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Chris Dupont is a professor in the Genomic Medicine, Environment & Sustainability, and Synthetic Biology groups at JCVI. His primary research focus is microbial physiology and the environmental and evolutionary influence on physiological variation. This involves work with model organisms in laboratory systems, domestication of wild microbes for model studies, and sequencing based profiling of microbial communities in a variety of environments, including organismal microbiomes. This includes metagenomic and metatranscriptomic studies of the microbiomes found in the human gut, respiratory pathways, skin, and oral surfaces.
Dr. Dupont is also working on applying synthetic biology and machine learning techniques to solve unique problems in big datasets associated with the human microbiome and the environment.
Dr. Dupont began his career at JCVI as a postdoctoral fellow. He received his PhD in oceanography from the Scripps Institution of Oceanography, as well as a bachelor's in natural resources and a master's of biological and environmental engineering from Cornell University.
Research Priorities
Systems biology of an emerging model photoautotrophic diatom
- Characterization and regulation of CO2 concentrating mechanisms
- Development of molecular tools for genome engineering
Genomics and physiology of marine microbes
- Bacteria and Archaea involved in nitrification
- Genomics of uncultivated heterotrophs
- Assembly-centric studies of oxygen minimum zones
Organism-organism and organism-environment interactions
- Systems biology of plant-cyanobacterial symbioses
- Gene coexpression network analyses of both simple and complex communities
- Coevolution of geochemistry and biological metal utilization
Publications
Stroke. 2024-10-01; 55.10: e266-e268.
Unveiling Molecular Diversity in Cerebral Thrombi via Spatial Transcriptomics
Walker M, Federico E, Espinoza JL, Dupont CL
PMID: 39206540
mBio. 2024-08-14; 15.8: e0003824.
Marine bacteria Alteromonas spp. require UDP-glucose-4-epimerase for aggregation and production of sticky exopolymer
Robertson JM, Garza EA, Stubbusch AKM, Dupont CL, Hwa T, Held NA
PMID: 38958440
Nucleic acids research. 2024-08-12; 52.14: e63.
Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing
Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL
PMID: 38909293
Frontiers in public health. 2024-08-09; 12.1399731.
Whole-genome sequencing-based genetic diversity, transmission dynamics, and drug-resistant mutations in Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
Chekesa B, Singh H, Gonzalez-Juarbe N, Vashee S, Wiscovitch-Russo R, Dupont CL, Girma M, Kerro O, Gumi B, Ameni G
PMID: 39185123
PloS one. 2024-07-25; 19.7: e0304060.
Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
Chekesa B, Singh H, Gonzalez-Juarbe N, Vashee S, Wiscovitch-Russo R, Dupont CL, Girma M, Kerro O, Gumi B, Ameni G
PMID: 39052555
PNAS nexus. 2024-04-01; 3.4: pgae126.
Host-microbiome associations in saliva predict COVID-19 severity
Alqedari H, Altabtbaei K, Espinoza JL, Bin-Hasan S, Alghounaim M, Alawady A, Altabtabae A, AlJamaan S, Devarajan S, AlShammari T, Ben Eid M, Matsuoka M, Jang H, Dupont CL, Freire M
PMID: 38617584
Science (New York, N.Y.). 2024-03-22; 383.6689: 1344-1349.
Efficient formation of single-copy human artificial chromosomes
Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE
PMID: 38513017
The ISME journal. 2024-01-08; 18.1:
Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron
Manck LE, Coale TH, Stephens BM, Forsch KO, Aluwihare LI, Dupont CL, Allen AE, Barbeau KA
PMID: 38624181
Environmental microbiology. 2023-12-01; 25.12: 2761-2775.
Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients
Bos RP, Kaul D, Zettler ER, Hoffman JM, Dupont CL, Amaral-Zettler LA, Mincer TJ
PMID: 37132662
ACS synthetic biology. 2023-11-17; 12.11: 3215-3228.
Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering
Garza EA, Bielinski VA, Espinoza JL, Orlandi K, Alfaro JR, Bolt TM, Beeri K, Weyman PD, Dupont CL
PMID: 37857380
Molecular biology and evolution. 2023-10-04; 40.10:
Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms
Walworth NG, Espinoza JL, Argyle PA, Hinners J, Levine NM, Doblin MA, Dupont CL, Collins S
PMID: 37874344
Cold Spring Harbor perspectives in biology. 2023-10-03;
Microbial Catalysis for CO2 Sequestration: A Geobiological Approach
Van Den Berghe M, Walworth NG, Dalvie NC, Dupont CL, Springer M, Andrews MG, Romaniello SJ, Hutchins DA, Montserrat F, Silver PA, Nealson KH
PMID: 37788887
Nature immunology. 2023-10-01; 24.10: 1616-1627.
SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)
Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ
PMID: 37667052
Nature immunology. 2023-10-01; 24.10: 1778.
Author Correction: SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)
Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ
PMID: 37723351
Nature communications. 2023-09-22; 14.1: 5918.
Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures
Badrane H, Cheng S, Dupont CL, Hao B, Driscoll E, Morder K, Liu G, Newbrough A, Fleres G, Kaul D, Espinoza JL, Clancy CJ, Nguyen MH
PMID: 37739935
PloS one. 2023-08-03; 18.8: e0289557.
Comparison of DNA concentration and bacterial pathogen PCR detection when using two DNA extraction kits for nasopharyngeal/oropharyngeal samples
Khan D, Thomas SA, Tientcheu PE, Suso SMS, Dupont C, Kwambana-Adams B, Mohammed NI, Nicol MP, Antonio M
PMID: 37535692
Cell reports. 2023-05-30; 42.5: 112494.
Competition between skin antimicrobial peptides and commensal bacteria in type 2 inflammation enables survival of S. aureus
Nakatsuji T, Brinton SL, Cavagnero KJ, O'Neill AM, Chen Y, Dokoshi T, Butcher AM, Osuoji OC, Shafiq F, Espinoza JL, Dupont CL, Hata TR, Gallo RL
PMID: 37167061
PNAS nexus. 2022-11-01; 1.5: pgac239.
Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries
Espinoza JL, Torralba M, Leong P, Saffery R, Bockmann M, Kuelbs C, Singh S, Hughes T, Craig JM, Nelson KE, Dupont CL
PMID: 36712365
BMC bioinformatics. 2022-10-12; 23.1: 419.
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
Espinoza JL, Dupont CL
PMID: 36224545
Proceedings of the National Academy of Sciences of the United States of America. 2022-09-13; 119.37: e2200014119.
Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean
Saunders JK, McIlvin MR, Dupont CL, Kaul D, Moran DM, Horner T, Laperriere SM, Webb EA, Bosak T, Santoro AE, Saito MA
PMID: 36067300
mBio. 2022-06-28; 13.3: e0070022.
A Silent Operon of Photorhabdus luminescens Encodes a Prodrug Mimic of GTP
Shahsavari N, Wang B, Imai Y, Mori M, Son S, Liang L, Böhringer N, Manuse S, Gates MF, Morrissette M, Corsetti R, Espinoza JL, Dupont CL, Laub MT, Lewis K
PMID: 35575547
Bioresource technology. 2022-05-01; 351.126936.
Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing
Gupta J, Rathour R, Dupont C, Mishra A, Shekhar Thakur I
PMID: 35247565
The ISME journal. 2022-02-01; 16.2: 358-369.
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean
Manck LE, Park J, Tully BJ, Poire AM, Bundy RM, Dupont CL, Barbeau KA
PMID: 34341506
EBioMedicine. 2021-11-01; 73.103644.
Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children
Nabwera HM, Espinoza JL, Worwui A, Betts M, Okoi C, Sesay AK, Bancroft R, Agbla SC, Jarju S, Bradbury RS, Colley M, Jallow AT, Liu J, Houpt ER, Prentice AM, Antonio M, Bernstein RM, Dupont CL, Kwambana-Adams BA
PMID: 34695658
Science advances. 2021-08-13; 7.33:
Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality
Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, Pereira LM, Vilela CLS, Rosado JG, Cardoso PM, Rosado PM, Assis JM, Duarte GAS, Perna G, Rosado AS, Macrae A, Dupont CL, Nelson KE, Sweet MJ, Voolstra CR, Peixoto RS
PMID: 34389536
BMC infectious diseases. 2021-04-13; 21.1: 348.
Molecular epidemiology of Staphylococcus aureus in African children from rural and urban communities with atopic dermatitis
Ndhlovu GON, Abotsi RE, Shittu AO, Abdulgader SM, Jamrozy D, Dupont CL, Mankahla A, Nicol MP, Hlela C, Levin ME, Lunjani N, Dube FS
PMID: 33849482
The ISME journal. 2021-04-01; 15.4: 1025-1039.
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions
Bayer B, Saito MA, McIlvin MR, Lücker S, Moran DM, Lankiewicz TS, Dupont CL, Santoro AE
PMID: 33230266
Nature biotechnology. 2021-04-01; 39.4: 521.
Author Correction: A genomic catalog of Earth's microbiomes
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
PMID: 33795890
Nature biotechnology. 2021-04-01; 39.4: 520.
Publisher Correction: A genomic catalog of Earth's microbiomes
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
PMID: 33208936
Nature biotechnology. 2021-04-01; 39.4: 499-509.
A genomic catalog of Earth's microbiomes
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
PMID: 33169036
PLoS computational biology. 2021-03-29; 17.3: e1008857.
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach
Espinoza JL, Dupont CL, O'Rourke A, Beyhan S, Morales P, Spoering A, Meyer KJ, Chan AP, Choi Y, Nierman WC, Lewis K, Nelson KE
PMID: 33780444
Nature microbiology. 2021-02-01; 6.2: 173-186.
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean
Cohen NR, McIlvin MR, Moran DM, Held NA, Saunders JK, Hawco NJ, Brosnahan M, Ditullio GR, Lamborg C, McCrow JP, Dupont CL, Allen AE, Saito MA
PMID: 33398100
Environmental research. 2021-01-01; 192.110277.
Genomic insights into waste valorized extracellular polymeric substances (EPS) produced by Bacillus sp. ISTL8
Gupta J, Rathour R, Dupont CL, Kaul D, Thakur IS
PMID: 33069701
Journal of proteome research. 2021-01-01; 20.1: 326-336.
Development of an Ocean Protein Portal for Interactive Discovery and Education
Saito MA, Saunders JK, Chagnon M, Gaylord DA, Shepherd A, Held NA, Dupont C, Symmonds N, York A, Charron M, Kinkade DB
PMID: 32897077
Microbial genomics. 2020-12-01; 6.12:
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients
Nguyen MH, Kaul D, Muto C, Cheng SJ, Richter RA, Bruno VM, Liu G, Beyhan S, Sundermann AJ, Mounaud S, Pasculle AW, Nierman WC, Driscoll E, Cumbie R, Clancy CJ, Dupont CL
PMID: 33245689
The ISME journal. 2020-12-01; 14.12: 3068-3078.
Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism
Stuart RK, Pederson ERA, Weyman PD, Weber PK, Rassmussen U, Dupont CL
PMID: 32814866
Science robotics. 2020-11-25; 5.48:
Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle
Breier JA, Jakuba MV, Saito MA, Dick GJ, Grim SL, Chan EW, McIlvin MR, Moran DM, Alanis BA, Allen AE, Dupont CL, Johnson R
PMID: 33239321
Journal of proteome research. 2020-11-06; 19.11: 4718-4729.
METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses
Saunders JK, Gaylord DA, Held NA, Symmonds N, Dupont C, Dupont CL, Shepherd A, Kinkade DB, Saito MA
PMID: 32897080
Current biology : CB. 2020-08-03; 30.15: 2951-2961.e5.
Reprogramming of Stem Cell Activity to Convert Thorns into Branches
Zhang F, Rossignol P, Huang T, Wang Y, May A, Dupont C, Orbovic V, Irish VF
PMID: 32559443
Environmental microbiology. 2020-08-01; 22.8: 3020-3038.
Applications of weighted association networks applied to compositional data in biology
Espinoza JL, Shah N, Singh S, Nelson KE, Dupont CL
PMID: 32436334
Nature communications. 2020-06-16; 11.1: 3132.
Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection
Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA
PMID: 32546784
Nature communications. 2020-05-21; 11.1: 2537.
Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection
Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Das S, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA
PMID: 32439901
Nature methods. 2020-05-01; 17.5: 481-494.
Genetic tool development in marine protists: emerging model organisms for experimental cell biology
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
PMID: 32251396
Nature methods. 2020-05-01; 17.5: 551.
Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology
Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J
PMID: 32296171
Cell reports. 2020-03-03; 30.9: 2923-2933.e7.
Interplay of Staphylococcal and Host Proteases Promotes Skin Barrier Disruption in Netherton Syndrome
Williams MR, Cau L, Wang Y, Kaul D, Sanford JA, Zaramela LS, Khalil S, Butcher AM, Zengler K, Horswill AR, Dupont CL, Hovnanian A, Gallo RL
PMID: 32130897
Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:
Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling
O'Rourke A, Beyhan S, Choi Y, Morales P, Chan AP, Espinoza JL, Dupont CL, Meyer KJ, Spoering A, Lewis K, Nierman WC, Nelson KE
PMID: 31907190
PloS one. 2020-02-19; 15.2: e0227152.
Genomic and phenotypic characterization of Burkholderia isolates from the potable water system of the International Space Station
O'Rourke A, Lee MD, Nierman WC, Everroad RC, Dupont CL
PMID: 32074104
Synthetic biology (Oxford, England). 2020-02-05; 5.1: ysaa001.
Universal loop assembly: open, efficient and cross-kingdom DNA fabrication
Pollak B, Matute T, Nuñez I, Cerda A, Lopez C, Vargas V, Kan A, Bielinski V, von Dassow P, Dupont CL, Federici F
PMID: 32161816
mSphere. 2020-01-29; 5.1:
Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation
Bartelme RP, Custer JM, Dupont CL, Espinoza JL, Torralba M, Khalili B, Carini P
PMID: 31996418
Nature communications. 2019-10-07; 10.1: 4552.
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO, Allen AE
PMID: 31591397
The New phytologist. 2019-05-01; 222.3: 1364-1379.
Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum
Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE
PMID: 30636322
Microbial ecology. 2019-01-01; 77.1: 87-95.
The Airplane Cabin Microbiome
Weiss H, Hertzberg VS, Dupont C, Espinoza JL, Levy S, Nelson K, Norris S, FlyHealthy Research Team
PMID: 29876609
mBio. 2018-11-27; 9.6:
Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease
Espinoza JL, Harkins DM, Torralba M, Gomez A, Highlander SK, Jones MB, Leong P, Saffery R, Bockmann M, Kuelbs C, Inman JM, Hughes T, Craig JM, Nelson KE, Dupont CL
PMID: 30482830
Molecular biology and evolution. 2018-05-01; 35.5: 1160-1175.
Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont
Warshan D, Liaimer A, Pederson E, Kim SY, Shapiro N, Woyke T, Altermark B, Pawlowski K, Weyman PD, Dupont CL, Rasmussen U
PMID: 29554291
Cell host & microbe. 2017-09-13; 22.3: 269-278.e3.
Host Genetic Control of the Oral Microbiome in Health and Disease
Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE
PMID: 28910633
Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 2017-09-05; 372.1728:
Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism
Matsuda Y, Hopkinson BM, Nakajima K, Dupont CL, Tsuji Y
PMID: 28717013
The Plant cell. 2017-08-01; 29.8: 2047-2070.
Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom
McCarthy JK, McCarthy JK, Smith SR, McCrow JP, Tan M, Zheng H, Beeri K, Roth RA, Roth R, Lichtle C, Lichtle C, Goodenough U, Bowler C, Bowler CP, Dupont CL, Dupont CL, Allen AE
PMID: 28765511
Journal of experimental botany. 2017-06-01; 68.14: 3937-3948.
The diversity of CO2-concentrating mechanisms in marine diatoms as inferred from their genetic content
Shen C, Dupont CL, Hopkinson BM
PMID: 28510761
PLoS genetics. 2017-03-29; 13.3: e1006688.
Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE
PMID: 28355217
The ISME journal. 2017-01-01; 11.1: 201-211.
Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly
Llorens-Marès T, Liu Z, Allen LZ, Rusch DB, Craig MT, Dupont CL, Bryant DA, Casamayor EO
PMID: 27392085
mSystems. 2017-01-01; 2.1:
Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels
Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K
PMID: 28217746
PLoS genetics. 2016-12-01; 12.12: e1006490.
Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Smith SR, Gillard JT, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE
PMID: 27973599
Frontiers in microbiology. 2016-07-06; 7.1043.
Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem
Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M
PMID: 27458440
The ISME journal. 2015-07-01; 9.7: 1648-61.
Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics
Llorens-Marès T, Yooseph S, Goll J, Hoffman J, Vila-Costa M, Borrego CM, Dupont CL, Casamayor EO
PMID: 25575307
The ISME journal. 2015-05-01; 9.5: 1076-92.
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities
Dupont CL, McCrow JP, Valas R, Moustafa A, Walworth N, Goodenough U, Roth R, Hogle SL, Bai J, Johnson ZI, Mann E, Palenik B, Barbeau KA, Venter JC, Allen AE
PMID: 25333462
Nature communications. 2015-04-21; 6.6925.
Designer diatom episomes delivered by bacterial conjugation
Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips AP, Noddings CM, Brunson JK, Valas RE, Deerinck TJ, Jablanovic J, Gillard JT, Beeri K, Ellisman MH, Glass JI, Hutchison CA, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD
PMID: 25897682
PloS one. 2014-02-27; 9.2: e89549.
Functional tradeoffs underpin salinity-driven divergence in microbial community composition
Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B
PMID: 24586863
Journal of biological engineering. 2013-12-10; 7.1: 30.
Assembly of eukaryotic algal chromosomes in yeast
Karas BJ, Molparia B, Jablanovic J, Hermann WJ, Lin YC, Dupont CL, Tagwerker C, Yonemoto IT, Noskov VN, Chuang RY, Allen AE, Glass JI, Hutchison CA, Smith HO, Venter JC, Weyman PD
PMID: 24325901
Proceedings of the National Academy of Sciences of the United States of America. 2013-06-25; 110.26: E2390-9.
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS
PMID: 23754396
The New phytologist. 2013-04-01; 198.2: 398-407.
Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
Konotchick T, Dupont CL, Valas RE, Badger JH, Allen AE
PMID: 23488966
Nucleic acids research. 2012-11-01; 40.20: 10375-83.
Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast
Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews-Pfannkoch C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA
PMID: 22941652
The ISME journal. 2012-06-01; 6.6: 1186-99.
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC
PMID: 22170421
Nature biotechnology. 2011-09-18; 29.10: 915-21.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS
PMID: 21926975
Proceedings of the National Academy of Sciences of the United States of America. 2011-03-08; 108.10: 3830-7.
Efficiency of the CO2-concentrating mechanism of diatoms
Hopkinson BM, Dupont CL, Allen AE, Morel FM
PMID: 21321195
Proceedings of the National Academy of Sciences of the United States of America. 2010-06-08; 107.23: 10567-72.
History of biological metal utilization inferred through phylogenomic analysis of protein structures
Dupont CL, Butcher A, Valas RE, Bourne PE, Caetano-Anollés G
PMID: 20498051
Applied and environmental microbiology. 2009-08-01; 75.15: 5047-57.
Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains
Stuart RK, Dupont CL, Johnson DA, Paulsen IT, Palenik B
PMID: 19502430
Environmental microbiology. 2009-06-01; 11.6: 1376-85.
The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi
Todd JD, Curson AR, Dupont CL, Nicholson P, Johnston AW
PMID: 19220400
Environmental microbiology. 2008-07-01; 10.7: 1831-43.
Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases
Dupont CL, Neupane K, Shearer J, Palenik B
PMID: 18412551
Applied and environmental microbiology. 2008-01-01; 74.1: 23-31.
Ni uptake and limitation in marine Synechococcus strains
Dupont CL, Barbeau K, Palenik B
PMID: 17951444
Proceedings of the National Academy of Sciences of the United States of America. 2007-05-01; 104.18: 7705-10.
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV
PMID: 17460045
Proceedings of the National Academy of Sciences of the United States of America. 2006-11-21; 103.47: 17822-7.
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry
Dupont CL, Yang S, Palenik B, Bourne PE
PMID: 17098870
Proceedings of the National Academy of Sciences of the United States of America. 2006-09-05; 103.36: 13555-9.
Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment
Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT
PMID: 16938853
02-Oct-2024
Press Release
J. Craig Venter Institute awarded 5-year, $5M grant to lead Center for Innovative Recycling and Circular Economy (CIRCLE)
CIRCLE is one of the six new NSF Global Centers focused on advancing bioeconomy research to solve global challenges
18-Apr-2024
Press Release
Groundbreaking study reveals oral microbiome’s role in immune response and COVID-19 severity
Newly developed AI model shows that saliva is a better predictor of COVID-19 severity than existing blood tests
21-Mar-2024
Press Release
Scientists develop method to efficiently construct single-copy human artificial chromosomes (HACs)
This new tool will allow scientists to work in mammalian systems in ways only previously available in bacteria and yeast
HACs have wide potential research applications to synthetic biologists and may eventually aid in delivering DNA in clinical applications
22-Feb-2024
Collaborator Release
New LongCOVID research launched by PolyBio’s global consortium of scientists
Funding will deepen research on the persistence of the SARS-CoV-2 virus in LongCOVID patients and launch new clinical trials
04-Sep-2023
Collaborator Release
PolyBio Research Foundation Consortium & colleagues publishes Nature position paper on SARS-CoV-2 reservoir in Long COVID/PASC
24-Mar-2023
Collaborator Release
What are the Drivers of Chronic Infectious Disease?
A $1 million grant from the Steven & Alexandra Cohen Foundation will launch a UC San Diego-led national effort to more deeply study tissue samples from patients with conditions ranging from long COVID-19 and relapsed Lyme disease to chronic fatigue syndrome
The Tissue Analysis Pipeline will be directed by scientists at UC San Diego and the J. Craig Venter Institute
08-Sep-2022
Reuters
Top scientists join forces to study leading theory behind long COVID
Several JCVI scientists will be contributing to the newly launched Long Covid Research Initiative — a collaboration of researchers, clinicians, and patients working to rapidly study and treat long Covid.
26-May-2020
Press Release
Maintaining a Healthy Upper Respiratory Tract Microbiome May Help Prevent Secondary Infections in Influenza A Patients
An influenza-impacted upper respiratory tract microbiome may invite opportunistic bacterial pathogens
26-Sep-2018
Blog
Ocean Microplastics Explained
24-May-2018
Collaborator Release
Researchers identify bacteria and viruses ejected from the ocean
Certain types of bacteria and viruses are readily ejected into the atmosphere when waves break while others less likely to be transported into the air
09-Nov-2015
Blog