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, 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. V., Elsen, S. V. D., 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. (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., 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., 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., 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., Jones, J. T., Opperman, C. H., Kikuchi, T., & Danchin, E. G. J. (2015). Signatures of adaptation to plant parasitism in nematode genomes. Parasitology, 142, 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. (2011). Computational and phylogenetic validation of nematode horizontal gene transfer. BMC Biology, 9. https://doi.org/10.1186/1741-7007-9-9

Dalzell, J. J., McVeigh, P., Warnock, N. D., Mitreva, M., Bird, D., 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. (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). 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). 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. In 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.

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., 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.

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.

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.

Mitreva, M., Blaxter, M. L., Bird, D., & McCarter, J. P. (2005). 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.

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. (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. K., & 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 transcripts 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. K. (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. (2004). 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.

Bird, D. M. K., & Kaloshian, I. (2003). 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.

Bird, D. M. K., Opperman, C. H., & Davies, K. G. (2003). 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. K. (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., 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.

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.

Koltai, H., & Bird, D. (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. (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. K. (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.

Bird, D. M., & Koltai, H. (2000). Plant parasitic nematodes: Habitats, hormones, and horizontally-acquired genes. Journal of Plant Growth Regulation, 19(2), 183–194.

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. K., Opperman, C. H., Jones, S. J. M., & Baillie, D. L. (1999). 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.

Opperman, C. H., & Bird, D. (1998). 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.

Bird, D. M. K. (1996). Manipulation of host gene expression by root-knot nematodes. Journal of Parasitology, 82(6), 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.

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.

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