For those interested in numbers, see Benjamin’s google scholar citations profile.
We try to include links for all of our papers. Some of the links open PDFs, others direct you to a journal’s site where that particular publication is available for download. If you cannot access one of our papers, let us know. The copyright notice for these papers is listed at the bottom of the page.
Hoang, M.T.V., Irinyi, L., Hu, Y., Schwessinger, B., Meyer, W., 2022. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front. Microbiol. 12. https://doi.org/10.3389/fmicb.2021.708550
Schwessinger, B.$, Jones, A., Albekaa, M., Hu, Y., Mackenzie, A., Tam, R., Nagar, R., Milgate, A., Rathjen, J.P$., Periyannan, S. $, 2022. A Chromosome Scale Assembly of an Australian Puccinia striiformis f. sp. tritici Isolate of the PstS1 Lineage. Mol. Plant-Microbe Interactions 35, 293–296. https://doi.org/10.1094/MPMI-09-21-0236-A
Duan, H.#, Jones, A.W.#, Hewitt, T., Mackenzie, A., Hu, Y., Sharp, A., Lewis, D., Mago, R., Upadhyaya, N.M., Rathjen, J.P., Stone, E.A., Schwessinger, B., Figueroa, M., Dodds, P.N., Periyannan, S., Sperschneider, J., 2022. Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data. Genome Biol. 23, 84. https://doi.org/10.1186/s13059-022-02658-2
Hu, Y., Irinyi, L., Hoang, M.T.V., Eenjes, T., Graetz, A., Stone, E.A., Meyer, W., Schwessinger, B.$, Rathjen, J.P.$, 2022. Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data. mBio 13, e02444-21. https://doi.org/10.1128/mbio.02444-21
Poudel, B., Purushotham, N., Jones, A., Nasim, J., Adorada, D.L., Sparks, A.H., Schwessinger, B., Vaghefi, N., 2022. The First Annotated Genome Assembly of Macrophomina tecta Associated with Charcoal Rot of Sorghum. Genome Biol. Evol. 14, evac081. https://doi.org/10.1093/gbe/evac081
Kent, B.A., Holman, C., Amoako, E., Antonietti, A., Azam, J.M., Ballhausen, H., Bediako, Y., Belasen, A.M., Carneiro, C.F.D., Chen, Y.-C., Compeer, E.B., Connor, C.A.C., Crüwell, S., Debat, H., Dorris, E., Ebrahimi, H., Erlich, J.C., Fernández-Chiappe, F., Fischer, F., Gazda, M.A., Glatz, T., Grabitz, P., Heise, V., Kent, D.G., Lo, H., McDowell, G., Mehta, D., Neumann, W.-J., Neves, K., Patterson, M., Penfold, N.C., Piper, S.K., Puebla, I., Quashie, P.K., Quezada, C.P., Riley, J.L., Rohmann, J.L., Saladi, S., Schwessinger, B., Siegerink, B., Stehlik, P., Tzilivaki, A., Umbers, K.D.L., Varma, A., Walavalkar, K., Winde, C.M. de, Zaza, C., Weissgerber, T.L., 2022. Recommendations for empowering early career researchers to improve research culture and practice. PLOS Biol. 20, e3001680. https://doi.org/10.1371/journal.pbio.3001680
Ferguson, S., Jones, A., Murray, K., Schwessinger, B., Borevitz, J.O., n.d. Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus. Mol. Ecol. n/a. https://doi.org/10.1111/mec.16608
Powell, D., Jones, A., Kent, N., Kaur, P., Bar, I., Schwessinger, B., Frère, C.H., 2021. Genome Sequence of the Fungus Nannizziopsis barbatae, an Emerging Reptile Pathogen. Microbiol. Resour. Announc. 10, e01213-20. https://doi.org/10.1128/MRA.01213-20.
Sarabipour, S., Khan, A., Seah, Y.F.S. et al. Changing scientific meetings for the better. Nat Hum Behav 5, 296–300 (2021). https://doi.org/10.1038/s41562-021-01067-y
Auer, S., Haeltermann, N.A., Weissberger, T.L., Erlich, J.C., Susilaradeya, D., Julkowska, M., Gazda, M.A., Schwessinger, B. $, Jadavji, N.M. $, Reproducibility for Everyone Team, 2021. A community-led initiative for training in reproducible research. eLife 10, e64719. https://doi.org/10.7554/eLife.64719
Jones, A.$, Torkel, C., Stanley, D., Nasim, J., Borevitz, J., Schwessinger, B., 2021. High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing. PLOS ONE 16, e0253830. https://doi.org/10.1371/journal.pone.0253830
Lane, C.R., Sherry, N.L., Porter, A.F., Duchene, S., Horan, K., Andersson, P., Wilmot, M., … Schwessinger, B. et al. (2021), Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study, The Lancet Public Health, pp. S2468-2667(21)00133-X. https://doi.org/10.1016/S2468-2667(21)00133-X
Sperschneider, J., Jones, A.W., Nasim, J., Xu, B., Jacques, S., Zhong, C., Upadhyaya, N.M., Mago, R., Hu, Y., Figueroa, M., Singh, K.B., Stone, E.A., Schwessinger, B., Wang, M.-B., Taylor, J.M., Dodds, P.N., 2021. The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation. BMC Biol. 19, 203. https://doi.org/10.1186/s12915-021-01123-z))))
Bender, K.W., Couto, D., Kadota, Y., Macho, A.P., Sklenar, J., Derbyshire, P., Bjornson, M., DeFalco, T.A., Petriello, A., Font Farre, M., Schwessinger, B., Ntoukakis, V., Stransfeld, L., Jones, A.M.E., Menke, F.L.H., Zipfel, C., 2021. Activation loop phosphorylation of a non-RD receptor kinase initiates plant innate immune signaling. Proc. Natl. Acad. Sci. 118, e2108242118. https://doi.org/10.1073/pnas.2108242118
Distinct life histories impact dikaryotic genome evolution in the rust fungus Puccinia striiformis causing stripe rust in wheat
Benjamin Schwessinger, Yan-Jun Chen, Richard Tien, Josef Korbinian Vogt, Jana Sperschneider, Ramawatar Nagar, Mark McMullan, Thomas Sicheritz-Ponten, Chris K Sørensen, Mogens Støvring Hovmøller, John P Rathjen, Annemarie Fejer Justesen. Genome Biology and Evolution, evaa071, doi: https://doi.org/10.1093/gbe/evaa071
Draft Genome Resource for Macrophomina phaseolina Associated With Charcoal Rot in Sorghum
Purushotham N, Jones A, Poudel B, Nasim J, Adorada D, Sparks A, Schwessinger B, Vaghefi N. Mol Plant Microbe Interact. 2020 May;33(5):724-726. doi: 10.1094/MPMI-12-19-0356-A. Epub 2020 Mar 24. PMID: 32096690
The Rice Xa3 Gene Confers Resistance to Xanthomonas oryzae pv. oryzae in the Model Rice Kitaake Genetic Background
Liu F, Zhang W, Schwessinger B, Wei T, Ruan D, Ronald P. Front Plant Sci. 2020 Feb 6;11:49. doi: 10.3389/fpls.2020.00049. eCollection 2020.
PMID: 32117387
The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies
Wang W, Das A, Kainer D, Schalamun M, Morales-Suarez A, Schwessinger B, Lanfear R. Gigascience. 2020 Jan 1;9(1):giz160. doi: 10.1093/gigascience/giz160. PMID: 31895413; PMCID: PMC6939829.
Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics
Laszlo Irinyi, Yiheng Hu, Minh Thuy Vi Hoang, Lana Pasic, Catriona Halliday, Menuk Jayawardena, Indira Basu, Wendy McKinney, Arthur J Morris, John Rathjen, Eric Stone, Sharon Chen, Tania C Sorrell, Benjamin Schwessinger, Wieland Meyer. Med Mycol. 2020 July;58(5):650-660. https://doi.org/10.1093/mmy/myz109. PMID: 31758176.
Blurred lines: integrating emerging technologies to advance plant biosecurity
Yiheng Hu, Salome Wilson, Benjamin Schwessinger, John P Rathjen. Current Opinion in Plant Biology. 2020 Aug;56:127-134. https://doi.org/10.1016/j.pbi.2020.04.011. PMID: 32610220.
Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia
Somasundhari Shanmuganandam, Yiheng Hu, Tanja Strive, Benjamin Schwessinger, Robyn N. Hall. PeerJ. 2020 Aug 18;8:e9564. doi: 10.7717/peerj.9564. PMID: 32874776; PMCID: PMC7441920.
Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene
Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Phytopathology. 2021 Jan;111(1):49-67. doi: 10.1094/PHYTO-08-20-0358-FI Epub 2020 Dec 18. PMID: 33200962.
Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
Peri A Tobias, Benjamin Schwessinger, Cecilia H Deng, Chen Wu, Chongmei Dong, Jana Sperschneider, Ashley Jones, Zhenyan Lou, Peng Zhang, Karanjeet Sandhu, Grant R Smith, Josquin Tibbits, David Chagné, Robert F Park, G3 GenesGenomesGenetics, Volume 11, Issue 3, March 2021, jkaa015, https://doi.org/10.1093/g3journal/jkaa015
Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics
Irinyi L, Hu Y, Hoang MTV, Pasic L, Halliday C, Jayawardena M, Basu I, McKinney W, Morris AJ, Rathjen J, Stone E, Chen S, Sorrell TC, Schwessinger B, Meyer W. Med Mycol. 2019 Nov 23:myz109. doi: 10.1093/mmy/myz109. Online ahead of print. PMID: 31758176
Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation
Li F, Upadhyaya NM, Sperschneider J, Matny O, Nguyen-Phuc H, Mago R, Raley C, Miller ME, Silverstein KAT, Henningsen E, Hirsch CD, Visser B, Pretorius ZA, Steffenson BJ, Schwessinger B, Dodds PN, Figueroa M. Nat Commun. 2019 Nov 7;10(1):5068. doi: 10.1038/s41467-019-12927-7. PMID: 31699975
Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens
Megan C. McDonald, Adam P. Taranto, Erin Hill, Benjamin Schwessinger, Zhaohui Liu, Steven Simpfendorfer, Andrew Milgate, Peter S. Solomon. mBio Sep 2019, 10 (5) e01515-19; doi: 10.1128/mBio.01515-19
Pathogen Detection and Microbiome Analysis of Infected Wheat Using a Portable DNA Sequencer
Y. Hu, G. S. Green, A. W. Milgate, E. A. Stone, J. P. Rathjen and B. Schwessinger Phytobiomes Journal, 0, PBIOMES-01-19-0004-R. doi: 10.1094/pbiomes-01-19-0004-r. PDF available here
On the value of preprints: An early career researcher perspective
S. Sarabipour, H. J. Debat, E. Emmott, S. J. Burgess, B. Schwessinger and Z. Hensel 2019. PLoS biology, 17, e3000151. doi: 10.1371/journal.pbio.3000151. PDF available here
Variation and inheritance of the Xanthomonas raxX-raxSTAB gene cluster required for activation of XA21-mediated immunity
F. Liu, M. McDonald, B. Schwessinger, A. Joe, R. Pruitt, T. Erickson, X. Zhao, V. Stewart and P. C. Ronald 2019. Molecular Plant Pathology, 20, 656-672. doi: 10.1111/mpp.12783. PDF available here
MinIONQC: fast and simple quality control for MinION sequencing data
R. Lanfear, M. Schalamun, D. Kainer, W. Wang and B. Schwessinger 2019. Bioinformatics (Oxford, England), 35, 523-525. doi: 10.1093/bioinformatics/bty654. PDF available here
Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora
M. Schalamun, R. Nagar, D. Kainer, E. Beavan, D. Eccles, J. P. Rathjen, R. Lanfear and B. Schwessinger 2019. Molecular Ecology Resources, 19, 77-89. doi: 10.1111/1755-0998.12938. PDF available here
Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case
W. Wang, M. Schalamun, A. Morales-Suarez, D. Kainer, B. Schwessinger and R. Lanfear 2018. BMC genomics, 19, 977. doi: 10.1186/s12864-018-5348-8. PDF available here
The rice XA21 ectodomain fused to the Arabidopsis EFR cytoplasmic domain confers resistance to Xanthomonas oryzae pv. oryzae
N. C. Thomas, N. Oksenberg, F. Liu, D. Caddell, A. Nalyvayko, Y. Nguyen, B. Schwessinger and P. C. Ronald 2018. PeerJ, 6, e4456. doi: 10.7717/peerj.4456. PDF available here
A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity
B. Schwessinger, J. Sperschneider, W. S. Cuddy, D. P. Garnica, M. E. Miller, J. M. Taylor, P. N. Dodds, M. Figueroa, R. F. Park and J. P. Rathjen 2018. mBio, 9. doi: 10.1128/mBio.02275-17. PDF available here
Author Correction: Phosphocode-dependent functional dichotomy of a common co-receptor in plant signalling
A. Perraki, T. A. DeFalco, P. Derbyshire, J. Avila, D. Séré, J. Sklenar, X. Qi, L. Stransfeld, B. Schwessinger, Y. Kadota, A. P. Macho, S. Jiang, D. Couto, K. U. Torii, F. L. H. Menke and C. Zipfel 2018. Nature, 563, E30. doi: 10.1038/s41586-018-0663-4. PDF available here
Phosphocode-dependent functional dichotomy of a common co-receptor in plant signalling
A. Perraki, T. A. DeFalco, P. Derbyshire, J. Avila, D. Séré, J. Sklenar, X. Qi, L. Stransfeld, B. Schwessinger, Y. Kadota, A. P. Macho, S. Jiang, D. Couto, K. U. Torii, F. L. H. Menke and C. Zipfel 2018. Nature, 561, 248-252. doi: 10.1038/s41586-018-0471-x. PDF available here
De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust
M. E. Miller, Y. Zhang, V. Omidvar, J. Sperschneider, B. Schwessinger, C. Raley, J. M. Palmer, D. Garnica, N. Upadhyaya, J. Rathjen, J. M. Taylor, R. F. Park, P. N. Dodds, C. D. Hirsch, S. F. Kianian and M. Figueroa 2018. mBio, 9. doi: 10.1128/mBio.01650-17. PDF available here
Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides
E. Thynne, I. M. L. Saur, J. Simbaqueba, H. A. Ogilvie, Y. Gonzalez-Cendales, O. Mead, A. Taranto, A.-M. Catanzariti, M. C. McDonald, B. Schwessinger, D. A. Jones, J. P. Rathjen and P. S. Solomon 2017. Molecular Plant Pathology, 18, 811-824. doi: 10.1111/mpp.12444. PDF available here
Tyrosine-610 in the Receptor Kinase BAK1 Does Not Play a Major Role in Brassinosteroid Signaling or Innate Immunity
V. Singh, A. Perraki, S. Y. Kim, S. Shrivastava, J. H. Lee, Y. Zhao, B. Schwessinger, M.-H. Oh, A. Marshall-Colon, C. Zipfel and S. C. Huber 2017. Frontiers in Plant Science, 8, 1273. doi: 10.3389/fpls.2017.01273. PDF available here
Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing
B. Schwessinger and J. P. Rathjen 2017. Methods in Molecular Biology (Clifton, N.J.), 1659, 49-57. doi: 10.1007/978-1-4939-7249-4_5.
Fundamental wheat stripe rust research in the 21st century
B. Schwessinger 2017. The New Phytologist, 213, 1625-1631. doi: 10.1111/nph.14159. PDF available here
A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone
R. N. Pruitt, A. Joe, W. Zhang, W. Feng, V. Stewart, B. Schwessinger, J. R. Dinneny and P. C. Ronald 2017. The New Phytologist, 215, 725-736. doi: 10.1111/nph.14609. PDF available here
A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination
W. Pornsiriwong, G. M. Estavillo, K. X. Chan, E. E. Tee, D. Ganguly, P. A. Crisp, S. Y. Phua, C. Zhao, J. Qiu, J. Park, M. T. Yong, N. Nisar, A. K. Yadav, B. Schwessinger, J. Rathjen, C. I. Cazzonelli, P. B. Wilson, M. Gilliham, Z.-H. Chen and B. J. Pogson 2017. eLife, 6. doi: 10.7554/eLife.23361. PDF available here
XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves
N. C. Thomas, B. Schwessinger, F. Liu, H. Chen, T. Wei, Y. P. Nguyen, I. W. F. Shaker and P. C. Ronald 2016. PeerJ, 4, e2446. doi: 10.7717/peerj.2446. PDF available here
A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection
B. Schwessinger, X. Li, T. L. Ellinghaus, L. J. G. Chan, T. Wei, A. Joe, N. Thomas, R. Pruitt, P. D. Adams, M. S. Chern, C. J. Petzold, C. C. Liu and P. C. Ronald 2016. Integrative Biology: Quantitative Biosciences from Nano to Macro, 8, 542-545. doi: 10.1039/c5ib00232j. PDF available here
Structural Analysis of an Avr4 Effector Ortholog Offers Insight into Chitin Binding and Recognition by the Cf-4 Receptor
A. C. Kohler, L.-H. Chen, N. Hurlburt, A. Salvucci, B. Schwessinger, A. J. Fisher and I. Stergiopoulos 2016. The Plant Cell, 28, 1945-1965. doi: 10.1105/tpc.15.00893. PDF available here
Bacterial Outer Membrane Vesicles Induce Plant Immune Responses
O. Bahar, G. Mordukhovich, D. D. Luu, B. Schwessinger, A. Daudi, A. K. Jehle, G. Felix and P. C. Ronald 2016. Molecular plant-microbe interactions: MPMI, 29, 374-384. doi: 10.1094/MPMI-12-15-0270-R. PDF available here
Changing SERKs and priorities during plant life
B. Schwessinger and J. P. Rathjen 2015. Trends in Plant Science, 20, 531-533. doi: 10.1016/j.tplants.2015.06.006. PDF available here
Focus issue on plant immunity: from model systems to crop species
B. Schwessinger, R. Bart, K. V. Krasileva and G. Coaker 2015. Frontiers in Plant Science, 6, 195. doi: 10.3389/fpls.2015.00195. PDF available here
Correction: Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses
B. Schwessinger, O. Bahar, N. Thomas, N. Holton, V. Nekrasov, D. Ruan, P. E. Canlas, A. Daudi, C. J. Petzold, V. R. Singan, R. Kuo, M. Chovatia, C. Daum, J. L. Heazlewood, C. Zipfel and P. C. Ronald 2015. PLoS pathogens, 11, e1004872. doi: 10.1371/journal.ppat.1004872. PDF available here
Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses
B. Schwessinger, O. Bahar, N. Thomas, N. Thomas, N. Holton, V. Nekrasov, D. Ruan, P. E. Canlas, A. Daudi, C. J. Petzold, V. R. Singan, R. Kuo, M. Chovatia, C. Daum, J. L. Heazlewood, C. Zipfel and P. C. Ronald 2015. PLoS pathogens, 11, e1004809. doi: 10.1371/journal.ppat.1004809. PDF available here
The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium
R. N. Pruitt, B. Schwessinger, A. Joe, N. Thomas, F. Liu, M. Albert, M. R. Robinson, L. J. G. Chan, D. D. Luu, H. Chen, O. Bahar, A. Daudi, D. De Vleesschauwer, D. Caddell, W. Zhang, X. Zhao, X. Li, J. L. Heazlewood, D. Ruan, D. Majumder, M. Chern, H. Kalbacher, S. Midha, P. B. Patil, R. V. Sonti, C. J. Petzold, C. C. Liu, J. S. Brodbelt, G. Felix and P. C. Ronald 2015. Science Advances, 1, e1500245. doi: 10.1126/sciadv.1500245. PDF available here
Proteome profile of the endomembrane of developing coleoptiles from switchgrass (Panicum virgatum)
J. Lao, M. K. Sharma, R. Sharma, S. M. G. Fernández-Niño, J. Schmutz, P. C. Ronald, J. L. Heazlewood and B. Schwessinger 2015. Proteomics, 15, 2286-2290. doi: 10.1002/pmic.201400487. PDF available here
OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae
S. Zuo, X. Zhou, M. Chen, S. Zhang, B. Schwessinger, D. Ruan, C. Yuan, J. Wang, X. Chen and P. C. Ronald 2014. Journal of Integrative Plant Biology, 56, 1179-1192. doi: 10.1111/jipb.12290. PDF available here
Antagonistic regulation of growth and immunity by the Arabidopsis basic helix-loop-helix transcription factor homolog of brassinosteroid enhanced expression2 interacting with increased leaf inclination1 binding bHLH1
F. G. Malinovsky, M. Batoux, B. Schwessinger, J. H. Youn, L. Stransfeld, J. Win, S.-K. Kim and C. Zipfel 2014. Plant Physiology, 164, 1443-1455. doi: 10.1104/pp.113.234625. PDF available here
A bacterial tyrosine phosphatase inhibits plant pattern recognition receptor activation
A. P. Macho, B. Schwessinger, V. Ntoukakis, A. Brutus, C. Segonzac, S. Roy, Y. Kadota, M.-H. Oh, J. Sklenar, P. Derbyshire, R. Lozano-Durán, F. G. Malinovsky, J. Monaghan, F. L. Menke, S. C. Huber, S. Y. He and C. Zipfel 2014. Science (New York, N.Y.), 343, 1509-1512. doi: 10.1126/science.1248849. PDF available here
An XA21-associated kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors
X. Chen, S. Zuo, B. Schwessinger, M. Chern, P. E. Canlas, D. Ruan, X. Zhou, J. Wang, A. Daudi, C. J. Petzold, J. L. Heazlewood and P. C. Ronald 2014. Molecular Plant, 7, 874-892. doi: 10.1093/mp/ssu003. PDF available here
The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles
O. Bahar, R. Pruitt, D. D. Luu, B. Schwessinger, A. Daudi, F. Liu, R. Ruan, L. Fontaine-Bodin, R. Koebnik and P. Ronald 2014. PeerJ, 2, e242. doi: 10.7717/peerj.242. PDF available here
How postdocs benefit from building a union
B. Cain, J. M. Budke, K. J. Wood, N. T. Sweeney and B. Schwessinger 2014. eLife, 3. doi: 10.7554/eLife.05614. PDF available here
A common signaling process that promotes mycorrhizal and oomycete colonization of plants
E. Wang, S. Schornack, J. F. Marsh, E. Gobbato, B. Schwessinger, P. Eastmond, M. Schultze, S. Kamoun and G. E. D. Oldroyd 2012. Current biology: CB, 22, 2242-2246. doi: 10.1016/j.cub.2012.09.043. PDF available here
Plant innate immunity: perception of conserved microbial signatures
B. Schwessinger and P. C. Ronald 2012. Annual Review of Plant Biology, 63, 451-482. doi: 10.1146/annurev-arplant-042811-105518. PDF available here
Tyrosine sulfation in a Gram-negative bacterium
S.-W. Han, S.-W. Lee, O. Bahar, B. Schwessinger, M. R. Robinson, J. B. Shaw, J. A. Madsen, J. S. Brodbelt and P. C. Ronald 2012. Nature Communications, 3, 1153. doi: 10.1038/ncomms2157. PDF available here
Non-arginine-aspartate (non-RD) kinases are associated with innate immune receptors that recognize conserved microbial signatures
C. Dardick, B. Schwessinger and P. Ronald 2012. Current Opinion in Plant Biology, 15, 358-366. doi: 10.1016/j.pbi.2012.05.002. PDF available here
Brassinosteroids inhibit pathogen-associated molecular pattern-triggered immune signaling independent of the receptor kinase BAK1
C. Albrecht, F. Boutrot, C. Segonzac, B. Schwessinger, S. Gimenez-Ibanez, D. Chinchilla, J. P. Rathjen, S. C. de Vries and C. Zipfel 2012. Proceedings of the National Academy of Sciences of the United States of America, 109, 303-308. doi: 10.1073/pnas.1109921108. PDF available here
An XA21-associated Kinase 1 (XAK1) regulates immunity mediated by the pattern-recognition receptor XA21
M. Chern, P. E. Canlas, B. Schwessinger and P. C. Ronald 2012. From Plant Science to Agricultural Development - Proceedings of the 2012 National Conference on Plant Biology. ed. China. doi:10.1093/mp/ssu003. PDF available here
Phosphorylation-dependent differential regulation of plant growth, cell death, and innate immunity by the regulatory receptor-like kinase BAK1
B. Schwessinger, M. Roux, Y. Kadota, V. Ntoukakis, J. Sklenar, A. Jones and C. Zipfel 2011. PLoS genetics, 7, e1002046. doi: 10.1371/journal.pgen.1002046. PDF available here
The Arabidopsis leucine-rich repeat receptor-like kinases BAK1/SERK3 and BKK1/SERK4 are required for innate immunity to hemibiotrophic and biotrophic pathogens
M. Roux, B. Schwessinger, C. Albrecht, D. Chinchilla, A. Jones, N. Holton, F. G. Malinovsky, M. Tör, S. de Vries and C. Zipfel 2011. The Plant Cell, 23, 2440-2455. doi: 10.1105/tpc.111.084301. PDF available here
Cautionary notes on the use of C-terminal BAK1 fusion proteins for functional studies
V. Ntoukakis, B. Schwessinger, C. Segonzac and C. Zipfel 2011. The Plant Cell, 23, 3871-3878. doi: 10.1105/tpc.111.090779. PDF available here
Genetic analysis of signalling components of PAMP-triggered immunity (PTI) in plants
B. Schwessinger. 2010. University of East Anglia. . PDF available here
Control of the pattern-recognition receptor EFR by an ER protein complex in plant immunity
V. Nekrasov, J. Li, M. Batoux, M. Roux, Z.-H. Chu, S. Lacombe, A. Rougon, P. Bittel, M. Kiss-Papp, D. Chinchilla, H. P. van Esse, L. Jorda, B. Schwessinger, V. Nicaise, B. P. H. J. Thomma, A. Molina, J. D. G. Jones and C. Zipfel 2009. The EMBO journal, 28, 3428-3438. doi: 10.1038/emboj.2009.262. PDF available here
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
B. J. Haas, S. Kamoun, M. C. Zody, R. H. Y. Jiang, R. E. Handsaker, L. M. Cano, M. Grabherr, C. D. Kodira, S. Raffaele, T. Torto-Alalibo, T. O. Bozkurt, A. M. V. Ah-Fong, L. Alvarado, V. L. Anderson, M. R. Armstrong, A. Avrova, L. Baxter, J. Beynon, P. C. Boevink, S. R. Bollmann, J. I. B. Bos, V. Bulone, G. Cai, C. Cakir, J. C. Carrington, M. Chawner, L. Conti, S. Costanzo, R. Ewan, N. Fahlgren, M. A. Fischbach, J. Fugelstad, E. M. Gilroy, S. Gnerre, P. J. Green, L. J. Grenville-Briggs, J. Griffith, N. J. Grünwald, K. Horn, N. R. Horner, C.-H. Hu, E. Huitema, D.-H. Jeong, A. M. E. Jones, J. D. G. Jones, R. W. Jones, E. K. Karlsson, S. G. Kunjeti, K. Lamour, Z. Liu, L. Ma, D. Maclean, M. C. Chibucos, H. McDonald, J. McWalters, H. J. G. Meijer, W. Morgan, P. F. Morris, C. A. Munro, K. O’Neill, M. Ospina-Giraldo, A. Pinzón, L. Pritchard, B. Ramsahoye, Q. Ren, S. Restrepo, S. Roy, A. Sadanandom, A. Savidor, S. Schornack, D. C. Schwartz, U. D. Schumann, B. Schwessinger, L. Seyer, T. Sharpe, C. Silvar, J. Song, D. J. Studholme, S. Sykes, M. Thines, P. J. I. van de Vondervoort, V. Phuntumart, S. Wawra, R. Weide, J. Win, C. Young, S. Zhou, W. Fry, B. C. Meyers, P. van West, J. Ristaino, F. Govers, P. R. J. Birch, S. C. Whisson, H. S. Judelson and C. Nusbaum 2009. Nature, 461, 393-398. doi: 10.1038/nature08358. PDF available here
News from the frontline: recent insights into PAMP-triggered immunity in plants
B. Schwessinger and C. Zipfel 2008. Current Opinion in Plant Biology, 11, 389-395. doi: 10.1016/j.pbi.2008.06.001. PDF available here
Small ubiquitin-like modifier proteases OVERLY TOLERANT TO SALT1 and -2 regulate salt stress responses in Arabidopsis
L. Conti, G. Price, E. O’Donnell, B. Schwessinger, P. Dominy and A. Sadanandom 2008. The Plant Cell, 20, 2894-2908. doi: 10.1105/tpc.108.058669. PDF available here
Engineering pathogen resistance in plants
B. S. Pamela Ronald, Rory Pruitt, Anna Joe, Weiguo Zhang. 2018. US patent application 15382461. PDF available here
Pathogen Detection and Microbiome Analysis of Infected Wheat Using a Portable DNA Sequencer
Y. Hu, G. S. Green, A. W. Milgate, E. A. Stone, J. P. Rathjen and B. Schwessinger 2019. bioRxiv, 429878. doi: 10.1101/429878
Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case
W. Wang, M. Schalamun, A. M. Suarez, D. Kainer, B. Schwessinger and R. Lanfear 2018. bioRxiv, 320085. doi: 10.1101/320085
A comprehensive toolkit to enable MinION long-read sequencing in any laboratory
M. Schalamun, D. Kainer, E. Beavan, R. Nagar, D. Eccles, J. Rathjen, R. Lanfear and B. Schwessinger 2018. bioRxiv, 289579. doi: 10.1101/289579
On the value of preprints: an early career researcher perspective
S. Sarabipour, H. J. Debat, E. Emmott, S. Burgess, B. Schwessinger and Z. Hensel 2018. PeerJ Preprints. doi: 10.7287/peerj.preprints.27400v1
Variation and inheritance of the Xanthomonas gene cluster required for activation of XA21-mediated immunity
F. Liu, M. McDonald, B. Schwessinger, A. Joe, R. Pruitt, T. Erickson, X. Zhao, V. Stewart and P. C. Ronald 2018. bioRxiv, 149930. doi: 10.1101/149930
De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust
M. E. Miller, Y. Zhang, V. Omidvar, J. Sperschneider, B. Schwessinger, C. Raley, J. M. Palmer, D. Garnica, N. Upadhyaya, J. Rathjen, J. M. Taylor, R. F. Park, P. N. Dodds, C. D. Hirsch, S. F. Kianian and M. Figueroa 2017. bioRxiv, 179226. doi: 10.1101/179226
A microbially derived tyrosine sulfated peptide mimics a plant peptide hormone
R. N. Pruitt, A. Joe, W. Zhang, W. Feng, V. Stewart, B. Schwessinger, J. R. Dinneny and P. C. Ronald 2017. bioRxiv, 116897. doi: 10.1101/116897
A near complete haplotype-phased genome of the dikaryotic wheat stripe rust fungus Puccinia striiformis f. sp. tritici reveals high inter-haplotype diversity
B. Schwessinger, J. Sperschneider, W. S. Cuddy, D. P. Garnica, M. E. Miller, J. M. Taylor, P. N. Dodds, M. Figueroa, P. F. Robert and J. Rathjen 2017. bioRxiv, 192435. doi: 10.1101/192435
The Rice XA21 Ectodomain Fused to the Arabidopsis EFR Cytoplasmic Domain Confers Resistance to Xanthomonas oryzae pv. oryzae
N. Thomas, N. Oksenberg, F. Liu, D. Caddell, A. Nalyvayko, Y. Nguyen, B. Schwessinger and P. Ronald 2017. bioRxiv, 119925. doi: 10.1101/119925
XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves
N. C. Thomas, B. Schwessinger, F. Liu, H. Chen, T. Wei, Y. P. Nguyen, I. W. F. Shaker and P. C. Ronald 2016. PeerJ Preprints. doi: 10.7287/peerj.preprints.2289v1
Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses
B. Schwessinger, O. Bahar, N. Thomas, N. Holton, V. Nekrasov, D. Ruan, P. E. Canlas, A. Daudi, C. J. Petzold, V. R. Singan, R. Kuo, M. Chovatia, C. Daum, J. L. Heazlewood, C. Zipfel and P. C. Ronald 2015. bioRxiv, 006155. doi: 10.1101/006155
An XA21-Associated Kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors
X. Chen, S. Zuo, B. Schwessinger, M. Chern, P. E. Canlas, D. Ruan, X. Zhou, J. Wang, A. Daudi, C. J. Petzold, J. L. Heazlewood and P. C. Ronald 2013. bioRxiv, 000950. doi: 10.1101/000950
The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles
O. Bahar, R. N. Pruitt, D. D. Luu, B. Schwessinger, R. Ruan, L. Fontaine-Bodin, R. Koebnik and P. Ronald 2013. PeerJ PrePrints. doi: 10.7282/peerjpr.preprints.109v1
Maintaining confidence in the reporting of scientific outputs
S. Sarabipour, E. M. Wissink, S. J. Burgess, Z. Hensel, H. Debat, E. Emmott, A. Akay, K. Akdemir and B. Schwessinger 2018. PeerJ Preprints. doi: 10.7287/peerj.preprints.27098v1
The stem rust fungus Puccinia graminis f. sp. tritici induces waves of small RNAs with opposing profiles during wheat infection
Jana Sperschneider, Silke Jacques, Bo Xu, Narayana M. Upadhyaya, Rohit Mago, Ashley W. Jones, Benjamin Schwessinger, Melania Figueroa, Karam B. Singh, Eric A. Stone, Ming-Bo Wang, Jennifer M. Taylor, Peter N. Dodds. bioRxiv 469338; doi: https://doi.org/10.1101/469338
Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
Peri A Tobias, Benjamin Schwessinger, Cecilia H Deng, Chen Wu, Chongmei Dong, Jana Sperschneider, Ashley Jones, Zhenyan Lou, Peng Zhang, Karanjeet Sandhu, Grant R Smith, Josquin Tibbits, David Chagné, Robert F Park. bioRxiv 2020.03.18.996108; doi: https://doi.org/10.1101/2020.03.18.996108
Evaluating features of scientific conferences: A call for improvements
Sarvenaz Sarabipour, Aziz Khan, Samantha Seah, Aneth D. Mwakilili, Fiona N. Mumoki, Pablo J. Sáez, Benjamin Schwessinger, Humberto J. Debat, Tomislav Mestrovic. bioRxiv 2020.04.02.022079; doi: https://doi.org/10.1101/2020.04.02.022079
Reproducibility for everyone: a community-led initiative with global reach in reproducible research training
Susann Auer, Nele Haelterman, Tracey Weissgerber, Jeffrey Erlich, Damar Susilaradeya, Magdalena Julkowska, Małgorzata Gazda, Angela Abitua, Anzela Niraulu, Aparna Shah, April Clyburne-Sherin, Benoit Guiquel, Bradly Alicea, Caroline LaManna, Diep Ganguly, Eric J. Perkins, Helena Jambor, Ian Li, Jennifer Tsang, Joanne Kamens, Lenny Teytelman, Mariella Paul, Santosh Phuyal, Nicolas Schmelling, Peter Crisp, Sarvenaz Sarabipour, Sonali Roy, Susanna Bachle, Tuan Tran, Tyler Ford, Vicky Steeves, Vinodh Ilangovan, Benjamin Schwessinger, Nafisa Jadavji. OSF Preprints. 2020 Oct 31. doi:10.31219/osf.io/dxw67
Departmental-level approaches to gender equity in biology
C. J. McDonald-Spicer, B. Schwessinger and S. Howitt 2018. PeerJ Preprints. doi: 10.7287/peerj.preprints.27325v1
Improving methodologies for rapid diagnosis of coinfection in plants
G. Green, A. Milgate, J. Rathjen and B. Schwessinger 2017. F1000Research, 6. doi:
Scalable high-molecular weight DNA extraction for longread sequencing
Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin Borevitz, Benjamin Schwessinger. 2020 Oct 19. https://dx.doi.org/10.17504/protocols.io.bnjhmcj6
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