Publications

  • 32 total publications including 2 first author, 7 second author, and 5 third author
  • Plan and conduct written and oral presentations in a professional manner 
  • Successfully gave dozens of BASF wide presentations, dozens of presentations in and around Penn State and LSU, and several high-profile presentations at Plant & Animal Genome Conference

Genome Papers

  • Ming R, Hou S, Feng Y, Yu Q, …, Wall K, …, Alam M.  Genome of the transgenic tropical fruit tree papaya (Carica papaya L.). Nature. 2008;452(7190):991-6.
  • Tuskan G, DiFazio S, …, Wall K, ..., Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw).  Science. 2006;313(5793):1596-604.

Genomics / RNA-seq Papers

  • Bliss BJ, Wanke S, …, Wall PK, Jiao Y, …, Ma H, dePamphilis CW. Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies. BMC Plant Biol. 2013 Jan 24;13:13.
  • Wall K, Leebens-Mack J, …, Soltis P, Altman N, dePamphilis C. 2009.  Comparison of next generation sequencing technologies for de novo transcriptome characterization. BMC Genomics, BMC Genomics 2009, 10:347 (1 August 2009). [highly accessed & most viewed article in BMC Genomics – FALL 2009]
  • Wall K, Leebens-Mack J, Muller K, …, dePamphilis C.  PlantTribes:  A gene family database for comparative genomics in plants. Nucleic Acids Res. 2008; 36(Database issue):D970-6.
  • Chanderbali AS, Yo M, Zahn L, Brokington S, Wall PK, …, Soltis PS. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower.  Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22570-5. Epub 2010 Dec 13.
  • Zahn LM, Ma X, Altman NS, Zhang Q, Wall PK, ..., Ma H.  Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies.  Genome Biol. 2010;11(10):R101. Epub 2010 Oct 15.
  • Oldham JT, Hincapie M, Rejtar T, Wall PK, Carlson JE, Lee-Parsons CW.  Shotgun proteomic analysis of yeast-elicited California poppy (Eschscholzia californica) suspension cultures producing enhanced levels of benzophenanthridine alkaloids.  J Proteome Res. 2010 Sep 3;9(9):4337-45.
  • Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, dePamphilis CW.  Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels.  BMC Evol Biol. 2010 Feb 24;10:61.
  • Shan H, Zahn L, Guindon S, Wall PK, Kong H, Ma H, DePamphilis CW, Leebens-Mack J.  Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications.  Mol Biol Evol. 2009 Oct;26(10):2229-44. Epub 2009 Jul 3.
  • Duarte J, Wall K, Leebens-Mack JH, and dePamphilis CW. 2007. Utility of Amborella trichopoda and Nuphar advena ESTs for comparative sequence analysis. Taxon, 2008;57(4):1110-383E(-726).
  • Liang L, Carlson JL, Leebens-Mack JH, Wall K, …, Field D, Tanksley S, Ma H, dePamphilis CW. An EST Database for Liriodendron tulipifera. Tree Genetics and Genomes. 2008;4(3):419-33.
  • Soltis D, Albert V, Leebens-Mack J, Wing R, dePamphilis C, Ma H, Carlson J, Altman N, Wall K, Zuccolo A, Sotis P.  The Amborella genome: an evolutionary reference for plant biology. Genome Biol. 2008;9(3):402
  • Soltis D, Albert V, Leebens-Mack J, Bell C, Patterson A, Zheng C, Sankoff D, dePamphilis C, Wall K, Sotis P.  Polyploidy and Angiosperm Diversification.  American Journal of Botany (2007).
  • Leebens-Mack J, Vision T, ..., Wall K, Warnow T, Zmasek C. Taking the first steps towards a standard for reporting on phylogenies: minimal information about a phylogenetic analysis (MIAPA). OMICS.  2006;10(2):231-7.
  • Cui L, Wall K, Leebens-Mack JH, Lindsay BG, …, Ma H, dePamphilis CW. Widespread genome duplications throughout the history of flowering plants. Genome Res. 2006;16(6):738-49.
  • Duarte JM, Cui L, Wall K, Zhang Q, Zhang X, Leebens-Mack J, Ma H, Altman N, dePamphilis CW. Expression pattern shifts following duplication indicative of sub and neo-functionalization in regulatory genes of Arabidopsis. Mol Biol Evol. 2006;23(2):469-478
  • Kim S, Soltis PS, Wall K, Soltis DE. Phylogeny and domain evolution in the APETALA2-like gene family. Mol Biol Evol. 2006;23(1):107-20.
  • Carlson JE, Leebens-Mack JH, Wall K, …, Ma H, dePamphilis CW. EST database for early flower development in California poppy tags over 6000 genes from a basal eudicot.  Plant Mol. Biol. 2006;62(3):351-69.
  • Albert V, Soltis D, Carlson J, Farmerie W, Wall K, …, dePamphilis C, Leebens-Mack J.  Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biology. 2005;5(1):5.

Bioinformatics Papers

  • Ali R, Yuannian J, Wall PK, Ahmad I, Patching S, dePamphilis CW.  In silico identification and structure function analysis of a putative coclaurine N-methyltransferase from Aristolochia fimbriata. Computational Biology and Chemistry. 2020 Apr. Volume 85.
  • Wang LS, Leebens-Mack J, Kerr Wall P, Beckmann K, Depamphilis CW, Warnow T.  The impact of multiple protein sequence alignment on phylogenetic estimation.  IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):1108-19.
  • Zheng C, Wall PK, Leebens-Mack J, Albert VA, dePamphilis C, Sankoff D.  The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral populus diploid.  Comput Syst Bioinformatics Conf. 2008;7:261-71.
  • Sankoff D, Zheng C, Wall PK, dePamphilis C, Leebens-Mack J, Albert VA.  Towards improved reconstruction of ancestral gene order in angiosperm phylogeny.  J Comput Biol. 2009 Oct;16(10):1353-67.
  • Sankoff D, Zheng C, Wall K, dePamphilis CW, Leebens-Mack J, Albert V.  Internal validation of ancestral gene order reconstruction in angiosperm phylogeny.  In: Viallette S, Nelson C (eds.) Proceedings of the RECOMB Satellite Conference on Comparative Genomics (RECOMB CG 2008)
  • Cui L, Veeraraghavan N, Richter A, Wall K, Jansen RK, Leebens-Mack J, Makalowska I, dePamphilis CW. ChloroplastDB: the chloroplast genome database. Nucleic Acids Res. 2006;34(Database issue):D692-6.
  • Wang JP, Lindsay BG, Cui L, Wall K, Marion J, Zhang J, Depamphilis CW. Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. BMC Bioinformatics. 2005 Dec;6(1):300.
  • Wang JP, Lindsay BG, Leebens-Mack J, Cui L, Wall K, Miller WC, dePamphilis CW.  EST clustering error evaluation and correction. Bioinformatics. 2004;20(17):2973-84.
  • Molbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D. The plasmid genome database.  Microbiology. 2003;149(Pt 11):3043-5.

miRNA Papers

  • Barakat A, Wall K, Diloreto S, dePamphilis CW, Carlson JE. Conservation and divergence of microRNAs in Populus. BMC Genomics. 2007;8:481.
  • Barakat A, Wall K, Leebens-Mack J, Carlson J, dePamphilis C. Conservation and divergence of microRNAs in California poppy. Plant Journal. 2007; 51(6):991-1003.

Book Chapters

  • Soltis DE, Albert VA, Kim S, …, Wall K, dePamphilis CW, Ma H. Diversity and Evolution of Plants: Genotypic and Phenotypic Variation in Higher Plants. Evolution of the flower.  2005;CABI:165-200.
  • Leebens-Mack JH, Wall K, Duarte J, Zheng ZG, Oppenheimer D, Depamphilis C.  A genomics approach to the study of ancient polyploidy and floral developmental genetics.  Advances in Botanical Reesearch: Incorporating Advances in Plant Pathology. 2006. 44: 527-549. 

Presentations

  • “Knowledge Management at BASF Geismar.”  Presentation at the TCC/LCA EHS conference in Galveston, TX.  June 9, 2016.
  • “Ultrahigh-throughput transcriptome tagging using pyrosequencing technology.” Presentation at the Institute of Molecular Evolutionary Genetics, University Park, PA.  October 25, 2006. 
  • “Populus Genome Aids Identification of Gene Families Across the Angiosperms.” Presentation at the Plant and Animal Genome Conference, San Diego, CA.  January 15, 2006. 
  • “PlantTribes:  A Global Classification of Arabidopsis and Rice Proteins.” Presentation at the Plant and Animal Genome Conference, San Diego, CA.  January 19, 2004.
  • “Bioinformatic Solutions in the Floral Genome Project.”  Presentation at the Plant and Animal Genome Conference, San Diego, CA.  January 13, 2002.