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Taj B, Adeolu M, Xiong X, Ang J, Nursimulu N, Parkinson J. MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities. Microbiome. 2023 Jun 27;11(1):143. doi: 10.1186/s40168-023-01562-6. PubMed PMID: 37370188; PubMed Central PMCID: PMC10294448.
Nursimulu N, Moses AM, Parkinson J. Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation. PLoS Comput Biol. 2022 Sep;18(9):e1010452. doi: 10.1371/journal.pcbi.1010452. eCollection 2022 Sep. PubMed PMID: 36074804; PubMed Central PMCID: PMC9488769.
Zou A, Nadeau K, Xiong X, Wang PW, Copeland JK, Lee JY, Pierre JS, Ty M, Taj B, Brumell JH, Guttman DS, Sharif S, Korver D, Parkinson J. Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure. Microbiome. 2022 Aug 15;10(1):127. doi: 10.1186/s40168-022-01319-7. PubMed PMID: 35965349; PubMed Central PMCID: PMC9377095.
Cromar GL, Epp JR, Popovic A, Gu Y, Ha V, Walters BJ, St Pierre J, Xiong X, Howland JG, Josselyn SA, Frankland PW, Parkinson J. Toxoplasma infection in male mice alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease. PLoS Negl Trop Dis. 2022 Jul;16(7):e0010600. doi: 10.1371/journal.pntd.0010600. eCollection 2022 Jul. PubMed PMID: 35857765; PubMed Central PMCID: PMC9342775.
Kairmi SH, Taha-Abdelaziz K, Yitbarek A, Sargolzaei M, Spahany H, Astill J, Shojadoost B, Alizadeh M, Kulkarni RR, Parkinson J, Sharif S. Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens. Poult Sci. 2022 Jun;101(6):101864. doi: 10.1016/j.psj.2022.101864. Epub 2022 Mar 17. PubMed PMID: 35477134; PubMed Central PMCID: PMC9061639.
Ty M, Taha-Abdelaziz K, Demey V, Castex M, Sharif S, Parkinson J. Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry. Anim Microbiome. 2022 Jan 3;4(1):2. doi: 10.1186/s42523-021-00157-6. PubMed PMID: 34980288; PubMed Central PMCID: PMC8722297.
Popovic A, Bourdon C, Wang PW, Guttman DS, Soofi S, Bhutta ZA, Bandsma RHJ, Parkinson J, Pell LG. Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut. Nat Commun. 2021 Nov 18;12(1):6729. doi: 10.1038/s41467-021-27010-3. PubMed PMID: 34795270; PubMed Central PMCID: PMC8602372.
Jiang JX, Wellhauser L, Laselva O, Utkina I, Bozoky Z, Gunawardena T, Ngan Z, Xia S, Di Paola M, Eckford PDW, Ratjen F, Moraes TJ, Parkinson J, Wong AP, Bear CE. A new platform for high-throughput therapy testing on iPSC-derived lung progenitor cells from cystic fibrosis patients. Stem Cell Reports. 2021 Nov 9;16(11):2825-2837. doi: 10.1016/j.stemcr.2021.09.020. Epub 2021 Oct 21. PubMed PMID: 34678210; PubMed Central PMCID: PMC8581165.
Dacquay LC, Tsang D, Chan D, Parkinson J, Philpott DJ, McMillen DR. E.coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis. Gut Microbes. 2021 Jan-Dec;13(1):1994832. doi: 10.1080/19490976.2021.1994832. PubMed PMID: 34751631; PubMed Central PMCID: PMC8583297.
Curran DM, Grote A, Nursimulu N, Geber A, Voronin D, Jones DR, Ghedin E, Parkinson J. Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. Elife. 2020 Aug 11;9. doi: 10.7554/eLife.51850. PubMed PMID: 32779567; PubMed Central PMCID: PMC7419141.
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, Abdullatif AA, 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, Emili A. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst. 2020 Apr 22;10(4):333-350.e14. doi: 10.1016/j.cels.2020.03.003. PubMed PMID: 32325033; PubMed Central PMCID: PMC7938770.
Bundalovic-Torma C, Whitfield GB, Marmont LS, Howell PL, Parkinson J. A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. PLoS Comput Biol. 2020 Apr;16(4):e1007721. doi: 10.1371/journal.pcbi.1007721. eCollection 2020 Apr. PubMed PMID: 32236097; PubMed Central PMCID: PMC7112194.
Whitfield GB, Marmont LS, Bundalovic-Torma C, Razvi E, Roach EJ, Khursigara CM, Parkinson J, Howell PL. Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster. PLoS Pathog. 2020 Apr;16(4):e1008281. doi: 10.1371/journal.ppat.1008281. eCollection 2020 Apr. PubMed PMID: 32236137; PubMed Central PMCID: PMC7112168.
Zou A, Nadeau K, Wang PW, Lee JY, Guttman DS, Sharif S, Korver DR, Brumell JH, Parkinson J. Accumulation of genetic variants associated with immunity in the selective breeding of broilers. BMC Genet. 2020 Jan 17;21(1):5. doi: 10.1186/s12863-020-0807-z. PubMed PMID: 31952471; PubMed Central PMCID: PMC6969402.
Yitbarek A, Astill J, Hodgins DC, Parkinson J, Nagy É, Sharif S. Commensal gut microbiota can modulate adaptive immune responses in chickens vaccinated with whole inactivated avian influenza virus subtype H9N2. Vaccine. 2019 Oct 16;37(44):6640-6647. doi: 10.1016/j.vaccine.2019.09.046. Epub 2019 Sep 18. PubMed PMID: 31542262.
Zhang J, Parkinson J. PopNetD3-A Network-Based Web Resource for Exploring Population Structure. Genome Biol Evol. 2019 Jul 1;11(7):1730-1735. doi: 10.1093/gbe/evz100. PubMed PMID: 31095319; PubMed Central PMCID: PMC6668580.
Comparative genomics of the major parasitic worms. Nat Genet. 2019 Jan;51(1):163-174. doi: 10.1038/s41588-018-0262-1. Epub 2018 Nov 5. PubMed PMID: 30397333; PubMed Central PMCID: PMC6349046.
Popovic A, Bourdon C, Wang PW, Guttman DS, Voskuijl W, Grigg ME, Bandsma RHJ, Parkinson J. Design and application of a novel two-amplicon approach for defining eukaryotic microbiota. Microbiome. 2018 Dec 20;6(1):228. doi: 10.1186/s40168-018-0612-3. PubMed PMID: 30572961; PubMed Central PMCID: PMC6302507.
Zou A, Sharif S, Parkinson J. Lactobacillus elicits a 'Marmite effect' on the chicken cecal microbiome. NPJ Biofilms Microbiomes. 2018;4:27. doi: 10.1038/s41522-018-0070-5. eCollection 2018. PubMed PMID: 30455975; PubMed Central PMCID: PMC6226495.
Nursimulu N, Xu LL, Wasmuth JD, Krukov I, Parkinson J. Improved enzyme annotation with EC-specific cutoffs using DETECT v2. Bioinformatics. 2018 Oct 1;34(19):3393-3395. doi: 10.1093/bioinformatics/bty368. PubMed PMID: 29722785; PubMed Central PMCID: PMC6157075.
Yitbarek A, Taha-Abdelaziz K, Hodgins DC, Read L, Nagy É, Weese JS, Caswell JL, Parkinson J, Sharif S. Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses. Sci Rep. 2018 Sep 4;8(1):13189. doi: 10.1038/s41598-018-31613-0. PubMed PMID: 30181578; PubMed Central PMCID: PMC6123399.
Swapna LS, Molinaro AM, Lindsay-Mosher N, Pearson BJ, Parkinson J. Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. Genome Biol. 2018 Aug 24;19(1):124. doi: 10.1186/s13059-018-1498-x. PubMed PMID: 30143032; PubMed Central PMCID: PMC6109357.
Yitbarek A, Alkie T, Taha-Abdelaziz K, Astill J, Rodriguez-Lecompte JC, Parkinson J, Nagy É, Sharif S. Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2. Benef Microbes. 2018 Apr 25;9(3):417-427. doi: 10.3920/BM2017.0088. Epub 2018 Jan 30. PubMed PMID: 29380643.
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 JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A. Global landscape of cell envelope protein complexes in Escherichia coli. Nat Biotechnol. 2018 Jan;36(1):103-112. doi: 10.1038/nbt.4024. Epub 2017 Nov 27. PubMed PMID: 29176613; PubMed Central PMCID: PMC5922438.
Adeolu M, Parkinson J, Xiong X. Analyzing Metabolic Pathways in Microbiomes. Methods Mol Biol. 2018;1849:291-307. doi: 10.1007/978-1-4939-8728-3_18. PubMed PMID: 30298261.
Yitbarek A, Weese JS, Alkie TN, Parkinson J, Sharif S. Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens. FEMS Microbiol Ecol. 2018 Jan 1;94(1). doi: 10.1093/femsec/fix165. PubMed PMID: 29228270.
Popovic A, Parkinson J. Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing. Methods Mol Biol. 2018;1849:29-48. doi: 10.1007/978-1-4939-8728-3_3. PubMed PMID: 30298246.
Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M. A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling. Cell Syst. 2017 Dec 27;5(6):564-577.e12. doi: 10.1016/j.cels.2017.10.010. Epub 2017 Nov 8. PubMed PMID: 29128334; PubMed Central PMCID: PMC5746455.
Xiong X, Bales ES, Ir D, Robertson CE, McManaman JL, Frank DN, Parkinson J. Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. Microbiome. 2017 Sep 6;5(1):117. doi: 10.1186/s40168-017-0327-x. PubMed PMID: 28877764; PubMed Central PMCID: PMC5588750.
Zhang J, Khan A, Kennard A, Grigg ME, Parkinson J. PopNet: A Markov Clustering Approach to Study Population Genetic Structure. Mol Biol Evol. 2017 Jul 1;34(7):1799-1811. doi: 10.1093/molbev/msx110. PubMed PMID: 28383661; PubMed Central PMCID: PMC5850731.
Swapna LS, Parkinson J. Genomics of apicomplexan parasites. Crit Rev Biochem Mol Biol. 2017 Jun;52(3):254-273. doi: 10.1080/10409238.2017.1290043. Epub 2017 Feb 22. Review. PubMed PMID: 28276701; PubMed Central PMCID: PMC6813780.
Vetere G, Kenney JW, Tran LM, Xia F, Steadman PE, Parkinson J, Josselyn SA, Frankland PW. Chemogenetic Interrogation of a Brain-wide Fear Memory Network in Mice. Neuron. 2017 Apr 19;94(2):363-374.e4. doi: 10.1016/j.neuron.2017.03.037. PubMed PMID: 28426969.
Bertschi NL, Toenhake CG, Zou A, Niederwieser I, Henderson R, Moes S, Jenoe P, Parkinson J, Bartfai R, Voss TS. Malaria parasites possess a telomere repeat-binding protein that shares ancestry with transcription factor IIIA. Nat Microbiol. 2017 Mar 13;2:17033. doi: 10.1038/nmicrobiol.2017.33. PubMed PMID: 28288093.
Di Giovanni V, Bourdon C, Wang DX, Seshadri S, Senga E, Versloot CJ, Voskuijl W, Semba RD, Trehan I, Moaddel R, Ordiz MI, Zhang L, Parkinson J, Manary MJ, Bandsma RH. Metabolomic Changes in Serum of Children with Different Clinical Diagnoses of Malnutrition. J Nutr. 2016 Dec;146(12):2436-2444. doi: 10.3945/jn.116.239145. Epub 2016 Nov 2. PubMed PMID: 27807038; PubMed Central PMCID: PMC5118769.
Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. The genome of Onchocerca volvulus, agent of river blindness. Nat Microbiol. 2016 Nov 21;2:16216. doi: 10.1038/nmicrobiol.2016.216. PubMed PMID: 27869790; PubMed Central PMCID: PMC5310847.
Cromar GL, Zhao A, Xiong X, Swapna LS, Loughran N, Song H, Parkinson J. PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. Database (Oxford). 2016;2016. doi: 10.1093/database/baw013. Print 2016. PubMed PMID: 26980519; PubMed Central PMCID: PMC4792532.
Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Data Brief. 2016 Mar;6:715-21. doi: 10.1016/j.dib.2015.11.062. eCollection 2016 Mar. PubMed PMID: 26870755; PubMed Central PMCID: PMC4738005.
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 AF, Babu M. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli. Cell Rep. 2016 Jan 26;14(3):648-661. doi: 10.1016/j.celrep.2015.12.060. Epub 2016 Jan 8. PubMed PMID: 26774489.
Jiang Y, Xiong X, Danska J, Parkinson J. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. Microbiome. 2016 Jan 12;4:2. doi: 10.1186/s40168-015-0146-x. PubMed PMID: 26757703; PubMed Central PMCID: PMC4710996.
Lorenzi H, Khan A, Behnke MS, Namasivayam S, Swapna LS, Hadjithomas M, Karamycheva S, Pinney D, Brunk BP, Ajioka JW, Ajzenberg D, Boothroyd JC, Boyle JP, Dardé ML, Diaz-Miranda MA, Dubey JP, Fritz HM, Gennari SM, Gregory BD, Kim K, Saeij JP, Su C, White MW, Zhu XQ, Howe DK, Rosenthal BM, Grigg ME, Parkinson J, Liu L, Kissinger JC, Roos DS, Sibley LD. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. Nat Commun. 2016 Jan 7;7:10147. doi: 10.1038/ncomms10147. PubMed PMID: 26738725; PubMed Central PMCID: PMC4729833.
Cromar GL, Zhao A, Yang A, Parkinson J. Hyperscape: visualization for complex biological networks. Bioinformatics. 2015 Oct 15;31(20):3390-1. doi: 10.1093/bioinformatics/btv385. Epub 2015 Jun 24. PubMed PMID: 26108529.
Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Panorama of ancient metazoan macromolecular complexes. Nature. 2015 Sep 17;525(7569):339-44. doi: 10.1038/nature14877. Epub 2015 Sep 7. PubMed PMID: 26344197; PubMed Central PMCID: PMC5036527.
Zhang Y, Rowehl L, Krumsiek JM, Orner EP, Shaikh N, Tarr PI, Sodergren E, Weinstock GM, Boedeker EC, Xiong X, Parkinson J, Frank DN, Li E, Gathungu G. Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PLoS One. 2015;10(6):e0130902. doi: 10.1371/journal.pone.0130902. eCollection 2015. PubMed PMID: 26125937; PubMed Central PMCID: PMC4509574.
Blazejewski T, Nursimulu N, Pszenny V, Dangoudoubiyam S, Namasivayam S, Chiasson MA, Chessman K, Tonkin M, Swapna LS, Hung SS, Bridgers J, Ricklefs SM, Boulanger MJ, Dubey JP, Porcella SF, Kissinger JC, Howe DK, Grigg ME, Parkinson J. Systems-based analysis of the Sarcocystis neurona genome identifies pathways that contribute to a heteroxenous life cycle. mBio. 2015 Feb 10;6(1). doi: 10.1128/mBio.02445-14. PubMed PMID: 25670772; PubMed Central PMCID: PMC4337577.
Wetzel J, Herrmann S, Swapna LS, Prusty D, John Peter AT, Kono M, Saini S, Nellimarla S, Wong TW, Wilcke L, Ramsay O, Cabrera A, Biller L, Heincke D, Mossman K, Spielmann T, Ungermann C, Parkinson J, Gilberger TW. The role of palmitoylation for protein recruitment to the inner membrane complex of the malaria parasite. J Biol Chem. 2015 Jan 16;290(3):1712-28. doi: 10.1074/jbc.M114.598094. Epub 2014 Nov 25. PubMed PMID: 25425642; PubMed Central PMCID: PMC4340414.
Bundalovic-Torma C, Parkinson J. Comparative Genomics and Evolutionary Modularity of Prokaryotes. Adv Exp Med Biol. 2015;883:77-96. doi: 10.1007/978-3-319-23603-2_4. Review. PubMed PMID: 26621462.
Celaj A, Markle J, Danska J, Parkinson J. Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. Microbiome. 2014;2:39. doi: 10.1186/2049-2618-2-39. eCollection 2014. PubMed PMID: 25411636; PubMed Central PMCID: PMC4236897.
Cromar G, Wong KC, Loughran N, On T, Song H, Xiong X, Zhang Z, Parkinson J. New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. Genome Biol Evol. 2014 Oct 15;6(10):2897-917. doi: 10.1093/gbe/evu228. PubMed PMID: 25323955; PubMed Central PMCID: PMC4224354.
Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Res. 2014 Oct;24(10):1676-85. doi: 10.1101/gr.168955.113. Epub 2014 Jul 11. PubMed PMID: 25015382; PubMed Central PMCID: PMC4199364.
Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet. 2014 Feb;10(2):e1004120. doi: 10.1371/journal.pgen.1004120. eCollection 2014 Feb. PubMed PMID: 24586182; PubMed Central PMCID: PMC3930520.
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