2024
MINING HUMAN MICROBIOMES REVEALS AN UNTAPPED SOURCE OF PEPTIDE ANTIBIOTICS
Marcelo D. T. Torres, Erin F. Brooks, Angela Cesaro, Hila Sberro, Matthew O. Gill, Cosmos Nicolaou, Ami S. Bhatt, and Cesar de la Fuente-Nunez*
Cell, 2024, August 19
DEEP-LEARNING-ENABLED ANTIBIOTIC DISCOVERY THROUGH MOLECULAR DE-EXTINCTION
Fangping Wan, Marcelo D. T. Torres, Jacqueline Peng, and Cesar de la Fuente-Nunez*
Nature Biomedical Engineering, 2024, June 11
DISCOVERY OF ANTIMICROBIAL PEPTIDES IN THE GLOBAL MICROBIOME WITH MACHINE LEARNING
Celio D. Santos-Junior, Marcelo D. T. Torres, Yiqian Duan, Alvaro Rodriguez del Rio, Thomas S. B. Schmidt, Hui Chong, Anthony Fullam, Michael Kuhn, Chengkai Zhu, Amy Houseman, Jelena Somborski, Anna Vines, Xing-Ming Zhao, Peer Bork, Jaime Huerta-Cepas, Cesar de la Fuente-Nunez*, and Luis Pedro Coelho*
Cell, 2024, June 5
MACHINE LEARNING FOR ANTIMICROBIAL PEPTIDE IDENTIFICATION AND DESIGN
Fangping Wan, Felix Wong, James J. Collins*, and Cesar de la Fuente-Nunez*
Nature Reviews Bioengineering, 2024, February 26
2023
MOLECULAR HYBRIDIZATION STRATEGY FOR TUNING BIOACTIVE PEPTIDE FUNCTION
Cibele N. Pedron, Marcelo D. T. Torres, Cyntia S. Oliveira, Adriana F. Silva, Gislaine P. Andrade, Yiming Wan, Maria A. S. Pinhal, Giselle Cerchiaro, Pedro I. Silva Junior, Fernanda D. Silva, Ravi Radhakrishnan, Cesar de la Fuente-Nunez*, and Vani X. Oliveira Junior
Nature Communications Biology, 6, 1067, 2023, October 19
RAPID AND ACCURATE DETECTION OF HERPES SIMPLEX VIRUS TYPE 2 USING A LOW-COST ELECTROCHEMICAL BIOSENSOR
Lucas F. de Lima, André L. Ferreira, Sita Awasthi, Marcelo D. T. Torres, Harvey M. Friedman, Gary H. Cohen, William R. de Araujo, Cesar de la Fuente-Nunez*
Cell Reports Physical Sciences, 2023, August 23
A BACTERIAL CELLULOSE-BASED AND LOW-COST ELECTROCHEMICAL BIOSENSOR FOR ULTRASENSITIVE DETECTION OF SARS-COV-2
Lucas F. de Lima, André L. Ferreira, Ishani Ranjan, Ronald G. Colman, William R. de Araujo, Cesar de la Fuente-Nunez*
Cell Reports Physical Sciences, 2023, August 17
MOLECULAR DE-EXTINCTION OF ANCIENT ANTIMICROBIAL PEPTIDES ENABLED BY MACHINE LEARNING
Jacqueline R. M. A. Maasch, Marcelo D. T. Torres, Marcelo C. R. Melo, Cesar de la Fuente-Nunez*
Cell Host Microbe, 2023, July 28
STRUCTURE-FUNCTION-GUIDED DESIGN OF SYNTHETIC PEPTIDES WITH ANTI-INFECTIVE ACTIVITY DERIVED FROM WASP VENOM
Andreia Boaro, Lucía Ageitos, Marcelo D. T. Torres, Esther B. Blasco, Sebahat Oztekin, Cesar de la Fuente-Nunez*
Cell Reports Physical Science, 4, 7, 101459, 2023, July 19
LEVERAGING ARTIFICIAL INTELLIGENCE IN THE FIGHT AGAINST INFECTION DISEASES
Felix Wong, Cesar de la Fuente-Nunez*, James J. Collins*
Science, 381, 6654, 164-170, 2023, July 13
ADVANCED DELIVERY SYSTEMS FOR PEPTIDE ANTIBIOTICS
Angelica Cesaro, Shuangzhe Lin, Norbert Pardi, Cesar de la Fuente-Nunez*
Advanced Drug Delivery Reviews, 196, 114733, 2023, May 14
MINING FOR ANTIMICROBIAL PEPTIDES IN SEQUENCE SPACE
Fangping Wan & Cesar de la Fuente-Nunez*
Nature Biomedical Engineering, 7, 707-708, 2023, April 24
2022
MOLECULAR DE-EXTINCTION OF ANCIENT ANTIMICROBIAL PEPTIDES ENABLED BY MACHINE LEARNING
Jacqueline R. M. A. Maasch, Marcelo D. T. Torres, Marcelo C. R. Melo, Cesar de la Fuente-Nunez*
bioRxiv, 2022, November 15
MOLECULAR TOOLS FOR PROBING THE MICROBIOME
Marcelo D. T. Torres, Cesar de la Fuente-Nunez*
Current Opinion in Structural Biology, 2022, August 16
IMPACT OF NATURAL SELECTION ON GLOBAL PATTERNS OF GENETIC VARIATION AND ASSOCIATION WITH CLINICAL PHENOTYPES AT GENES INVOLVED IN SARS-COV-2 INFECTION
Chao Zhang, Anurag Verma, Yuanqing Feng, Marcelo C. R. Melo, Michael McQuillan, Matthew Hansen, Anastasia Lucas, Joseph Park, Alessia Ranciaro, Simon Thompson, Meagan A. Rubel, Michael C. Campbell, William Beggs, Jibril Hirbo, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Regeneron Genetic Center, Thomas Nyambo, Dawit Wolde Meskel, Gurja Belay, Charles Fokunang, Alfred K. Njamnshi, Sabah A. Omar, Scott M. Williams, Daniel J. Rader, Marylyn D. Ritchie, Cesar de la Fuente-Nunez, Giorgio Sirugo, and Sarah A. Tishkoff
PNAS, 2022, May 17
ANTIBIOTIC DISCOVERY WITH MACHINE LEARNING
Cesar de la Fuente-Nunez*
Nature Biotechnology, 2022, May 6
AUTONOMOUS TREATMENT OF BACTERIAL INFECTIONS IN VIVO USING ANTIMICROBIAL MICRO- AND NANOMOTORS
Xavier Arqué, Marcelo D. T. Torres, Tania Patiño, Andreia Boaro, Samuel Sánchez*, Cesar de la Fuente-Nunez*
ACS Nano, 2022, April 29
DEEP GENERATIVE MODELS FOR PEPTIDE DESIGN
Fangping Wan, Daphne Kontogiorgos-Heintz, Cesar de la Fuente-Nunez*
Digital Discovery, 2022, March 31
DETECTION OF SARS-COV-2 WITH RAPID: A PROSPECTIVE COHORT STUDY
Marcelo D.T. Torres, Lucas F. de Lima, André L. Ferreira, William R. de Araujo, Paul Callahan, Antonio Dávila, Benjamin S. Abella, Cesar de la Fuente-Nunez*
iScience, 2022, March 11
MACHINE LEARNING FOR DRUG DISCOVERY
Marcelo C.R. Melo, Jacqueline R.M.A. Maasch, Cesar de la Fuente-Nunez*
American Chemical Society, 2022, March 11
SYNTHETIC ANTIBIOTIC DERIVED FROM SEQUENCES ENCRYPTED IN A PROTEIN FROM HUMAN PLASMA
Angela Cesaro, Marcelo Der Torossian Torres, Rosa Gaglione, Eliana Dell'Olmo, Rocco Di Girolamo, Andrea Bosso, Elio Pizzo, Henk P. Haagsman, Edwin J. A. Veldhuizen, Cesar de la Fuente-Nunez*, and Angela Arciello
ACS Nano, 2022, Feb 3
2021
MINING FOR ENCRYPTED PEPTIDE ANTIBIOTICS IN THE HUMAN PROTEOME
Marcelo Der Torossian Torres, Marcelo C. R. Melo, Laurice Flowers, Orlando Crescenzi, Eugenio Notomista, Cesar de la Fuente-Nunez*
Nature Biomedical Engineering, 2021, Nov 4
LOW-COST OPTODIAGNOSTIC FOR MINUTE-TIME SCALE DETECTION OF SARS-COV-2
Andre Lopes Ferreira, Lucas Felipe de Lima, Marcelo Der Torossian Torres, William Reis de Araujo*, Cesar de la Fuente-Nunez*
ACS Nano, 2021, Oct 20
PROBIOTIC ENGINEERING STRATEGIES FOR THE HETEROLOGOUS PRODUCTION OF ANTIMICROBIAL PEPTIDES
Adriana Mejia-Pitta, Esther Broset, Cesar de la Fuente-Nunez*
Advanced Drug Delivery Reviews, 2021, 176:113863
ACCELERATING ANTIBIOTIC DISCOVERY THROUGH ARTIFICIAL INTELLIGENCE
Marcelo C. R. Melo, Jacqueline R. M. A. Maasch, Cesar de la Fuente-Nunez*
Communications Biology, 2021, 4(1):1050
MINUTE-SCALE DETECTION OF SARS-COV-2 USING A LOW-COST BIOSENSOR COMPOSED OF PENCIL GRAPHITE ELECTRODES
Lucas F. de Lima, André L. Ferreira, Marcelo D. T. Torres, William R. de Araujo, Cesar de la Fuente-Nunez*
PNAS, 2021, 118, 30, e2106724118
LOW-COST BIOSENSOR FOR RAPID DETECTION OF SARS-COV-2 AT POINT-OF-CARE
Marcelo D. T. Torres, William R. de Araujo, Lucas F. de Lima, André L. Ferreira, Cesar de la Fuente-Nunez*
Matter (Cell Press), 2021, 4, 7, 2403-2416
SYNTHETIC BIOLOGY AND COMPUTER-BASED FRAMEWORKS FOR ANTIMICROBIAL PEPTIDE DISCOVERY
Marcelo D. T. Torres, Jicong Cao, Octavio L. Franco, Timothy K. Lu, Cesar de la Fuente-Nunez*
ACS Nano, 2021, 15, 2, 2143-2164
COATABLE AND RESISTANCE-PROOF IONIC LIQUID FOR PATHOGEN ERADICATION
Marcelo D. T. Torres, Sahag Voskian, Paul Brown, Andong Liu, Timothy K. Lu, T. Alan Hatton, and Cesar de la Fuente-Nunez*
ACS Nano, 2021, 15, 1, 966-978
2020
LIGHT-EMITTING PROBES FOR LABELING PEPTIDES
Andreia Boaro, Lucia Ageitos, Marcelo Der Torossian Torres, Fernando H. Bartoloni, Cesar de la Fuente-Nunez*
Cell Reports Physical Science, 2020
REPURPOSING A PEPTIDE TOXIN FROM WASP VENOM INTO ANTIINFECTIVES WITH DUAL ANTIMICROBIAL AND IMMUNOMODULATORY PROPERTIES
Osmar N. Silva, Marcelo Der Torossian Torres, Jicong Cao, Eliane S. F. Alves, Leticia V. Rodrigues, Jarbas M. Resende, Luciano M. Liao, William F. Porto, Isabel C. M. Fensterseifer, Timothy K. Lu, Octavio L. Franco*, Cesar de la Fuente-Nunez*
PNAS, 2020, 117, 43, 26936-26945
THE VALUE OF ANTIMICROBIAL PEPTIDES IN THE AGE OF RESISTANCE
Maria Magana, Muthuirulan Pushpanatan, Ana L. Santos, Leon Leanse, Michael Fernandez, Anastasios Ionnidis, Marc A. Giulianotti, Yiorgos Apidianakis, Steven Bradfute, Andrew L. Ferguson, Artem Cherkasov, Mohamed N. Seleem, Clemencia Pinilla, Cesar de la Fuente-Nunez, Themis Lazaridis, Tianhong Dai, Richard A Houghten, Robert E. W. Hancock, Geroge P. Tegos
The Lancet Infectious Diseases, 2020
2019
REPROGRAMMING BIOLOGICAL PEPTIDES TO COMBAT INFECTIOUS DISEASES
Marcelo Der Torossian Torres and Cesar de la Fuente-Nunez*
Chemical Communications, 2019
EMERGING FRONTIERS IN MICROBIOME ENGINEERING
María Eugenia Inda, Esther Broset, Timothy K. Lu, Cesar de la Fuente-Nunez*
Trends in Immunology, 2019
ENGINEERING PHAGE HOST-RANGE AND SUPPRESSING BACTERIAL RESISTANCE THROUGH PHAGE TAIL FIBER MUTAGENESIS
Kevin Yehl, Sébastien Lemire, Andrew C. Yang, Hiroki Ando, Mark Mimee, Marcelo Der Torossian Torres, Cesar de la Fuente-Nunez, and Timothy K. Lu
Cell, 2019, 179, 2, 459-469
TOWARD COMPUTER-MADE ARTIFICIAL ANTIBIOTICS
Marcelo Der Torossian Torres and Cesar de la Fuente-Nunez*
Current Opinion in Microbiology, 2019, 51, 30-38
PEPTIDE DESIGN PRINCIPLES FOR ANTIMICROBIAL APPLICATIONS
Marcelo Der Torossian Torres, Shanmugapriya Sothiselvam, Timothy K. Lu, and Cesar de la Fuente-Nunez*
Journal of Molecular Biology, 2019
2018
STRUCTURE-FUNCTION-GUIDED EXPLORATION OF THE ANTIMICROBIAL PEPTIDE POLYBIA-CP IDENTIFIES ACTIVITY DETERMINANTS AND GENERATES SYNTHETIC THERAPEUTICS CANDIDATES
Marcelo Der Torossian Torres, Cibele N. Pedron, Yasutomi Higashikuni, Robin M. Kramer, Marlon H. Cardoso, Karen G. N. Oshiro, Octávio L. Franco, Pedro I. Silva Junior, Fernanda D. Silva, Vani X. Oliveira Junior*, Timothy K. Lu*, Cesar de la Fuente-Nunez*
Nature Communications Biology, 2018, 1, 221 (Editor's pick)
IDENTIFICATION OF NOVEL CRYPTIC MULTIFUNCTIONAL ANTIMICROBIAL PEPTIDES FROM THE HUMAN STOMACH ENABLED BY A COMPUTATIONAL–EXPERIMENTAL PLATFORM
Katia Pane, Valeria Cafaro, Angela Avitable, Marcelo Der Torossian Torres, Adriana Vollaro, Eliana De Gregorio, Maria Rosaria Catania, Antimo Di Maro, Andrea Bosso, Giovanni Gallo, Anna Zanfardino, Mario Varcamonti, Elio Pizzo, Alberto Di Donato, Thimothy K. Lu, Cesar de la Fuente-Nunez*, and Eugenio Notomista*
ACS Synthetic Biology, 2018, 7 (9), 2105–2115
IN SILICO OPTIMIZATION OF A GUAVA ANTIMICROBIAL PEPTIDE ENABLES COMBINATORIAL EXPLORATION FOR PEPTIDE DESIGN
William F. Porto, Luz Irazazabal, Eliane S. F. Alves, Suzana M. Ribeiro, Carolina O. Matos, Állan S. Pires, Isabel C. M. Fensterseifer, Vivian J. Miranda, Evan F. Haney, Vincent Humblot, Marcelo D. T. Torres, Robert E. W. Hancock, Luciano M. Liao, Ali Ladram, Timothy K. Lu, Cesar de la Fuente-Nunez*, and Octavio L. Franco*
Nature Communications, 2018, 9, 1490
VERSATILE AND ON-DEMAND BIOLOGICS CO-PRODUCTION IN YEAST
Jicong Cao, Pablo Perez-Pinera, Ky Lowenhaupt, Ming-Ru Wu, Oliver Purcell, Cesar de la Fuente-Nunez, and Timothy K. Lu
Nature Communications, 2018, 9, 77
YEAST-BASED SYNTHETIC BIOLOGY PLATFORM FOR ANTIMICROBIAL PEPTIDE PRODUCTION
Jicong Cao#, Cesar de la Fuente-Nunez#, Rui Wen Ou, Marcelo Der Torossian Torres, Santosh G. Pande, Anthony J. Sinskey, and Timothy K. Lu
ACS Synthetic Biology, 2018, 7 (3), 896–902
2017
3D PRINTING OF LIVING RESPONSIVE MATERIALS AND DEVICES
Xinyue Liu, Hyunwoo Yuk, Shaoting Lin, German Alberto, Parada Tzu‐Chieh Tang, Eléonore Tham, Cesar de la Fuente‐Nunez, Timothy K. Lu, and Xuanhe Zhao
Advanced Materials, 2017, 1704821
NEUROMICROBIOLOGY: HOW MICROBES INFLUENCE THE BRAIN
Cesar de la Fuente-Nunez*, Beatriz Torres Meneguetti, Octávio Luiz Franco, and Timothy K. Lu*
ACS Chemical Neuroscience, 2018, 9 (2), 141–150
NEXT-GENERATION PRECISION ANTIMICROBIALS: TOWARDS PERSONALIZED TREATMENT OF INFECTIOUS DISEASES
Cesar de la Fuente-Nunez*, Marcelo D. T. Torres, Francisco J. M. Mojica, and Timothy K. Lu*
Current Opinion in Microbiology, 2017, 37, 95-102
