David Bird

Kranse, O., Beasley, H., Adams, S., Pires-daSilva, A., Bell, C., Lilley, C. J., … Akker, S. (2021). Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles. G3-GENES GENOMES GENETICS, 11(2). https://doi.org/10.1093/g3journal/jkaa058

Schoonmaker, A., Hao, Y., Bird, D. M. K., & Conant, G. C. (2020). A Single, Shared Triploidy in Three Species of Parasitic Nematodes. G3-GENES GENOMES GENETICS, 10(1), 225–233. https://doi.org/10.1534/g3.119.400650

Yergaliyev, T. M., Alexander-Shani, R., Dimerets, H., Pivonia, S., Bird, D. M. K., Rachmilevitch, S., & Szitenberg, A. (2020). Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions. MSPHERE, 5(4). https://doi.org/10.1128/mSphere.00306-20

Levin, K. A., Tucker, M. R., Bird, D. M., & Mather, D. E. (2020). Infection by cyst nematodes induces rapid remodelling of developing xylem vessels in wheat roots. SCIENTIFIC REPORTS, 10(1). https://doi.org/10.1038/s41598-020-66080-z

Schreeg, M. E., Marr, H. S., Tarigo, J. L., Sherrill, M. K., Outi, H. K., Scholl, E. H., … Birkenheuer, A. J. (2018). Identification of Cytauxzoon felis antigens via protein microarray and assessment of expression library immunization against cytauxzoonosis. CLINICAL PROTEOMICS, 15(1). https://doi.org/10.1186/s12014-018-9218-9

Holterman, M., Karegar, A., Mooijman, P., Megen, H., Elsen, S., Vervoort, M. T. W., … Helder, J. (2017). Disparate gain and loss of parasitic abilities among nematode lineages. PLOS ONE, 12(9). https://doi.org/10.1371/journal.pone.0185445

Guo, Y., Fudali, S., Gimeno, J., DiGennaro, P., Chang, S., Williamson, V. M., … Nielsen, D. M. (2017). Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping. Genetics, 206(4), 2175–2184. https://doi.org/10.1534/genetics.117.202531

Szitenberg, A., Cha, S., Opperman, C. H., Bird, D. M., Blaxter, M. L., & Lunt, D. H. (2016). Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements. GENOME BIOLOGY AND EVOLUTION, 8(9), 2964–2978. https://doi.org/10.1093/gbe/evw208

Schreeg, M. E., Marr, H. S., Tarigo, J. L., Cohn, L. A., Bird, D. M., Scholl, E. H., … Birkenheuer, A. J. (2016). Mitochondrial Genome Sequences and Structures Aid in the Resolution of Piroplasmida phylogeny. PLOS ONE, 11(11). https://doi.org/10.1371/journal.pone.0165702

Schreeg, M. E., Marr, H. S., Griffith, E. H., Tarigo, J. L., Bird, D. M., Reichard, M. V., … Birkenheuer, A. J. (2016). PCR amplification of a multi-copy mitochondrial gene (cox3) improves detection of Cytauxzoon felis infection as compared to a ribosomal gene (18S). VETERINARY PARASITOLOGY, 225, 123–130. https://doi.org/10.1016/j.vetpar.2016.06.013

Bird, D. M., Williamson, V. M., & Opperman, C. H. (2015). Exploiting solved genomes of plant-parasitic nematodes to understand parasitism. In Advances in Botanical Research (Vol. 73, pp. 241–258). https://doi.org/10.1016/bs.abr.2014.12.008

Bird, D. M. K., Jones, J. T., Opperman, C. H., Kikuchi, T., & Danchin, E. G. J. (2015). Signatures of adaptation to plant parasitism in nematode genomes. Parasitology, 142(S1), S71–S84. https://doi.org/10.1017/s0031182013002163

Burke, M., Scholl, E. H., Bird, D. M. K., Schaff, J. E., Colman, S. D., Crowell, R., … Opperman, C. H. (2015). The plant parasite Pratylenchus coffeae carries a minimal nematode genome. NEMATOLOGY, 17(6), 621–637. https://doi.org/10.1163/15685411-00002901

Tarigo, J. L., Scholl, E. H., Bird, D. M. K., Brown, C. C., Cohn, L. A., Dean, G. A., … Birkenheuer, A. J. (2013). A Novel Candidate Vaccine for Cytauxzoonosis Inferred from Comparative Apicomplexan Genomics. PLOS ONE, 8(8). https://doi.org/10.1371/journal.pone.0071233

Bobay, B. G., Digennaro, P., Scholl, E., Imin, N., Djordjevic, M. A., & McK Bird, D. (2013). Solution NMR studies of the plant peptide hormone CEP inform function. FEBS Letters, 587(24), 3979–3985. https://doi.org/10.1016/j.febslet.2013.10.033

Thomas, V. P., Fudali, S. L., Schaff, J. E., Liu, Q., Scholl, E. H., Opperman, C. H., … Williamson, V. M. (2012). A sequence-anchored linkage map of the plant-parasitic nematode meloidogyne hapla reveals exceptionally high genome-wide recombination. G3: Genes, Genomes, Genetics, 2(7), 815–824. https://doi.org/10.1534/g3.112.002261

Stock, S. P., Bird, D. M. K., Ghedin, E., & Goodrich-Blair, H. (2011). Abstracts of NEMASYM: The Third Nematode-Bacteria Symbioses Research Coordination Network Meeting. Symbiosis, 55(3), 97–109. https://doi.org/10.1007/s13199-011-0135-1

Scholl, E. H., & Bird, D. M. K. (2011, February 22). Computational and phylogenetic validation of nematode horizontal gene transfer. BMC BIOLOGY, Vol. 9. https://doi.org/10.1186/1741-7007-9-9

Dalzell, J. J., McVeigh, P., Warnock, N. D., Mitreva, M., Bird, D. M. K., Abad, P., … Maule, A. G. (2011). RNAi Effector Diversity in Nematodes. PLOS NEGLECTED TROPICAL DISEASES, 5(6). https://doi.org/10.1371/journal.pntd.0001176

Mbeunkui, F., Scholl, E. H., Opperman, C. H., Goshe, M. B., & Bird, D. M. K. (2010). Proteomic and Bioinformatic Analysis of the Root-Knot Nematode Meloidogyne hapla: The Basis for Plant Parasitism. Journal of Proteome Research, 9(10), 5370–5381. https://doi.org/10.1021/pr1006069

Torto-Alalibo, T., Collmer, C. W., Gwinn-Giglio, M., Lindeberg, M., Meng, S., Chibucos, M. C., … Tyler, B. M. (2010). [Review of Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology]. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 74(4), 479–503. https://doi.org/10.1128/mmbr.00017-10

Torto-Alalibo, T., Collmer, C. W., Lindeberg, M., Bird, D., Collmer, A., & Tyler, B. M. (2009). [Review of Common and contrasting themes in host cell-targeted effectors from bacterial, fungal, oomycete and nematode plant symbionts described using the Gene Ontology]. BMC MICROBIOLOGY, 9(SUPPL. 1). https://doi.org/10.1186/1471-2180-9-s1-s3

Opperman, C. H., Bird, D. M., & Schaff, J. E. (2009). Genomic analysis of the root-knot nematode genome. In Plant Cell Monographs (Vol. 15, pp. 221–237). https://doi.org/10.1007/978-3-540-85215-5_8

Bird, D. M., Opperman, C. H., & Williamson, V. M. (2009). Plant infection by root-knot nematode. In Plant Cell Monographs (Vol. 15, pp. 1–13). https://doi.org/10.1007/978-3-540-85215-5_1

Bird, D. M. K., Williamson, V. M., Abad, P., McCarter, J., Danchin, E. G. J., Castagnone-Sereno, P., & Opperman, C. H. (2009). The Genomes of Root-Knot Nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY, Vol. 47, pp. 333–351. https://doi.org/10.1146/annurev-phyto-080508-081839

Bird, D. M., & Opperman, C. H. (2009). [Review of The secret(ion) life of worms]. GENOME BIOLOGY, 10(1). https://doi.org/10.1186/gb-2009-10-1-205

Bird, D. M., & Opperman, C. H. (2009). The secret(ion) life of worms. Genome Biology, 10(1), 205. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-69449107507&partnerID=MN8TOARS

Schaff, J. E., Mbeunkui, F., Blackburn, K., Bird, D. M., & Goshe, M. B. (2008). A sequence-anchored genetic linkage map for the moss, Physcomitrella patens. Plant Journal, 56(5), 840–854.

Schaff, J. E., Mbeunkui, F., Blackburn, K., Bird, D. M. K., & Goshe, M. B. (2008). SILIP: A novel stable isotope labeling method for in planta quantitative proteomic analysis. Plant Journal, 56(5), 840–854. https://doi.org/10.1111/j.1365-313X.2008.03639.x

Opperman, C. H., Bird, D. M., Williamson, V. M., Rokhsar, D. S., Burke, M., Cohn, J., … Windham, E. (2008). Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(39), 14802–14807. https://doi.org/10.1073/pnas.0805946105

Schaff, J. E., Nielsen, D. M., Smith, C. P., Scholl, E. H., & Bird, D. M. K. (2007). Comprehensive Transcriptome Profiling in Tomato Reveals a Role for Glycosyltransferase in Mi-Mediated Nematode Resistance. Plant Physiology, 144(2), 1079–1092. https://doi.org/10.1104/pp.106.090241

Elling, A. A., Mitreva, M., Recknor, J., Gai, X., Martin, J., Maier, T. R., … Baum, T. J. (2007). Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. GENOME BIOLOGY, 8(10). https://doi.org/10.1186/gb-2007-8-10-r211

Snyder, D. W., Opperman, C. H., & Bird, D. M. K. (2006). A method for generating Meloidogyne incognita males. Journal of Nematology, 38(2), 192–194. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-33750134280&partnerID=MN8TOARS

Waterman, J. T., Bird, D. M. K., & Opperman, C. H. (2006). A method for isolation of Pasteuria penetrans endospores for bioassay and genomic studies. Journal of Nematology, 38(1), 165–167. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-34248330929&partnerID=MN8TOARS

Bird, D. M., Blaxter, M. L., McCarter, J. P., Mitreva, M., Sternberg, P. W., & Thomas, W. K. (2006). A white paper on nematode comparative genomics. Journal of Nematology, 37(4), 408–416.

Vanholme, B., Mitreva, M., Van Criekinge, W., Logghe, M., Bird, D., McCarter, J. P., & Gheysen, G. (2006). Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii. Parasitology Research, 98(5), 414–424. https://doi.org/10.1007/s00436-005-0029-3

McCarter, J. P., Bird, D. M., & Mitreva, M. (2006). Nematode gene sequences: Update for December 2005. Journal of Nematology, 37(4), 417–421.

Bird, D. M. K., Blaxter, M. L., McCarter, J. P., Mitreva, M., Sternberg, P. W., & Thomas, W. K. (2005). A white paper on nematode comparative genomics. Journal of Nematology, 37(4), 408–416. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-33744994353&partnerID=MN8TOARS

Mitreva, M., Blaxter, M. L., Bird, D. M., & McCarter, J. P. (2005). [Review of Comparative genomics of nematodes]. TRENDS IN GENETICS, 21(10), 573–581. https://doi.org/10.1016/j.tig.2005.08.003

Bird, D. M. (2005). Model systems in agriculture: Lessons from worms. Annals of Applied Biology, 146(2), 147–154. https://doi.org/10.1111/j.1744-7348.2005.040066.x

McCarter, J. P., Bird, D. M. K., & Mitreva, M. (2005). Nematode gene sequences: Update for December 2005. Journal of Nematology, 37(4), 417–421. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-33744980477&partnerID=MN8TOARS

Charles, L., Carbone, I., Davies, K. G., Bird, D., Burke, M., Kerry, B. R., & Opperman, C. H. (2005). Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci. JOURNAL OF BACTERIOLOGY, 187(16), 5700–5708. https://doi.org/10.1128/JB.187.16.5700-5708.2005

Scholl, E. H., & Bird, D. M. (2005). Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data. MOLECULAR PHYLOGENETICS AND EVOLUTION, 36(3), 536–545. https://doi.org/10.1016/j.ympev.2005.03.016

Weerasinghe, R. R., Bird, D. M., & Allen, N. S. (2005). Root-knot nematodes and bacterial Nod factors elicit common signal transduction events in Lotus japonicus. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102(8), 3147–3152. https://doi.org/10.1073/pnas.0407926102

Mitreva, M., Elling, A. A., Dante, M., Kloek, A. P., Kalyanaraman, A., Aluru, S., … McCarter, J. P. (2004). A survey of SL1-spliced transcipts from the root-lesion nematode Pratylenchus penetrans. MOLECULAR GENETICS AND GENOMICS, 272(2), 138–148. https://doi.org/10.1007/s00438-004-1054-0

Lohar, D. P., Schaff, J. E., Laskey, J. G., Kieber, J. J., Bilyeu, K. D., & Bird, D. M. (2004). Cytokinins play opposite roles in lateral root formation, and nematode and Rhizobial symbioses. PLANT JOURNAL, 38(2), 203–214. https://doi.org/10.1111/j.1365-313X.2004.02038.x

Bird, D. M. K. (2004). High society (of nematologists). Genome Biology, 5(11). https://doi.org/10.1186/gb-2004-5-11-353

Bird, D. M. (2004). [Review of Signaling between nematodes and plants]. CURRENT OPINION IN PLANT BIOLOGY, 7(4), 372–376. https://doi.org/10.1016/j.pbi.2004.05.005

McCarter, J. P., Mitreva, M. D., Martin, J., Dante, M., Wylie, T., Rao, U., … Waterston, R. H. (2003). Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biology, 4(4), R26–1. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-9444261296&partnerID=MN8TOARS

Bird, D. M., & Kaloshian, I. (2003). [Review of Are roots special? Nematodes have their say]. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY, 62(2), 115–123. https://doi.org/10.1016/S0885-5765(03)00045-6

Scholl, E. H., Thorne, J. L., McCarter, J. P., & Bird, D. M. (2003). Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biology, 4(6), R39–1. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0038576862&partnerID=MN8TOARS

Bird, D. M., Opperman, C. H., & Davies, K. G. (2003). [Review of Interactions between bacteria and plant-parasitic nematodes: now and then]. INTERNATIONAL JOURNAL FOR PARASITOLOGY, 33(11), 1269–1276. https://doi.org/10.1016/S0020-7519(03)00160-7

Lohar, D. P., & Bird, D. M. (2003). Lotus japonicus: A new model to study root-parasitic nematodes. PLANT AND CELL PHYSIOLOGY, 44(11), 1176–1184. https://doi.org/10.1093/pcp/pcg146

Hirsch, A. M., Bauer, W. D., Bird, D. M., Cullimore, J., Tyler, B., & Yoder, J. I. (2003). Molecular signals and receptors: Controlling rhizosphere interactions between plants and other organisms. ECOLOGY, 84(4), 858–868. https://doi.org/10.1890/0012-9658(2003)084[0858:msarcr]2.0.co;2

McCarter, J. P., Mitreva, M., Clifton, S. W., Bird, D. M. K., & Waterston, R. H. (2003). Nematode gene sequences: Update for December 2003. Journal of Nematology, 35(4), 465–469. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-1842510703&partnerID=MN8TOARS

McCarter, J. P., Clifton, S. W., Bird, D. M. K., & Waterston, R. H. (2002). Nematode gene sequences, update for June 2002. Journal of Nematology, 34(2), 71–74. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0036618995&partnerID=MN8TOARS

Koltai, H., & Bird, D. M. (2002). Recovery and sequence validation of the histological signal following in situ RT-PCR localization of plant gene transcripts. PLANT MOLECULAR BIOLOGY REPORTER, 20(4), 391–397. https://doi.org/10.1007/BF02772126

Bradshaw, R. E., Bird, D. M., Brown, S., Gardiner, R. E., & Hirst, P. (2001). Cytochrome c is not essential for viability of the fungus Aspergillus nidulans. Molecular Genetics and Genomics, 266(1), 48–55. https://doi.org/10.1007/s004380100517

Koltai, H., Dhandaydham, M., Opperman, C., Thomas, J., & Bird, D. (2001). Overlapping plant signal transduction pathways induced by a parasitic nematode and a rhizobial endosymbiont. MOLECULAR PLANT-MICROBE INTERACTIONS, 14(10), 1168–1177. https://doi.org/10.1094/MPMI.2001.14.10.1168

Bird, D. M. (2000). Alan Francis Bird: 1928-99. Journal of Nematology, 32(1), 1–3.

Koltai, H., & Bird, D. M. (2000). Epistatic repression of PHANTASTICA and class 1 KNOTTED genes is uncoupled in tomato. PLANT JOURNAL, 22(5), 455–459. https://doi.org/10.1046/j.1365-313X.2000.00754.x

Koltai, H., & Bird, D. M. (2000). High throughput cellular localization of specific plant mRNAs by liquid-phase in situ reverse transcription-polymerase chain reaction of tissue sections. PLANT PHYSIOLOGY, 123(4), 1203–1212. https://doi.org/10.1104/pp.123.4.1203

McCarter, J. P., Bird, D. M. K., Clifton, S. W., & Waterston, R. H. (2000). Nematode gene sequences, December 2000 update. Journal of Nematology, 32(4), 331–333. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0034353966&partnerID=MN8TOARS

Bird, D. M., & Koltai, H. (2000). Plant parasitic nematodes: Habitats, hormones, and horizontally-acquired genes. Journal of Plant Growth Regulation, 19(2), 183–194. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0033758702&partnerID=MN8TOARS

McCarter, J., Abad, P., Jones, J. T., & Bird, D. (2000). Rapid gene discovery in plant parasitic nematodes via Expressed Sequence Tags. NEMATOLOGY, 2(7), 719–731. https://doi.org/10.1163/156854100509574

Bird, D. M., Opperman, C. H., Jones, S. J. M., & Baillie, D. L. (1999). [Review of The Caenorhabditis elegans genome: A guide in the post genomics age]. ANNUAL REVIEW OF PHYTOPATHOLOGY, 37(1999), 247–265. https://doi.org/10.1146/annurev.phyto.37.1.247

Bird, D. M., & Opperman, C. H. (1998). Caenorhabditis elegans: A genetic guide to parasitic nematode biology. Journal of Nematology, 30(3), 299–308. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0032357095&partnerID=MN8TOARS

Opperman, C. H., & Bird, D. M. (1998). [Review of The soybean cyst nematode, Heterodera glycines: a genetic model system for the study of plant-parasitic nematodes]. CURRENT OPINION IN PLANT BIOLOGY, 1(4), 342–346. https://doi.org/10.1016/1369-5266(88)80057-8

Bird, D., & Bradshaw, R. (1997). Gene targeting is locus dependent in the filamentous fungus Aspergillus nidulans. Molecular and General Genetics, 255(2), 219–225. https://doi.org/10.1007/s004380050492

Bird, D. M., Kaloshian, I., & Molinari, S. (1997). Promoter structure of the RNA polymerase II large subunit gene in caenorhabditis elegans and C. Briggsae. Journal of Nematology, 29(2), 144–152. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0030786968&partnerID=MN8TOARS

Bird, D. M. (1996, December). Manipulation of host gene expression by root-knot nematodes. JOURNAL OF PARASITOLOGY, Vol. 82, pp. 881–888. https://doi.org/10.2307/3284193

Wilson, M. A., Bird, D. M., & Knaap, E. (1994). A comprehensive subtractive cDNA cloning approach to identify nematode-induced transcripts in tomato. Phytopathology, 84(3), 299–303. https://doi.org/10.1094/Phyto-84-299

Bird, D. M., & Riddle, D. L. (1994). A genetic nomenclature for parasitic nematodes. Journal of Nematology, 26(2), 138–143. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0028054366&partnerID=MN8TOARS

Bird, D. M., & Wilson, M. A. (1994). DNA sequence and expression analysis of root-knot nematode-elicited giant cell transcripts. Molecular Plant-Microbe Interactions, 7(3), 419–424. https://doi.org/10.1094/MPMI-7-0419

Peloquin, J. J., Bird, D. M., & Platzer, E. G. (1993). Rapid miniprep isolation of mitochondrial DNA from metacestodes, and free- living and parasitic nematodes. Journal of Parasitology, 79(6), 964–967. https://doi.org/10.2307/3283741

Kaloshian, I., & Bird, D. M. (1992). Efficient removal of hybridization signal from Southern blots probed with radiolabeled oligonucleotides. BioTechniques, 13(1), 34–36. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-0026653183&partnerID=MN8TOARS

Bird, D. M. K. (1992). Sequence comparison of the Caenorhabditis elegans dpy-13 and col-34 genes, and their deduced collagen products. Gene, 120(2), 261–266. https://doi.org/10.1016/0378-1119(92)90102-U

Bird, D. M., & Riddle, D. L. (1989). Molecular cloning and sequencing of ama-1, the gene encoding the largest subunit of Caenorhabditis elegans RNA polymerase II. Molecular and Cellular Biology, 9(10), 4119–4130. https://doi.org/10.1128/MCB.9.10.4119

Mende, N., Bird, D. M., Albert, P. S., & Riddle, D. L. (1988). dpy-13: A nematode collagen gene that affects body shape. Cell, 55(4), 567–576. https://doi.org/10.1016/0092-8674(88)90215-2