Paul Kirk - Publications

Affiliations: 
Biological Sciences California State University, Chico, Chico, CA, United States 

95 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Boonmee S, Wanasinghe DN, Calabon MS, Huanraluek N, Chandrasiri SKU, Jones GEB, Rossi W, Leonardi M, Singh SK, Rana S, Singh PN, Maurya DK, Lagashetti AC, Choudhary D, Dai YC, ... ... Kirk PM, et al. Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa. Fungal Diversity. 1-335. PMID 34899100 DOI: 10.1007/s13225-021-00489-3  1
2021 Voigt K, James TY, Kirk PM, Santiago ALCMA, Waldman B, Griffith GW, Fu M, Radek R, Strassert JFH, Wurzbacher C, Jerônimo GH, Simmons DR, Seto K, Gentekaki E, Hurdeal VG, et al. Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals. Fungal Diversity. 1-40. PMID 34608378 DOI: 10.1007/s13225-021-00480-y  1
2021 Nguyen TTT, Frisvad JC, Kirk PM, Lim HJ, Lee HB. Discovery and Extrolite Production of Three New Species of Belonging to Sections and from Freshwater in Korea. Journal of Fungi (Basel, Switzerland). 7. PMID 34575760 DOI: 10.3390/jof7090722  1
2021 Karapanagiotis S, Benedetto U, Mukherjee S, Kirk PDW, Newcombe PJ. Tailored Bayes: a risk modeling framework under unequal misclassification costs. Biostatistics (Oxford, England). PMID 34363680 DOI: 10.1093/biostatistics/kxab023  0.01
2021 Nguyen TTT, Voigt K, Santiago ALCMA, Kirk PM, Lee HB. Discovery of Novel (Backusellaceae, Mucorales) Isolated from Invertebrates and Toads in Cheongyang, Korea. Journal of Fungi (Basel, Switzerland). 7. PMID 34199055 DOI: 10.3390/jof7070513  1
2021 Fang S, Kirk PDW, Bantscheff M, Lilley KS, Crook OM. A Bayesian semi-parametric model for thermal proteome profiling. Communications Biology. 4: 810. PMID 34188175 DOI: 10.1038/s42003-021-02306-8  1
2021 Lücking R, Aime MC, Robbertse B, Miller AN, Aoki T, Ariyawansa HA, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, ... Kirk PM, et al. Author Correction: Fungal taxonomy and sequence-based nomenclature. Nature Microbiology. PMID 34045712 DOI: 10.1038/s41564-021-00921-z  1
2021 Gong S, Gaccioli F, Dopierala J, Sovio U, Cook E, Volders PJ, Martens L, Kirk PDW, Richardson S, Smith GCS, Charnock-Jones DS. The RNA landscape of the human placenta in health and disease. Nature Communications. 12: 2639. PMID 33976128 DOI: 10.1038/s41467-021-22695-y  1
2021 Aime MC, Miller AN, Aoki T, Bensch K, Cai L, Crous PW, Hawksworth DL, Hyde KD, Kirk PM, Lücking R, May TW, Malosso E, Redhead SA, Rossman AY, Stadler M, et al. How to publish a new fungal species, or name, version 3.0. Ima Fungus. 12: 11. PMID 33934723 DOI: 10.1186/s43008-021-00063-1  1
2021 Lücking R, Aime MC, Robbertse B, Miller AN, Aoki T, Ariyawansa HA, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, ... Kirk PM, et al. Fungal taxonomy and sequence-based nomenclature. Nature Microbiology. PMID 33903746 DOI: 10.1038/s41564-021-00888-x  1
2021 Gisby J, Clarke CL, Medjeral-Thomas N, Malik TH, Papadaki A, Mortimer PM, Buang NB, Lewis S, Pereira M, Toulza F, Fagnano E, Mawhin MA, Dutton EE, Tapeng L, Richard AC, ... Kirk PD, et al. Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death. Elife. 10. PMID 33704068 DOI: 10.7554/eLife.64827  0.01
2021 Li H, Tian Y, Menolli N, Ye L, Karunarathna SC, Perez-Moreno J, Rahman MM, Rashid MH, Phengsintham P, Rizal L, Kasuya T, Lim YW, Dutta AK, Khalid AN, Huyen LT, ... ... Kirk PM, et al. Reviewing the world's edible mushroom species: A new evidence-based classification system. Comprehensive Reviews in Food Science and Food Safety. PMID 33599116 DOI: 10.1111/1541-4337.12708  0.01
2021 Foley CN, Staley JR, Breen PG, Sun BB, Kirk PDW, Burgess S, Howson JMM. A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits. Nature Communications. 12: 764. PMID 33536417 DOI: 10.1038/s41467-020-20885-8  1
2020 Burren OS, Reales G, Wong L, Bowes J, Lee JC, Barton A, Lyons PA, Smith KGC, Thomson W, Kirk PDW, Wallace C. Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases. Genome Medicine. 12: 106. PMID 33239102 DOI: 10.1186/s13073-020-00797-4  0.01
2020 Crook OM, Geladaki A, Nightingale DJH, Vennard O, Lilley KS, Gatto L, Kirk PDW. A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. Plos Computational Biology. 16: e1008288. PMID 33166281 DOI: 10.1371/journal.pcbi.1008288  1
2020 Foley CN, Mason AM, Kirk PDW, Burgess S. MR-Clust: Clustering of genetic variants in Mendelian randomization with similar causal estimates. Bioinformatics (Oxford, England). PMID 32915962 DOI: 10.1093/bioinformatics/btaa778  1
2020 Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, ... Kirk PM, et al. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? Ima Fungus. 11: 14. PMID 32714773 DOI: 10.1186/s43008-020-00033-z  1
2020 Piepenbring M, Maciá-Vicente JG, Codjia JEI, Glatthorn C, Kirk P, Meswaet Y, Minter D, Olou BA, Reschke K, Schmidt M, Yorou NS. Mapping mycological ignorance - checklists and diversity patterns of fungi known for West Africa. Ima Fungus. 11: 13. PMID 32699745 DOI: 10.1186/s43008-020-00034-y  0.01
2020 Cabassi A, Kirk PDW. Multiple kernel learning for integrative consensus clustering of 'omic datasets. Bioinformatics (Oxford, England). PMID 32592464 DOI: 10.1093/bioinformatics/btaa593  0.01
2020 Yao YJ, Li Y, Du Z, Wang K, Wang XC, Kirk PM, Spooner BM. On the Typification of Ganoderma sichuanense (Agaricomycetes)-the Widely Cultivated Lingzhi Medicinal Mushroom. International Journal of Medicinal Mushrooms. 22: 45-54. PMID 32463997 DOI: 10.1615/IntJMedMushrooms.2019033189  1
2019 Crook OM, Gatto L, Kirk PDW. Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics. Statistical Applications in Genetics and Molecular Biology. 18. PMID 31829970 DOI: 10.1515/sagmb-2018-0065  1
2019 Strauss ME, Kirk PDW, Reid JE, Wernisch L. GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution. Bioinformatics (Oxford, England). PMID 31608923 DOI: 10.1093/Bioinformatics/Btz778  0.01
2019 Krah FS, Büntgen U, Schaefer H, Müller J, Andrew C, Boddy L, Diez J, Egli S, Freckleton R, Gange AC, Halvorsen R, Heegaard E, Heideroth A, Heibl C, Heilmann-Clausen J, ... ... Kirk PM, et al. European mushroom assemblages are darker in cold climates. Nature Communications. 10: 2890. PMID 31253790 DOI: 10.1038/S41467-019-10767-Z  1
2019 Crook OM, Breckels LM, Lilley KS, Kirk PDW, Gatto L. A Bioconductor workflow for the Bayesian analysis of spatial proteomics. F1000research. 8: 446. PMID 31119032 DOI: 10.12688/f1000research.18636.1  1
2019 Andrew C, Büntgen U, Egli S, Senn-Irlet B, Grytnes JA, Heilmann-Clausen J, Boddy L, Bässler C, Gange AC, Heegaard E, Høiland K, Kirk PM, Krisai-Greilhüber I, Kuyper TW, Kauserud H. Open-source data reveal how collections-based fungal diversity is sensitive to global change. Applications in Plant Sciences. 7: e01227. PMID 30937219 DOI: 10.1002/Aps3.1227  1
2018 Scambler R, Niskanen T, Assyov B, Ainsworth AM, Bellanger JM, Loizides M, Moreau PA, Kirk PM, Liimatainen K. Diversity of (, ) in Europe, and typification of . Ima Fungus. 9: 271-290. PMID 30622883 DOI: 10.5598/imafungus.2018.09.02.04  1
2018 Crook OM, Mulvey CM, Kirk PDW, Lilley KS, Gatto L. A Bayesian mixture modelling approach for spatial proteomics. Plos Computational Biology. 14: e1006516. PMID 30481170 DOI: 10.1371/journal.pcbi.1006516  1
2018 Niskanen T, Liimatainen K, Nuytinck J, Kirk P, Ibarguren IO, Garibay-Orijel R, Norvell L, Huhtinen S, Kytövuori I, Ruotsalainen J, Niemelä T, Ammirati JF, Tedersoo L. Identifying and naming the currently known diversity of the genus Hydnum, with an emphasis on European and North American taxa. Mycologia. 1-29. PMID 30215579 DOI: 10.1080/00275514.2018.1477004  1
2018 Abarenkov K, Somervuo P, Nilsson RH, Kirk PM, Huotari T, Abrego N, Ovaskainen O. Protax-fungi: a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences. The New Phytologist. 220: 517-525. PMID 30035303 DOI: 10.1111/nph.15301  0.01
2018 Lücking R, Kirk PM, Hawksworth DL. Sequence-based nomenclature: a reply to Thines and Zamora and provisions for an amended proposal "from the floor" to allow DNA sequences as types of names. Ima Fungus. 9: 185-198. PMID 30018879 DOI: 10.5598/imafungus.2018.09.01.12  1
2018 Andrew C, Heegaard E, Høiland K, Senn-Irlet B, Kuyper TW, Krisai-Greilhuber I, Kirk PM, Heilmann-Clausen J, Gange AC, Egli S, Bässler C, Büntgen U, Boddy L, Kauserud H. Explaining European fungal fruiting phenology with climate variability. Ecology. PMID 29655179 DOI: 10.1002/Ecy.2237  1
2017 Hansel TT, Tunstall T, Trujillo-Torralbo MB, Shamji B, Del-Rosario A, Dhariwal J, Kirk PD, Stumpf MP, Koopmann J, Telcian A, Aniscenko J, Gogsadze L, Bakhsoliani E, Stanciu L, Bartlett N, et al. A Comprehensive Evaluation of Nasal and Bronchial Cytokines and Chemokines Following Experimental Rhinovirus Infection in Allergic Asthma: Increased Interferons (IFN-γ and IFN-λ) and Type 2 Inflammation (IL-5 and IL-13). Ebiomedicine. PMID 28373098 DOI: 10.1016/j.ebiom.2017.03.033  1
2016 Kirk PD, Huvet M, Melamed A, Maertens GN, Bangham CR. Retroviruses integrate into a shared, non-palindromic DNA motif. Nature Microbiology. 2: 16212. PMID 27841853 DOI: 10.1038/nmicrobiol.2016.212  1
2016 Hibbett D, Abarenkov K, Koljalg U, Opik M, Chai B, Cole JR, Wang Q, Crous PW, Robert VA, Helgason T, Herr J, Kirk P, Lueschow S, O'Donnell K, Nilsson H, et al. Sequence-based classification and identification of Fungi. Mycologia. PMID 27760854 DOI: 10.3852/16-130  1
2016 Imoulan A, Wu HJ, Lu WL, Li Y, Li BB, Yang RH, Wang WJ, Wang XL, Kirk PM, Yao YJ. Beauveria medogensis sp. nov., a new fungus of the entomopathogenic genus from China. Journal of Invertebrate Pathology. PMID 27449678 DOI: 10.1016/j.jip.2016.07.006  1
2016 Filippi S, Barnes CP, Kirk PD, Kudo T, Kunida K, McMahon SS, Tsuchiya T, Wada T, Kuroda S, Stumpf MP. Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling. Cell Reports. PMID 27264188 DOI: 10.1016/j.celrep.2016.05.024  1
2016 Fan S, Geissmann Q, Lakatos E, Lukauskas S, Ale A, Babtie AC, Kirk PD, Stumpf MP. MEANS: python package for Moment Expansion Approximation, iNference and Simulation. Bioinformatics (Oxford, England). PMID 27153663 DOI: 10.1093/bioinformatics/btw229  1
2016 Žurauskienė J, Kirk PD, Stumpf MP. A graph theoretical approach to data fusion. Statistical Applications in Genetics and Molecular Biology. 15: 107-22. PMID 26992203 DOI: 10.1515/sagmb-2016-0016  1
2016 Mason SA, Sayyid F, Kirk PD, Starr C, Wild DL. MDI-GPU: accelerating integrative modelling for genomic-scale data using GP-GPU computing. Statistical Applications in Genetics and Molecular Biology. 15: 83-6. PMID 26910751 DOI: 10.1515/sagmb-2015-0055  1
2016 Penev L, Paton A, Nicolson N, Kirk P, Pyle RL, Whitton R, Georgiev T, Barker C, Hopkins C, Robert V, Biserkov J, Stoev P. A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank). Zookeys. 233-46. PMID 26877662 DOI: 10.3897/zookeys.550.9551  0.01
2015 Rossman AY, Crous PW, Hyde KD, Hawksworth DL, Aptroot A, Bezerra JL, Bhat JD, Boehm E, Braun U, Boonmee S, Camporesi E, Chomnunti P, Dai DQ, D'souza MJ, Dissanayake A, ... ... Kirk PM, et al. Recommended names for pleomorphic genera in Dothideomycetes. Ima Fungus. 6: 507-23. PMID 26734553 DOI: 10.5598/imafungus.2015.06.02.14  1
2015 de Jong Y, Kouwenberg J, Boumans L, Hussey C, Hyam R, Nicolson N, Kirk P, Paton A, Michel E, Guiry MD, Boegh PS, Pedersen HÆ, Enghoff H, von Raab-Straube E, Güntsch A, et al. PESI - a taxonomic backbone for Europe. Biodiversity Data Journal. e5848. PMID 26491393 DOI: 10.3897/Bdj.3.E5848  1
2015 MacLean AL, Kirk PD, Stumpf MP. Cellular population dynamics control the robustness of the stem cell niche. Biology Open. 4: 1420-6. PMID 26453624 DOI: 10.1242/bio.013714  1
2015 Lakatos E, Ale A, Kirk PD, Stumpf MP. Multivariate moment closure techniques for stochastic kinetic models. The Journal of Chemical Physics. 143: 094107. PMID 26342359 DOI: 10.1063/1.4929837  1
2015 Donnelly P, Kirk P. Use the PDSA model for effective change management. Education For Primary Care : An Official Publication of the Association of Course Organisers, National Association of Gp Tutors, World Organisation of Family Doctors. 26: 279-81. PMID 26253069 DOI: 10.1080/14739879.2015.11494356  1
2015 Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, Cavalier-Smith T, Guiry MD, Kirk PM. Correction: A Higher Level Classification of All Living Organisms. Plos One. 10: e0130114. PMID 26068874 DOI: 10.1371/Journal.Pone.0130114  1
2015 Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, Cavalier-Smith T, Guiry MD, Kirk PM. A higher level classification of all living organisms. Plos One. 10: e0119248. PMID 25923521 DOI: 10.1371/Journal.Pone.0119248  1
2015 Jovanovic G, Sheng X, Ale A, Feliu E, Harrington HA, Kirk P, Wiuf C, Buck M, Stumpf MP. Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB. Molecular Biosystems. 11: 1348-59. PMID 25797699 DOI: 10.1039/c4mb00720d  1
2015 Johnson R, Kirk P, Stumpf MP. SYSBIONS: nested sampling for systems biology. Bioinformatics (Oxford, England). 31: 604-5. PMID 25399028 DOI: 10.1093/bioinformatics/btu675  1
2014 Wijayawardene NN, Crous PW, Kirk PM, Hawksworth DL, Boonmee S, Braun U, Dai DQ, D'souza MJ, Diederich P, Dissanayake A, Doilom M, Hongsanan S, Jones EB, Groenewald JZ, Jayawardena R, et al. Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names. Fungal Diversity. 69: 1-55. PMID 27284275 DOI: 10.1007/S13225-014-0309-2  1
2014 Babtie AC, Kirk P, Stumpf MP. Topological sensitivity analysis for systems biology. Proceedings of the National Academy of Sciences of the United States of America. 111: 18507-12. PMID 25512544 DOI: 10.1073/pnas.1414026112  1
2014 Crous PW, Giraldo A, Hawksworth DL, Robert V, Kirk PM, Guarro J, Robbertse B, Schoch CL, Damm U, Trakunyingcharoen T, Groenewald JZ. The Genera of Fungi: fixing the application of type species of generic names. Ima Fungus. 5: 141-60. PMID 25083414 DOI: 10.5598/imafungus.2014.05.01.14  1
2014 Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH, Hughes K, Miller AN, Kirk PM, Abarenkov K, Aime MC, Ariyawansa HA, Bidartondo M, et al. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database : the Journal of Biological Databases and Curation. 2014. PMID 24980130 DOI: 10.1093/Database/Bau061  1
2014 Silk D, Kirk PD, Barnes CP, Toni T, Stumpf MP. Model selection in systems biology depends on experimental design. Plos Computational Biology. 10: e1003650. PMID 24922483 DOI: 10.1371/journal.pcbi.1003650  1
2014 Zurauskienė J, Kirk P, Thorne T, Pinney J, Stumpf M. Derivative processes for modelling metabolic fluxes. Bioinformatics (Oxford, England). 30: 1892-8. PMID 24578401 DOI: 10.1093/bioinformatics/btu069  1
2014 Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MP. A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nature Protocols. 9: 439-56. PMID 24457334 DOI: 10.1038/nprot.2014.025  1
2013 Kirk PM, Stalpers JA, Braun U, Crous PW, Hansen K, Hawksworth DL, Hyde KD, Lücking R, Lumbsch TH, Rossman AY, Seifert KA, Stadler M. A without-prejudice list of generic names of fungi for protection under the International Code of Nomenclature for algae, fungi, and plants. Ima Fungus. 4: 381-443. PMID 24563844 DOI: 10.5598/imafungus.2013.04.02.17  1
2013 Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, ... ... Kirk PM, et al. Towards a unified paradigm for sequence-based identification of fungi. Molecular Ecology. 22: 5271-7. PMID 24112409 DOI: 10.1111/Mec.12481  1
2013 Kirk P, Witkover A, Bangham CR, Richardson S, Lewin AM, Stumpf MP. Balancing the robustness and predictive performance of biomarkers. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 979-89. PMID 23909374 DOI: 10.1089/cmb.2013.0018  1
2013 Ale A, Kirk P, Stumpf MP. A general moment expansion method for stochastic kinetic models. The Journal of Chemical Physics. 138: 174101. PMID 23656108 DOI: 10.1063/1.4802475  1
2013 Kirk P, Thorne T, Stumpf MP. Model selection in systems and synthetic biology. Current Opinion in Biotechnology. 24: 767-74. PMID 23578462 DOI: 10.1016/j.copbio.2013.03.012  1
2013 Darkins R, Cooke EJ, Ghahramani Z, Kirk PD, Wild DL, Savage RS. Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm. Plos One. 8: e59795. PMID 23565168 DOI: 10.1371/Journal.Pone.0059795  1
2013 Kauserud H, Heegaard E, Büntgen U, Halvorsen R, Egli S, Senn-Irlet B, Krisai-Greilhuber I, Dämon W, Nordén J, Høiland K, Kirk PM, Semenov M, Stenseth NC, Boddy L. Reply to Gange et al.: Climate-driven changes in the fungal fruiting season in the United Kingdom. Proceedings of the National Academy of Sciences of the United States of America. 110: E335. PMID 23479781 DOI: 10.1073/Pnas.1221131110  1
2013 Taylor HB, Liepe J, Barthen C, Bugeon L, Huvet M, Kirk PD, Brown SB, Lamb JR, Stumpf MP, Dallman MJ. P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish. Immunology and Cell Biology. 91: 60-9. PMID 23165607 DOI: 10.1038/icb.2012.57  1
2013 Natarajan A, Khokhar AA, Kirk P, Westwood M, Davies JR. Coronary anomalies in Klippel-Trenaunay-Weber syndrome: multidetector computed tomography and cardiac magnetic resonance study of a rare association. European Heart Journal Cardiovascular Imaging. 14: 88. PMID 22898712 DOI: 10.1093/ehjci/jes171  1
2013 Natarajan A, Khokhar AA, Kirk P, Patel HH, Turner D. Coronary-pulmonary artery fistula: value of 64-MDCT imaging. Qjm : Monthly Journal of the Association of Physicians. 106: 91-2. PMID 22187506 DOI: 10.1093/qjmed/hcr254  1
2012 Appeltans W, Ahyong ST, Anderson G, Angel MV, Artois T, Bailly N, Bamber R, Barber A, Bartsch I, Berta A, Błażewicz-Paszkowycz M, Bock P, Boxshall G, Boyko CB, Brandão SN, ... ... Kirk P, et al. The magnitude of global marine species diversity. Current Biology : Cb. 22: 2189-202. PMID 23159596 DOI: 10.1016/J.Cub.2012.09.036  1
2012 Kirk P, Griffin JE, Savage RS, Ghahramani Z, Wild DL. Bayesian correlated clustering to integrate multiple datasets. Bioinformatics (Oxford, England). 28: 3290-7. PMID 23047558 DOI: 10.1093/Bioinformatics/Bts595  1
2012 Kauserud H, Heegaard E, Büntgen U, Halvorsen R, Egli S, Senn-Irlet B, Krisai-Greilhuber I, Dämon W, Sparks T, Nordén J, Høiland K, Kirk P, Semenov M, Boddy L, Stenseth NC. Warming-induced shift in European mushroom fruiting phenology. Proceedings of the National Academy of Sciences of the United States of America. 109: 14488-93. PMID 22908273 DOI: 10.1073/Pnas.1200789109  1
2012 David J, Garrity GM, Greuter W, Hawksworth DL, Jahn R, Kirk PM, McNeill J, Michel E, Knapp S, Patterson DJ, Tindall BJ, Todd JA, van Tol J, Turland NJ. Biological nomenclature terms for facilitating communication in the naming of organisms. Zookeys. 67-72. PMID 22639540 DOI: 10.3897/Zookeys.192.3347  1
2012 Toni T, Ozaki Y, Kirk P, Kuroda S, Stumpf MP. Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection. Molecular Biosystems. 8: 1921-9. PMID 22555461 DOI: 10.1039/c2mb05493k  1
2011 Cooke EJ, Savage RS, Kirk PD, Darkins R, Wild DL. Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. Bmc Bioinformatics. 12: 399. PMID 21995452 DOI: 10.1186/1471-2105-12-399  1
2011 Kirk PD, Witkover A, Courtney A, Lewin AM, Wait R, Stumpf MP, Richardson S, Taylor GP, Bangham CR. Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis. Retrovirology. 8: 81. PMID 21992623 DOI: 10.1186/1742-4690-8-81  1
2011 Silk D, Kirk PD, Barnes CP, Toni T, Rose A, Moon S, Dallman MJ, Stumpf MP. Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes. Nature Communications. 2: 489. PMID 21971504 DOI: 10.1038/ncomms1496  1
2011 Carpenter JP, He T, Kirk P, Roughton M, Anderson LJ, de Noronha SV, Sheppard MN, Porter JB, Walker JM, Wood JC, Galanello R, Forni G, Catani G, Matta G, Fucharoen S, et al. On T2* magnetic resonance and cardiac iron. Circulation. 123: 1519-28. PMID 21444881 DOI: 10.1161/CIRCULATIONAHA.110.007641  1
2011 Voigt K, Kirk PM. Recent developments in the taxonomic affiliation and phylogenetic positioning of fungi: impact in applied microbiology and environmental biotechnology. Applied Microbiology and Biotechnology. 90: 41-57. PMID 21336930 DOI: 10.1007/s00253-011-3143-4  1
2011 Kirk P, Carpenter JP, Tanner MA, Pennell DJ. Low prevalence of fibrosis in thalassemia major assessed by late gadolinium enhancement cardiovascular magnetic resonance. Journal of Cardiovascular Magnetic Resonance : Official Journal of the Society For Cardiovascular Magnetic Resonance. 13: 8. PMID 21241474 DOI: 10.1186/1532-429X-13-8  1
2010 Kirk P, Smith GC, Roughton M, He T, Pennell DJ. Myocardial T2* is not affected by ageing, myocardial fibrosis, or impaired left ventricular function. Journal of Magnetic Resonance Imaging : Jmri. 32: 1095-8. PMID 21031513 DOI: 10.1002/jmri.22348  1
2010 Donnelly P, Kirk P. How to . . . give effective feedback. Education For Primary Care : An Official Publication of the Association of Course Organisers, National Association of Gp Tutors, World Organisation of Family Doctors. 21: 267-9. PMID 20836932 DOI: 10.1080/14739879.2010.11493919  1
2010 Kirk P, He T, Anderson LJ, Roughton M, Tanner MA, Lam WW, Au WY, Chu WC, Chan G, Galanello R, Matta G, Fogel M, Cohen AR, Tan RS, Chen K, et al. International reproducibility of single breathhold T2* MR for cardiac and liver iron assessment among five thalassemia centers. Journal of Magnetic Resonance Imaging : Jmri. 32: 315-9. PMID 20677256 DOI: 10.1002/jmri.22245  1
2010 Liepe J, Barnes C, Cule E, Erguler K, Kirk P, Toni T, Stumpf MP. ABC-SysBio--approximate Bayesian computation in Python with GPU support. Bioinformatics (Oxford, England). 26: 1797-9. PMID 20591907 DOI: 10.1093/bioinformatics/btq278  1
2010 Carpenter JP, Alpendurada F, Deac M, Maceira A, Garbowski M, Kirk P, Walker JM, Porter JB, Shah F, Banya W, He T, Smith GC, Pennell DJ. Right ventricular volumes and function in thalassemia major patients in the absence of myocardial iron overload. Journal of Cardiovascular Magnetic Resonance : Official Journal of the Society For Cardiovascular Magnetic Resonance. 12: 24. PMID 20416084 DOI: 10.1186/1532-429X-12-24  1
2010 Alpendurada F, Carpenter JP, Deac M, Kirk P, Walker JM, Porter JB, Banya W, He T, Smith GC, Pennell DJ. Relation of myocardial T2* to right ventricular function in thalassaemia major. European Heart Journal. 31: 1648-54. PMID 20413399 DOI: 10.1093/eurheartj/ehq106  1
2009 Kirk P, Roughton M, Porter JB, Walker JM, Tanner MA, Patel J, Wu D, Taylor J, Westwood MA, Anderson LJ, Pennell DJ. Cardiac T2* magnetic resonance for prediction of cardiac complications in thalassemia major. Circulation. 120: 1961-8. PMID 19801505 DOI: 10.1161/CIRCULATIONAHA.109.874487  1
2009 Hibbett DS, Ohman A, Kirk PM. Fungal ecology catches fire. The New Phytologist. 184: 279-82. PMID 19796334 DOI: 10.1111/J.1469-8137.2009.03042.X  1
2009 Kirk PD, Stumpf MP. Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. Bioinformatics (Oxford, England). 25: 1300-6. PMID 19289448 DOI: 10.1093/bioinformatics/btp139  1
2009 Carpenter J, He T, Kirk P, Anderson LJ, Porter JB, Wood J, Galanello R, Forni G, Catani G, Fucharoen S, Fleming A, House M, Black G, Firmin DN, Pierre TGS, et al. Calibration of myocardial iron concentration against T2-star Cardiovascular Magnetic Resonance Journal of Cardiovascular Magnetic Resonance. 11: 224. DOI: 10.1186/1532-429X-11-S1-P224  1
2008 He T, Gatehouse PD, Kirk P, Mohiaddin RH, Pennell DJ, Firmin DN. Myocardial T*2 measurement in iron-overloaded thalassemia: an ex vivo study to investigate optimal methods of quantification. Magnetic Resonance in Medicine. 60: 350-6. PMID 18666131 DOI: 10.1002/mrm.21625  1
2008 Kirk PD, Toni T, Stumpf MP. Parameter inference for biochemical systems that undergo a Hopf bifurcation. Biophysical Journal. 95: 540-9. PMID 18456830 DOI: 10.1529/biophysj.107.126086  1
2008 He T, Kirk P, Firmin DN, Lam WM, Chu WC, Au WY, Chan GC, Tan RS, Ng I, Biceroglu S, Aydinok Y, Fogel MA, Cohen AR, Pennell DJ. Multi-center transferability of a breath-hold T2 technique for myocardial iron assessment. Journal of Cardiovascular Magnetic Resonance : Official Journal of the Society For Cardiovascular Magnetic Resonance. 10: 11. PMID 18291040 DOI: 10.1186/1532-429X-10-11  1
2007 Ramnarain N, Kirk P. Fraud and deceit in medical research. British Journal of Hospital Medicine (London, England : 2005). 68: 543-6. PMID 17974302 DOI: 10.12968/hmed.2007.68.10.27325  0.01
2007 Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Thorsten Lumbsch H, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, et al. A higher-level phylogenetic classification of the Fungi. Mycological Research. 111: 509-47. PMID 17572334 DOI: 10.1016/J.Mycres.2007.03.004  1
2007 He T, Gatehouse PD, Kirk P, Tanner MA, Smith GC, Keegan J, Mohiaddin RH, Pennell DJ, Firmin DN. Black-blood T2* technique for myocardial iron measurement in thalassemia. Journal of Magnetic Resonance Imaging : Jmri. 25: 1205-9. PMID 17520740 DOI: 10.1002/jmri.20929  1
2004 Ramachandran K, Kirk P. Massive hemorrhage in a previously undiagnosed abdominal pregnancy presenting for elective Cesarean delivery. Canadian Journal of Anaesthesia = Journal Canadien D'Anesthã©Sie. 51: 57-61. PMID 14709462 DOI: 10.1007/BF03018548  0.01
2000 Siboe GM, Murray J, Kirk PM. Genetic similarity among Cercospora apii-group species and their detection in host plant tissue by PCR/RFLP analyses of the rDNA internal transcribed spacer (ITS). The Journal of General and Applied Microbiology. 46: 69-78. PMID 12483593 DOI: 10.2323/jgam.46.69  0.01
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