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Miriam Konkel

Assistant Professor
Genetics and Biochemistry Department

Office: 308 Biosystems Research Complex
Phone: 864-656-3346
Email: mkonkel@clemson.edu

 

 Educational Background

M.D.
Humboldt University, Berlin, Germany 2000

 Research Interests

My laboratory centers upon primate genomics and focuses on genome-mobilome interactions. The term “mobilome” refers to the global mobile element content of a genome. We are interested in how genomes evolve with respect to mobile elements, and how mobile elements evolve over time. Moreover, we are intrigued by observations that the fate of mobile elements varies in different primate lineages. We are interested in identifying reasons for higher and lower mobilization rates of mobile elements; e.g., the quiescence of Alu propagation in the lineage leading to orangutan. These variations occasionally even are such that a new repeat family does not establish itself in a primate lineage, while it maintains activity over millions of years in another. One such example recently identified by us is the case of Platy-1 in New World monkeys.

Another research focus centers upon human genomics and health. My laboratory is particularly interested in contributing genetic factors of multifactorial disease. The identification of risk factors will enable a path toward precision medicine where treatments can be customized, and in other cases disease potentially prevented.

Our third area of research is the development of cyberphysical genomics interfaces. Here, we are working within interdisciplinary teams to develop new approaches for data interaction. Toward this, we are investigating different interaction modalities integrating tablets, interactive walls, and tangible user interfaces. We believe that novel approaches for data interaction of large datasets (e.g. several to thousands of genomes) will lead to a better understanding of datasets and consequently higher quality datasets. Our goal is to provide interfaces to wide range of target groups: from domain experts to lay people, and from bioinformaticians to counselors and patients.

 Publications

Publications since 2008

Peer-reviewed publications:
1. Walker, J. A., V. E. Jordan, C. J. Steely, T. O. Beckstrom, C. L. McDaniel, C. P. St. Romain, E. C. Bennett, A. Robichaux, B. N. Clement, M. K. Konkel, The Baboon Genome Analysis Consortium, and M. A. Batzer (2017) Papio baboon species indicative Alu elements. Genome Biology and Evolution 9 (6):1788–1796

2. 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.

3. The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation. Nature 526: 68-74 [cover article].

4. 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.

5. 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.)

6. 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.

7. 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, 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]

8. The Marmoset Genome Sequencing and Analysis Consortium. (2014) The common marmoset genome provides insight into primate biology and evolution. Nature Genetics, 46:850-857.

9. 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).

10. 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

11. 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

12. 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.

13. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature; 491: 56-65.

14. 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].

15. 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.

16. 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.

17. 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.

18. 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. 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.

19. 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]

20. Konkel, M.K., J.A. Walker, and M.A. Batzer (2010) LINEs and SINEs of primate evolution. Evolutionary Anthropology; 19: 236-249.

21. 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]

22. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population scale sequencing. Nature; 467: 1061-1073. [cover article]

23. 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.)

24. 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.

25. 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.

26. 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]

Peer-reviewed Louisiana Healthy Aging Study corporate authorship publications:

1. 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

2. 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.

3. 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.

4. 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.

5. 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. 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.

6. 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.

7. 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.

Book chapters:

1. 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.

2. Karcher H. and M. Konkel. (2008) Gasbrand und andere Clostridieninfektionen. In Harrisons Innere Medizin; 17. edition (German).