Josh L Espinoza

ORCID

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 32

Top Venues

PNAS nexus

Science (New York, N.Y.)

bioRxiv : the preprint server for biology

Science advances

J. Craig Venter Institute

Durban University of Technology (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

J. Craig Venter Institute Jun 20 2016

United States

Bioinformatics Analyst :: Microbial Informatics

Education History

Durban University of Technology

South Africa

PHD :: Applied Sciences

University of California, Santa Cruz

United States

MSC :: Bioinformatics

San Diego State University Aug 23 2007 - Mar 03 2013

United States

BSC :: Cellular and Molecular Biology

Publications

Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath, Karen G Lloyd, Chris L Dupont
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. Nucleic acids research (2024)
Hend Alqaderi, Khaled Altabtbaei, Josh L Espinoza, Saadoun Bin Hasan, Mohammad Alghounaim, Abdullah Alawady, Abdullah Altabtabae, Sarah AlJamaan, Sriraman Devarajan, Tahreer AlShammari, Mohammed Ben Eid, Michele Matsuoka, Hyesun Jang, Christopher L Dupont, Marcelo O Freire
Host-microbiome associations in saliva predict COVID-19 severity. PNAS nexus 3 (4) (2024)
Hend Alqaderi, Khaled Altabtbaei, Josh L Espinoza, Saadoun Bin Hasan, Mohammad Alghounaim, Abdullah Alawady, Abdullah Altabtabae, Sarah AlJamaan, Sriraman Devarajan, Tahreer AlShammari, Mohammed Ben Eid, Michele Matsuoka, Hyesun Jang, Christopher L Dupont, Marcelo O Freire
Host-microbiome associations in saliva predict COVID-19 severity. PNAS nexus 3 (4) (2024)
Hend Alqaderi, Khaled Altabtbaei, Josh L Espinoza, Saadoun Bin Hasan, Mohammad Alghounaim, Abdullah Alawady, Abdullah Altabtabae, Sarah AlJamaan, Sriraman Devarajan, Tahreer AlShammari, Mohammed Ben Eid, Michele Matsuoka, Hyesun Jang, Christopher L Dupont, Marcelo O Freire
Host-microbiome associations in saliva predict COVID-19 severity. PNAS nexus 3 (4) (2024)
Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Christopher L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black
Efficient formation of single-copy human artificial chromosomes. Science (New York, N.Y.) 383 (6689) (2024)
Hend Alqaderi, Khaled Altabtbaei, Josh L Espinoza, Saadoun Bin Hasan, Mohammad Alghounaim, Abdullah Alawady, Abdullah Altabtabae, Sarah AlJamaan, Sriraman Devarajan, Tahreer AlShammari, Mohammed Ben Eid, Michele Matsuoka, Hyesun Jang, Christopher L Dupont, Marcelo O Freire
Host-microbiome associations in saliva predict COVID-19 severity. PNAS nexus 3 (4) (2024)
Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath, Karen G Lloyd, Chris L Dupont
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. Nucleic acids research 52 (14) (2024)
Isaac Josh Abecassis, Emma M Federico, Josh L Espinoza, Christopher L Dupont
Unveiling Molecular Diversity in Cerebral Thrombi via Spatial Transcriptomics. Stroke (2024)
Manish Kumar, Juan D Tibocha-Bonilla, Zoltan Fussy, Chloe Lieng, Sarah M Schwenck, Alice V Levesque, Mahmoud M Al-Bassam, Anurag Passi, Maxwell Neal, Cristal Zuñiga, Farrah Kaiyom, Josh L Espinoza, Hyun Gyu Lim, Shawn W Polson, Lisa Zeigler Allen, Karsten Zengler
Mixotrophic growth of a ubiquitous marine diatom. Science advances 10 (29) (2024)
Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Christopher L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black
Efficient formation of single-copy human artificial chromosomes. Science (New York, N.Y.) 383 (6689) (2024)
Hend Alqaderi, Khaled Altabtbaei, Josh L Espinoza, Saadoun Bin Hasan, Mohammad Alghounaim, Abdullah Alawady, Abdullah Altabtabae, Sarah AlJamaan, Sriraman Devarajan, Tahreer AlShammari, Mohammed Ben Eid, Michele Matsuoka, Hyesun Jang, Christopher L Dupont, Marcelo O Freire
Host-microbiome associations in saliva predict COVID-19 severity. PNAS nexus 3 (4) (2024)
Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath, Karen G Lloyd, Chris L Dupont
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. bioRxiv : the preprint server for biology (2024)
Manish Kumar, Juan D Tibocha-Bonilla, Zoltan Fussy, Chloe Lieng, Sarah M Schwenck, Alice V Levesque, Mahmoud M Al-Bassam, Anurag Passi, Maxwell Neal, Cristal Zuñiga, Farrah Kaiyom, Josh L Espinoza, Hyun Gyu Lim, Shawn W Polson, Lisa Zeigler Allen, Karsten Zengler
Mixotrophic growth of a ubiquitous marine diatom. Science advances 10 (29) (2024)
Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Christopher L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black
Efficient formation of single-copy human artificial chromosomes. Science (New York, N.Y.) 383 (6689) (2024)
Manish Kumar, Juan D Tibocha-Bonilla, Zoltan Fussy, Chloe Lieng, Sarah M Schwenck, Alice V Levesque, Mahmoud M Al-Bassam, Anurag Passi, Maxwell Neal, Cristal Zuñiga, Farrah Kaiyom, Josh L Espinoza, Hyun Gyu Lim, Shawn W Polson, Lisa Zeigler Allen, Karsten Zengler
Mixotrophic growth of a ubiquitous marine diatom. Science advances 10 (29) (2024)
Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Christopher L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black
Efficient formation of single-copy human artificial chromosomes. Science (New York, N.Y.) 383 (6689) (2024)
Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Christopher L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black
Efficient formation of single-copy human artificial chromosomes. Science (New York, N.Y.) 383 (6689) (2024)
Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath, Karen G Lloyd, Chris L Dupont
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. bioRxiv : the preprint server for biology (2024)
Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath, Karen G Lloyd, Chris L Dupont
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. Nucleic acids research (2024)
Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Christopher L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black
Efficient formation of single-copy human artificial chromosomes. Science (New York, N.Y.) 383 (6689) (2024)
Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Christopher L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black
Efficient formation of single-copy human artificial chromosomes. Science (New York, N.Y.) 383 (6689) (2024)
Hend Alqaderi, Khaled Altabtbaei, Josh L Espinoza, Saadoun Bin Hasan, Mohammad Alghounaim, Abdullah Alawady, Abdullah Altabtabae, Sarah AlJamaan, Sriraman Devarajan, Tahreer AlShammari, Mohammed Ben Eid, Michele Matsuoka, Hyesun Jang, Christopher L Dupont, Marcelo O Freire
Host-microbiome associations in saliva predict COVID-19 severity. PNAS nexus 3 (4) (2024)
Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath, Karen G Lloyd, Chris L Dupont
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. bioRxiv : the preprint server for biology (2024)
Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath, Karen G Lloyd, Chris L Dupont
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. Nucleic acids research 52 (14) (2024)
Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath, Karen G Lloyd, Chris L Dupont
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. bioRxiv : the preprint server for biology (2024)
Hend Alqaderi, Khaled Altabtbaei, Josh L Espinoza, Saadoun Bin Hasan, Mohammad Alghounaim, Abdullah Alawady, Abdullah Altabtabae, Sarah AlJamaan, Sriraman Devarajan, Tahreer AlShammari, Mohammed Ben Eid, Michele Matsuoka, Hyesun Jang, Christopher L Dupont, Marcelo O Freire
Host-Microbiome Associations in Saliva Predict COVID-19 Severity. bioRxiv : the preprint server for biology (2023)
Hend Alqaderi, Khaled Altabtbaei, Josh L Espinoza, Saadoun Bin Hasan, Mohammad Alghounaim, Abdullah Alawady, Abdullah Altabtabae, Sarah AlJamaan, Sriraman Devarajan, Tahreer AlShammari, Mohammed Ben Eid, Michele Matsuoka, Hyesun Jang, Christopher L Dupont, Marcelo O Freire
Host-Microbiome Associations in Saliva Predict COVID-19 Severity. bioRxiv : the preprint server for biology (2023)
Josh L Espinoza, Manolito Torralba, Pamela Leong, Richard Saffery, Michelle Bockmann, Claire Kuelbs, Suren Singh, Toby Hughes, Jeffrey M Craig, Karen E Nelson, Chris L Dupont
Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries. PNAS nexus 1 (5) (2022)
Josh L Espinoza, Manolito Torralba, Pamela Leong, Richard Saffery, Michelle Bockmann, Claire Kuelbs, Suren Singh, Toby Hughes, Jeffrey M Craig, Karen E Nelson, Chris L Dupont
Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries. PNAS nexus 1 (5) (2022)
Josh L Espinoza, Chris L Dupont, Aubrie O'Rourke, Sinem Beyhan, Pavel Morales, Amy Spoering, Kirsten J Meyer, Agnes P Chan, Yongwook Choi, William C Nierman, Kim Lewis, Karen E Nelson
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. PLoS computational biology 17 (3) (2021)
Erika P Santoro, Ricardo Moreira Borges, Josh L Espinoza, Marcelo O Freire, Camila S M A Messias, Helena D M Villela, Leandro de Mattos Pereira, Caren L S Vilela, João G Rosado, Pedro M Cardoso, Phillipe M Rosado, Juliana M Assis, Gustavo A S Duarte, Gabriela Perna, Alexandre Soares Rosado, Andrew Macrae, Christopher L Dupont, Karen E Nelson, Michael J Sweet, Christian R Voolstra, Raquel Silva Peixoto
Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Science advances 7 (33) (2021)
Josh L Espinoza, Naisha Shah, Suren Singh, Karen E Nelson, Christopher L Dupont
Applications of weighted association networks applied to compositional data in biology. Environmental microbiology 22 (8) (2020)

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Publication Activity (10 Years)

Top Topics

Top Venues

Josh L Espinoza