COMPLETE CURRICULUM VITAE (September, 2015)

 

 

MICHAEL FREELING

Professor of Genetics

freeling@berkeley.edu

Lab website: http://plantbio.berkeley.edu/~freeling/labweb/welcome.html

 

                                                Freeling’s Bio-Bibliographical Data

 

Born:                                       January 14, 1945, Ft. Wayne, Indiana, USA

 

Address:                                  Department of Plant Biology

                                                111 Koshland Hall

                                                University of California

                                                Berkeley, CA  94720

                                                510-642-8058

                                                FAX 510-642-4995

 

Education:                               University of Oregon, Eugene, OR  A.B.  1968

 

                                                Indiana University, Bloomington, IN  Ph.D.  1973

                                                Thesis Advisor:  Drew Schwartz

 

Honors:                                   Guggenheim Fellow, 1980-81

                                                Member, National Academy of Sciences, USA, 1994

                                                Coen portrait, Named Lecture Series, JIC, UK  2006

 

Major Research                       Comparative genomics in plants.

Current Funding                      NIFA, USDA.

 

Lab Status                               Open to talent if co-mentored by another, younger PI. 

 

Professional                            1984-present, University of California, Berkeley

Experience:                              Professor of Genetics

                                               

                                                1996 Visiting Prof., Jodrell Laboratory, Kew                                                Gardens, UK                                         

1988-1995 

                                                Director, NSF Center of Plant Developmental Biology

                                                1979-1984

                                                Associate Professor of Genetics, University of California at            Berkeley; Associate Geneticist in California Agricultural          Experiment Station

 

                                                1980-1981

                                                Guggenheim Fellow

Visiting Professor, Department of Biochemistry, Rothamsted Experimental Station, England

 

                                                1973-1978

                                                Assistant Professor of Genetics, University of California at             Berkeley

 

 

Freeling's Summary of Activities

 

Professor of Genetics and Principal Investigator (PI) at UC-Berkeley since 1973.

 

Teaching-related at UCB. Taught one large liberal arts course entitled "Heredity and Society (MCB 41X)" for nonscience majors 1977-2006, about every other year, and PMB13, which evolved into a new course:  Genetic Revolutions,  every year  2006- present.  One graduate course in genetics recently titled "PMB200A or B-part 1" about every year  from 1974-2007;  will teach PMB200 again in 2016.   Graduate Advisor, Graduate Group in Genetics, 1981-1989; Plant Biology, 1991-1996.   Member, Executive Committee, College of Natural Resources, 87-88 and 1995-1997; Steering Committee, Graduate Group in Genetics, 81-89 and 94- 98 and 2010-2015.  Member of CNR Internal Review Committee, 1990-91.

 

Summer Internship Program.  Damon Lisch and Michael Freeling mentor 1-3 underserved high school students each summer, or, in one case, a high school teacher, during an intensive summer program.  

 

At UCB. Director and PI of NSF Center of Plant Developmental Biology, 1988-1995.  There after, chair of the faculty oversight committee, CNR Biological Imaging Facility 1995-2015. (Steve Ruzin, PI).

 

Member, National Academy of Science (USA), 1994

 

Total number of graduate students: current candidates (incl. jointly sponsored) + completed Ph.Ds): ca. 26

Total number of postdoctoral students: ca. 44.

Ph.D. Visitors: several

 

Recent editorial boards (since 2000): Development,1987-2004; The Plant Journal 1990-2000; Genome Research 2000-2007, Associate Editor Frontiers of Plant Genetics and Genomics, 2010-2015.   

 

Organizer, Panel and Professional Committee Functions.:  Panalist for funding agencies: NSF, 1980-84, 1986-1988, 1993, 1997, 2007;  NAS, COSAPUP, on Agricultural Sciences, 1983; American Cancer Society, 1986-1988.  Ad hoc member, NRC Plant Biology and Agriculture Subcommittee, Committee on Research Opportunities in Biology, 1987-1988; DOE-JGI Community Genome Sequencing, 2005 to 2009. Organizer of international scientific meetings  (esp. Keystones)  in 1982, two in 1985, 1990, 1993 , two in 1997 and one in 1999.  Executive Committee, Annual Maize Genetics Workshop (Allerton Meeting); 1983-87; Maize Genetics Executive Committee, 2000 – 2003.  Member USDA Steering Comm, MaizeGDB, 2003-2010.  Member, DOE Plant Genome Advisory Committee, 2006-2009.

 

Michael Freeling  BIBLIOGRAPHY (193 total, dateline 07-30-15)

For an automated record of publications with citation data, go to Mike Freeling‘s Google Citation Index.

 

1. Freeling, M. and D. Schwartz. 1973. Genetics relationships between the multiple

alcohol dehydrogenases of maize. Biochem. Genet. 8:27-36.

2. Freeling, M. 1973. Simultaneous induction by anaerobiosis or 2,4-D of multiple

enzymes specified by two unlinked genes: Differential Adh1-Adh1 expression in

maize. Molec. Gen. Genet. 127:215-227.

3. Freeling, M. 1974. Dimerization of multiple maize ADHs studied in vivo and in vitro.

Biochem. Genet. 12:407-417.

4. Freeling, M. (1975.) Further studies on the balance between Adh1 and Adh2 in maize:

Gene Competitive Programs Genetics. 1975 Dec; 81(4): 641–654.

5. Freeling, M. 1976. Intragenic recombination in maize: Pollen analysis methods and the

effect of parental Adh1 isoalleles. Genetics 83:701-717.

6. Freeling, M., J.C. Woodman and D.S.K. Cheng. 1976. Developmental potentials of

maize tissue cultures. Maydica 21:97-112.

7. Freeling, M. 1977. Spontaneous forward mutation versus reversion frequencies for

maize Adh1 in pollen. Nature 267:154-156.

8. Freeling, M. and D.S.K. Cheng. 1978. Radiation-induced alcohol dehydrogenase

mutants in maize following allyl alcohol selection of pollen. Genet. Res. 31:107-129.

9. Freeling, M. 1978. Allelic variation at the level of intragenic recombination. Genetics

89:211-224.

10. Sachs, M. and M. Freeling. 1978. Selective synthesis of alcohol dehydrogenase during anaerobic treatment of maize. Molec. Gen. Genet. 161:111-115.

11. Freeling, M. 1979. Maize Adh1 as a monitor of environmental mutagens. Environ.

Health Perspt. 27:91-98.

12. Freeling, M. and J.C. Woodman. 1979. Regulatory variant and mutant alleles in higherorganisms and their possible origin via chromosomal breaks. In The Plant Seed:

Development, Preservation and Germination (Eds. Rubenstein, I., et al.) Academic

Press, N.Y.

13. Kelly, J. and M. Freeling. 1980. Purification of maize alcohol dehydrogenase-1

allozymes and comparison of their tryptic peptides. Biochimica et Biophysica Acta

624:102-110.

14. Sachs, M.M., M. Freeling and R. Okimoto. 1980. The anaerobic proteins of maize. Cell 20:761-767.

15. Okimoto, R., M.M. Sachs, E.K. Porter and M. Freeling. 1980. Patterns of polypeptide

synthesis in various maize organs under anaerobiosis. Planta 150:89-94.

16. Freeling, M. 1980. Toward monitoring specific DNA lesions in the gene using pollen

systems. Environ. Health Perspt. 37:13-17.

17. Woodman, J.C. and M. Freeling. 1981. Identification of a genetic element which

controls the organ-specific expression of Adh1 in maize. Genetics 98:357-378.

18. Freeling, M. and J.A. Birchler. 1981. Mutants and variants of the alcohol

dehydrogenase-1 gene in maize. In Genetic Engineering: Principles and Methods (Eds.

Setlow, J. K. and A. Hollaender) Plenum Press, N. Y., pp. 223-264.

19. Birchler, J.A., M. Alleman and M. Freeling. 1981. The construction of a segmental

tetrasomic line of maize. Maydica 26:3-10.

20. Freeling, J., D.S.K. Cheng and M.L. Alleman. 1982. Mutant alleles that are altered in

quantitative, organ-specific behavior. Develop. Genet. 3:179-196.

21. Kelley, P.M. and M. Freeling. 1982. A preliminary comparison of maize anaerobic andheat shock proteins. In Heat Shock Induction of Proteins. Cold Spring Harbor

Laboratory, N.Y., pp. 315-319.

22. Johns, M.A., M. Alleman and M. Freeling. 1982. Differential regulation of the Adh1

gene in maize: facts and theories. In Genetic Engineering in Plants (Ed. Hollaender,

A.) Plenum Press, N.Y., pp. 61-79.23.

23. Strommer, J.N., S. Hake, J. Bennetzen, W.C. Taylor and M. Freeling. 1982. Regulatorymutants of the maize Adh1 gene caused by DNA insertions. Nature 300:542-44.

24. Karoly, C.W., Woodman, J.C., Chen, C.-H., Alleman, M.L., Johns, M.A. and M.

Freeling. 1982. An annotated bibliography of the Adh genes of maize, from 1966

through 1981, and prediction on the future of classical genetics. In Maize for Biological

Research, Sheridan, W.F. Ed. Plant Molecular Biology Association, Charlottesville,

VA.

25. Johns, M.A., J.N. Strommer and M. Freeling. 1983. Exceptionally high levels of

restriction site polymorphism in DNA near the maize Adh1 gene. Genetics 105:733-

743.

26. Freeling, M. 1983. Isozyme systems to study gene regulation during development: a

lecture. In Isozymes in Plant Genetics and Breeding (Eds. Tanksley, S. D. and Orton,

T. J.) Elsevier, Amsterdam, pp. 61-83.

27. Kelley, P.M. and M. Freeling. 1984. Anaerobic expression of maize glucose phosphateisomerase-1. J. Biol. Chem. 259:673-677.

28. Doring, H.-P., M. Freeling, S. Hake, M.A. John, A. Merckelbach, F. Salamini and P.

Starlinger. 1983. A Ds-induced mutation of the Adh1 gene in Zea mays L. Molec. Gen.

Genet. 193:199-204.

29. Hake, S., W.C. Taylor and M. Freeling. 1984. Molecular studies of genetically stable

mutants at the Adh1 gene of maize. Molec. Gen. Gent. 194:42-48.

30. Freeling, M. 1984. Plant transposable elements and insertion sequences. Ann. Rev.

Plant Physiol. 35:277-298 (Contains data of Mu1 not published elsewhere).

31. Bennetzen, J.L., J. Swanson, W.C. Taylor and Michael Freeling. 1984. DNA insertion

in the first intron of maize Adh1 affects message levels: cloning of progenitor and

mutant alleles. Proc. Natl. Acad. Aci. USA 81:4125-4128.

32. Mottinger, J.P., M.L. Johns and M. Freeling. 1984. Mutations of the Adh1 gene in

maize plants infected with barley stripe mosaic virus. Molec. Gen. Genet. 195:367-369.

33. Kelley, P.M. and M. Freeling. 1984. Anaerobic expression of maize fructose-1,6-

diphosphate aldolase. J. Biol. Chem. 259:14180.

34. Hake, S., P.M. Kelley, W.C. Taylor and M. Freeling. 1985. Coordinate induction of

ADH1, aldolase and other anaerobic RNAs in maize. J. Biol. Chem. 260:5050-5054.

35. Roberts, J.K.M., O. Jardetzky, J. Callis, V. Walbot and M. Freeling. 1984. Cytoplasmic acidosis as a determinant of flooding intolerance in plants. Proc. Natl. Acad. Sci. USA81:6029.

36. Johns, M.L., J.P. Mottinger and M. Freeling. 1985. A low copy number, copia-like

transposon in maize. EMBO J. 4:1093-1102.

37. Alleman, M. and M. Freeling. 1986. The Mu transposable element of maize: evidence

for transposition and copy number regulation during plant development. Genetics

112:107-119.

38. Freeling, M. and S. Hake. 1985. Developmental genetics of mutants that specify

knotted leaves in maize. Genetics 111:617-634.

39. Bennett, D.C. and M. Freeling. 1985. Flooding and the anaerobic stress response. In

Model Building in Plant Physiology/Biochemistry, volume III, (Eds. Newman, D. W.

and K. G. Wilson) CRC Press, Boca Raton, FL 1987, pp. 79-84.

40. Freeling, M. and D.C. Bennett. 1985. Maize Adh1. Ann. Rev. Genet. 19:297-323.

41. Hake, S., Bird, R.McK., Neuffer, M.G. and M. Freeling. 1985. The maize ligule and

mutants that affect it. In Plant Genetics (Ed. Freeling, M.) Alan R. Liss, N.Y., pp. 61-

72.

42. Chen, C.-H., M. Freeling and A. Mercklebach. 1986. Enzymatic and morphological

consequences of Ds excisions from maize Adh1. Maydica 31:93-108 (This issue is

dedicated to Barbara McClintock).

43. Hake, S. and M. Freeling. 1986. Analysis of genetic mosaics shows that the extra

epidermal cell divisions in Knotted mutant maize plants are induced by adjacent

mesophyll cells. Nature 320:621-623.

44. Vayda, M.E. and M. Freeling. 1986. Insertion of the Mu1 transposable element into the first intron of maize Adh1 interferes with transcript elongation but does not disrupt

chromatin structure. Plant Molec. Biol. 6:441-454.

45. Lillis, M. and M. Freeling. 1986. Mu transposons of maize. Trends in Genetics 2:183-188.

46. Freeling, M. and 12 other authors (a compendium). 1986. Developmentally interesting new mutants in plants. Ibid. item 41, pp. 817-836.

47. Phinney, B.O., M. Freeling, D.S. Robertson, C.R. Spray and J. Silverthorn. 1986.

Dwarf mutants in maize--the gibberellin biosynthetic pathway and its molecular future.

Plant Growth Substances. (Ed. Bopp, M.) Springer-Verlag, Heidelberg, pp. 55-64.

48. Springer, B., W. Werr, P. Starlinger (Cologne) and D.C. Bennett, M. Zokolica and M.

Freeling. 1986. The Shrunken gene on chromosome 9 of Zea mays L. is expressed in

various plant tissues and encodes an anaerobic protein. Molec. Gen. Genet. 205:461-

468.

49. Chen, C.-H., K.K. Oishi, B. Kloeckener-Gruissem and M. Freeling. 1987. Organspecific expression of maize Adh1 is altered after a Mu transposon insertion. Genetics 116:469-477.

50. Sundaresan, V. and M. Freeling. 1987. An extrachromosomal form of the Mu

transposons in maize. Proc. Natl. Acad. Sci. 84:4924-4928.

51. Kloeckener-Gruissem, B. and M. Freeling. 1987. Relationship between anaerobic

inducibility and tissue-specific expression for the maize anaerobic genes. In The

Proceedings of the NATO Advanced Study Institute: Plant Molecular Biology, Plenum

Press, New York. pp. 293-303.

52. Freeling, M. 1988. Mutagenesis using Robertson's mutator lines and consequent

insertions at the Adh1 gene in maize. In Plant Transposable Elements, Oliver Nelson et

al, eds. Plenum Press, New York. pp. 279-288.

53. Oishi, K. and M. Freeling. 1988. The Mu3 transposon in maize. In Plant Transposable Elements, Oliver Nelson et al, eds. Plenum Press, New York. pp. 289-292.

54. Freeling, M., D.K. Bongard-Pierce, N. Harberd, B. Lane and S. Hake. 1988. Genes

involved in the patterns of maize leaf cell division. In Plant Gene Research: Temporal

and Spatial Regulation of Plant Genes. Eds. D.P.S. Verma and R.B. Goldberg.

Springer-Verlag, Wien.pp. 41-62.

55. Bailey-Serres, J., B. Kloeckener-Gruissem and M. Freeling. 1988. Genetic and

molecular approaches to the study of the anaerobic response and tissue specific gene

expression in maize. Plant, Cell and Environment 11:351-357.

56. Johns, M.A., M.S. Babcock, S.M. Fuerstenberg, S.I. Fuerstenberg, M. Freeling and

R.B. Simpson. 1989. An unusually compact retrotransposon in maize. Plant Molecular

Biology 12:633-642.

57. Hake, S., E. Vollbrecht and M. Freeling. 1989. Cloning Knotted, the dominant

morphological mutant in maize using Ds2 as a transposon tag. EMBO J. 8:15-22.

58. Harberd, N. and M. Freeling. 1989. Genetics of dominant gibberellin-insensitive

dwarfism in maize. Genetics 121:837-838.

59. Langdale, J.A., B. Lane, M. Freeling and T. Nelson. 1989. Cell lineage analysis of

maize bundle sheath and mesophyll cells. Developmental Biology 133:128-139.

60. Martienssen, R., A. Barkan, W.C. Taylor and M. Freeling. 1990. Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize. Genes and Development 4:331-343.

61. Martienssen, R., A. Barkan, M. Freeling and W.C. Taylor. 1989. Molecular cloning of a maize gene involved in photosynthetic membrane organization that is regulated by

Robertson’s Mutator. EMBO J. 8(6):1633-1639.

62. Becraft, P.W., D.K. Bongard-Pierce, A.W. Sylvester, R.S. Poethig and M. Freeling.

1990. The liguleless-1 gene acts tissue-specifically in maize leaf development.

Developmental Biology 141:220-232.

63. Dawe, R.K. and M. Freeling. 1990. Clonal analysis of the cell lineages in the male

flower of maize. Developmental Biology 142:233-245.

64. Williams, C., B. Kloeckener-Gruissem and M. Freeling. 1990. Naturally occurring

variants of maize Adh1 differ in organ-specific expression both in quantity and

developmental timing. Maydica 36:115-128. (Drew Schwartz commemorative

volume.)

65. Bailey-Serres, J. and M. Freeling. 1990. Hypoxic stress induced changes in ribosomes

of maize seedling roots. Plant Physiology 94:1237-1243.

66. Sylvester, A.W., W.Z. Cande and Michael Freeling. 1990. Division and differentiation during normal and liguleless-1 maize leaf development. Development 110:985-1000.

67. Bertrand-Garcia, R. and M. Freeling. 1991. Hairy-Sheath-Frayed 1-O: A systemic,

heterochronic mutant of maize which specifies slow developmental stage transitions.

Amer. J. Bot. 78(6):747-765.

68. Becraft, P. and M. Freeling. 1990. Sectors of liguleless-1 tissue interrupt a short-range intercellular signal during maize leaf development. The Plant Cell 3:801-807.

69. Freeling, M. and A. Pryor. 1991. Drew Schwartz: an appreciation. Maydica 36:109-

113.

70. Dawe, R.K. and M. Freeling. 1991. Cell lineage and its consequences in higher plants. The Plant Journal 1:3-7.

71. Chomet, P., D. Lisch, K.J. Hardeman, V.L. Chandler and M. Freeling. 1991.

Identification of a regulatory transposon that controls the Mutator transposable element

system in maize. Genetics 129:261-270.

72. Dawe, R.K. and M. Freeling. 1992. The role of initial cells in maize anther

morphogenesis. Development 116: 1077-1085.

73. Bailey-Serres, J., J. Tom and M. Freeling. 1992. Expression and distribution of

cytosolic 6-phosphogluconate dehydrogenase isozymes in maize. Biochem. Genet. 30

(5/6):233-246.

74. Kloeckener-Gruissem, B., Vogel, J.M. and M. Freeling. 1992. The TATA-box

promoter region of maize alcohol dehydrogenase-1 (Adh1) affects its organ-specific

expression. EMBO J. 11:157-166.

75. Freeling, M., R. Bertrand-Garcia and N. Sinha. 1992. Maize mutants and variants

altering developmental time and their heterochronic interactions. BioEssays 14:227-

236. Special invited issue on “Evolution and Development.”

76. Freeling, M. and B. Lane. 1994. The maize leaf. In The Maize Handbook, Freeling, M. & V. Walbot, Eds. Springer-Verlag, N.Y.

77. Freeling, M. and J. Fowler. 1994. Nine steps to characterize a morphological mutant. In The Maize Handbook, Freeling, M. & V. Walbot, Eds. Springer-Verlag, N.Y.

78. Sinha, N., S. Hake and M. Freeling. 1993. Genetic and molecular analysis of leaf

development. Current Topics in Develop. Biol. 28: 47-80.

79. Freeling, M. 1992. A conceptual framework for maize leaf development. Develop. Biol. 153:44-58.

80. Becraft, P. and M. Freeling. 1992. Cell interactions in plants. Curr. Opin. Genet. and

Develop. 2:571-575.

81. Winkler, R. and M. Freeling. 1994. Physiological genetics of the dominant

gibberellinnonresponsive maize dwarfs, Dwarf8 and Dwarf9. Planta 193:341-348.

82. Dawe, R.K., A.R. Lachmansingh and M. Freeling. 1993. Transposon-mediated

mutations in the untranslated leader of maize Adh1 that increase and decrease pollen specific gene expression. The Plant Cell 5: 311-319.

83. Becraft, P.W. and M. Freeling. 1994. Genetic analysis of Rough sheath1 developmental mutants of maize. Genetics 136: 295-311.

84. Vogel, J.M., B. Roth, M. Cigan and M. Freeling. 1993. Expression of the two maize

TATAbinding protein genes, and function of the encoded TBP proteins by

complementation in yeast. The Plant Cell 5:1627-1638.

85. Bennetzen, J.L. and M. Freeling. 1993. Grasses as a single genetic system: genome

composition, collinearity and compatability. (An argument.) Trends in Genetics 9 (8):

259-261.

86. Lisch, D., P. Chomet and M. Freeling. 1995. Genetic characterization of the Mutator

system in maize: behavior and regulation of Mu transposons in a minimal line. Genetics

139: 1777-1796.

87. Winkler, R.G. and M. Freeling. 1994. Analysis of the autonomy of maize Dwarf1

action in genetic mosaics. J. Heredity 85 (5).

88. Fowler, J. and M. Freeling. 1996. Genetic analysis of mutations that alter cell fates in maize leaves: dominant Liguleless mutations. Developmental Genetics 18 (3): 198-222.

89. Lisch, D. and M. Freeling. 1994. Loss of mutator activity in a minimal line. Maydica

39:289-300. Robertson commemorative issue.

90. Kloeckener-Gruissem, B. and M. Freeling. 1995. Transposon-induced promoter

scrambling: a mechanism for the evolution of new alleles. PNAS 92:1836-1840.

91. Schneeberger, R.G., Becraft, P.W., Hake, S. and M. Freeling. 1995. Ectopic expression of the knox homeo box gene rough sheath1 alters cell fate in the maize leaf. Genes & Development 9: 2292-2304.

92. Scanlon, M.J., Schneeberger, R.G. and M. Freeling. 1996. The maize mutant narrow

sheath fails to establish leaf margin identity in a meristematic domain. Development

122:1683-1691.

93. Donlin, M.J., Lisch, D. and M. Freeling. 1995. Tissue specific accumulation of MURB,a protein encoded by MuDR, the autonomous regulator of the MUTATOR transposable element family. The Plant Cell 7: 1989-2000.

94. Fowler, J.E., Muehlbauer, G.J. and M. Freeling. 1996. Mosaic analysis of the

Liguleless3 mutant phenotype in maize by coordinate suppression of Mutator-insertion

alleles. Genetics 143: 489-503.

95. Sylvester, A., Smith, L. and M. Freeling. 1996. Acquisition of identity in the

developing leaf. Annual Review of Cell and Developmental Biology 12: 257-304.

96. Harper, L. and M. Freeling. 1996. Studies on early leaf development. Current Opinions in Biotechnology 7:139-144.

97. Harper, L. and M. Freeling. 1996. Interactions of liguleless1 and liguleless2 function

during ligule induction in maize. Genetics 144:1871-1882.

98. Schichnes, D., Schneeberger, R. and M. Freeling. 1997. Induction of leaves directly

from leaves in the maize mutant Lax midrib1-O. Developmental Biology 186: 36-45.

99. Scanlon, M.J. and M. Freeling. 1996. Clonal sectors in norrow sheath versus nonmutant maize reveal early events in leaf margin development. Developmental Biology 182: 52-66.

100. Bennetzen, J.L. and M. Freeling. 1997. The unified grass genome: synergy in synteny. Invited by Genome Research 7: 301-306.

101. Moreno, M.A., Harper, L.C., Krueger, R., Dellaporta, S.L and M. Freeling. 1997.

Liguleless1 encodes a nuclear localized protein required for induction of ligules and

auricles during maize leaf organogenesis. Genes and Development 11:616-628.

102. Schichnes, D.E. and M. Freeling. 1997. Lax Midrib1-O, a systematic, heterochronic

mutant of maize. American Journal of Botany 85: 481-491.

103. Mooney, M. and M. Freeling. 1997. Using morphological genes to investigate the

evolution of leaf form. A special edition to honor Dr. David Walden. Maydica 42: 173-

184.

104. Scanlon, M.J., Meyers, A.M., Schneeberger, R.G. and M. Freeling. 1997. The maize

gene empty pericarp2 is required for progression beyond early stages of

embryogenesis. The Plant Journal 12: 901-909.

105. Lisch, D., Girard, L., Donlin, M. and M. Freeling. 1999. Functional analysis of deletion derivatives of the maize transposon MuDR deliniates roles of the MURA and MURB proteins. Genetics 151: 331-341.

106. Scanlon, M.J. and M. Freeling, 1998. The narow sheath leaf domain deletion: a genetic tool used to reveal developmental homologies among modified maize organs. The

Plant Journal 13: 547-561.

107. Muehlbauer, G. J., J.E. Fowler and M. Freeling, 1997. Sectors expressing the

homeobox gene liguleless3 implicate a time-dependent mechanism for cell-fate

aquisition along the proximo-distal axis of the maize leaf. Development 124: 5097-

5106.

108. Walsh, J. Waters, C. and M. Freeling, 1998. The maize gene liguleless2 encodes a

basicleucine zipper protein involved in the precision of the blade-sheath boundary in

the maize leaf. Genes and Development 11: 208-218.

109. Schneeberger, R.S., M. Tsiantis, M. Freeling and J. Langdale, 1998. The rough sheath2 gene negatively regulates homeobox gene expresion during maize leaf development. Development 125: 2857-2865.

110. Phillips, R.L. and M. Freeling, 1998. Plant genomics and our food supply: An

introduction. Proc. Natl. Acad. Sci. USA 95: 1969-1970.

111. Meuhlbauer, G.J., J,E, Fowler, L. Girard, R. Tyers, L. Harper, and M. Freeling, 1999. Ectopic expression of the maize homeobox gene liguleless3 alters cell fates in a

quantitative fashion. Plant Physiology 119: 651-662.

112. Tsiantis, M., R. Schneeberger, M. Freeling and J. A. Langdale, 1999. The maize rough sheath2 gene and leaf development programs in monocot and dicot plants. Science 284: 154-56.

113. Hay, J.O., B. Mouilia, B. Lane, M. Freeling and W. K. Silk, 2000. Biomechanical

analysis of the Rolled (RLD) leaf phenotype of maize. American J. of Bot. 87: 625-633.

114. Walsh, J. and M. Freeling, 1999. The liguleless2 gene in maize functions during the

transition from the vegetative to the reproductive shoot apex. The Plant Journal 19,

489-495.

115. Girard, L. and M. Freeling, 1999. Regulatory changes as a consequence of transposon insertion. Develop. Genetics 25: 291-296.

116. Girard, L. and M. Freeling, 2000. Mutator supressible alleles of rough sheath1 and

liguleless3 in maize reveal multiple mechanisms for suppression. Genetics 154: 437-

446.

117. Bennetzen et al. (Doebly, including M. Freeling), 2000. Genetic evidence and the

origin of maize. Latin American Antiquity 12: 84-86.

118 Lisch, D., M. Freeling, R.J. Langham, and M. Choy, 2001. Mutator transposon is

widespread in grasses. Plant Physiol. 125: 1293-1303.

119. Freeling, M., 2001. Grasses as a single Genetic System: Reassessment 2001. Plant

Physiology 125: 1-7.

120. Nelson, J., B. Lane and M. Freeling, 2002. Trans-epidermal signaling along the

dorsoventral axis controls patterning of the maize leaf. Development 129: 4581-4589.

121. Kaplinsky, N., D. Braun, D. Lisch, A. Hay, S. Hake and M. Freeling,. 2002. Maize

transgene results in Mexico are artifacts. Nature 416, 601 (This brief communication is

the most peer-reviewed publication in Freeling lab history).

122. Kaplinsky, N., D.Braun, J. Penterman, S.A., Goff and M. Freeling, 2002. Utility and

distribution of conserved noncoding sequences (CNSs) in the grasses. PNAS 99, 6147-

6151.

123. Kasplinsky, N.and M. Freeling, 2003.Combinatorial control of meristem identity in

maize. Development 130: 1149-1158.

124. Theodoris, G,, N., Inada and M. Freeling, 2003. Genetic dissection of RS2/AS1

function in Arabidopsis. PNAS 100: 6837-6842.

125. Dong, Q., L. Roy, M. Freeling, V. Walbot and V. Brendel, 2003. ZmDB—An

integrated database for maize genome research. Nucleic Acids Research 31: 244-247.

126. May, Bruce P.*, Hong Liu*, Erik Vollbrecht*, Lynn Senior, Pablo Rabinowicz, Donna Roh, Xiaokang Pan, Lincoln Stein, Mike Freeling, Danny Alexander, Rob Martienssen, 2003. Maize targeted mutagenesis: a knockout resource for maize. PNAS 100: 11541-1546.

127. Langham, R.J., J. Walsh, M. Dunn, C, Ko, S.A. Goff and M. Freeling, 2003. Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166: 935-945.

128. Inada, D. C., A. Bashir, C. Lee, B.C. Thomas, C. Ko, S.A. Goff and M. Freeling, 2003. Conserved noncoding sequences in grasses. Genome Research 13: 2030-2041.

129. Slotkin, R. Keith, Michael Freeling and Damon Lisch 2003. Mu killer causes the

heritable inactivation of the Mutator family of transposable elements in Zea mays.

Genetics 165: 781-797.

130. Osmont, K. S., and M. Freeling, 2004. The extended auricle1 (eta1) gene provides an essential component of the genetic network controlling post-initiation maize leaf

development. Genetics 165: 1507-1519.

131. Slotkin, R.K, M. Freeling and D. Lisch, 2005. Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nature Genetics 17: 641-645.

132. Woodhouse, M.R., M. Freeling, and D. Lisch, 2005. The mop1 (modifier of

paramutation1) mutant progressively reactivates one of the two genes encoded by the

MuDR transposon in maize. Genetics 172: 579-592.

133. Freeling, M. and B.C. Thomas, 2006. Gene balanced duplications, like tetraploidy,

provide predictable drive to increase morphological complexity. Genome Research 16:

805-814.

134. Osmont, K.S., N. Sadeghian, and M. Freeling, 2006. Mosaic analysis of extended

auricle1 (eta1) suggests a two-way signaling pathway positioning the boundary

between blade/sheath in Zea mays. Developmental Biology 295: 1-12.

135. Diao, X., M. Freeling and D. Lisch, 2006. Horizontal transfer of a plant transposon.

PLOS Biology 4: 119-128.

136. Paterson, AH, M. Freeling and T. Sasaki, 2006. Genomics of model cereals. Genome Research 15: 1643-1650.

137. Thomas, B.C., B. Pedersen and M. Freeling, 2006. Following tetraploidy in an

Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving

clusters enriched in dose-sensitive genes. Genome Research 16: 934-946.

138. Freeling, M., Rapaka, L., Lyons, E., Pedersen, B., and Thomas, B.C. 2007. G-boxes,

bigfoot genes, and environmental response: characterization of intragenomic conserved

noncoding sequences in Arabidopsis. Plant Cell 19: 1441-1457.

139. Thomas, B.C., Rapaka, L., Lyons, E., Pedersen, B., and Freeling, M. 2007. Arabidopsis

intragenomic conserved noncoding sequence. Proc Natl Acad Sci U S A 104: 3348-3353.

140. Freeling, M. 2008. The evolutionary position of subfunctionalization, downgraded.

Genome Dynamics 4: 25-40. (peer-reviewed; evolutionary theory)

141 Lyons, E. and Freeling, M. 2008. How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J 53: 661-673.

142 Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J.H., Senin, P., Wang, W., Ly, B.V., Lewis, K.L. et al. 2008. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991-996.

143 Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R., and Lisch, D. 2008. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res 18: 1924-1937.

144 Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D. and Freeling, M. 2008. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 148: 1772-1781.

145. Lyons, E., Castelletti, S., Pedersen, B., Lisch, D., and Freeling, M. 2008. Maize GEvo: A comparative DNA sequence alignment visualization tool . In The Maize Handbook (eds. J. Bennetzen and S. Hake). Springer, New York.

146. Lyons, E., Pederson, B., Kane, J., and Freeling, M. 2008. The value of nonmodel

genomes and an example using SynMap within CoGe to dissect the paleohexaploidy at

preceeds the rosids. Tropical Plant Biology 1: 246-277.

147 Freeling, M. and Subramaniam, S. 2009. Conserved noncoding sequences (CNSs) in

higher plants. Curr Opin Plant Biol 12: 126-132. (peer reviewed, but invited)

148 Freeling, M. 2009. Bias in plant gene content following different sorts of duplication:

tandem, whole-genome, segmental, or by transposition. Annual Review of Plant Biology

60: 433-453. (peer reviewed, evolutionary theory)

149 Paterson, A., Freeling, M., Tang, H., and Wang, X. 2010. Insights from the comparison of plant genome sequences. Annu. Rev. Plant Biol. 60.

150 Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H.,Haberer, G., Hellsten, U., Mitros, T., Poliakov, A. et al. 2009. The Sorghum bicolor

genome and the diversification of grasses. Nature 457: 551-556.

151 Woodhouse, M. and Freeling, M. 2010. Tandem duplications and gene transposition inplants. Maydica 54:457-462. (Ron Phillips commemorative issue)

152 Woodhouse, M., Pedersen, B., and Freeling, M. 2010. Transposed genes in Arabidopsisare often associated with flanking repeats. PLoS Genetics: 6: e1000949.

153 Woodhouse, M., Schnable, J., Pedersen, B., Lyons, E., Lisch, D., Subramaniam, S., and Freeling, M. 2010. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biology (cover and splash editorial, Faculty of 1000 pick) 8, e1000409 (June)

154 Kane, J., Freeling, M., and Lyons, E. 2010. The evolution of a high copy gene array in Arabidopsis. Journal of Molecular Evolution 70: 531-544.

155.  Li H, Freeling M, Lisch D (2010) Epigenetic reprogramming during vegetative phase change in maize. Proceedings of the National Academy of Sciences of the United States of America 107: 22184-22189

156. Woodward JB, Abeydeera ND, Paul D, Phillips K, Rapala-Kozik M, Freeling M, Begley TP, Ealick SE, McSteen P, Scanlon MJ (2010) A maize thiamine auxotroph is defective in shoot meristem maintenance. The Plant cell 22: 3305-3317

157. Cande WZ, Freeling M (2011) Inna Golubovskaya: the life of a geneticist studying meiosis. Genetics 188: 491-498

158. Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM (2011) Heritable epigenetic variation among maize inbreds. PLoS genetics 7: e1002372

159.Lyons E, Freeling M, Kustu S, Inwood W (2011) Using genomic sequencing for classical genetics in E. coli K12. PloS one 6: e16717

160. Pedersen BS, Tang H, Freeling M (2011) Gobe: an interactive, web-based tool for comparative genomic visualization. Bioinformatics 27: 1015-1016

161. Reneker J, Lyons E, Conant GC, Pires JC, Freeling M, Shyu CR, Korkin D (2012) Long identical multispecies elements in plant and animal genomes. Proceedings of the National Academy of Sciences of the United States of America 109: E1183-1191

162. Schnable JC, Pedersen BS, Subramaniam S, Freeling M (2011b) Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses. Frontiers in plant science 2: 2

163. Schnable JC, Springer NM, Freeling M (2011c) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proceedings of the National Academy of Sciences of the United States of America 108: 4069-4074

164. Schnable JC, Freeling M (2011) Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PloS one 6: e17855

165. Tang H, Lyons E, Pedersen B, Paterson A, Freeling M (2011a) Guided synteny alignment between duplicated genomes through integer programming. BMC Bioinformatics 12, 102

166. Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M (2011b) Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics 12: 102

167. Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z (2011) The genome of the mesopolyploid crop species Brassica rapa. Nature genetics 43: 1035-1039

168. Woodhouse MR, Tang H, Freeling M (2011) Different Gene Families in Arabidopsis thaliana Transposed in Different Epochs and at Different Frequencies throughout the Rosids. The Plant cell 23: 4241-4253

169. Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J (2012) High-resolution mapping of open chromatin in the rice genome. Genome research 22: 151-162

170. Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant GC, Wang X, Freeling M, Pires JC (2012) Altered Patterns of Fractionation and Exon Deletions in Brassica rapa Support a Two-step Model of Paleohexaploidy. Genetics

171. Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC (2012) Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Current opinion in plant biology 15: 131-139

172. D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengelle J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, McKain MR, Leebens-Mack J, Burgess D, Freeling M, Mbeguie AMD, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quetier F, Yahiaoui N, Wincker P (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488: 213-217

173. Freeling M (2012) Response to Birchler:  heterosis is partly a sub-probem of quantitative genetics, but its solution may depend on understanding the mysterious genetics of quantity. Maydica 57: 96-97

174. Schnable JC, Freeling M (2012) Maize (Zea mays) as a model for studying the impact of gene and regulatory sequence loss following whole-genome duplication. In Polyploidy and Genome Evolution, Soltis PS, Soltis DE (eds). Berlin/Heidelberg: Springer

175. Schnable JC, Freeling M, Lyons E (2012a) Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biology and Evolution 4: 265-277

176. Schnable JC, Wang X, Pires JC, Freeling M (2012b) Escape from preferential retention following repeated whole genome duplications in plants. Frontiers in plant science 3: 94

177. Spangler JB, Ficklin SP, Luo F, Freeling M, Feltus FA (2012a) Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules. PloS one 7: e45041

178. Spangler JB, Subramaniam S, Freeling M, Feltus FA (2012b) Evidence of function for conserved noncoding sequences in Arabidopsis thaliana. The New phytologist 193: 241-252

179. Subramaniam S, Freeling M (2012) Conserved noncoding sequences in plant  genomes. In Plant Genome Diversity, Wendel JF (ed), Vol. Volume 1: Plant genomes, their residents, and their evolutionary dynamics. Springer

180. Freeling M (2013) A short course on the impact of gene duplications on the evolution of novelty. In Advances in Botanical Research, Paterson AH (ed), Vol. 69, 13, p 27pp. Elsevier

181. Schnable J, Freeling M (2013) Maize (Zea mays ) as a model for studying the impact of gene and regulatory sequence loss following whole-genome duplication. In Polyploidy and Gene Evolution, Soltis P, Soltis D (eds), Vol. VIII, 8, pp 137-146. New York: Springer

182. Subramaniam S, Wang X, Freeling M, Pires JC (2013) The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa. Genome biology and evolution 5: 646-660

183.Turco G, Schnable J, Pedersen B, Freeling M (2013) Automated conserved noncoding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. Frontiers in Plant Genetics and Genomics 4: 170-180

184. Garsmeur O, Schnable JC, Almeida A, Jourda C, D'Hont A, Freeling M (2014) Two evolutionarily distinct classes of paleopolyploidy. Molecular biology and evolution 31: 448-454

185. Bolduc N, Tyers RG, Freeling M, Hake S (2014) Unequal redundancy in maize knotted1 homeobox genes. Plant physiology 164: 229-238

186. Burgess D, Freeling M (2014) The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates. The Plant cell 26: 1-16

187. Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X (2014) Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proceedings of the National Academy of Sciences of the United States of America 111: 5283-5288.

188. AMR de Almeida, R Yockteng, J Schnable, ER Alvarez-Buylla, M Freeling, ...(2014).  Co-option of the polarity gene network shapes filament morphology in angiosperms.  Scientific reports 4

189.  DG Burgess, J Xu, M Freeling, 2015. Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics. Current Opinion in Plant Biology 27, 141-147

190. M Freeling, J Xu, M Woodhouse, D Lisch, 2015. A solution to the C-value paradox and the function of junk DNA: the Genome Balance Hypothesis

Molecular Plant 1, 12

191. de Almeida, A. M. Yockteng, R. Schnable, J. Alvarez-Buylla, E. R.Freeling, M. Specht, C. D. (2014).  Co-option of the polarity gene network shapes filament morphology in angiosperms. Science Rep.4: 6194-.

192. Burgess2, Dinakar Challabathula4, Kristi Spittle5, Richard Hall5, Jenny Gu5, Eric Lyons3, Michael Freeling2, Dorothea Bartels4, Todd P. Michael6*, Todd C. Mockler (2015)*  Single-molecule sequencing of the desiccation tolerant grass Oropetium thomaeum.  Nature, accepted.

193. Ray Ming1,2*, †, Robert VanBuren1,2,3*, Ching Man Wai1,2*, Haibao Tang1,4*, Michael C. Schatz5, John E. Bowers6, Eric Lyons4, Ming-Li Wang7, Jung Chen8, Eric Biggers5, Jisen Zhang1, Lixian Huang1, Lingmao Zhang1, Wenjing Miao1, Jian Zhang1, Zhangyao Ye1, Chenyong Miao1, Zhicong Lin1, Hao Wang6, Hongye Zhou6, Won C. Yim9, Henry D. Priest3, Chunfang Zheng10, Margaret Woodhouse11, Patrick P. Edger11, Romain Guyot12,  Hao-Bo Guo13, Hong Guo13, Guangyong Zheng14, Ratnesh Singh15, Anupma Sharma15, Xiangjia Min16, Yun Zheng17, Hayan Lee5, James Gurtowski5, Fritz J. Sedlazeck5, Alex Harkess6, Michael R. McKain3, Zhenyang Liao1, Jingping Fang1, Juan Liu1, Xiaodan Zhang1,  Qing Zhang1, Weichang Hu1, Yuan Qin1, Kai Wang1, Li-Yu Chen1, Neil Shirley18, Yann-Rong Lin19, Li-Yu Liu19, Alvaro G. Hernandez20, Chris L. Wright20, Vincent Bulone18, Gerald A. Tuskan21, Katy Heath2, Francis Zee22, Paul H. Moore7, Ramanjulu Sunkar23, James H. Leebens-Mack6, Todd Mockler3, Jeffrey L. Bennetzen6, Michael Freeling11, David Sankoff10, Andrew H. Paterson24, Xinguang Zhu14, Xiaohan Yang21,  J. Andrew C. Smith25, John C. Cushman9, Robert E. Paull8, †, Qingyi Yu15, † (2015)  The pineapple genome and the evolution of CAM photosynthesis Nature Genetics, accepted 7-2015

 

                                   *** Dateline to be accepted for publication:  7-2015***

 

Recent (2008-present)  peer reviewed website: websites going online before 2006 have been minimally updated, and are not listed here although they are still online. Newer web applications on our servers  or powered by iPlant, University of Arizona:

 

I. CoGe. Now at iPlant, administered by it’s lead developer, E. Lyons.  (Peer reviewed with each of the E. Lyons publications above, beginning with Lyons and Freeling, 2008.) This tool box is highly utilized by comparative genome biologists, especially working with plants and microbes, from all over the world.

CoGe= Compare Genomes, an online suit of tools for the comparison of multiple genomes, segments, genes, sequences, ENCODE-like features and motifs in an evolutionarily useful way:

https://genomevolution.org/CoGe/index.pl Get started thru CoGePedia, our wiki, with

links to movies and animated tutorials:

http://genomevolution.org/wiki/index.php/Main_Page

 

II.  http://qTeller.com .  Coded by James Schnable while in the Freeling lab. This RNAseq reads rendering and graphic analysis pipeline is open to the public, and is actively utilized.  The code has been released at GitHub but the announcement has not been published. 

 

III.  Arabidopsis gene positional history website. Peer reviewed

 

Some past websites carrying Freeling lab data 7/98- 2006.

http://128.32.88.35/grassweb/  Under re-construction with serious database issues; 14 years old.   This is the Grass Hybrids Database, located on a Department of Plant and Microbial Biology server. Here the public can research evidence for or against interspecies and intergeneric hybridizability among the about 10,000 species in the grass family. Funding from the Syngenta Corp via a grant to UC-Berkeley. Collaborator: E.A. Kellogg.

http://mtm.cshl.edu/  This is the Maize Targeted Mutagenesis (reverse genetics: maize gene knockout project) database, an NSF Plant Genome Project centered at Cold Spring Harbor Laboratory. Freeling is one of three PIs, and the PI in charge of seedling phenotypes; R. Martienssen is PI. About 8,000 families of segregating maize are included on this website. Many (total of 20%) of these families segregate useful new mutants caused by transposon Mu insertion. The public may search. Server at Cold Spring Harbor.

http://www.maizegdb.org/rescuemu-phenotype.php  The is the maizeGDB website,

phenotypes subsection. Freeling is one of several PIs of this NSF project centered at Stanford. (Walbot, PI). Several thousand families have been screened for segregating new mutants. Data is available to the public. Server at Iowa State University.

 

Publications from research in the Freeling lab from which Freeling removed his name from the byline, ending in 2009.  The most common reason was because the paper was the result of a collaboration initiated by Damon Lisch, a PI in the Freeling lab.

1. Porter, E.K. 1981. Origins and genetic nonvariability of the proteins which diffuse from maize pollen. Environ. Health Perspt. 37:53-59.

2. Hake, S. 1987. Tissue interactions in plant development. BioEssays 6:58-60.

3. Hake, S., R. Walko, B. Lane and B. Lowe. 1989. Transposon mutagenesis in developmental biology: methodology and results. Curr. Topics in Plant Biochem. and Physiol. 8:237-250.

4. Sylvester, A.W. and J. Fowler. 1994. Boundaries in the maize leaf: Cellular analysis of threedevelopmental mutations Lg3, Lg4 and Lxm. Submitted.

5. Fennoy, S.L. and J.B. Serres, 1995. Post-transcriptional regulation of gene expression inoxygen-deprived roots of maize. The Plant Journal 7: 287-295. Initial work in my lab (NIH).

6. Bailey-Serres, J. and R. Kelly Dawe, 1996. Both 5' and 3' sequences of maize adh1 mRNA are required for enhanced translation under low oxygen conditions. Plant Physiol. 112: 685-695. Initial work in my lab (NIH).

7. Lisch, D., C.C. Cary, J.E. Dorwiler and V.L. Chandler, 2002. A mutation that prevents

paramutation in maize also reverses MutatorI transposon methylation and silencing. PNAS 99: 6130-5

8. Hudson ME, Lisch DR, Quail PH (2003) The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J 34: 453-471.

9.  Diao XM, Lisch D (2006) Mutator transposon in maize and MULEs in the plant genome. Yi Chuan Xue Bao 33: 477-487.

10. Hale, C., Erhard, L., Lisch, D., and J. Hollick, 2009. Distinct roles of RNAdirected

DNA methylation factors in the processing of maize repetitive RNAs.

PLoS Genetics. PMID: 19680464

11. Hanada, K., Vallejo, V., Nobuta, K., Slotkin, R.K., Lisch, D., Meyers, B.C.,

Shiu, S-H. and N. Jiang, 2009. Expression and evidence for function of Pack-

MULEs in rice. Plant Cell. PMID: 19136648

12. Schnable, P.S et al. (Lisch, D., author 121 of 160), 2009. The B73 maize

genome: complexity, diversity and dynamics. Science 326(5956):1112-5.

13. Jia, Y., Ohtsu, K, Lisch, D., Nettleton, D and P.S. Schnable, 2009. Loss of

RNA-dependent RNA Polymerase 2 (RDR2) function causes widespread and

unexpected changes in the expression of transposons and genes in maize shoot

apical meristems. PLoS Genet. 2009 Nov;5(11):e1000737.

14. Ramirez, J., Bolduc, N., Lisch, D, and S. Hake, 2009. Position dependent

effects of knotted1 on leaf shape in maize. Plant Physiol. 2009

Dec;151(4):1878-88.

Freeling no longer recorded these publications as of 2010.