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United States Department of Agriculture

Agricultural Research Service

Alejandro P. Rooney (Alex)

Supervisory Research Geneticist

Alejandro P. Rooney (Alex)


Research Leader and Supervisory Research Geneticist
Telephone: (309)-681-6395
Fax: (309)-681-6693
Email: alejandro.rooney@ars.usda.gov
http://www.ars.usda.gov/mwa/ncaur/cbp

 

Research Specialties


Microbial systematics, taxonomy and evolutionary biology; molecular evolution; discovery and development of living microbial biological control agents for use against arthropod vectors of disease and plant pathogens.

 

Education


1998    Ph.D., Genetics    Texas A&M University

1994    B.S., Biology         University of Cincinnati

 

Professional Appointments


2010 – Present   Research Leader, Crop Bioprotection Research Unit, USDA, ARS, Peoria, IL

2010 – Present   Director, Microbial Biological Control Agent Resource Center, USDA, ARS, Peoria, IL

2009 – 2010       Director, ARS (NRRL) Culture Collection, USDA, ARS, Peoria, IL

2002 – 2010       Research Geneticist, Microbial Genomics Research Unit, USDA, ARS, Peoria, IL

2002 – 2010       Curator of Bacteria, ARS (NRRL) Culture Collection, USDA, ARS, Peoria, IL

2000 – 2002       Assistant Professor, Department of Biological Sciences, Mississippi State University

1998 – 2000       Postdoctoral Scholar, Inst. of Molecular Evolutionary Genetics, Penn State University

 

Honors and Awards


·         President’s Volunteer Service Award (Gold Level), 2013. Awarded for outstanding community service.

·         Extra Effort Award, U.S. Department of Agriculture, Agricultural Research Service, 2010. Awarded for exceeding performance expectations while serving on special detail.

·         Gene, Top Reviewer Award, 2010. Awarded for meritorious service to the journal Gene.

·         Early Career Research Scientist of the Year.  U.S. Department of Agriculture, Agricultural Research Service, Midwest Area, 2008. Awarded for research accomplishments on the systematics and population genetics of public health and biodefense microorganisms

·         Centers for Disease Control and Prevention, Certificate of Merit. 2008. Awarded for research accomplishments resulting in the development of novel subtyping methods for the human pathogen Aspergillus fumigatus and candidate for the Charles C. Shepard Science Award (Laboratory and Methods).

·         The Wildlife Society, Outstanding Article of the Year, 2004. Awarded for research on the population genetics of translocated deer populations.

·         Journal of Molecular Evolution, Zuckerkandl Prize (Best Paper of the Year), 2003. Awarded for research on the molecular evolution of snake venom protein multigene families.

·         Mississippi State University, Office of the Vice President for Research, Faculty Research Award, 2001. Awarded for faculty research achievement.

·         Texas A&M University, Faculty of Genetics, Graduate Student Research Award, 1996. Awarded for student research achievement.

·         Texas A&M University, College of Veterinary Medicine, Graduate Student Research Award, College of Veterinary Medicine, 1995. Awarded for student research achievement.

·         Texas A&M University, College of Veterinary Medicine, Graduate Student Presentation Award, 1995. Awarded for best oral presentation.

 

Editorial Boards


·         Plant Gene, Editor-in-Chief, 2014 – present

·         Gene, Executive Editor, 2013 – present

·         International Journal of Systematic and Evolutionary Microbiology, Assoc. Editor, 2013 – present

·         Frontiers in Ecology and Evolution: Phylogenetics, Phylogenomics, and Systematics, Assoc. Editor, 2013 – present

·         Frontiers in Ecology and Evolution: Evolutionary and Population Genetics, Editorial Board, 2011 – present

·         Gene, Assoc. Editor, 2010 – 2013

·         Current Microbiology, Assoc. Editor, 2009 – 2013

 

Professional Consultation Activities


·         USDA representative, Scientific Collections International (SciColl), Food Security Research Advisory Group, 2013 present.

·         USDA representative, Federal Experts Security Advisory Panel, Select Agent Regulatory Changes Working Group, 2014

·         External scientific reviewer, Canadian Domestic Substances List (living organisms), Safe Environments Directorate, Health Canada (Government of Canada), 2014.

·         USDA representative, White House Office of Science and Technology Policy working group to establish guidelines for strain exchange among U.S. federal agencies working in biodefense and bioforensics, 2011.

·         Consultant, Federal Bureau of Investigation, Amerithrax Investigation, 2003 2010.

·         Consultant, Centers for Disease Control and Prevention, genomics of Rhizopus, 2010.

·         Member, American Type Culture Collection Standards Working Group, 2009 2010.

·         Consultant, California Almond Board, establishment of guidelines for the use of bacterial thermal validation strain surrogates for foodborne pathogens in food processing production lines and testing facilities, 2008 2009.

·         Consultant, Centers for Disease Control and Prevention, the establishment of guidelines for the identification and subtyping of Aspergillus fumigatus, 2008.

·         Consultant, National Aeronautics and Space Administration (Jet Propulsion Laboratory), microbial diversity, long-term preservation, and curation, 2004 2007.

·         Consultant, U.S. Army Center for Health Promotion and Preventative Medicine, bacterial species identification, 2003 2005.

·         Consultant to the National Aeronautics and Space Administration (Kennedy Space Center), microbial diversity, species identification, and long-term preservation, 2004.

·         United States Delegate, Scientific Committee, International Whaling Commission, 1998 – 2002.

 

Students and Visiting Scientists


Visiting Scientists

·         Alessandro Airo, Stanford University, 2004.

·         Soo-Jin Kim, Korean Agricultural Culture Collection (National Academy of Agricultural Science, Republic of Korea), 2013 2014 

Postdoctoral Researchers

·         Lina Flor-Weiler, 2013 present 

Master’s Students

·         April Harlan, Mississippi State University, 2000 2002

·         Jason Sumners, Mississippi State University, 2000 2002 

Undergraduate Students

·         Paul Holze, University of Illinois, 2003 2004

·         Tabitha Williams, Western Illinois University, 2006

·         Marley Brimberry, Indiana University, 2014

·         Kirsten Zeman, Bradley University, 2014 – present

Doctoral dissertations externally reviewed

·         José-María Eírin-López, University of A Coruña (Spain), 2005

·         Tamara M. Sirey, University of Auckland (New Zealand), 2006

 

Invited Conference Lectures and Departmental Seminars (Last 5 Years)


·          Invited conference lecturer, “Know Your Food, Know Your Farmer” Symposium, sponsored by the USDA Rural Development Agency, 2014

·         Seminar speaker, University of Kentucky, Department of Biology, 2013.

·          Invited conference lecturer, Symposium on Molecular Evolution, National Institute of Genetics (Japan) held in conjunction with the 2013 Kyoto Prize in Basic Sciences (Inamori Foundation, Japan), 2013.

·          Invited conference lecturer, Annual meeting of the U.S. Culture Collection Network, 2013.

·          Invited conference lecturer, Annual meeting of the Society for Molecular Biology and Evolution, 2012.

·         Seminar speaker, North Carolina Central University, Department of Biology, 2011.

·         Seminar speaker, North Carolina State Museum of Natural History, 2011.

·         Seminar speaker, Auburn University, Department of Biological Sciences, 2011.

·          Invited conference lecturer, Symposium on Molecular and Genomic Evolution, sponsored by the Society for Molecular Biology and Evolution, 2011.

·         Invited conference lecturer, Fourth National Bio-Threat Conference, 2010.

·         Invited conference lecturer, Bioforensics Resources and Repositories Forum, 2010.

·         Seminar speaker, Natural Sciences Division, Pepperdine University, 2010.

·         Seminar speaker, University of Illinois, College of Veterinary Medicine, Department of Pathology, 2009.

·          Invited conference lecturer,International Symposium on Olfaction & Taste, 2008.

·          Invited conference lecturer, New Insight of Genome Evolution into Fundamental Activities of Life conference, hosted by National Institute of Genetics (Japan), 2008.

 

Publications


·         Liu Q.Q., Li X.L., Rooney A.P., Du Z.J., Chen G.J. 2014. Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae. International Journal of Systematic and Evolutionary Microbiology 64:3473-3477. 

·         Du Z.-J., Wang Y., Dunlap C., Rooney A. P., and Chen G.-J. 2014. Draconibacterium orientalis gen. nov., sp. nov., isolated from two distinct marine environments. International Journal of Systematic and Evolutionary Microbiology 64:1690-1696.

·         Hughes T.J., O'Donnell K., Rooney A.P., Sink S., Scandiani M.M., Luque A., Bhattacharyya M.K., and Huang X. 2014. Genetic architecture and evolution of the mating type locus in fusaria that cause soybean sudden death syndrome and bean root rot. Mycologia 106:686-697.

·         Schisler D. A., Core A. B., Boehm M. J., Horst L., Krause C., Dunlap C.A., and Rooney A.P.  2014. Population dynamics of the Fusarium head blight biocontrol agent Cryptococcus flavescens OH182.9 on wheat anthers and heads. Biological Control, 70:17-27.

·         Venkateswaran K., Vaishampayan P., Benardini J.N. 3rd, Rooney A.P., and Spry J.A. 2014. Deposition of extreme-tolerant bacterial strains isolated during different phases of Phoenix spacecraft assembly in a public culture collection. Astrobiology 14:24-26.

·         Ma L.J., Geiser D. M., Proctor R. H., Rooney A. P., O’Donnell K., Trail F., Gardiner D. M., Manners J. M., and Kazan K., 2013. Fusarium pathogenomics. Annual Review of Microbiology. 67:399-416.

·         Du Z.-J., Miao T. T., Rooney A. P., Liu Q.-Q. and Chen G. J.  2013. Neiella marina gen. nov., sp. nov., isolated from sea cucumber Apostichopus japonicus.  International Journal of Systematic and Evolutionary Microbiology 65:1597-1601.

·         Kasson M. T., O'Donnell K., Rooney A. P., Sink S., Ploetz R. C, Ploetz J. N., Konkol J. L., Carrillo D., Freeman S., Mendel Z., Smith J. A., Black A. W., Hulcr J., Bateman C., Stefkova K., Campbell P. R., Geering A. D., Dann E. K., Eskalen A., Mohotti K., Short D. P., Aoki T., Fenstermacher K. A., Davis D. D., Geiser D. M. An inordinate fondness for Fusarium: phylogenetic diversity of fusaria cultivated by ambrosia beetles in the genus Euwallacea on avocado and other plant hosts. Fungal Genetics and Biology 56:147-157.

·         Geiser D. M., Aoki T., Bacon C. W., Baker S. E., Bhattacharyya M. K., Brandt M. E., Brown D. W., Burgess L. W., Chulze S. N., Coleman J. J., Correll J. C., Covert S., Crous P. W., Cuomo C. A., de Hoog G. S., Di Pietro A., Elmer W. H., Epstein L., Frandsen R. J., Freeman S., Gagkaeva T., Glenn A. E., Gordon T., Gregory N. F., Hammond-Kosack K., Hanson L., Jimenez-Gasco M. D., Kang S., Kistler H. C., Kuldau G. A., Leslie J. F., Logrieco A., Lü G., Lysøe E., Ma L. J., McCormick S., Migheli Q., Moretti A., Munaut F., O'Donnell K., Pfenning L. H., Ploetz R., Proctor R., Rehner S. A., Robert V. A., Rooney A. P., Salleh B., Scandiani M. M., Scauflaire J., Short D. P., Steenkamp E., Suga H., Summerell B. A., Sutton D. A., Thrane U., Trail F., van Diepeningen A., Vanetten H., Viljoen A., Waalwijk C., Ward T., Wingfield M. J., Xu J. R., Yang X. B., Yli-Matilla T., and Zhang N. 2013. One fungus, one name: Defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology 103:400-408.

·         O'Donnell K., Rooney A. P., Proctor R. H., Brown D. W., McCormick S. P., Ward T. J., Frandsen R. J., Lysøe E., Rehner S. A., Aoki T., Robert V. A., Crous P. W., Groenewald J. Z., Kang S., and Geiser D. M. 2013. Phylogenetic analysis of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal Genetics and Biology 52:20-31.

·         Kubo Y., Rooney A. P., Tukakoshi Y., Nakagawa R., Hasegawa H., and Kimura K. 2012. Phylogenetic analysis of Bacillus subtilis strains applicable to natto (fermented soybean) production. Applied and Environmental Microbiology 77:6463-6469.

·         Du X.-H., Zhao Q., Yang Z. L., Hansen K., Taskin H., Büyükalaca S., Dewsbury D., Moncalvo J. M., Douhan G. W., Robert V. A., Crous P. W., Rehner S. A., Rooney A. P., Sink S. and O'Donnell K. 2012. How well do ITS rDNA sequences differentiate species of true morels (Morchella)?  Mycologia 104:1351-1368.

·         Du X.-H., Zhao Q., O'Donnell K., Rooney A. P. and Yang Z. L. 2012. Multigene molecular phylogenetics reveals true morels (Morchella) are especially species-rich in China.  Fungal Genetics and Biology 49:455-469.

·         Xue B., Rooney A. P., and Roelofs W. L. 2012. Genome-wide screening and transcriptional profile analysis of desaturase genes in the European corn borer moth. Insect Science 19:55-63.

·         Eirín-López J. M., Rebordinos L., Rooney A. P. and Rozas J.  2012. The birth-and-death evolution of multigene families revisited.  Genome Dynamics 7:170-96.

·         O'Donnell K., Humber R. A., Geiser D. M., Kang S., Park B., Robert V. A., Crous P. W., Johnston P. R., Aoki T., Rooney A. P. and Rehner S. A.  2012. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST.  Mycologia 104:427-445. 

·         Rooney A. P., Swezey J. L., Pukall R., Schumann P. and Spring S. 2011.  Peptoniphilus methioninivorax sp. nov., a gram-positive anaerobic coccus isolated from retail ground beef.  International Journal of Systematic and Evolutionary Microbiology 61:1962-1967.

·         O'Donnell K., Rooney A. P., Mills G. L., Kuo M., Weber N. S., and Rehner S. A. 2011. Phylogeny and historical biogeography of true morels (Morchella) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic. Fungal Genetics and Biology 48:252-265.

·         Adiyaman T., Schisler D. A., Slininger P. J., Sloan J. M., Jackson M. A., and Rooney A. P. 2011. Selection of biocontrol agents of pink rot based on efficacy and growth kinetics index rankings. Plant Disease 95:24-30.

·         Du Z. J., Lu G. Q., Rooney A. P., Miao T. T., Xu Q. Q., and Chen G. J. 2011. Agarivorans gilvus sp. nov., isolated from seaweed. International Journal of Systematic and Evolutionary Microbiology 61: 493-496.

·         Rooney A. P. 2011. Pheromone emergencies and drifting moth genomes. Proceedings of the National Academy of Sciences 108:8069-8070.

·         Park M., Rooney A. P., Hecht D. W, Li J., McClane B. A., Nayak R., Paine D. D., and Rafii F. 2010. Phenotypic and genotypic characterization of tetracycline and minocycline resistance in Clostridium perfringens. Archives of Microbiology 192:803-810.

·         Slack W. S., Sumners J. A., Rooney A. P., and Taylor C. M. 2010. Conservation Genetics of the Threatened Bayou Darter (Percidae: Etheostoma rubrum) in the Bayou Pierre System of Southwestern Mississippi. Copeia 2010:176-180.

·         Du Z. J., Jordan E. M., Rooney A. P., Chen G. J., and Austin B. 2010. Corynebacterium marinum sp. nov. isolated from coastal sediment in Qingdao, China. International Journal of Systematic and Evolutionary Microbiology 60:1944-1947.

·         Connor N., Sikorski J., Rooney A. P., Kopac S., Koeppel A. F., Burger A., Cole S. G., Perry E. B., Krizanc D., Field N. C., Slaton M., and Cohan F. M. 2010. Ecology of speciation in the genus Bacillus. Applied and Environmental Microbiology 76:1349-1358.

·         Kato A., Rooney A. P., Furutani Y., and Hirose S. 2010. Evolution of trappin genes in mammals. BMC Evolutionary Biology 10:31.

·         Rooney A. P., Price N. P., Erhardt C., Swezey J. L. and Bannan J. D. 2009. Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. International Journal of Systematic and Evolutionary Microbiology 54:2429-2436.

·         Rooney A. P., Price N. P., Ray K. J., and Kuo T. M. 2009. Isolation and characterization of rhamnolipid-producing strains from a biodiesel facility. FEMS Microbiology Letters 295:82-87.

·         Vaishampayan P., Miyashita M., Ohnishi A., Satomi M., Rooney A. P., La Duc M. T. and Venkateswaran K. 2009. Description of Rummeliibacillus stabekisii gen. nov., sp. nov. and reclassification of Bacillus pycnus Nakamura et al. 2002 as Rummeliibacillus pycnus comb. nov. International Journal of Systematic and Evolutionary Microbiology 59:1094-1099.

·         Frank D.N., Wysocki A., Specht-Glick D. D., Rooney A. P., Feldman R. A., St. Amand A. L., Pace N. R., and Trent J. D. 2009. Microbial diversity in chronic open wounds. Wound Repair and Regeneration 17:163-172.

·         Rooney A. P. 2009. Evolution of moth sex pheromone desaturases. Annals of the New York Academy of Sciences 1170:506-510.

·         Rooney A. P., Ward T. J. 2008. Birth-and-death evolution of the internalin multigene family in Listeria. Gene 427:124-128.

·         Mertens J. A., Burdick R. C., Rooney A. P. 2008. Identification, biochemical characterization and evolution of the Rhizopus oryzae 99-880 polygalacturonase gene family. Fungal Genetics and Biology 45:1616-1624.

·         Koeppel A., Perry E. B., Sikorski J., Krizanc D., Warner A., Ward D. M., Rooney A. P., Brambilla E., Connor N., Ratcliff R. M., Nevo E., Cohan F. M. 2008. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proceedings of the National Academy of Sciences USA 105:2504-2509.

·         Ward T. J., Clear R., Rooney A. P., O’Donnell K., Gaba D., Patrick S., Starkey D. E., Gilbert J., Geiser D. and Nowicki T. 2008. An adaptive evolutionary shift in Fusarium head blight pathogen populations is driving the rapid spread of more toxigenic Fusarium graminearum in North America. Fungal Genetics and Biology 45:473-84.

·         Kuo T. M., Rooney A. P. and Isbell T. A. 2008. Conversion of lesquerolic acid to 14-oxo-11(Z)-eicosenoic acid by genetically variable Sphingobacterium multivorum strains. Current Microbiology 57:55-60.

·         Balajee S. A., Tay S. T., Lasker B. A., Hurst S. F. and Rooney A. P. 2007. Characterization of a novel gene for strain typing reveals substructuring of Aspergillus fumigatus across North America.  Eukaryotic Cell 6:1392-1399. 

·         Perry E. B., Krizan D, Rooney A. P., Sikorski J., Nevo E. and Cohan F. M. 2007. Identifying the fundamental units of diversity among Bacillus isolates from “Evolution Canyon” III.  Israel Journal of Ecology & Evolution 52:543-552. 

·         Kuo T.-M., Isbell T. A., Rooney A. P., Levinson W. E., and Frykman H. 2007. Production of 14-Oxo-cis-11-eicosenoic acid from lesquerolic acid by Sphingobacterium multivorum NRRL B-23212.  Journal of the American Oil Chemists’ Society 54:639-643. 

·         Price N. P., Rooney A. P., Swezey J. L., Perry E., and Cohan F. M. 2007. Mass spectrometric analysis of lipopeptides from Bacillus strains isolated from diverse geographical locations.  FEMS Microbiology Letters 271:83-89. 

·         Xue B., Rooney A. P., Kajikawa M., Okada N., and Roelofs W. L. 2007. Cryptic sex pheromone desaturase genes in the genomes of moths: generation of evolutionary novelty through retroposon fusion. Proceedings of the National Academy of Sciences USA 104: 4467-4472.

·         Rooney A. P., Swezey J. L., Friedman R., Hecht D. W., and Maddox C. W. 2006. Analysis of core housekeeping and virulence genes reveals cryptic lineages of Clostridium perfringens that are associated with distinct disease presentations. Genetics 172:2081-2092.

·         Bischoff K. M., Rooney A. P., Li X. L., Liu S., and Hughes S. R. 2006. Purification and characterization of a family 5 endoglucanase from a moderately thermophilic strain of Bacillus licheniformis. Biotechnology Letters 28:1761-1765.

·         Louis Jr. E.E., Engberg S. E., Lei R., Geng H., Sommer J. A., Randriamampionona R., Randriamanana J. C., Zaonarivelo J. R., Andriantompohavana R., Randria G., Ramaromilanto B., Rakotoarisoa G., Rooney A. P., and Brenneman R. A. 2006. Molecular and morphological analyses of the sportive lemurs (Family Megaladapidae: Genus Lepilemur) reveals 11 previously unrecognized species.  Special Publications of the Museum of Texas Tech University 49:1-47. 

·         Rooney A. P. and Ward T. J. 2005. Evolution of a large ribosomal RNA multigene family in filamentous fungi: birth-and-death of a concerted evolution paradigm. Proceedings of the National Academy of Sciences of the USA 102: 5084-5089

·         Nei M. and Rooney A. P. 2005. Concerted and birth-and-death evolution of multigene families. Annual Review of Genetics 39: 121-152.

·         Rooney A. P., Swezey J. L., Wicklow D. T. and McAtee M. 2005. Bacterial species diversity in cigarettes linked to an investigation of severe pneumonitis in U.S. military personnel deployed in Operation Iraqi Freedom. Current Microbiology 51: 46-52.

·         Kostinek M., Pukall R., Rooney A P, Schillinger U., Hertel C., Holzapfel W. H. and Franz C. M. A. P. 2005. Lactobacillus arizonensis is a later heterotypic synonym of Lactobacillus plantarum. International Journal of Systematic and Evolutionary Microbiology 55: 2485-2489.

·         Hou C. T., Labeda, D. P., Rooney, A. P. 2005. Evaluation of microbial strains for linoleic acid hydroxylation and reclassification of strain ALA2. Antonie Van Leeuwenhoek 88:167-171.

·         Rooney A. P. 2004. Mechanisms underlying the evolution and maintenance of functionally heterogeneous 18S rRNA genes in apicomplexans. Molecular Biology and Evolution 21: 1704-1711.

·         Seabury C. M., Honeycutt R. L., Rooney A. P., Halbert N. D. and Derr J. N. 2004. Novel prion protein gene (PRNP) variants and evidence for strong purifying selection in functionally important regions of bovine exon 3. Proceedings of the National Academy of Sciences of the USA 101:15142-15147.

·         Rodríguez S., Liu W., Hao G., Piña B., Rooney A. P., Camps F., Roelofs W. L. and Fabriàs G. 2004. Expression and evolution of delta-9 and delta-11 desaturase genes in the moth Spodoptera littoralis. Insect Biochemistry and Molecular Biology 334:1315-1328.

·         Liu, W. Rooney A. P., Xue B. and Roelofs W. L. 2004. Desaturases from the spotted fireworm moth (Choristoneura parallela) shed light on the evolutionary origins of novel moth sex pheromone desaturases. Gene 342:303-311.

·         Rooney A. P. 2003. Selection for highly biased amino acid frequency in the TolA cell envelope protein of proteobacteria.  Journal of Molecular Evolution 57: 731-736.

·         Roelofs W. L. and Rooney A. P. 2003. Molecular genetics and evolution of pheromone biosynthesis in Lepidoptera.  Proceedings of the National Academy of Sciences of the USA 100:9179-9184.

·         Fry B. G., Wüster W., Kini R. M., Brusic V., Khan A., Venkataraman D. and Rooney A. P. 2003. Molecular evolution and phylogeny of elapid snake venom three finger toxins.  Journal of Molecular Evolution 57:110-129.

·         DeYoung R. W., Demarais S., Honeycutt R. L., Rooney A. P., Gonzalez R. A. and Gee K. L. 2003. Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi.  Molecular Ecology 12:3237-3252.

·         Rugh D., DeMaster D., Rooney A. P., Breiwick J., Shelden K. and Moore S. 2003. Review of studies on stock identity in the bowhead whale (Balaena mysticetus).  Journal of Cetacean Research and Management 5:267-279.

·         Rooney A. P., Piontkivska H. and Nei M. 2002. Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family.  Molecular Biology and Evolution 19:68-75.

·         Piontkivska H., Rooney A. P. and Nei M. 2002. Purifying selection and birth-and-death evolution in the Histone 4 gene family.  Molecular Biology and Evolution 19:689-697.

·         Roelofs W. L., Liu W., Hao G., Jiao H., Rooney A. P. and Linn C. E. Jr. 2002. Evolution of moth sex pheromones via ancestral genes.  Proceedings of the National Academy of Sciences of the USA 99:13621-13626. 

·         Patterson C. E., Gao J., Rooney A. P. and Davis E. C. 2002. Genomic organization of mouse and human 65 kDa FK506-binding protein genes and evolution of the FKBP multigene family.  Genomics 79:881-889. 

·         Rooney A. P., Honeycutt R. L. and Derr J. N. 2001. Historical population size change of bowhead whales inferred from DNA sequence polymorphism data.  Evolution 55:1678-1985.

·         Rooney A. P., Zhang J. and Nei M. 2000. An unusual form of purifying selection in a sperm protein.  Molecular Biology and Evolution 17:278-283.

·         Takahashi K., Rooney A. P. and Nei M. 2000. Origins and divergence times of mammalian class II MHC gene clusters. Journal of Heredity 91:198-204. 

·         Schroeder J. W., Honeycutt R. L., Rooney A. P., Han G., Begall S. and Gallardo M. H. 2000. Microsatellites from the South American Coruro, Spalacopus cyanus.  Molecular Ecology 9:1447-1449. 

·         Rooney A. P. and Zhang J. 1999. Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive Darwinian selection?  Molecular Biology and Evolution 16:706-710.

·         Rooney A. P., Honeycutt R. L., Davis S. K. and Derr J. N. 1999. Evaluating a putative botttleneck in a population of bowhead whales from patterns of microsatellite diversity and genetic disequilibria.  Journal of Molecular Evolution 49:682-690.

·         Rooney A. P., Merritt D. B. and Derr J. N. 1999. Microsatellite diversity in captive bottlenose dolphins (Tursiops truncatus).  Journal of Heredity 90:228-31. 

·         Nikaido M., Rooney A. P. and Okada N. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: Hippopotamuses are the closest extant relatives of whales.  Proceedings of the National Academy of Sciences of the USA.  96:10261-10266.

·         Slowinski J. B., Knight A. and Rooney A. P.  1997. Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins.  Molecular Phylogenetics and Evolution 8:349-362.

 

Additional Publications (Conference Proceedings, Trade Journals, etc.)

·         O’Donnell K., Du X., Zhao Q., Yang Z. L., Taskin H., Hansen K., Dewsbury D., Moncalvo J., Rehner S. A., Rooney A. P., Crous P. W. and Robert V. A. 2012. Morchella MLST database. .

·         Rooney A. P. 2008. Molecular evolution of moth sex pheromone desaturases. Chemical Senses 33:S7–S8.

·         DeYoung R. W., Demarais S., Honeycutt R. L., Rooney A. P., Gonzalez R. A. and Gee K. L.  2004. White-tailed deer restoration in the southeastern United States: genetic insights from the greatest wildlife conservation success story.  Quality Whitetails 11:68-72. 

·         Hou C.T., Labeda D.P. and Rooney A.P.  2004. Value-added products from vegetable oil: Screening of microbial strains for linoleic acid bioconversion and reclassification of strain ALA2. UJNR Food & Agricultural Panel Proceedings. pp. 235-239. 

·         Rooney A. P., George J. C. and Tarpley R. J. 2002. Phylogenetic and morphometric analyses of the ingutuk, a morphological variant of the bowhead whale (Balaena mysticetus). International Whaling Commission Scientific Committee Paper #SC/54/BRG19. 14 pp. 

·         Rooney A. P.  2000. Estimating the necessary sample size for studies of genetic polymorphism in a group of bowhead whales from the Chukchi Peninsula. International Whaling Commission Scientific Committee Paper #SC/52/SD15. 6 pp. 

·         DeMaster D., Rugh D., Rooney A. P., Breiwick J., Shelden K. and Moore S. 2000. A review of bowhead whale (Balaena mysticetus) stock identity. International Whaling Commission Scientific Committee Paper #SC/52/SD4. 34 pp.

·         Rooney A. P. 1999. Inferring historical demographic patterns of the Bering‑Chukchi‑Beaufort seas stock of bowhead whales (Balaena mysticetus) from genetic polymorphism data. International Whaling Commission Scientific Committee Paper #SC/51/AS17. 9 pp. 

·         Rooney A. P., Davis S. K., Honeycutt R. L. and Derr J. N. 1999. Evaluating the likelihood of a potential recent bottleneck in a population of bowhead whales (Balaena mysticetus) from patterns of microsatellite diversity and genetic disequilibria. International Whaling Commission Scientific Committee Paper #SC/51/AS16. 33 pp. 

·         Rooney A. P., Honeycutt R. L., Nei M., Chakraborty R. and Derr J. N.  1998. Evaluating the likelihood of a potential recent bottleneck in the Bering-Chukchi-Beaufort Seas stock of bowhead whales (Balaena mysticetus). International Whaling Commission Scientific Committee Paper #SC/50/AS13, 15 pp.

·         Rooney A. P.  1998. Asssesment of recent bottlenecks: a case study of the Bering‑Chukchi‑Beaufort Seas stock of bowhead whales (Balaena mysticetus). Texas A&M University. 100 pp.  (Dissertation).

·         Breen A., Rooney A. P., Ward T., Loper J. C., Govind R. and Haines J. R. 1994. Characterization of bacteria in a TCE degrading biofilter. pp 229-233 in Symposium on Bioremediation of Hazardous Wastes. United States Environmental Protection Agency, San Francisco, California. 


Last Modified: 11/14/2014