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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Small-Molecule Procaspase-3 Activation Sensitizes Cancer to Treatment with Diverse Chemotherapeutics
Botham, R. C.; Roth, H. S.; Book, A. P.; Roady, P. J.; Fan, T. M.; Hergenrother, P. J.
ACS Central Science 2016, 2, 545-559.

A Small Molecule that Induces Intrinsic Pathway Apoptosis with Unparalleled Speed
Palchaudhuri, R.; Lambrecht, M. J.; Botham, R. C.; Partlow, K. C.; Van Ham, T. J.; Putt, K. S.; Nguyen, L. T.; Kim, S.-H.; Peterson, R. T.; Fan, T. M.; Hergenrother, P. J.
Cell Reports 201513, 2027-2036.

Deoxynyboquinones as NQO1-Activated Cancer Therapeutics
Parkinson, E. I.; Hergenrother, P. J.
Acc. Chem. Res. 201548, 2715-2733.

Removal of Metabolic Liabilities Enables Development of Derivatives of Procaspase-Activating Compound 1 (PAC-1) with Improved Pharmacokinetics
Roth, H. S.; Botham, R. C.; Schmid, S. C.; Fan, T. M.; Dirikolu, L.; Hergenrother, P. J.  
J. Med. Chem. 201558, 4046-4065.

Putting Non-coding RNA on Display with CRISPR. 
Perez-Pinera P, Jones MF, Lal A, Lu TK.
Mol Cell. 2015 Jul 16;59(2):146-8.

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.
Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, Safi A, Crawford GE, Reddy TE, Gersbach CA.
Genome Res. 2015 May 29.

Correction of dystrophin expression in cells from duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases.
Ousterout DG, Kabadi AM, Thakore PI, Perez-Pinera P, Brown MT, Majoros WH, Reddy TE, Gersbach CA.
Mol Ther. 2015 Mar;23(3):523-32.

DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors.
T. Mazor1, A. Pankov1, B.E. Johnson, C. Hong, E.G. Hamilton, R.J.A. Bell, I.V. Smirnov, G.F. Reis, J.J. Phillips, M.J. Barnes, A. Idbaih, A. Alentorn, J.J. Kloezeman, M.L.M. Lamfers, A.W. Bollen, B.S. Taylor, A.M. Molinaro, A.B. Olshen, S.M. Chang, J.S. Song,2,* and J.F. Costello2,*. (1co-first authors, 2co-senior authors, *co-corresponding authors).
Cancer Cell, 28(3), 307-317, 2015.

KnowEnG: A knowledge engine for genomics.
S. Sinha, J.S. Song, R. Weinshilboum, V. Jongeneel, J. Han.
 J Am Med Inform Assoc, 2015.

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer
R.J.A. Bell, H.T. Rube, A. Kreig, A. Mancini, S.D. Fouse, R.P. Nagarajan, S. Choi, C. Hong, D. He, M. Pekmezci, J.K. Wiencke, M.R. Wrensch, S.M. Chang, K.M. Walsh, S. Myong, J.S. Song*,# and J.F. Costello*,#. (*co-corresponding authors, #equal contribution). 
Science, 348, 1036-1039, 2015.

TCGA analysis predicts microRNA for targeting cancer growth and vascularization in glioblastoma
H.A. Wong, R.E. Fatimy, C. Onodera, Z. Wei, M. Yi, A. Mohan, S. Gowrisankaran, P. Karmali, E. Marcusson, H. Wakimoto, R. Stephens, E.J. Uhlmann, J.S. Song, B. Tannous and A.M. Krichevsky.
Molecular Therapy, 23(7), 1234-47, 2015.

Transcription factor Tfe3 directly regulates Pgc-1alpha in muscle,
N. Salma, J.S. Song, Z. Arany, D.E. Fisher.
J. Cell. Physiology, 230(10), 2330-6, 2015.

The genetics of splicing in neuroblastoma. Cancer Discovery
Chen J, Hackett CS, Zhang S, Song YK, Bell RJA, Molinaro AM, Quigley DA, Balmain A, Song JS, Costello JF, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA. 
5(4), 380-95, 2015.

HiTSelect: A Comprehensive Tool for High-Complexity Pooled Screen Analysis
A. Diaz1, H. Qin1, M. Ramalho-Santos*, J.S. Song* (1co-first authors, *co-corresponding authors).
Nucleic Acids Research, 43(3):e16, 2015.

Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast
M. Guzman-Ayala, M. Sachs, F.M. Koh, C. Onodera, A. Bulut-Karslioglu, C.J. Lin, P. Wong, R. Nitta, J.S. Song, and M. Ramalho-Santos.
Development, 142(1), 118-27, 2015.

COG Osteosarcoma Biology Group. A summary of the osteosarcoma banking efforts: a report from the Children's Oncology Group and the QuadW Foundation.
Glover J, Krailo M, Tello T, Marina N, Janeway K, Barkauskas D, Fan TM, Gorlick R, Khanna C
Pediatr Blood Cancer. 2015 Mar;62(3):450-5.

The immunotherapy of canine osteosarcoma: a historical and systematic review.
Wycislo KL, Fan TM.
J Vet Intern Med. 2015 May-Jun;29(3):759-69.

Targeting tumor vasculature with aptamer-functionalized doxorubicin-polylactide nanoconjugates for enhanced cancer therapy.
Tang L, Tong R, Coyle VJ, Yin Q, Pondenis H, Borst LB, Cheng J, Fan TM.
ACS Nano. 2015 May 26;9(5):5072-81.

The Association of Endothelin-1 Signaling with Bone Alkaline Phosphatase Expression and Protumorigenic Activities in Canine Osteosarcoma.
Neumann ZL, Pondenis HC, Masyr A, Byrum ML, Wycislo KL, Fan TM.
J Vet Intern Med. 2015 Nov;29(6):1584-94.

Comparative Aspects of Osteosarcoma Pathogenesis in Humans and Dogs.
Fan TM, Khanna C.
Vet. Sci. 2015; 2(3):210-230.

Targeted Gene Activation Using RNA-Guided Nucleases.
Brown A, Woods WS, Perez-Pinera P.
Methods Mol Biol. In Press.

Engineering Synthetic Circuits in Living Cells with CRISPR-Cas9 Technology. 
Jusiak B, Cleto S, Perez-Pinera P, Timothy K. Lu.
Trends Biotechnol. In Press.

Dual Small-Molecule Targeting of Procaspase-3 Dramatically Enhances Zymogen Activation and Anticancer Activity.
Botham, R. C.; Fan, T. M.; Im, I.; Borst, L. B.; Dirikolu, L.; Hergenrother, P. J.  
J. Am. Chem. Soc. 2014136, 1312-1319.

Activating human genes with zinc finger proteins, transcription activator-like effectors and CRISPR/Cas9 for gene therapy and regenerative medicine.
Gersbach CA, Perez-Pinera P.
Expert Opin Ther Targets. 2014 Aug;18(8):835-9.

Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells.
Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK.
Mol Cell. 2014 May 22;54(4):698-710.

Scaffold-mediated lentiviral transduction for functional tissue engineering of cartilage.
Brunger JM, Huynh NP, Guenther CM, Perez-Pinera P, Moutos FT, Sanchez-Adams J, Gersbach CA, Guilak F.
Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):E798-806.

Systematic Identification of Barriers to Human iPSC Generation
H. Qin1, A. Diaz1, L. Blouin, R.J. Lebbink, W. Patena, P. Tanbun, E.M. LeProust, M.T. McManus2, J.S. Song2,*, M. Ramalho-Santos2,* (1co-first authors, 2co-senior authors, *co-corresponding authors).
Cell, 158(2), 449-461, 2014.

Recurrent epimutations activate gene body promoters in primary glioblastoma
R.P. Nagarajan , B. Zhang, R.J. Bell, B.E. Johnson, A.B. Olshen, V. Sundaram, D. Li, A.E. Graham, A. Diaz, S.D Fouse, I. Smirnov, J. Song, P.L. Paris, T. Wang, J.F. Costello
Genome Research, 24(5), 761-74, 2014.

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma
B.E. Johnson, T. Mazor, et al.
Science, 343(6167), 189-93, 2014.

Quantifying the Role of Steric Constraints in Nucleosome Positioning
T. Rube and J.S. Song
Nucleic Acids Research, 42(4), 2147-58, 2014.

Pro-tumorigenic effects of transforming growth factor beta 1 in canine osteosarcoma.
Portela RF, Fadl-Alla BA, Pondenis HC, Byrum ML, Garrett LD, Wycislo KL, Borst LB, Fan TM. 
J Vet Intern Med. 2014 May-Jun;28(3):894-904.

Toward a drug development path that targets metastatic progression in osteosarcoma.
Khanna C, Fan TM, Gorlick R, Helman LJ, Kleinerman ES, Adamson PC, Houghton PJ, Tap WD, Welch DR, Steeg PS, Merlino G, Sorensen PH, Meltzer P, Kirsch DG, Janeway KA, Weigel B, Randall L, Withrow SJ, Paoloni M, Kaplan R, Teicher BA, Seibel NL, Smith M, Uren A, Patel SR, Trent J, Savage SA, Mirabello L, Reinke D, Barkaukas DA, Krailo M, Bernstein M.
Clin Cancer Res. 2014 Aug 15;20(16):4200-9.

Efficient NQO1 Substrates are Potent and Selective Anticancer Agents
Parkinson, E. I.; Bair, J. S.; Cismesia, M.; Hergenrother, P. J. 
ACS Chem. Biol. 20138, 2173-2183.

RNA-Guided Human Gene Activation by CRISPR/Cas9-Based Engineered Transcription Factors. 
Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW, Guilak F, Crawford GE, Reddy TE, and Gersbach CA.
Nat Methods. 2013 Oct;10(10):973-6.

Template-Free Reading Frame Restoration by Genome Editing with TALE Nucleases.
Ousterout DG, Perez-Pinera P, Thakore PI, Kabadi AM, Brown MT, Qin X, Fedrigo O, Mouly V, Tremblay JP, Gersbach CA.
Mol. Therapy. 2013 Sep;21(9):1718-26.

Synergistic and Tunable Gene Activation in Human Cells by Combinations of Synthetic Transcription Factors.
Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, and Gersbach CA.
Nat Methods. 2013 Mar;10(3):239-42.

Somatic cells regulate maternal mRNA translation and development competence of mouse oocytes
J. Chen, S. Torcia, F. Xie, C-J Lin, H. Cakmak, F. Franciosi, K. Horner, C. Onodera, J.S. Song, M.I. Cedars, M. Ramalho-Santos, and M. Conti.
Nature Cell Biology, 15(12), 1415-23, 2013.

Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline in vivo
M. Sachs, C. Onodera, K. Blaschke, K.T. Ebata, J.S. Song, M. Ramalho-Santos.
Cell Reports, 3(6), 1777-84, 2013.

Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo
A.D. Ramos, A. Diaz, A. Nellore, R.N. Delgado, K.-Y. Park, G. Gonzales-Roybal, M.C. Oldham, J.S. Song, D.A. Lim.
Cell Stem Cell 12, 616-628, 2013.

Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF
R. Haq, J. Shoag, P. Andreu-Perez, S. Yokoyama, A. Edelman, A.D. Hunley, A. Nellore, J. Wargo, J.S. Song, D.E. Fisher, Z. Arany, H. Widlund.
Cancer Cell, 23 (3), 302-315, 2013.

BCL2A1 is a lineage-specific anti-apoptotic melanoma oncogene that confers resistance to BRAF inhibition
R. Haq, S. Yokoyama, K. McHenry, J. Li, D. Porter, L. Duncan, J.S. Song*, D.E. Fisher* (*co-corresponding authors).
PNAS, 110(11), 4321-4326, 2013.

NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data
A. Nellore, K. Bobkov, E. Howe, A. Pankov, A. Diaz, J.S. Song.
Frontiers in Genetics, 3:320 2013.

Categorical spectral analysis of periodicity in human and viral genomes
E. Howe and J.S. Song.
Nucleic Acids Research, 41(3), 1395-1405, 2013.

Feasibility and dose discovery analysis of zoledronic acid with concurrent chemotherapy in the treatment of newly diagnosed metastatic osteosarcoma: a report from the Children's Oncology Group.
Goldsby RE, Fan TM, Villaluna D, Wagner LM, Isakoff MS, Meyer J, Randall RL, Lee S, Kim G, Bernstein M, Gorlick R, Krailo M, Marina N. 
Eur J Cancer. 2013 Jul;49(10):2384-91.

An NQO1 Substrate with Potent Anti-Tumor Activity that Selectively Kills by PARP-1-Induced Programmed Necrosis
Huang, X.; Dong, Y.; Bey, E. A.; Kilgore, J. A.; Bair, J. S.; Li, L.-S.; Patel, M.; Parkinson, E. I.; Wang, Y.; Williams, N. S.; Gao, J.; Hergenrother, P. J.; Boothman, D. A. 
Cancer Res. 201272, 3038-3047.

Differential effects of procaspase-3 activating compounds in the induction of cancer cell death
West, D. C.; Qin, Y.; Peterson, Q. P.; Thomas, D. L.; Palchaudhuri, R. P.; Morrison, K. C.; Lucas, P. W.; Palmer, A. E.; Fan, T. M; Hergenrother, P. J.
Mol. Pharmaceutics 20129, 1425-1434.

Advances in targeted genome editing.
Perez-Pinera P, Ousterout DG, Gersbach CA.
Curr Opin Chem Biol. 2012 Aug;16(3-4):268-77.

Gene Targeting to the ROSA26 Locus Directed By Engineered Zinc Finger Nucleases.
Perez-Pinera P, Ousterout D, Brown M, Gersbach C.
Nucleic Acid Res. 2012 Apr;40(8):3741-52.

CHANCE - CHip-seq ANalytics and Confidence Estimation: comprehensive software for quality control and validation of ChIP-seq data
A. Diaz, A. Nellore, J.S. Song.
Genome Biology 13:R98, 2012.

Sox1 marks an activated neural stem/progenitor cell in the hippocampus
M. Venere, Y.-G. Han, R. Bell, J.S. Song, A. Alvarez-Buylla, R. Blelloch,
Development 139, 3938-3949 2012.

YY1 regulates melanocyte development and function by co-operating with MITF
J. Li#, J.S. Song#,*, R.J.A. Bell, T-N T. Tran, R. Haq, H. Liu, K.T. Love, R. Langer, D.G. Anderson, L. Larue, D.E. Fisher* (#co-first authors, *co-corresponding authors).
PLoS Genetics 8(5): e1002688, 2012.

Polycomb-like 3 promotes Polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal
J. Hunkapiller, Y. Shen, A. Diaz, G. Cagney, D. McCleary, M. Ramalho-Santos, N. Krogan, B. Ren, J.S. Song*, and J.F. Reiter* (*co-corresponding authors).
PLoS Genetics 8(3): e1002576, 2012.

Normalization, bias correction, and peak calling for ChIP-seq
Aaron Diaz, Kiyoub Park, Daniel A. Lim, and Jun S. Song.
Statistical Applications in Genetics and Molecular Biology, Vol 11: Iss. 3, Article 9, 2012.

Pharmacokinetics and Derivation of an Anticancer Dosing Regimen for PAC-1, a Preferential Small Molecule Activator of Procaspase-3, in Healthy Dogs
Lucas, P. W.; Schmit, J. M.; Peterson, Q. P.; West, D. C.; Hsu, D. C.; Novotny, C. J.; Dirikoul, L.; Deorge, D. R.; Garrett, L. D.; Hergenrother, P. J.; Fan, T. M. 
Invest. New Drugs 201129, 901-911. 

Discovery and Canine Preclinical Assessment of a Nontoxic Procaspase-3-Activating Compound
Peterson, Q. P.; Hsu, D. C.; Novotny, C. J.; West, D. C.; Kim, D.; Schmit, J. M.; Dirikolu, L.; Hergenrother, P. J.; Fan, T. M.  
Cancer Res. 201070, 7232-7241.

Chemistry and Biology of Deoxynyboquinone, a Potent Inducer of Cancer Cell Death
Bair, J. S.; Palchaudhuri, R.; Hergenrother, P. J. 
J. Am. Chem. Soc. 2010132, 5469-5478.

Rapamycin Pharmacokinetic and Pharmacodynamic Relationships in Osteosarcoma: A Comparative Oncology Study in Dogs.
Paoloni M, Mazcko C, Fox E, Fan TM, Lana S, Kisseberth W, Vail D, Nuckolls K, Osborne T, Yalkowsy S, Gustafson D, Yu Y, Cao L, Khanna C.
PLoS One. 2010 Jun 8;5(6):e11013.

Animal models of osteosarcoma.
Fan TM.
Expert Reviews of Anticancer Therapy. September 2010, Vol. 10, No. 8, 1327-1338.