Shrestha R, Zhang M, Sjöström M, Feng S, Anderson JA, Han W, Chesner LN, Shin HJ, Farsh T, Suarez HJ, Nath S, Chou J, Das R, Egusa EA, Calvert M, Kishishita A, Barpanda A, Zhu…
• Loss of Fanconi anemia proteins causes a reliance on lysosomal exocytosis.
  Cell death & disease 2025 Fu BXH, Xu A, Li H, Johnson DE, Grandis JR, Gilbert LA
• Integrated epigenetic and genetic programming of primary human T cells.
  Nature biotechnology 2025 Goudy L, Ha A, Borah AA, Umhoefer JM, Chow L, Tran C, Winters A, Talbot A, Hernandez R, Li Z, Subramanya S, Arab A, Kale N, Lee JHJ, Muldoon JJ, Liu C, Schmidt R, Santangelo P, Carnevale J, Eyquem J, …
• Multiplexed epigenetic memory editing using CRISPRoff sensitizes glioblastoma to chemotherapy.
  Neuro-oncology 2025 Lin K, Zou C, Hubbard A, Sengelmann S, Goudy L, Wang IC, Sharma R, Pak J, Foster K, Ozawa T, de Groot JF, Phillips J, Vasudevan HN, Raleigh DR, Marson A, Murthy N, Gilbert LA, Berger MS, Liu SJ
• Exploitable mechanisms of antibody and CAR mediated macrophage cytotoxicity.
  Nature communications 2025 Liu T, Zhang M, Farsh T, Li H, Kishishita A, Barpanda A, Leung SG, Zhu J, Jung H, Hua JT, Zhu X, Kim AB, Goo YA, Son M, Kim J, Subramanian A, Sjöström M, Fuh KC, Chapman JS, Carnevale J, Gilbert LA, …
• Virtual Cell Challenge: Toward a Turing test for the virtual cell.
  Cell 2025 Roohani YH, Hua TJ, Tung PY, Bounds LR, Yu FB, Dobin A, Teyssier N, Adduri A, Woodrow A, Plosky BS, Mehta R, Hsu B, Sullivan J, Ricci-Tam C, Li N, Kazaks J, Gilbert LA, Konermann S, Hsu PD, Goodarzi H…
• Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator.
  bioRxiv : the preprint server for biology 2025 Li H, Melnyk JE, Fu BXH, Shrestha R, Zhang M, Sjöström M, Feng S, Anderson JA, Han W, Chesner LN, Shin HJ, Farsh T, Suarez HJ, Nath S, Chou J, Das R, Egusa EA, Zhu J, Winters A, Maheshwari A, Hua JT, …
• EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs.
  bioRxiv : the preprint server for biology 2025 Yi H, Zhang S, Swinderman J, Wang Y, Kanakaveti V, Hung KL, Wong IT, Srinivasan S, Curtis EJ, Bhargava-Shah A, Li R, Jones MG, Luebeck J, Zhao Y, Belk JA, Kraft K, Shi Q, Yan X, Pritchard SK, Liang FM…
• Neddylation as a target in PIK3CA-mutated head and neck cancer.
  Biochemical and biophysical research communications 2025 Naara S, Cui Z, Izgutdina A, VanLandingham NK, Nazarenko A, Woerner LC, Hua Fu BX, Gilbert LA, Johnson DE, Grandis JR
• Androgen Receptor Inhibition Increases MHC Class I Expression and Improves Immune Response in Prostate Cancer.
  Cancer discovery 2025 Chesner LN, Polesso F, Graff JN, Hawley JE, Smith AK, Lundberg A, Das R, Shenoy T, Sjöström M, Zhao F, Hu YM, Linder S, Chen WS, Hawkins RM, Shrestha R, Zhu X, Foye A, Li H, Kim LM, Bhalla M, O'…
• MorPhiC Consortium: towards functional characterization of all human genes.
  Nature 2025 Adli M, Przybyla L, Burdett T, Burridge PW, Cacheiro P, Chang HY, Engreitz JM, Gilbert LA, Greenleaf WJ, Hsu L, Huangfu D, Hung LH, Kundaje A, Li S, Parkinson H, Qiu X, Robson P, Schürer SC, Shojaie A…
• Loss of Fanconi anemia proteins causes a reliance on lysosomal exocytosis.
  bioRxiv : the preprint server for biology 2025 Fu BXH, Xu A, Li H, Johnson DE, Grandis JR, Gilbert LA
• Cis-Regulatory Element and Transcription Factor Circuitry Required for Cell-Type Specific Expression of FOXP3.
  bioRxiv : the preprint server for biology 2025 Umhoefer JM, Arce MM, Whalen S, Dajani R, Goudy L, Kasinathan S, Belk JA, Zhang W, Zhou R, Subramanya S, Hernandez R, Tran C, Kirthivasan N, Freimer JW, Mowery CT, Nguyen V, Ota M, Gowen BG, Simeonov …
• EXTH-68. EPIGENETIC EDITING BY MRNA-BASED CRISPROFF ENABLES FLEXIBLE AND DURABLE TARGETING OF GLIOBLASTOMA DRIVERS MGMT AND TERT.
  Neuro-Oncology 2024 Katie Lin, Christopher Zou, Laine Goudy, Rohit Sharma, Nicholas O Stevers, Joanna Pak, Kyla Foster, Emily Payne, Anny Shai, Tomoko Ozawa, John F de Groot, Harish Vasudevan, Joanna J Phillips, David R …
• CDK8 Inhibition Represses Monocyte-like Gene Expression in Acute Myeloid Leukemia Cells and Antagonizes In Vivo Resistance to FLT3 Inhibition.
  Blood 2024 Timothy T. Ferng, Samantha M. Pintar, Vanessa E. Kennedy, Shaheen Kabir, Theodore C. Tarver, Veronica Steri, Paul Phojanakong, Juwita Hübner, Carolina E. Morales, Jose M. Rivera, Aaron C. Logan, …
• A multi-subunit autophagic capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer.
  bioRxiv : the preprint server for biology 2024 Berquez M, Li AL, Luy MA, Venida AC, O'Loughlin T, Rademaker G, Barpanda A, Hu J, Yano J, Wiita A, Gilbert LA, Bruno PM, Perera RM
• A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation.
  Scientific reports 2024 Ge AY, Arab A, Dai R, Navickas A, Fish L, Garcia K, Asgharian H, Goudreau J, Lee S, Keenan K, Pappalardi MB, McCabe MT, Przybyla L, Goodarzi H, Gilbert LA
• Combinatorial effector targeting (COMET) for transcriptional modulation and locus-specific biochemistry.
  bioRxiv : the preprint server for biology 2024 Wilson CM, Pommier GC, Richman DD, Sambold N, Hussmann JA, Weissman JS, Gilbert LA
• OS07.1.A INTEGRATIVE SINGLE NUCLEI, SPATIAL, AND FUNCTIONAL GENOMIC ANALYSES REVEAL DNA-PK DRIVES GLIOBLASTOMA RADIORESISTANCE THROUGH TUMOR CELLS AND THE MYELOID MICROENVIRONMENT.
  Neuro-Oncology 2024 J Liu, N Majd, C Zou, K Mirchia, J Pak, K Foster, K Lin, T Casey-Clyde, K Seo, S Pan, E Payne, H Vasudevan, T Ozawa, M Berger, J de Groot, W Weiss, L Gilbert, D Raleigh
• In vivo perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma.
  Genome biology 2024 Liu SJ, Zou C, Pak J, Morse A, Pang D, Casey-Clyde T, Borah AA, Wu D, Seo K, O'Loughlin T, Lim DA, Ozawa T, Berger MS, Kamber RA, Weiss WA, Raleigh DR, Gilbert LA
• 261 (PB249): ENPP1 is an innate immune checkpoint of the anticancer cGAMPSTING pathway in breast cancer.
  European Journal of Cancer 2024 S. Wang, V. Böhnert, A. Joseph, V. Sudaryo, G. Skariah, J. Swinderman, F. Yu, V. Subramanyam, D. Wolf, X. Lyu, L. Gilbert, L. van’t Veer, H. Goodarzi, L. Li
• Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.
  Cell reports 2024 Woo BJ, Moussavi-Baygi R, Karner H, Karimzadeh M, Yousefi H, Lee S, Garcia K, Joshi T, Yin K, Navickas A, Gilbert LA, Wang B, Asgharian H, Feng FY, Goodarzi H
• A systematic search for RNA structural switches across the human transcriptome.
  Nature methods 2024 Khoroshkin M, Asarnow D, Zhou S, Navickas A, Winters A, Goudreau J, Zhou SK, Yu J, Palka C, Fish L, Borah A, Yousefi K, Carpenter C, Ansel KM, Cheng Y, Gilbert LA, Goodarzi H
• Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.
  Molecular cell 2024 Ietswaart R, Smalec BM, Xu A, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN, Churchman LS
• Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations.
  Nature biotechnology 2024 Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA
• Improving prime editing with an endogenous small RNA-binding protein.
  Nature 2024 Yan J, Oyler-Castrillo P, Ravisankar P, Ward CC, Levesque S, Jing Y, Simpson D, Zhao A, Li H, Yan W, Goudy L, Schmidt R, Solley SC, Gilbert LA, Chan MM, Bauer DE, Marson A, Parsons LR, Adamson B
• Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics.
  bioRxiv : the preprint server for biology 2024 Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, Teyssier N, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA
• Epigenetic reprogramming shapes the cellular landscape of schwannoma.
  Nature communications 2024 Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez…
• ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway in breast cancer.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Wang S, Böhnert V, Joseph AJ, Sudaryo V, Skariah G, Swinderman JT, Yu FB, Subramanyam V, Wolf DM, Lyu X, Gilbert LA, Van't Veer LJ, Goodarzi H, Li L
• Base-editing mutagenesis maps alleles to tune human T cell functions.
  Nature 2023 Schmidt R, Ward CC, Dajani R, Armour-Garb Z, Ota M, Allain V, Hernandez R, Layeghi M, Xing G, Goudy L, Dorovskyi D, Wang C, Chen YY, Ye CJ, Shy BR, Gilbert LA, Eyquem J, Pritchard JK, Dodgson SE, …
• Mediator Kinase/CDK8 Inhibition As a Strategy to Improve FLT3 Inhibitor Activity in Acute Myeloid Leukemia.
  Blood 2023 Timothy T. Ferng, Samantha M. Pintar, Vanessa E. Kennedy, Theodore C. Tarver, Shaheen Kabir, Veronica Steri, Juan Antonio Camara Serrano, Fernando Salangsang, Paul Phojanakong, Juwita Hübner, Carolina…
• EPCO-12. IN VIVO PERTURB-SEQ DEFINES BIOLOGICAL DRIVERS AND THERAPEUTIC VULNERABILITIES UNDERLYING RADIOTHERAPY RESISTANCE IN GLIOBLASTOMA.
  Neuro-Oncology 2023 John Liu, Joanna Pak, Christopher Zou, Sixuan Pan, Emily Payne, Kyla Foster, Katie Lin, Tim Casey-Clyde, Kyounghee Seo, Thomas O'Loughlin, David Wu, Daniel Lim, Harish Vasudevan, Aaron Diaz, Tomoko …
• EXTH-78. CRISPROFF EPIGENOME EDITING AND FUNCTIONAL GENOMICS DEFINE MEDIATORS OF CHEMOTHERAPY RESISTANCE IN GLIOBLASTOMA.
  Neuro-Oncology 2023 Katie Lin, Laine Goudy, Joanna Pak, Kyla Foster, Emily Payne, Tomoko Ozawa, John de Groot, Harish Vasudevan, David Raleigh, Luke Gilbert, Mitchel Berger, John Liu
• CRISPR-Based Epigenome Editing and Genome Wide Screening Define Mediators of Chemotherapy Response in Glioblastoma.
  International Journal of Radiation Oncology • Biology • Physics 2023 K. Lin, L. Goudy, J. Pak, K. Foster, E. Payne, T. Ozawa, J. de Groot, H. Vasudevan, D. Raleigh, L.A. Gilbert, M.S. Berger, S.J. Liu
• Identifying Gene-Treatment Interactions and Targetable Radiation Vulnerabilities in Glioblastoma through Coupling of In Vivo CRISPR Perturbation and Single Cell Transcriptomics.
  International Journal of Radiation Oncology • Biology • Physics 2023 S.J. Liu, J. Pak, C. Zou, E. Payne, K. Foster, H. Vasudevan, T. Casey-Clyde, K. Seo, T. O'Loughlin, D. Wu, D. Lim, T. Ozawa, J. de Groot, M.S. Berger, W. Weiss, L.A. Gilbert, D. Raleigh
• Environmental challenge rewires functional connections among human genes.
  bioRxiv : the preprint server for biology 2023 Herken BW, Wong GT, Norman TM, Gilbert LA
• ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway.
  bioRxiv : the preprint server for biology 2023 Wang S, Böhnert V, Joseph AJ, Sudaryo V, Swinderman J, Yu FB, Lyu X, Skariah G, Subramanyam V, Gilbert LA, Goodarzi H, Lingyin L
• Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.
  bioRxiv : the preprint server for biology 2023 Woo BJ, Moussavi-Baygi R, Karner H, Karimzadeh M, Garcia K, Joshi T, Yin K, Navickas A, Gilbert LA, Wang B, Asgharian H, Feng FY, Goodarzi H
• Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors.
  eLife 2022 Replogle JM, Bonnar JL, Pogson AN, Liem CR, Maier NK, Ding Y, Russell BJ, Wang X, Leng K, Guna A, Norman TM, Pak RA, Ramos DM, Ward ME, Gilbert LA, Kampmann M, Weissman JS, Jost M
• IFITM proteins assist cellular uptake of diverse linked chemotypes.
  Science (New York, N.Y.) 2022 Lou K, Wassarman DR, Yang T, Paung Y, Zhang Z, O'Loughlin TA, Moore MK, Egan RK, Greninger P, Benes CH, Seeliger MA, Taunton J, Gilbert LA, Shokat KM
• The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
  Cancer research 2022 Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, …
• Abstract B021: Long non-coding RNAs that are required for robust cell growth in ewing Sarcoma.
  Clinical Cancer Research 2022 Marcela C. Briones Martin del Campo, Alex Lee, Max Horlbeck, Truc Dinh, Marta Roman-Moreno, Leanne Sayles, Bokyung Seong, Kimberly Stegmaier, Luke Gilbert, E. Alejandro Sweet-Cordero
• Highly efficient generation of isogenic pluripotent stem cell models using prime editing.
  eLife 2022 Li H, Busquets O, Verma Y, Syed KM, Kutnowski N, Pangilinan GR, Gilbert LA, Bateup HS, Rio DC, Hockemeyer D, Soldner F
• A campaign targeting a conserved Hsp70 binding site uncovers how subcellular localization is linked to distinct biological activities.
  Cell chemical biology 2022 Shao H, Taguwa S, Gilbert L, Shkedi A, Sannino S, Guerriero CJ, Gale-Day ZJ, Young ZT, Brodsky JL, Weissman J, Gestwicki JE, Frydman J
• Applications of CRISPRi and CRISPRa in Drug Discovery.
  2022 Luke A. Gilbert
• A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments.
  Nature communications 2022 Zhao B, Rao Y, Leighow S, O'Brien EP, Gilbert L, Pritchard JR
• RNA Polymerase II Is a Therapeutic Target to Overcome FLT3 Inhibitor Resistance Mediated By the Bone Marrow Microenvironment.
  Blood 2021 Timothy T. Ferng, Theodore C. Tarver, Shaheen Kabir, Benjamin Braun, Aaron C. Logan, Luke A. Gilbert, Catherine C. Smith
• A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy.
  Genome medicine 2021 Yogodzinski C, Arab A, Pritchard JR, Goodarzi H, Gilbert LA
• A new era in functional genomics screens.
  Nature reviews. Genetics 2021 Przybyla L, Gilbert LA
• An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer.
  Nature communications 2021 Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA
• Revealing molecular pathways for cancer cell fitness through a genetic screen of the cancer translatome.
  Cell reports 2021 Kuzuoglu-Ozturk D, Hu Z, Rama M, Devericks E, Weiss J, Chiang GG, Worland ST, Brenner SE, Goodarzi H, Gilbert LA, Ruggero D
• Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.
  Cell 2021 Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, …
• Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
  Cell 2021 Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA
• Mapping cancer genetics at single-cell resolution.
  Science translational medicine 2020 Gilbert LA
• The DNA methylation landscape of advanced prostate cancer.
  Nature genetics 2020 Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, …
• Pharmaceutical-Grade Rigosertib Is a Microtubule-Destabilizing Agent.
  Molecular cell 2020 Jost M, Chen Y, Gilbert LA, Horlbeck MA, Krenning L, Menchon G, Rai A, Cho MY, Stern JJ, Prota AE, Kampmann M, Akhmanova A, Steinmetz MO, Tanenbaum ME, Weissman JS
• Keap1ing an eye on Slc33A1.
  Nature cancer 2020 Gilbert LA
• Clonal ZEB1-Driven Mesenchymal Transition Promotes Targetable Oncologic Antiangiogenic Therapy Resistance.
  Cancer research 2020 Chandra A, Jahangiri A, Chen W, Nguyen AT, Yagnik G, Pereira MP, Jain S, Garcia JH, Shah SS, Wadhwa H, Joshi RS, Weiss J, Wolf KJ, Lin JG, Müller S, Rick JW, Diaz AA, Gilbert LA, Kumar S, Aghi MK
• Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.
  Science (New York, N.Y.) 2019 Norman TM, Horlbeck MA, Replogle JM, Ge AY, Xu A, Jost M, Gilbert LA, Weissman JS
• A Bounty of New Challenging Targets in Oncology for Chemical Discovery.
  Biochemistry 2019 Lou K, Gilbert LA, Shokat KM
• DNA-Dependent Protein Kinase Drives Prostate Cancer Progression through Transcriptional Regulation of the Wnt Signaling Pathway.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2019 Kothari V, Goodwin JF, Zhao SG, Drake JM, Yin Y, Chang SL, Evans JR, Wilder-Romans K, Gabbara K, Dylgjeri E, Chou J, Sun G, Tomlins SA, Mehra R, Hege K, Filvaroff EH, Schaeffer EM, Karnes RJ, Quigley …
• KRASG12C inhibition produces a driver-limited state revealing collateral dependencies.
  Science signaling 2019 Lou K, Steri V, Ge AY, Hwang YC, Yogodzinski CH, Shkedi AR, Choi ALM, Mitchell DC, Swaney DL, Hann B, Gordan JD, Shokat KM, Gilbert LA
• Lethal clues to cancer-cell vulnerability.
  Nature 2019 Feng FY, Gilbert LA
• Cellular response to small molecules that selectively stall protein synthesis by the ribosome.
  PLoS genetics 2019 Liaud N, Horlbeck MA, Gilbert LA, Gjoni K, Weissman JS, Cate JHD
• Functional Genomics for Cancer Research: Applications In Vivo and In Vitro.
  Annual Review of Cancer Biology 2019 Thomas A. O'Loughlin, Luke A. Gilbert
• Finding and Interpreting Genetic Interactions using Perturb-Seq Single Cell RNA-Seq CRISPR Screens.
  Biophysical Journal 2019 Jonathan Weissman, Thomas Norman, Max Horlbeck, Luke Gilbert
• DRES-01. ZEB1-MEDIATED INVASIVE MESENCHYMAL TRANSITION AT THE SINGLE CELL LEVEL PROMOTES ANTI-ANGIOGENIC THERAPY RESISTANCE IN GLIOBLASTOMA.
  Neuro-Oncology 2018 Ankush Chandra, Arman Jahangiri, William Chen, Garima Yagnik, Joseph Garcia, Alan Nguyen, Jacob Weiss, Kayla Wolf, Jung-Ming Lin, Soeren Mueller, Jonathan Rick, Aaron Diaz, Luke Gilbert, Sanjay Kumar,…
• Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.
  Cell 2018 Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, …
• A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure.
  PLoS biology 2018 Mendelsohn BA, Bennett NK, Darch MA, Yu K, Nguyen MK, Pucciarelli D, Nelson M, Horlbeck MA, Gilbert LA, Hyun W, Kampmann M, Nakamura JL, Nakamura K
• Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.
  Cell 2018 Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, …
• Mapping the Genetic Landscape of Human Cells.
  Cell 2018 Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA
• Exploration of Benzothiazole Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70).
  Journal of medicinal chemistry 2018 Shao H, Li X, Moses MA, Gilbert LA, Kalyanaraman C, Young ZT, Chernova M, Journey SN, Weissman JS, Hann B, Jacobson MP, Neckers L, Gestwicki JE
• Combinatorial genetics in liver repopulation and carcinogenesis with a in vivo CRISPR activation platform.
  Hepatology (Baltimore, Md.) 2018 Wangensteen KJ, Wang YJ, Dou Z, Wang AW, Mosleh-Shirazi E, Horlbeck MA, Gilbert LA, Weissman JS, Berger SL, Kaestner KH
• The Promise and Challenge of In Vivo Delivery for Genome Therapeutics.
  ACS chemical biology 2017 Wilson RC, Gilbert LA
• Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent.
  Molecular cell 2017 Jost M, Chen Y, Gilbert LA, Horlbeck MA, Krenning L, Menchon G, Rai A, Cho MY, Stern JJ, Prota AE, Kampmann M, Akhmanova A, Steinmetz MO, Tanenbaum ME, Weissman JS
• A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.
  Cell 2016 Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS
• CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.
  Science (New York, N.Y.) 2016 Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA
• A senescence secretory switch mediated by PI3K/AKT/mTOR activation controls chemoprotective endothelial secretory responses.
  Genes & development 2016 Bent EH, Gilbert LA, Hemann MT
• Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity.
  Nature communications 2016 Nguyen DP, Miyaoka Y, Gilbert LA, Mayerl SJ, Lee BH, Weissman JS, Conklin BR, Wells JA
• Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Braun CJ, Bruno PM, Horlbeck MA, Gilbert LA, Weissman JS, Hemann MT
• Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification.
  Nature chemical biology 2016 Deans RM, Morgens DW, Ökesli A, Pillay S, Horlbeck MA, Kampmann M, Gilbert LA, Li A, Mateo R, Smith M, Glenn JS, Carette JE, Khosla C, Bassik MC
• Versatile protein tagging in cells with split fluorescent protein.
  Nature communications 2016 Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert LA, Ishikawa H, Leonetti MD, Marshall WF, Weissman JS, Huang B
• Nucleosomes impede Cas9 access to DNA in vivo and in vitro.
  eLife 2016 Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS
• CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.
  Cell stem cell 2016 Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP,…
• Abstract IA27: Retooling CRISPR to turn genes on and off.
  New Technologies in Cancer Research 2016 Luke A. Gilbert, Max A. Horlbeck, Jacqueline Villalta, Shao Hao, Jason E. Gestwicki, Jonathan S. Weissman
• Abstract A2-56: Cancer-specific synthetic lethality and network rewiring elucidated by genetic interaction maps and CRISPR-based gain- and loss-of-function screens.
  Network-Based Cancer Biology 2015 Martin Kampmann, Diego Acosta-Alvear, Luke A. Gilbert, Max A. Horlbeck, Min Y. Cho, Britt Adamson, Jacqueline Villalta, Yuwen Chen, Peter Walter, Jonathan S. Weissman
• Abstract PR05: Using genome-scale CRISPR-mediated loss-of-function and gain-of-function screens to analyze gene-drug interactions in cancer.
  Genomics and Target Discovery 2015 Luke A. Gilbert, Marvin E. Tanenbaum, Max A. Horlbeck, Britt Adamson, Jacqueline E. Villalta, Ronald D. Vale, Martin Kampmann, Jonathan S. Weissman
• Unraveling the Mechanism of SBRT Response in EGFR-Addicted Pulmonary Adenocarcinoma by CRISPR/Cas9 Functional Genomics.
  International Journal of Radiation Oncology • Biology • Physics 2015 A.L. Polishchuk, J. Flanagan, L.A. Gilbert, M. Horlbeck, X. Yang, A. Olow, M. Bassik, J.S. Weissman, D.A. Haas-Kogan, J.A. Wells, T.G. Bivona
• Next-generation libraries for robust RNA interference-based genome-wide screens.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Kampmann M, Horlbeck MA, Chen Y, Tsai JC, Bassik MC, Gilbert LA, Villalta JE, Kwon SC, Chang H, Kim VN, Weissman JS
• Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds.
  Cell 2014 Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA
• Abstract IA10: Improving existing cancer therapy by targeting the tumor microenvironment.
  Target Discovery and Validation 2014 Christian Pallasch, Luke Gilbert, Michael Hemann
• Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System.
  Cell 2014 Baohui Chen, Luke A. Gilbert, Beth A. Cimini, Joerg Schnitzbauer, Wei Zhang, Gene-Wei Li, Jason Park, Elizabeth H. Blackburn, Jonathan S. Weissman, Lei S. Qi, Bo Huang
• Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.
  Cell 2013 Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B
• CRISPR interference (CRISPRi) for sequence-specific control of gene expression.
  Nature protocols 2013 Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS
• Abstract PR07: Systematic genetic interaction maps reveal rewiring of the stress response network and resulting vulnerabilities in leukemia and multiple myeloma cells.
  Interpreting the Cancer Genome 2013 Martin Kampmann, Diego Acosta-Alvear, Min Cho, Yuwen Chen, Xiaokai Li, Luke Gilbert, Blake T. Aftab, Jason Gestwicki, Peter Walter, Jonathan S. Weissman
• Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
  Cell 2013 Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA
• Defining principles of combination drug mechanisms of action.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Pritchard JR, Bruno PM, Gilbert LA, Capron KL, Lauffenburger DA, Hemann MT
• Context-specific roles for paracrine IL-6 in lymphomagenesis.
  Genes & development 2012 Gilbert LA, Hemann MT
• Bcl-2 family genetic profiling reveals microenvironment-specific determinants of chemotherapeutic response.
  Cancer research 2011 Pritchard JR, Gilbert LA, Meacham CE, Ricks JL, Jiang H, Lauffenburger DA, Hemann MT
• Chemotherapeutic resistance: surviving stressful situations.
  Cancer research 2011 Gilbert LA, Hemann MT
• A thioredoxin family protein of the apicoplast periphery identifies abundant candidate transport vesicles in Toxoplasma gondii.
  Eukaryotic cell 2008 DeRocher AE, Coppens I, Karnataki A, Gilbert LA, Rome ME, Feagin JE, Bradley PJ, Parsons M
• Toxoplasma gondii targets a protein phosphatase 2C to the nuclei of infected host cells.
  Eukaryotic cell 2006 Gilbert LA, Ravindran S, Turetzky JM, Boothroyd JC, Bradley PJ