Utkina, I., Fan, Y., Willing, BP., and Parkinson, J. Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation. BioArxiv 2024.10.14.618310

Campisi, SC., Zhang F., Seo, M., Muha, J., Schumacher, A., DeLuca I., Bradley-Ridout G., Merriman K., Parkinson, J., and Korczak, DJ. The gut microbiome and child and adolescent depression and anxiety: A systematic review and meta-analysis with youth consultation.

Peng, H.,*^,# Kotelnikov, S.*, Egbert, ME., Ofaim, S.,* Stevens, GC.,* Phanse, S.,* Saccon, T., Ignatov, M., Dutta, S., Istace, Z., Moutaoufik, MT., Aoki, H., Kewalramani, N., Sun, J., Gong, Y., Padhorny, D., Poda, G., Alekseenko, A., Jones, G., Rodionova I., Guo H., Pogoutse, O., Datta, S., Saier, M., Crovella, M., Vajda, S., Moreno-Hagelsieb, G., Parkinson^#, J., Segre, D.,^# Babu, M.,^# Kozakov, D.^# and Emili, A.^# (2024) The native small molecule interaction landscape of transcription factors and essential enzymes in E. coli. *These authors contributed equally to the work; ^#Corresponding authors.

Alves-Ferreira, EVC., Galac, MR., Lorenzi, HA., Ho, MCW., Tjhin, ET., Popovic, A., Parkinson, J. and Grigg, ME. Whole Genome Sequence of the gut commensal protist Tritrichomonas musculus isolated from laboratory mice.

Curran, DM., Ng, D., Parkinson, J., Moraes, T., Gray-Owen, S, and Fegan, JE Phylogeny-based selection of representative variants with Navargator: Proof of principle using humoral cross-reactivity data from two immunization studies. BioArxiv 2024.09.08.611914

Binepal, G.,* Jurga, E., *, Carruthers-Lay, D., Krüger, S., Zitterman, S., Alexander, D., Martin, I., Allen, V., Parkinson, J.^# and Gray-Owen, SD.^# Phenotypic diversity and shared genomic determinants among isolates causing a large incidence of disseminated gonococcal infections in Canada. BioArxiv 2024.611862; *Both authors contributed equally to the work; ^#These authors are considered co-senior/corresponding authors.

2024

Swapna, L.,* Stevens, G.,* Sardinha da Silva, A., Hu, LZ., Brand, V., Fusca, DD., Xiong, X., Boyle, JP., Grigg, ME., Emili, A. and Parkinson J. (2024) ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii reveals novel virulence factors implicated in host cell invasion. PLoS Computational Biology. 20(6):e1012208. doi: 10.1371/journal.pcbi.1012208. *Both authors contributed equally to the work.

Cao, EY., Burrows, K., Chiaranunt, P., Popovic, A., Zhou, X., Xie, C., Thakur, A., Britton, GJ., Spindler, MP., Ngai, L., Tai, SL., Dasoveanu, DC., Nguyen, A., Faith, JJ., Parkinson, J., Gommerman, J. and Mortha A. (2024) The protozoan commensal Tritrichomonas musculis is a natural adjuvant for mucosal IgA. Journal of Experimental Medicine. 221(12): e20221727.

Wasan, Y., Baxter, JB., Spiegel-Feld, C., Begum, K., Rizvi, A., Iqbal, J., Hulst, JM., Bandsma, R., Suleman, S., Soofi, SB., Parkinson, J.,^# and Bhutta, ZA^# (2024) Elucidating the Dynamics and Impact of the Gut Microbiome on Maternal Nutritional Status During Pregnancy in Rural Pakistan. Study Protocol for a Prospective, Longitudinal Observational Study. BMJ Open. 14(8):e081629. ^#These authors are considered co-senior authors (BMJ only include one corresponding author).

Chieu, R.,* Hamilton, K.,* Ryan, PM., Copeland, J., Wang, PW., Retnakaran, R., Guttman, DS., Parkinson, J.^# and Hamilton, J.^# (2024) The impact of gestational diabetes on functional capacity of the infant gut microbiome is modest and transient. Gut Microbes. 16(1): 2356277. *Both authors contributed equally to the work; ^#These authors are considered co-senior/corresponding authors.

Popovic, A., Cao, E.Y., Han, J., Nursimulu, N., Alves-Ferreira, E.V.C., Kennard, A., Alsmadi, N. Grigg, M.E., Mortha, A. and Parkinson, J. (2024) Commensal protist Tritrichomonas musculus exhibits a dynamic life cycle that induces B cell-modulated remodeling of the gut microbiota. ISME J. 18(1): wrae023.

Chan, D.,* Cromar, GL.,* Taj, B. and Parkinson, J. (2024) Cell4D: A general purpose spatial stochastic simulator for cellular pathways. BMC Bioinformatics. 25: 121. *Both authors contributed equally to the work

Verma, B. and Parkinson, J. (2024) HiTaxon: A hierarchical ensemble framework for taxonomic classification of short reads. Bioinformatics Advances. 4(1): vbae016.

Kairmi, SH., Taha-Abdelaziz, K., Spahany, H., Astill J., Trott, D., Wang, B., Wang, A., Parkinson, J. and Sharif, S. (2024) Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens. PLoS ONE. 19(4): e0301110.

2023

Romano, K., Shah, AN., Schumacher, A., Zasowski, C., Zhang, T., Bradley-Ridout, G., Merriman, K., Parkinson, J., Szatmari, P., Campisi, SC., and Korczak, DJ (2003) The gut microbiome in children with mood, anxiety, and neurodevelopmental disorders: An umbrella review. Gut Microbiome. 4: e18

Taj , B.,* Adeolu, M.,* Xiong, X., Nursimulu, N., Ang, J. and Parkinson, J. (2023) MetaPro: A scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities. Microbiome. 11: 143. *Both authors contributed equally to the work

Popovic, A., Bourdon, C., Wang, PW., Guttman, DS., Soofi, S., Bhutta, ZA., Bandsma, RHJ., Parkinson, J.* and Pell, LG. (2021) Micronutrient supplements with iron promote disruptive protozoan and fungal communities in the developing infant gut. Nature Communications. 12(1):6729. *Senior corresponding author. Editors Highlight.

Dacquay, LC., Tsang, T., Chan, D., Parkinson, J., Philpott, DJ. and McMillen, DR. (2021) E. coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis. Gut Microbes. 13(1): 1994832.

Jiang, JX., Wellhauser, L., Laselva, O., Utkina, I., Bozoky, Z., Gunawardena, T., Ngan, Z., Xia, S., Eckford, PDW., Ratjen, F., Moraes, TJ., Parkinson, J.,Wong, AP. and Bear, CE. (2021) A new platform for high-throughput therapy testing on iPSC-derived, immature airway from Cystic Fibrosis Patients. Stem Cell Reports. 16:1–13

Shokrollahi, P., Lai, YP., Rash-Ahmadi, S., Stewart, V., Mohammadigheisar, M., Huber, L., Matsuura, N., Zavodni, A., Parkinson, J. and Diller, E. (2021) Blindly Controlled Magnetically Actuated Capsule for Noninvasive Sampling of the Gastrointestinal Microbiome. IEEE/ASME Transactions on Mechatronics. 26(5)” 2616-2628.

Curran, DM.,* Grote, A.,* Nursimulu, N., Geber, A., Voronin, D., Jones, DR., Ghedin, E.# and Parkinson, J..# (2020) Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. eLife. 9:e51850. *Both authors contributed equally to the work; #Co-corresponding authors eLife news release

Bundalovic-Torma, C., Whitfield, GB., Marmont, LS., Howell, PL. and Parkinson, J. (2020) A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. PLoS Computational Biology. 16(4): e1007721.

Whitfield, GB., Marmont, LS., Bundalovic-Torma, C., Razvi, E., Roach, EJ., Khursigara, CM., Parkinson, J. and Howell, PL. (2020) Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster. PLoS Pathogens. 16(4): e1008281.

Pourhaghighi, R., Ash, PEA., Phanse, S., Goebels, F., Hu, LZM., Chen, S., Zhang, Y., Wierbowski, SD., Boudeau, S., Moutaoufik, MT., Malty, RH., Malolepsza, E., Tsafou, K., Nathan, A., Cromar, G.,Guo, H., AlAbdullatif, A., Apicco, DJ., Becker, LA., Gitler, AD., Pulst, SM., Youssef, A., Hekman, R., Havugimana, PC., White, CA., Blum, BC., Ratti, A., Bryant, CD., Parkinson, J., Lage, K., Babu, M., Yu, H., Bader, GD., Wolozin, B. and Emili, A. (2020) BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Systems. 10: 333-350.e14

Zou, A., Nadeau, K., Wang, PW., Lee, JY., Guttman, DS., Sharif, S., Korver, D., Brumell, JH. and Parkinson, J.. (2020) Accumulation of genetic variants associated with immunity in the selective breeding of broilers. BMC Genetics. 21: 5.

Yitbarek, A., Astill, J., Hodgins, DC., Parkinson, J.,Nagy, E. and Sharif, S. (2019) Commensal gut microbiota can modulate adaptive immune responses in chickens vaccinated with whole inactivated influenza virus subtype H9N2. Vaccine. 37(44):6640-6647.

Zhang, J. and Parkinson, J. (2019) PopNetD3 – A network based web resource for exploring population structure. Genome Biology and Evolution. 11(7):1730-1735.

International Helminths Genome Consortium (2019) Comparative genomics of the major parasitic worms. Nature Genetics. 51(1):163-174.

Popovic, A., Bourdon, C., Wang, P., Guttmann, D., Voskuijl, W., Grigg, M., Bandsma, R. and Parkinson, J. (2018) Design and application of a novel two-barcode approach for defining the eukaryotic microbiome. Microbiome. 6(1):228.

Zou, A., Sharif, S. and Parkinson, J. (2018) Lactobacillus elicits a “Marmite effect” on the chicken cecal microbiome. NPJ Biofilms and Microbiome. 4: 27.

Adeolu, M., Parkinson, J. and Xiong, X. (2018) Analyzing Metabolic Pathways in Microbiomes. Methods Mol Biol. 1849:291-307.

Popovic, A. and Parkinson, J. (2018) Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing. Methods Mol Biol. 1849:29-48.

Swapna L.S., Molinaro A.M., Lindsay-Mosher N., Pearson B.J.,# and Parkinson, J.# (2018). Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identifies major cell types and pathway conservation. Genome Biology. 19:124. #jointly supervised this work

Yitbarek A., Taha-Abdelaziz K., Hodgins D.C., Read L., Nagy E., Weese J.S., Caswell J.L., Parkinson J., and Sharif S. (2018). Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses. Scientific Reports. 8(1):13189.

Nursimulu N., Xu L.Y., Wasmuth J.D., Krukov I. and Parkinson J. (2018). Improved enzyme annotation with EC-specific cutoffs using DETECT v2. Bioinformatics. 34(19):3393-3395.

Yitbarek A., Weese J.S., Alkie T., Parkinson J. and Sharif S. (2018) Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens. FEMS Microbiology Ecology. 94(1): fix165

Babu M.*#, Bundalovic-Torma C.*, Calmettes C.,* Phanse S., Zhang Q., Jiang Y., Minic Z., Kim S., Mehla J., Gagarinova A., Rodionova I., Kumar A., Guo H., Kagan O., Pogoutse O., Aoki H., Deineko V., Caufield J. H., Holtzapple E., Zhang Z., Vastermark A., Pandya Y., Lai C.C., El Bakkouri M., Hooda Y., Shah M., Burnside D., Hooshyar M., Vlasblom J., Rajagopala S.V., Golshani A., Wuchty S., Greenblatt J.F., Saier M.,# Uetz P.,# Moraes T.F.,# Parkinson J.# and Emili A.# (2018) Global landscape of cell envelope protein complexes in Escherichia coli. Nature Biotechnology. 36: 103-112. *contributed equally; #jointly supervised this work

Yitbarek A., Alkie T., Taha-Abdelaziz K., Astill J., Rodriguez-Lecompte J.C., Parkinson J., Nagy E. and Sharif S. (2018) Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2. Beneficial Microbes. 9: 417-427.

Malty R.H., Aoki H., Kumar A., Phanse S., Amin S., Zhang Q., Minic Z., Goebels F., Musso G., Wu Z., Abou-tok H., Meyer M.J., Deineko V., Kassir S., Sidhu V., Jessulat M., Scott N.E., Xiong X., Vlasblom J., Prasad B., Foster L.J., Alberio T., Garavaglia B., Yu H., Bader G.D., Nakamura K., Parkinson J., and Babu M. (2017) A map of human mitochondrial protein interactions linked to neurodegeneration reveals new mechanisms of redox homeostasis and NF-kB signaling. Cell Systems. 5(6):564-577.e12

Xiong X., Bales C.E., Ir D., Robertson C.E., McManaman J.L., Frank D.N.# and Parkinson J.# (2017) Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. Microbiome. 5:117. #jointly supervised this work

Zhang J., Khan A., Kennard A., Grigg M.E. and Parkinson J. (2017) PopNet: A Markov Clustering Approach to Study Population Genetic Structure. Molecular Biology and Evolution. 34(7):1799-1811.

Swapna L.S. and Parkinson J. (2017) Genomics of Apicomplexan Parasites. Critical Reviews in Biochemistry and Molecular Biology. 52(3): 254-273

Vetere G., Kenney J.W., Tran L.M., Xia F., Steadman P.E., Parkinson J., Josselyn S.A. and Frankland P.W. (2017) Chemogenetic interrogation of a brain-wide fear memory network in mice. Neuron. 94: 363-374.e4

Bertschi N.L., Toenhake C.G., Zou A., Niederwieser I., Henderson R., Moes S., Jenoe P., Parkinson J.,, Bartfai R. and Voss T.S. (2017) Malaria parasites possess a telomere repeat-binding protein that shares ancestry with transcription factor IIIA. Nature Microbiology. 2:17033.

Cotton J.A., Bennuru S., Grote A., Harsha B., Tracey A., Beech R., Doyle S.R., Dunn M., Hotopp J.C.D., Holroyd N., Kikuchi T., Lambert O., Mhashilkar A., Mutowo P., Nursimulu N., Ribeiro J.M.C., Rogers M.B., Stanley E., Swapna L.S., Tsai I.J., Unnasch T.R., Voronin D., Parkinson J., Nutman T.B., Ghedin E., Berriman M. and Lustigman S. (2016) The genome of Onchocerca volvulus, agent of river blindness. Nature Microbiology. 2:16216

Di Giovanni V., Bourdon C., Wang D., Swapna L., Senga E., Versloot C., Voskuijl W., Semba R., Trehan I., Moaddel R., Ordiz M., Zhang L., Parkinson J., Manary M. and Bandsma R. (2016) Metabolomic changes in serum of children with different clinical diagnoses of malnutrition. The Journal of Nutrition. 146(12):2436-2444.

Cromar, GL., Zhao, A., Xiong, X., Swapna, LS., Loughran, N., Song, H. and Parkinson, J.(2016) PhyloPro2.0: A database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. Database. pii: baw013.

Phanse, S., Wan, C., Borgeson, B., Tu, F., Drew, K., Clark, G., Xiong, X., Kagan, O., Kwan, J., Berzginov, A., Chessman, K., Pal, S., Cromar, G., Papoulas, O., Ni, Z., Boutz, DR., Stoilova, S., Havugimana, P., Guo, X., Malty, R., Sarov, M., Greenblatt, J., Babu, M., Derry, WB., Tillier, E., Wallingford, J., Parkinson, J., Marcotte, E. and Emili, A. (2016). Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Data in Brief. 6: 715–721.

Jiang, Y., Xiong, X., Danska, J. and Parkinson, J.(2016) Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. Microbiome. 4:2

Kumar, A.*, Beloglazova, N.*, Bundalovic-Torma, C.*, Phanse, S., Deineko, V., Gagarinova, A., Musso, G., Vlasblom, J., Lemak, S., Hooshyar, M., Minic, Z., Wagih, O., Mosca, R., Aloy, P., Golshani, A., Parkinson, J.,* Emili A.*, Yakunin, A.*, and Babu, M.* (2016) Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli. Cell Reports. pii: S2211-1247(15)01501-6.

Lorenzi, H., Khan, A., Behnke, M., Namasivayam, S., Swapna, LS., Hadjithomas, M., Karamycheva, S., Pinney, D., Brunk, B., Ajioka, J., Ajzenberg, D., Boothroyd, J., Boyle, J., Darde, M., Diaz-Miranda, MA, Dubey, JP., Fritz, H., Gennari, SM., Gregory, B., Kim, K., Saeij, JPJ., Su, C., White, MW., Zhu, X-Q., Howe, DK., Rosenthal, BM., Grigg, ME., Parkinson, J.,Liu, L., Kissinger, JC., Roos, DS. and Sibley, LD. (2016) Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. Nature Communications. 7:10147

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