Curriculum vitae
Michael John Axtell, Ph.D.
Professor of Biology
The Pennsylvania State University
Phone: 814-867-0241
[email protected]
http://sites.psu.edu/axtell
Educational Background
Institution
Degree, year
Advisor
Ithaca College
B.A. in Biology, Summa cum
laude, 1998
Dr. Susan Swensen
University of California, Berkeley
Ph.D., Plant Biology, 2003
Dr. Brian J. Staskawicz
Whitehead Institute / Massachusetts
Institute of Technology
Helen Hay Whitney
Postdoctoral Fellow, 20032006
Dr. David P. Bartel
Academic Appointments
July 2016 to present: Professor of Biology, Pennsylvania State University
July, 2011 to June, 2016: Associate Professor of Biology, Pennsylvania State University
August, 2006 to June, 2011: Assistant Professor of Biology, Pennsylvania State University
April, 2003 to July, 2006: Helen Hay Whitney Postdoctoral Fellow, Whitehead Institute for
Biomedical Research
Honors, Awards, and Fellowships
Searle Scholar, 2008
Beckman Young Investigator, 2008
Helen Hay Whitney Postdoctoral Fellowship, 2004.
National Science Foundation (USA) Graduate Research Fellowship, 1998.
The Berkeley Fellowship, 1998. (Three-year fellowship awarded to approximately 30 incoming
graduate students University-wide based on exceptional merit)
Dean’s Award: Most outstanding student in Natural Sciences and Mathematics (Ithaca College),
1998.
Phi Kappa Phi past presidents award, 1998.
Barry M. Goldwater Fellowship, 1997.
Professional Memberships
American Society of Plant Biologists
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Curriculum vitae, Michael John Axtell
Updated September 18, 2016
Citation Impact Analysis (September 18, 2016 - Google Scholar )
http://scholar.google.com/citations?user=fNX1mOIAAAAJ
total citations: 8,327
citations last five years: 5,296
h-index: 30
h-index last five years: 29
i10-index: 35
i10-index last five years: 35
Peer-reviewed Publications (a = Principal Author, b = Co-Author, c = Supervising Author;
Bold author indicates members of Axtell Lab at Penn State or MJ Axtell).
47. Wang F, Johnson NR, Coruh C, Axtell MJc. (2016). Genome-Wide Analysis of Single
Non-Tempated Nucleotides in Plant Endogenous siRNAs and miRNAs. Nucleic Acids
Research. 44:7395-7405. doi: 10.1093/nar/gkw457
46. Johnson NR, Yeoh JM, Coruh C, Axtell MJc. (2016). Improved placement of multimapping small RNAs. G3 (Genes, Genomes, & Genetics) 6:2103-2111. doi:
10.1534/g3.116.030452.
45. Lunardon A, Forestan C, Farinati S, Axtell MJb, Varotto S. (2016). Genome-Wide
Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain
repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses. Plant Physiology
170:1535-1548. doi: 10.1104/pp.15.01205
44. Margaria P, Miozzi L, Ciuffo M, Rosa C, Axtell MJb, Pappu HR, Turina M. (2015).
Comparison of small RNA profiles in Nicotiana benthamiana and Solanum
lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to
viral infection. Virus Res. 211:38-45 doi: 10.1016/j.virusres.2015.09.019
43. Coruh C, Cho SH, Shahid S, Liu Q, Wierzbicki A, and Axtell MJc. (2015).
Comprehensive annotation of Physcomitrella patens small RNA loci reveals that the
heterochromatic short interfering pathway is largely conserved in land plants. The Plant
Cell. 27: 2148-2162. doi: 10.1105/tpc.15.00228
42. Wang F, Polydore S, and Axtell MJc. (2015). More than meets the eye? Factors that
affect target selection by plant miRNAs and heterochromatic siRNAs. Current Opinion in
Plant Biology 27: 118-124. doi: 10.1016/j.pbi.2015.06.012
41. Paolo M, Miozzi L, Rosa C, Axtell MJb, Pappu HR, and Turina, M. (2015). Small RNA
profiles of wild-type and silencing suppressor-deficient Tomato spotted wilt virus infected
Nicotiana benthamiana Virus Res. 208: 30-38. doi: 10.1016/j.virusres.2015.05.021
40. Liu Q, and Axtell MJc. (2015). Quantitating plant microRNA-mediated target repression
using a dual-luciferase transient expression system. Methods in Molecular Biology 24. doi:
10.1007/978-1-4939-2444-8_14.
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Curriculum vitae, Michael John Axtell
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39. Kaja E, Szcześniak MW, Jensen PJ, Axtell MJb, McNellis T, and Makałowska I. (2014).
Identification of apple miRNAs and their potential role in fire blight resistance. Tree
Genetics and Genomes 11 doi: 10.1007/s11295-014-0812-3
38. Coruh C, Shahid S, and Axtell MJc. (2014). Seeing the forest for the trees: Annotating
small RNA producing genes in plants. Current Opinion in Plant Biology 18C: 87-95. doi:
10.1016/j.pbi.2014.02.008
37. Brousse C, Liu Q, Beauclair L, Deremetz A, Axtell MJb, and Bouche N. (2014). A noncanonical plant microRNA target site. Nucleic Acids Research. 42: 5270-5279. doi:
10.1093/nar/gku157
36. Liu Q, Wang F, and Axtell MJc. (2014). Analysis of complementarity requirements for
plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay. The
Plant Cell 26: 741-753 doi: 10.1105/tpc.113.120972
35. Ma Z. and Axtell M.Jc. (2013). Long-range Genomic Enrichment, Sequencing, and
Assembly to Determine Unknown Sequences Flanking a Known microRNA. PLoS ONE 8:
e83721 doi: 10.1371/journal.pone.0083721
34. Amborella Genome Project (Including Shahid S and Axtell MJb from the Axtell Lab).
(2013). The Amborella Genome and the Evolution of Flowering Plants. Science 342 doi:
10.1126/science.1241089
33. Shahid S. and Axtell MJc. (2013) Identification and annotation of small RNA genes
using ShortStack. Methods 67: 20-27 doi:10.1016/j.ymeth.2013.10.004
32. Zhu H, Zhou Y, Castillo-Gomex C, Lu A, Ge C, Zhao YT, Duan L, Li Z, Axtell MJb,
Wang XJ, Zhang X. (2013). Bidirectional processing of pri-miRNAs with branched terminal
loops by Arabidopsis Dicer-like1. Nature Structural and Molecular Biology 20: 11061115. doi: 10.1038/nsmb.2646
31. Axtell MJa. (2013). ShortStack: Comprehensive annotation and quantification of small
RNA genes. RNA 19: 740-751. doi: 10.1261/rna.035279.112
30. Axtell MJa. (2013). Classification and comparison of small RNAs from plants. Annual
Review of Plant Biology, 64: 137-159. doi: 10.1146/annurev-arplant-050312-120043
29. Cho SH, Coruh C, Axtell MJc. (2012). miR156 and miR390 Regulate tasiRNA
Accumulation and Developmental Timing in Physcomitrella patens. The Plant Cell 24:
4837-4849. doi: 10.1105/tpc.112.103176
28. Liu C, Axtell MJb, Fedoroff NV. (2012). The helicase and RNaseIIIa domains of
Arabidopsis DCL1 modulate catalytic parameters during microRNA biogenesis. Plant
Physiology 159: 748-758. doi: 10.1104/pp.112.193508
27. Arif MA, Fattash I, Ma Z, Cho SH, Beike A, Reski R, Axtell MJb, Frank W. (2012).
DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe
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Curriculum vitae, Michael John Axtell
Updated September 18, 2016
developmental dysfunction and sterility. Molecular Plant 5: 1281-1294. doi:
10.1093/mp/sss036
26. Puzey JR, Karger A, Axtell Mb, Kramer EM. (2012). Deep annotation of Populus
trichocarpa microRNAs from diverse tissue sets. PLoS ONE. 7: e33034 doi:
10.1371/journal.pone.0033034
25. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert
VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, bAxtell MJ, Barker E, Barker MS,
Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer
I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T,
Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M,
Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y,
Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S,
Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N,
Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y,
Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE,
Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G,
Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD,
Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H,
Lindquist E, Lucas S, Rokhsar D, Grigoriev IV. (2011). The Selaginella genome identifies
genetic changes associated with the evolution of vascular plants. Science. 332: 960-963.
doi: 10.1126/science.1203810
24. bAxtell, MJ, Westholm, JO, and Lai, EC. (2011). Vive la difference: Biogenesis and
evolution of microRNAs in plants and animals. Genome Biol. 12: 221 doi: 10.1186/gb2011-12-4-221
23. Argout, X, Salse, J, Aury, J-M, Guiltinan, MJ, Droc, G, Gouzy, J, Allegre, M, Chaparro,
C, Legavre, T, Maximova, SN, Abrouk, M, Murat, F, Fouet, O, Poulain, J, Ruiz, M, Roguet,
Y, Rodier-Goud, M, Barbosa-Neto, JF, Sabot, F, Kudrna, D, Ammiraju, JSS, Schuster, SC,
Carlson, JE, Sallet, E, Schiex, T, Dievart, A, Kramer, M, Gelley, L, Shi, Z, Bérard, A, Viot,
C, Boccara, M, Risterucci, AM, Guignon, V, Sabau, X, bAxtell, MJ, Ma, Z, Zhang, Y,
Brown, S, Bourge, M, Golser, W, Song, X, Clement, D, Rivallan, R, Tahi, M, Akaza, JM,
Pitollat, B, Gramacho, K, D'Hont, A, Brunel, D, Infante, D, Kebe, I, Costet, P, Wing, R,
McCombie, WR, Guiderdoni, E, Quetier, F, Panaud, O, Wincker, P, Bocs, S, and Lanaud, C.
(2011). The genome of Theobroma cacao. Nat Genet. 43: 101-108. doi: 10.1038/ng.736
22. Li, Y-F, Zheng, Y, Addo-Quaye, C, Zhang, L, Saini, A, Jagadeeswaran, G, bAxtell, MJ,
Zhang, W, and Sunkar, R. (2010). Transcriptome-wide identification of microRNA targets in
rice. Plant Journal 62: 742-759. doi: 10.1111/j.1365-313X.2010.04187.x
21. Ma, Z, Coruh, C, and cAxtell, MJ. (2010). Arabidopsis lyrata Small RNAs: Transient
MIRNA and Small Interfering RNA Loci within the Arabidopsis Genus. The Plant Cell 22:
1090-1103. doi: 10.1105/tpc.110.073882
20. aAxtell, MJ. (2010). A method to discover phased siRNA loci. In Plant microRNAs:
Methods and Protocols. Meyers, B.C., and Green, P.J. eds. Series: Methods in Molecular
Biology 592: 59-70. doi: 10.1007/978-1-60327-005-2_5
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19. Song, L, bAxtell, MJ, and Fedoroff, N. (2010). RNA Secondary Structural
Determinants of miRNA Precursor Processing in Arabidopsis. Current Biology 20: 37-41.
doi: 10.1016/j.cub.2009.10.076
18. Addo-Quaye, C, Snyder, JA, Park, YB, Li, Y-F, Sunkar, R, and cAxtell, MJ. (2009).
Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by
analysis of the Physcomitrella patens degradome. RNA 15: 2112-2121. doi:
10.1261/rna.1774909
17. aAxtell, MJ. (2009). The small RNAs of Physcomitrella patens: Expression, function,
and evolution. Annual Plant Reviews 36: 113-142. doi:
10.1111/b.9781405181891.2009.00005.x
16. Addo-Quaye, C, Miller, W, and cAxtell, MJ. (2009). CleaveLand: A pipeline for using
degradome data to find cleaved small RNA targets. Bioinformatics 25: 130-131. doi:
10.1093/bioinformatics/btn604
15. Cho, SH, Addo-Quaye, C, Coruh, C, Asif Arif, M, Ma, Z, Frank, W, and cAxtell, MJ.
(2008). Physcomitrella patens DCL3 is required for 22-24nt siRNA accumulation,
suppression of retrotransposon-derived transcripts, and normal development. PLoS Genetics
4: e1000314. doi: 10.1371/journal.pgen.1000314
14. cMeyers, BC, cAxtell, MJ, Bartel, B, Bartel, DP, Baulcombe, D, Bowman, JL, Cao, X,
Carrington, JC, Chen, X, Green, PJ, Griffiths-Jones, S, Jacobsen, SE, Mallory, AC,
Martienssen, RA, Poethig, RS, Qi, Y, Vaucheret, H, Voinnet, O, Watanabe, Y, Weigel, D,
and Zhu, J-K. (2008). Criteria for annotation of plant microRNAs. The Plant Cell 20:
3186-3190. doi: 10.1105/tpc.108.064311
13. aAxtell, MJ, and Bowman, JL. (2008). Evolution of plant microRNAs and their targets.
Trends in Plant Science 13: 343-349 doi: 10.1016/j.tplants.2008.03.009
12. Addo-Quaye, C, Eshoo, TW, Bartel, DP, and cAxtell, MJ. (2008). Endogenous
siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current
Biology 18: 758-762. doi: 10.1016/j.cub.2008.04.042
11. aAxtell, MJ. (2008). Evolution of microRNAs and their targets: Are all microRNAs
biologically relevant? Biochimica et Biophysica Acta. 1779: 725-734. doi:
10.1016/j.bbagrm.2008.02.007
10. a, cAxtell, MJ, Snyder JA, and Bartel, DP. (2007). Common functions for diverse small
RNAs of land plants. The Plant Cell 19: 1750-1769 doi: 10.1105/tpc.107.051706
9. Ruby, JG, Jan, C, Player, C, bAxtell, MJ, Lee, W, Nusbaum, C, Ge, H, and Bartel, D.
(2006). Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
endogenous siRNAs in Caenorhabditis elegans. Cell 127: 1193-1207. doi:
10.1016/j.cell.2006.10.040
8. aAxtell, MJ, Rajagopalan, R, Jan, C, and Bartel, DP. (2006). A two-hit trigger for
siRNA biogenesis in plants. Cell 127: 565-577. doi: 10.1016/j.cell.2006.09.032
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7. aAxtell, MJ, and Bartel, DP. (2005). Antiquity of microRNAs and their targets in land
plants. Plant Cell 17: 1658-1673. doi: 10.1105/tpc.105.032185
6. aAxtell, MJ, Chisholm, ST, Dahlbeck, D, and Staskawicz, BJ. (2003). Genetic and
molecular evidence that the Pseudomonas syringae type III effector protein AvrRpt2 is a
cysteine protease. Molecular Microbiology 49: 1537-1546. doi: 10.1046/j.13652958.2003.03666.x
5. aAxtell, MJ, and Staskawicz, BJ. (2003). Initiation of RPS2-specified disease resistance
in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4. Cell 112: 369-377.
doi: 10.1016/S0092-8674(03)00036-9
4. Jin, H, bAxtell, M, Dahlbeck, D, Ekwenna, O, Zhang, S, Staskawicz, B, and Baker, B.
(2002). NPK1, an MEKK1-like mitogen-zctivated proein kinase kinase kinase, regulates
innate immunity and development in plants. Developmental Cell 3: 291-297. doi:
10.1016/S1534-5807(02)00205-8
3. aAxtell, MJ, McNellis, TW, Mudgett, MB, Hsu, CS, and Staskawicz, BJ. (2001).
Mutational analysis of the Arabidopsis RPS2 disease resistance gene and the corresponding
Pseudomonas syringae avrRpt2 avirulence gene. Molecular Plant Microbe Interactions 14:
181-188. doi: 10.1094/MPMI.2001.14.2.181
2. Soltis, DE, Soltis, PS, Chase, MW, Mort, ME, Albach, DC, Zanis, M, Savolainen, V,
Hahn, WH, Hoot, SB, Fay, MF, bAxtell, M, Swensen, SM, Prince, LM, Kress, WJ, Nixon,
KC, and Farris, JS. (2000). Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB
sequences. Botanical Journal of the Linnean Society 133: 381-461. doi: 10.1111/j.10958339.2000.tb01588.x
1. Erickson, FL, Holzberg, S, Calderon-Urrea, A, Handley, V, bAxtell, M, Corr, C, and
Baker, B. (1999). The helicase domain of the TMV replicase proteins induces the N-mediated
defence response in tobacco. Plant Journal 18: 67-75. doi: 10.1046/j.1365313X.1999.00426.x
Non peer-reviewed publications
2. Axtell, MJc. (2015). Non-coding RNAs: The small mysteries of males. Nature Plants 1
doi:10.1038/nplants.2015.55
1. Axtell, MJc. (2014). Butter: High-precision genomic alignment of small RNA-seq data.
bioRXiv doi: 10.1101/007427 [preprint]
Major Open-Source Software
2. ShortStack : Comprehensive annotation and quantification of small RNA genes.
https://github.com/MikeAxtell/ShortStack
1. CleaveLand4 : Analysis of degradome data to find sliced miRNA and siRNA targets.
https://github.com/MikeAxtell/CleaveLand4
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Curriculum vitae, Michael John Axtell
Updated September 18, 2016
Invited talks at national/international conferences since joining Penn State faculty
July 9, 2016: American Society of Plant Biologists annual national meeting - Gibbs Medal
Symposium. Austin, TX.
May 3, 2016: The 11th Microsymposium on Small RNAs, IMBA, Vienna, Austria.
January 26, 2016: Keystone Symposium - Small RNA Silencing: Little Guides, Big Biology.
Keystone, CO.
January 9, 2016: Plant and Animal Genome Meeting XXIV, San Diego, CA.
April 18, 2015: Mid-Atlantic Section American Society of Plant Biologists meeting. Swarthmore
College, Swarthmore, PA.
August 29, 2014: Regulatory and non-coding RNAs. Cold Spring Harbor Laboratory, Cold
Spring Harbor, NY.
April 6, 2013: Mid-Atlantic Section American Society of Plant Biologists meeting. University of
Delaware, Newark DE.
May 16, 2011: The 6th Microsymposium on Small RNAs, IMBA, Vienna, Austria.
October 2, 2010: Eighth Annual Symposium in Plant Biology: Biology without borders:
Synergies between plant and animal biology. University of Massachusetts, Amherst, MA.
March 27, 2010: University of Maryland Plant Biology Minisymposium. College Park, MD.
February 25, 2010: Keystone Symposium on RNA silencing mechanisms in plants. Santa Fe,
NM.
October 27, 2009: 9th International Plant Molecular Biology Congress, St. Louis, MO.
June 23, 2009: Gatsby Foundation Plant Biology Meeting (invitation only). Telluride, CO.
November 15, 2008: Ohio Plant Biotechnology Consortium 11th Annual Meeting, Columbus,
OH.
August 18, 2008: Moss 2008, Tampere, Finland
July 17, 2008: 20th International Congress of Genetics, Berlin, Germany
February 17, 2008: 29th Annual Lorne genome conference, Lorne, Victoria, Australia.
January 16, 2007: Plant and Animal Genome Conference XV, San Diego, CA
September 7, 2006: International Symposium of Plant Regulatory RNAs, Academica Sinica,
Taipei, Taiwan.
Contributed talks at national/international conferences since joining Penn State faculty
August 19, 2014 : Penn State MCIBS retreat. Genomic views of small RNA production in plants.
Tussey Mountain, Boalsburg PA.
May 21, 2011 : 18th Penn State Plant Biology Symposium - Plant Evolutionary Genetics and
Genomics, Penn State University Park. "Evolutionary perspectives on small RNA biogenesis and
functions in plants"
April 12, 2011 : Searle Scholars Annual Meeting, Chicago, IL. "Function and Evolution of
microRNAs in Plants"
August 18, 2008: Moss 2008, Tampere, Finland
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Updated September 18, 2016
June 30, 2008: Plant Biology 2008, Merida, Mexico (poster abstract selected for a talk)
August 4, 2007: Moss 2007, Seoul, South Korea
Invited talks at Universities or Research Institutes since joining Penn State faculty
June 6, 2016: Ohio State University, Columbus, OH.
January 8, 2016: University of California, Riverside, CA
November 9, 2015: University of Georgia, Athens, GA.
October 19, 2015: Agricultural Biotechnology Research Center, Academia Sinica, Taiwan, ROC.
July 8, 2015: Adam Mickiewicz University, Poznan, Poland (Gave a seminar and directed a
hands-on workshop for the Poznan Summer School of Bioinformatics).
December 8, 2014: Instituto de Biotecnología, UNAM, Cuernavaca, Mexico.
September 19, 2014: Fudan University, Shanghai, China.
September 16, 2014: Xinyang Normal University, Xinyang, China.
May 19, 2014: Dow Agrosciences, LLC. Indianapolis, IN.
May 12, 2014: Washington University of St. Louis, St. Louis MO.
April 23, 2014: University of Nebraska, Lincoln NE.
March 28, 2013: Monsanto, Inc. St. Louis, MO.
November 28, 2012 : Texas A & M University, Department of Biochemistry and Biophysics
April 13, 2012 : Cornell University, Ithaca, NY, Department of Plant Sciences
March 16, 2012 : University of Illinois, Urbana, IL, Energy Biosciences Institute
October 25, 2011 : Franklin and Marshall College, Lancaster PA, Department of Biology.
September 30, 2010: University of Pennsylvania, Department of Biology
January 26, 2010: Harvard University, Department of Organismal and Evolutionary Biology
May 21, 2009: Samuel Robert Nobel Foundation, Ardmore, OK
May 7, 2009: Delaware Biotechnology Institute / University of Delaware
April 27, 2009: Rice University, Department of Biochemistry and Cell Biology
April 23, 2009: University of Texas, Austin, Institute of Cellular and Molecular Biology
January 18, 2008: Oklahoma State University, Department of Biochemistry and Molecular
Biology .
January 16, 2008: Texas Tech. University, Department of Biological Sciences.
November 2, 2006: University of Massachusetts Amherst, Plant Biology Graduate Program.
Research Support (since joining Penn State Faculty)
May 15, 2014 - April 30, 2017
Reference annotations for small RNA-producing genes in plants
National Science Foundation (#1339207)
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Curriculum vitae, Michael John Axtell
Updated September 18, 2016
Role: PI
coPI: Matthew Jones-Rhoades (Knox College)
$885,370 ($625,685 Direct, $259,685 F&A)
Status: In Progress
October 1, 2012 - September 30, 2015
MRI: Acquisition of an Illumina HiSeq2000 as a core sequencing instrument for genomics and
gene expression research.
National Science Foundation (#1229046)
Role: PI
coPIs: Albert I, dePamphilis CW, Marden JH, Roosinck MJ.
$569,419 ($569,419 direct, $0 Indirect)
Status: Completed
November 1, 2011 - October 31, 2014
(No-cost extension Nov. 1, 2014 - Oct 31, 2015)
Sequence Requirements for Small RNA Targeting in Plants
National Science Foundation ( #1121438)
Role: Sole PI
$525,000 ($363,407 Direct; $161,593 Indirect)
Status: Completed
February 1, 2009 – January 31, 2014
Functional and Evolutionary Genomics of Ancient Small RNAs
National Institutes of Health (Award R01GM84051)
Role: Sole PI.
$895,836 ($610,000 Direct; $285,836 F&A).
Status: Completed
April 1, 2011 - March 31, 2012
Conference: The 18th Penn State Plant Biology Symposium: Plant Evolutionary Genetics and
Genomics to be held May19-21, 2011 in University Park, PA
Nationl Science Foundation (#1062246)
Role: PI
coPIs: Hong Ma, Claude dePamphilis, Teh-Hui Kao, John Carlson.
$26,140 ($26,140 Direct; $0 Indirect)
Status: Completed
March 1, 2010 – February 28, 2011
(no cost extension: March 1, 2011 - February 29, 2012)
EAGER: Rapid enrichment, sequencing, and assembly of targeted genomic DNA
National Science Foundation (Award MCB-0964859)
Role: Sole PI.
$102,930 ($75,999 Direct; $26,931 F&A).
Status: Completed.
September 1, 2008 – August 31, 2011
(no cost extension: September 1, 2011 - August 31, 2012)
Functional Genomic Analysis of Ancient microRNAs
Arnold and Mabel Beckman Foundation
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Curriculum vitae, Michael John Axtell
Updated September 18, 2016
Role: Sole PI
$300,000 ($300,000 Direct; $0 Indirect)
Status: Completed.
July 1, 2008 – June 30, 2011
(no cost extension: July 1, 2011 - June 30, 2012)
Functional Genomic Analysis of Ancient microRNAs
Searle Scholars Program
Role: Sole PI
$300,000 ($277,779 Direct; $22,221 Indirect)
Status: Completed.
September 1, 2007 – August 31, 2010
(no cost extension: September 1, 2010 - August 31, 2011)
Empirical Detection of Small RNA Targets
National Science Foundation (Award MCB-0718051)
Role: Sole PI
$461,595 ($329,238 Direct; $132,357 Indirect)
Status: Completed.
Courses taught as instructor of record
Course
Title
Semester
Enrollment
BIOL497D
PLBIO 512*
BIOL240W**
BIOL497A
BIOL240W**
BIOL497A
BIOL240W**
BIOL497A
BIOL240W**
BIOL497A
BIOL240W**
BIOL497A
BIOL240W**
BIOL451
BIOL240W**
BIOL451
BIOL240W**
PLBIO516***
Biology of RNA
Plant Resource Acquisition & Utilization
Function and Development of Organisms
Biology of RNA
Function and Development of Organisms
Biology of RNA
Function and Development of Organisms
Biology of RNA
Function and Development of Organisms
Biology of RNA
Function and Development of Organisms
Biology of RNA
Function and Development of Organisms
Biology of RNA
Function and Development of Organisms
Biology of RNA
Function and Development of Organisms
Techniques in Plant Molecular Biology
Fall 2007
Fall 2007
Spring 2008
Fall 2008
Spring 2009
Fall 2009
Spring 2010
Fall 2010
Spring 2011
Fall 2011
Spring 2012
Fall 2012
Spring 2013
Spring 2014
Spring 2014
Spring 2015
Spring 2016
Spring 2016
22
7
593
12
498
35
548
24
539
33
593
30
541
15
559
7
532
10
*Course coordinator
** Co-taught: Responsible for ½ of lectures
*** Co-taught: Responsible for laboratory portion of the course
Guest Lectures / Graduate Courses (Typically 1-3 lectures each)
Course
Title
Semester
Enrollment
Page 10 of 15
Curriculum vitae, Michael John Axtell
IBIOS597G
PLBIO513
IBIOS592
GEN597A
PLBIO512
GEN597A
IBIOS592
BIOL497B
PLBIO512
GEN597A
IBIOS572
PLBIO512
BIOL497B
PLBIO512
PLBIO512
PLBIO513
PLBIO513
PLBIO513
Updated September 18, 2016
Plant Genomics
Spring 2007
Integrative Plant Communication & Growth Spring 2007
Current Seminars
Spring 2007
Eukaryotic Genetic Model Systems
Fall 2007
Plant Resource Acquisition & Utilization
Fall 2008
Eukaryotic Genetic Model Systems
Fall 2008
Current Seminars
Fall 2008
Reproductive Biology
Spring 2009
Plant Resource Acquisition & Utilization
Fall 2009
Eukaryotic Genetic Model Systems
Fall 2009
Benchmark Papers
Fall 2009
Plant Resource Acquisition & Utilization
Fall 2010
Reproductive Biology
Spring 2011
Plant Resource Acquisition & Utilization
Fall 2011
Plant Resource Acquisition & Utilization
Fall 2012
Plant Communication and Growth Regulation Spring 2014
Plant Communication and Growth Regulation Spring 2015
Plant Communication and Growth Regulation Spring 2016
10
9
8
4
7
4
11
52
7
6
8
9
64
7
10
7
8
7
Compilation of SRTEs
(SRTE: Student rating of teaching effectiveness. A Penn State specific metric, scored from 1
[poor] to 7 [excellent]).
Overall Quality of
Course
Enrolment
Semester/Yr.
Course
Instructor
# of SRTEs
BIOL 497D
22
Fall / 2007
6.47
6.87
15
BIOL240W
593
Spring / 2008
4.58
5.46
unknown*
BIOL497A
12
Fall / 2008
6.14
6.57
7
BIOL240W
498
Spring / 2009
4.97
6.21
301
BIOL497A
35
Fall / 2009
6.10
6.40
20
BIOL240W
548
Spring / 2010
5.10
5.23
258
BIOL497A
24
Fall / 2010
6.08
6.69
14
BIOL240W
539
Spring / 2011
5.19
5.15
248
BIOL497A
33
Fall / 2011
5.88
6.38
16
BIOL240W
593
Spring / 2012
5.31
5.56
270
BIOL497A
30
Fall / 2012
5.83
6.38
13
BIOL240W
541
Spring / 2013
5.22
5.48
258
BIOL451
15
Spring / 2014
6.50
6.75
7
BIOL240W
559
Spring / 2014
5.35
5.93
226
BIOL451
7
Spring / 2015
6.20
6.80
5
BIOL240W
532
Spring / 2016
5.21
5.55
247
PLBIO516
10
Spring / 2016
6.33
6.83
6
*Technical difficulties with online SRTEs in Sp 2008 prevented me from obtaining this tally.
Undergraduate Research Supervision
Chris Rainville: Fall 2009 - Summer 2010
Shane Denecke: Spring 2010 - Summer 2011
Page 11 of 15
Curriculum vitae, Michael John Axtell
Updated September 18, 2016
Charles Page: Fall 2011 - Spring 2014 (Honors thesis)
Shreela Natarajan: Summer 2013 - Spring 2014
Evan Callaghan: Fall 2014 - Spring 2015
Kinsey Douglas: Summer 2015 (REU summer student from Knox College, IL)
Jonathan Yeoh: Summer 2015 (REU summer student from Knox College, IL)
Rebecca Benner: Summer 2016 (REU summer student from Knox College, IL)
Katarina Whittenburg: Summer 2016 (REU summer student from Knox College, IL)
Rajeev Joshi: Fall 2016 - present
Graduate Student Supervision
Name
Tifani Eshoo
Charles Addo-Quaye*
Zhaorong Ma
Ceyda Coruh
Qikun Liu
Hang Zhang
Saima Shahid
Feng Wang
Seth Polydore
Nathan Johnson
Degree
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Program
IBIOS CDB
CSE
IBIOS BG
Plant Biol.
Plant Biol.
IBIOS BG
Plant Biol.
Plant Biol.
Genetics
Plant Biol.
Semester Graduated
Withdrew, May 2008
Graduated, Summer 2009
Graduated, Summer 2013
Graduated, Summer 2014
Graduated, Summer 2014
Terminated, January 2011
Ongoing, Ph.D. candidate
Ongoing, Ph.D. candidate
Ongoing, Ph.D. candidate
Ongoing, Ph.D. candidate
*Co-advised with Prof. Webb Miller, Dept. of Biology and Dept. of Computer Science and
Engineering
Membership on graduate degree candidates’ committees
a. Candidacy Exam Committees
Name
Program
Joshua Herr
Plant Biology
Xu Xu
Cell & Devel. Biology
Dihong Lu
Plant Biology
Ceyda Coruh*
Plant Biology
Zhaorong Ma*
Bioinformatics & Genomics
Melissa Long
Cell & Devel. Biology
Kumar, Sushant
Bioinformatics & Genomics
Zhang, Tian
Cell & Devel. Biology
Liu, Qikun*
Plant Biology
Wang, Yanming
Cell & Devel. Biology
Han, Celine
Bioinformatics & Genomics
Morrissey, Chris
Bioinformatics & Genomics
Zhang, Tian
Plant Biology
Shih, Han-Wei
Plant Biology
Zhang, Hang*
Bioinformatics & Genomics
Chen, Li
Cell & Devel. Biology
Li, Shu
Plant Biology
Byrska-Bishop, Marta Cell & Devel. Biology
Lin, Xin
Plant Biology
Hu, Jingjie
Cell & Devel. Biology
Degree
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Semester
Fall 2007, Spring 2008
Fall 2007
Fall 2008
Fall 2008
Fall 2008
Fall 2008
Fall 2009
Fall 2009
Fall 2009
Fall 2009
Spring 2010
Spring 2010
Summer 2010
Fall 2010
Fall 2010
Fall 2010
Summer 2011
Fall 2011
Fall 2012
Fall 2012
Page 12 of 15
Curriculum vitae, Michael John Axtell
Minkenberg, Bastian
Zhu, Xiaoyu
Jung, Yong
Wu, Di
Yamada, Naomi
Polydore, Seth*
Wang, Xuan
Johnson, Nathan*
Jia, Mengyuan
Juengst, Brendon
Updated September 18, 2016
Plant Biology
Cell & Devel. Biology
Bioinformatics & Genomics
Bioinformatics & Genomics
Bioinformatics & Genomics
Genetics
Plant Biology
Plant Biology
Plant Biology
Plant Biology
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Summer 2013
Fall 2013
Summer 2014
Summer 2014
Spring 2015
Fall 2014
Fall 2014
Fall 2015
Fall 2015
Fall 2016
*Major adviser
b. Thesis Committees
Name
Charles Addo-Quaye*
Ceyda Coruh**
Zhaorong Ma**
Suting Zheng***
Dennis Lee***
Heather Simmons
Liang Song
Gue Su Chang
Gaurav Bhardwaj
Kumar, Sushant
Zhang, Shuyi***
El-Mowafi, Shaima***
Hill, Joseph***
Miura, Sayaka
Morrissey, Chris
Fisher, Michael***
Mishra, Tejaswini
Li, Shu
Wittmeyer, Kameron
Shahid, Saima**
Wang, Feng**
Matsui, Yurika
McCarthy, Thomas
Srikanth, Abhinaya***
Zhu, Xiaoyu
Sun, Penglin
Miller, Jason***
Program
Comp. Sci. & Eng.
Plant Biology
Bioinformatics & Genomics
Biochem. &Mol. Biol.
Biochem. &Mol. Biol.
Biology
Plant Biology
Bioinformatics & Genomics
Cell & Devel. Biology
Bioinformatics & Genomics
Biochem. &Mol. Biol.
Biochem. &Mol. Biol.
Biochem. &Mol. Biol.
Biology
Bioinformatics & Genomics
Biochem. &Mol. Biol.
Cell & Devel. Biology
Plant Biology
Plant Biology
Plant Biology
Plant Biology
Cell & Devel. Biology
Plant Biology
Biochem. &Mol. Biol.
MCIBS
Plant Biology
Biochem. &Mol. Biol.
Degree
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Ph.D.
Semesters
SP07 – SU09
FA08 – SU14
FA08 - SU13
SP08 - SU11
SP08 – SP10(?)
FA08 – SU11
FA08 – SP09
FA08 – FA13
SP08 - SP10
SP10 - FA13
SP11 - SU15
SP11 - SU14
SP11 - SP15
SP11 - SU12
SU11 - FA13
SU11 - present
FA11 - SP14
FA12 - present
FA12 - present
FA13 - present
FA13 - present
FA13 - present
FA13 - SU16
SU14 - present
FA14 - present
SP15 - SP15
SU15 - SU16
* Co-advisor
** Advisor
*** Outside Member
Course Development
Fall 2007: Developed and taught “Biology of RNA” for the first time as 400-level elective. Was
later transitioned to a permanent course, BIOL451.
Page 13 of 15
Curriculum vitae, Michael John Axtell
Updated September 18, 2016
Spring 2012: Developed a new laboratory module for BIOL240W .. a microRNA / plant
nutrition lab delivered to over 500 students.
Spring 2015: Added computational laboratory to BIOL451, teaching basic programming in a
linux environment (perl, R, various bioinformatic tools) and focusing on analysis of RNA-seq
data.
Service to Penn State
A. Departmental

Graduate Admissions Committee: 2006-2014

Plant Biology Faculty Search Committee: Fall 2008 – Spring 2009

Penn State Institutes for Energy and the Environment / Plant Biology Search Committee:
Fall 2009 - Spring 2010

Departmental Promotion and Tenure Committee: 2011-present

Chair: Plant Biology Faculty Search Committee: Summer 2014 - present

Department head search committee: Summer 2015 - Spring 2016

Chair: Peer evaluation of teaching committee: Fall 2015 - present
B. Inter-College Graduate Degree Programs

Cell & Developmental Biology Graduate Admissions Committee: 2007 – 2009

Plant Biology Graduate Admissions Committee: 2009 – 2013

Plant Biology Seminar Series Organizer: Spring 2010 - present
C. University Level

Schreyer Honors College Advisor: March 2012 - present

Institutional Biosafety Committee: January 2008 – present

Beckman Young Investigator Internal Downselect Committee: Fall 2008

Searle Scholar’s Internal Downselect Committee: 2008-2013, 2016.
Service to Governmental, National, and International Agencies

Member, NSF grant panel
Fall, 2016

Member, NSF grant panel
Summer, 2015

Member, NSF grant panel
Fall, 2012

NSF grant panel, invited
Fall, 2011
*Invitation to serve declined due to teaching obligations

Member, NSF grant panel
Spring, 2009

Member, NSF grant panel
Spring, 2008

NSF grant panel, invited
Fall, 2007
*Invitation to serve declined due to teaching obligations

Ad-Hoc grant reviewer, NSF
2007 – present
Page 14 of 15
Curriculum vitae, Michael John Axtell
Updated September 18, 2016

Member, NSF grant panel, Gene Expression II
Fall, 2006

Outside grant reviewer, BARD*
2006
The US-Israel Binational Agricultural Research and Development Fund

Ad Hoc grant reviewer, Academica Sinica (Taipei, Taiwan)
2007
Service to the Profession


Since 2006, I have peer-reviewed manuscripts at a average rate of 2-4 per month. I've
refereed manuscripts for many journals including: Nature, Nature Genetics, Nature
Chemical Biology, Nature Methods, Proceedings of the National Academy (USA), The
Plant Cell, Plant Physiology, Genome Research, Genome Biology, RNA, Molecular
Biology and Evolution, EMBO Reports, Trends in Plant Science, Nucleic Acids Research,
FEBS Letters, The Plant Journal, Plant Cell Reports, Plant Molecular Biology, Gene,
BMC Plant Biology, BMC Genomics, BMC Evolutionary Biology, BMC Plant Biology,
Silence, PLoS Genetics, PLoS One, PLoS Computational Biology, Gene, and New
Phytologist.
Chaired the Organizing Committee for the 18th Biennial Plant Biology Symposium held
in Spring 2011. This was a National Symposium sponsored by the Plant Biology Ph.D.
program. The theme for 2011 was “Plant Evolutionary Genetics and Genomics”. The
event was held on the University Park Campus from May 18, 2011 to May 21, 2011 and
was organized with the logistical support of the College of Agriculture’s Office of
Conferences and Short Courses.
Editorial Service




Guest Editor, PLoS Genetics. 2013 - present
Associate Editor, BMC Genomics. 2012 - 2014
Reviewing Editor, Molecular Plant. 2014 - present
Reviewing Editor, The Plant Cell. 2015 - present
Page 15 of 15