Bennett JM, Narwal SK, Kabeche S, Abegg D, Hackett F, Yeo T, Li VL, Muir RK, Faucher FF, Lovell S, Blackman MJ, Adibekian A, Yeh E, Fidock DA, Bogyo M. Mixed Alkyl/Aryl Phosphonates Identify Metabolic Serine Hydrolases as Antimalarial Targets. bioRxiv [Preprint]. 2024 Jan 11:2024.01.11.575224. doi: 10.1101/2024.01.11.575224.

Jo J, Upadhyay T, Woods EC, Park KW, Pedowitz NJ, Jaworek-Korjakowska J, Wang S, Valdez TA, Fellner M, Bogyo M. Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections. J Am Chem Soc. 2024 Feb 27. doi: 10.1021/jacs.3c13974.pdf

Bennett JM, Ward KE, Muir RK, Kabeche S, Yoo E, Yeo T, Lam G, Zhang H, Almaliti J, Berger G, Faucher FF, Lin G, Gerwick WH, Yeh E, Fidock DA, Bogyo M. Covalent Macrocyclic Proteasome Inhibitors Mitigate Resistance in Plasmodium falciparum. ACS Infect Dis 2023 Oct 13;9(10):2036-2047. pdf

Keller LJ, Nguyen TH, Liu LJ, Hurysz BM, Lakemeyer M, Guerra M, Gelsinger DJ, Chanin R, Ngo N, Lum KM, Faucher F, Ipock P, Niphakis MJ, Bhatt AS, O'Donoghue AJ, Huang KC, Bogyo M. Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron. Nat Chem Biol. 2023 Jun 22. pdf

Faucher FF, Liu KJ, Cosco ED, Widen JC, Sorger J, Guerra M, Bogyo M. Protease Activated Probes for Real-Time Ratiometric Imaging of Solid Tumors. ACS Cent Sci. 2023 May 4;9(5):1059-1069. pdf

Deni I, Stokes BH, Ward KE, Fairhurst KJ, Pasaje CFA, Yeo T, Akbar S, Park H, Muir R, Bick DS, Zhan W, Zhang H, Liu YJ, Ng CL, Kirkman LA, Almaliti J, Gould AE, Duffey M, O'Donoghue AJ, Uhlemann AC, Niles JC, da Fonseca PCA, Gerwick WH, Lin G, Bogyo M, Fidock DA. Mitigating the risk of antimalarial resistance via covalent dual-subunit inhibition of the Plasmodium proteasome. Cell Chem Biol. 2023 May 18;30(5):470-485.e6. pdf

Faucher FF, Abegg D, Ipock P, Adibekian A, Lovell S, Bogyo M. Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows. Israel Journal of Chemistry. 2023 Mar;63(3-4):e202300020. https://doi.org/10.1002/ijch.202300020. pdf

Bogyo M. Finding optimal drug target sites in parasite pathogens. Trends Parasitol. 2023 Feb;39(2):83-85. pdf

Brown RWB, Sharma AI, Villanueva MR, Li X, Onguka O, Zilbermintz L, Nguyen H, Falk BA, Olson CL, Taylor JM, Epting CL, Kathayat RS, Amara N, Dickinson BC, Bogyo M, Engman DM. Trypanosoma brucei Acyl-Protein Thioesterase-like (TbAPT-L) Is a Lipase with Esterase Activity for Short and Medium-Chain Fatty Acids but Has No Depalmitoylation Activity. Pathogens. 2022 Oct 27;11(11):1245. pdf 

Richards CM, Jabs S, Qiao W, Varanese LD, Schweizer M, Mosen PR, Riley NM, Klüssendorf M, Zengel JR, Flynn RA, Rustagi A, Widen JC, Peters CE, Ooi YS, Xie X, Shi PY, Bartenschlager R, Puschnik AS, Bogyo M, Bertozzi CR, Blish CA, Winter D, Nagamine CM, Braulke T, Carette JE. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Science. 2022 Oct 7;378(6615):eabn5648. pdf 

Walker E, Linders DGJ, Abenojar E, Wang X, Hazelbag HM, Straver ME, Bijlstra OD, March TL, Vahrmeijer AL, Exner A, Bogyo M, Basilion JP, Straight B. Formulation of a Thermosensitive Imaging Hydrogel for Topical Application and Rapid Visualization of Tumor Margins in the Surgical Cavity. Cancers (Basel). 2022 Jul 16;14(14):3459. pdf 

Kennedy GT, Holt DE, Azari FS, Bernstein E, Nadeem B, Chang A, Sullivan NT, Segil A, Deshpande C, Bensen E, Santini JT, Kucharczuk JC, Delikatny EJ, Bogyo M, Egan AJM, Bradley CW, Eruslanov E, Lickliter JD, Wright G, Singhal S. A cathepsin targeted quenched activity-based probe facilitates enhanced detection of human tumors during resection. Clin Cancer Res. 2022. Jul 6:ccr.22.1215. doi: 10.1158/1078-0432.CCR-22-1215. pdf 

Keller LJ, Lakemeyer M, Bogyo M. Integration of bioinformatic and chemoproteomic tools for the study of enzyme conservation in closely related bacterial species. Methods Enzymol. 2022. 664:1-22. pdf

Lakemeyer M, Bogyo M. Uncovering an overlooked consequence of phosphorylation: change in cysteine reactivity. Nat Methods. 2022. 19(3):281-283. pdf

Muir RK, Guerra M, Bogyo M. Activity-Based Diagnostics: Recent Advances in the Development of Probes for Use with Diverse Detection Modalities. ACS Chem Biol. 2022. 17(2):281-291. pdf

Babin BM, Keller LJ, Pinto Y, Li VL, Eneim AS, Vance SE, Terrell SM, Bhatt AS, Long JZ, Bogyo M. Identification of covalent inhibitors that disrupt M. tuberculosis growth by targeting multiple serine hydrolases involved in lipid metabolism. Cell Chem Biol. 2022. 29(5):897-909.e7.  pdf

Bogyo M. A 'Swiss army knife' probe for metastatic cancers. Nat. Mater. 2022. 20(10):1312-1314. pdf

Amara N, Cooper MP, Voronkova MA, Webb BA, Lynch EM, Kollman JM, Ma T, Yu K, Lai Z, Sangaraju D, Kayagaki N, Newton K, Bogyo M, Staben ST, Dixit VM. Selective activation of PFKL suppresses the phagocytic oxidative burst. Cell. 2021 184(17):4480-4494.e15. pdf

Onguka O, Babin BM, Lakemeyer M, Foe IT, Amara N, Terrell SM, Lum KM, Cieplak P, Niphakis MJ, Long JZ, Bogyo M. Toxoplasma gondii serine hydrolases regulate parasite lipid mobilization during growth and replication within the host. Cell Chem Biol. 2021 May 25:S2451-9456(21)00218-X. doi: 10.1016/j.chembiol.2021.05.001. pdf

Rompikuntal PK, Kent RS, Foe IT, Deng B, Bogyo M, Ward GE. Blocking Palmitoylation of Toxoplasma gondii Myosin Light Chain 1 Disrupts Glideosome Composition but Has Little Impact on Parasite Motility. mSphere. 2021 May 19;6(3):e00823-20. pdf

Babin BM, Fernandez-Cuervo G, Sheng J, Green O, Ordonez AA, Turner ML, Keller LJ, Jain SK, Shabat D, Bogyo M. Chemiluminescent Protease Probe for Rapid, Sensitive, and Inexpensive Detection of Live Mycobacterium tuberculosis. ACS Cent Sci. 2021. 7(5):803-814. pdf

Steuten K, Kim H, Widen JC, Babin BM, Onguka O, Lovell S, Bolgi O, Cerikan B, Neufeldt CJ, Cortese M, Muir RK, Bennett JM, Geiss-Friedlander R, Peters C, Bartenschlager R, Bogyo M. Challenges for Targeting SARS-CoV-2 Proteases as a Therapeutic Strategy for COVID-19. ACS Infect Dis. 2021. 7(6):1457-1468. pdf

Venugopalan V, Al-Hashimi A, Rehders M, Golchert J, Reinecke V, Homuth G, Völker U, Manirajah M, Touzani A, Weber J, Bogyo MS, Verrey F, Wirth EK, Schweizer U, Heuer H, Kirstein J, Brix K. The Thyroid Hormone Transporter Mct8 Restricts Cathepsin-Mediated Thyroglobulin Processing in Male Mice through Thyroid Auto-Regulatory Mechanisms That Encompass Autophagy. Int J Mol Sci. 2021 22(1):462. pdf

Yim JJ, Harmsen S, Flisikowski K, Flisikowska T, Namkoong H, Garland M, van den Berg NS, Vilches-Moure JG, Schnieke A, Saur D, Glasl S, Gorpas D, Habtezion A, Ntziachristos V, Contag CH, Gambhir SS, Bogyo M, Rogalla S. A protease-activated, near-infrared fluorescent probe for early endoscopic detection of premalignant gastrointestinal lesions. Proc Natl Acad Sci U S A. 2021 Jan 5;118(1):e2008072118. pdf

Chen S, Lovell S, Lee S, Fellner M, Mace PD, Bogyo M. Identification of highly selective covalent inhibitors by phage display. Nat Biotechnol. 2021 39(4):490-498. pdf

Al-Hashimi A, Venugopalan V, Rehders M, Sereesongsaeng N, Hein Z, Springer S, Weber E, Führer D, Bogyo MS, Scott CJ, Burden RE, Brix K. Procathepsin V Is Secreted in a TSH Regulated Manner from Human Thyroid Epithelial Cells and Is Accessible to an Activity-Based Probe. Int J Mol Sci. 2020 21(23):9140. pdf

Brodzicki A, Jaworek-Korjakowska J, Kleczek P, Garland M, Bogyo M. Pre-Trained Deep Convolutional Neural Network for Clostridioides Difficile Bacteria Cytotoxicity Classification Based on Fluorescence Images. Sensors (Basel). 2020 20(23):6713. pdf

Yim JJ, Singh SP, Xia A, Kashfi-Sadabad R, Tholen M, Huland DM, Zarabanda D, Cao Z, Solis-Pazmino P, Bogyo M, Valdez TA. Short-Wave Infrared Fluorescence Chemical Sensor for Detection of Otitis Media. ACS Sens. 2020 5(11):3411-3419. pdf

Simwela NV, Stokes BH, Aghabi D, Bogyo M, Fidock DA, Waters AP. Plasmodium berghei K13 Mutations Mediate In Vivo Artemisinin Resistance That Is Reversed by Proteasome Inhibition. mBio. 2020 11(6):e02312-20. pdf

Suurs FV, Qiu SQ, Yim JJ, Schröder CP, Timmer-Bosscha H, Bensen ES, Santini JT Jr, de Vries EGE, Bogyo M, van Dam GM. Fluorescent image-guided surgery in breast cancer by intravenous application of a quenched fluorescence activity-based probe for cysteine cathepsins in a syngeneic mouse model. EJNMMI Res. 2020 10(1):111. pdf

Widen JC, Tholen M, Yim JJ, Antaris A, Casey KM, Rogalla S, Klaassen A, Sorger J, Bogyo M. AND-gate contrast agents for enhanced fluorescence-guided surgery. Nat Biomed Eng. 2020 Sep 28. doi: 10.1038/s41551-020-00616-6. pdf

Bilverstone TW, Garland M, Cave RJ, Kelly ML, Tholen M, Bouley DM, Kaye P, Minton NP, Bogyo M, Kuehne SA, Melnyk RA. The glucosyltransferase activity of C. difficile Toxin B is required for disease pathogenesis. PLoS Pathog 2020 16(9):e1008852. pdf

Fellner M, Lentz CS, Jamieson SA, Brewster JL, Chen L, Bogyo M, Mace PD. Structural Basis for the Inhibitor and Substrate Specificity of the Unique Fph Serine Hydrolases of Staphylococcus aureus. ACS Infect Dis. 2020 6(10):2771-2782. pdf

Telpoukhovskaia MA, Liu K, Sayed FA, Etchegaray JI, Xie M, Zhan L, Li Y, Zhou Y, Le D, Bahr BA, Bogyo M, Ding S, Gan L. Discovery of small molecules that normalize the transcriptome and enhance cysteine cathepsin activity in progranulin-deficient microglia. Sci Rep. 2020 10(1):13688. pdf

Faucher F, Bennett JM, Bogyo M, Lovell S. Strategies for Tuning the Selectivity of Chemical Probes that Target Serine Hydrolases. Cell Chem Biol. 2020 27(8):937-952. pdf

Tholen M, Yim JJ, Groborz K, Yoo E, Martin BA, van den Berg NS, Drag M, Bogyo M. Design of optical imaging probes by screening of diverse substrate libraries directly in disease tissue extracts. Angew Chem Int Ed Engl. 2020 59(43):19143-19152. pdf

Garland M, Hryckowian AJ, Tholen M, Bender KO, Van Treuren WW, Loscher S, Sonnenburg JL,Bogyo M. The Clinical Drug Ebselen Attenuates Inflammation and Promotes Microbiome Recovery in Mice after Antibiotic Treatment for CDI. Cell Rep Med. 2020 Apr 21;1(1):100005. doi: 10.1016/j.xcrm.2020.100005. pdf

Widen JC, Tholen M, Yim JJ, Bogyo M. Methods for analysis of near-infrared (NIR) quenched-fluorescent contrast agents in mouse models of cancer. Methods Enzymol. 2020 639:141-166. pdf

Keller LJ, Lentz CS, Chen YE, Metivier RJ, Weerapana E, Fischbach MA, Bogyo M. Characterization of Serine Hydrolases Across Clinical Isolates of Commensal Skin Bacteria Staphylococcus epidermidis Using Activity-Based Protein Profiling. ACS Infect Dis. 2020 6(5):930-938. doi: 10.1021/acsinfecdis.0c00095. pdf

Walker E, Liu Y, Kim I, Biro M, Iyer SR, Ezaldein H, Scott J, Merati M, Mistur R, Zhou B, Straight B, Yim JJ, Bogyo M, Mann M, Wilson DL, Basilion JP, Popkin DL. A Protease-Activated Fluorescent Probe Allows Rapid Visualization of Keratinocyte Carcinoma during Excision. Cancer Res. 2020 80(10):2045-2055. doi: 10.1158/0008-5472.CAN-19-3067. pdf

Yoo E, Schulze CJ, Stokes BH, Onguka O, Yeo T, Mok S, Gnädig NF, Zhou Y, Kurita K, Foe IT, Terrell SM, Boucher MJ, Cieplak P, Kumpornsin K, Lee MCS, Linington RG, Long JZ, Uhlemann AC, Weerapana E, Fidock DA, Bogyo M. The Antimalarial Natural Product Salinipostin A Identifies Essential α/β Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites. Cell Chem Biol. 2020 Feb 20;27(2):143-157.e5. doi: 10.1016/j.chembiol.2020.01.001. pdf

Sanchez MI, de Vries LE, Lehmann C, Lee JT, Ang KK, Wilson C, Chen S, Arkin MR, Bogyo M, Deu E. Identification of Plasmodium dipeptidyl aminopeptidase allosteric inhibitors by high throughput screening. PLoS One. 2019 Dec 18;14(12):e0226270. doi: 10.1371/journal.pone.0226270. pdf

Keller LJ, Babin BM, Lakemeyer M, Bogyo M. Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Curr Opin Chem Biol. 2020 Feb;54:45-53. doi: 10.1016/j.cbpa.2019.10.007. pdf

Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem. 2019 Dec 18;401(1):165-182. doi: 10.1515/hsz-2019-0332. pdf

Babin BM, Kasperkiewicz P, Janiszewski T, Yoo E, Dra G M, Bogyo M. Leveraging Peptide Substrate Libraries to Design Inhibitors of Bacterial Lon Protease. ACS Chem Biol. 2019 2019 Nov 15;14(11):2453-2462. doi: 10.1021/acschembio.9b00529.  pdf

Szumska J, Batool Z, Al-Hashimi A, Venugopalan V, Skripnik V, Schaschke N, Bogyo M, Brix K. Treatment of rat thyrocytes in vitro with cathepsin B and L inhibitors results in disruption of primary cilia leading to redistribution of the trace amine associated receptor 1 to the endoplasmic reticulum. Biochimie. 2019 Jul 11. pii: S0300-9084(19)30201-9. pdf

Veillard F, Sztukowska M, Nowakowska Z, Mizgalska D, Thøgersen IB, Enghild JJ, Bogyo M, Potempa B, Nguyen KA, Potempa J. Proteolytic processing and activation of gingipain zymogens secreted by T9SS of Porphyromonas gingivalis. Biochimie. 2019 Jun 15. pii: S0300-9084(19)30175-0. pdf

de Vries LE, Sanchez MI, Groborz K, Kuppens L, Poreba M, Lehmann C, Nevins N, Withers-Martinez C, Hirst DJ, Yuan F, Arastu-Kapur S, Horn M, Mares M, Bogyo M, Drag M, Deu E. Characterization of P. falciparum dipeptidyl aminopeptidase 3 specificity identifies differences in amino acid preferences between peptide-based substrates and covalent inhibitors. FEBS J. 2019 Jun 8. doi: 10.1111/febs.14953. pdf

Stokes BH, Yoo E, Murithi JM, Luth MR, Afanasyev P, da Fonseca PCA, Winzeler EA, Ng CL, Bogyo M, Fidock DA. Covalent Plasmodium falciparum-selective proteasome inhibitors exhibit a low propensity for generating resistance in vitro and synergize with multiple antimalarial agents. PLoS Pathog. 2019 Jun 6;15(6):e1007722. pdf

Liu Y, Walker E, Iyer SR, Biro M, Kim I, Zhou B, Straight B, Bogyo M, Basilion JP, Popkin DL, Wilson DL. Molecular imaging and validation of margins in surgically excised nonmelanoma skin cancer specimens. J Med Imaging (Bellingham). 2019 Jan;6(1):016001. pdf

Chen L, Keller LJ, Cordasco E, Bogyo M, Lentz CS. Fluorescent Triazole Urea Activity-Based Probes for the Single-Cell Phenotypic Characterization of Staphylococcus aureus. Angew Chem Int Ed Engl. 2019 Apr 16;58(17):5643-5647 pdf

Garland M, Babin BM, Miyashita SI, Loscher S, Shen Y, Dong M, Bogyo M. Covalent Modifiers of Botulinum Neurotoxin Counteract Toxin Persistence. ACS Chem Biol. 2019 Jan 18;14(1):76-87. pdf

Amara N, Foe IT, Onguka O, Garland M, Bogyo M. Synthetic Fluorogenic Peptides Reveal Dynamic Substrate Specificity of Depalmitoylases. Cell Chem Biol. 2019 Jan 17;26(1):35-47. pdf

Seth-Pasricha M, Senn S, Sanman LE, Bogyo M, Nanda V, Bidle KA, Bidle KD. Catalytic linkage between caspase activity and proteostasis in Archaea. Environ Microbiol.2019 Jan;21(1):286-298. pdf

Shrivastav M, Gounaris E, Khan MW, Ko J, Ryu SH, Bogyo M, Larson A, Barret TA, Bentrem DJ. Validation of near infrared fluorescence (NIRF) probes in vivo with dual laser NIRF endoscope. PLoS One. 2018 Nov 2;13(11):e0206568. pdf

Foe IT, Onguka O, Amberg-Johnson K, Garner RM, Amara N, Beatty W, Yeh E, Bogyo M. The Toxoplasma gondii Active Serine Hydrolase 4 Regulates Parasite Division and Intravacuolar Parasite Architecture. mSphere2018 Sep 19;3(5). pii: e00393-18. pdf

Amara N, Tholen M, Bogyo M. Chemical Tools for Selective Activity Profiling of Endogenously Expressed MMP-14 in Multicellular Models. ACS Chem Biol. 2018 Sep 21;13(9):2645-2654. pdf

Yoo E, Stokes BH, de Jong H, Vanaerschot M, Kumar T, Lawrence N, Njoroge M, Garcia A, Van der Westhuyzen R, Momper JD, Ng CL, Fidock DA, Bogyo M. Defining the Determinants of Specificity of Plasmodium Proteasome Inhibitors. J Am Chem Soc. 2018 Sep 12;140(36):11424-11437. pdf

Stathopoulou C, Gangaplara A, Mallett G, Flomerfelt FA, Liniany LP, Knight D, Samsel LA, Berlinguer-Palmini R, Yim JJ, Felizardo TC, Eckhaus MA, Edgington-Mitchell L, Martinez-Fabregas J, Zhu J, Fowler DH, van Kasteren SI, Laurence A, Bogyo M, Watts C, Shevach EM, Amarnath S.PD-1 Inhibitory Receptor Downregulates Asparaginyl Endopeptidase and Maintains Foxp3 Transcription Factor Stability in Induced Regulatory T Cells. Immunity. 2018 Aug 21;49(2):247-263.e7. pdf

Lentz CS, Sheldon JR, Crawford LA, Cooper R, Garland M, Amieva MR, Weerapana E, Skaar EP, Bogyo M.Identification of a S. aureus virulence factor by activity-based protein profiling (ABPP). Nat Chem Biol. 2018 14, 609-617. pdf

Hewings DS, Heideker J, Ma TP, AhYoung AP, El Oualid F, Amore A, Costakes GT, Kirchhofer D, Brasher B, Pillow T, Popovych N, Maurer T, Schwerdtfeger C, Forrest WF, Yu K, Flygare J, Bogyo M, Wertz IE. Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes. Nat Commun. 2018 Mar 21;9(1):1162. pdf

Flanagan-Steet H, Christian C, Lu PN, Aarnio-Peterson M, Sanman L, Archer-Hartmann S, Azadi P, Bogyo M, Steet RA. TGF-ß Regulates Cathepsin Activation during Normal and Pathogenic Development. Cell Rep. 2018 Mar 13;22(11):2964-2977. pdf

Bogyo M, Yim JJ, Rosenthal EL. New Blood Test SEEKs To Detect and Localize Cancer before It's Too Late. Biochemistry. 2018 Mar 13;57(10):1561-1562. pdf

Garland M, Schulze CJ, Foe IT, van der Linden WA, Child MA, Bogyo M. Development of an activity-based probe for acyl-protein thioesterases. PLoS One. 2018 Jan 24;13(1):e0190255. pdf

Tomlin FM, Gerling-Driessen UIM, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR. Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity. ACS Cent Sci. 2017 Nov 22;3(11):1143-1155. pdf

Yim JJ, Tholen M, Klaassen A, Sorger J, Bogyo M. Optimization of a Protease Activated Probe for Optical Surgical Navigation. Mol Pharm. 2017 Mar 5;15(3):750-758. pdf

Aillaud C, Bosc C, Peris L, Bosson A, Heemeryck P, Van Dijk J, Le Friec J, Boulan B, Vossier F, Sanman LE, Syed S, Amara N, Couté Y, Lafanechère L, Denarier E, Delphin C, Pelletier L, Humbert S, Bogyo M, Andrieux A, Rogowski K, Moutin MJ. Live Vasohibins/SVBP are tubulin carboxypeptidases (TCPs) that regulate neuron differentiation. Science. 2017 Dec 15;358(6369):1448-1453. pdf

Duivenvoorden HM, Rautela J, Edgington-Mitchell LE, Spurling A, Greening DW, Nowell CJ, Molloy TJ, Robbins E, Brockwell NK, Lee CS, Chen M, Holliday A, Selinger CI, Hu M, Britt KL, Stroud DA, Bogyo M, Möller A, Polyak K, Sloane BF, O'Toole SA, Parker BS. Myoepithelial cell-specific expression of stefin A as a suppressor of early breast cancer invasion. J Pathol. 2017 Dec;243(4):496-509. pdf

Hopp CS, Bennett BL, Mishra S, Lehmann C, Hanson KK, Lin JW, Rousseau K, Carvalho FA, van der Linden WA, Santos NC, Bogyo M, Khan SM, Heussler V, Sinnis P. Deletion of the rodent malaria ortholog for falcipain-1 highlights differences between hepatic and blood stage merozoites. PLoS Pathog. 2017 Sep 18;13(9):e1006586.pdf

Lee CW, Stankowski JN, Chew J, Cook CN, Lam YW, Almeida S, Carlomagno Y, Lau KF, Prudencio M, Gao FB, Bogyo M, Dickson DW, Petrucelli L. The lysosomal protein cathepsin L is a progranulin protease. Mol Neurodegener. 2017 Jul 25;12(1):55. pdf

Ng CL, Fidock DA, Bogyo M. Protein Degradation Systems as Antimalarial Therapeutic Targets. Trends Parasitol. 2017 Sep;33(9):731-743. pdf

Di Cristina M, Dou Z, Lunghi M, Kannan G, Huynh MH, McGovern OL, Schultz TL, Schultz AJ, Miller AJ, Hayes BM, van der Linden W, Emiliani C, Bogyo M, Besteiro S, Coppens I, Carruthers VB. Toxoplasma depends on lysosomal consumption of autophagosomes for persistent infection. Nat Microbiol. 2017 Jun 19;2:17096.pdf

Bogyo M. Introduction to the Special Issue on Proteases and Proteolysis in Health and Disease. FEBS J. 2017 May;284(10):1392-1393. pdf

Ward ME, Chen R, Huang HY, Ludwig C, Telpoukhovskaia M, Taubes A, Boudin H, Minami SS, Reichert M, Albrecht P, Gelfand JM, Cruz-Herranz A, Cordano C, Alavi MV, Leslie S, Seeley WW, Miller BL, Bigio E, Mesulam MM, Bogyo MS, Mackenzie IR, Staropoli JF, Cotman SL, Huang EJ, Gan L, Green AJ.Individuals with progranulin haploinsufficiency exhibit features of neuronal ceroid lipofuscinosis. Sci Transl Med. 2017 Apr 12;9(385). pdf

Child MA, Garland M, Foe I, Madzelan P, Treeck M, van der Linden WA, Oresic Bender K, Weerapana E, Wilson MA, Boothroyd JC, Reese ML, Bogyo M. Toxoplasma DJ-1 Regulates Organelle Secretion by a Direct Interaction with Calcium-Dependent Protein Kinase 1. MBio. 2017 Feb 28;8(1). pii: e02189-16. pdf

Garland M, Loscher S, Bogyo M.Chemical Strategies To Target Bacterial Virulence. Chem Rev. 2017 Mar 8;117(5):4422-4461. pdf

Hewings DS, Flygare JA, Bogyo M, Wertz IE. Activity-based probes for the ubiquitin conjugation-deconjugation machinery: new chemistries, new tools, and new insights. FEBS J. 2017 May;284(10):1555-1576. pdf

Tipirneni KE, Rosenthal EL, Moore LS, Haskins AD, Udayakumar N, Jani AH, Carroll WR, Morlandt AB, Bogyo M, Rao J, Warram JM. Fluorescence Imaging for Cancer Screening and Surveillance. Mol Imaging Biol. 2017 Oct;19(5):645-655. pdf

Hewings DS, Flygare JA, Wertz IE, Bogyo M. Activity-based probes for the multicatalytic proteasome.Methods FEBS J. 2017 May;284(10):1540-1554. pdf

Orlowski GM, Sharma S, Colbert JD, Bogyo M, Robertson SA, Kataoka H, Chan FK, Rock KL. Frontline Science: Multiple cathepsins promote inflammasome-independent, particle-induced cell death during NLRP3-dependent IL-1β activation. J Leukoc Biol. 2017 Jul;102(1):7-17.pdf

Walker E, Mann M, Honda K, Vidimos A, Schluchter MD, Straight B, Bogyo M, Popkin D, Basilion JP. Rapid visualization of nonmelanoma skin cancer. J Am Acad Dermatol. 2017 Feb;76(2):209-216. pdf

Dubey R, Staker BL, Foe IT, Bogyo M, Myler PJ, Ngô HM, Gubbels MJ. Membrane skeletal association and post-translational allosteric regulation of Toxoplasma gondii GAPDH. Mol Microbiol. 2017 Feb;103(4):618-634. pdf

Edgington-Mitchell LE, Bogyo M, Verdoes M. Live Cell Imaging and Profiling of Cysteine Cathepsin Activity Using a Quenched Activity-Based Probe. Methods Mol Biol. 2017;1491:145-159. pdf

Bender KO, Garland M, Bogyo M.Response to Comment on "A small-molecule antivirulence agent for treating Clostridium difficile infection".Sci Transl Med. 2016 Dec 21;8(370):370tr2. pdf

Sensarn S, Zavaleta CL, Segal E, Rogalla S, Lee W, Gambhir SS, Bogyo M, Contag CH.A Clinical Wide-Field Fluorescence Endoscopic Device for Molecular Imaging Demonstrating Cathepsin Protease Activity in Colon Cancer. Mol Imaging Biol. 2016 Dec;18(6):820-829.pdf

Edgington-Mitchell LE, Bogyo M, Verdoes M. Live Cell Imaging and Profiling of Cysteine Cathepsin Activity Using a Quenched Activity-Based Probe. Methods Mol Biol. 2017;1491:145-159.

Lentz CS, Ordonez AA, Kasperkiewicz P, La Greca F, O'Donoghue AJ, Schulze CJ, Powers JC, Craik CS, Drag M, Jain SK, Bogyo M. Design of selective substrate and activity-based probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis. ACD Infect. Dis. 2016 11;2(11):807-815. pdf

Grüner BM, Schulze CJ, Yang D, Ogasawara D, Dix MM, Rogers ZN, Chuang CH, McFarland CD, Chiou SH, Brown JM, Cravatt BF, Bogyo M, Winslow MM. An in vivo multiplexed small-molecule screening platform. Nat Methods. 2016 13(10):883-889.pdf

Abd-Elrahman I, Kosuge H, Wises Sadan T, Ben-Nun Y, Meir K, Rubinstein C, Bogyo M, McConnell MV, Blum G. Cathepsin Activity-Based Probes and Inhibitor for Preclinical Atherosclerosis Imaging and Macrophage Depletion. PLoS One. 2016 Aug 17;11(8):e0160522.pdf

Edgington-Mitchell LE, Wartmann T, Fleming AK, Gocheva V, van der Linden WA, Withana NP, Verdoes M, Aurelio L, Edgington-Mitchell D, Lieu T, Parker BS, Graham B, Reinheckel T, Furness JB, Joyce JA, Storz P, Halangk W, Bogyo M, Bunnett NW. Legumain is activated in macrophages during pancreatitis. Am J Physiol Gastrointest Liver Physiol. 2016 311(3):G548-60. pdf

Sanman LE, van der Linden WA, Verdoes M, Bogyo M. Bifunctional Probes of Cathepsin Protease Activity and pH Reveal Alterations in Endolysosomal pH during Bacterial Infection. Cell Chem Biol. 2016 23(7):793-804. pdf

van der Linden, W.A., Schulze, C.J., Herbert, A.S., Krause, T.B., Wirchnianski, A.A., Dye, J.M., Chandran, K., Bogyo M. Cysteine Cathepsins as anti-ebola agents. ACS Infect Dis. 2016 2(3):173-179. pdf

Li H, Bogyo M, da Fonseca PC. The cryo-EM structure of the Plasmodium falciparum 20S proteasome and its use in the fight against malaria. FEBS J. 2016 Jun 11. doi: 10.1111/febs.13780. [Epub ahead of print] pdf

Withana NP, Saito T, Ma X, Garland M, Liu C, Kosuge H, Amsallem M, Verdoes M, Ofori LO, Fischbein M, Arakawa M, Cheng Z, McConnell MV, Bogyo M. Dual Modality Activity Based Probes as Molecular Imaging Agents for Vascular Inflammation. J Nucl Med. 2016 May 19. pii: jnumed.115.171553. [Epub ahead of print] pdf

Sensarn S, Zavaleta CL, Segal E, Rogalla S, Lee W, Gambhir SS, Bogyo M, Contag CH. A Clinical Wide-Field Fluorescence Endoscopic Device for Molecular Imaging Demonstrating Cathepsin Protease Activity in Colon Cancer. Mol Imaging Biol. 2016 May 6. [Epub ahead of print] pdf

Edgington-Mitchell LE, Bogyo M. Detection of Active Caspases During Apoptosis Using Fluorescent Activity-Based Probes. Methods Mol Biol. 2016 1419:27-39. pdf

Sanman LE, Qian Y, Eisele NA, Ng TM, van der Linden WA, Monack DM, Weerapana E, Bogyo M. Disruption of glycolytic flux is a signal for inflammasome signaling and pyroptotic cell death. Elife. 2016 5:e13663. pdf

Garland M, Yim JJ, Bogyo M. A Bright Future for Precision Medicine: Advances in Fluorescent Chemical Probe Design and Their Clinical Application. Cell Chem Biol. 2016 23(1):122-36. pdf

Li H, O'Donoghue AJ, van der Linden WA, Xie SC, Yoo E, Foe IT, Tilley L, Craik CS, da Fonseca PC, Bogyo M. Structure- and function-based design of Plasmodium-selective proteasome inhibitors. Nature. 2016 530(7589):233-6. pdf

Withana NP, Ma X, McGuire HM, Verdoes M, van der Linden WA, Ofori LO, Zhang R, Li H, Sanman LE, Wei K, Yao S, Wu P, Li F, Huang H, Xu Z, Wolters PJ, Rosen GD, Collard HR, Zhu Z, Cheng Z, Bogyo M.Non-invasive Imaging of Idiopathic Pulmonary Fibrosis Using Cathepsin Protease Probes. Sci Rep. 2016 6:19755. pdf

Withana NP, Garland M, Verdoes M, Ofori LO, Segal E, Bogyo M. Labeling of active proteases in fresh-frozen tissues by topical application of quenched activity-based probes. Nat Protoc. 2016 11(1):184-91. pdf

Lauterwasser EM, Fontaine SD, Li H, Gut J, Katneni K, Charman SA, Rosenthal PJ, Bogyo M, Renslo AR. Trioxolane-Mediated Delivery of Mefloquine Limits Brain Exposure in a Mouse Model of Malaria. ACS Med Chem Lett. 2015 6(11):1145-9. pdf

Foe IT, Child MA, Majmudar JD, Krishnamurthy S, van der Linden WA, Ward GE, Martin BR, Bogyo M. Global Analysis of Palmitoylated Proteins in Toxoplasma gondii. Cell Host Microbe. 2015 18(4):501-11 pdf

Oresic Bender K, Garland M, Ferreyra JA, Hryckowian AJ, Child MA, Puri AW, Solow-Cordero DE, Higgenbottom SK, Segal E, Banaei N, Shen A, Sonnenburg JL, Bogyo M. A small-molecule antivirulance agent for treating Clostridium difficile infection. Science Translational Medicine. 2015 7(306):306ra148. pdf

Staniec D, Ksiazek M, Thøgersen IB, Enghild JJ, Sroka A, Bryzek D, Bogyo M, Abrahamson M, Potempa J.Calcium Regulates the Activity and Structural Stability of Tpr, a Bacterial Calpain-like Peptidas. J Biol Chem. 2015 290(45):27248-60.

Hou L, Cooley J, Swanson R, Ong PC, Pike RN, Bogyo M, Olson ST, Remold-O'Donnell E. The protease cathepsin L regulates Th17 cell differentiation. J Autoimmun. 2015 65:56-63. pdf

Edgington-Mitchell LE, Rautela J, Duivenvoorden HM, Jayatilleke KM, van der Linden WA, Verdoes M, Bogyo M, Parker BS. Cysteine cathepsin activity suppresses osteoclastogenesis of myeloid-derived suppressor cells in breast cancer. Oncotarget. 2015 6(29):27008-22. pdf

van der Linden WA, Segal E, Child MA, Byzia A, Drag M, Bogyo M. Design and Synthesis of Activity-Based Probes and Inhibitors for Bleomycin Hydrolase. Chem Biol. 2015 Aug 20;22(8):995-1001. pdf

Orlowski GM, Colbert JD, Sharma S, Bogyo M, Robertson SA, Rock KL. Multiple Cathepsins Promote Pro-IL-1β Synthesis and NLRP3-Mediated IL-1β Activation. J Immunol. 2015 Aug 15;195(4):1685-97. pdf

Lu H, Chandrasekar B, Oeljeklaus J, Misas-Villamil JC, Wang Z, Shindo T, Bogyo M, Kaiser M, van der Hoorn RA. Subfamily-specific Fluorescent Probes for Cys proteases Display Dynamic Protease Activities During Seed Germination. Plant Physiol. 2015 Jun 5. pii: pp.114.254466. [Epub ahead of print] pdf

Ofori LO, Withana NP, Prestwood TR, Verdoes M, Brady JJ, Winslow MM, Sorger J, Bogyo M. Design of Protease Activated Optical Contrast Agents That Exploit a Latent Lysosomotropic Effect for Use in Fluorescence-Guided Surgery. ACS Chem Biol. 2015 10(9):1977-88. pdf

Gangoda L, Keerthikumar S, Fonseka P, Edgington LE, Ang CS, Ozcitti C, Bogyo M, Parker BS, Mathivanan S. Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin. Oncotarget. 2015 6(13):11175-90. pdf

Oresic Bender K, Ofori L, van der Linden WA, Mock ED, Datta GK, Chowdhury S, Li H, Segal E, Sanchez Lopez M, Ellman JA, Figdor CG, Bogyo M, Verdoes M. Design of a highly selective quenched activity-based probe and its application in dual color imaging studies of cathepsin S activity localization. J Am Chem Soc. 2015 137(14):4771-7. pdf

Segal E, Prestwood TR, van der Linden WA, Carmi Y, Bhattacharya N, Withana N, Verdoes M, Habtezion A, Engleman EG, Bogyo M. Detection of intestinal cancer by local, topical application of a quenched fluorescence probe for cysteine cathepsins. Chem Biol.2015 22(1):148-58. doi: 10.1016/j.chembiol.2014.11.008. pdf

Hachmann J, Edgington-Mitchell LE, Poreba M, Sanman LE, Drag M, Bogyo M, Salvesen GS. Probes to monitor activity of the paracaspase MALT1. Chem Biol. 2015 Jan 22;22(1):139-47. doi: 10.1016/j.chembiol.2014.11.011. pdf

Li H, Tsu C, Blackburn C, Li G, Hales P, Dick L, Bogyo M. Identification of potent and selective non-covalent inhibitors of the Plasmodium falciparum proteasome. J Am Chem Soc. 2014 Oct 1;136(39):13562-5. doi: 10.1021/ja507692y. pdf

Godinat A, Budin G, Morales AR, Park HM, Sanman LE, Bogyo M, Yu A, Stahl A, Dubikovskaya EA. A biocompatible "split luciferin" reaction and its application for non-invasive bioluminescent imaging of protease activity in living animals. Curr Protoc Chem Biol. 2014 Sep 9;6(3):169-89. doi: 10.1002/9780470559277.ch140047. pdf

Gangoda L, Doerflinger M, Srivastava R, Narayan N, Edgington LE, Orian J, Hawkins C, O'Reilly LA, Gu H, Bogyo M, Ekert P, Strasser A, Puthalakath H. Loss of Prkar1a leads to Bcl-2 family protein induction and cachexia in mice. Cell Death Differ. 2014 Nov;21(11):1815-24. doi: 10.1038/cdd.2014.98. pdf

Li H, van der Linden WA, Verdoes M, Florea BI, McAllister FE, Govindaswamy K, Elias JE, Bhanot P, Overkleeft HS, Bogyo M. Assessing subunit dependency of the Plasmodium proteasome using small molecule inhibitors and active site probes. ACS Chem Biol. 2014 Aug 15;9(8):1869-76. pdf

Sanman LE, Bogyo M. Activity-based profiling of proteases. Annu Rev Biochem. 2014;83:249-73. pdf

Haedke UR, Frommel SC, Hansen F, Hahne H, Kuster B, Bogyo M, Verhelst SH. Phosphoramidates as novel activity-based probes for serine proteases. Chembiochem. 2014 May 26;15(8):1106-10. pdf

Cattaruzza F, Amadesi S, Carlsson JF, Murphy JE, Lyo V, Kirkwood K, Cottrell GS, Bogyo M, Knecht W, Bunnett NW. Serine proteases and protease-activated receptor 2 mediate the proinflammatory and algesic actions of diverse stimulants. Br J Pharmacol. 2014 Aug;171(16):3814-26. pdf

Walker E, Gopalakrishnan R, Bogyo M, Basilion JP. Microscopic Detection of Quenched Activity-Based Optical Imaging Probes Using an Antibody Detection System: Localizing Protease Activity. Mol Imaging Biol. 2014 Apr 5. [Epub ahead of print] pdf

Razorenova OV, Castellini L, Colavitti R, Edgington LE, Nicolau M, Huang X, Bedogni B, Mills EM, Bogyo M, Giaccia AJ. The apoptosis repressor with a CARD domain (ARC) gene is a direct hypoxia-inducible factor 1 target gene and promotes survival and proliferation of VHL-deficient renal cancer cells. Mol Cell Biol. 2014 Feb;34(4):739-51. pdf

Rothberg JM, Bailey KM, Wojtkowiak JW, Ben-Nun Y, Bogyo M, Weber E, Moin K, Blum G, Mattingly RR, Gillies RJ, Sloane BF. Acid-mediated tumor proteolysis: contribution of cysteine cathepsins. Neoplasia. 2013 Oct;15(10):1125-37. pdf

Deu E, Chen IT, Lauterwasser EM, Valderramos J, Li H, Edgington LE, Renslo AR, Bogyo M. Ferrous iron-dependent drug delivery enables controlled and selective release of therapeutic agents in vivo. Proc Natl Acad Sci U S A. 2013 Nov 5;110(45):18244-9. pdf

Ruffell B, Affara NI, Cottone L, Junankar S, Johansson M, DeNardo DG, Korets L, Reinheckel T, Sloane BF, Bogyo M, Coussens LM. Cathepsin C is a tissue-specific regulator of squamous carcinogenesis. Genes Dev. 2013 27(19):2086-98. pdf

Verdoes M, Oresic Bender K, Segal E, van der Linden WA, Syed S, Withana NP, Sanman LE, Bogyo M. An improved quenched fluorescent probe for imaging of cysteine cathepsin activity. J Am Chem Soc. 2013 135(39):14726-30. pdf

Puri AW, Bogyo M. Applications of Small Molecule Probes in Dissecting Mechanisms of Bacterial Virulence and Host Responses. Biochemistry. 2013 52(35):5985-96. pdf

Child MA, Hall CI, Beck JR, Ofori LO, Albrow VE, Garland M, Bowyer PW, Bradley PJ, Powers JC, Boothroyd JC, Weerapana E, Bogyo M. Small-molecule inhibition of a depalmitoylase enhances Toxoplasma host-cell invasion. Nat Chem Biol. 2013 9(10):651-6. pdf

Tanaka TQ, Deu E, Molina-Cruz A, Ashburne MF, Ali O, Suri A, Kortagere S, Bogyo M, Williamson KC. Plasmodium dipeptidyl aminopeptidases as malaria transmission blocking drug targets. Antimicrob Agents Chemother. 2013 Oct;57(10):4645-52. pdf

Gloeckl S, Ong VA, Patel P, Tyndall JD, Timms P, Beagley KW, Allan JA, Armitage CW, Turnbull L, Whitchurch CB, Merdanovic M, Ehrmann M, Powers JC, Oleksyszyn J, Verdoes M, Bogyo M, Huston WM. Identification of a serine protease inhibitor which causes inclusion vacuole reduction and is lethal to Chlamydia trachomatis. Mol Microbiol. 2013 Aug;89(4):676-89. pdf

Xiao J, Broz P, Puri AW, Deu E, Morell M, Monack DM, Bogyo M. Coupled protein and probe engineering approach for selective inhibition and activity-based probe labeling of the caspases. J Am Chem Soc. 2013 Jun 19;135(24):9130-8. pdf

Morell M, Nguyen Duc T, Willis AL, Syed S, Lee J, Deu E, Deng Y, Xiao J, Turk BE, Jessen JR, Weiss SJ, Bogyo M. Coupling protein engineering with probe design to inhibit and image matrix metalloproteinases with controlled specificity. J Am Chem Soc. 2013 Jun 19;135(24):9139-48. pdf

Godinat A, Park HM, Miller SC, Cheng K, Hanahan D, Sanman LE, Bogyo M, Yu A, Nikitin GF, Stahl A, Dubikovskaya EA. A Biocompatible in Vivo Ligation Reaction and Its Application for Noninvasive Bioluminescent Imaging of Protease Activity in Living Mice. ACS Chem Biol. 2013 May 17;8(5):987-99. pdf

Edgington LE, Bogyo M. In vivo imaging and biochemical characterization of protease function using fluorescent activity-based probes. Curr Protoc Chem Biol. 2013 Mar 1;5(1):25-44.

Lu H, Wang Z, Shabab M, Oeljeklaus J, Verhelst SH, Kaschani F, Kaiser M, Bogyo M, van der Hoorn RA. A substrate-inspired probe monitors translocation, activation, and subcellular targeting of bacterial type III effector protease AvrPphB. Chem Biol. 2013 Feb 21;20(2):168-76. pdf

Bogyo M, Rudd PM. New technologies and their impact on 'omics' research. Curr Opin Chem Biol. 2013 Feb;17(1):1-3. pdf

Lee J, Bogyo M. Target deconvolution techniques in modern phenotypic profiling. Curr Opin Chem Biol. 2013 Feb;17(1):118-26. pdf

Misas-Villamil JC, Toenges G, Kolodziejek I, Sadaghiani AM, Kaschani F, Colby T, Bogyo M, van der Hoorn RA. Activity profiling of vacuolar processing enzymes reveals a role for VPE during oomycete infection. Plant J. 2013 Feb;73(4):689-700. pdf

Edgington LE, Verdoes M, Ortega A, Withana NP, Lee J, Syed S, Bachmann MH, Blum G, Bogyo M. Functional imaging of legumain in cancer using a new quenched activity-based probe. J Am Chem Soc. 2013 Jan 9;135(1):174-82. pdf

Mullins SR, Sameni M, Blum G, Bogyo M, Sloane BF, Moin K. Three-dimensional cultures modeling premalignant progression of human breast epithelial cells: role of cysteine cathepsins. Biol Chem. 2012 Dec;393(12):1405-16. pdf

Stolze SC, Deu E, Kaschani F, Li N, Florea BI, Richau KH, Colby T, van der Hoorn RA, Overkleeft HS, Bogyo M, Kaiser M. The antimalarial natural product symplostatin 4 is a nanomolar inhibitor of the food vacuole falcipains. Chem Biol. 2012 Dec 21;19(12):1546-55. pdf

Li H, Ponder EL, Verdoes M, Asbjornsdottir KH, Deu E, Edgington LE, Lee JT, Kirk CJ, Demo SD, Williamson KC, Bogyo M. Validation of the proteasome as a therapeutic target in Plasmodium using an epoxyketone inhibitor with parasite-specific toxicity. Chem Biol. 2012 Dec 21;19(12):1535-45. pdf

Sztukowska M, Veillard F, Potempa B, Bogyo M, Enghild JJ, Thogersen IB, Nguyen KA, Potempa J. Disruption of gingipain oligomerization into non-covalent cell-surface attached complexes. Biol Chem. 2012 Sep;393(9):971-7. pdf

Salvesen GS, Bogyo M. Highlight: the universe of proteolytic networks and mechanisms. Biol Chem. 2012 Sep;393(9):841. pdf

Lyo V, Cattaruzza F, Kim TN, Walker AW, Paulick M, Cox D, Cloyd J, Buxbaum J, Ostroff J, Bogyo M, Grady EF, Bunnett NW, Kirkwood KS. Active cathepsins B, L, and S in murine and human pancreatitis. Am J Physiol Gastrointest Liver Physiol. 2012 Oct 15;303(8):G894-903. pdf

Goussetis DJ, Gounaris E, Wu EJ, Vakana E, Sharma B, Bogyo M, Altman JK, Platanias LC. Autophagic degradation of the BCR-ABL oncoprotein and generation of antileukemic responses by arsenic trioxide. Blood. 2012 Oct 25;120(17):3555-62. pdf

Puri AW, Broz P, Shen A, Monack DM, Bogyo M. Caspase-1 activity is required to bypass macrophage apoptosis upon Salmonella infection. Nature Chemical Biology. 2012; 8(9): 745-7. pdf

Verdoes M, Edgington LE, Scheeren FA, Leyva M, Blum G, Weiskopf K, Bachmann MH, Ellman JA, Bogyo M. A nonpeptidic cathepsin s activity-based probe for noninvasive optical imaging of tumor-associated macrophages. Chemistry & Biology. 2012; 19(5):619-28. pdf

Cutter JL, Cohen NT, Wang J, Sloan AE, Cohen AR, Panneerselvam A, Schluchter M, Blum G, Bogyo M, Basilion JP. Topical application of activity-based probes for visualization of brain tumor tissue. PLoS One. 2012;7(3):e33060. Epub 2012 Mar 13. pdf

Richau KH, Kaschani F, Verdoes M, Pansuriya TC, Niessen S, Stüber K, Colby T, Overkleeft HS, Bogyo M, Van der Hoorn RA. Subclassification and biochemical analysis of plant papain-like cysteine proteases displays subfamily-specific characteristics. Plant Physiol. 2012 Apr;158(4):1583-99. pdf

Edgington LE, van Raam BJ, Verdoes M, Wierschem C, Salvesen GS, Bogyo, M. An optimized activity-based probe for the study of caspase-6 activation. Chemistry & Biology. 2012; 19(3): 340-52 pdf

Fritz HM, Bowyer PW, Bogyo M, Conrad PA, Boothroyd JC. Proteomic analysis of fractionated toxoplasma oocysts reveals clues to their environmental resistance. PLoS One. 2012;7(1):e29955. pdf

Withana NP, Blum G, Sameni M, Slaney C, Anbalagan A, Olive MB, Bidwell BN, Edgington L, Wang L, Moin K, Sloane BF, Anderson RL, Bogyo MS, Parker BS. Cathepsin B inhibition limits bone metastasis in breast cancer. Cancer Res. 2012 Jan 19. [Epub ahead of print]. pdf

Ferreira KS, Kreutz C, Macnelly S, Neubert K, Haber A, Bogyo M, Timmer J, Borner C. Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes. Apoptosis. 2012 Jan 13. [Epub ahead of print]. pdf

Lee J and Bogyo M. Synthesis and evaluation of aza-peptidyl inhibitors of the lysosomal asparaginyl endopeptidase, legumain. Bioorg Med Chem Lett. 2012 Feb 1;22(3):1340-3. pdf

Deu E, Verdoes M, Bogyo M. New approaches for dissecting protease functions to improve probe development and drug discovery. Nat Struct Mol Biol. 2012 Jan 5;19(1):9-16. pdf

Li H, Child MA, Bogyo M. Proteases as regulators of pathogenesis: Examples from the apicomplexa. Biochim Biophys Acta. 2012 1824(1):177-85 pdf

Kalinska M, Kantyka T, Greenbaum DC, Larsen KS, Wadyka B, Jabaiah A, Bogyo M, Daugherty PS, Wysocka M, Jaros M, Lesner A, Rolka K, Schaschke N, Stennicke H, Dubin A, Potempa J, Dubin G. Substrate specificity of Staphylococcus aureus cysteine proteases - Staphopains A, B and C. Biochimie. 2012 94(2):318-27. pdf

Edgington LE and Bogyo M. (2011) Applications for Activity-based Probes in Drug Discovery. Royal Society of Chemistry. Ed. Bunage M. P. 33-63. pdf

Ren G, Blum G, Verdoes M, Liu H, Syed S, Edgington LE, Gheysens O, Miao Z, Jiang H, Gambhir SS, Bogyo M, Cheng Z. Non-invasive imaging of cysteine cathepsin activity in solid tumors using a 64Cu-labeled activity-based probe. PLoS One. 2011;6(11):e28029. pdf

Edgington LE, Verdoes M, Bogyo M. Functional imaging of proteases: recent advances in the design and application of substrate-based and activity-based probes. Curr Opin Chem Biol. 2011 Dec;15(6):798-805. pdf

Li J, Hsu HC, Yang P, Wu Q, Li H, Edgington LE, Bogyo M, Kimberly RP, Mountz JD. Treatment of arthritis by macrophage depletion and immunomodulation: Testing an apoptosis-mediated therapy in a humanized death receptor mouse model. Arthritis Rheum. 2011 Oct 17. doi: 10.1002/art.33423. [Epub ahead of print]. pdf

Tedelind S, Jordans S, Resemann H, Blum G, Bogyo M, Führer D, Brix K. Cathepsin B trafficking in thyroid carcinoma cells. Thyroid Res. 2011 Aug 3;4 Suppl 1:S2. pdf

Mikhaylov G, Mikac U, Magaeva AA, Itin VI, Naiden EP, Psakhye I, Babes L, Reinheckel T, Peters C, Zeiser R, Bogyo M, Turk V, Psakhye SG, Turk B, Vasiljeva O. Ferri-liposomes as an MRI-visible drug-delivery system for targeting tumours and their microenvironment. Nat Nanotechnol. 2011 6(9):594-602. pdf

Cattaruzza F, Lyo V, Jones E, Pham D, Hawkins J, Kirkwood K, Valdez-Morales E, Ibeakanma C, Vanner SJ, Bogyo M, Bunnett NW. Cathepsin S is activated during colitis and causes visceral hyperalgesia by a PAR2-dependent mechanism in mice. Gastroenterology. 2011 141(5):1864-74. pdf

Hall CI, Reese ML, Weerapana E, Child MA, Bowyer PW, Albrow VE, Haraldsen JD, Phillips MR, Sandoval ED, Ward GE, Cravatt BF, Boothroyd JC, Bogyo M. Chemical genetic screen identifies Toxoplasma DJ-1 as a regulator of parasite secretion, attachment, and invasion. Proc Natl Acad Sci U S A. 2011 108(26):10568-73. pdf

Boutté AM, Friedman DB, Bogyo M, Min Y, Yang L, Lin PC. Identification of a myeloid-derived suppressor cell cystatin-like protein that inhibits metastasis. FASEB J. 2011 25(8):2626-37 pdf

Ponder EL, Albrow VE, Leader BA, Békés M, Mikolajczyk J, Fonovic UP, Shen A, Drag M, Xiao J, Deu E, Campbell AJ, Powers JC, Salvesen GS, Bogyo M. Functional Characterization of a SUMO Deconjugating Protease of Plasmodium falciparum Using Newly Identified Small Molecule Inhibitors. Chem Biol. 2011 18:711-721. pdf

Albrow VE, Ponder EL, Fasci D, Békés M, Deu E, Salvesen GS, Bogyo M. Development of Small Molecule Inhibitors and Probes of Human SUMO Deconjugating Proteases. Chem Biol. 2011 18:722-732. pdf

Ewald SE, Engel A, Lee J, Wang M, Bogyo M, Barton GM. Nucleic acid recognition by Toll-like receptors is coupled to stepwise processing by cathepsins and asparagine endopeptidase. J Exp Med. 2011 208:643-51. pdf

Paulick MG, Bogyo M. Development of Activity-Based Probes for Cathepsin X. ACS Chem Biol. 2011 6:563-72. pdf

Mahajan SS, Deu E, Lauterwasser EM, Leyva MJ, Ellman JA, Bogyo M, Renslo AR. A fragmenting hybrid approach for targeted delivery of multiple therapeutic agents to the malaria parasite. ChemMedChem. 2011 6:415-9. pdf

Shen A, Lupardus PJ, Gersch MM, Puri AW, Albrow VE, Garcia KC, Bogyo M. Defining an allosteric circuit in the cysteine protease domain of Clostridium difficile toxins. Nature Struc. Mol. Bio. 2011. 18: 364-7. pdf

Wang F, Krai P, Deu E, Bibb B, Lauritzen C, Pedersen J, Bogyo M, Klemba M. Biochemical characterization of Plasmodium falciparum dipeptidyl aminopeptidase 1. Mol Biochem Parasitol. 2011 175:10-20. pdf

Bowyer PW, Simon GM, Cravatt BF, Bogyo M. Global profiling of proteolysis during rupture of P. falciparum from the host erythrocyte. Mol Cell Proteomics. 2011 10(5):M110.001636. pdf

Puri AW, Lupardus PJ, Deu E, Albrow VE, Garcia KC, Bogyo M, Shen A. Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB. Chem Biol. 2010 17: 1201-1211. pdf

Deu E, Leyva MJ, Albrow VE, Rice MJ, Ellman JA, Bogyo M. Functional studies of Plasmodium falciparum dipeptidyl aminopeptidase I using small molecule inhibitors and active site probes. Chem Biol. 2010 17:808-19. pdf

Deu E, Yang Z, Wang F, Klemba M, Bogyo M. Use of activity-based probes to develop high throughput screening assays that can be performed in complex cell extracts. PLoS One. 2010 5(8). pii: e11985. pdf

Tedelind S, Poliakova K, Valeta A, Hunegnaw R, Yemanaberhan EL, Heldin NE, Kurebayashi J, Weber E, Kopitar-Jerala N, Turk B, Bogyo M, Brix K. Nuclear cysteine cathepsin variants in thyroid carcinoma cells. Biol Chem. 2010 391:923-35. pdf

Staudt ND, Aicher WK, Kalbacher H, Stevanovic S, Carmona AK, Bogyo M, Klein G. Cathepsin X is secreted by human osteoblasts, digests CXCL-12 and impairs adhesion of hematopoietic stem and progenitor cells to osteoblasts. Haematologica. 2010 95(9):1452-60. pdf

Konjar S, Yin F, Bogyo M, Turk B, Kopitar-Jerala N. Increased nucleolar localization of SpiA3G in classically but not alternatively activated macrophages. FEBS Lett. 2010 Mar 23. [Epub ahead of print]. pdf

Bogyo M. Finding enzymes that are actively involved in cancer. Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2379-80. pdf

Lee J and Bogyo M. Development of near-infrared fluorophore (NIRF)-labeled activity-based probes for in vivo imaging of legumain.  ACS Chem Biol. 2010 19:233-43. pdf

Drag M, Bogyo M, Ellman JA, Salvesen GS. Aminopeptidase fingerprints. An integrated approach for identification of good substrates and optimal inhibitors. J Biol Chem. (2010) 285:3310-8. pdf

Ravindran S, Lodoen MB, Verhelst SH, Bogyo M, Boothroyd JC. 4-bromophenacyl bromide specifically inhibits rhoptry secretion during Toxoplasma invasion. PLoS One. (2009) Dec 2;4(12):e8143. pdf

Shen A, Lupardus PJ, Morell M, Ponder EL, Sadaghiani AM, Garcia KC, Bogyo M. Simplified, enhanced protein purification using an inducible, autoprocessing enzyme tag. PLoS One. (2009) Dec 2;4(12):e8119.pdf

Horn M, Nussbaumerová M, Sanda M, Kovárová Z, Srba J, Franta Z, Sojka D, Bogyo M, Caffrey CR, Kopácek P, Mares M. Hemoglobin digestion in blood-feeding ticks: mapping a multipeptidase pathway by functional proteomics. Chem Biol. (2009) 16:1053-63. pdf

Zhang J, Fonovic M, Suyama K, Bogyo M, Scott MP. Rab35 controls actin bundling by recruiting fascin as an effector protein. Science. (2009) 325:1250-4. pdf

Blum G, Weimer RM, Edgington LE, Adams W, Bogyo M. Comparative assessment of substrates and activity based probes as tools for non-invasive optical imaging of cysteine protease activity. PLoS One(2009) 4(7): e6374 pdf

Puri AW, Bogyo M. Using Small Molecules to Dissect Mechanisms of Microbial Pathogenesis. ACS Chem. Biol. (2009) 4, 603-16. pdf     about the author

Lee JT, Chen DY, Yang Z, Ramos AD, Hsieh JJD, Bogyo M. Design, synthesis, and evaluation of Taspase1 inhibitors. Bioorg. Med. Chem. Let. (2009) 19:5086-5090 pdf

Edgington LE, Berger AB, Blum G, Albrow VE, Paulick MG, Lineberry N, Bogyo M. Noinvasive optical imaging of apoptosis by caspase-targeted activity based probes. Nat Med (2009) 15:967-73 pdf    Stanford Press Release

Larson ET, Parussini F, Huynh MH, Giebel JD, Kelley AM, Zhang L, Bogyo M, Merritt EA, Carruthers VB. Toxoplasma gondii cathepsin l is the primary target of the invasion inhibitory compound LHVS. J. Biol. Chem. (2009) July 17. [Epub ahead of print]. pdf

Shen A, Lupardus PJ, Albrow VE, Guzzetta A, Powers JC, Garcia KC, Bogyo M. Mechanistic and structural insights into the proteolytic activation of Vibrio cholerae MARTX toxin. Nat Chem Biol. (2009) 5:469-478. pdf

Chang SH, Kanasaki K, Gocheva V, Blum G, Harper J, Moses MA, Shih SC, Nagy JA, Joyce J, Bogyo M, Kalluri R, Dvorak HF. VEGF-A induces angiogenesis by perturbing the cathepsin-cysteine protease inhibitor balance in venules, causing basement membrane degradation and mother vessel formation. Cancer Res. (2009) 69:4537-44. pdf

Beckham SA, Piedrafita D, Phillips CI, Samarawickrema N, Law RH, Smooker PM, Quinsey NS, Irving JA, Greenwood D, Verhelst SH, Bogyo M, Turk B, Coetzer TH, Wijeyewickrema LC, Spithill TW, Pike RN. A major cathepsin B protease from the liver fluke Fasciola hepatica has atypical active site features and a potential role in the digestive tract of newly excysted juvenile parasites. Int J Biochem Cell Biol. (2009) 41:1601-12. pdf

Barbero S, Mielgo A, Torres V, Teitz T, Shields DJ, Mikolon D, Bogyo M, Barilà D, Lahti JM, Schlaepfer D, Stupack DG. Caspase-8 association with the focal adhesion complex promotes tumor cell migration and metastasis. Cancer Res. (2009) 69:3755-63. pdf

Cavallo-Medved D, Rudy D, Blum G, Bogyo M, Caglic D, Sloane BF. Live-cell imaging demonstrates extracellular matrix degradation in association with active cathepsin B in caveolae of endothelial cells during tube formation. Exp Cell Res. (2009) 315:1234-46. pdf

Obermajer N, Jevnikar Z, Doljak B, Sadaghiani AM, Bogyo M, Kos J. Cathepsin X-mediated beta2 integrin activation results in nanotube outgrowth. Cell Mol Life Sci. (2009) 66:1126-34. pdf

Pungercar JR, Caglic D, Sajid M, Dolinar M, Vasiljeva O, Pozgan U, Turk D, Bogyo M, Turk V, Turk B. Autocatalytic processing of procathepsin B is triggered by proenzyme activity. FEBS J. (2009) 276:660-8. pdf

Liz MA, Fleming CE, Nunes AF, Almeida MR, Mar FM, Choe Y, Craik CS, Powers JC, Bogyo M, Sousa MM. Substrate specificity of transthyretin: identification of natural substrates in the nervous system. Biochem J. (2009) Biochem J. 2009 Apr 15;419(2):467-74. pdf

Bogyo M. Metabolomics cuts to the chase to chase the cuts. Nat Chem Biol. (2009) 5:5-6. pdf

Fonovic M, Bogyo M. Activity-based probes as a tool for functional proteomic analysis of proteases. Expert Rev Proteomics. (2008) 5:721-30. pdf

Lupardus PJ, Shen A, Bogyo M, Garcia KC. Small molecule-induced allosteric activation of the Vibrio cholerae RTX cysteine protease domain. Science. (2008) 322:265-8. pdf Sup. Mat.

Shen A, Bogyo M. Friend or Foe? Turning a Host Defense Protein Into a Pathogen's Accomplice. Chem Biol.(2008) 15:879-80. pdf

Kaschani F, Verhelst SH, van Swieten PF, Verdoes M, Wong CS, Wang Z, Kaiser M, Overkleeft HS, Bogyo M, van der Hoorn RA. Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using 'click-chemistry' Plant J. (2008) 57:373-85. pdf

Schurigt U, Sevenich L, Vannier C, Gajda M, Schwinde A, Werner F, Stahl A, von Elverfeldt D, Becker AK, Bogyo M, Peters C, Reinheckel T. Trial of the cysteine cathepsin inhibitor JPM-OEt on early and advanced mammary cancer stages in the MMTV-PyMT-transgenic mouse model. Biol Chem. (2008) 389:1067-74. pdf

Obermajer N, Svajger U, Bogyo M, Jeras M, Kos J. Maturation of dendritic cells depends on proteolytic cleavage by cathepsin X. J Leukoc Biol. (2008) 84:1306-14. pdf

Jevnikar Z, Obermajer N, Bogyo M, Kos J. The role of cathepsin X in the migration and invasiveness of T lymphocytes. J Cell Sci. (2008) 121:2652-61. pdf

Yang Z, Fonovic M, Verhelst SH, Blum G and Bogyo M. Evaluation of alpha,beta-unsaturated ketone-based probes for papain-family cysteine proteases. Bioorg Med Chem. (2008) Mar 2. [Epub ahead of print]. pdf

Paulick MG and Bogyo M. Application of activity-based probes to the study of enzymes involved in cancer progression. Curr Opin Genet Dev. (2008) 18:97-106. pdf

Arastu-Kapur S, Ponder EL, Fonovic UP, Yeoh S, Yuan F, Fonovic M, Grainger M, Phillips CI, Powers JC, and Bogyo M. Identification of proteases that regulate erythrocyte rupture by the malaria parasite Plasmodium falciparum. Nature Chemical Biology (2008) 4:203-213. pdf. News and Views pdf

Ponder EL and Bogyo M. Ubiquitin-like modifiers and their deconjugating enzymes in medically important parasitic protozoa. Eukaryot Cell. (2007) 6:1943-1952. pdf

Goulet B, Sansregret L, Leduy L, Bogyo M, Weber E, Chauhan SS, Nepveu A. Increased expression and activity of nuclear cathepsin L in cancer cells suggests a novel mechanism of cell transformation. Mol Cancer Res. (2007) 5:899-907. pdf

Blum, G., von Degenfeld, G., Merchant, M.J., Blau, H.M., and Bogyo, M. Noinvasive optical imaging of cysteine protease activity using fluorescently quenched activity-based probes. (2007) Nature Chemical Biology. 3: 668-677. pdf

Fonovic M, Verhelst SH, Sorum MT, Bogyo M. Proteomic evaluation of chemically cleavable activity based probes. (2007) Mol Cell Proteomics. 6: 1761-1770. pdf

Bell-McGuinn KM, Garfall AL, Bogyo M, Hanahan D, Joyce JA. Inhibition of cysteine cathepsin protease activity enhances chemotherapy regimens by decreasing tumor growth and invasiveness in a mouse model of multistage cancer. (2007) Cancer Res. 67:7378-85. pdf

Burster T, Giffon T, Dahl ME, Bjorck P, Bogyo M, Weber E, Mahmood K, Lewis DB, Mellins ED. Influenza A virus elevates active cathepsin B in primary murine DC. (2007) Int Immunol. 19:645-55. pdf

Rose PP, Bogyo M, Moses AV, Fruh K. Insulin-like growth factor II receptor-mediated intracellular retention of cathepsin B is essential for transformation of endothelial cells by Kaposi's sarcoma-associated herpesvirus. (2007) J Virol. 81:8050-62. pdf

Sadaghiani, A.M.,.Verhelst, S.H.L., Gocheva, V., Hill, K., Majerova, E., Stinson, S. Joyce, J.A. and Bogyo, M. Design, synthesis and evaluation of in vivo potency and selectivity of epoxysuccinyl-based inhibitors of papain family cysteine proteases. (2007) Chem Biol 14:499-511. pdf

Sojka D, Hajdusek O, Dvorak J, Sajid M, Franta Z, Schneider EL, Craik CS, Vancova M, Buresova V, Bogyo M, Sexton KB, McKerrow JH, Caffrey CR, Kopacek P. IrAE - An asparaginyl endopeptidase (legumain) in the gut of the hard tick Ixodes ricinus. (2007) Int J Parasitol. 37:713-724.

Cuerrier D, Moldoveanu T, Campbell RL, Kelly J, Yoruk B, Verhelst SH, Greenbaum D, Bogyo M, Davies PL. Development of calpain-specific inactivators by screening of positional-scanning epoxide libraries. (2007) J Biol Chem. 282:9600-96011. pdf

Bogyo, M and Cravatt BF. Genomics and proteomics From genes to function: advances in applications of chemical and systems biology. (2007) Curr Opin Chem Biol. 11:1-3. pdf

Teo CF, Zhou XW, Bogyo, M, Carruthers VB. Cysteine protease inhibitors block Toxoplasma gondii microneme secretion and cell invasion. (2007) Antimicrob Agents Chemother. 51, 679-88. pdf

Verhelst, S.H.L., Fonovic, M. and Bogyo, M. A Mild Chemically Cleavable Linker System for Functional Proteomic Applications. (2007) Angew. Chemie. 46:1284-1286. pdf

Fonovic, M. and Bogyo, M. Activity Based Probes for Proteases: Applications to Biomarker Discovery, Molecular Imaging and Drug Screening. (2007) Current Pharmaceutical Design. 13:253-261 pdf

Sadaghiani, A.M., Verhelst, S.H.L., and Bogyo, M. Tagging and Detection Strategies for Activity-Based Proteomics. (2007) Cur Opin Chem. Bio. 11:20-28. pdf

Sexton, K.B., Witte, M.D., Blum, G., and Bogyo, M. Design of cell permeable, fluorescent activity based probes of the lysosomal cysteine protease asparaginyl endopeptidase (AEP)/legumain. (2007) Bioorg. Med. Chem. Let. 17:649-653. pdf

Sexton, K.B., Kato, D., Berger, A.B., Fonovic, M., Verhelst, S.H.L. and Bogyo, M. Specificity if aza-peptide electrophile activity based probes of caspases. (2007) Cell Death Differ 14:727-732. pdf

Berger, A.B., Sexton, K.B., and Bogyo, M. Commonly used caspase inhibitors designed based on substrate specificity profiles lack selectivity. (2006) Cell Research. 16:961-963. pdf

Sadaghiani, A. M.,Verhelst, S. H. L. and Bogyo, M. Solid-Phase Methods for the Preparation of Epoxysuccinate-Based Inhibitors of Cysteine Proteases. (2006) J. Comb. Chem. 8: 802-804. pdf Sup Mat

Pandey, K.C., Singh, N., Arastu-Kapur, S., Bogyo, M. and Rosenthal P.J. Falstatin, a Cysteine Protease Inhibitor of Plasmodium falciparum, Facilitates Erythrocyte Invasion. (2006) PloS Pathogens. 2: e117 pdf

Denault, J.-B., Bekes, M., Scott, F.L., Sexton, K.B., Bogyo, M. and Salvesen, G.S., Engineered hybrid dimers: tracking the activation pathway of caspase-7. (2006) Molecular Cell. 23:523-533. pdf

Berger, A.B., Witte, M.D., Denault, J.-B., Sadaghiani, A.M., Sexton, K.B., Salvesen, G.S. and Bogyo, M. Identification of early intermediates of caspase activation using selective inhibitors and activity-based probes . (2006) Molecular Cell. 23:509-521. pdf

Vasiljeva, O., Papazoglou, A., Kruger, A., Brodoefel, H., Korovin, M., Deussing, J., Augustin, N., Nielsen, B.S., Almholt, K., Bogyo, M., Peters, C. and Reinheckel, T. Tumor cell-derived and macrophage-derived cathepsin B promotes progression and lung metastasis of mammary cancer. (2006) Cancer Res. 66:5242-5250. pdf

Yuan, F., Verhelst,  S., Blum, G., Coussens, L. and Bogyo, M. A selective activity-based probe for the papain family cysteine protease dipeptidyl peptidase I/cathepsin C. (2006) J. Am. Chem. Soc. 128:5616-5617. pdf

Verhelst, S.H.L., Witte, M.D., Arastu-KApur, S., Fonovic M., and Bogyo, M. Novel aza peptide inhibitors and active site probes of papain family cysteine proteases. (2006) ChemBioChem, epub ahead of print. pdf

Pan Z, Jeffery DA, Chehade K, Beltman J, Clark JM, Grothaus P, Bogyo M, and Baruch A. Development of activity-based probes for trypsin-family serine proteases. (2006) Bioorg Med Chem Lett. 16:2882-2885. pdf

Choe Y., Leonetti F., Greenbaum D.C., Lecaille F., Bogyo M., Bromme D., Ellman J.A. andCraik C.S. Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique specificities.(2006) J Biol Chem. 281:12824-12832. pdf

Kato, D., Verhelst, S.H.L., Sexton, K.B. and Bogyo, M. A General Solid Phase Method for the Preparation of Diverse Azapeptide Probes Directed Against Cysteine Proteases. (2005) Organic Letters, 7:5649-5652.pdf

Blum, G., Mullins, S.R., Keren, K., Fonovic, M., Jedeszko, C., Rice, M.J., Sloane, B.F. and Bogyo, M. Dynamic imaging of protease activity with fluorescently quenched activity-based probes. (2005) Nature Chemical Biology, 1:203-209.pdf News and Views

Kato, D., Boatright, K.M., Berger, A.B., Nazif, T., Blum, G., Ryan, C., Chehade, K.A.H., Salvesen, G., and Bogyo, M. Activity based probes that target diverse cysteine protease families. (2005) Nature Chemical Biology 1:33-38. pdf  

Verhelst, S.H.L, and Bogyo, M. Dissecting protein function using chemical proteomic methods. (2005) QSAR 

Phillips, C.I., and Bogyo, M. Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. (2005) Cellular Microbiology 7(8):1061-76.  pdf

Verhelst S.H.L. and Bogyo, M. Solid-Phase Synthesis of Double-Headed Epoxysuccinyl Activity-Based Probes for Selective Targeting of Papain Family Cysteine Proteases. (2005) ChemBioChem 6(5):824-827.  pdf

Verhelst S.H.L. and Bogyo, M. Chemical proteomics applied to target identification and drug discovery. (2005) Biotechniques 38(2):175-7. pdf

Chehade, K.A.H., Baruch, A., Verhelst, S.H.L. and Bogyo, M. An improved preparation of the activity-based probe JPM-OEt and in situ applications. (2005) Synthesis 2: 240-244. pdf

Borodovsky, A., Ovaa. H., Meester, W.J., Venanzi, E.S., Bogyo, M., Hekking B.G., Ploegh, H.L., Kessler, B.M. and Overkleeft, H.S. Small-molecule inhibitors and probes for ubiquitin- and ubiquitin-like-specific proteases. (2005) Chembiochem 6(2):287-91. pdf

Berger, A.B., Vitorino, P.M., Bogyo, M. Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery. (2004) Am J Pharmacogenomics 4(6):371-81. pdf

Snipas, SJ, Wildfang E, Nazif T, Christensen L, Boatright KM, Bogyo M, Stennicke HR, Salvesen GS. Characteristics of the caspase-like catalytic domain of human paracaspase. (2004) Biol Chem 385(11):1093-8.  pdf

van der Hoorn RA, Leeuwenburgh MA, Bogyo M, Joosten MH, Peck SC. Activity profiling of papain-like cysteine proteases in plants. (2004) Plant Physiol 135(3):1170-8.  pdf

Oleksy A, Golonka E, Banbula A, Szmyd G, Moon J, Kubica M, Greenbaum D, Bogyo M, Foster TJ, Travis J, Potempa J. Growth phase-dependent production of a cell wall-associated elastinolytic cysteine proteinase by Staphylococcus epidermidis. (2004) Biol Chem 385(6):525-35.  pdf

Hook V, Yasothornsrikul S, Greenbaum D, Medzihradszky KF, Troutner K, Toneff T, Bundey R, Logrinova A, Reinheckel T, Peters C, Bogyo M. Cathepsin L and Arg/Lys aminopeptidase: a distinct prohormone processing pathway for the biosynthesis of peptide neurotransmitters and hormones. (2004) Biol Chem 385(6):473-80.  pdf

Eksi S, Czesny B, Greenbaum DC, Bogyo M, Williamson KC. Targeted disruption of Plasmodium falciparum cysteine protease, falcipain 1, reduces oocyst production, not erythrocytic stage growth. (2004) Mol Microbiol 53(1):243-50. pdf

Yasuda Y, Li Z, Greenbaum D, Bogyo M, Weber E, Bromme D. Cathepsin V, a novel and potent elastolytic activity expressed in activated macrophages. (2004) J Biol Chem 279(35):36761-70. pdf

Joyce JA, Baruch A, Chehade K, Meyer-Morse N, Giraudo E, Tsai FY, Greenbaum DC, Hager JH, Bogyo M, Hanahan D. Cathepsin cysteine proteases are effectors of invasive growth and angiogenesis during multistage tumorigenesis. (2004) Cancer Cell 5(5):443-53. pdf

Goulet B, Baruch A, Moon NS, Poirier M, Sansregret LL, Erickson A, Bogyo M, Nepveu A.  A cathepsin L isoform that is devoid of a signal peptide localizes to the nucleus in S phase and processes the CDP/Cux transcription factor. (2004) Mol Cell 14(2):207-19. Abstract pdf

Medzihradszky KF, Darula Z, Perlson E, Fainzilber M, Chalkley RJ, Ball H, Greenbaum D, Bogyo M, Tyson DR, Bradshaw RA, Burlingame AL. O-sulfonation of serine and threonine: mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes. (2004) Mol Cell Proteomics 3(5):429-40. Abstract pdf

Baruch A, Jeffery DA, Bogyo M. Enzyme activity--it's all about image. (2004) Trends Cell Biol 14(1):29-35. Abstract pdf

Li Z, Yasuda Y, Li W, Bogyo M, Katz N, Gordon RE, Fields GB, Bromme D. Regulation of collagenase activities of human cathepsins by glycosaminoglycans. (2004) J Biol Chem 279(7):5470-9. Abstract pdf

Sajid M, McKerrow JH, Hansell E, Mathieu MA, Lucas KD, Hsieh I, Greenbaum D, Bogyo M, Salter JP, Lim KC, Franklin C, Kim JH, Caffrey CR. Functional expression and characterization of Schistosoma mansoni cathepsin B and its trans-activation by an endogenous asparaginyl endopeptidase. (2003) Mol Biochem Parasitol 131(1):65-75. pdf

Yasothornsrikul S, Greenbaum D, Medzihradszky KF, Toneff T, Bundey R, Miller R, Schilling B, Petermann I, Dehnert J, Logvinova A, Goldsmith P, Neveu JM, Lane WS, Gibson B, Reinheckel T, Peters C, Bogyo M, Hook V. Cathepsin L in secretory vesicles functions as a prohormone-processing enzyme for production of the enkephalin peptide neurotransmitter. (2003) Proc Natl Acad Sci 100(16):9590-5. pdf

Rozman-Pungercar J, Kopitar-Jerala N, Bogyo M, Turk D, Vasiljeva O, Stefe I, Vandenabeele P, Bromme D, Puizdar V, Fonovic M, Trstenjak-Prebanda M, Dolenc I, Turk V, Turk B. Inhibition of papain-like cysteine proteases and legumain by caspase-specific inhibitors: when reaction mechanism is more important than specificity. (2003) Cell Death Differ 10(8):881-8. pdf

Wang CC, Bozdech Z, Liu CL, Shipway A, Backes BJ, Harris JL, Bogyo M Biochemical analysis of the 20S proteasome of Trypanosoma brucei. (2003) J Biol Chem 278(18):15800-8. pdf

Mikolajczyk J, Boatright KM, Stennicke HR, Nazif T, Potempa J, Bogyo M, Salvesen GS Sequential autolytic processing activates the zymogen of Arg-gingipain. (2003) J Biol Chem 278(12):10458-64. pdf

Kessler B, Hong X, Petrovic J, Borodovsky A, Dantuma NP, Bogyo M, Overkleeft HS, Ploegh H, Glas R Pathways accessory to proteasomal proteolysis are less efficient in major histocompatibility complex class I antigen production. (2003) J Biol Chem 278(12):10013-21. pdf

Jeffery DA, Bogyo M Chemical proteomics and its application to drug discovery. (2003) Curr OpinBiotechnol 14(1):87-95. pdf

Greenbaum DC, Baruch A, Grainger M, Bozdech Z, Medzihradszky KF, Engel J, DeRisi J, Holder AA, Bogyo M. A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. (2002) Science 298(5600):2002-6. pdf

Greenbaum DC, Arnold WD, Lu F, Hayrapetian L, Baruch A, Krumrine J, Toba S, Chehade K, Bromme D, Kuntz ID, Bogyo M. Small molecule affinity fingerprinting. A tool for enzyme family subclassification, target identification, and inhibitor design. (2002) Chem Biol 9(10):1085-94. pdf

Groll M, Nazif T, Huber R, Bogyo M. Probing structural determinants distal to the site of hydrolysis that control substrate specificity of the 20S proteasome. (2002) Chem Biol 9(5):655-62. pdf

Mathieu MA, Bogyo M, Caffrey CR, Choe Y, Lee J, Chapman H, Sajid M, Craik CS, McKerrow JH. Substrate specificity of schistosome versus human legumain determined by P1-P3 peptide libraries. (2002) Mol Biochem Parasitol 121(1):99-105. pdf

Bogyo M, Wang EW. Proteasome inhibitors: complex tools for a complex enzyme. (2002) Curr Top Microbiol Immunol 268:185-208. pdf

Greenbaum D, Baruch A, Hayrapetian L, Darula Z, Burlingame A, Medzihradszky KF, Bogyo M. Chemical approaches for functionally probing the proteome. (2002) Mol Cell Proteomics 1(1):60-8. pdf

Caffrey CR, Hansell E, Lucas KD, Brinen LS, Alvarez Hernandez A, Cheng J, Gwaltney SL 2nd, Roush WR, Stierhof YD, Bogyo M, Steverding D, McKerrow JH. Active site mapping, biochemical properties and subcellular localization of rhodesain, the major cysteine protease of Trypanosoma brucei rhodesiense. (2001) Mol Biochem Parasitol 118(1):61-73. pdf

Baruch A, Greenbaum D, Levy ET, Nielsen PA, Gilula NB, Kumar NM, Bogyo M. Defining a link between gap junction communication, proteolysis, and cataract formation. (2001) J Biol Chem 276(31):28999-9006. pdf

Li J, Gao X, Ortega J, Nazif T, Joss L, Bogyo M, Steven AC, Rechsteiner M. Lysine 188 substitutions convert the pattern of proteasome activation by REGgamma to that of REGs alpha and beta. (2001) EMBO J 20(13):3359-69. pdf

Nazif T and Bogyo M. Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors. (2001) Proc Natl Acad Sci 98(6):2967-72. pdf

Weihofen A, Lemberg MK, Ploegh HL, Bogyo M, Martoglio B. Release of signal peptide fragments into the cytosol requires cleavage in the transmembrane region by a protease activity that is specifically blocked by a novel cysteine protease inhibitor. (2000) J. Biol. Chem. 275(40):30951-6. pdf

Wang EW, Kessler BM, Borodovsky A, Cravatt BF, Bogyo M, Ploegh HL, Glas R. Integration of the ubiquitin-proteasome pathway with a cytosolic oligopeptidase activity. (2000) Proc Natl Acad Sci 97(18):9990-5. pdf

Greenbaum D, Medzihradszky KF, Burlingame A, Bogyo M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. (2000) Chem Biol 7(8):569-81. pdf

Caffrey CR, Mathieu MA, Gaffney AM, Salter JP, Sajid M, Lucas KD, Franklin C, Bogyo M, McKerrow JH. Identification of a cDNA encoding an active asparaginyl endopeptidase of Schistosoma mansoni and its expression in Pichia pastoris. (2000) FEBS Lett 466(2-3):244-8. pdf

Bogyo M, Verhelst S, Bellingard-Dubouchaud V, Toba S, Greenbaum D. Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs. (2000) Chem Biol 7(1):27-38. pdf supplemental materials

Schmidtke G, Holzhutter HG, Bogyo M, Kairies N, Groll M, de Giuli R, Emch S, Groettrup M. How an inhibitor of the HIV-I protease modulates proteasome activity. (1999) J Biol Chem 274(50):35734-40. pdf

Selzer PM, Pingel S, Hsieh I, Ugele B, Chan VJ, Engel JC, Bogyo M, Russell DG, Sakanari JA, McKerrow JH. Cysteine protease inhibitors as chemotherapy: lessons from a parasite target. (1999) Proc Natl Acad Sci 96(20):11015-22. pdf

Bogyo M, Ploegh HL. Antigen presentation. A protease draws first blood. (1998) Nature 396(6712):625-627. pdf

Bogyo M, Shin S, McMaster JS, Ploegh HL. Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes. (1998) Chem Biol 5(6):307-20. pdf

Glas R, Bogyo M, McMaster JS, Gaczynska M, Ploegh HL. A proteolytic system that compensates for loss of proteasome function. (1998) Nature 392(6676):618-22. pdf

Ruepp A, Eckerskorn C, Bogyo M, Baumeister W. Proteasome function is dispensable under normal but not under heat shock conditions in Thermoplasma acidophilum. (1998) FEBS Lett 425(1):87-90. pdf

Bogyo M, McMaster JS, Gaczynska M, Tortorella D, Goldberg AL, Ploegh HL. Covalent modification of the active site threonine of proteasomal beta subunits and the Escherichia coli homolog HslV by a new class of inhibitors. (1997) Proc Natl Acad Sci 94(13):6629-34. 9316392 pdf

Bogyo M, Gaczynska M, Ploegh HL. Proteasome inhibitors and antigen presentation. (1997) Biopolymers 94(13):6629-34. pdf

Wiertz EJ, Tortorella D, Bogyo M, Yu J, Mothes W, Jones TR, Rapoport TA, Ploegh HL. Sec61-mediated transfer of a membrane protein from the endoplasmic reticulum to the proteasome for destruction. (1996) Nature 384(6608):432-8. pdf

Wiertz EJ, Jones TR, Sun L, Bogyo M, Geuze HJ, Ploegh HL. The human cytomegalovirus US11 gene product dislocates MHC class I heavy chains from the endoplasmic reticulum to the cytosol. (1996) Cell 84(5):769-79. pdf

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