Desert Southwest Genomics Center

Research

The aim of the Desert Southwest Genomics Center is to serve the research community — both on and off campus — with the resources and support researchers need to achieve their goals.

2026

Cao, T. T. T., Herckes, P., Straub, D., Sarkar, S., & Garcia-Pichel, F. (2026). Growth and formaldehyde degradation of photoheterotrophic Methylobacterium within radiation fogs. Mbio, 17(6), e00463-26.

Evangelista, D. A., Medina-Espinoza, E. F., Yáñez, S. K. M., Drager, K., Swichtenberg, K. L., Gile, G., … & Sanchez-Herrera, M. (2026). Xylomycophagy in a close relative of termites: Lamproblattidae (Blattodea) systematics, ecology, and diet. Arthropod Systematics & Phylogeny, 84, 309-342.

Gao, W., Lan, Y. W., Deng, Z., Li, E., Acharya, A., Do, J., … & Kalin, T. V. (2026). Emergence of fibrotic pericytes and their transcriptional regulation in pulmonary fibrosis. Nature communications.

Sakthikumar, S., Hendricks, W. P., Rainford, D., Selleck, W., Briones, N., Coggins, C., … & Trent, J. M. (2026). Genomic Landscape Analysis of Canine Pulmonary Adenocarcinoma Reveals Candidate Targetable Gene Fusions. Veterinary and Comparative Oncology, 24(2), 393-406.

Scott, E., Rand, T., Ronalds, S., Mirza, E., Wang, V., Tullo, A., & Gile, G. H. (2026). Microbiome communities with different transmission modes respond differently to host diet changes in a wood-feeding insect.

Vinuesa, P., Argueta-Zepeda, F. S., Valerdi-Negreros, J. C., Vázquez-Enciso, D. M., Osorio-Herrera, M. D., Gutiérrez-Hernández, D., … & Ochoa-Sánchez, L. E. (2026). Complete genome sequence of Stenotrophomonas maltophilia ESTM1D_MKCAZ16_6a (Sm18), a Mexican environmental multidrug-and amoeba-resistant strain. Microbiology Resource Announcements, 15(4), e01304-25.

Wright, S. L., Joslin, M., Kim, Y., Olson, M., Hall, A., Peter, B., Whisner, C. M. (2026). Distinct gut and oral microbiome patterns associated with dyslexia in a family-based cohort: A preliminary exploratory study. PloS one, 21(7), e0353463.

Zongo, V. S., Zhou, Y., Djigma, F. W., Roamba, E., Yonli, A. T., Sorgho, A. P., … & Simpore, J. K. (2026). Identification of Novel TERT Promoter Mutations in Chronic Hepatitis B-Induced HCC Patients in Burkina Faso. American Journal of Molecular Biology, 16(1), 46-59.

2025

Aguilar, S. G., Shevat, J., Jasso-Selles, D. E., Swichtenberg, K. L., Vecco-Giove, C. D., Šobotník, J., … & Gile, G. H. (2025). Distinct Patterns of Co-Evolution Among Protist Symbionts of Neoisoptera Termites. Diversity, 17(8), 537.

Cao, T. T. T., López, L. N., Ervens, B., Garcia-Pichel, F., & Herckes, P. (2025). Impact of bacterial biodegradation in fog on formaldehyde and hydroxymethanesulfonate (HMS) concentrations. Atmospheric Environment, 360, 121402.

Coots, N. L., Blanco-Bercial, L., & Gile, G. H. (2025). Polycystine radiolarians associate with diverse phytoplankton. Journal of Plankton Research, 47(3), fbaf010.

Coots, N. L., Jasso-Selles, D. E., Swichtenberg, K. L., Aguilar, S. G., Nguyen, L., Sidles, P. G., … & Gile, G. H. (2025). The protist symbionts of Reticulitermes tibialis: Unexpected diversity enables a new taxonomic framework. Protist, 176, 126087.

Harwood, G., Leipart, V., Elsik, C., Ng, J. C., Drabløs, F., & Amdam, G. V. (2025). Evidence for vitellogenin DNA‐binding in honey bees. Protein Science, 34(10), e70291.

Kulasekara, H. M. I. P., Rajapakshe, D., Zhang, Y., & Papelis, C. (2025). Microbial co-reduction of selenate and selenite in zeolite-packed columns in the presence of sulfate and nitrate: effects on removal efficiency and transformation of microbial community structure. Journal of Environmental Management, 394, 127383.

Long, M., Zheng, C. W., Zhou, C., & Rittmann, B. E. (2025). Mitigating chromate toxicity through concurrent denitrification in the H2-based membrane biofilm reactor. Journal of Hazardous Materials, 492, 138073.

Márquez-Sanz, R., Garrido-Benavent, I., Durán, J., & de Los Ríos, A. (2025). The Establishment of a Terrestrial Macroalga Canopy Impacts Microbial Soil Communities in Antarctica. Microbial ecology, 88(1), 4.

Mirza, E., Jasso‐Selles, D. E., Mizumoto, N., & Gile, G. H. (2025). Intragenomic 18S Sequence Variability in the Termite Symbionts Kofoidia loriculata and Kofoidia repleta n. sp.(Parabasalia). Journal of Eukaryotic Microbiology, 72(5), e70039.

Romo, R., Ricks, E., Ogden, R., Bonnette, P. E., Olson, S. C., Pearman, K., … & Chaston, J. M. (2025). Whole-body homogenates restore disrupted microbiota composition in a model insect better than feces or no restoration treatment. bioRxiv, 2025-11.

Skyler, H., Felipe, B., Zhang, Y., Roy, O., Akshansh, K., Park, J., … & Anderson, K. (2025). 327 Personalized neoepitope mRNA-based dendritic cell therapies against breast cancer. Journal for Immunotherapy of Cancer, 13(Suppl 2), A374-A374.

2024

Badshah, S. L., Stirbet, A., Siddiquee, M., Govindjee, G., Kang, D. W., Bridgeman, T., & Seo, Y. (2024). Inhibition of CO2 fixation as a potential target for the control of freshwater cyanobacterial harmful algal blooms. ACS ES&T Water, 4(8), 3309-3319.

Emery, M. V., Bolhofner, K., Spake, L., Ghafoor, S., Versoza, C. J., Rawls, E. M., … & Stone, A. C. (2024). Targeted enrichment of whole‐genome SNPs from highly burned skeletal remains. Journal of Forensic Sciences, 69(5), 1558-1577.

Flores-Díaz, A., Alatriste-Mondragón, F., Rittmann, B., Rangel-Mendez, R., & Ontiveros-Valencia, A. (2024). Biotransformation of microplastics from three-layer face masks by nitrifying-denitrifying consortia. Journal of Hazardous Materials, 480, 136161.

Ghosh, D., Yaron, J. R., Abedin, M. R., Godeshala, S., Kumar, S., Kilbourne, J., … & Rege, K. (2024). Bioactive nanomaterials kickstart early repair processes and potentiate temporally modulated healing of healthy and diabetic wounds. Biomaterials, 306, 122496.

Hackney, J. F., Broatch, J. E., Dallal, R. A., Brotherson, C., Livingston, S., Sabir, Z., … & Marshall, P. A. (2024). Rexinoids Induce Differential Gene Expression in Human Glioblastoma Cells and Protein–Protein Interactions in a Yeast Two-Hybrid System. ACS chemical neuroscience, 15(15), 2897-2915.

Koelbel, C., Ruiz, Y., Wan, Z., Wang, S., Ho, T., & Lake, D. (2024). Development of tandem antigen capture ELISAs measuring QSOX1 isoforms in plasma and serum. Free Radical Biology and Medicine, 210, 212-220.

Koroli, S., Buss, K., Blain, J. M., Nakka, G. S., Hong, M., McLean, R. J., … & Yang, J. (2024). Draft genome sequence of Sphingomonas paucimobilis strain Sph5, isolated from tap water filtration membrane. Microbiology Resource Announcements, 13(1), e00345-23.

Nirmalkar, K., Patel, J., Kang, D. W., Bellinghiere, A., Bowes, D. A., Qureshi, F., … & Krajmalnik-Brown, R. (2024). Bimodal distribution of intestinal Candida in children with autism and its potential link with worse ASD symptoms. Gut Microbes Reports, 1(1), 2358324.

Zheng, C. W., Lai, Y. S., Luo, Y. H., Cai, Y., Wu, W., & Rittmann, B. E. (2024). A two-stage design enhanced biodegradation of high concentrations of a C16-alkyl quaternary ammonium compound in oxygen-based membrane biofilm reactors. Water research, 250, 120963.

2023

Andre, A. B., Rees, K. P., O’Connor, S., Severson, G. W., Newbern, J. M., Wilson-Rawls, J., … & Rawls, A. (2023). Single cell analysis reveals satellite cell heterogeneity for proinflammatory chemokine expression. Frontiers in Cell and Developmental Biology, 11, 1084068.

Faleye, T. O., Driver, E. M., Bowes, D. A., Smith, A., Kaiser, N. A., Wright, J. M., … & Scotch, M. (2023). Canine Parvovirus 2C Identified in Dog Feces from Poop Bags Collected from Outdoor Waste Bins in Arizona USA, June 2022. Transboundary and Emerging Diseases, 2023(1), 5596886.

Luo, Y. H., Long, X., Cai, Y., Zheng, C. W., Roldan, M. A., Yang, S., … & Rittmann, B. E. (2023). A synergistic platform enables co-oxidation of halogenated organic pollutants without input of organic primary substrate. Water Research, 234, 119801.

Montoya-Rosales, J. D. J., Ontiveros-Valencia, A., Esquivel-Hernandez, D. A., Etchebehere, C., Celis, L. B., & Razo-Flores, E. (2023). Metatranscriptomic analysis reveals the coexpression of hydrogen-producing and homoacetogenesis genes in dark fermentative reactors operated at high substrate loads. Environmental Science & Technology, 57(31), 11552-11560.

Ortiz-Rivero, J., Garrido-Benavent, I., Heiðmarsson, S., & de Los Ríos, A. (2023). Moss and liverwort covers structure soil bacterial and fungal communities differently in the Icelandic highlands. Microbial Ecology, 86(3), 1893-1908.

Pal, A., Gonzalez-Malerva, L., Eaton, S., Xu, C., Zhang, Y., Grief, D., … & LaBaer, J. (2023). Multidimensional quantitative phenotypic and molecular analysis reveals neomorphic behaviors of p53 missense mutants. NPJ Breast Cancer, 9(1), 78.

Robles, A., Sundar, S. V., Mohana Rangan, S., & Delgado, A. G. (2023). Butanol as a major product during ethanol and acetate chain elongation. Frontiers in Bioengineering and Biotechnology, 11, 1181983.

Sadeghi, N., Kaur, K., & Soby, S. (2022). Draft Genomic Sequences of Pseudomonas moorei Strains Isolated from Wild Cranberry Bogs in Massachusetts. Microbiology Resource Announcements, 11(10), e00650-22.

Schreiber, M., Harrison, A., & Soby, S. (2023). Aquitalea palustris sp. nov., isolated from a wild cranberry bog in the Cape Cod National Seashore. International Journal of Systematic and Evolutionary Microbiology, 73(4), 005790.

Stephens, K., Harrison, A., & Soby, S. (2023). Draft Genome Sequence of Priestia megaterium MWU16-30321, Isolated from a Cranberry Stem Gall in Massachusetts. Microbiology Resource Announcements, 12(1), e01052-22.

Zheng, C. W., Luo, Y. H., Lai, Y. J. S., Ilhan, Z. E., Ontiveros-Valencia, A., Krajmalnik-Brown, R., … & Rittmann, B. E. (2023). Identifying biodegradation pathways of cetrimonium bromide (CTAB) using metagenome, metatranscriptome, and metabolome tri-omics integration. Water Research, 246, 120738.

2022

Anasi, A., & Soby, S. (2022). Draft genome sequences of Pseudomonas sp. strains MWU12-2037 and MWU12-2345, isolated from peat and sandy bog soils in the Cape Cod National Seashore, Massachusetts. Microbiology Resource Announcements, 11(8), e00536-22.

Baker, S. T. (2022). Identification of Cytospora Species Isolated from Canker in Peach Trees in South Carolina.

Barrila, J., Yang, J., Franco Meléndez, K. P., Yang, S., Buss, K., Davis, T. J., … & Nickerson, C. A. (2022). Spaceflight analogue culture enhances the host-pathogen interaction between Salmonella and a 3-D biomimetic intestinal co-culture model. Frontiers in Cellular and Infection Microbiology, 12, 705647.

De los Rios, A., Garrido-Benavent, I., Limón, A., Cason, E. D., Maggs-Kölling, G., Cowan, D., & Valverde, A. (2022). Novel lichen-dominated hypolithic communities in the Namib Desert. Microbial Ecology, 83(4), 1036-1048.

Emery, M. V., Bolhofner, K., Ghafoor, S., Winingear, S., Buikstra, J. E., Fulginiti, L. C., & Stone, A. C. (2022). Whole mitochondrial genomes assembled from thermally altered forensic bones and teeth. Forensic Science International: Genetics, 56, 102610.

Faleye, T. O., Driver, E. M., Bowes, D. A., Holm, R. H., Talley, D., Yeager, R., … & Scotch, M. (2022). Detection of human, porcine and canine picornaviruses in municipal sewage sludge using pan-enterovirus amplicon-based long-read Illumina sequencing. Emerging Microbes & Infections, 11(1), 1339-1342.

Faleye, T. O., Skidmore, P. T., Elyaderani, A., Smith, A., Kaiser, N., Adhikari, S., … & Scotch, M. (2022). Canine picornaviruses detected in wastewater in Arizona, USA 2019 and 2021. Infection, Genetics and Evolution, 103, 105315. bes & Infections, 11(1), 1339-1342.

Graham, B., Castañeda, T., Harrison, A., & Soby, S. (2022). Draft genomic sequences of four Pseudomonas spp. and a Xanthomonas sp. from cranberry stem galls. Microbiology Resource Announcements, 11(3), e00999-21.

Jackson, A. C., Jorna, J., Chaston, J. M., & Adams, B. J. (2022). Glacial legacies: microbial communities of Antarctic refugia. Biology, 11(10), 1440.

Knowles, S. J., Holter, M. C., Li, G., Bjorklund, G. R., Rees, K. P., Martinez-Fuentes, J. S., … & Newbern, J. M. (2022). Multifunctional requirements for ERK1/2 signaling in the development of ganglionic eminence derived glia and cortical inhibitory neurons. bioRxiv, 2022-08.

Kooner, A., & Soby, S. (2022). Draft genome sequence of Curtobacterium sp. strain MWU13-2055, isolated from a wild cranberry fruit surface in Massachusetts, USA. Microbiology resource announcements, 11(10), e00565-22.

Kooner, A., & Soby, S. (2022). Draft Genome Sequence of Pseudomonas sp. Strain MWU13-3659, Isolated from Commercial Cranberry Bog Soil in Massachusetts, USA. Microbiology Resource Announcements, 11(11), e00880-22.

Kurgan, G., Onyeabor, M., Holland, S. C., Taylor, E., Schneider, A., Kurgan, L., … & Wang, X. (2022). Directed evolution of Zymomonas mobilis sugar facilitator Glf to overcome glucose inhibition. Journal of Industrial Microbiology and Biotechnology, 49(2), kuab066.

Manthena, A., Pittman, A., & Soby, S. (2022). Draft genome sequences of Pseudomonas sp. strains MWU 12-2029, MWU 12-3088, and MWU 12-3091, isolated from wild and cultivated Massachusetts cranberry bogs. Microbiology Resource Announcements, 11(11), e00889-22.

Mayer, B., & Soby, S. (2022). Draft Genome Sequences of Pseudomonas sp. Strains MWU13-2100 and MWU13-2105 Isolated from Wild Cranberry Bog Soil in the Cape Cod National Seashore. Microbiology Resource Announcements, 11(10), e00557-22.

Nirmalkar, K., Qureshi, F., Kang, D. W., Hahn, J., Adams, J. B., & Krajmalnik-Brown, R. (2022). Shotgun metagenomics study suggests alteration in sulfur metabolism and oxidative stress in children with autism and improvement after microbiota transfer therapy. International journal of molecular sciences, 23(21), 13481.

Ormsby, A., & Soby, S. (2022). Draft Genome Sequence of Pseudomonas sp. Strains MWU12-2020 and MWU12-3103b, Isolated from Wild and Cultivated Cranberry Bogs in Massachusetts. Microbiology Resource Announcements, 11(10), e00568-22.

Pittman, A., & Soby, S. (2022). Draft Genome Sequence of Pseudomonas sp. Strains MWU12-2319 and MWU12-2311, Isolated from a Wild Cranberry Bog in the Cape Cod National Seashore. Microbiology Resource Announcements, 11(11), e00869-22.

Sadeghi, N., Kaur, K., & Soby, S. (2022). Draft Genomic Sequences of Pseudomonas moorei Strains Isolated from Wild Cranberry Bogs in Massachusetts. Microbiology Resource Announcements, 11(10), e00650-22.

Sholl, T., & Soby, S. (2022). Draft genome sequence of Pseudomonas sp. strain MWU15-20650, isolated from wild cranberry fruit in the Cape Cod National Seashore. Microbiology Resource Announcements, 11(8), e00547-22.

Stephens, K., Gnambani, E. J., Bilgo, E., Diabate, A., & Soby, S. (2022). Draft Genome of a Member of the Family Chromobacteriaceae Isolated from Anopheles Mosquitoes in West Africa. Microbiology Resource Announcements, 11(10), e00524-22.

Wood, M., & Soby, S. D. (2022). Draft Genome Sequence of Pseudomonas protegens Strain MWU12-2233, Isolated from Wild Cranberry Fruit in Provincetown, Massachusetts. Microbiology Resource Announcements, 11(8), e00546-22.

Yaeger, J., & Soby, S. (2022). Draft genome sequence of Pseudomonas sp. strain MWU13-2517, isolated from a wild cranberry bog in Provincetown, MA. Microbiology Resource Announcements, 11(8), e00545-22.

2021

Bering, J., McAulay, K., Grys, T., & Ruff, K. C. (2021). S1371 Small Intestinal Microbiome Assessed by Deep Enteroscopy. Official journal of the American College of Gastroenterology| ACG, 116, S630.

Blain, J. M., Grote, D. L., Watkins, S. M., Goshu, G. M., Muller, C., Gorman, J. L., … & Hagen, T. J. (2021). Structural and biophysical characterization of the Burkholderia pseudomallei IspF inhibitor L-tryptophan hydroxamate. Bioorganic & medicinal chemistry letters, 48, 128273.

Cho, H., & Misra, R. (2021). Mutational activation of antibiotic-resistant mechanisms in the absence of major drug efflux systems of Escherichia coli. Journal of bacteriology, 203(14), 10-1128.

Collins, C. L., DeNardo, D. F., Blake, M., Norton, J., Schmidlin, K., Fontenele, R. S., … & Varsani, A. (2021). Genome sequences of microviruses identified in Gila monster feces. Microbiology Resource Announcements, 10(11), 10-1128.

Del Moral, Á., Garrido-Benavent, I., Duran, J., Lehmann, J. R., Rodríguez, A., Heiðmarsson, S., & de Los Ríos, A. (2021). Are recently deglaciated areas at both poles colonised by the same bacteria?. FEMS Microbiology Letters, 368(3), fnab011.

Duran, J., Rodriguez, A., Heiðmarsson, S., Lehmann, J. R., Del Moral, Á., Garrido-Benavent, I., & De los Rios, A. (2021). Cryptogamic cover determines soil attributes and functioning in polar terrestrial ecosystems. Science of the Total Environment, 762, 143169.

Faleye, T. O., Driver, E., Bowes, D., Adhikari, S., Adams, D., Varsani, A., … & Scotch, M. (2021). Pan-enterovirus amplicon-based high-throughput sequencing detects the complete capsid of a EVA71 genotype C1 variant via wastewater-based epidemiology in Arizona. Viruses, 13(1), 74.

Faleye, T. O., Adams, D., Adhikari, S., Sandrolini, H., Halden, R. U., Varsani, A., & Scotch, M. (2021). Use of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting. BMC Infectious Diseases, 21(1), 810.

Luo, Y. H., Lai, Y. S., Zheng, C., Ilhan, Z. E., Ontiveros-Valencia, A., Long, X., … & Rittmann, B. E. (2021). Increased expression of antibiotic-resistance genes in biofilm communities upon exposure to cetyltrimethylammonium bromide (CTAB) and other stress conditions. Science of The Total Environment, 765, 144264.

Nelson, C., & Garcia-Pichel, F. (2021). Beneficial cyanosphere heterotrophs accelerate establishment of cyanobacterial biocrust. Applied and environmental microbiology, 87(20), e01236-21.

Nelson, C., Giraldo-Silva, A., & Garcia-Pichel, F. (2021). A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus. The ISME Journal, 15(1), 282-292.

Richard Jr, Harold B., et al. “Optimization of translation enhancing element use to increase protein expression in a vaccinia virus system.” Journal of General Virology 102.8 (2021): 001624.

Sagaser, S., Butterfield, R., Kosiorek, H., Kusne, Y., Maldonado, J., Fautsch, M. P., … Shen, J. F. (2021). Effects of Intense Pulsed Light on Tear Film TGF-β and Microbiome in Ocular Rosacea with Dry Eye. Clinical Ophthalmology, 15, 323–330.

Skidmore, P. T., Kaelin, E. A., Holland, L. A., Maqsood, R., Wu, L. I., Mellor, N. J., … & Lim, E. S. (2021). Genomic sequencing of SARS-CoV-2 E484K variant B. 1.243. 1, Arizona, USA. Emerging infectious diseases, 27(10), 2718.

Skidmore, P. T., Kaelin, E. A., Holland, L. A., Maqsood, R., Wu, L. I., Mellor, N. J., … & Lim, E. S. (2021). Emergence of a SARS-CoV-2 E484K variant of interest in Arizona. medRxiv, 2021-03.

Velazquez, J. J., LeGraw, R., Moghadam, F., Tan, Y., Kilbourne, J., Maggiore, J. C., … & Ebrahimkhani, M. R. (2021). Gene regulatory network analysis and engineering directs development and vascularization of multilineage human liver organoids. Cell systems, 12(1), 41-55.

2020

Avelar, S., Ramos-Sobrinho, R., Conner, K., Nichols, R. L., Lawrence, K., & Brown, J. K. (2020). Characterization of the complete genome and P0 protein for a previously unreported genotype of cotton leafroll dwarf virus, an introduced polerovirus in the United States. Plant Disease, 104(3), 780-786.

Emami-Khoyi, A., Parbhu, S. P., Ross, J. G., Murphy, E. C., Bothwell, J., Monsanto, D. M., … & Paterson, A. M. (2020). De novo transcriptome assembly and annotation of liver and brain tissues of common brushtail possums (Trichosurus vulpecula) in New Zealand: Transcriptome diversity after decades of population control. Genes, 11(4), 436.

Emery, M. V., Bolhofner, K., Winingear, S., Oldt, R., Montes, M., Kanthaswamy, S., … & Stone, A. C. (2020). Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques. Forensic Science International: Genetics, 46, 102272.

Flores-Valdez, M. A., Aceves-Sánchez, M. D. J., Peterson, E. J., Baliga, N., Bravo-Madrigal, J., De la Cruz-Villegas, M. Á., … & Espinoza-Jorge, M. G. (2020). Transcriptional portrait of M. bovis BCG during biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment. Scientific Reports, 10(1), 12578.

Holland, L. A., Kaelin, E. A., Maqsood, R., Estifanos, B., Wu, L. I., Varsani, A., … & Lim, E. S. (2020). An 81-nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (January to March 2020). Journal of virology, 94(14), 10-1128.

Lenkiewicz, E., Malasi, S., Hogenson, T. L., Flores, L. F., Barham, W., Phillips, W. J., … & Barrett, M. T. (2020). Genomic and epigenomic landscaping defines new therapeutic targets for adenosquamous carcinoma of the pancreas. Cancer research, 80(20), 4324-4334.

Mondal, Mosharrof, Judith K. Brown, and Alex Flynt. “Exploiting somatic piRNAs in Bemisia tabaci enables novel gene silencing through RNA feeding.” Life science alliance 3.10 (2020).

Powell, G. L., Vannan, A., Bastle, R. M., Wilson, M. A., Dell’Orco, M., Perrone-Bizzozero, N. I., & Neisewander, J. L. (2020). Environmental enrichment during forced abstinence from cocaine self-administration opposes gene network expression changes associated with the incubation effect. Scientific reports, 10(1), 11291.

Yaron, J. R., Ambadapadi, S., Zhang, L., Chavan, R. N., Tibbetts, S. A., Keinan, S., … & Lucas, A. R. (2020). Immune protection is dependent on the gut microbiome in a lethal mouse gammaherpesviral infection. Scientific reports, 10(1), 2371.

2019

Giner-Lamia, J., Vinuesa, P., Betancor, L., Silva, C., Bisio, J., Soleto, L., … & García-del Portillo, F. (2019). Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256. BMC genomics, 20(1), 99.

Kurgan, G., Sievert, C., Flores, A., Schneider, A., Billings, T., Panyon, L., … & Wang, X. (2019). Parallel experimental evolution reveals a novel repressive control of GalP on xylose fermentation in Escherichia coli. Biotechnology and bioengineering, 116(8), 2074-2086.

Maarsingh, J. D., Yang, S., Park, J. G., & Haydel, S. E. (2019). Comparative transcriptomics reveals PrrAB-mediated control of metabolic, respiration, energy-generating, and dormancy pathways in Mycobacterium smegmatis. BMC genomics, 20(1), 942.

Voth-Gaeddert, L. E., Torres, O., Maldonado, J., Krajmalnik-Brown, R., Rittmann, B. E., & Oerther, D. B. (2019). Aflatoxin exposure, child stunting, and dysbiosis in the intestinal microbiome among children in Guatemala. Environmental Engineering Science, 36(8), 958-968.

Yang, D., Kong, Y., Sun, W., Kong, W., & Shi, Y. (2019). A dopamine-responsive signal transduction controls transcription of salmonella enterica Serovar Typhimurium virulence genes. MBio, 10(2), 10-1128.

2018

Ebadzadsahrai, G., & Soby, S. (2018). Draft genome sequence of Aquitalea sp. strain MWU14-2217, isolated from a wild cranberry bog in Provincetown, Massachusetts. Microbiology Resource Announcements, 7(21), 10-1128.

Ebadzadsahrai, G., Thomson, J., & Soby, S. (2018). Draft genome sequence of Pseudomonas sp. strain MWU13-2860, isolated from a wild cranberry bog in Truro, Massachusetts. Microbiology resource announcements, 7(13), 10-1128.

Ebadzadsahrai, G., Thomson, J., & Soby, S. (2018). Draft genome sequences of Pseudomonas MWU13-2625 and MWU12-2115, isolated from a wild cranberry bog at the Cape Cod National Seashore. Microbiology Resource Announcements, 7(12), 10-1128.

Esquivel-Elizondo, S., Maldonado, J., & Krajmalnik-Brown, R. (2018). Anaerobic carbon monoxide metabolism by Pleomorphomonas carboxyditropha sp. nov., a new mesophilic hydrogenogenic carboxydotroph. FEMS microbiology ecology, 94(6), fiy056.

Gillum, D., Carrera, L. A. O., Mendoza, I. A., Bates, P., Bowens, D., Jetson, Z., … & Kiani, S. (2018). The 2017 Arizona biosecurity workshop: an open dialogue about biosecurity. Applied Biosafety, 23(4), 233-241.

Heinitz, S., Piaggi, P., Yang, S., Bonfiglio, S., Steel, J., Krakoff, J., & Votruba, S. B. (2018). Response of skeletal muscle UCP2-expression during metabolic adaptation to caloric restriction. International journal of obesity, 42(5), 974-984.

Kämpfer, P., Glaeser, S. P., & Soby, S. D. (2018). Chromobacterium pseudoviolaceum Kämpfer et al. 2009 is a later heterotypic synonym of Chromobacterium violaceum Bergonzini 1880. International Journal of Systematic and Evolutionary Microbiology, 68(9), 2967-2968.

Maldonado, J., Yaron, J. R., Zhang, L., & Lucas, A. (2018). Next-generation sequencing library preparation for 16S rRNA microbiome analysis after serpin treatment. In Serpins: Methods and Protocols (pp. 213-221). New York, NY: Springer New York.

O’Hara-Hanley, K., Harrison, A., & Soby, S. D. (2018). Draft genomic sequences of Chromobacterium sp. nov. strains MWU13-2610 and MWU14-2602, isolated from wild cranberry bogs in Massachusetts. Genome Announcements, 6(15), 10-1128.

Whisner, C. M., Maldonado, J., Dente, B., Krajmalnik-Brown, R., & Bruening, M. (2018). Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study. Bmc Microbiology, 18(1), 210.

2017

Copetti, D., Búrquez, A., Bustamante, E., Charboneau, J. L., Childs, K. L., Eguiarte, L. E., … & Sanderson, M. J. (2017). Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. Proceedings of the National Academy of Sciences, 114(45), 12003-12008.

Moremen, K. W., Ramiah, A., Stuart, M., Steel, J., Meng, L., Forouhar, F., … & Jarvis, D. L. (2018). Expression system for structural and functional studies of human glycosylation enzymes. Nature chemical biology, 14(2), 156-162.

Sievert, C., Nieves, L. M., Panyon, L. A., Loeffler, T., Morris, C., Cartwright, R. A., & Wang, X. (2017). Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR. Proceedings of the National Academy of Sciences, 114(28), 7349-7354.

Soby, S. D. (2017). Draft genome sequence of Chromobacterium pseudoviolaceum LMG 3953T, an enigmatic member of the genus Chromobacterium. Genome Announcements, 5(12), 10-1128.

Soby, S. D. (2017). Draft genome sequence of Chromobacterium aquaticum CC-SEYA-1, a nonpigmented member of the genus Chromobacterium. Genome Announcements, 5(12), 10-1128.

Song, L., Wallstrom, G., Yu, X., Hopper, M., Van Duine, J., Steel, J., … & Achkar, J. M. (2017). Identification of antibody targets for tuberculosis serology using high-density nucleic acid programmable protein arrays. Molecular & Cellular Proteomics, 16(4), S277-S289.

Vöing, K., Harrison, A., & Soby, S. D. (2017). Draft genome sequence of Chromobacterium subtsugae MWU12-2387 isolated from a wild cranberry bog in Truro, Massachusetts. Genome announcements, 5(12), 10-1128.

2016

Bian, X., Wallstrom, G., Davis, A., Wang, J., Park, J., Throop, A., … & LaBaer, J. (2016). Immunoproteomic profiling of antiviral antibodies in new-onset type 1 diabetes using protein arrays. Diabetes, 65(1), 285-296.

Hingorani, P., McEachron, T., Park, J., Steel, J., Gastier-Foster, J. M., Rodriguez-Galindo, C., … & Dinu, V. (2016). RNA profiling of desmoplastic small round cell tumors (DSRCTs) using next-generation sequencing.

The ORFeome Collaboration (2016). The ORFeome Collaboration: A genome-scale human ORF-clone resource. Nature Methods 13: 191.

2015

Anderson, K. S., Cramer, D. W., Sibani, S., Wallstrom, G., Wong, J., Park, J., … & LaBaer, J. (2015). Autoantibody signature for the serologic detection of ovarian cancer. Journal of proteome research, 14(1), 578-586.

Sanderson, M. J., Copetti, D., Búrquez, A., Bustamante, E., Charboneau, J. L., Eguiarte, L. E., … & Wojciechowski, M. F. (2015). Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat. American Journal of Botany, 102(7), 1115-1127.

Vöing, K., Harrison, A., & Soby, S. D. (2015). Draft genome sequences of three Chromobacterium subtsugae isolates from wild and cultivated cranberry bogs in southeastern Massachusetts. Genome Announcements, 3(5), 10-1128.

Vöing, K., Harrison, A., & Soby, S. D. (2015). Draft genome sequence of Chromobacterium vaccinii, a potential biocontrol agent against mosquito (Aedes aegypti) larvae. Genome announcements, 3(3), 10-1128.

2014

Paul, R., Jinkerson, R. E., Buss, K., Steel, J., Mohr, R., Hess, W. R., … & Fromme, P. (2014). Draft genome sequence of the filamentous cyanobacterium Leptolyngbya sp. strain Heron Island J, exhibiting chromatic acclimation. Genome announcements, 2(1), 10-1128.

Seiler, C. Y., Park, J. G., Sharma, A., Hunter, P., Surapaneni, P., Sedillo, C., … & LaBaer, J. (2014). DNASU plasmid and PSI: Biology-Materials repositories: resources to accelerate biological research. Nucleic acids research, 42(D1), D1253-D1260.

Yu, X., Bian, X., Throop, A., Song, L., Del Moral, L., Park, J., … & LaBaer, J. (2014). Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions. Theranostics, 4(8), 808.