CURRICULUM VITAE JAMES B HICKS PAGE 14 CURRICULUM VITAE

curriculum vitae james b. hicks page 14 curriculum vitae james b. hicks, ph.d. university of southern california email: james.hic

CURRICULUM VITAE
JAMES B. HICKS PAGE 14
CURRICULUM VITAE
JAMES B. HICKS, Ph.D.
University of Southern California Email: [email protected]
1002 W Childs Way, MCB 354, MC3502 Phone: (213) 821 1481
Los Angeles, CA 90089-3502 Cell: (503) 351 4414
CURRENT POSITION
2014 – Present Professor (Research) CSI: Cancer Inst., Michelson
Center for Convergent Biosciences, University of Southern California,
Los Angeles CA
2014 – Present Adjunct Professor, Charles University, Pilsen, Czech
Republic
PREVIOUS SCIENTIFIC AND MANAGEMENT EXPERIENCE
1978 – 1981 Senior Staff Investigator, Cold Spring Harbor Laboratory,
Cold Spring Harbor, NY
1981 – 1985 Senior Scientist, Cold Spring Harbor Laboratory
1986 – 1990 Director, PPG Industries/Scripps Joint Research Program,
Research Institute of Scripps Clinic, La Jolla, CA
1990 – 1992 Director, Yeast Genetics Program, ICOS Corporation
1992 – 1994 Senior Director, Science, ICOS Corporation, Bothell, WA
1994 – 1999 President and Chief Science Officer, Hedral Therapeutics,
Inc. Portland, OR
1996 – 1999 Co-founder and Technical Consultant, Sapient Health
Network, Portland, OR
1999 – 2003 Co-founder and Chief Technology Officer, Virogenomics,
Inc., Tigard, OR
2003 Senior Research Fellow, National Cancer Institute, Frederick, MD
2004 – 2016 Research Professor of Cancer Genomics, Cold Spring Harbor
Laboratory, NY
EDUCATION
1964 – 1968 B.A. Biology, Willamette University, Salem, OR
Phi Beta Kappa (Alumni Chapter)
1970 – 1975 Ph.D. Molecular Biology/Genetics, University of Oregon
Institute of Molecular Biology, Eugene, OR, Advisor: Dr. Ira
Herskowitz
1975 – 1978 Postdoctoral Fellowship, Molecular Genetics, Cornell
University, Ithaca, NY Advisor: Dr. Gerald R. Fink
OTHER PROFESSIONAL ACTIVITIES:
1979 – 1987 Instructor, Summer Postgraduate Course on Yeast Genetics,
Cold Spring Harbor Laboratory, NY
1981 – 1982 NIH Postdoctoral Fellowship Study Section
1981 – 1985 NSF Genetic Biology Study Section
1982 – 1984 Editorial Board, Cell
1984 – 1988 Editorial Board, Yeast
1984 – 1989 Editorial Board, Molecular and Cellular Biology
1986 – 1987 Member, NSF Plant Genetics Postdoctoral Fellowship Panel
1986 – 1991 Member, Board of Directors, The Infergene Corporation,
Benicia, CA
1987 – 1990 Member, Scientific Advisory Board, Damon Runyon Walter
Winchell Cancer Fund
1988 – 1994 Editorial Board, Infection and Immunity
1988 – 1997 Member, Board of Directors, California Institute of
Biological Science, La Jolla, CA
1989 Summer session course, “Management of Technology,” Sloan School
of Management, Massachusetts Institute of Technology
1997 – 2007 Member, Board of Directors, AVI Biopharma, Inc, Portland,
OR
(NASDAQ: AVII)
2001 – Present Member, Board of Directors, BBSI, Inc, Vancouver
WA.(NASDAQ: BBSI)
2009 – Present Member, Scientific Advisory Board, Celmatix Inc., NY,
NY
2014 – Present Member, Board of Directors, Virogenomics, Inc., Tigard
OR
2013 – Present Member, Clinical Advisory Board, Epic Sciences, La
Jolla, CA
RESEARCH ARTICLES:
1.
Hicks JB and Herskowitz I. (1976) Interconversion of yeast mating
types. I. Direct bservations of the action of the homothallism
(HO) gene. Genet. 83: 245-258.
2.
Hicks JB and Herskowitz I. (1976) Evidence for a new diffusible
element of mating pheromones in yeast. Nature 260: 246-248.
3.
Hicks J and Strathern JN. (1977) Interconversion of mating type in
S. Cerevisiae and the cassette model for gene transfer. Brookhaven
Symp. Biol. 29: 233-242.
4.
Hicks J and Fink GR. (1977) Identification of chromosomal location
of yeast DNA from hybrid plasmid pYeleul0. Nature 269:265-267.
5.
Hicks JB, Strathern JN and Herskowitz I. (1977) The cassette model
of mating-type interconversion. In, DNA Insertion Elements,
Plasmids and Episomes. A. Bukhari, J. Shapiro and S. Adhya, Eds.,
Cold Spring Harbor Laboratory, NY, Pp. 457-462.
6.
Hicks JB and Herskowitz I. (1977) Interconversion of yeast mating
types. II. Restoration of mating ability to sterile mutants in
homothallic and heterothallic strains. Genet. 8-5: 373-393.
7.
Hicks JB, Strathern JN and Herskowitz I. (1977) Interconversion of
yeast mating types. In. Action of the homothallism (HO) gene in
cells homozygous for mating type locus' Genet. 85: 395-405.
8.
Herskowitz I, Strathern JN, Hicks JB and Rine J. (1977) Mating
type interconversion in yeast and its relationship to development
in higher eucaryotes. In, Proceedings of the 1977 ICN-UCLA
Symposium: Molecular Approaches to Eukaryotic Genetic Systems. G.
Wilcox, J. Abelson and C.F. Fox, Eds., Academic Press, NY, pp.
193-202.
9.
Hinnen A, Hicks JB and Fink GR. (1978) Transformation of yeast.
Proc. Natl. Acad. Sci. USA 75: 1929-1933.
10.
Fink GR, Hicks JB and Hinnen A. (1978) Yeast as a host for hybrid
DNA. in, International Symposium on Genetic Engineering,
Scientific Development and Practical Applications. H.W. Boyer and
S. Nicosia, Eds., Elsevier, North Holland Biomedical Press.
11.
Strathern JN, Newlon CS, Herskowitz I and Hicks JB. (1979)
Isolation of a circular derivative of yeast chromosome IH:
Implications for the mechanism of mating type interconversion.
Cell 18: 309-319.
12.
Hicks J, Klar A, Strathern JN and Newlon CS. (1979) Control of
mating type in yeast. In, Proceedings of the 1979 ICN-UCLA
Symposium: Eucaryotic Gene Regulation. T. Maniatis, R. Axel and
C.F. Fox, Eds., Academic Press, NY.
13.
Rine J, Strathern JN, Hicks JB and Herskowitz I. (1979) A
suppressor of mating-type locus mutations in Saccharomyces
cerevisiae: Evidence for and identification of cryptic mating-type
loci. Genet. 93: 877-901.
14.
Broach JR, Strathern JN and Hicks JB. (1979) Transformation in
yeast: Development of a hybrid cloning vector and isolation of the
CAN1 gene. Gene 8: 121-133.
15.
Hicks J, Strathern JN and Klar AJ. (1979) Transposable mating type
genes in Saccharomyces cerevisiae. Nature (London) 282: 478-483.
16.
Strathern JN, Spatola E, McGill C and Hicks JB. (1980) Structure
and organization of transposable mating type cassettes in
Saccharomyces yeasts. Proc. Natl. Acad. Sci. USA 77: 2839-2843.
17.
Broach JR and Hicks JB. (1980) Replication and recombination
functions associated with the yeast plasmid, 2 u circle. Cell 21:
501-508.
18.
Klar AJ, Mclndoo J, Strathern JN and Hicks JB. (1980) Evidence for
a physical interaction between the transposed and the substituted
sequences during mating type gene transposition in yeast. Cell 22:
291-298.
19.
Herskowitz 1, Blair L, Forbes D, Hicks J, Kassir Y, Kushner P,
Rine J, Sprague G Jr and Strathern J. (1980) Control of cell type
in Saccharomyces cerevisiae and.a hypothesis for development in
higher eucaryotes. In, Molecular Genetics of Development. W.
Loomis and T. Leighton, Eds., Academic Press, NY.
20.
Klar AJ, McIndoo J, Hicks JB and Strathern JN. (1980) Precise
mapping of the homothallism genes HML and HMR in Saccharomyces
cerevisiae. Genet. 96: 315-320.
21.
Klar AJ, Hicks JB and Strathern JN. (1981) Irregular
transpositions of mating-type genes in yeast. Cold Spring Harbor
Symp. Ouant. Biol. 45: 983-990.
22.
Strathern J, Hicks JB and Herskowitz 1. (1981) Control of cell
type in yeast by the mating type locus: The a-1 and a-2
hypothesis. J. Mol. Biol. 147: 357-372.
23.
Klar AJ, Strathern JN, Broach JR and Hicks JB. (1981) Regulation
of transcription in expressed and unexpressed mating type
cassettes of yeast. Nature (London) 289: 239-244.
24.
Klar AJ, Strathern JN and Hicks JB. (1981) A position-effect
control for gene transposition: State of expression of yeast
mating-type genes affects their ability to switch. Cell 25:
517-524.
25.
Klar AJ, Hicks JB and Strathern JN. (1982) Directionality of yeast
mating-type interconversion. Cell 28: 551-561.
26.
Strathern JN, Klar AJ, Hicks JB, Abraham JA, Ivy JM, Nasmyth KA
and McGill C. (1982) Homothallic switching of yeast mating type
cassettes is initiated by a double-stranded cut in the MAT locus.
Cell 31: 183-192.
27.
Abraham J, Feldman J, Nasmyth KA, Strathern JN, Klar AJ, Broach JR
and Hicks JB. (1983) Sites required for position-effect regulation
of mating-type information in yeast. Cold Spring Harbor Symi).
Quant. Biol. 47: 989-998.
28.
Broach JR, Li Y-Y, Feldman J, Jayarain M, Abraham J, Nasmyth KA
and Hicks JB. (1983) Localization and sequence analysis of yeast
origins of DNA replication. Cold Spring Harbor Symp. Ouant. Biol.
47: 1165-1173.
29.
Kassir Y, Hicks JB and Herskowitz 1. (1983) SAD mutation of
Saccharomyces cerevisiae is an extra a cassette. Mol Cell. Biol.
3: 871-880.
30.
Dellaporta SL, Wood J and Hicks JB (1983) Maize DNA miniprep
procedure. Maize Genetic Coop. Newsletter 53: 11-12.
31.
Klar AJ, Strathern JN, Hicks JB and Prudente D. (1983) Efficient
production of a ring derivative of chromosome IR by the
mating-type switching mechanism in Saccharomyces cerevisiae. Mol.
Cell. Biol. 3: 803-810.
32.
Kostriken R, Strathern JN, Klar AJ, Hicks JB and Heffron F. (1983)
A site-specific endonuclease essential for rnating-type switching
in Saccharomyces cerevisiae. Cell 35: 167-174.
33.
Abraham J, Nasmyth KA, Strathern JN, Klar AJ and Hicks JB (1984)
Regulation of mating-type information in yeast: Negative control
requiring sequences both 5'and 3'to the regulated region. J. Mol.
Biol. 176: 307-33 1.
34.
Feldman JB, Hicks JB and Broach JR. (1984) Identification of sites
required for repression of a silent mating type locus in yeast. J.
Mol. Biol. 178: 815-834.
35.
Hicks J, Strathern J, Klar A, Ismail S and Broach J. (1984)
Structure of the SAD mutation and the location of control sites at
silent mating type genes in Saccharomyces cerevisiae. Mol. Cell.
Biol. 4: 1278-1285.
36.
Dellaporta SL, Chomet PS, Mottinger JP, Wood JA, Yu S-M and Hicks
JB. (1984) Endogenous transposable elements associated with virus
infection in maize. Cold Spring Harbor Symp.. Quant. Biol. 49:
321-328.
37.
Dellaporta SL, Wood J and Hicks JB. (1984) A microscale plant DNA
isolation procedure. Plant Molec. Biol. Reporter .1: 2-4.
38.
Ivy JM, Hicks JB and Klar AJ. (1985) Map positions of yeast genes:
SIR1, SIR3, and SIR4. Genet. 111:: 735-744.
39.
Klar AJ, Kakar SN, Ivy JM, Hicks JB, Livi GP and Miglio LM. (1985)
SUM 1, an apparent positive regulator of the cryptic mating-type
loci in Saccharomyces cerevisiae. Genet. 111: 745- 758.
40.
Ivy JM, Klar AJ and Hicks JB. (1986) Cloning and characterization
of four SIR genes of Saccharomyces cerevisiae. Mol. Cell. Biol. 6:
688-702.
41.
Hicks JB. (1987) Mechanisms of differentiation. Nature (London)
326: 444-445.
42.
Soll DR, Langtimm CJ, McDowell J, Hicks J and Galask R. (1987)
High-frequency switching in Candida strains isolated from
vaginitis patients. J. Clin. Microbiol. 25: 1611-1622.
43.
Marshall M, Mahoney D, Rose A, Hicks JB and Broach JR. (1987)
Functional domains of SIR4, a gene required for position effect
regulation Saccharomyces cerevisiae. Mol. Cell. Biol. 7:
4441-4452.
44.
Soll DR, Staebell M, Langtimm C, PfaNer M, Hicks J and Rao TVG.
(1987) Multiple Candida strains in the course of a single systemic
infection. J. Clin. Microbiol. 26: 1448-1459.
45.
Strathern J, Shafer B, Hicks J and McGill C. (1988) A specific
repression by MAT-a2. Genet. 120:75-81.
46.
Soll DR, Galask R, Isley S, Rao TVG, Stone D, Hicks J, Schmid J,
Mac K and Hanna C. (1989) Switching of Candida albicans during
successive episodes of recurrent vaginitis. J. Clin. Microbiol.
27: 681-69,0.
47.
Kwong-Chung KJ, Rigsby WS, Uphoff RA, Hicks JB, Whelan WL, Reiss
E, Magee BB and Wickes BL. (1989) Genetic differences between type
I and type II Candida stellatoidea. Infect. Immun. 57: 527-532.
48.
Livi GP, Hicks JB and Klar AJ., (I 990) The sum I - I mutation
affects silent mating-type gene transcription in Saccharomyces
cerevisiae. Mol. Cell. Biol. 10: 409-412.
49.
Rustchenko-Bulgac EP, Sherman F and Hicks JB. (1990) Chromosomal
rearrangements associated with morphological mutants provide a
means for genetic variation of Candida albicans. J. Bacteriol.
172: 1276-1283.
50.
Kwon-Chung KJ, Hicks JB and Lipke PN. (1990) Evidence that Candida
stellatoidea type H is a mutant of Candida albicans that does not
express sucrose-inhibitable a-glucosidase. Infect. Immun. 58:
2804-2808.
51.
Sadhu C, McEachern MJ, Rustchenko-Bulgac EP, Schmid J, Soll DR and
Hicks JB. (1991) Telomeric and dispersed repeat sequences in
Candida yeasts and their use in strain identification. J.
Bacterol. 173: 842-850.
52.
Stone EM, Swanson MJ, Romeo AM, Hicks JB and Stemglanz R. (1991)
The SIR1 gene of Saccharomyces cerevisiae and its role as an
extragenic suppressor of several mating-defective mutants. Mol.
Cell. Biol. It: 2253-2262.
53.
Bowdish K, Tang Y, Hicks JB and Hilvert D. (1991) Yeast expression
of a catalytic antibody with chorismate mutase activity. J. Biol.
Chem. 266: 11901-11908.
54.
Tang Y, Hicks JB and Hilvert D. (1991) In vivo catalysis of a
metabolically essential reaction by an antibody. Proc. Natl. Acad.
Sci. U.S.A. 88: 8784-8786.
55.
McEachem MJ and Hicks JB. (1991) Dosage of the smallest chromosome
affects both the yeast- hyphal transition and the white-opaque
transition of Candida albicans WO-1. J. Bacterol. 173: 7436-7442.
56.
Sherman F and Hicks JB. (1991) Micromanipulation and dissection of
asci. Meth. In Enzym. 194:21-37.
57.
Sadhu C, Hoekstra D, MeEachem MJ, Reed SI and Hicks JB. (1992) A
G-protein a subunit from asexual Candida albicans functions in the
mating signal transduction pathway of Saccharomyces cerevisiae and
is regulated by the al-a2 repressor. Mol. Cell. Biol. 12:
1977-1985.
58.
Polacheek I, Lebens G and Hicks JB. (1992) Development of DNA
probes for early diagnosis and epidemiological study of
cryptococcosis in AIDS patients. J. Clin. Microbiol. 30: 925-930.
59.
Wickes BL, Hicks JB, Merz WG and Kwong-Chung KJ. (1992) The
molecular analysis of synonymy among medically important yeasts
within the genus Candida. J. Gen. Microbiol. 138: 901-907.
60.
Miyasaki SH, Hicks JB, Greenspan D, Polacheck 1, MacPhail LA,
White TC, Agabian N and Greenspan JS. (1992) The identification
and tracking of Candida albicans isolates from oral lesions in
HIV-seropositive individuals. J. AIDS 5: 1039-1046
61.
McEachern MJ, Sadhu C and Hicks JB. (1993) Unusually large
telomeric repeats in the yeast Candida albicans. Mol. Cell. Biol.
13: 551-560.
62.
Coghlan VM, Perrino BA, Howard M, Langeberg LK, Hicks JB, Gallatin
WM and Scott JD. (1995) Association of protein kinase A and
protein phosphatase 2B with a common anchoring protein. Science
267: 108-1 1 1.
63.
Loughney K, Martins TJ, Harris EAS, Sadhu K, Hicks JB, Sonnenburg
WK, Beavo JA and Ferguson K. (1996) Isolation and characterization
of cDNAs corresponding to two human calcium calmodulin-regulated
3',5'cyclic nucleotide phosphodiesterases. J. Biol. Chem. 12:27(2)
796-806.
64.
Sebat J, Lakshmi B, Troge, J, Hicks J, Ye K, Reiner A, Gilliam TC
Trask B Patterson N, Zetterberg A, Wigler M. (2004) Large-Scale
Copy Number Polymorphism in the Human Genome. Science 267:108-111.
65.
Navin N, Grubor V, Hicks J, Leibu E, Thomas E, Troge J, Riggs M,
Lundin P, Maner S, Sebat J, Zetterberg A. and Wigler, M. (2006)
Prober: Oligonucleotide FISH probe design software.
Bioinformatics, 22: 2437-2438.
66.
Hicks J, Krasnitz A, Lakshmi B, Navin N, Riggs M, Leibu E,
Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye
K, Børresen-Dale A-L, Naume B, Schlicting E, Norton L, Hagerstrom
T, Skoog L, Auer G, Maner S, Lundin P, and Zetterberg A. (2006)
Genome Novel Patterns of Genomic rearrangement and their
association with survival in breast cancer. Genome Research
16:1465–1479.
67.
Pelham RJ, Rodgers L, Hall I, Lucito R, Nquyen KCQ, Navin N, Hicks
J, Mu D, Powers S, Wigler M. and Botstein M. (2006).
Identification of alterations in DNA copy number in host stromal
cells during tumor progression. Proc. Natl. Acad. Sci. USA 103:
19848-19853.
68.
Sebat J, Lakshmi B, Malhotra D, Lese-Martin C, Troge J, Walsh T,
Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R,
Lee Y-H, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimäki T,
Ledbetter D, Gregersen,PK, Bregman J, Sutcliffe JS, Jobanputra V,
Chung W, Warburton D, King M-C, Skuse D, Geschwind DH, Gilliam,
TC, Ye K, Wigler M. (2007) Strong association of de novo copy
number mutation with autism. Science 316: 445-449.
69.
Zender L, Xue W, Zuber J, Semighini CP, Krasnitz A, Ma B, Zender
P, Kubicka S, Luk JM, Schirmacher P, McCombie RW, Wigler M, Hicks
J, Hannon GJ, Powers S, Lowe SW. (2008) An Oncogenomics-Based In
Vivo RNAi Screen Identifies Tumor Suppressors in Liver Cancer Cell
135: 852-864.
70.
Xiang, B, Chatti K, Qiu H, Lakshmi B, Kransnitz A, Hicks J, Yu M,
Miller WT, Muthuswamy SK. (2008) Brk is coamplified with ErbB2 to
promote proliferation in breast cancer. Proc. Natl. Acad. Sci. USA
105: 12463-12468. PMCID: PMC2527934
71.
Kamalakaran S, Kendall J, Zhao X, Tang C, Khan S, Ravi K, Auletta
T, Riggs M, Wang Y, Helland A, Naume B, Dimitrova N, Borresen-Dale
A-L, Hicks J and Lucito, R (2009) Methylation Detection
Oligonucleotide Microarray Analysis: a high-resolution method for
CpG island methylation. Nucleic Acid Research, 37, e89. PMCID:
PMC2709589.
72.
McArthur HL, Tan LK, Patil S, Wigler M, Hudis CA, Hicks J, Norton
L (2009) High resolution representational oligonucleotide
microarray analysis (ROMA) suggests that TOPO2 and HER2
co-amplification is uncommon in human breast cancer. Cancer
Research, 69: 2023
73.
Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ,
Ye K, Bhattacharjee A, Brizuela L, McCombie R, Wigler M, Hannon GJ
and Hicks J. (2009) High definition profiling of mammalian DNA
methylation by array capture and single molecule bisulfite
sequencing. Genome Research, 19: 1593-1605.
74.
Bric A, Miething C, Bialucha CU, Scuoppo C, Zender L, Krasnitz A,
Xuan Z, Zuber J, Wigler M, Hicks J, et al. (2009). Functional
identification of tumor-suppressor genes through an in vivo RNA
interference screen in a mouse lymphoma model. Cancer Cell 16:
324-335.
75.
Navin N, Krasnitz A, Rodgers R, Cook K, Meth J, Kendall J, Riggs
M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S,
Zetterberg A, Hicks J and Wigler, M. (2010) Inferring Tumor
Progression from Genomic Heterogeneity. Genome Research, 20:
68-80.
76.
Floer M, Wang X, Prabhu V, Berrozpe G, Narayan S, Spagna D,
Alvarez D, Kendall J, Krasnitz A, Stepansky A, Hicks J, Bryant GO,
Ptashne M (2010) A RSC/nucleosome complex determines chromatin
architecture and facilitates activator binding. Cell, 141:
407-18.Russnes HG, Moen Vollan HK, Lingjærde OC, Krasnitz A,
Lundin P, Naume B, Sørlie T, Borgen E, Rye IH, Langerød A, Chin
S-F, Teschendorff AE, Stephens PJ, Susanne Månér S, Schlichting E,
Baumbusch LO, Kåresen R, Stratton MP, Wigler M, Caldas C,
Zetterberg A, Hicks J, Børresen-Dale A-L. (2010) Genomic
architecture characterizes tumor progression paths and fate in
breast cancer patients. Science: Translational Medicine, 2:
38ra47. PMID: 20592421.
77.
Kamalakaran, S., Vinay Varadan, V., Giercksky Russnes, H.E., Levy,
D., Kendall, J., Janevski, A., Riggs, M., Banerjee, N.,
Synnestvedt, M., Schlichting, E., Kåresen, R., Prasada, S., Rotti,
H., Ramachandara, R., Laxmi, R., Man-Hung, E.T., Satyamoorthy, K.,
Lucito, R., Wigler, M., Dimitrova, N., Naume, B., Borresen-Dale,
A.-L., Hicks, J.B. (2011) DNA methylation patterns in breast
cancer differ from non-luminal subtypes and can identify relapse
risk independent of other clinical variables. Molecular Oncology,
5: 77-92. PMID: 20434983
78.
Tafe, L.J., Janjigian, Y.Y., Barbashina, V.V., Kelsen, D.P.,
Ilson, D.H., Tang, L.H., Hicks, J.B., Shah, M.A. (2011) Human
epidermal growth factor receptor 2 testing in gastro esophageal
cancer: correlation between immunohistochemistry and fluorescence
in-situ hybridization. Archives of Pathology & Laboratory
Medicine, 135: 1460-1465.
79.
Navin, N., Kendall, J., Troge, J., Andrews, P., Rodgers, L.,
McIndoo, J., Cook, K., Stepansky, A., Levy, D., Esposito, D.,
Muthuswamy, L., Krasnitz, A., McCombie, R., Hicks, J. Wigler, M.
(2011). Tumor evolution inferred by single cell sequencing.
Nature, 472: 90-94. PMID: 21399628
80.
Russnes, HG, Navin, N, Hicks, J, Borressen-Dale, A-L, (2011)
Insight into the heterogeneity of breast cancer through next
generation sequencing. J. Clin. Inv., 121: 3810-3818.
81.
Shakya, R., Reid, L.J., Reczek, C.R., Cole, F., Egli, D., Lin,
C.S., deRooij, D.g., Hirsch, S., Ravi, K., Hicks,J.B., Szablocs,
M., Jasin, M., Baer, R., Ludwig, T. (2011) BRAC1 tumor suppression
depends on BRCT phosphoprotein binding, but not its E3 ligase
activity. Science, 334:525-528.
82.
Png, K.J., Yoshida, M., Zhang, X.H., Shu, W., Lee, H., Rimner, A.,
Chan, T.A., Comen, E., Andrade, V.P., Kim, S.W., King, T.A.,
Hudis, C.A., Norton, L., Hicks, J., Massague, J., Tavazoie S.F.
(2011) MicroRNA-335 inhibits tumor reinitiation and is silenced
through genetic and epigenetic mechanisms in human breast cancer.
Genes Div., 25: 226-231.
83.
Baslan, T., Kendall, J., Rodgers, L., Cox, H., Riggs, R.,
Stepansky, A., Troge, J., Kandasamy, R., Esposito, D., B. Lakshmi,
Wigler, M., Navin, N., and Hicks, J. (2012) Genome wide copy
number analysis of single cells. Nature Protocols, 7: 1024-1041.
84.
Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A.,
Schultz, N., Revill, K., Weissmueller, S., Rappaport, A.R., Simon,
J., Zhang, J., Luo, W., Hicks, J., Zender, L., Wang, X-W., Powers,
S., Wigler, M., Lowe, S.W. (2012) A cluster of cooperating
tumor-suppressor gene candidates in chromosomal deletions. Proc.
Natl. Acad. Sci., USA, 109: 8212-8217. PMCID: 3361457
85.
Mazurek, A., Luo, W., Krasnitz, A., Hicks, J., Scott Powers, R.,
Stillman, B. (2012) DDX5 regulates DNA replication and is required
for cell proliferation in a subset of breast cancer cells. Cancer
Discovery, 2: 812-825.
86.
Tang, M.H., Varadan, V., Kamalakaran, S., Zhang, M.Q., Dimitrova,
N., and Hicks, J. (2012). Major chromosomal breakpoint intervals
in breast cancer co-localize with differentially methylated
regions. Front Oncol 2, 197.
87.
Donnenberg, A.D., Hicks, J.B., Wigler, M., and Donnenberg, V.S.
(2013). The cancer stem cell: Cell type or cell state? Cytometry A
83, 5-7.
88.
Regulski, M., Zhenyuan, L., Kendall, J., Donoghue, M.T.A.,
reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, A.,
McCombie, W.R., Tingey, S., Rafalski, A., Hicks, J., Ware, D.,
Martienssen, R. (2013) The maize methylome influences mRNA splice
sites and reveals widespread paramutation-like switches guided by
small RNA. Genome Research, 23: 1651-1664.
89.
Miething, C., Scuoppo, C., Bosbach, B., Appelmann, I., Nakitandwe,
J., Ma, Wu, G., J., Lintault, L., Auer, M., Premsrirut, P.,
Teruya-Feldstein, J., Hicks, J., Benveniste, H., Speicher, M.,
Downing, J., and Lowe, SW. (2014) PTEN action in leukemia dictated
by the tissue microenvironment. Nature. Jun 19; 520(7505):402-6.
90.
Dago, A.E., Stepansky, A., Carlsson, A., Luttgen, M., Kendall, J.,
Baslan, Kolatkar, A., Wigler, M., Bethel, K., Gross, M.E., Hicks,
J., Kuhn, P. (2014) Rapid Phenotypic and Genomic Change in
Response to Therapeutic Pressure in Prostate Cancer. PLOS One, 9:
e101777. PMCID 4118839.
91.
Pratt ED, Stepansky A, Hicks J, Kirby BJ Single cell copy number
analysis of prostate cancer cells captured with geometrically
enhanced differential immunocapture microdevices (2014) Anal Chem
66(22):11013-7
92.
Ruiz C, Li J, Luttgen MS, Kolatkar A, Kendall JT, Flores E, Topp
Z, Samlowski WE, McClay E, Bethel K, Ferrone S, Hicks J, Kuhn P.
Limited genomic heterogeneity of circulating melanoma cells in
advanced stage patients. Phys Biol 2015;12:016006. PMCID: PMC502
93.
Baslan T, Kendall J, Ward B, Cox H, Leotta A, Rodgers L, Riggs M,
D'Italia S, Sun G, Yong M, Miskimen K, Gilmore H, Saborowski M,
Dimitrova N, Krasnitz A, Harris L, Wigler M, Hicks J.(2015)
Optimizing sparse sequencing of single cells for highly multiplex
copy number profiling. Genome Res. 2015 May;25(5):714-24. doi:
10.1101/gr.188060.114. Epub 2015 Apr 9.
94.
Williamson, S, Metcalf, R, Trapani, F, Sumitra Mohan, Antonell, J,
Abbott, B, Leong, H, Chester C, Simms, N, Palanski R, Nonaka, D,
Priest, L, Fusi,A, Carlsson, F, Carlsson, A, Hendrix M, Seftor R,
Seftor E, Rothwell D, Hughes A, Hicks J, Miller C, Kuhn P, Brady
G, Simpson K, Blackhall F, Dive C. Vascular mimicry in small cell
lung cancer. Nat Commun 2016;7:13322. PMCID: MPC5105195
95.
Martelotto LG, Baslan T, Kendall J, Rodgers , Cox H, Piscuoglio S,
Ng C, da Cruz Paula A, Schizas M, Stepansky A, Norton L, King T,
Weigelt B, Hicks JB, & Reis-Filho JS. Single-cell sequencing from
formalin-fixed paraffin-embedded samples: a powerful tool to
address intra-tumor genetic heterogeneity. Nat Med. 2017
Mar;23(3):376-385. doi: 10.1038/nm.4279. Epub 2017 Feb 6.
96.
Grossman RL, Abel B, Angiuoli S, Barrett JC, Bassett D, Bramlett
K, Blumenthal GM, Carlsson A, Cortese R, DiGiovanna J,
Davis-Dusenbery B, Dittamore R, Eberhard DA, Febbo P, Fitzsimons
M, Flamig Z, Godsey J, Goswami J, Gruen A, Guzman FO, Han J, Hayes
D, Hicks J, Holloway D, Hovelson D, Johnson J, Juhl H, Kalamegham
R, Kamal R, Kang Q, Kelloff GJ, Klozenbuecher M, Kolatkar A, Kuhn
P, Langone K, Leary R, Loverso P, Manmathan H, Martin AM, Martini
J, Miller D, Mitchell M, Morgan T, Mulpuri R, Nguyen T, Otto G,
Pathak A, Peters E, Philip R, Posadas E, Reese D, Reese MG,
Robinson D, Rossi AD, Sakul H, Schageman J, Singh S, Scher HI,
Schmitt K, Silvestro A, Simmons J, Simmons T, Sislow J, Talasaz A,
Tang P, Tewari M, Tomlins S, Toukhy H, Tseng HR, Tuck M, Tzou A,
Vinson J, Wang Y, Wells W, Welsh A, Wilbanks J, Wolf J, Young L,
Lee JS, Leiman LC. Collaborating to Compete: Blood Profiling Atlas
in Cancer (BloodPAC) Consortium. Clin Pharmacol Ther
2017;101:589-592. PMCID: PMC5525192
97.
Berry JL, Xu L, Murphree AL, Krishnan S, Stachelek K, Zolfaqhari
E, Mc Govern K, Lee TC, garlsson A, Kuhn P, Kim JW, Cobrinik D,
Hicks J. Potential of aqueous humor as a surrogate tumor biopsy
for retinoblastoma. JAMA Ophthalmol 2017 135:1221-30. PMCID:
PMC5710399
98.
Carlsson A, Kuhn P, Luttgen MS, Dizon KK, Troncoso P, Corn PG,
Kolatkar A, Hicks, JB, Logothetis C, Zurita AJ. Paired
high-content analysis of prostate cancer cells in bone marrow and
Blood characterizes increased androgen receptor expression in
tumor cell clusters. Clin Cancer Res 2017;23:1722-1732. PMCID:
PMC5661959.
99.
Alexander J, Kendall J, McIndoo J, Rodgers L, Aboukhalil R, Levy
D, Stepansky A, Sun G, Chobardjiev L, Riggs M, Cox H, Hakker I,
Nowak DG, Laze J, Llukani E, Srivastava A, Gruschow S, Yadav SS,
Robinson B, Atwal G, Trotman LC, Lepor H, Hicks J, Wigler M,
Krasnitz A. Utility of Single-Cell Genomics in Diagnostic
Evaluation of Prostate Cancer. Cancer Res. 2018 Jan 15;78:348-358.
PMCID: PMC5771881
100.
Rodriguez-Lee M, Kolatkar A, McCormick M, Dago, AE, Kendall J,
Carlsson NA, Bethel K, Greenspan E, Hwang S, Waitman K, Nieva J,
Hicks J, Kuhn P. Effect of blood collection tube type and time to
processing on the enumeration and high-content characterization of
circulating tumor cells using the high-definition single cell
assay. Arch Pathol Lab Med 2018;142:198-207.
101.
Gerdtsson E, Pore M, Thiele J-A, Sandstrom Gerdtsson A, Malihi PD,
Nevarez R, Kolatkar A, Ruiz Velasco C, Wix S, Singh M, Carlsson A,
Zurita AJ, Logothetis C, Merchant AA, Hicks J, Kuhn P. Multiplex
protein detection on circulating tumor cells from liquid biopsies
using imaging mass cytometry. Converg Sci Phys Oncol
2018;4:015002. PMID: 3128701
102.
Malihi P, Morikado M, Welter L, Liu ST, Miller ET, Cadaneanu RM,
Knudsen BS, Lewis MS, Carlsson A, Ruiz Velasco C, Kolatkar A,
Rodriguez-Lee M, Garraway IP, Hicks J, Kuhn P. Clonal diversity
revealed by morphoproteomic and copy number profiles of single
prostate cancer cells at diagnosis. Converg Sci Phys Oncol
2018;4:015003.
103.
Berry JL, Xu L, Kooi I, Murphree AL, Prabakar RK, Reid MW,
Stachelek K, Le BHA, Welter L, Reiser BJ, Chevez-Barrios P, Jubran
R, Lee TC, Kim JW, Kuhn P, Cobrinik D, Hicks J. Genomic cfDNA
Analysis of Aqueous Humor in Retinoblastoma Predicts Eye Salvage:
The Surrogate Tumor Biopsy for Retinoblastoma. Mol Cancer Res.
2018 Jul 30. pii: molcanres.0369.2018. doi:
10.1158/1541-7786.MCR-18-0369. [Epub ahead of print] PMID:
30061114
104.
Ho YJ, Anaparthy N, Molik D, Mathew G, Aicher T, Patel A, Hicks J,
Hammell MG. Single-cell RNA-seq analysis identifies markers of
resistance to targeted BRAF inhibitors in melanoma cell
populations. Genome Res. 2018 Jul 30. doi: 10.1101/gr.234062.117.
[Epub ahead of print] PMID: 30061114
105.
Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff
D, Hicks J, Loe J, Ratan A, McConnell MJ. Improved molecular
karyotyping in glioblastoma. Mutat.Res. 2018 Jul 8;811:16-26. doi:
10.1016/j.mrfmmm.2018.06.002. [Epub ahead of print] PMID: 30055482
106.
Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder
P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin CS, Beck
T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J,
McCombie WR, Schatz MC. Complex rearrangements and oncogene
amplifications revealed by long-read DNA and RNA sequencing of a
breast cancer cell line. Genome Res. 2018 Aug;28(8):1126-1135.
doi: 10.1101/gr.231100.117. Epub 2018 Jun 28. PMID: 29954844
107.
Prabakar RK, Xu L, Hicks J, Smith AD. SMURF-seq: efficient copy
number profiling on long-read sequencers. Genome Biol. 2019 Jul
8:20(1):134. doi: 10.1186/s13059-019-1732-1. PMID: 3128701
108.
Klotz, R, Thomas A, Teng T, Han SM, Iriondo O, Li L,
Restrepo-Vassalli S, Wang A, Izadian N, MacKay M, Moon BS, Liu KJ,
Ganesan SK, Lee G, Kang DS, Walmsley CS, Pinto CJ, Press MF, Lu W,
Lu J, Juric D, Bardia A, Hicks J, Salhia B, Attenello FJ, Smith
AD, Yu M. Circulating tumor cells exhibit metastatic tropism and
reveal brain metastasis drivers. Cancer Discov. 2019 Oct 10. pii:
CD-19-0384. doi: 10.1158/2159-8290.CD-19-0384. PMID:31601552
109.
Shishido SN, Carlsson A, Nieva J, Bethel K, Hicks JB, Bazhenova L,
Kuhn P. Circulating tumor cells as a response monitor in stage IV
non-small cell lung cancer. J Transl Med. 2019 Aug 28;17(1):294.
doi: 10.1186/s12967-019-2035-8. PMID: 31462312
110.
Shishido SN, Welter L, Rodriguez-Lee M, Kolatkar A, Xu L,
Gerdtsson AS, Restrepo-Vassalli S,
Carlsson A, Larsen J, Greenspan EJ, Hwang SE, Waitman KR, Nieva J,
Bethel K, Hicks J, and Kuhn P. Pre-analytical variables for the
genomic assessment of the cellular and acellular fractions of the
liquid biopsy in a cohort of breast cancer patients. Journal of
Molecular Diagnostics. 2019 (In Press).
111.
Welter L, Xu L, McKinley D, Dago AE, Restrepo-Vassalli S,
Rodriguez-Lee M, Kolatkar A, Ruiz-Velasco C, Nieva J, Kuhn P,
Hicks J. Liquid biopsy traces tumor evolution and treatment
resistance in a metastatic breast cancer patient. Submitted to
Cancer Discovery.
REVIEW ARTICLES:
1.
Hicks JB, Hinnen A and Fink GR. (1979) Properties of yeast
transformation. Cold Spring Harbor Symp. Ouant. Biol. 43:
1305-1313.
2.
Hicks JB, Strathern JN, Klar AJ and Dellaporta S. (1982) Cloning
by complementation in yeast: The mating type genes. In, Genetic
Engineering, Vol. IV., J. Setlow and A. Hollander, Eds., Plenum
Publishing Corp., NY, Pp. 219-248.
3.
Klar AJ, Strathern JN and Hicks JB. (1984) Developmental pathways
in yeast. in, Microbial Development. R. Losick and L. Shapiro,
Eds., Cold Spring Harbor Laboratory, NY, pp. 151-195.
4.
Hicks JB, Ivy JM, Strathern JN and Klar AJ. (1985) Sex in budding
yeast: How and why. In, The Origin and Evolution of Sex, H.O.
Halvorson and A. Monroy, Eds., A.R. Liss, Inc., NY, pp. 97-111.
5.
Navin, N., Hicks, J. (2010) Tracing the Tumor Lineage. Molecular
Oncology, 4: 267-283.
6.
Navin, N., Hicks, J. (2011) Future medical applications of
single-cell sequencing in cancer. Genome Med. 5: 31.
7.
Cowell, C.F., Weigelt, B., Sakr, R.A., Ng, C.K., Hicks, J., King,
T.a., Reis-Filho, J.S. (2013) progression from ductal carcinoma in
situ to invasive breast cancer: Revisited. Mol Oncol., 13:
S1574-7891
8.
Crockford, A., Jamal-Hanjani, M., Hicks, J., Swanton, C. (2014)
Implications of intratumour heterogeneity for treatment
stratification. Journal of Pathology 232: 264-273.
9.
Grosseman, RL, Abel, B, et al. Collaborating to Compete: Blood
Profiling Atlas in
Cancer (BloodPAC) Consortium. Clin Pharmacol Ther. 2017
May;101(5):589-592.
doi: 10.1002/cpt.666. Epub 2017 Apr 12. Review
10.
Baslan, T. and Hicks, J. (2014) Single cell sequencing approaches
for complex biological systems. Current Opinions in Genetics and
Development. Jul 10; 26C: 59-65
11.
Thiele JA, Pitule P, Hicks J, Kuhn P. (2019) Single-Cell Analysis
of Circulating Tumor Cells. Methods Mol Biol. 2019;1908:243-264.
doi: 10.1007/978-1-4939-9004-7_17. PMID: 3064973
12.
Anaparthy N, Ho YJ, Martelotto L, Hammell M, Hicks J. (2019)
Single Cell Applications of Next Generation Sequencing. Cold
Spring Harb Perspect Med. Jan 7 pii: a026898. doi:
10.1101/cshperspect.a026898 PMID: 30617056
BOOK REVIEWS:
The Man Who Protested Too Much. (1985) Science 85: October.
BOOKS:
Yeast Cell Biology, J. Hicks, Ed., John Wiley & Sons, NY, 1986.
Methods in Yeast Genetics: A Laboratory Course Manual, F. Sherman,
G.R. Fink and J.B. Hicks, Cold Spring Harbor Laboratory, NY, 1987.
RECENT INVITED TALKS and ABSTRACTS
James Hicks. AACR Annual Meeting, Atlanta World Congress Center,
Atlanta, Georgia. Meet-the-Expert Sessions: Deconvoluting Tumor
Heterogeneity Using Single-Cell Genomics. April 3, 2019.
Lisa Welter, James Hicks et al. Investigating the multimodal
relationship between cell-free DNA and circulating tumor cells in
metastatic breast cancer patients. Podium Presentation: Gordon
Conference on Liquid biopsy for Cancer August 7, 2018
PATENTS ISSUED:
USPTO 8,652,777
“METHOD for the anlysis of ovarian cancer disorders”.
With Robert Lucito, et al
Awarded: Feb 18, 2014.
Assignee: Cold Spring Harbor Laboratory
USPTO 9,404,156
“VARIETAL COUNTING OF NUCLEIC ACIDS FOR OBTAINING GENOMIC COPY NUMBER
INFORMATION” with M. Wigler, et al
Provisional Application Filing Date: October 22, 2010
Assignee: Cold Spring Harbor Laboratory
PATENTS APPLIED FOR:
"METHODS FOR ASSESSING PROBABILISTIC MEASURES OF CLINICAL OUTCOME
USING GENOMIC PROFILING" with M. Wigler and A. Krasnitz.
Applied: Dec14, 2006
Assignee: Cold Spring Harbor Laboratory, NY
“USE OF ROMA FOR CHARACTERIZING GENOMIC REARRANGEMENTS”
With M. Wigler
Applied: December 14, 2006
Assignee: Cold Spring Harbor Laboratory, NY
"METHODS AND ARRAYS FOR PROFILING DNA METHYLATION" with G. Hannon, J.
Kendall and A. Smith
Filed: January 23, 2009
Assignee: Cold Spring Harbor Laboratory, NY
“GENETIC MARKERS INDICATIVE OF A CANCER PATIENT RESPONSE TO
TRASTUZUMAB (HERCEPTIN)” with M. Wigler
Filing date: December 10, 2010
Assignee: Cold Spring Harbor Laboratory
“GENOTYPIC AND PHENOTYPIC ANALYSIS OF CIRCULATING TUMOR CELLS TO
MONITOR TUMOR EVOLUTION IN PROSTATE CANCER PATIENTS” with P. Kuhn,
A.E. Dago Rodriguez, Carlsson A. and Liu W.
Filed: September 30, 2014
Assignee: The Scripps Research Institute, La Jolla, CA; Cold Spring
Harbor Laboratory, Cold Spring Harbor, NY.
14