Miriam Kristine Konkel
• Department of Genetics and Biochemistry • Clemson University • • Tel.: +1 (864) 656-3346 • E-mail: [email protected] •
Curriculum Vitae
Research employment: 2017-present Assistant Professor (tenure track) in the Dept. of Genetics & Clemson, USA Biochemistry, Clemson University 2011-2017 Assistant Professor for Research (with teaching responsibilities Baton Rouge, USA since Spring 2015) Batzer Laboratory of Comparative Genomics, Dept. of Biological Sciences, Louisiana State University (LSU) Research interests: Genomics (wet bench and computational); Structural variation of primate genomes; Evolution; Impact of mobile elements upon genome structure and fluidity; Evolution of retrotransposons in mammalian genomes, esp. primates; Population and phylogenetic approaches (using retrotransposon markers); Personalized genomics, precision medicine with emphasis on Women’s Health; Development of tangible user interfaces for genomics; Development of interactive posters Participant of multiple genome projects (rhesus macaque, platypus, zebra finch, orangutan, marmoset, gibbon, baboon, mouse lemur, 1000 Genomes, human genome structural variation) and the Louisiana Healthy Aging Study
2007-2017 Co-manager of LSU Genomics Facility, including Illumina and Baton Rouge, USA Ion Torrent sequencers 2005-2011 Postdoctoral Researcher, Batzer Laboratory of Comparative Baton Rouge, USA Genomics, Dept. of Biological Sciences, LSU
Medical residency: 2004 Internal Medicine, Charité University Hospital, Berlin, Germany Universitätsmedizin Berlin, (Campus Benjamin-Franklin). Dept. of Gastroenterology, Rheumatology, Infectious Diseases; head Prof. Dr. M. Zeitz, lead Infectious Diseases Prof. Dr. T. Schneider. 2001-2002 Pediatrics, Charité University Hospital, Universitätsmedizin Berlin, Berlin, Germany (Campus Mitte and Virchow) and Emil von Behring Clinic, Heckeshorn. Clinic for Pediatrics with focus on Pneumology and Immunology; head Prof. Dr. U. Wahn. Clinical work on following wards: Infectious Diseases, Immunology, Pneumology, Rheumatology; General Pediatrics (4 weeks to 4 years); Nephrology (all Charité); Pneumology and Allergy with focus on cystic fibrosis and tuberculosis (Heckeshorn).
1 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • Teaching: Spring 2016 Principles of Genetics (BIOL 2153) Baton Rouge, Louisiana Spring 2015 Human Molecular Genetics (BIOL 4753) Baton Rouge, Louisiana 2004 Instructor, 4th and 5th year medical students Berlin, Germany (Internal Medicine, in association with clinical position) 2002 Visiting co-instructor for human-computer interaction course at the Hong Kong, China School of Design, Interactive Systems Stream, Hong Kong Polytechnic University 1996-2000 Instructor, Clinical Chemistry, Institute for Laboratory Medicine Berlin, Germany and Pathobiochemistry, Charité, Universitätsmedizin Berlin 1991-1993 Instructor for children sports and athletics Leichlingen, Germany
Academic studies:
2000 M.D. (Humboldt University) Berlin, Germany Third state medical exam; cumulative grade: very good (‘A’ level) 1995-2000 Clinical studies at Humboldt University Berlin, Germany 1999 Second state medical exam 1996-1997 Research semester for experimental laboratory work 1996 First state medical exam 1993-1995 Preclinical studies at Free University Berlin, Germany 1995 Physikum
Research and other electives during medical school: 1996-2000 Identification and characterization of polymorphisms of HIV Berlin, Germany Co-receptors, Dept. of Clinical Chemistry, Molecular Biology Laboratory, Charité – Universitätsmedizin Berlin, Campus Virchow, Group of Dr. Reinhard Gessner, co-mentored by Dr. Heiko Witt 1998 Neurology Summer School Poznan, Poland 1998 HIV Research in Dept. of Human Retrovirology, Dana-Farber Boston, USA Cancer Institute, group of Dr. Joseph Sodroski, Dr. Hyeryun Choe; co-mentored by Dr. Michael Farzan 1997 HIV Research in Dept. of Human Retrovirology, Dana-Farber Boston, USA Cancer Institute, group of Dr. Joseph Sodroski, Dr. Hyeryun Choe; co-mentored by Dr. Michael Farzan
Other professional responsibilities and positions: 2015-present Member, Editorial Board of Analytical Biochemistry 2014 Reviewer of NIH INBRE proposal for the Louisiana Biomedical Research Network (LBRN) 2013 Reviewer of proposal for the Netherlands Organisation for Scientific Research (NWO), Chemical & Physical Sciences Division 2013 Session Chair at FASEB “Mobile DNA in Mammalian Genomes,” Big Sky, Montana (Session: Genetics and Genomics) 2007-2017 Co-manager of Genomics Facility, Biological Sciences, LSU Baton Rouge, USA 2 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • 2011 Trained to prep samples and operate Ion Torrent sequencer Baton Rouge, USA 2009 Certified to prep samples and operate Illumina sequencer Baton Rouge, USA 2009 Participant and judge at Intermedia Summer School Crete, Greece 1991-1993 Instructor for children sports and athletics Leichlingen, Germany 1987-1990 Assistant for children sports and athletics Leichlingen, Germany
Other schooling: 1988-1993 Landrat-Lucas-Gymnasium (Abitur; overall mark 1.2, A level) Leverkusen, Germany 1984-1988 Gymnasium am Hammer Leichlingen, Germany 1980-1984 Grundschule Ost Wermelskirchen, Germany
Stipends: 1998 Carl Duisberg Stipend 1997 Boehringer Ingelheim Stipend (for research training at the Dana-Farber Cancer Institute, Dept. of Human Retrovirology)
Peer-reviewed publications: Konkel, M. K.*^, B. Ullmer*, E. L. Arceneaux, S. Sanampudi, S. A. Brantley, R. Hubley, A. F. A. Smit, M. A. Batzer^ (2016) Discovery of a new repeat family in the Callithrix jacchus genome. Genome Research 26(5): 649-59. * These authors contributed equally; ^ corresponding authors. The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation. Nature 526: 68-74 [cover article]. Sudmant, P. H.*, T. Rausch*, E. J. Gardner*, R. E. Handsaker*, A. Abyzov*, J. Huddleston*, Y. Zhang*, K. Ye*, G. Jun, M. H.-Y. Fritz, M. K. Konkel, A. Malhotra, A. M. Stütz, X. Shi, F. P. Casale, J. Chen, F. Hormozdiari, G. Dayama, K. Chen, M. Malig, M. J. P. Chaisson, K. Walter, S. Meiers, S. Kashin, E. Garrison, C. Alkan, D. Antaki, T. Bae, P. Chines, Z. Chong, L. Clarke, E. Dal, L. Ding, S. Emery, X. Fan, M. Gujral, F. Kahveci, J. M. Kidd, H. Y. K. Lam, S. McCarthy, P. Flicek, R. A. Gibbs, G. Marth, A. Menelaou, X. J. Mu, D. M. Muzny, B. Nelson, A. Noor, N. F. Parrish, A. Quitadamo, B. Raeder, E. Schadt, A. Schlattl, A. Shabalin, A. Untergasser, E.-W. Lameijer, J. A. Walker, M. Wang, F. Yu, C. Zhang, J. Zhang, X. Zheng-Bradley, W. Zhou, T. Zichner, J. Sebat, M. A. Batzer, S. A. McCarroll, The 1000 Genomes Project Consortium, R. E. Mills, M. B. Gerstein, A. Bashir, O. Stegle, S. E. Devine, C. Lee, E. E. Eichler and J. O. Korbel (2015) An integrated map of structural variation in 2,504 human genomes. Nature 526: 75-81 [cover article]. * These authors contributed equally to this work. Konkel, M. K.*, J. A. Walker*, A. B. Hotard, M. C. Ranck, C. C. Fontenot, J. Storer, C. Stewart, G. T. Marth, the 1000 Genomes Consortium and Mark A. Batzer (2015) Sequence analysis and characterization of active human Alu subfamilies based on the 1000 Genomes pilot project. Genome Biology and Evolution 7: 2608. * These authors contributed equally to this work. (Received ASHG reviewers’ choice award for abstract in 2015.) Wu, J., W.-P. Lee, A. Ward, E. Garrison, J. A. Walker, M. K. Konkel, M. A. Batzer and G. T. Marth (2014) Tangram: A comprehensive toolbox for mobile element insertion detection. BMC Genomics, 15: 795. Carbone, L., R. A. Harris, S. Gnerre, K. R. Veeramah, B. Lorente-Galdos, J. Huddleston, T. J. Meyer, J. Herrero, C. Roos, B. Aken, F. Anaclerio, N. Archidiacono, C. Baker, D. Barrell, M. A. Batzer, K. Bea, A. Blancher, C. L. Bohrson, M. Brameier, M. S. Campbell, O. Capozzi, C. Casola, G. Chiatante, A. Cree, A. Damert, P. J. de Jong, L. Dumas, M. Fernandez-Callejo, P. Flicek, N. V. Fuchs, M. Gut, I. Gut, M. W. Hahn, J. Hernández-Rodríguez, L. Hillier, R. Hubley, B. Ianc, Z. Izsvák, N. G. Jablonski, L. Johnstone,
3 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • A. Karimpour-Fard, M. K. Konkel, D. Kostka, N. H. Lazar, S. L. Lee, L. R. Lewis, Y. Liu, D. P. Locke, S. Mallick, F. L. Mendez, M. Muffato, L. Nazareth, K. A. Nevonen, M. O'Bleness, T. K. O'Connor, C. Ochis, D. T. Odom, K. S. Pollard, J. Quilez, D. Reich, M. Rocchi, G. G. Schumann, S. Searle, J. M. Sikela, G. Skollar, A. Smit, K. Sonmez, B. T. Hallers, E. Terhune, G. W.C. Thomas, B. Ullmer, M. Ventura, J. A. Walker, J. D. Wall, L. Walter, M. C. Ward, S. Wheelan, C. Whelan, L. J. Wilhelm, S. White, A. E. Woerner, M. Yandell, B. Zhu, M. Hammer, T. Marques-Bonet, E. E. Eichler, L. Fulton, C. Fronick, D. M. Muzny, W. C. Warren, K. C. Worley, J. Rogers, R. K. Wilson & R. A. Gibbs (2014) The gibbon genome provides a novel perspective on the accelerated karyotype evolution of small apes. Nature, 513(7517): 195-201. [cover article] The Marmoset Genome Sequencing and Analysis Consortium. (2014) The common marmoset genome provides insight into primate biology and evolution. Nature Genetics, 46:850-857. Valdes, C., D. Eastman, C. Grote, S. Thatte, O. Shaer, A. Mazalek, B. Ullmer, and M.K. Konkel. (2014) Exploring the Design Space of Gestural Interaction with Active Tokens through User-Defined Gestures. Proceedings of ACM CHI Conference on Human Factors in Computing Systems, pp. 4107-4116. (Best paper honorable mention award, top 5% of accepted manuscripts). Hormozdiari, F., M.K. Konkel, J. Prado-Martinez, G. Chiatante, I.H. Herraez, J.A. Walker, B. Nelson, C. Alkan, P.H. Sudmant, J. Huddleston, C. R. Catacchio, A. Ko, M. Malig, C. Baker, the Great Ape Genome Project, T. Marques-Bonet, M. Ventura, M.A. Batzer and E.E. Eichler (2013) Rates and patterns of great ape retrotransposition. Proceedings of the National Academy of Sciences, USA; 110:13457-13462 Cook, G.W., M.K. Konkel, J.A. Walker, M.G. Bourgeois, M.L. Fullerton, J.T. Fussell, H.D. Herbold and M.A. Batzer (2013) A comparison of 100 human genes using an Alu element-based instability model. PLOS ONE; 8: e65188 Shaer, O., A. Mazalek, B. Ullmer, and M. Konkel (2013) From Big Data to Insights: Opportunities and Challenges for TEI in Genomics. Proceedings of ACM TEI'13 (Tangible, Embedded, and Embodied Interaction), pp. 109-116. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature; 491: 56-65. Carbone, L., R.A. Harris, A.R. Mootnick, A. Milosavljevic, D.I.K. Martin, M. Rocchi, O. Capozzi, N. Archidiacono, M.K. Konkel, J.A. Walker, M.A. Batzer and P.J. de Jong (2012) Centromere remodeling in Hoolock leuconedys (Hylobatidae) uncovers a new transposable element unique to the gibbons. Genome Biology and Evolution 4: 648-658 [cover article]. Walker, J.A.*, M.K. Konkel*, B. Ullmer, C.P. Monceaux, O.A. Ryder, R. Hubley, A.F.A. Smit and M.A. Batzer (2012) Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. Mobile DNA; 8: 10. * These authors contributed equally to this work. Cook, G.W., M.K. Konkel, J.D. Major III, J.A. Walker, K. Han and M. A. Batzer (2011) Alu Pair Exclusions in the Human Genome. Mobile DNA; 2: 10. Stewart, C.*, D. Kural*, M.P. Stromberg*, J.A. Walker, M.K. Konkel, A.M. Stütz, A.E. Urban, F. Grubert, H.Y.K. Lam, W.-P. Lee, M. Busby, A.R. Indap, E. Garrison, C. Huff, J. Xing, M.P. Snyder, L.B. Jorde, M.A. Batzer, J.O. Korbel, G.T. Marth and the 1000 Genomes Project (2011) A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genetics; 7: e1002236. * These authors contributed equally to this work. Mills, R.E.*, K. Walter*, D.A. Stewart*, R. Handsaker*, K. Chen*, C. Alkan*, A. Abyzov*, S.C. Yoon*, K. Ye*, R.K. Cheetham, A. Chinwalla, D.F. Conrad, Y. Fu, F. Grubert, I. Hajirasouliha, F. Hormozdiari, Z. Iqbal, J.M. Kidd, M.K. Konkel, J. Korn, E. Khurana, D. Kura, H.J.K. Lam, J. Leng, R. Li, Y. Li, C.-Y. Lin, R. Luo, X.J. Mu, J. Nemesh, H.E. Peckham, T. Rausch, A. Scally, X. Shi, M.P. Stromberg, A.M. Stutz, A.E. Urban, J.A. Walker, J.Wu, Y. Zhang, Z. Zhang, M.A. Batzer, L. Ding, G.T. Marth, G. McVean, J. 4 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • Sebat, M. Snyder, J. Wang, K. Ye, E.E. Eichler*, M.B. Gerstein*, M.E. Hurles*, C. Lee*, S.A. McCarroll* and J.O. Korbel* on behalf of the 1000 Genomes Project (2011) Mapping copy number variation by population-scale genome sequencing. Nature; 470, 59–65. *These authors contributed equally. Locke, D.P., L.W. Hillier, W.C. Warren, K.C. Worley, L.V. Nazareth, D.M. Muzny, S.-P. Yang, Z. Wang, A.T. Chinwalla, P. Minx, M. Mitreva, L. Cook, K.D. Delehaunty, C. Fronick, L.A. Fulton, R.S. Fulton, J.O. Nelson, V. Magrini, S.D. McGrath, C. Pohl, T.A. Graves, C. Markovic, A. Cree, H.H. Dinh, J. Hume, C.L.Kovar, G.R. Fowler, G. Lunter, S. Meader., A. Heger, C.P. Ponting, T. Marques-Bonet, C. Alkan, L. Chen, Z. Cheng, J.M. Kidd, E.E. Eichler, S. White, S. Searle, A. J. Vilella, P. Flicek, E. Birney, J. Ma, B. Raney, B. Suh, R. Burhans, J. Herrero, D. Haussler, R. Faria, O. Fernando, F. Darré, D. Farré, E. Gazave, M. Oliva, A. Navarro, R. Roberto, O. Capozzi, N. Archidiacono, G.D. Valle, S. Purgato, M. Rocchi, M.K. Konkel, J.A. Walker, B. Ullmer, M.A. Batzer, A.F.A. Smit, R. Hubley, C. Casola, D.R. Schrider, M.W. Hahn, V. Quesada, X.S. Puente, G.R. Ordoñez, C. López-Otín, T. Vinar, B. Brejova, A. Ratan, R.S. Harris, W. Miller, K. Prüfer, J. Kelso, B. Nickel, S. Pääbo, C. Kosiol, H.A. Lawson, V. Taliwal, A.L. Martins, A. Siepel, A. RoyChoudhury, X. Ma, J. Degenhardt, C.D. Bustamante, R.N. Gutenkunst, T. Mailund, J.Y. Dutheil, A. Hobolth, M.H. Schierup, L. Chemnick, O.A. Ryder, Y. Yoshinaga, P.J. de Jong, G.M. Weinstock, J. Rogers, E.R. Mardis, R.A. Gibbs, and R.K. Wilson (2011) Comparative and demographic analysis of orang-utan genomes. Nature; 469: 529-533. [cover article] Konkel, M.K., J.A. Walker, and M.A. Batzer (2010) LINEs and SINEs of primate evolution. Evolutionary Anthropology; 19: 236-249. Byerley, L. O., L. Leamy, S. W. Tam, C.-W. Chou, and E. Ravussin for the Louisiana Healthy Aging Study (2010) Development of a serum profile for healthy aging. Age; 32: 497-507. [LHAS corporate authorship] The 1000 Genomes Project Consortium (2010) A map of human genome variation from population scale sequencing. Nature; 467: 1061-1073. [cover article] Brown, J.S., K.E. Cherry, L.D. Marks, E.M. Jackson, J. Volaufova, C. Lefante, S.M. Jazwinski for the Louisiana Healthy Aging Study (2010) After Hurricanes Katrina and Rita: gender differences in health and religiosity in middle-aged and older adults. Health Care Women International. 31: 997-1012 [LHAS corporate authorship] Konkel, M.K. and M.A. Batzer. (2010) A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome. Seminars in Cancer Biology; 20(4): 211-21. (On list of most cited Seminars in Cancer Biology Articles since 2010.) Jazwinski, S.M., S. Kim*, J. Dai*, L. Li, X. Bi, J.C. Jiang, J. Arnold, M.A. Batzer, J.A. Walker, D.A. Welsh, C.M. Lefante, J. Volaufova, L. Myers, L.J. Su, D.B. Hausman, M.V. Miceli, E. Ravussin, L.W. Poon, K.E. Cherry and M.A. Welsh for the Georgia Centenarian Study and the Louisiana Healthy Aging Study (2010) Interaction of APOE, HRAS1, and LASS1 associated with exceptional longevity and healthy aging. Aging Cell; 9:698-708. * These authors contributed equally to this work. [LHAS corporate authorship] Warren, W.C., D.F. Clayton, H. Ellegren, A.P. Arnold, L.W. Hillier, A. Künstner, S. Searle, S. White, A.J. Vilella, S. Fairley, A. Heger, L. Kong, C.P. Ponting, E.D. Jarvis, C.V. Mello, P. Minx, P. Lovell, T.A.F. Velho, M. Ferris, C.N. Balakrishnan, S. Sinha, C. Blatti, S.E. London, Y. Li, Y.-C. Lin, J. George, J. Sweedler, B. Southey, P. Gunaratne, M. Watson, K. Nam, N. Backström, L. Smeds, B. Nabholz, Y. Itoh, O. Whitney, A.R. Pfenning, J. Howard, M. Völker, B.M. Skinner, D.K. Griffin, L. Ye, W.M. McLaren, P. Flicek, V. Quesada, G. Velasco, C. Lopez-Otin, X.S. Puente, T. Olender, D. Lancet, A.F.A. Smit, R. Hubley, M.K. Konkel, J.A. Walker, M.A. Batzer, W. Gu, D.D. Pollock, L. Chen, Z. Cheng, E.E. Eichler, J. Stapley, J. Slate, R. Ekblom, T. Birkhead, T. Burke, D. Burt, C. Scharff, I. Adam, H. Richard, M. Sultan, A. Soldatov, H. Lehrach, S.V. Edwards, S.-P. Yang, X. Li, T. Graves, L. Fulton, J. Nelson, A. Chinwalla, S. Hou, E.R. Mardis, and R.K. Wilson (2010) The genome of a songbird. Nature; 464: 757-762.
5 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • Cordaux, R. S.K. Sen, M.K. Konkel, and M.A. Batzer (2010) Computational methods for the analysis of primate mobile elements. Methods in Molecular Biology; 628: 137-5. Dobrosielski, D.A., F.L. Greenway, D.A. Welsh, S.M. Jazwinski, M.A. Welsch; Louisiana Healthy Aging Study (2009) Modification of vascular function after handgrip exercise training in 73- to 90-yr-old men. Medicine and Science in Sports and Exercise; 41: 1429-1435. [LHAS corporate authorship] Frisard, M.I., J.C. Rood, X. Fang, J. Su, D.A. Welsh, S.M. Jazwinski, E. Ravussin for the Louisiana Healthy Aging Study (2009) Metabolic syndrome and risk factors for cardiovascular disease: are nonagenarians protected? AGE; 31: 67-75. [LHAS corporate authorship] Johannsen, D.L., J.P. DeLany, M.I. Frisard, M.A. Welsch, C.K. Rowley, X. Fang, S.M. Jazwinski, E. Ravussin for the Louisiana Healthy Aging Study (2008) Physical activity in aging: comparison among young, aged, and nonagenarian individuals. Journal of Applied Physiology; 105: 495-501. [LHAS corporate authorship] Welsch, M.A., D.A. Dobrosielski, A.A. Arce-Esquivel, R.H. Wood, E. Ravussin, C. Rowley, S.M. Jazwinski for the Louisiana Healthy Aging Study (2008) The association between flow-mediated dilation and physical function in older men. Medical and Science Sports and Exercise; 40: 1237-43. [LHAS corporate authorship] Cherry, K.E., K.S. Hawley, E.M. Jackson, J. Volaufova, L.J. Su, S.M. Jazwinski for the Louisiana Healthy Aging Study (2008) Pictorial superiority effects in oldest-old people. Memory; 23: 1-14. [LHAS corporate authorship] Cherry, K.E., S. Galea, J.L. Silva and the Louisiana Healthy Aging Study (2008) Successful aging and natural disasters: Role of adaptation and resiliency in late life. In M. Hersen and A. M. Gross (Eds.) “Handbook of Clinical Psychology” 1: 810-833, John Wiley & Sons, Ltd., Chichester, UK. [LHAS corporate authorship] Warren, W.C., L.W. Hillier, J.A. Marshall Graves, E. Birney, C.P. Ponting, F. Grützner, K. Belov, W. Miller, L. Clarke, A.T. Chinwalla, S.-P. Yang, A. Heger, D. Locke, P. Miethke, P.D. Waters, F. Veyrunes, L. Fulton, B. Fulton, T. Graves, J. Wallis, X.S. Puente, C. López-Otín, G.R. Ordóñez, E.E. Eichler, L. Chen, Z. Cheng, J.E. Deakin, A. Alsop, K. Thompson, P. Kirby, A.T. Papenfuss, M.J. Wakefield, T. Olender, D. Lancet, G.A. Huttley, A.F.A. Smit, A. Pask, P. Temple-Smith, M.A. Batzer, J.A. Walker, M.K. Konkel, R.S. Harris, C.M. Whittington, E.S.W. Wong, N. Gemmell, E. Buschiazzo, I.V. Jentzsch, A. Merkel, J. Schmitz, A. Zemann, G. Churakov, J.O. Kriegs, J. Brosius, E. Murchison, R. Sachidanandam, C. Smith, A. Stark, P. Kheradpour, G. Hannon, E. Tsend-Ayush, D. McMillan, R. Attenborough, W. Rens, M. Ferguson- Smith, C.M. Lefèvre, J.A. Sharp, K.R. Nicholas, D.A. Ray, M. Kube, R. Reinhard, T.H. Pringle, J. Taylor, R.C. Jones, B. Nixon, J.-L. Dacheux, H. Niwa, Y. Sekita, X. Huang, P. Flicek, C. Webber, R. Hardison, J. Nelson, K. Hallsworth-Pepin, K. Delehaunty, C. Markovic. P. Minx, Y. Feng, C. Kremitzki, M. Mitreva, J. Glasscock, T. Whylie, P. Wohldmann, P. Thiru, M. Nahn, C. Pol, S.M. Smith, S. Hou, M. Nefedov, P.J. de Jong, M. B. Renfree, E.R. Mardis, and R.K. Wilson. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature; 452: 175-183. [cover article] Dai, J., L. Li, S. Kim, B. Kimball, S.M. Jazwinski, J. Arnold for the Georgia Centenarian Study (2007) Exact sample size needed to detect dependence in 2 x 2 x 2 tables. Biometrics; 63: 1245-1252. [Georgia Centenarian Study corporate authorship] Frisard, M.I., J.M. Fabre, R.D. Russell, C.M. King, J.P. DeLany, R.H. Wood, E. Ravussin, for the Louisiana Healthy Aging Study (2007) Physical activity level and physical functionality in nonagenarians compared to individuals aged 60-74 years. The Journals of Gerontology Series A: Biological Sciences and Medical Sciences; 62: 783-788. [LHAS corporate authorship] Frisard, M.I., A. Broussard, S.S. Davies, L.J. Roberts, II, J. Rood, L. de Jonge, X. Fang, S.M. Jazwinski, W.A. Deutsch, E. Ravussin, for the Louisiana Healthy Aging Study (2007) Aging, resting metabolic rate,
6 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • and oxidative damage: results from the Louisiana Healthy Aging Study. The Journals of Gerontology Series A: Biological Sciences and Medical Sciences; 62: 752-759. [LHAS corporate authorship] Fabre, J.M., R.H. Wood, K.E. Cherry, L.J. Su, M.E. Cress, C.M. King, M.J. deVeer, R.E. Gardner, S.M. Jazwinski and the Louisiana Healthy Aging Study (2007) Age-related deterioration in flexibility is associated with health-related quality of life in nonagenarians. Journal of Geriatric Physical Therapy; 30: 16-22. [LHAS corporate authorship] Han, K.*, M.K. Konkel*, J. Xing*, H. Wang*, J. Lee, T.J. Meyer, C.T. Huang, E. Sandifer, K. Hebert, E.W. Barnes, R. Hubley, W. Miller, A.F.A. Smit, B. Ullmer, and M.A. Batzer (2007) Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome. Science; 316: 238-240. * These authors contributed equally to this work. Gibbs, R.A., J. Rogers, M.G. Katze, R. Bumgarner, G.M. Weinstock, E.R. Mardis, K.A. Remington, R.L. Strausberg, J.C. Venter, R.K. Wilson, M.A. Batzer, C.D. Bustamante, E.E. Eichler, M.W. Hahn, R.C. Hardison, K.D. Makova, W. Miller, A. Milosavljevic, R.E. Palermo, A. Siepel, J.M. Sikela, T. Attaway, S. Bells, K.E. Bernard, C.J. Buhay, M.N. Chandrabose, M. Dao, C. Davis, K.D. Delehaunty, Y. Ding, H.H. Dinh, S. Dugan-Rocha, L.A. Fulton, R.A. Gabisi, T.T. Garner, J. Godfrey, A.C. Hawes, J. Hernandez, S. Hines, M. Holder, J. Hume, S.N. Jhangiani, V. Joshi, Z. M. Khan, E. F. Kirkness, A. Cree, R.G. Fowler, S. Lee, L.R. Lewis, Z. Li, Y.S. Liu, S.M. Moore, D. Muzny, L.V. Nazareth, D.N. Ngo, G.O. Okwuonu, G. Pai, D. Parker, H.A. Paul, C. Pfannkoch, C.S. Pohl, Y.H. Rogers, S.J. Ruiz, A. Sabo, J. Santibanez, B.W. Schneider, S.M. Smith, E. Sodergren, A.F. Svatek, T.R. Utterback, S. Vattathil, W. Warren, C.S. White, A.T. Chinwalla, Y. Feng, A.L. Halpern, L.W. Hillier, X. Huang, P. Minx, J.O. Nelson, K.H. Pepin, X. Qin, G.G. Sutton, E. Venter, B.P. Walenz, J.W. Wallis, K.C. Worley, S.P. Yang, S.M. Jones, M. A. Marra, M. Rocchi, J.E. Schein, R. Baertsch, L. Clarke, M. Csürös, J. Glasscock, R.A. Harris, P. Havlak, A.R. Jackson, H. Jiang, Y. Liu, D.N. Messina, Y. Shen, H.X. Song, T. Wylie, L. Zhang, E. Birney, K. Han, M.K. Konkel, J. Lee, A.F. Smit, B. Ullmer, H. Wang, J. Xing, R. Burhans, Z. Cheng, J.E. Karro, J. Ma, B. Raney, X. She, M.J. Cox, J.P. Demuth, L.J. Dumas, S.G. Han, J. Hopkins, A. Karimpour-Fard, Y.H. Kim, J.R. Pollack, T. Vinar, C. Addo-Quaye, J. Degenhardt, A. Denby, M.J. Hubisz, A. Indap, C. Kosiol, B.T. Lahn, H.A. Lawson, A. Marklein, R. Nielsen, E.J. Vallender, A.G. Clark, B. Ferguson, R.D. Hernandez, K. Hirani, H. Kehrer-Sawatzki, J. Kolb, S. Patil, L.L. Pu, Y. Ren, D.G. Smith, D. A. Wheeler, I. Schenck, E.V. Ball, R. Chen, D.N. Cooper, B. Giardine, F. Hsu, W.J. Kent, A. Lesk, D.L. Nelson, W.E. O'Brien, K. Prüfer, P.D. Stenson, J.C. Wallace, H. Ke, X. M. Liu, P. Wang, A.P. Xiang, F. Yang, G.P. Barber, D. Haussler, D. Karolchik, A.D. Kern, R.M. Kuhn, K.E. Smith, A.S. Zwieg. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science; 316: 222-234. [cover article]. Konkel, M.K.*, J. Wang*, P. Liang, and M.A. Batzer. (2007) Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. Gene; 390:28-38. * These authors contributed equally to this work. Hawley, K.S., K.E. Cherry, J. Su, Y.W. Chiu, S.M. Jazwinski for the Louisiana Healthy Aging Study (2006) Knowledge of memory aging in adulthood. International Journal of Aging and Human Development; 63: 317-334. [LHAS corporate authorship] Dobrosielski, D.A.*, A.A. Arce*, J.D. Allen*, R.H. Wood*, M.A. Welsch* and the Louisiana Healthy Aging Study (2006) Biphasic responses of the brachial artery diameter following forearm occlusion: a blunted response in the elderly. Dynamic Medicine; 5: 4. * These authors contributed equally to this work. [LHAS corporate authorship] Hsu, H.C., D.K. Scott, P. Zhang, J. Zhou, P. Yang, Q. Wu, H.W. Schroeder, L.B. Gerald, E. Ravussin, S.M. Jazwinski, J.D. Mountz and the Louisiana Healthy Aging Study (2006) CD8 T-cell immune phenotype of successful aging. Mechanisms of Ageing and Development; 127: 231-239. [LHAS corporate authorship]
7 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • Wood, R.H., R.E. Gardner, K.A. Ferachi, C. King, A. Ermolao, K.E. Cherry, M.E. Cress, S.M. Jazwinski for the Louisiana Healthy Aging Study (2005) Physical function and quality of life in older adults: sex differences. Southern Medical Journal; 98: 504-512. [LHAS corporate authorship] Konkel, M., Leung, V., Ullmer, B., and Hu, C. Tagaboo: a collaborative children’s game based upon wearable RFID technologies. (2004) Personal and Ubiquitous Computing; 8(5): 382-384. H. Choe, M. Farzan, M. Konkel, K. Martin, Y. Sun, L. Marcon, M. Cayabyab, M. Berman, M. E. Dorf, N. Gerard, C. Gerard, J. Sodroski. (1998) The orphan-transmembrane receptor apj supports the entry of primary dual- and T-tropic HIV-1. Journal of Virology; 72 (7): 6113-6118. Non peer-reviewed book chapters: Ullmer, B., A. Siqueira, C. Branton, and M. K. Konkel (2016) Weaving peripheral interaction within habitable architectures. In Peripheral Interaction, Chapter 12, S. Bakker, D. Hausen, and T. Selker, eds., Springer. Karcher H. and M. Konkel. (2008) Gasbrand und andere Clostridieninfektionen. (2008) Harrisons Innere Medizin; 17. edition (German). Konkel, M. and T. Schneider. (2005) Salmonellosen. Harrisons Innere Medizin; 16. Edition (German). Konkel, M. and T. Schneider. (2005) Cholera und andere Vibrosen. Harrisons Innere Medizin; 16. Edition (German). Konkel, M. and T. Schneider. (2005) Infektionen durch Campylobacter und verwandte Spezies. Harrisons Innere Medizin; 16. Edition (German). Konkel, M. and T. Schneider. (2005) Gasbrand und andere Clostridieninfektionen. Harrisons Innere Medizin; 16. Edition (German).
Talks and poster awards: 2016 Mobile elements in primates: investigations and implication of inter- and intraspecies variation. Seminar, Louisiana State University (Department of Biological and Agricultural Engineering) Baton Rouge, LA
2016 Mobile elements in primates: investigations and implications of inter- and intraspecies variation. Clemson University, Department of Clemson, SC
2016 Mobile elements in primates: investigations and implications of inter- and intraspecies variation. The Pennsylvania State University, University Park, PA
2015 Sequence analysis and characterization of active human Alu subfamilies Poster, Reviewers’ choice award, American Society of Human Genetics Conference, Baltimore, MD 2015 Baboon Alus gone wild Selected short talk, The Mobile Genome: Genetic and Physiological Impacts of Transposable Elements, EMBL/EMBO Symposium, Heidelberg, Germany 2015 Mobile elements in primates - major contributors to variation within and between species Invited talk, Max-Dellbrueck Center, Berlin, Germany 2014 Discovery of a novel retrotransposon family in the Callithrix jacchus genome Platform presentation, American Society of Human Genetics Conference, San Diego, CA
8 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • 2014 Exploring the Design Space of Gestural Interaction with Active Tokens through User-Defined Gestures. ACM CHI Conference on Human Factors in Computing Systems. Presented by O. Shaer, A. Mazalek, B. Ullmer, and M.K. Konkel 2013 Retrotransposition expansion dynamics in primates FASEB “Mobile DNA in Mammalian Genomes,” Big Sky, Montana [Invited speaker] (Focus on gibbon genome project and 1000 Genomes project) 2012 Toward computational genomics support via ecologies of tangible interfaces and interactive supercomputing Invited talk, Wellesley College, Wellesley, MA 2012 Mobile elements in primate genomes: every lineage has its own unique tale 63rd Fujihara Seminar, “A new horizon of retroposon research,” Kyoto, Japan [Invited speaker] 2012 Mobile elements in primate genomes: every lineage has its own unique tale 5th International Primate Conference on Primate Genomics, Houston, Texas [Invited speaker] 2011 Emerging Perspectives of non-LTR Retrotransposons in Primates FASEB “Mobile DNA in Mammalian Genomes,” Snowmass, Colorado [Invited speaker] (Focus on marmoset genome project and 1000 Genomes project) 2011 Emerging Perspectives on Retrotransposons in Primates BMB/CDIB Seminar Series, Louisiana State University, Louisiana (Focus on orangutan genome project and 1000 Genomes project) 2010 Retrotransposons in the orangutan (Pongo) lineage: A new evolutionary tale Biology of Genomes Meeting, Cold Spring Harbor, NY
2009 Whole genome analysis of mobile elements on LSU and LONI resources LBRN Computational Biology workshop, Louisiana State University, Louisiana
Student supervision and service on committees 2017-present Member of graduate student committee (co-advisor) of Jun Wang, Clemson University 2017-present Mentor of Brianna Tennie, undergraduate student, Clemson University 2005-2017 Training, supervision, and administrative management of undergraduate student workers. 2016-2017 Mentor of Yahor Sukharuski, undergraduate scholar of President’s Student Aide program, LSU. 2015-2017 Mentor of Kacie Philippe, undergraduate scholar of President’s Future Leaders in Research program, LSU. 2014-2017 Co-advisor of Michael Denham, undergraduate scholar of President’s Future Leaders in Research program, LSU. 2013-2017 Co-mentor of Cody Steely toward his Ph.D. dissertation, LSU. 2013-2017 Co-mentor of Vallmer Jordan toward his Ph.D. dissertation, LSU. 2013-2017 Co-mentor of Jasmine Brown toward her Ph.D. dissertation, LSU. 2013-2017 Co-advisor of Sarah Brantley, undergraduate scholar of President’s Future Leaders in Research program, LSU. 2012-2016 Co-advisor of Thomas Beckstrom, undergraduate scholar of President’s Future Leaders in Research program, LSU; Howard Hughes Medical Institute (HHMI) summer scholar;
9 Miriam Kristine Konkel • Laboratory of Comparative Genomics • • Department of Biological Sciences • Louisiana State University • • Baton Rouge, LA 70803 • Tel.: +1 (225) 578-7103 • E-mail: [email protected] • serving on undergraduate honors thesis committee. 2012-2015 Co-advisor of Emily Bennett, Chancellor’s Student Aide program, LSU; Howard Hughes Medical Institute (HHMI) summer scholar; served on undergraduate honors thesis committee. 2011-2015 Co-advisor of Sreeja Sanampudi, Chancellor’s Student Aide program, LSU; EPSCoR Supervised Undergraduate Research Experiences (SURE) scholar; Howard Hughes Medical Institute (HHMI) summer scholar; served on undergraduate honors thesis committee. 2011-2014 Co-advisor of Erika L. Arceneaux, Chancellor’s Student Aide program, LSU; Howard Hughes Medical Institute (HHMI) summer scholar; served on committee for undergraduate honors thesis committee. 2010-2014 Co-advisor of Michelle Limbaugh, Chancellor’s Student Aide program, LSU; Howard Hughes Medical Institute (HHMI) summer scholar; served on committee for undergraduate honors thesis. 2009-2014 Co-advisor of Catherine C. Fontenot, undergraduate scholar of Chancellor’s Future Leaders in Research program, LSU; Howard Hughes Medical Institute (HHMI) summer scholar, recipient of The Harry S. Truman Scholarship Foundation; served on committee for undergraduate honors thesis. 2009-2013 Co-mentor of George Windham Cook toward his Ph.D. dissertation, LSU. 2009-2013 Co-advisor of Megan C. Ranck, Chancellor’s Student Aide program, LSU; Howard Hughes Medical Institute (HHMI) summer scholar; served on committee for undergraduate honors thesis. Funded Grants: 2013-2017 NIH U41 grant “An integrative analysis of structural variation for the 1000 Genomes Project.” [Co-PI; PI Lee, LSU PI Batzer; LSU part: $621,600, funding: 09/13-08/17] 2012-2013 EPSCoR Supervised Undergraduate Research Experiences (SURE) [Co-PI; PI Ullmer; $4,500, funding: 06/12-05/13] 2011-2015 NSF grant "Development of Melete: an interaction-oriented, software-rich compute cluster with tangible interface support for collaborative research and the classroom." [Senior Investigator; PI Ullmer; $1.2 million ($900,000 NSF + $300,000 LSU match), funding: 09/11-08/16] Ad hoc reviewer for: Analytical Biochemistry, Bioinformatics, BMC Evolutionary Biology, Computational Biology and Chemistry, Gene, Genetics, Genome Biology and Evolution, Genome Research, Genomics, Modern Pathology, Molecular Biology and Evolution, Molecular Evolution, Nucleic Acids Research, PeerJ, PLOS One, Science, and Science in Translational Medicine.
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