Skip to main content

Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Cao, J., Perez-Pinera, P., Lowenhaupt, K., Wu, M. R., Purcell, O., De La Fuente-Nunez, C., & Lu, T. K. (2018). Versatile and on-demand biologics co-production in yeast. Nature Communications, 9(1), [77]. DOI: 10.1038/s41467-017-02587-w

Phillips, H., Maxwell, E. A., Schaeffer, D. J., & Fan, T. M. (2018). Simulation of spatial diffusion of platinum from carboplatin-impregnated calcium sulfate hemihydrate beads by use of an agarose gelatin tissue phantom. American journal of veterinary research, 79(6), 592-599. DOI: 10.2460/ajvr.79.6.592

McLean, M. A., Gregory, M. C., & Sligar, S. G. (2018). Nanodiscs: A Controlled Bilayer Surface for the Study of Membrane Proteins. Annual Review of Biophysics, 47, 107-124. DOI: 10.1146/annurev-biophys-070816-033620

Yin, Q., Tang, L., Cai, K., Yang, X., Yin, L., Zhang, Y., ... Cheng, J. (2018). Albumin as a "trojan Horse" for polymeric nanoconjugate transendothelial transport across tumor vasculatures for improved cancer targeting. Biomaterials Science, 6(5), 1189-1200. DOI: 10.1039/c8bm00149a

Mak, P. J., Duggal, R., Denisov, I. G., Gregory, M. C., Sligar, S. G., & Kincaid, J. R. (Accepted/In press). Human cytochrome CYP17A1. the structural basis for compromised lyase activity with 17-hydroxyprogesterone. Journal of the American Chemical Society. DOI: 10.1021/jacs.8b03901

Zhang, Y., Manjunath, M., Zhang, S., Chasman, D., Roy, S., & Song, J. S. (2018). Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer–associated genetic variant rs4415084. Cancer Research, 78(7), 1579-1591. DOI: 10.1158/0008-5472.CAN-17-3486

Saba, C. F., Vickery, K. R., Clifford, C. A., Burgess, K. E., Phillips, B., Vail, D. M., ... Thamm, D. H. (2018). Rabacfosadine for relapsed canine B-cell lymphoma: Efficacy and adverse event profiles of 2 different doses. Veterinary and Comparative Oncology, 16(1), E76-E82. DOI: 10.1111/vco.12337

Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., ... Wysocki, V. H. (2018). How many human proteoforms are there? Nature chemical biology, 14(3), 206-214. DOI: 10.1038/nchembio.2576

Denisov, I. G., Baylon, J. L., Grinkova, Y. V., Tajkhorshid, E., & Sligar, S. G. (2018). Drug-Drug Interactions between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4. Biochemistry, 57(5), 805-816. DOI: 10.1021/acs.biochem.7b01012

Gregory, M. C., Mak, P. J., Khatri, Y., Kincaid, J. R., & Sligar, S. G. (2018). Human P450 CYP17A1: Control of Substrate Preference by Asparagine 202. Biochemistry, 57(5), 764-771. DOI: 10.1021/acs.biochem.7b01067

Harris, D. T., Hager, M. V., Smith, S. N., Cai, Q., Stone, J. D., Kruger, P., ... Kranz, D. M. (2018). Comparison of t cell activities mediated by human TCRs and CARs that use the same recognition domains. Journal of Immunology, 200(3), 1088-1100. DOI: 10.4049/jimmunol.1700236

Maxwell, E. A., Phillips, H., Schaeffer, D. J., & Fan, T. M. (2018). In vitro chemosensitivity of feline injection site-associated sarcoma cell lines to carboplatin. Veterinary Surgery, 47(2), 219-226. DOI: 10.1111/vsu.12709

Peh, J., Boudreau, M. W., Smith, H. M., & Hergenrother, P. J. (Accepted/In press). Overcoming Resistance to Targeted Anticancer Therapies through Small-Molecule-Mediated MEK Degradation. Cell Chemical Biology. DOI: 10.1016/j.chembiol.2018.05.008

Hejna, M., Jorapur, A., Zhang, Y., Song, J. S., & Judson, R. L. (2018). Quantification of mammalian tumor cell state plasticity with digital holographic cytometry. In Quantitative Phase Imaging IV (Vol. 10503). [1050312] SPIE. DOI: 10.1117/12.2290462

Sharma, P., & Kranz, D. M. (2018). Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity. Journal of Biological Chemistry, 293(5), 1820-1834. DOI: 10.1074/jbc.M117.814152

Gapinske, M., Tague, N., Winter, J., Underhill, G. H., & Perez-Pinera, P. (2018). Targeted gene knock out using nuclease-assisted vector integration: Hemi- and Homozygous deletion of JAG1. In Methods in Molecular Biology (pp. 233-248). (Methods in Molecular Biology; Vol. 1772). Humana Press Inc.. DOI: 10.1007/978-1-4939-7795-6_13

Zheng, X., Andruska, N., Lambrecht, M. J., He, S., Parissenti, A., Hergenrother, P. J., ... Shapiro, D. J. (2018). Targeting multidrug-resistant ovarian cancer through estrogen receptor a dependent ATP depletion caused by hyperactivation of the unfolded protein response. Oncotarget, 9(19), 14741-14753. DOI: 10.18632/oncotarget.10819

Purcell, O., Opdensteinen, P., Chen, W., Lowenhaupt, K., Brown, A., Hermann, M., ... Lu, T. K. (2017). Production of Functional Anti-Ebola Antibodies in Pichia pastoris. ACS Synthetic Biology, 6(12), 2183-2190. DOI: 10.1021/acssynbio.7b00234

Hejna, M., Jorapur, A., Song, J. S., & Judson, R. L. (2017). High accuracy label-free classification of single-cell kinetic states from holographic cytometry of human melanoma cells. Scientific Reports, 7(1), [11943]. DOI: 10.1038/s41598-017-12165-1

Doǧanay, S., Lee, M. Y., Baum, A., Peh, J., Hwang, S. Y., Yoo, J. Y., ... Ha, T. (2017). Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic: IFNB1 expression. Integrative Biology (United Kingdom), 9(11), 857-867. DOI: 10.1039/c7ib00146k

Guo, Z., Sevrioukova, I. F., Denisov, I. G., Zhang, X., Chiu, T. L., Thomas, D. G., ... Potter, D. A. (2017). Heme Binding Biguanides Target Cytochrome P450-Dependent Cancer Cell Mitochondria. Cell Chemical Biology, 24(10), 1259-1275.e6. DOI: 10.1016/j.chembiol.2017.08.009

Kim, M., Kim, Y., Qian, L., & Song, J. S. (2017). TeachEnG: A Teach ing en gine for G enomics. Bioinformatics, 33(20), 3296-3298. DOI: 10.1093/bioinformatics/btx447

Roy, J., Wycislo, K. L., Pondenis, H., Fan, T. M., & Das, A. (2017). Comparative proteomic investigation of metastatic and non-metastatic osteosarcoma cells of human and canine origin. PloS one, 12(9), [e0183930]. DOI: 10.1371/journal.pone.0183930

Ye, J., Jin, H., Pankov, A., Song, J. S., & Blelloch, R. (2017). NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation. RNA, 23(8), 1270-1284. DOI: 10.1261/rna.061499.117

Salma, N., Song, J. S., Kawakami, A., Devi, S. P., Khaled, M., Cacicedo, J. M., & Fisher, D. E. (2017). Tfe3 and Tfeb transcriptionally regulate peroxisome proliferator-activated receptor γ2 expression in adipocytes and mediate adiponectin and glucose levels in mice. Molecular and Cellular Biology, 37(15), [e00608-16]. DOI: 10.1128/MCB.00608-16

Granchi, C., Fortunato, S., Meini, S., Rizzolio, F., Caligiuri, I., Tuccinardi, T., ... Minutolo, F. (2017). Characterization of the Saffron Derivative Crocetin as an Inhibitor of Human Lactate Dehydrogenase 5 in the Antiglycolytic Approach against Cancer. Journal of Agricultural and Food Chemistry, 65(28), 5639-5649. DOI: 10.1021/acs.jafc.7b01668

Raman, R., Grant, L., Seo, Y., Cvetkovic, C., Gapinske, M., Palasz, A., ... Bashir, R. (2017). Damage, Healing, and Remodeling in Optogenetic Skeletal Muscle Bioactuators. Advanced Healthcare Materials, 6(12), [1700030]. DOI: 10.1002/adhm.201700030

Black, J. B., Perez-Pinera, P., & Gersbach, C. A. (2017). Mammalian Synthetic Biology: Engineering Biological Systems. Annual Review of Biomedical Engineering, 19, 249-277. DOI: 10.1146/annurev-bioeng-071516-044649

Chaudhary, R., Gryder, B., Woods, W. S., Subramanian, M., Jones, M. F., Li, X. L., ... Lal, A. (2017). Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3. eLife, 6, [e23244]. DOI: 10.7554/eLife.23244

Gregory, M. C., McLean, M. A., & Sligar, S. G. (2017). Interaction of KRas4b with anionic membranes: A special role for PIP2. Biochemical and Biophysical Research Communications, 487(2), 351-355. DOI: 10.1016/j.bbrc.2017.04.063

Zhang, D., Lee, J., Sun, M. B., Pei, Y., Chu, J., Gillette, M. U., ... Kilian, K. A. (2017). Combinatorial Discovery of Defined Substrates That Promote a Stem Cell State in Malignant Melanoma. ACS Central Science, 3(5), 381-393. DOI: 10.1021/acscentsci.6b00329

Tasker, S. Z., & Hergenrother, P. J. (2017). Natural products: Taming reactive benzynes. Nature Chemistry, 9(6), 504-506. DOI: 10.1038/nchem.2786

Lee, H. Y., Parkinson, E. I., Granchi, C., Paterni, I., Panigrahy, D., Seth, P., ... Hergenrother, P. J. (2017). Reactive Oxygen Species Synergize to Potently and Selectively Induce Cancer Cell Death. ACS Chemical Biology, 12(5), 1416-1424. DOI: 10.1021/acschembio.7b00015

Thamm, D. H., Vail, D. M., Post, G. S., Fan, T. M., Phillips, B. S., Axiak-Bechtel, S., ... Ruslander, D. A. (2017). Alternating Rabacfosadine/Doxorubicin: Efficacy and Tolerability in Naïve Canine Multicentric Lymphoma. Journal of Veterinary Internal Medicine, 31(3), 872-878. DOI: 10.1111/jvim.14700

Fan, T. M. (2017). Cancer Patients. In Veterinary Anesthesia and Analgesia: The Fifth Edition of Lumb and Jones (pp. 993-1003). wiley. DOI: 10.1002/9781119421375.ch55

Van Eps, N., Caro, L. N., Morizumi, T., Kusnetzow, A. K., Szczepek, M., Hofmann, K. P., ... Hubbell, W. L. (2017). Conformational equilibria of light-activated rhodopsin in nanodiscs. Proceedings of the National Academy of Sciences of the United States of America, 114(16), E3268-E3275. DOI: 10.1073/pnas.1620405114

Zhao, C., & Song, J. S. (2017). Emergent community agglomeration from data set geometry. Physical Review E, 95(4), [042307]. DOI: 10.1103/PhysRevE.95.042307

Lundberg, A. P., Francis, J. M., Pajak, M., Parkinson, E. I., Wycislo, K. L., Rosol, T. J., ... Fan, T. M. (2017). Pharmacokinetics and derivation of an anticancer dosing regimen for the novel anti-cancer agent isobutyl-deoxynyboquinone (IB-DNQ), a NQO1 bioactivatable molecule, in the domestic felid species. Investigational New Drugs, 35(2), 134-144. DOI: 10.1007/s10637-016-0414-z

Wang, H., Wang, R., Cai, K., He, H., Liu, Y., Yen, J., ... Cheng, J. (2017). Selective in vivo metabolic cell-labeling-mediated cancer targeting. Nature Chemical Biology, 13(4), 415-424. DOI: 10.1038/nchembio.2297

Denisov, I. G., & Sligar, S. G. (2017). Nanodiscs in Membrane Biochemistry and Biophysics. Chemical Reviews, 117(6), 4669-4713. DOI: 10.1021/acs.chemrev.6b00690

di Chiara, T., DiNunno, N., Clark, J., Bu, R. L., Cline, E. N., Rollins, M. G., ... Klein, W. L. (2017). Alzheimer’s toxic amyloid beta oligomers: Unwelcome visitors to the Na/K ATPase alpha3 docking station. Yale Journal of Biology and Medicine, 90(1), 45-61.

Huang, Q., Peh, J., Hergenrother, P. J., & Cunningham, B. T. (2017). Porous photonic crystal external cavity laser biosensor for drug screening. In IEEE Sensors, SENSORS 2016 - Proceedings [7808619] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/ICSENS.2016.7808619

Schmitt, T. M., Aggen, D. H., Ishida-Tsubota, K., Ochsenreither, S., Kranz, D. M., & Greenberg, P. D. (2017). Generation of higher affinity T cell receptors by antigen-driven differentiation of progenitor t cells in vitro. Nature biotechnology, 35(12), 1188-1195. DOI: 10.1038/nbt.4004

Lee, J., Abdeen, A. A., Hedhli, J., Wycislo, K. L., Dobrucki, I. T., Fan, T. M., ... Kilian, K. A. (2017). Melanoma topology reveals a stem-like phenotype that promotes angiogenesis. Science Advances, 3(10), [e1701350]. DOI: 10.1126/sciadv.1701350

Wade, J. H., Jones, J. D., Lenov, I. L., Riordan, C. M., Sligar, S. G., & Bailey, R. C. (2017). Microfluidic platform for efficient Nanodisc assembly, membrane protein incorporation, and purification. Lab on a Chip, 17(17), 2951-2959. DOI: 10.1039/c7lc00601b

Brown, A., Woods, W. S., & Perez-Pinera, P. (2017). Targeted gene activation using RNA-guided nucleases. Methods in Molecular Biology, 1468, 235-250. DOI: 10.1007/978-1-4939-4035-6_16

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 2015, 13, 2027-2036.

Deoxynyboquinones as NQO1-Activated Cancer Therapeutics
Parkinson, E. I.; Hergenrother, P. J.
Acc. Chem. Res. 2015, 48, 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. 2015, 58, 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. 2014, 136, 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. 2013, 8, 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. 2012, 72, 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 2012, 9, 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 2011, 29, 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. 2010, 70, 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. 2010, 132, 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.