Works by Sperschneider, Jana

Results: 32

DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 7, p. e103, doi. 10.1093/nar/gkq021

By:

Sperschneider, Jana;
Datta, Amitava

Publication type:

Article

A functional genomics approach to dissect spotted alfalfa aphid resistance in Medicago truncatula.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-78904-z

By:

Jacques, Silke;
Sperschneider, Jana;
Garg, Gagan;
Thatcher, Louise F.;
Gao, Ling-Ling;
Kamphuis, Lars G.;
Singh, Karam B.

Publication type:

Article

Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat.

Published in:

Genome Biology & Evolution, 2020, v. 12, n. 5, p. 597, doi. 10.1093/gbe/evaa071

By:

Schwessinger, Benjamin;
Chen, Yan-Jun;
Tien, Richard;
Vogt, Josef Korbinian;
Sperschneider, Jana;
Nagar, Ramawatar;
McMullan, Mark;
Sicheritz-Ponten, Thomas;
Sørensen, Chris K;
Hovmøller, Mogens Støvring;
Rathjen, John P;
Justesen, Annemarie Fejer

Publication type:

Article

Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity.

Published in:

Genome Biology & Evolution, 2015, v. 7, n. 6, p. 1613, doi. 10.1093/gbe/evv092

By:

Sperschneider, Jana;
Gardiner, Donald M.;
Thatcher, Louise F.;
Lyons, Rebecca;
Singh, Karam B.;
Manners, John M.;
Taylor, Jennifer M.

Publication type:

Article

Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2486-8

By:

Williams, Angela H.;
Sharma, Mamta;
Thatcher, Louise F.;
Azam, Sarwar;
Hane, James K.;
Sperschneider, Jana;
Kidd, Brendan N.;
Anderson, Jonathan P.;
Ghosh, Raju;
Garg, Gagan;
Lichtenzveig, Judith;
Kistler, H. Corby;
Shea, Terrance;
Young, Sarah;
Buck, Sally-Anne G.;
Kamphuis, Lars G.;
Saxena, Rachit;
Pande, Suresh;
Li-Jun Ma;
Varshney, Rajeev K.

Publication type:

Article

A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-807

By:

Sperschneider, Jana;
Gardiner, Donald M.;
Taylor, Jennifer M.;
Hane, James K.;
Singh, Karam B.;
Manners, John M.

Publication type:

Article

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation.

Published in:

BMC Biology, 2021, v. 19, n. 1, p. 1, doi. 10.1186/s12915-021-01123-z

By:

Sperschneider, Jana;
Jones, Ashley W.;
Nasim, Jamila;
Xu, Bo;
Jacques, Silke;
Zhong, Chengcheng;
Upadhyaya, Narayana M.;
Mago, Rohit;
Hu, Yiheng;
Figueroa, Melania;
Singh, Karam B.;
Stone, Eric A.;
Schwessinger, Benjamin;
Wang, Ming-Bo;
Taylor, Jennifer M.;
Dodds, Peter N.

Publication type:

Article

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-12927-7

By:

Li, Feng;
Upadhyaya, Narayana M.;
Sperschneider, Jana;
Matny, Oadi;
Nguyen-Phuc, Hoa;
Mago, Rohit;
Raley, Castle;
Miller, Marisa E.;
Silverstein, Kevin A. T.;
Henningsen, Eva;
Hirsch, Cory D.;
Visser, Botma;
Pretorius, Zacharias A.;
Steffenson, Brian J.;
Schwessinger, Benjamin;
Dodds, Peter N.;
Figueroa, Melania

Publication type:

Article

An RNAi supplemented diet as a reverse genetics tool to control bluegreen aphid, a major pest of legumes.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-58442-4

By:

Jacques, Silke;
Reidy-Crofts, Jenny;
Sperschneider, Jana;
Kamphuis, Lars G.;
Gao, Ling-Ling;
Edwards, Owain R.;
Singh, Karam B.

Publication type:

Article

Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02658-2

By:

Duan, Hongyu;
Jones, Ashley W.;
Hewitt, Tim;
Mackenzie, Amy;
Hu, Yiheng;
Sharp, Anna;
Lewis, David;
Mago, Rohit;
Upadhyaya, Narayana M.;
Rathjen, John P.;
Stone, Eric A.;
Schwessinger, Benjamin;
Figueroa, Melania;
Dodds, Peter N.;
Periyannan, Sambasivam;
Sperschneider, Jana

Publication type:

Article

Haplotype‐phased and chromosome‐level genome assembly of Puccinia polysora, a giga‐scale fungal pathogen causing southern corn rust.

Published in:

Molecular Ecology Resources, 2023, v. 23, n. 3, p. 601, doi. 10.1111/1755-0998.13739

By:

Liang, Junmin;
Li, Yuanjie;
Dodds, Peter N.;
Figueroa, Melania;
Sperschneider, Jana;
Han, Shiling;
Tsui, Clement K. M.;
Zhang, Keyu;
Li, Leifu;
Ma, Zhanhong;
Cai, Lei

Publication type:

Article

Predicting pseudoknotted structures across two RNA sequences.

Published in:

Bioinformatics, 2012, v. 28, n. 23, p. 3058, doi. 10.1093/bioinformatics/bts575

By:

Sperschneider, Jana;
Datta, Amitava;
Wise, Michael J.

Publication type:

Article

A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis.

Published in:

G3: Genes | Genomes | Genetics, 2023, v. 13, n. 6, p. 1, doi. 10.1093/g3journal/jkad077

By:

Manley, Bethan F.;
Lotharukpong, Jaruwatana S.;
Barrera-Redondo, Josué;
Llewellyn, Theo;
Yildirir, Gokalp;
Sperschneider, Jana;
Corradi, Nicolas;
Uta Paszkowski;
Miska, Eric A.;
Dallaire, Alexandra

Publication type:

Article

A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts.

Published in:

G3: Genes | Genomes | Genetics, 2022, v. 12, n. 8, p. 1, doi. 10.1093/g3journal/jkac149

By:

Henningsen, Eva C.;
Hewitt, Tim;
Dugyala, Sheshanka;
Nazareno, Eric S.;
Gilbert, Erin;
Feng Li;
Kianian, Shahryar F.;
Steffenson, Brian J.;
Dodds, Peter N.;
Sperschneider, Jana;
Figueroa, Melania

Publication type:

Article

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements.

Published in:

G3: Genes | Genomes | Genetics, 2021, v. 11, n. 3, p. 1, doi. 10.1093/g3journal/jkaa015

By:

Tobias, Peri A.;
Schwessinger, Benjamin;
Deng, Cecilia H.;
Chen Wu;
Chongmei Dong;
Sperschneider, Jana;
Jones, Ashley;
Zhenyan Lou;
Peng Zhang;
Sandhu, Karanjeet;
Smith, Grant R.;
Tibbits, Josquin;
Chagné, David;
Park, Robert F.

Publication type:

Article

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12864-019-5521-8

By:

DeBoer, Kathleen;
Melser, Su;
Sperschneider, Jana;
Kamphuis, Lars G.;
Garg, Gagan;
Gao, Ling-Ling;
Frick, Karen;
Singh, Karam B.

Publication type:

Article

Advances and Challenges in Computational Prediction of Effectors from Plant Pathogenic Fungi.

Published in:

PLoS Pathogens, 2015, v. 11, n. 5, p. 1, doi. 10.1371/journal.ppat.1004806

By:

Sperschneider, Jana;
Dodds, Peter N.;
Gardiner, Donald M.;
Manners, John M.;
Singh, Karam B.;
Taylor, Jennifer M.

Publication type:

Article

A high-resolution haplotype collection uncovers somatic hybridization, recombination and intercontinental movement in oat crown rust.

Published in:

PLoS Genetics, 2024, v. 20, n. 11, p. 1, doi. 10.1371/journal.pgen.1011493

By:

Henningsen, Eva C.;
Lewis, David;
Nazareno, Eric S.;
Mangelson, Hayley;
Sanchez, Monica;
Langford, Kyle;
Huang, Yung-Fen;
Steffenson, Brian J.;
Boesen, Brendan;
Kianian, Shahryar F.;
Liachko, Ivan;
Stone, Eric;
Dodds, Peter N.;
Sperschneider, Jana;
Figueroa, Melania

Publication type:

Article

LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell.

Published in:

Scientific Reports, 2017, p. 44598, doi. 10.1038/srep44598

By:

Sperschneider, Jana;
Catanzariti, Ann-Maree;
DeBoer, Kathleen;
Petre, Benjamin;
Gardiner, Donald M.;
Singh, Karam B.;
Dodds, Peter N.;
Taylor, Jennifer M.

Publication type:

Article

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0.

Published in:

Molecular Plant Pathology, 2018, v. 19, n. 9, p. 2094, doi. 10.1111/mpp.12682

By:

Sperschneider, Jana;
Dodds, Peter N.;
Gardiner, Donald M.;
Singh, Karam B.;
Taylor, Jennifer M.

Publication type:

Article

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen <i>Rhizoctonia solani</i> AG8.

Published in:

PLoS Genetics, 2014, v. 10, n. 5, p. 1, doi. 10.1371/journal.pgen.1004281

By:

Hane, James K.;
Anderson, Jonathan P.;
Williams, Angela H.;
Sperschneider, Jana;
Singh, Karam B.

Publication type:

Article

AvrSr27 is a zinc‐bound effector with a modular structure important for immune recognition.

Published in:

New Phytologist, 2024, v. 243, n. 1, p. 314, doi. 10.1111/nph.19801

By:

Outram, Megan A.;
Chen, Jian;
Broderick, Sean;
Li, Zhao;
Aditya, Shouvik;
Tasneem, Nuren;
Arndell, Taj;
Blundell, Cheryl;
Ericsson, Daniel J.;
Figueroa, Melania;
Sperschneider, Jana;
Dodds, Peter N.;
Williams, Simon J.

Publication type:

Article

Long reads and Hi‐C sequencing illuminate the two‐compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.

Published in:

New Phytologist, 2022, v. 233, n. 3, p. 1097, doi. 10.1111/nph.17842

By:

Yildirir, Gökalp;
Sperschneider, Jana;
Malar C, Mathu;
Chen, Eric C. H.;
Iwasaki, Wataru;
Cornell, Calvin;
Corradi, Nicolas

Publication type:

Article

The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro‐domain protease processing of fungal effectors.

Published in:

New Phytologist, 2021, v. 231, n. 6, p. 2282, doi. 10.1111/nph.17516

By:

Outram, Megan A.;
Sung, Yi‐Chang;
Yu, Daniel;
Dagvadorj, Bayantes;
Rima, Sharmin A.;
Jones, David A.;
Ericsson, Daniel J.;
Sperschneider, Jana;
Solomon, Peter S.;
Kobe, Bostjan;
Williams, Simon J.

Publication type:

Article

Machine learning in plant–pathogen interactions: empowering biological predictions from field scale to genome scale.

Published in:

New Phytologist, 2020, v. 228, n. 1, p. 35, doi. 10.1111/nph.15771

By:

Sperschneider, Jana

Publication type:

Article

ApoplastP: prediction of effectors and plant proteins in the apoplast using machine learning.

Published in:

New Phytologist, 2018, v. 217, n. 4, p. 1764, doi. 10.1111/nph.14946

By:

Sperschneider, Jana;
Dodds, Peter N.;
Singh, Karam B.;
Taylor, Jennifer M.

Publication type:

Article

E ffectorP: predicting fungal effector proteins from secretomes using machine learning.

Published in:

New Phytologist, 2016, v. 210, n. 2, p. 743, doi. 10.1111/nph.13794

By:

Sperschneider, Jana;
Gardiner, Donald M.;
Dodds, Peter N.;
Tini, Francesco;
Covarelli, Lorenzo;
Singh, Karam B.;
Manners, John M.;
Taylor, Jennifer M.

Publication type:

Article

Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes.

Published in:

PLoS ONE, 2019, v. 14, n. 12, p. 1, doi. 10.1371/journal.pone.0226106

By:

Wu, Wenjie;
Nemri, Adnane;
Blackman, Leila M.;
Catanzariti, Ann-Maree;
Sperschneider, Jana;
Lawrence, Gregory J.;
Dodds, Peter N.;
Jones, David A.;
Hardham, Adrienne R.

Publication type:

Article

Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici.

Published in:

Frontiers in Plant Science, 2016, p. 1, doi. 10.3389/fpls.2016.00205

By:

Figueroa, Melania;
Upadhyaya, Narayana M.;
Sperschneider, Jana;
Park, Robert F.;
Szabo, Les J.;
Steffenson, Brian;
Ellis, Jeff G.;
Dodds, Peter N.;
Gijze, Mark;
Mcdonald, Bruce A.

Publication type:

Article

Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors.

Published in:

Frontiers in Plant Science, 2015, p. 1, doi. 10.3389/fpls.2015.01168

By:

Sperschneider, Jana;
Williams, Angela H.;
Hane, James K.;
Singh, Karam B.;
Taylor, Jennifer M.

Publication type:

Article

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.

Published in:

Frontiers in Plant Science, 2015, v. 5, p. 1, doi. 10.3389/fpls.2014.00759

By:

Upadhyaya, Narayana M.;
Sperschneider, Jana;
Nemri, Adnane;
Bo Xu;
Mago, Rohit;
Ellis, Jeffrey G.;
Dodds, Peter N.;
Garnica, Diana P.;
Rathjen, John P.;
Karaoglu, Haydar;
Park, Robert F.;
Cuomo, Christina A.

Publication type:

Article

Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors.

Published in:

Frontiers in Plant Science, 2014, v. 5, p. 1, doi. 10.3389/fpls.2014.00372

By:

Sperschneider, Jana;
Singh, Karam B.;
Hua Ying;
Dodds, Peter N.;
Upadhyaya, Narayana M.;
Manners, John M.;
Taylor, Jennifer M.;
Gardiner, Donald M.

Publication type:

Article