Keywan Hassani-Pak

Name	Keywan Hassani-Pak
Job title	Senior Research Scientist - Head of Bioinformatics
Email address	keywan.hassani-pak@rothamsted.ac.uk
Department	Intelligent Data Ecosystems
Research cluster	CAS: Genomics and Bioinformatics
ORCID	https://orcid.org/0000-0001-9625-0511
Office	Harpenden

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Research outputs

The complete genome assemblies of 19 insect pests of worldwide importance to agriculture

King, R., Buer, B., Davies, T. G. E., Ganko, E., Guest, M., Hassani-Pak, K., Hughes, D. J., Raming, K., Rawlings, C. J., Williamson, M. S., Crossthwaite, A., Nauen, R. and Field, L. M. 2023. The complete genome assemblies of 19 insect pests of worldwide importance to agriculture. Pesticide Biochemistry and Physiology. 191, p. 105339. https://doi.org/10.1016/j.pestbp.2023.105339

Novel molecules and target genes for vegetative heat tolerance in wheat

Rose, T., Wilkinson, M. D., Lowe, C., Xu, J., Hughes, D. J., Hassall, K. L., Hassani-Pak, K., Amberkar, S., Noleto-Dias, C., Ward, J. L. and Heuer, S. 2022. Novel molecules and target genes for vegetative heat tolerance in wheat. Plant Environmental Interactions. 3 (6), pp. 264-289. https://doi.org/10.1002/pei3.10096

Proanthocyanidin Biosynthesis in the Developing Wheat Seed Coat Investigated by Chemical and RNA-seq Analysis

Phillips, A. L., Vaughan, S., Baker, J., Primavesi, L. F., Patil, A., King, R., Hassani-Pak, K., Kulasekaran, S., Coghill, J., Ward, J. L. and Huttly, A. K. 2022. Proanthocyanidin Biosynthesis in the Developing Wheat Seed Coat Investigated by Chemical and RNA-seq Analysis. Plant Direct. 6 (10), p. e453. https://doi.org/10.1002/pld3.453

A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators

Bailey, E., Field, L. M., Rawlings, C. J., King, R., Mohareb, F., Hassani-Pak, K., Hughes, D. J., Williamson, M. S., Ganko, E., Buer, B. and Nauen, R. 2022. A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators. BMC Genomics. 23 (1), p. 198. https://doi.org/10.1186/s12864-022-08436-5

A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus, and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests

Bailey, E., Field, L. M., Rawlings, C. J., King, R., Mahareb, F., Hassani-Pak, K., Hughes, D. J., Williamson, M. S., Ganko, E., Buer, B. and Nauen, R. 2022. A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus, and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests. BMC Genomics. 23, p. 45. https://doi.org/10.1186/s12864-021-08249-y

Daisychain Search and Interactive Visualisation of Homologs in Genome Assemblies

Schliebs, O., Chan, C-K. K., Bayer, P. E., Petereit, J., Singh, A., Hassani-Pak, K., Batley, J. and Edwards, D. 2021. Daisychain Search and Interactive Visualisation of Homologs in Genome Assemblies. Agronomy. 11 (12), p. 2587. https://doi.org/10.3390/agronomy11122587

High-quality, haplotype-phased de novo assembly of the highly heterozygous fig genome, a major genetic resource for fig breeding

Usai, G., Mascagni, F., Giordani, T., Vangelisti, A., Bosi, E., Zuccolo, A., Ceccarelli, M., King, R., Hassani-Pak, K., Solorzano, L. S., Cavallini, A. and Natali, L. 2021. High-quality, haplotype-phased de novo assembly of the highly heterozygous fig genome, a major genetic resource for fig breeding. International Society of Horticultural Science (ISHS). https://doi.org/10.17660/ActaHortic.2021.1310.4

Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel

Lyra, D. H., Griffiths, C. A., Watson, A., Joynson, R., Molero, G., Igna, A. A., Hassani-Pak, K., Reynolds, M. P., Hall, A. and Paul, M. J. 2021. Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel. Food and Energy Security. p. e292. https://doi.org/10.1002/fes3.292

KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species

Hassani-Pak, K., Singh, A., Brandizi, M., Hearnshaw, J., Parsons, J. D., Amberkar, S., Phillips, A. L., Doonan, J. H. and Rawlings, C. J. 2021. KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13583

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

Harrington, S. A., Backhaus, A. E., Singh, A., Hassani-Pak, K. and Uauy, C. 2020. The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat. G3: Genes, Genomes, Genetics. 10 (10), pp. 3675-3686. https://doi.org/10.1534/g3.120.401436

A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat

Adamski, N. M., Borril, P., Brinton, J., Harrington, S. A., Marchal, C., Bentley, A. R., Bovill, W. D., Cattivelli, L., Cockram, J., Contreras-Moreira, B., Ford, B., Ghosh, S., Harwood, W., Hassani-Pak, K., Hayta, S., Hickey, L. T., Kanyuka, K., King, J., Maccaferri, M., Naamati, G., Pozniak, C. J., Ramirez-Gonzalez, R. H., Sansaloni, C., Trevaskis, B., Wingen, L. U., Wulff, B. B. H. and Uauy, C. 2020. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife. 9, p. e55646. https://doi.org/10.7554/eLife.55646

A roadmap for gene functional characterisation in wheat

Adamski, N. M., Borril, P., Brinton, J., Harrington, S. A., Marchal, C., Bentley, A. R., Bovill, W. D., Cattivelli, L., Cockram, J., Contreras-Moreira, B., Ford, B., Ghosh, S., Harwood, W., Hassani-Pak, K., Hayta, S., Hickey, L. T., Kanyuka, K., King, J., Maccaferri, M., Naamati, G., Pozniak, C. J., Ramirez-Gonzalez, R. H., Sansaloni, C., Trevaskis, B., Wingen, L. U., Wulff, B. B. H. and Uauy, C. 2019. A roadmap for gene functional characterisation in wheat. PeerJ. 7, p. e26877v2. https://doi.org/10.7287/peerj.preprints.26877v2

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

Usai, G., Mascagni, F., Giordani, T., Vangelisti, A., Bose, E., Zuccolo, A., Ceccarelli, M., King, R., Hassani-Pak, K., Zambrano, L. S., Cavallini, A. and Natali, L. 2020. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. The Plant Journal. https://doi.org/10.1111/tpj.14635

PHI-base - the Pathogen–Host Interactions database

Urban, M., Cuzick, A., Seager, J., Wood, V., Rutherford, K., De Silva, N., Venkatesh, S. Y, Martinez, M. C., Pedro, H., Yates, A. D., Hassani-Pak, K. and Hammond-Kosack, K. E. 2020. PHI-base - the Pathogen–Host Interactions database . Nucleic Acids Research. 48 (Database issue D1), pp. D613-D620. https://doi.org/10.1093/nar/gkz904

A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization

Alabdullah AK., Borrill, P., Martin, AC., Ramirez-Gonzalez, RH., Hassani-Pak, K., Uauy, C., Shaw, P. and Moore, G. 2019. A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization. Frontiers in Plant Science. 10 (1325), p. 24pp. https://doi.org/10.3389/fpls.2019.01325

Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis

Bryant, F. M., Hughes, D. J., Hassani-Pak, K. and Eastmond, P. J. 2019. Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis. The Plant Cell. https://doi.org/10.1105/tpc.18.00892

Natural variation in acyl editing is a determinant of seed storage oil composition

Menard, G. N., Bryant, F. M., Kelly, A. A., Craddock, C. P., Lavagi, I., Hassani-Pak, K., Kurup, S. and Eastmond, P. J. 2018. Natural variation in acyl editing is a determinant of seed storage oil composition. Scientific Reports. 8, p. 17346. https://doi.org/10.1038/s41598-018-35136-6

KnetMaps: a BioJS component to visualize biological knowledge networks

Singh, A., Rawlings, C. J. and Hassani-Pak, K. 2018. KnetMaps: a BioJS component to visualize biological knowledge networks. F1000Research. 7, p. 1651. https://doi.org/10.12688/f1000research.16605.1

Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach

Brandizi, M., Singh, A., Rawlings, C. J. and Hassani-Pak, K. 2018. Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. Journal of Integrative Bioinformatics. 15 (3), pp. 1-10. https://doi.org/10.1515/jib-2018-0023

The Role of Trehalose 6-Phosphate in Crop Yield and Resilience

Paul, M. J., Gonzalez-Uriarte, A., Griffiths, C. A. and Hassani-Pak, K. 2018. The Role of Trehalose 6-Phosphate in Crop Yield and Resilience. Plant Physiology. 177, pp. 12-23. https://doi.org/10.1104/pp.17.01634

Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots

Vangelisti, A., Natali, L., Bernardi, R., Sbrana, C., Turrini, A., Hassani-Pak, K., Hughes, D. J., Cavallini, A., Giovannetti, M. and Giordani, T. 2018. Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots. Scientific Reports. 8 (4), pp. 1-14. https://doi.org/10.1038/s41598-017-18445-0

KnetMiner - An integrated data platform for gene mining and biological knowledge discovery

Hassani-Pak, K. 2017. KnetMiner - An integrated data platform for gene mining and biological knowledge discovery. F - Theses Rothamsted Research Computational and Analytical Sciences

Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress

Wan, Y., King, R., Mitchell, R. A. C., Hassani-Pak, K. and Hawkesford, M. J. 2017. Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress. Scientific Reports. 7 (1), p. 5461. https://doi.org/10.1038/s41598-017-04473-3

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

Hassani-Pak, K. and Rawlings, C. J. 2017. Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. Journal of Integrative Bioinformatics. 14 (1), pp. 1-9. https://doi.org/10.1515/jib-2016-0002

Genome wide analysis of fatty acid desaturation and its response to temperature

Menard, G. N., Martin-Moreno, J., Bryant, F. M., Munoz-Azcarate, O., Kelly, A. A., Hassani-Pak, K., Kurup, S. and Eastmond, P. J. 2017. Genome wide analysis of fatty acid desaturation and its response to temperature. Plant Physiology. 173 (3), pp. 1594-1605. https://doi.org/10.1104/pp.16.01907

Developing integrated crop knowledge networks to advance candidate gene discovery

Hassani-Pak, K., Castellote, M., Esch, M., Hindle, M. M., Lysenko, A., Taubert, J. and Rawlings, C. J. 2016. Developing integrated crop knowledge networks to advance candidate gene discovery. Applied and Translational Genomics. 11 (December), pp. 18-26. https://doi.org/10.1016/j.atg.2016.10.003

Insecticide resistance mediated by an exon skipping event.

Berger, M., Puinean, A. M., Randall, E., Zimmer, C. T., Silva, W. M., Bielza, P., Field, L. M., Hughes, D. J., Mellor, I., Hassani-Pak, K., Siqueira, H. A. A., Williamson, M. S. and Bass, C. 2016. Insecticide resistance mediated by an exon skipping event. Molecular Ecology. 25 (22), pp. 5692-5704. https://doi.org/10.1111/mec.13882

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

King, R., Urban, M., Hammond-Kosack, M. C. U., Hassani-Pak, K. and Hammond-Kosack, K. E. 2015. The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum. BMC Genomics. 16, p. 544. https://doi.org/10.1186/s12864-015-1756-1

Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition

Rudd, J. J., Kanyuka, K., Hassani-Pak, K., Derbyshire, M., Andongabo, A. E., Devonshire, J., Lysenko, A., Saqi, M., Desai, N. M., Powers, S. J., Hooper, J., Ambroso, L., Bharti, A., Farmer, A., Hammond-Kosack, K. E., Dietrich, R. A. and Courbot, M. 2015. Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition. Plant Physiology. 167 (3), pp. 1158-1185. https://doi.org/10.1104/pp.114.255927

Mutation scanning in wheat by exon capture and next-generation sequencing

King, R., Bird, N., Ramirez-Gonzalez, R., Coghill, J. A., Patil, A., Hassani-Pak, K., Uauy, C. and Phillips, A. L. 2015. Mutation scanning in wheat by exon capture and next-generation sequencing. PLOS ONE. 10, p. e0137549. https://doi.org/10.1371/journal.pone.0137549

Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions

Urban, M., King, R., Hassani-Pak, K. and Hammond-Kosack, K. E. 2015. Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions. BMC Genomics. 16, p. 261. https://doi.org/10.1186/s12864-015-1412-9

Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems

Wan, Y., Gritsch, C., Tryfona, T., Ray, M. J., Andongabo, A. E., Hassani-Pak, K., Jones, H. D., Dupree, P., Karp, A., Shewry, P. R. and Mitchell, R. A. C. 2014. Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems. Planta. 239, pp. 1041-1053. https://doi.org/10.1007/s00425-014-2034-1

A tale of one fungal pathogen of wheat: how it evades host surveillance and then hijacks host defences

Kanyuka, K., Lysenko, A., Saqi, M., Derbyshire, M., Andongabo, A. E., Hassani-Pak, K., Hammond-Kosack, K. E., Courbot, M. and Rudd, J. J. 2014. A tale of one fungal pathogen of wheat: how it evades host surveillance and then hijacks host defences. Abstracts 16th International Congress on Molecular Plant-Microbe Interactions (IS-MPMI 2014), Rhodes, 6-10 July 2014 . pp. P069

Identification and analysis of differentially expressed genes in the wheat- Zymoseptoria tritici interaction

Kanyuka, K., Andongabo, A. E., Hassani-Pak, K., Powers, S. J., Lysenko, A., Saqi, M., Derbyshire, M., Lee, W-S., Hammond-Kosack, K. E., Courbot, M. and Rudd, J. J. 2014. Identification and analysis of differentially expressed genes in the wheat- Zymoseptoria tritici interaction. Abstracts Plant Genomics Congress, London, 12-13 May 2014 .

A query suggestion workflow for life science IR-systems

Esch, M., Chen, J., Weise, S., Hassani-Pak, K., Scholz, U. and Lange, M. 2014. A query suggestion workflow for life science IR-systems. Journal of Integrative Bioinformatics. 11, p. 237. https://doi.org/10.2390/biecoll-jib-2014-237

Ondex Web: web-based visualization and exploration of heterogeneous biological networks

Taubert, J., Hassani-Pak, K., Castells-Brooke, N. I. D. and Rawlings, C. J. 2014. Ondex Web: web-based visualization and exploration of heterogeneous biological networks. Bioinformatics. 30, pp. 1034-1035. https://doi.org/10.1093/bioinformatics/btt740

Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits

Defoin-Platel, M., Hassani-Pak, K. and Rawlings, C. J. 2011. Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits. Systems Approaches to Crop Improvement. Aspects of Applied Biology 107 . Association of Applied Biologists (AAB) Wellesbourne Warwick . pp. 79-87

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

Lysenko, A., Defoin-Platel, M., Hassani-Pak, K., Taubert, J., Hodgman, C., Rawlings, C. J. and Saqi, M. 2011. Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. BMC Bioinformatics. 12, p. 203 (14pp). https://doi.org/10.1186/1471-2105-12-203

Enhancing data integration with text analysis to find proteins implicated in plant stress response

Hassani-Pak, K., Legaie, R., Canevet, C., Van Den Berg, H. A., Moore, J. D. and Rawlings, C. J. 2010. Enhancing data integration with text analysis to find proteins implicated in plant stress response. Journal of Integrative Bioinformatics. 7, p. 121 (13pp). https://doi.org/10.2390/biecoll-jib-2010-121

Graph-based sequence annotation using a data integration approach

Pesch, R., Lysenko, A., Hindle, M. M., Hassani-Pak, K., Thiele, R., Rawlings, C. J., Kohler, J. and Taubert, J. 2008. Graph-based sequence annotation using a data integration approach. Journal of Integrative Bioinformatics. 5(2):94, p. 15pp. https://doi.org/10.2390/biecoll-jib-2008-94

Keywan Hassani-Pak

Research outputs

Projects