Carolyn J Lawrence-Dill

Research Description

Dr. Lawrence’s group develops computational systems and tools that enable researchers to leverage plant genetics and genomics information to better understand basic biology as well as to engineer improved plants.  Her group is interested in application of technologies to predict plant phenotype and coordinates activities to overcome challenges in the emerging field of high-throughput phenotyping. Although work by group members is not specifically limited to maize, it is by far the group’s favorite model system.

Publications – Publications list at Google Scholar

• MaizeGDB: The Maize Genetics and Genomics Database. 2016. Harper L, Gardiner J, Andorf C, Lawrence CJ. Methods Mol Biol. 2016;1374:187-202.
  doi: 10.1007/978-1-4939-3167-5_9.
• MaizeGDB update: new tools, data and interface for the maize model organism database. 2016. Andorf CM, Cannon EK, Portwood JL nd, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ. Nucleic Acids Res. 2016 Jan 4;44(D1):D1195-201. doi: 10.1093/nar/gkv1007. Epub 2015 Oct 1. 2016
• A Quick Guide to CRISPR sgRNA Design Tools. 2016. Brazelton VA Jr, Zarecor S, Wright DA, Wang Y, Liu J, Chen K, Yang B, Lawrence-Dill CJ.
• Emerging semantics to link phenotype and environment. 2015. Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. PeerJ. 2015 Dec 14;3:e1470.  doi: 10.7717/peerj.1470. eCollection 2015.
• An Ontology Approach to Comparative Phenomics in Plants. 2015. Anika Oellrich, Ramona L. Walls, Ethalinda K.S. Cannon, Steven B. Cannon, Laurel Cooper, Jack Gardiner, Georgios V. Gkoutos, Lisa Harper, Mingze He, Robert Hoehndorf, Pankaj Jaiswal, Scott Kalberer, John P. Lloyd, David Meinke, Naama Menda, Laura Moore, Rex Nelson, Anuradha Pujar, Carolyn J. Lawrence and Eva Huala Plant Methods. 2015 Feb 25;11:10. doi: 10.1186/s13007-015-0053-y. eCollection 2015.
• Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. 2015. MeiYee Law, Kevin L. Childs, Michael S. Campbell, Joshua C. Stein, Andrew J. Olson, Carson Holt, Nicholas Panchy, Jikai Lei, Dian Jiao, Carson M. Andorf, Carolyn J. Lawrence, Doreen Ware, Shin-Han Shiu, Yanni Sun, Ning Jiang, Mark Yandell. Plant Physiology, January 2015; 167(1):25-39. doi: 10.1104/pp.114.245027.
• Finding our way through phenotypes. 2015. Andrew R Deans, Suzanna E Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csősz, Hong Cui, Wasila Dahdul, Sandip Das, T. Alexander Dececchi, Agnes Dettai, Rui Diogo, Robert E. Druzinsky, Michel Dumontier, Nico M. Franz, Frank Friedrich, George V. Gkoutos, Melissa Haendel, Luke J. Harmon, Terry F. Hayamizu, Yongqun He, Heather M. Hines, Nizar Ibrahim, Laura M. Jackson, Pankaj Jaiswal, Christina James-Zorn, Sebastian Köhler, Hilmar Lapp, Carolyn J. Lawrence, Nicolas Le Novère, Guillaume Lecointre, John G. Lundberg, James Macklin, Austin R. Mast, Peter E. Midford, István Mikó, Christopher J. Mungall, Anika Oellrich, David Osumi-Sutherland, Helen Parkinson, Martín J. Ramírez, Stefan Richter, Peter N. Robinson, Alan Ruttenberg, Katja S. Schulz, Erik Segerdell, Katja C. Seltmann, Michael J. Sharkey, Aaron D. Smith, Barry Smith, Chelsea D. Specht, R. Burke Squires, Robert W. Thacker, Anne Thessen, Jose Fernandez Triana, Mauno Vihinen, Peter D. Vize, Lars Vogt, Ramona L. Walls, Monte Westerfield, Robert A. Wharton, Christian S. Wirkner, James B. Woolley, Matthew J. Yoder, Aaron M. Zorn, Paula M. Mabee. doi: 10.1371/journal.pbio.1002033.
• G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation. 2014. Carson M. Andorf, Mykhailo Kopylovc, Drena Dobbs, Karen E. Koch, M.Elizabeth Stroupec, Carolyn J. Lawrence Hank W. Bass. Journal of Genetics and Genomics, November 4, 2014
  doi: 10.1016/j.jgg.2014.10.004.
• Databases (Book Chapter). 2014. Schaeffer, Mary L, Sen TZ and Lawrence C. 2014. Databases. IN: Genetics, Genomics and Breeding of Maize, Martin Bohn, Jinsheng Lai,Ramakrishna Wusirika (eds), pp 215-235 CRC Press, Boca Raton, FL. Aug 5 2014.
• MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations. 2014. Campbell M, Law M, Holt C, Stein J, Moghe G, Hufnagel D, Lei J, Achawanantakun R, Jiao D, Lawrence C, Ware D, Shiu SH, Childs K, Sun Y, Jiang N, Yandell M.; Feb 2014; 164(2): 513–524
  doi: 10.1104/pp.113.230144.
• Maize chromosomal knobs are located in gene-dense areas and suppress local recombination.
  Ghaffari R, Cannon EK, Kanizay LB, Lawrence CJ, Dawe RK.
  Chromosoma. 2013 Mar;122(1-2):67-75. doi: 10.1007/s00412-012-0391-8. Epub 2012 Dec 9.
• RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.
  Robbins RJ, Amaral-Zettler L, Bik H, Blum S, Edwards J, Field D, Garrity G, Gilbert JA, Kottmann R, Krishtalka L, Lapp H, Lawrence C, Morrison N, Tuama EÓ, Parr C, San Gil I, Schindel D, Schriml L, Vieglas D, Wooley J.
  Stand Genomic Sci. 2012 Oct 10;7(1):159-65. doi: 10.4056/sigs.3156511. Epub 2012 Jul 28.
• POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.
  Cannon EK, Birkett SM, Braun BL, Kodavali S, Jennewein DM, Yilmaz A, Antonescu V, Antonescu C, Harper LC, Gardiner JM, Schaeffer ML, Campbell DA, Andorf CM, Andorf D, Lisch D, Koch KE, McCarty DR, Quackenbush J, Grotewold E, Lushbough CM, Sen TZ, Lawrence CJ. Int J Plant Genomics. 2011;2011:923035.
• MaizeGDB: curation and outreach go hand-in-hand.
  Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Sen TZ, Lawrence CJ.
  Database (Oxford). 2011 May 29;2011:bar022.
• The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.
  Harper LC, Schaeffer ML, Thistle J, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Braun BL, Birkett SM, Lawrence CJ, Sen TZ. Database (Oxford). 2011 May 9;2011:bar016.
• Multi-source and ontology-based retrieval engine for maize mutant phenotypes.
  Green JM, Harnsomburana J, Schaeffer ML, Lawrence CJ, Shyu CR. Database (Oxford). 2011 May 10;2011:bar012.
• Sen, TZ, Harper, LC, Schaeffer, ML, Andorf, CM, Seigfried, T., Campbell, DA, Lawrence, CJ (2010) Choosing a genome browser for a Model Organism Database: surveying the Maize community. Database 2010:baq007
• Andorf, CM, Lawrence, CJ, Harper, LC, Schaeffer, ML, Campbell, DA, Sen, TZ. (2010) The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps Bioinformatics. 2010 26: 434-436.
• Sen, TZ, Andorf, CM, Schaeffer, ML, Harper, LC, Sparks, ME, Duvick, J, Brendel, VP, Cannon, E, Campbell, DA, Lawrence, CJ. (2009) MaizeGDB becomes ‘sequence-centric’ Database. 2009:Vol. 2009:bap020.
• Lushbough C, Bergman MK, Lawrence CJ, Jennewein D, Brendel V. BioExtract server–an integrated workflow-enabling system to access and analyze heterogeneous, distributed biomolecular data.  IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):12-24.
• Yi G, Luth D, Goodman TD, Lawrence CJ, Becraft PW. High-throughput linkage analysis of Mutator insertion sites in maize. Plant J. 2009 Jun;58(5):883-92. Epub 2009 Feb 4.
• Gray J, Bevan M, Brutnell T, Buell CR, Cone K, Hake S, Jackson D, Kellogg E, Lawrence C, McCouch S, Mockler T, Moose S, Paterson A, Peterson T, Rokshar D, Souza GM, Springer N, Stein N, Timmermans M, Wang GL, Grotewold E. A recommendation for naming transcription factor proteins in the grasses. Plant Physiol. 2009 Jan;149(1):4-6.
• Lushbough CM, Bergman MK, Lawrence CJ, Jennewein D, Brendel V. Implementing bioinformatic workflows within the bioextract server. Int J Comput Biol Drug Des. 2008;1(3):302-12.
• Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V. PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D959-65.
• Lawrence, CJ, Harper, LC, Schaeffer, ML, Sen, TZ, Seigfried, TE, Campbell, DA. (2008) MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research. Int J Plant Genomics. 2008:496957.
• Carolyn J. Lawrence. 2007. MaizeGDB, the Maize Genetics and Genomics Database. in Plant Bioinformatics, D. Edwards (Editor) for the series Methods in Molecular Biology Humana Press, Totowa, New Jersey, USA .
• Carolyn J. Lawrence and Virginia Walbot. 2007. Translational Genomics for Bioenergy Production from Fuelstock Grasses: Maize as the Model Species. The Plant Cell 19(7):2091-2094.
• Carolyn J. Lawrence, Mary L. Schaeffer, Trent E. Seigfried, Darwin A. Campbell, and Lisa C. Harper. 2007. MaizeGDB’s New Data Types, Resources, and Activities. Nucleic Acids Research 35(Database):D895-900.
• Lincoln D. Stein, William D. Beavis, Damian D. Gessler, Eva Huala, Carolyn J. Lawrence, Doreen Main, Lukas A. Mueller, Sue Y. Rhee, and Daniel S. Rokhsar. 2006. Save Our Data!. The Scientist 20(4):24-25.
• Carolyn J. Lawrence, Trent E. Seigfried, Hank W. Bass, and Lorinda K. Anderson. 2006. Predicting Chromosomal Locations of Genetically Mapped Loci in Maize Using the Morgan2McClintock Translator. Genetics 172(3):2007-2009.
• Carolyn J. Lawrence, Trent E. Seigfried, and Volker Brendel. 2005. The Maize Genetics and Genomics Database. The Community Resource for Access to Diverse Maize Data. Plant Physiology 138(1):55-58.
• Qunfeng Dong, Carolyn J. Lawrence, Shannon D. Schlueter, Matthew D. Wilkerson, Stefan Kurtz, Carol Lushbough, and Volker Brendel. 2005. Comparative Plant Genomics Resources at PlantGDB. Plant Physiology 139(2):610-618.
• Carolyn J. Lawrence, Qunfeng Dong, Mary L. Polacco, Trent E. Seigfried, and Volker Brendel. 2004. MaizeGDB, the Community Database for Maize Genetics and Genomics. Nucleic Acids Research 32:D393-397.
• Sanford Baran, Carolyn J. Lawrence, and Volker Brendel. 2004. PGROP – A Gateway to Plant Genome Research ‘Outreach’ Programs. Plant Physiology 134(3):889.
• Carolyn J. Lawrence, Christian M. Zmasek, R. Kelly Dawe, and Russell L. Malmberg. 2004. LumberJack: A Heuristic Tool for Sequence Alignment Exploration and Phylogenetic Inference. Bioinformatics 20(12):1977-1979.
• Carolyn J. Lawrence, R. Kelly Dawe. 2004. A Standardized Kinesin Nomenclature. The Journal of Cell Biology 167(1):19-22.
• Carolyn J. Lawrence, Russell L. Malmberg, Michael G. Muszynski, and R. Kelly Dawe. 2002. Maximum Likelihood Methods Reveal Conservation of Function Among Closely Related Kinesin Families. Journal of Molecular Evolution 54(1):42-53.
• Carolyn J. Lawrence, N. Ronald Morris, Richard B. Meagher, and R. Kelly Dawe. 2001. Dyneins Have Run Their Course in Plant Lineage. Traffic 2(5):362-363.
• Carolyn J. Lawrence and A. Scott Holaday. 2000. Effects of Mild Night Chilling on Respiration of Expanding Cotton Leaves. Plant Science 157(2):233-244.