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(Contributions from lab members, past and present, in bold)


  1. Swapna L., Stevens G., Sardinha da Silva A., Hu LZ., Brand V., Fusca DD., Xiong X., Boyle JP., Grigg ME., Emili A., Parkinson J.: ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii reveals novel virulence factors implicated in host cell invasion. BioArxiv 2021.09.14.460186; doi:
  2. Taj , B.,* Adeolu, M.,* Xiong, X., Nursimulu, N., Ang, J. and Parkinson, J. MetaPro: A scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities. BioArxiv 2021.02.23.432558; doi: *Both authors contributed equally to the work


  1. Nursimulu, N., Moses, AM. andParkinson J. (2022) Architect: a tool for producing high-quality metabolic models through improved enzyme annotation. PLoS Computational Biology. 18(9): e1010452.
  2. Zou, A.†, Nadeau, K.†, Xiong, X.†, Wang, PW., Copeland, JK., Lee, JY., St Pierre, J., Ty, M., Taj, B., Brumell, JH., Guttman, DS., Sharif, S., Korver, D. and Parkinson, J. (2022) 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. 10:127. †These authors contributed equally
  3. Cromar, GL.†, Epp J.,†, Popovic, A., Gu, Y., Ha, V., Walters, B., St. Pierre, J., Xiong, X., Howland, J., Josselyn, S., Frankland, PW.* and Parkinson, J.* (2022) Toxoplasma infection alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease. PLoS Neglected Tropical Diseases. 16(7): e0010600. † These authors contributed equally; * These authors are considered co-senior/corresponding authors
  4. Ty, M., Taha-Abdelaziz, K., Demey, V., Castex, M., Sharif, S. and Parkinson, J. (2022) Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry. Animal Microbiome. 4:2.
  5. Kairimi, SH., Taha-Abdelaziz, K., Yitbarek, A.. Sargolzaei, M., Spahany, H., Astill, J., Shojadoost, B., Alizadeh, M., Kulkarni, RR., Parkinson, J. and Sharif, S. (2022) Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens. Poultry Science. 101(6):101864.


  1. 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.
  2. 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.
  3. 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
  4. 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.


  1. 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
  2. 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.
  3. 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.
  4. 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
  5. 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.


  1. 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.
  2. Zhang, J. and Parkinson, J. (2019) PopNetD3 – A network based web resource for exploring population structure. Genome Biology and Evolution. 11(7):1730-1735.
  3. International Helminths Genome Consortium (2019) Comparative genomics of the major parasitic worms. Nature Genetics. 51(1):163-174.


  1. 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.
  2. Zou, A., Sharif, S. and Parkinson, J. (2018) Lactobacillus elicits a “Marmite effect” on the chicken cecal microbiome. NPJ Biofilms and Microbiome. 4: 27.
  3. Adeolu, M., Parkinson, J. and Xiong, X. (2018) Analyzing Metabolic Pathways in Microbiomes. Methods Mol Biol. 1849:291-307.
  4. Popovic, A. and Parkinson, J. (2018) Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing. Methods Mol Biol. 1849:29-48.
  5. 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
  6. 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.
  7. 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.
  8. 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
  9. 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
  10. 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.

  1. 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
  2. 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
  3. 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.
  4. Swapna L.S. and Parkinson J. (2017) Genomics of Apicomplexan Parasites. Critical Reviews in Biochemistry and Molecular Biology. 52(3): 254-273
  5. 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
  6. 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.


  1. 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
  2. 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.
  3. 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.
  4. 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.
  5. 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
  6. 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.
  7. 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


  1. Bundalovic-Torma, C. & Parkinson, J. (2015) Comparative Genomics and Evolutionary Modularity of Prokaryotes. in Prokaryotic Systems Biology, Vol. 883 (eds. Krogan, P.N.J. & Babu, P.M.) 77-96 (Springer International Publishing).
  2. Wan, C., Borgeson, B., Phanse, S., 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. (2015). Panorama of ancient metazoan macromolecular complexes. Nature. 525(7569):339-44.
  3. Cromar, G., Zhao, A., Yang, A. and Parkinson, J.(2015) Hyperscape: Visualization for complex biological networks. Bioinformatics. 31(20): 3390-1.
  4. Zhang, Y., Rowehl, L., Krumsiek, J.F., Orner, E.P., Shaikh, N., Tarr, P.I., Sodergren, E., Weinstock, G.M., Boedeker, E.C., Xiong, X., Parkinson, J.,Frank, D.N., Li, E., Gathungu, G.(2015) Identification of candidate adherent-invasive E. coli signature transcripts by genomic/transcriptomic analysis. PLoS ONE. 10(6): e0130902.
  5. Blazejewski T., Nursimulu N., Pszenny V., Dangoudoubiyam S., Namasivayam S., Chiasson M.A., Chessman K., Tonkin M., Swapna L.S., Hung S.S., Bridgers J., Ricklefs S.M., Boulanger M.J., Dubey J.P., Porcella S.F., Kissinger J.C., Howe D.K., Grigg M.E. and Parkinson J. (2015) Systems based analysis of the Sarcocystis neurona genome identified pathways that contribute to a heteroxenous life cycle. mBio. 6(1). pii: e02445-14.
  6. Wetzel, J., Herrmann, S., Prusty, D., John Peter, A., Swapna LS, Saini, S., Nellimarla, S., Wong, T., Kono, K., Wilcke, L., Cabrera, A., Biller, L., Spielmann, T., Mossman, K., Ungermann , C., Parkinson, J. and Gilberger, T. (2015) Sequence specific recruitment of proteins to the Inner Membrane Complex of the malaria parasite. Journal of Biological Chemistry. 290(3):1712-28


  1. Cromar, G., Wong, K-C., Loughran, N.B., On, T., Song, H., Xiong, X., Zhang, Z. and Parkinson, J. (2014) New tricks for ‘old’ domains: How novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. Genome Biology and Evolution. 6: 2897-2917.
  2. Celaj, A., Markle, J., Danska, J. and Parkinson, J. (2014) Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. Microbiome. 2:39.
  3. Reid, A.J., Blake, D.P., Ansari, H.R., Billington, K., Browne, H.P., Dunn, M., Hung, S.S., Kawahara, F., Miranda-Saavedra, D., Malas, T.B., Mourier, T., Nagra, H., Nair, M., Otto, T.D., Rawlings, N.D., Rivailler, P., Sanchez-Flores, A., Sanders, M., Subramaniam, C., Tay, Y-L.L., Wu, X., Dear, P.H., Doerig, C., Gruber, A., Ivens, A.C., Parkinson, J., Shirley, M.W., Wan, K-L., Berriman, M., Tomley, F.M. and Pain, A. (2014) Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Research. 24: 1676-1685.
  4. Babu M.*, Arnold, R.*, Bundalovic-Torma, C.*, Gagarinova, A.*, Wong, K.S.*, Kumar, A., Stewart, G., Samanfar, B., Aoki, H., Wagih, O., Vlasblom, J., Phanse, S., Lad, K., Yu, A.Y.H., Graham, C., Jin, K., Brown, E., Golshani, A., Kim, P., Moreno-Hagelsieb, G., Greenblatt, J., Houry, W.A., Parkinson, J. and Emili, A. (2014) Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli. PLoS Genetics. 10(2): e1004120. *these authors contributed equally.


  1. Song, C., Chiasson, M.A., Nursimulu, N., Hung, S.S., Wasmuth, J., Grigg, M.E., and Parkinson, J. (2013) Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii. Molecular Systems Biology. 9: 708.
  2. Leung, H.C.M., Yiu, S-M., Parkinson, J. and Chin, F.Y.L. (2013) IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology. Journal of Computational Biology. 20(7): 540-550.
  3. Tsai, I.J., Zarowiecki, M., Holroyd, N., Garciarrubio, A., Sanchez-Flores, A., Brooks, K.L., Tracey, A., Bobes, R.J., Fragoso, G., Sciutto, E., Aslett, M., Beasley, H., Bennett, H.M., Cai, J., Camicia, F., Clark, R., Cucher, M., De Silva, N., Day, T.A., Deplazes, P., Estrada, K., Fernández, C., Holland, P.W.H., Hou, J., Hu, S., Huckvale, T., Hung, S.S., Kamenetzky, L., Keane, J.A., Kiss, F., Koziol, U., Lambert, O., Liu, K., Luo, X., Luo, Y., Macchiaroli, N., Nichol, S., Paps, J., Parkinson, J., Pouchkina-Stantcheva, N., Riddiford, N., Rosenzvit, M., Salinas, G., Wasmuth, J.D., Zamanian, M., Zheng, Y., The Taenia solium Genome Consortium, Cai, X., Soberón, X., Olson, P.D., Laclette, J.P., Brehm, K. and Berriman, M. (2013) The genomes of four tapeworm species reveal adaptations to parasitism. Nature.496: 57-63
  4. Khoshraftar, S., Hung, S.S., Khan, S., Gong, Y., Tyagi, V., Parkinson, J., Sain, M., Moses, A.M. and Christendat, D. (2013) Sequencing and annotation of the Ophiostoma ulmi genome. BMC Genomics. 14:162
  5. Kono, M., Prusty, D., Parkinson, J. and Gilberger, T.W. (2013) A membranous system in the spotlight. Frontiers in Bioscience. 18: 982-992.
  6. Wheeler, A.L., Teixeira, C.M., Wang, A.H., Xiong, X., Lerch, J.P., McIntosh, A.R., Parkinson, J. and Frankland, P.W. (2013) Identification of a functional connectome for long-term fear memory in mice. PLoS Computational Biology. 9(1):e1002853.


  1. Parkinson, J., Wasmuth, J.D., Salinas, G., Bizarro, C.V., Sanford, C., Berriman, M., Ferreira, H.B., Zaha, A., Blaxter, M.L., Maizels, R.M., Fernandez, C. (2012) A Transcriptomic Analysis of Echinococcus granulosus Larval Stages: Implications for Parasite Biology and Host Adaptation. PLoS Neglected Tropical Diseases. 6(11): e1897.
  2. Wasmuth, J.D., Pszenny, V., Haile, S., Jansen, E.M., Gast, A.T., Boyle, J., Boulanger, M.J., Parkinson, J.* and Grigg, M.E.* (2012) Integrated bioinformatic and targeted deletion analyses of the SRS gene superfamily identify SRS2 as a negative regulator of Toxoplasma virulence. mBio. 3(6):e00321-12.*co-corresponding authors
  3. Urban, D., Li, L., Christensen, H., Pluthero, F.G., Chen, S.Z., Puhacz, M., Garg, P.M., Lanka, K.K., Cummings, J.J., Kramer, H., Wasmuth, J.D., Parkinson, J. and Kahr, W.H.A. (2012) The VPS33B binding protein VPS16B is required in megakaryocyte and platelet ?-granule biogenesis. Blood. 120(25): 5032-40.
  4. He, D., Miao, M., Sitarz, E.E., Muiznieks, L.D., Reichheld, S., Stahl, R.J., Keeley, F.W. and Parkinson, J. (2012) Polymorphisms in the Human Tropoelastin Gene Modify in vitro Self-Assembly and Mechanical Properties of Elastin-like Polypeptides. PLoS ONE. 7(9): e46130.
  5. Xiong, X., Frank, D.N., Robertson, C.E., Hung, S.S., Markle, J., Canty, A.J., McCoy, K.D., Macpherson, A.J., Poussier, P., Danska, J.S., and Parkinson, J. (2012) Generation and Analysis of a Mouse Intestinal Metatranscriptome Through Illumina Based RNA-Sequencing. PLoS ONE. 7(4):e36009.
  6. Kono, M., Herrmann, S., Loughran, N.B., Cabrera, A., Engelberg, K., Lehmann, C., Sinha, D., Prinz, B., Ruch, U., Heussler, V., Spielman, T., Parkinson, J.* and Gilberger, T.W.* (2012) Evolution and architecture of the inner membrane complex in the asexual and sexual stages of the malaria parasite. Mol. Biol. Evol. 29(9):2113-32. *co-corresponding authors
  7. Reid, A.J., Vermont, S.J., Cotton, J.A., Harris, D., Hill-Cawthorne, G.A., Könen-Waisman, S., Latham, S., Mourier, T., Norton, R., Quail, M.A., Sanders, M., Shanmugam, D., Sohal, A., Wasmuth, J.D., Brunk, B., Grigg, M.E., Howard, J.C., Parkinson, J., Roos, D.S., Trees, A.J., Berriman, M., Pain, A. and Wastling, J.M. (2012) Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathogens.8(3): e1002567.
  8. Song, H. and Parkinson, J. (2012) Modelling the self-assembly of elastomeric proteins provides insights into the evolution of their domain architectures. PLoS Computational Biol. 8(3): e1002406
  9. Cromar, G.L., Xiong, X., Chautard, E., Ricard-Blum, S. and Parkinson, J. (2012) Towards a systems level view of the ECM and related proteins: A framework for the systematic definition and analysis of biological systems. Proteins. 80:1522–1544.


  1. Babu, M., Díaz-Mejía, J.J., Vlasblom, J., Gagarinova, A., Phanse, S., Graham, C., Arnold, R., Yousif, F., Ding, H., Xiong, X., Nazarians-Armavil, A., Alamgir, M., Ali, M., Pogoutse, O., Pe?er, A., Parkinson, J., Golshani, A., Whitfield, C., Wodak, S.J., Moreno-Hagelsieb, G., Greenblatt, J.F. and Emil, A. (2011) Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways. PLoS Genetics. 7(11): e1002377.
  2. Kahr, W.H.A., Hinckley, J., Li, L., Schwertz, H., Christensen, H., Rowley, J.W., Pluthero, F.G., Urban, D., Fabbro, S., Nixon, B., Gadzinski, R., Storck, M., Wang, K., Ryu, G-Y., Jobe, S.M., Schutte, B.C., Moseley, J., Loughran, N.B., Parkinson, J., Weyrich, A.S., Di Paola, J. (2011) Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome. Nature Genetics. 43(8): 738-40.
  3. Xiong, X., Song, H., On, T., Lochovsky, L., Provart, N. and Parkinson, J. (2011) Phylopro: A web based tool for the generation and visualization of phylogenetic profiles across Eukarya. Bioinformatics. 27(6):877-8
  4. Turinsky, A.L., Turner, B., Borja, R.C., Gleeson, J.A., Heath, M., Pu, S., Switzer, T., Dong, D., Gong, Y., On, T., Xiong, X., Emili, A., Greenblatt, J., Parkinson, J., Zhang, Z., Wodak, S.J. (2011) DAnCER: Disease-Annotated Chromatin Epigenetics Resource. Nucleic Acids Res. 39:D889-94.
  5. Hung, S. and Parkinson, J. (2011) Post-genomics Resources and Tools for Studying Apicomplexan Metabolism. Trends in Parasitology. 27(3):131-40..


  1. Pu, S., Turinsky, A.L., Vlasblom, J., On, T., Xiong, X., Emili, A., Zhang, Z., Greenblatt, J., Parkinson, J., and Wodak, S.J. (2010) Expanding the Landscape of Chromatin Modification (CM)-Related Functional Domains and Genes in Human. PloS ONE 5(11):e14122
  2. Yu, Z., Reichheld, S.E., Savchenko, A., Parkinson, J. and Davidson, A.R. (2010) A Comprehensive Analysis of Structural and Sequence Conservation in the TetR Family Transcriptional Regulators. J. Mol. Biol. 400: 847-864
  3. Hung, S., Wasmuth, J., Sanford, C. and Parkinson, J. (2010) DETECT - A Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum. Bioinformatics. 26: 1690-1698
  4. On, T., Xiong, X., Pu, S., Turinsky, A., Gong, Y., Emili, A., Zhang, Z., Greenblatt, J., Wodak, SJ. and Parkinson, J. (2010) The evolutionary landscape of the chromatin modification machinery. Proteins. 78:2075-2089
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  1. Peregrin-Alvarez, J.M., Xiong, X., Su, C. and Parkinson, J. (2009) The modular organization of protein interactions in Escherichia coli. PLoS Computational Biol. 5(10): e1000523.
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  1. Aznarez, I., Barash, Y., Shai, O., He, D., Zielenski, J., Tsui, L-C., Parkinson, J., Frey, B.J., Rommens, J.M. and Blencowe, B.J. (2008) A systematic analysis of intronic sequences downstream of 5´ splice sites reveals a widespread role for U-rich motifs and TIA-1/TIAR proteins in alternative splicing regulation. Genome Research. 18: 1247-1258.
  2. He, D. and Parkinson, J. (2008) SubSeqer: A graph-based approach for the detection and identification of repetitive elements in low-complexity sequences. Bioinformatics. 24: 1016-17.
  3. Su, C., Peregrin-Alvarez, J.M., Butland, G., Phanse, S., Fong, V., Emili, A. and Parkinson, J. (2008) – An integrated protein interaction database for E. coli. Nucleic Acids Research. 36: D632-36


  1. Peregrin-Alvarez, J.M. and Parkinson, J. (2007) The Global Landscape of Sequence Diversity. Genome Biology. 8:R238
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  1. Sanford, C.*, Yip, M.L.K.*, White, C. and Parkinson, J. (2006) Cell++ - simulating biochemical pathways within a spatial context. Bioinformatics. 22(23):2918-25.
  2. Chung, M.I.S., Miao, M., Stahl, R.J., Chan, E., Parkinson, J. and Keeley, F.W. (2006) Sequences and domain structures of mammalian, avian, amphibian and teleost tropoelastins: clues to the evolutionary history of elastins. Matrix Biology. 25(8):492-504.
  3. Mitreva, M., Wendl, M.C., Martin, J., Wylie, T., Yin, Y., Larson, A., Parkinson, J., Waterston, R.H. and McCarter, J.P. (2006) Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biology 7, R75.
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  1. Soares D.C., Gerloff D.L., Syme N.R., Coulson A.F., Parkinson J., Barlow P.N. (2005) Large-scale modelling as a route to multiple surface comparisons of the CCP module family. Protein Eng Des Sel. 18, 379-88.
  2. Butland, G., Peregrin-Alvarez, J.M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J., Emili, A. (2005) Interaction Network Containing Conserved and Essential Protein Complexes in Escherichia coli. Nature. 433, 531-537.
  3. Peregrin-Alvarez, J., Yam, A., Sivakumar, G., Parkinson, J. (2005) PartiGeneDB - Collating partial genomes. Nucleic Acids Research. 33, D303-307
  4. Gordon, R., Parkinson, J., (2005) Potential Roles for Diatomists in Nanotechnology. J. NanoSci. Nanotech. 5, 35-40.


  1. Parkinson, J., Mitreva, M., Whitton, C., Thomson, M., Daub, J., Martin, J., Schmid, R., Hall, N., Barrell, B., Waterston, R.H., McCarter, J.P., Blaxter, M.L., (2004) A transcriptomic analysis of the phylum Nematoda. Nature Genetics. 36, 1259-1267.
  2. Parkinson, J., Anthony, A., Wasmuth, J., Hedley, B.A. Blaxter, M. (2004) PartiGene - Constructing Partial Genomes. Bioinformatics 20, 1398-1404.
  3. Harcus, Y.M., Parkinson, J., Fernandez, C., Daub, J., Selkirk, M.E., Blaxter, M.L., Maizels, R.M. (2004) Signal sequence analysis of ESTs from the nematode Nippostrongylus brasiliensis and the evolution of parasite secreted proteins. Genome Biology. 5, R39.
  4. Parkinson, J., Whitton, C., Schmid, R., Thomson, M., Blaxter, M. (2004) NEMBASE - a resource for parasitic nematode ESTs. Nucleic Acids Research, 32, D427-D430.
  5. Parkinson, J., Blaxter, M. (2004) Expressed sequence tags: analysis and annotation. Methods Mol Biol. 270, 93-126.


  1. Sturzenbaum, S.R., Parkinson, J., Blaxter, M., Morgan, A.J., Kille, P., Georgiev, O. (2003) The earthworm EST sequencing project. Pedobiologia. 47, 447-451.
  2. Parkinson, J., Mitreva, M., Hall, N., Blaxter, M., McCarter, J. (2003) 400,000 Nematode ESTs on the Net. TRENDS in Parasitol. 19, 283-286.
  3. Kenyon, F., Welsh, M., Parkinson, J., Whitton, C., Blaxter, M.L., Knox, D.P. (2003) Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis allergens, proteinases and free radical scavengers. Parasitology, 126, 451-460.
  4. Gregory, W., Parkinson, J. (2003) Caenorhabditis elegans - Entering the Post-Genomic Era. Comp. Funct. Genom. 4, 194-202.
  5. Parkinson, J. Blaxter, M.L. (2003) SimiTri - Visualising similarity relationships for groups of sequences. Bioinformatics. 19, 390-395.


  1. Parkinson J., Guiliano D.B., Blaxter M. (2002) Making sense of EST sequences by CLOBBing them. BMC Bioinformatics. 3, 31.
  2. Loke P., Nair M.G., Parkinson J., Guiliano D., Blaxter M., Allen J.E. (2002) IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype. BMC Immunol. 3, 7.
  3. Parkinson, J., Blaxter, M. (2002) NEMBASE: Dealing with fragmented genomes. Comp. Biochem. Physiol. A. 132, S90-S91.
  4. Blaxter, M., Daub, J., Guiliano, D., Parkinson, J., Whitton, C., (2002) The Brugia malayi genome project: expressed sequence tags and gene discovery. Trans. Roy. Soc. Trop. Med. Hyg. 96, 7-17.


  1. Parkinson, J., Whitton, C., Guiliano, D., Daub, J., Blaxter, M. (2001) 200 000 nematode expressed sequence tags on the net. TRENDS in Parasitol. 17, 394-396.
  2. Loukas, A., Hintz, M., Linder, D., Mullin, N.P., Parkinson, J., Tetteh, K.K., Maizels, R.M. (2000) A family of secreted mucins from the parasitic nematode Toxocara canis bears diverse mucin domains but shares similar flanking six-cysteine repeat motifs. J. Biol. Chem. 275, 39600-39607.
  3. Liszewski, M.K., Leung, M., Cui, W., Subramanian, V.B., Parkinson, J., Barlow, P.N., Manchester, M., Atkinson, J.P (2000) Dissecting sites important for complement regulatory activity in membrane cofactor protein (MCP; CD46). J. Biol. Chem. 275, 37692-37701.
  4. Smith, S.A., Mullin, N.P., Parkinson, J., Shchelkunov, S.N., Totmenin, A.V., Loparev, V.N., Srisatjaluk, R., Reynolds, D.N., Keeling, K.L., Justus, D.E., Barlow, P.N., Kotwal, G.J. (2000) Conserved surface-exposed K/R-X-K/R motifs and net positive charge on poxvirus complement control proteins serve as putative heparin binding sites and contribute to inhibition of molecular interactions with human endothelial cells: a novel mechanism for evasion of host defense. J. Virol. 74, 5659-5666.
  5. Kirkitadze, M.D., Henderson, C., Price, N.C., Kelly, S.M., Mullin, N.P., Parkinson J., Dryden, D.T., Barlow, P.N. (1999) Central modules of the vaccinia virus complement control protein are not in extensive contact. Biochem J. 344, 167-175.
  6. Parkinson, J., Brechet, Y. & Gordon, R. (1999) Centric Diatom Morphogenesis : A Model Based on a DLA Algorithm Investigating the Potential Role of Microtubules. Biochim. Biophys. Acta. 1452, 89-102.
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  8. Parkinson, J., Brass, A., Canova, G. & Brechet, Y. (1997) Mechanical properties of simulated collagen fibrils. J. Biomech. 30, 549-554.
  9. Mack, D., Nishimura, K., Dennehey, B. K., Arbogast, T., Parkinson, J., Toh-E, A., Pringle, J. R., Bender, A. & Matsui, Y. (1996). Identification of the bud emergence gene BEM4 and its interactions with Rho-type GTPases in Saccharomyces cerevsiae. Mol. Cell. Biol. 16, 4387-4395.
  10. Parkinson, J., Kadler, K. E. & Brass, A. (1995). A model of type I collagen fibrillogenesis based on diffusion limited aggregation. J. Biol. Sys. 3, 1033-1039.
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