Publications

Selected Published Peer-Reviewed Articles:

2021 Ivanova M, Oh B, Khan IUH, Nightingale K, Bugarel M, Brown AMV, Loneragan GH. Draft genome assemblies of two Campylobacter novaezeelandiae and gour unclassified thermophilic Campylobacter isolates from Canadian agricultural surface water. Microbiology Resource Announcements 10(17): e00249-21.

2021 Aghdam SA, Brown AMV. Deep learning approaches for natural product discovery from plant endophytic microbiomes. Environmental Microbiome 16:6.

2021 Kaitlyn N. Myers, Daniel Conn, Brown AMV  Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont’s Role in a Global Virus-Vectoring Pest mSystems 6: e01048-20.

2019 SK. Wasala, Brown AMV, Jiwon Kang, Howe DK, Peetz AB, Zasada IA, Denver DR Variable Abundance and Distribution of Wolbachia and Cardinium Endosymbionts in Plant-Parasitic Nematode Field Populations. Frontiers in Microbiology 10:964.

2018 Howe DK, Smith M, Tom D, Brown AMV, Peetz AB, Zasada IA, Denver DR Analysis of nematode-endosymbiont coevolution in the Xiphinema americanum species complex using molecular markers of variable evolutionary rates. Nematology 21(5): 533–546.

2018 Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR Comparative genomics of WolbachiaCardinium dual endosymbiosis in a plant-parasitic nematode. Frontiers in Microbiology 9:2482.

2018 Brown AMV Endosymbionts of plant-parasitic nematodes. Annual Review of Phytopathology 56:225-242

2017 Phillips WS, Howe DK, Brown AMV, Eves-van Den Akker S, Dettwyler L, Peetz AB, Denver DR, Zasada IA. The draft genome of Globodera ellingtonae. Journal of Nematology 42(2):127-128 PMC5507130

2016 Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR. Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts. Scientific Reports 6: 34955.

2016 Phillips WS, Brown AMV, Howe DK, Peetz AB, Blok VC, Denver DR, Zasada IA. The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers. BMC Genomics 17:706.

2016 Denver DR, Brown AMV, Howe DK, Peetz AB, Zasada IA Genome skimming: a rapid approach to gaining diverse biological insights into multicellular pathogens. PLoS Pathogens 12(8): e1005713.

2015 Brown AMV, Howe DK, Peetz AB, Wasala SK, Zasada IA, Denver DR. Comparative genomics of an endosymbiont in a plant-parasitic nematode suggest a role in nutritional symbiosis. Genome Biology & Evolution 7(9):2727-2746.

2014 Brown, A.M.V., Huynh, L.Y., Bolender, C.M., Nelson, K.G., McCutcheon, J.P. Population genomics of a symbiont in the early stages of a pest invasion. Molecular Ecology 23:1516-1530. (Invited paper for Nature’s Microbiome).

2014 Brown AMV.  Microevolution of insect-bacterial mutualists: a population genomics perspective. In Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life. Pontarotti, P. (ed.). Springer International, Switzerland p. 247-259.

2010 Brown, A.M.V., Kent, M.L., Adamson, M.L. Description of five new Loma (Microsporidia) species in pacific fishes with redesignation of the type species Loma morhua Morrison & Sprague, 1981, based on morphological and molecular species-boundaries tests. Journal of Eukaryotic Microbiology 57(6): 529-553.

2010 Brown, A.M.V., Kent, M.L., Adamson, M.L. Low genetic variation in the salmon and trout parasite Loma salmonae (Microsporidia) supports marine transmission and clarifies species boundaries. Diseases of Aquatic Organisms 91(1): 35-46.

2008 Lee, R., Williams, B.A.P., Brown, A.M.V., Adamson, M.L., Keeling, P.J. and Fast, N.M. Alpha and beta-tubulin phylogenies support a close relationship between the microsporidia Brachiola algerae and Antonospora locustae. Journal of Eukaryotic Microbiology 55(5): 388-392.

2006 Brown, A.M.V., Adamson, M.L. Phylogenetic distance of Thelohania butleri Johnston, Vernick and Sprague, 1978 (Microsporidia; Thelohaniidae), a parasite of the smooth pink shrimp Pandalus jordani, from its congeners suggests need for major revision of the genus Thelohania Henneguy, 1892. Journal of Eukaryotic Microbiology 53(6): 445-455.

2002 Brown AMV, Kent ML.  Molecular diagnostics for Loma salmonae and Nucleospora salmonis (Microsporidia) In Molecular diagnostics of salmonid diseases. Cunningham, C. O. (ed.). Kluwer Academic Publishers, Dordrecht p. 267-283

2001 Matthews, J.L., Brown, A.M., Larison, K., Bishop-Stewart, J.K., Kent, M.L. Pseudoloma neurophilia n. g., n. sp., a new microsporidium from the central nervous system of the zebrafish (Danio rerio). Journal of Eukaryotic Microbiology 48(2): 227-233.

2000 Shaw, R.W., Kent, M.L., Brown, A.M.V., Whipps, C.M., Adamson, M.L. Experimental and natural host specificity of Loma salmonae (Microsporidia). Diseases of Aquatic Organisms 40(2): 131-136.

1997 Shaw, R.W., Kent, M.L., Docker, M.F., Brown, A.M.V., Devlin, R.H., Adamson, M.L. A new species of Loma (Microsporea) in shiner perch (Cymatogaster aggregata). Journal of Parasitology 83(2): 296-301.

Book Chapters:

Brown, A.M.V. (2014) Microevolution of insect-bacterial mutualists: a population genomics perspective. In Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life. Pontarotti, P. (ed.). Springer International, Switzerland p. 247-259.

Brown, A.M.V., Kent M.L. (2002) Molecular diagnostics for Loma salmonae and Nucleospora salmonis (microsporidia) In Molecular diagnostics of salmonid diseases. Cunningham, C. O. (ed.). Kluwer Academic Publishers, Dordrecht p. 267-283.

Software:

Brown, Amanda M.V., Coury, Michael (2002) REALEM: Realistic Evolutionary Models for DNA Analysis. Version 1.0. Computer Software Package in Java 1.3.1, distributed upon personal request from authors.

Posters:

2020 Vásquez-Weber L* (presenter), DePugh M*, Brown AMV. An initial computer model of biochemical signals through the gut-brain-axis. Annual Biomedical Research Conference for Minority Students (ABRCMS), Virtual, Nov 9-13.

2020 Aghdam S* (presenter), Singh S*, Lahowetz RM*, Brown AMV. Bioinformatic analysis of banana’s microbiome using a modified enrichment method. ASM Microbe 2020, Jun 18-22, Chicago, IL. (Changed to virtual conference due to Covid-19; withdrawn due to Covid-19)

2020 Hill BM* (presenter), Bisht K, Rumbaugh K, Wakeman C, Brown AMV. HiC Innovation to Study Polymicrobial Infections. ASM Microbe 2020, Jun 18-22, Chicago, IL. (Changed to virtual conference due to Covid-19; withdrawn due to Covid-19)

2020 Kucera T* (co-presenter), Mendoza B* (co-presenter), Brown AMV. Exploring microbial symbiont loss in Typhlocybinae and Acanaloniidae insects. 12th Annual TTU Undergraduate Research Conference Mar 30-31, Lubbock, TX. (Changed to virtual conference due to Covid-19)

2020 Lewis M* (presenter), Pupo MT, Brown AMV. Genomic and Metabolic Characterization of Endosymbionts Found in the Bacteriomes of Brazilian Membracids. 12th Annual TTU Undergraduate Research Conference Mar 30-31, Lubbock, TX. (Changed to virtual conference due to Covid-19)

2020 Vásquez-Weber L* (presenter), Brown AMV. Computer modeling gut-brain-axis biochemical flows. 12th Annual TTU Undergraduate Research Conference Mar 30-31, Lubbock, TX. (Changed to virtual conference due to Covid-19)

2020 Atkins GR* (presenter), Hill BM*, Bisht K, Wakeman CA, Brown AMV. Lysis HiC: A novel approach to determining the spatial make-up of a polymicrobial biofilm. 12th Annual TTU Undergraduate Research Conference Mar 30-31, Lubbock, TX. (Changed to virtual conference due to Covid-19)

2020 Gomez A* (presenter), Hill BM*, Bisht K, Wakeman CA, Brown AMV. Origins of Extracellular DNA Using Fluorescence in situ Hybridization. 12th Annual TTU Undergraduate Research Conference Mar 30-31, Lubbock, TX. (Changed to virtual conference due to Covid-19)

2020 Lahowetz RM* (presenter), Aghdam S*, Singh S*, Brown AMV. Bioinformatic Analysis of Banana Disease-Protective Microbiome. Jan. 11-15, Plant and Animal Genomes Conference XXVIII, San Diego, CA.

2020 Singh S* (presenter), Aghdam S*, Lahowetz RM*, Brown AMV. Genomic Diversity Analysis of Endophytic Microbes in Banana (Musa sp.). Jan. 11-15, Plant and Animal Genomes Conference XXVIII, San Diego, CA.

2019 Hill BM* (presenter), Bisht K, Wakeman C, Rumbaugh K, Brown AMV. New Hi-C and FISH methods for determining spatial context in polymicrobial infections. ASM Microbe June 20-24, San Francisco, CA.

2019 Sihaloho HF* (presenter), Brown AMV. Ophiocordyceps fungi in potato leafhopper (Empoasca fabae): Possible new symbiont recruitment. Integrative Omics Conference (NMBIST) March 14-15, Santa Fe, NM.

2019 Hill BM* (presenter), Brown AMV. Evolutionary microgeography in polymicrobial infections through a new Hi-C approach. Integrative Omics Conference (NMBIST) March 14-15, Santa Fe, NM.
2019 Nutt A* (co-presenter), Lahowetz R* (co-presenter), Alviña K, Brown AMV. Characterizing the microbiome along the gut-brain axis in an insect model, the cricket. 11th Annual TTU Undergraduate Research Conference, April 2-3, Lubbock, TX.
2019 Mendoza B* (presenter), Sihaloho HF*, Brown AMV. The missing microbe hypothesis explored in Typhlocybinae and Acanaloniidae insects. 11th Annual TTU Undergraduate Research Conference, April 2-3, Lubbock, TX.

2019 Joshi S* (presenter), Hill B*, Brown AMV. Lysis-Hi-C interactomics: new solution for combatting polymicrobial infections. 11th Annual TTU Undergraduate Research Conference, April 2-3, Lubbock, TX.
2019 Ball R* (co-presenter), Weyandt N* (co-presenter), Brown AMV. Genomic and transcriptomic study of plant-parasitic nematodes and their bacterial endosymbionts. 11th Annual TTU Undergraduate Research Conference, April 2-3, Lubbock, TX.
2019 Saltus S* (presenter), Brown AMV. Multi-omic study of membracid/endosymbiont relationship. 11th Annual TTU Undergraduate Research Conference, April 2-3, Lubbock, TX.
2018 Bell A* (co-presenter), Weyandt N* (co-presenter), Brown AMV. It’s what’s inside that counts: genome analysis of plant-parasitic nematode endosymbionts. Texas Tech Undergraduate Research Conference, March 27-28, Lubbock, TX.

2017 Murphy ED* (presenter) and Brown AMV. Analyzing Aedes aegypti and Aedes albopictus in search for a Zika virus cure. SACNAS National Diversity in STEM Conference, October 19-21, Salt Lake City, UT.

2017 Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Comparative genomics getting at the roots of a dual symbiosis: the importance of HGT. Society for Molecular Biology and Evolution Meetings, July 2-6, Austin, TX.

2017 White G*, Brown AMV. Sulcia, the great symbiotic facilitator in times of loss. Animal-Microbe Symbioses Gordon Research Conference, June 11-16, Mt. Snow, VT.

2017 Eaton C* (presenter), White G* (co-presenter), Brown AMV. A novel approach to isolate and sequence the banana (Musa spp.) microbiome. Texas Tech Undergraduate Research Conference, March 28-29, Lubbock, TX.

2016      Brown, AMV, Howe DK, Denver DR. Inferring symbiotic innovation through a shotgun metagenomics lens: progress and pitfalls of the latest techniques. Society for Molecular Biology and Evolution Meetings, July 3-7, 2016, Gold Coast, Australia.

2016      Howe DK, Tom DM, Smith M, Brown, AMV, Peetz AB, Zasada IA, Denver DR. Investigation of coevolution between Xiphinema spp. and bacterial endosymbionts. Society of Nematologists Meetings, Jul 17-21, 2016, Montreal, QC.

2015      Wasala SK, Brown AMV, Howe DK, Peetz AB, Zasada IA, Denver DR. Discovery and characterization of Wolbachia endosymbionts in plant-parasitic nematodes Pratylenchus penetrans. Fall Conference of the Center for Genomics and Biocomputing, Oregon State University.

2015      Tom, DM, Smith M, Brown AMV, Howe DK, Peetz AB, Zasada IA, Denver DR. Unraveling the relationship between a plant-parasitic nematode and its endosymbiont. Fall Conference of the Center for Genomics and Biocomputing, Oregon State University.

2014      Brown AMV, Howe DK, Dettwyler L, Peetz AB, Phillips WS, Zasada IA, Denver DR. Genome skimming reveals insights into symbiosis and chromosome dynamics in six plant-parasitic nematode species. Spring Conference of the Center for Genomics and Biocomputing, Oregon State University.

2014      Phillips WS, Howe DK, Brown AMV, Denver DR, Zasada IA. The unusual structuring of mitochondrial DNA into multiple mini-circles in the nematode Globodera ellingtonae. Spring Conference of the Center for Genomics and Biocomputing, Oregon State University.

Invited Talks:

2020 Brown AMV. Community genome skimming yields comparative and population genomic insights into rhizosphere microbiomes. American Society for Microbiology, Texas Branch, Virtual Fall 2020 Meeting Nov. 5-6.

2019 Brown AMV. Genomics of convergence and replacement in ecdysozoan symbioses. Sept. 24, Department of Microbiology and Molecular Genetics, Michigan State University (Departmental Seminar).

2018 Brown AMV. Comparative genomics insights into the wonderful world of plant-feeding invertebrate microbiomes. Apr. 17, Department of Plant Pathology and Microbiology Iowa State University, Ames, IA.

2017 Brown AMV, Pupo MT. Metabolic processes in the cooperative microbial symbionts of Brazilian membracids. TTU/FAPESP – STEM Across Continents Workshop. Sept. 21-22, TTU

2015 Brown AMV, Howe DK, Peetz AB, Phillips WS, Zasada IA, Denver DR. Genome skimming: novel insights into plant-parasitic nematode genomics and potential avenues for management. Symposium: Building Applied and Genomic Nematology Partnerships, Society of Nematologists Meetings, Jul 19-24, East Lansing, MI.

2014    Brown AMV, Huynh LY, McCutcheon JP. Population genomic and transcriptomic insights into symbiont adaptation during a rapid insect invasion. Horizons in the Field of Symbiosis Member Symposium, Entomological Society of America Meetings, Nov 15-19, 2014, Portland, OR.

2013    Brown AMV, McCutcheon JP. Microevolution of insect-bacterial mutualists: a population genomics perspective. 17th Evolutionary Biology Meeting at Marseilles, September 17-20, 2013, Marseille, France.

2008    Brown AMV. Pondering parasitism: meaning out of madness in the microsporidia. Invited talk to faculty at the Hawaiian Institute of Marine Biology (HIMB), University of Hawaii.

2008      Brown AMV. Meaning out of madness in the microsporidia. Invited talk to the Integrative Graduate Education and Research Traineeship (IGERT) group, University of Hawaii.

Recent Contributed Talks:

2016      Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Evolutionary genomics of an ancestral Wolbachia from plant-parasitic nematodes. Jun 28-Jul 3, Lamington Park, Queensland, Australia.

2016      Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Evolutionary genomics of rhizosphere endosymbionts: getting to the root of it. Yosemite Symbiosis Workshop, May 6-8. Wawona, Yosemite National Park, CA.

2015      Brown, A.M.V., Dettwyler, L., Wernick, R.I., Denver, D.R.  DeNAngler: a DNA untangling algorithm for mixed strain de novo assembly. Spring Conference of the Center for Genomics and Biocomputing, Oregon State University.

2013      Brown, A.M.V., Huynh, L.Y., Bolender, C.M., Nelson, K.G., McCutcheon, J.P. (2013) Population genomic study uncovers signs of selection in a nutritional symbiont, Ishikawaella, during a soybean pest invasion. Evolution Meetings, June 21-26, 2013, Snowbird, UT.

2012      Brown, A.M.V., McCutcheon, J.P. Population genomics of a nutritional symbiont affecting the pest status of an invasive bug: Ishikawaella in Megacopta cribraria. Yosemite Symbiosis Institute Workshop, May 19-20, 2012, Yosemite, CA.

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