J Craig Venter Institute

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Founded in 1992, J. Craig Venter Institute is a not-for-profit research institute whose primary research interests are in structural, functional and comparative analysis of genomes and gene products from a wide variety of organisms

J Craig Venter Institute's Articles

J Craig Venter Institute's articles RSS

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Whole-genome characterization of common rotavirus strains circulating in Vellore, India from 2002 to 2017: emergence of non-classical genomic constellations

Authors: Shainey Alokit Khakha, Tintu Varghese, Sidhartha Giri, Alan Durbin, Gene S. Tan, Maheswari Kalaivanan, Jasmin Helan Prasad and Gagandeep Kang

Citation: Gut Pathogens 2023 15:44

Content type: Research Published on: 20 September 2023
Characteristics and genomic epidemiology of colistin-resistant Enterobacterales from farmers, swine, and hospitalized patients in Thailand, 2014–2017

Authors: Adhiratha Boonyasiri, Lauren M. Brinkac, Elita Jauneikaite, Richard C. White, Chris Greco, Chakkraphong Seenama, Teerawit Tangkoskul, Kevin Nguyen, Derrick E. Fouts and Visanu Thamlikitkul

Citation: BMC Infectious Diseases 2023 23:556

Content type: Research Published on: 28 August 2023
Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household

Authors: Jessica Chopyk, Ana Georgina Cobián Güemes, Claudia Ramirez-Sanchez, Hedieh Attai, Melissa Ly, Marcus B. Jones, Roland Liu, Chenyu Liu, Kun Yang, Xin M. Tu, Shira R. Abeles, Karen Nelson and David T. Pride

Citation: BMC Microbiology 2023 23:206

Content type: Research Published on: 2 August 2023
Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort

Authors: Shantelle Claassen-Weitz, Sugnet Gardner-Lubbe, Yao Xia, Kilaza S. Mwaikono, Stephanie Harris Mounaud, William C. Nierman, Lesley Workman, Heather J. Zar and Mark P. Nicol

Citation: Microbiome 2023 11:127

Content type: Research Published on: 5 June 2023
Major adverse cardiovascular events are associated with necroptosis during severe COVID-19

Authors: Rosana Wiscovitch-Russo, Elsa D. Ibáñez-Prada, Cristian C. Serrano-Mayorga, Benjamin L. Sievers, Maeve A. Engelbride, Surya Padmanabhan, Gene S. Tan, Sanjay Vashee, Ingrid G. Bustos, Carlos Pachecho, Lina Mendez, Peter H. Dube, Harinder Singh, Luis Felipe Reyes and Norberto Gonzalez-Juarbe

Citation: Critical Care 2023 27:155

Content type: Research Published on: 20 April 2023
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

Authors: Josh L. Espinoza and Chris L. Dupont

Citation: BMC Bioinformatics 2022 23:419

Content type: Research Published on: 12 October 2022
Evaluation of feasibility and user acceptance of lateral-flow self-testing for viral illness in a residential treatment rehabilitation facility

Authors: Benjamin L. Sievers, James Klotzle and Tipu V. Khan

Citation: Health & Justice 2022 10:10

Content type: Research Article Published on: 26 February 2022
Transcriptomics of type 2 diabetic and healthy human neutrophils

Authors: Sarah E. Kleinstein, Jamison McCorrison, Alaa Ahmed, Hatice Hasturk, Thomas E. Van Dyke and Marcelo Freire

Citation: BMC Immunology 2021 22:37

Content type: Research article Published on: 16 June 2021
Molecular epidemiology of Staphylococcus aureus in African children from rural and urban communities with atopic dermatitis

Authors: Gillian O. N. Ndhlovu, Regina E. Abotsi, Adebayo O. Shittu, Shima M. Abdulgader, Dorota Jamrozy, Christopher L. Dupont, Avumile Mankahla, Mark P. Nicol, Carol Hlela, Michael E. Levin, Nonhlanhla Lunjani and Felix S. Dube

Citation: BMC Infectious Diseases 2021 21:348

Content type: Research article Published on: 13 April 2021
Genomic and clinical characterisation of multidrug-resistant carbapenemase-producing ST231 and ST16 Klebsiella pneumoniae isolates colonising patients at Siriraj hospital, Bangkok, Thailand from 2015 to 2017

Authors: Adhiratha Boonyasiri, Elita Jauneikaite, Lauren M. Brinkac, Chris Greco, Kanokorn Lerdlamyong, Teerawit Tangkoskul, Kevin Nguyen, Visanu Thamlikitkul and Derrick E. Fouts

Citation: BMC Infectious Diseases 2021 21:142

Content type: Research article Published on: 4 February 2021
Differences in plasma proteomes for active tuberculosis, latent tuberculosis and non-tuberculosis mycobacterial lung disease patients with and without ESAT-6/CFP10 stimulation

Authors: Takele Teklu, Biniam Wondale, Biruhalem Taye, Milkessa Hailemariam, Shiferaw Bekele, Mesfin Tamirat, Aboma Zewude, Temesgen Mohamed, Girmay Medhin, Mengistu Legesse, Yanbao Yu, Gobena Ameni and Rembert Pieper

Citation: Proteome Science 2020 18:10

Content type: Research Published on: 31 October 2020
Molecular epidemiology of clinical Mycobacterium tuberculosis complex isolates in South Omo, Southern Ethiopia

Authors: Biniam Wondale, Kwon Keehwan, Girmay Medhin, Takele Teklu, Temesgen Mohammed, Samuel Tolosa, Aboma Zewude, Friehiwot Amsalu, Rembert Pieper and Gobena Ameni

Citation: BMC Infectious Diseases 2020 20:750

Content type: Research article Published on: 13 October 2020
Gapless assembly of maize chromosomes using long-read technologies

Authors: Jianing Liu, Arun S. Seetharam, Kapeel Chougule, Shujun Ou, Kyle W. Swentowsky, Jonathan I. Gent, Victor Llaca, Margaret R. Woodhouse, Nancy Manchanda, Gernot G. Presting, David A. Kudrna, Magdy Alabady, Candice N. Hirsch, Kevin A. Fengler, Doreen Ware, Todd P. Michael…

Citation: Genome Biology 2020 21:121

Content type: Short Report Published on: 20 May 2020
The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation

Authors: Camilla Urbaniak, Hernan Lorenzi, James Thissen, Crystal Jaing, Brian Crucian, Clarence Sams, Duane Pierson, Kasthuri Venkateswaran and Satish Mehta

Citation: Microbiome 2020 8:56

Content type: Research Published on: 20 April 2020
An unsupervised learning approach to identify novel signatures of health and disease from multimodal data

Authors: Ilan Shomorony, Elizabeth T. Cirulli, Lei Huang, Lori A. Napier, Robyn R. Heister, Michael Hicks, Isaac V. Cohen, Hung-Chun Yu, Christine Leon Swisher, Natalie M. Schenker-Ahmed, Weizhong Li, Karen E. Nelson, Pamila Brar, Andrew M. Kahn, Timothy D. Spector, C. Thomas Caskey…

Citation: Genome Medicine 2020 12:7

Content type: Research Published on: 10 January 2020
Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure

Authors: Yun Zhang, Gautam Bandyopadhyay, David J. Topham, Ann R. Falsey and Xing Qiu

Citation: BMC Bioinformatics 2019 20:185

Content type: Methodology article Published on: 15 April 2019
OMeta: an ontology-based, data-driven metadata tracking system

Authors: Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger Sutton, Derrick E. Fouts and Karen E. Nelson

Citation: BMC Bioinformatics 2019 20:8

Content type: Software Published on: 7 January 2019
Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers’ diarrhea

Authors: Qiyun Zhu, Christopher L. Dupont, Marcus B. Jones, Kevin M. Pham, Zhi-Dong Jiang, Herbert L. DuPont and Sarah K. Highlander

Citation: Microbiome 2018 6:201

Content type: Research Published on: 8 November 2018
Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

Authors: Alexandra R. Buckley, Trey Ideker, Hannah Carter, Olivier Harismendy and Nicholas J. Schork

Citation: Genome Medicine 2018 10:69

Content type: Research Published on: 14 September 2018
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes

Authors: Thomas H. Clarke, Lauren M. Brinkac, Jason M. Inman, Granger Sutton and Derrick E. Fouts

Citation: BMC Bioinformatics 2018 19:246

Content type: Software Published on: 27 June 2018

J Craig Venter Institute

J Craig Venter Institute's Articles

Whole-genome characterization of common rotavirus strains circulating in Vellore, India from 2002 to 2017: emergence of non-classical genomic constellations

Characteristics and genomic epidemiology of colistin-resistant Enterobacterales from farmers, swine, and hospitalized patients in Thailand, 2014–2017

Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household

Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort

Major adverse cardiovascular events are associated with necroptosis during severe COVID-19

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

Evaluation of feasibility and user acceptance of lateral-flow self-testing for viral illness in a residential treatment rehabilitation facility

Transcriptomics of type 2 diabetic and healthy human neutrophils

Molecular epidemiology of Staphylococcus aureus in African children from rural and urban communities with atopic dermatitis

Genomic and clinical characterisation of multidrug-resistant carbapenemase-producing ST231 and ST16 Klebsiella pneumoniae isolates colonising patients at Siriraj hospital, Bangkok, Thailand from 2015 to 2017

Differences in plasma proteomes for active tuberculosis, latent tuberculosis and non-tuberculosis mycobacterial lung disease patients with and without ESAT-6/CFP10 stimulation

Molecular epidemiology of clinical Mycobacterium tuberculosis complex isolates in South Omo, Southern Ethiopia

Gapless assembly of maize chromosomes using long-read technologies

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data

Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure

OMeta: an ontology-based, data-driven metadata tracking system

Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers’ diarrhea

Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes