Christopher J Fields

2025

Fecal Microbiome and Metabolomic Profiles of Mixed-Fed Infants Are More Similar to Formula-Fed than Breastfed Infants

Wang, M., Valizadegan, N., Fields, C. J. & Donovan, S. M., Jan 2025, In: Microorganisms. 13, 1, 166.

Research output: Contribution to journal › Article › peer-review

Open Access

2024

A Gram-negative-selective antibiotic that spares the gut microbiome

Muñoz, K. A., Ulrich, R. J., Vasan, A. K., Sinclair, M., Wen, P.-C., Holmes, J. R., Lee, H. Y., Hung, C.-C., Fields, C. J., Tajkhorshid, E., Lau, G. W. & Hergenrother, P. J., Jun 13 2024, In: Nature. 630, 8016, p. 429-436 8 p.

Research output: Contribution to journal › Article › peer-review

Effects of yeast-enriched functionalized canola meal supplementation on apparent total tract macronutrient digestibility and fecal characteristics, fecal microbiota, and immune function of healthy adult dogs

De La Guardia-Hidrogo, V. M., Soto-Diaz, K., Rummell, L. M., Valizadegan, N., Fields, C. J., Steelman, A. J. & Swanson, K. S., 2024, In: Journal of animal science. 102, skae224.

Research output: Contribution to journal › Article › peer-review

Genome sequences of nine Clostridium scindens strains isolated from human feces

Fernandez-Materan, F. V., Olivos-Caicedo, K. Y., Daniel, S. L., Walden, K. K. O., Fields, C. J., Hernandez, A. G., Alves, J. M. P. & Ridlon, J. M., Nov 2024, In: Microbiology Resource Announcements. 13, 11, e00848-24.

Research output: Contribution to journal › Article › peer-review

Open Access

High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera)

Walden, K. K. O., Cao, Y., Fields, C. J., Hernandez, A. G., Rendon, G. A., Robinson, G. E., Skinner, R. K., Stein, J. A. & Dietrich, C. H., Nov 2024, In: Molecular ecology resources. 24, 8, e14010.

Research output: Contribution to journal › Article › peer-review

Open Access

Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

Farjo, M., Koelle, K., Martin, M. A., Gibson, L. L., Walden, K. K. O., Rendon, G., Fields, C. J., Alnaji, F. G., Gallagher, N., Luo, C. H., Mostafa, H. H., Manabe, Y. C., Pekosz, A., Smith, R. L., McManus, D. D. & Brooke, C. B., Jan 2024, In: Journal of virology. 98, 1

Research output: Contribution to journal › Article › peer-review

Open Access

2023

BOSC 2023, the 24th annual Bioinformatics Open Source Conference

Harris, N. L., Fields, C. J., Hokamp, K., Just, J., Khetani, R., Maia, J., Ménager, H., Munoz-Torres, M. C., Unni, D. & Williams, J., 2023, In: F1000Research. 12, 1568.

Research output: Contribution to journal › Editorial › peer-review

Open Access

First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing

Arora, D., Hernandez, A. G., Walden, K. K. O., Fields, C. J. & Yan, G., Apr 2023, In: International journal of molecular sciences. 24, 8, 7311.

Research output: Contribution to journal › Article › peer-review

Open Access

2022

Complete Genome Sequences of Three Staphylococcus haemolyticus Strains Isolated from the Lung of a TGFb1 Transgenic Mouse with Lung Fibrosis

Abdel-Hamid, A. M., D'Alessandro-Gabazza, C. N., Yasuma, T., Walden, K. K. O., Fields, C. J., Gabazza, E. C. & Cann, I., Apr 2022, In: Microbiology Resource Announcements. 11, 4

Research output: Contribution to journal › Article › peer-review

Open Access

Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

Ke, R., Martinez, P. P., Smith, R. L., Gibson, L. L., Mirza, A., Conte, M., Gallagher, N., Luo, C. H., Jarrett, J., Zhou, R., Conte, A., Liu, T., Farjo, M., Walden, K. K. O., Rendon, G., Fields, C. J., Wang, L., Fredrickson, R., Edmonson, D. C. & Baughman, M. E. & 19 others, Chiu, K. K., Choi, H., Scardina, K. R., Bradley, S., Gloss, S. L., Reinhart, C., Yedetore, J., Quicksall, J., Owens, A. N., Broach, J., Barton, B., Lazar, P., Heetderks, W. J., Robinson, M. L., Mostafa, H. H., Manabe, Y. C., Pekosz, A., McManus, D. D. & Brooke, C. B., May 2022, In: Nature Microbiology. 7, 5, p. 640-652 13 p.

Research output: Contribution to journal › Article › peer-review

Effects of a mildly cooked human-grade dog diet on gene expression, skin and coat health measures, and fecal microbiota of healthy adult dogs

Geary, E. L., Oba, P. M., Applegate, C. C., Clark, L. V., Fields, C. J. & Swanson, K. S., Oct 1 2022, In: Journal of animal science. 100, 10, skac265.

Research output: Contribution to journal › Article › peer-review

Open Access

Feeding Practice and Delivery Mode Are Determinants of Vitamin K in the Infant Gut: An Exploratory Analysis

Ellis, J. L., Wang, M., Fu, X., Fields, C. J., Donovan, S. M. & Booth, S. L., Mar 1 2022, In: Current Developments in Nutrition. 6, 3, nzac019.

Research output: Contribution to journal › Article › peer-review

Open Access

H3AGWAS: a portable workflow for genome wide association studies

Brandenburg, J. T., Clark, L., Botha, G., Panji, S., Baichoo, S., Fields, C. & Hazelhurst, S., Dec 2022, In: BMC bioinformatics. 23, 1, 498.

Research output: Contribution to journal › Article › peer-review

Open Access

Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution

Ke, R., Martinez, P. P., Smith, R. L., Gibson, L. L., Achenbach, C. J., McFall, S., Qi, C., Jacob, J., Dembele, E., Bundy, C., Simons, L. M., Ozer, E. A., Hultquist, J. F., Lorenzo-Redondo, R., Opdycke, A. K., Hawkins, C., Murphy, R. L., Mirza, A., Conte, M. & Gallagher, N. & 23 others, Luo, C. H., Jarrett, J., Conte, A., Zhou, R., Farjo, M., Rendon, G., Fields, C. J., Wang, L., Fredrickson, R., Baughman, M. E., Chiu, K. K., Choi, H., Scardina, K. R., Owens, A. N., Broach, J., Barton, B., Lazar, P., Robinson, M. L., Mostafa, H. H., Manabe, Y. C., Pekosz, A., McManus, D. D. & Brooke, C. B., Jul 2022, In: Open Forum Infectious Diseases. 9, 7, ofac192.

Research output: Contribution to journal › Article › peer-review

Open Access

Sulfate-reducing bacteria streamers and iron sulfides abruptly occlude porosity and increase hydraulic resistance in proppant-filled shale fractures

Fouke, B. W., Bhattacharjee, A. S., Fried, G. A., Sivaguru, M., Sanford, R. A., Zhou, L., Alcalde, R. E., Wunch, K., Stephenson, A., Ferrar, J. A., Hernandez, A. G., Wright, C., Fields, C. J., Todorov, L. G., Fouke, K. W., Bailey, C. M. & Werth, C. J., Jan 1 2022, In: AAPG Bulletin. 106, 1, p. 179-208 30 p.

Research output: Contribution to journal › Article › peer-review

2021

BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference

Harris, N. L., Cock, P. J. A., Fields, C. J., Hokamp, K., Maia, J., Munoz-Torres, M., Sharan, M. & Williams, J., 2021, In: F1000Research. 10, 1054.

Research output: Contribution to journal › Editorial › peer-review

Open Access

Children Tooth Brushing Behavior and Oral Microbiota: A Pilot Study

Calderon, S. J., Chung, S. Y., Fields, C. J. & Mortimer, N. T., May 2021, In: Oral. 1, 2, p. 112-121 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

In vivo competitions between fibrobacter succinogenes, ruminococcus flavefaciens, and ruminoccus albus in a gnotobiotic sheep model revealed by multi-omic analyses

Yeoman, C. J., Fields, C. J., Lepercq, P., Ruiz, P., Forano, E., White, B. A. & Mosoni, P., 2021, In: mBio. 12, 2, p. 1-16 16 p., e03533-20.

Research output: Contribution to journal › Article › peer-review

Open Access

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

Saw, J. J., Sivaguru, M., Wilson, E. M., Dong, Y., Sanford, R. A., Fields, C. J., Cregger, M. A., Merkel, A. C., Bruce, W. J., Weber, J. R., Lieske, J. C., Krambeck, A. E., Rivera, M. E., Large, T., Lange, D., Bhattacharjee, A. S., Romero, M. F., Chia, N. & Fouke, B. W., Feb 1 2021, In: Kidney360. 2, 2, p. 298-311 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Pursuing Advances in DNA Sequencing Technology to Solve a Complex Genomic Jigsaw Puzzle: The Agglutinin-Like Sequence (ALS) Genes of Candida tropicalis

Oh, S. H., Isenhower, A., Rodriguez-Bobadilla, R., Smith, B., Jones, J., Hubka, V., Fields, C., Hernandez, A. & Hoyer, L. L., Jan 20 2021, In: Frontiers in Microbiology. 11, 594531.

Research output: Contribution to journal › Article › peer-review

Open Access

Subacute exposure to an environmentally relevant dose of di-(2-ethylhexyl) phthalate during gestation alters the cecal microbiome, but not pregnancy outcomes in mice

Chiu, K., Bashir, S. T., Gao, L., Gutierrez, J., de Godoy, M. R. C., Drnevich, J., Fields, C. J., Cann, I., Flaws, J. A. & Nowak, R. A., Sep 2021, In: Toxics. 9, 9, 215.

Research output: Contribution to journal › Article › peer-review

Open Access

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa

Ras, V., Botha, G., Aron, S., Lennard, K., Allali, I., Weitz, S. C., Mwaikono, K. S., Kennedy, D., Holmes, J. R., Rendon, G., Panji, S., Fields, C. J. & Mulder, N., Feb 25 2021, In: PLoS computational biology. 17, 2, e1008640.

Research output: Contribution to journal › Article › peer-review

Open Access

Using Genomics to Shape the Definition of the Agglutinin-Like Sequence (ALS) Family in the Saccharomycetales

Oh, S. H., Schliep, K., Isenhower, A., Rodriguez-Bobadilla, R., Vuong, V. M., Fields, C. J., Hernandez, A. G. & Hoyer, L. L., Dec 14 2021, In: Frontiers in Cellular and Infection Microbiology. 11, 794529.

Research output: Contribution to journal › Article › peer-review

Open Access

2020

Acute PFOA exposure promotes epigenomic alterations in mouse kidney tissues

Rashid, F., Ramakrishnan, A., Fields, C. & Irudayaraj, J., 2020, In: Toxicology Reports. 7, p. 125-132 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis

D’alessandro-gabazza, C. N., Kobayashi, T., Yasuma, T., Toda, M., Kim, H., Fujimoto, H., Hataji, O., Takeshita, A., Nishihama, K., Okano, T., Okano, Y., Nishii, Y., Tomaru, A., Fujiwara, K., D’alessandro, V. F., Abdel-hamid, A. M., Ren, Y., Pereira, G. V., Wright, C. L. & Hernandez, A. & 15 others, Fields, C. J., Yau, P. M., Wang, S., Mizoguchi, A., Fukumura, M., Ohtsuka, J., Nosaka, T., Kataoka, K., Kondoh, Y., Wu, J., Kawagishi, H., Yano, Y., Mackie, R. I., Cann, I. & Gabazza, E. C., Dec 1 2020, In: Nature Communications. 11, 1, 1539.

Research output: Contribution to journal › Article › peer-review

Open Access

DNA punch cards for storing data on native DNA sequences via enzymatic nicking

Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J. P., Soloveichik, D., Zhao, H. & Milenkovic, O., Dec 1 2020, In: Nature communications. 11, 1, 1742.

Research output: Contribution to journal › Article › peer-review

Open Access

Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest

Soybean aphid research community, May 2020, In: Insect Biochemistry and Molecular Biology. 120, 103334.

Research output: Contribution to journal › Article › peer-review

Open Access

The 21st annual Bioinformatics Open Source Conference (BOSC 2020, part of BCC2020)

Harris, N. L., Cock, P. J. A., Fields, C. J., Hokamp, K., Maia, J., Munoz-Torres, M., Taschuk, M. & Yehudi, Y., 2020, In: F1000Research. 9, 1160.

Research output: Contribution to journal › Editorial

Open Access

The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice

Ridlon, J. M., Devendran, S., Alves, J. M., Doden, H., Wolf, P. G., Pereira, G. V., Ly, L., Volland, A., Takei, H., Nittono, H., Murai, T., Kurosawa, T., Chlipala, G. E., Green, S. J., Hernandez, A. G., Fields, C. J., Wright, C. L., Kakiyama, G., Cann, I. & Kashyap, P. & 2 others, McCracken, V. & Gaskins, H. R., May 3 2020, In: Gut Microbes. 11, 3, p. 381-404 24 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2019

Agglutinin-Like Sequence (ALS) Genes in the Candida parapsilosis Species Complex: Blurring the Boundaries Between Gene Families That Encode Cell-Wall Proteins

Oh, S.-H., Smith, B., Miller, A. N., Staker, B., Fields, C., Hernandez, A. & Hoyer, L. L., 2019, In: Frontiers in Microbiology. 10, 781.

Research output: Contribution to journal › Article › peer-review

BOSC 2019, the 20th annual Bioinformatics Open Source Conference

Harris, N. L., Cock, P. J. A., Fields, C. J., Greshake Tzovaras, B., Heuer, M., Hokamp, K., Munoz-Torres, M., Peltzer, A., Rieck, B., Wiencko, H. & Yehudi, Y., 2019, In: F1000Research. 8, 2132.

Research output: Contribution to journal › Editorial › peer-review

Open Access

Clostridium scindens ATCC 35704: Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids

Devendran, S., Shrestha, R., Alves, J. M. P., Wolf, P. G., Ly, L., Hernandez, A. G., Méndez-García, C., Inboden, A., Wiley, J., Paul, O., Allen, A., Springer, E., Wright, C. L., Fields, C. J., Daniel, S. L. & Ridlon, J. M., Apr 1 2019, In: Applied and environmental microbiology. 85, 7, e00052-19.

Research output: Contribution to journal › Article › peer-review

Open Access

Exercise and the Gut Microbiome: A Review of the Evidence, Potential Mechanisms, and Implications for Human Health

Mailing, L. J., Allen, J. M., Buford, T. W., Fields, C. J. & Woods, J. A., Apr 1 2019, In: Exercise and Sport Sciences Reviews. 47, 2, p. 75-85 11 p.

Research output: Contribution to journal › Review article › peer-review

Open Access

Host species and site of collection shape the microbiota of rift valley fever vectors in Kenya

Tchouassi, D. P., Muturi, E. J., Arum, S. O., Kim, C. H., Fields, C. J. & Torto, B., Jun 2019, In: PLoS neglected tropical diseases. 13, 6, e0007361.

Research output: Contribution to journal › Article › peer-review

Open Access

Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats

Dong, Y., Sanford, R. A., Inskeep, W. P., Srivastava, V., Bulone, V., Fields, C. J., Yau, P. M., Sivaguru, M., Ahrén, D., Fouke, K. W., Weber, J., Werth, C. R., Cann, I. K., Keating, K. M., Khetani, R. S., Hernandez, A. G., Wright, C., Band, M., Imai, B. S. & Fried, G. A. & 1 others, Fouke, B. W., Dec 2019, In: Astrobiology. 19, 12, p. 1442-1458 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Sequencing framework for the sensitive detection and precise mapping of defective interfering particle-associated deletions across influenza A and B viruses

Alnaji, F. G., Holmes, J. R., Rendon, G., Cristobal Vera, J., Fields, C. J., Martin, B. E. & Brooke, C. B., 2019, In: Journal of virology. 93, 11, e0035419.

Research output: Contribution to journal › Article › peer-review

Open Access

Sharing programming resources between bio* projects

Bonnal, R. J. P., Yates, A., Goto, N., Gautier, L., Willis, S., Fields, C., Katayama, T. & Prins, P., 2019, Methods in Molecular Biology. Humana Press Inc., p. 747-766 20 p. (Methods in Molecular Biology; vol. 1910).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

2018

Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243^T

Harris, S. C., Devendran, S., Méndez- García, C., Mythen, S. M., Wright, C. L., Fields, C. J., Hernandez, A. G., Cann, I., Hylemon, P. B. & Ridlon, J. M., Nov 2 2018, In: Gut Microbes. 9, 6, p. 523-539 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Defense against territorial intrusion is associated with DNA methylation changes in the honey bee brain

Herb, B. R., Shook, M. S., Fields, C. J. & Robinson, G. E., Mar 26 2018, In: BMC genomics. 19, 1, 216.

Research output: Contribution to journal › Article › peer-review

Open Access

Genome sequence of the soybean cyst nematode (Heterodera glycines) endosymbiont "Candidatus Cardinium hertigii" strain cHgTN10

Showmaker, K. C., Walden, K. K. O., Fields, C. J., Lambert, K. N. & Hudson, M. E., Jun 1 2018, In: Genome Announcements. 6, 26, e00624-18.

Research output: Contribution to journal › Article › peer-review

Open Access

Mosquito microbiota cluster by host sampling location

Muturi, E. J., Lagos-Kutz, D., Dunlap, C., Ramirez, J. L., Rooney, A. P., Hartman, G. L., Fields, C. J., Rendon, G. & Kim, C. H., Aug 14 2018, In: Parasites and Vectors. 11, 1, 468.

Research output: Contribution to journal › Article › peer-review

Open Access

The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018)

Harris, N. L., Wiencko, H., Chapman, B., Cock, P. J. A., Hokamp, K., Lapp, H., Fields, C. & Greshake Tzovaras, B., 2018, In: F1000Research. 7

Research output: Contribution to journal › Article › peer-review

Open Access

2017

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Sun, J., Zhang, Y., Xu, T., Zhang, Y., Mu, H., Zhang, Y., Lan, Y., Fields, C. J., Hui, J. H. L., Zhang, W., Li, R., Nong, W., Cheung, F. K. M., Qiu, J. W. & Qian, P. Y., Apr 3 2017, In: Nature Ecology and Evolution. 1, 5, 0121.

Research output: Contribution to journal › Article › peer-review

Open Access

A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee

Avalos, A., Pan, H., Li, C., Acevedo-Gonzalez, J. P., Rendon, G., Fields, C. J., Brown, P. J., Giray, T., Robinson, G. E., Hudson, M. E. & Zhang, G., Dec 1 2017, In: Nature communications. 8, 1, 1550.

Research output: Contribution to journal › Article › peer-review

Open Access

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

Jongeneel, C. V., Achinike-Oduaran, O., Adebiyi, E., Adebiyi, M., Adeyemi, S., Akanle, B., Aron, S., Ashano, E., Bendou, H., Botha, G., Chimusa, E., Choudhury, A., Donthu, R., Drnevich, J., Falola, O., Fields, C. J., Hazelhurst, S., Hendry, L., Isewon, I. & Khetani, R. S. & 20 others, Kumuthini, J., Kimuda, M. P., Magosi, L., Mainzer, L. S., Maslamoney, S., Mbiyavanga, M., Meintjes, A., Mugutso, D., Mpangase, P., Munthali, R., Nembaware, V., Ndhlovu, A., Odia, T., Okafor, A., Oladipo, O., Panji, S., Pillay, V., Rendon, G., Sengupta, D. & Mulder, N., Jun 2017, In: PLoS computational biology. 13, 6, e1005419.

Research output: Contribution to journal › Article › peer-review

Open Access

Effect of pesticides on microbial communities in container aquatic habitats

Muturi, E. J., Donthu, R. K., Fields, C. J., Moise, I. K. & Kim, C. H., Mar 16 2017, In: Scientific reports. 7, 44565.

Research output: Contribution to journal › Article › peer-review

Open Access

Whole genome comparative analysis of four Georgian grape cultivars

Tabidze, V., Pipia, I., Gogniashvili, M., Kunelauri, N., Ujmajuridze, L., Pirtskhalava, M., Vishnepolsky, B., Hernandez, A. G., Fields, C. J. & Beridze, T., Dec 1 2017, In: Molecular Genetics and Genomics. 292, 6, p. 1377-1389 13 p.

Research output: Contribution to journal › Article › peer-review

2016

Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Hirsch, C. N., Hirsch, C. D., Brohammer, A. B., Bowman, M. J., Soifer, I., Barad, O., Shem-Tov, D., Baruch, K., Lu, F., Hernandez, A. G., Fields, C. J., Wright, C. L., Koehler, K., Springer, N. M., Buckler, E., Buell, C. R., de Leon, N., Kaeppler, S. M., Childs, K. L. & Mikel, M. A., Nov 2016, In: Plant Cell. 28, 11, p. 2700-2714 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

The H3ABioNet Consortium, Feb 2016, In: Genome Research. 26, 2, p. 271-277 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

Harris, N. L., Cock, P. J. A., Lapp, H., Chapman, B., Davey, R., Fields, C., Hokamp, K. & Munoz-Torres, M., Feb 2016, In: PLoS computational biology. 12, 2, e1004691.

Research output: Contribution to journal › Article › peer-review

Open Access

Christopher J Fields

Research output

Search results