Items where Community is "Cancer Genetics and Genomics Program"

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Breschi, A., Muñoz-Aguirre, M., Wucher, V., Davis, C. A., Garrido-Martín, D., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Reverter, F., Snyder, M. P., Gingeras, T. R., Guigó, R. (July 2020) A limited set of transcriptional programs define major cell types. Genome Res, 30 (7). pp. 1047-1059. ISSN 1088-9051 (Print)1088-9051

Adrion, JR, Cole, C. B., Dukler, N., Galloway, JG, Gladstein, AL, Gower, G, Kyriazis, CC, Ragsdale, AP, Tsambos, G, Baumdicker, F, Carlson, J., Cartwright, R. A., Durvasula, A, Gronau, I., Kim, BY, McKenzie, P, Messer, PW, Noskova, E, Ortega-Del Vecchyo, D., Racimo, F, Struck, TJ, Gravel, S, Gutenkunst, R. N., Lohmueller, K. E., Ralph, PL, Schrider, D. R., Siepel, A., Kelleher, J. E., Kern, A. D. (June 2020) A Community-Maintained Standard Library of Population Genetic Models. Elife, 9. ISSN 2050-084X (Electronic)2050-084X (Linking)

Lin, A., Sheltzer, J.M. (June 2020) Discovering and Validating Cancer Genetic Dependencies: Approaches and Pitfalls. Nat Rev Genet. ISSN 1471-0056

Gryder, B. E., Wachtel, M., Chang, K., El Demerdash, O., Aboreden, N.G., Mohammed, W., Ewert, W., Pomella, S., Rota, R., Wei, J.S., Song, Y., Stanton, B. Z., Schafer, B., Vakoc, C.R., Khan, J. (May 2020) Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage. iScience, 23 (5). p. 101103. ISSN 2589-0042

Chorbadjiev, L., Kendall, J., Alexander, J., Zhygulin, V., Song, J., Wigler, M., Krasnitz, A. (May 2020) Integrated Computational Pipeline for Single-Cell Genomic Profiling. JCO Clinical Cancer Informatics, 4. pp. 464-471.

Smith, J.C., Sausville, E. L., Girish, V., Yuan, M.L., Vasudevan, A., John, K.M., Sheltzer, J. M. (May 2020) Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract. Dev Cell, 53 (5). 514-529.e3. ISSN 1534-5807

Baslan, T., Kendall, J., Volyanskyy, K., McNamara, K., Cox, H., D'Italia, S., Ambrosio, F., Riggs, M., Rodgers, L., Leotta, A., Song, J., Mao, Y., Wu, J., Shah, R., Gularte-Merida, R., Chadalavada, K., Nanjangud, G., Varadan, V., Gordon, A., Curtis, C., Krasnitz, A., Dimitrova, N., Harris, L., Wigler, M., Hicks, J. (May 2020) Novel Insights Into Breast Cancer Copy Number Genetic Heterogeneity Revealed by Single-Cell Genome Sequencing. Elife, 9. e51480. ISSN 2050-084X

Somerville, T. D. D., Biffi, G., DaBler-Plenker, J., Hur, S.K., He, X.-Y., Vance, K.E., Miyabayashi, K., Xu, Y., Maia-Silva, D., Klingbeil, O., Demerdash, O. E., Preall, J. B., Hollingsworth, M. A., Egeblad, M., Tuveson, D. A., Vakoc, C. R. (April 2020) Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation. Elife, 9. e53381. ISSN 2050-084x (Public Dataset)

Zhou, J., McCandlish, D. M. (April 2020) Minimum Epistasis Interpolation for Sequence-Function Relationships. Nature Communication, 11 (1782). pp. 1-11. ISSN 2041-1723 (Public Dataset)

O'Neill, K., Brocks, D., Hammell, M. G. (March 2020) Mobile Genomics: Tools and Techniques for Tackling Transposons. Philos Trans R Soc Lond B Biol Sci, 375 (1795). ISSN 0962-8436

Sahai, E., Astsaturov, I., Cukierman, E., DeNardo, D. G., Egeblad, M., Evans, R. M., Fearon, D., Greten, F. R., Hingorani, S. R., Hunter, T., Hynes, R. O., Jain, R. K., Janowitz, T., Jorgensen, C., Kimmelman, A. C., Kolonin, M. G., Maki, R. G., Powers, R. S., Pure, E., Ramirez, D. C., Scherz-Shouval, R., Sherman, M. H., Stewart, S., Tlsty, T. D., Tuveson, D. A., Watt, F. M., Weaver, V., Weeraratna, A. T., Werb, Z. (March 2020) A framework for advancing our understanding of cancer-associated fibroblasts. Nat Rev Cancer, 20 (3). pp. 174-186. ISSN 1474-175x

Dukler, N., Huang, Y-F., Siepel, A. (March 2020) Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data. Mol Biol Evol, 37 (7). pp. 2137-2152. ISSN 0737-4038

Vasudevan, A., Baruah, P.S., Smith, J.C., Wang, Z., Sayles, N. M., Andrews, P., Kendall, J., Leu, J., Chunduri, N.K., Levy, D., Wigler, M., Storchova, Z., Sheltzer, J. M. (February 2020) Single-Chromosomal Gains Can Function as Metastasis Suppressors and Promoters in Colon Cancer. Developmental Cell, 4 (52). pp. 413-428. ISSN 1534-5807

Moffitt, A. B., Spector, M. S., Andrews, P., Kendall, J., Alexander, J., Stepansky, A., Ma, B., Kolitz, J., Chiorazzi, N., Allen, S.L., Krasnitz, A., Wigler, M., Levy, D., Wang, Z. (February 2020) Multiplex Accurate Sensitive Quantitation (MASQ) With Application to Minimal Residual Disease in Acute Myeloid Leukemia. Nucleic Acids Research, 48 (7). e40. ISSN 0305-1048 (Public Dataset)

Hubisz, M., Siepel, A. (January 2020) Inference of Ancestral Recombination Graphs Using ARGweaver. Methods Mol Biol, 2090. pp. 231-266. ISSN 1064-3745

Li, S., Kendall, J., Park, S., Wang, Z., Alexander, J., Moffitt, A., Ranade, N., Danyko, C., Gegenhuber, B., Fischer, S., Robinson, B. D., Lepor, H., Tollkuhn, J., Gillis, J., Brouzes, E., Krasnitz, A., Levy, D., Wigler, M. (January 2020) Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res, 30 (1). pp. 49-61. ISSN 1088-9051 (Public Dataset)

Foronda, M., Tarumoto, Y., Schatoff, E. M., Leach, B. I., Diaz, B. J., Zimmerman, J., Goswami, S., Shusterman, M., Vakoc, C. R., Dow, L. E. (December 2019) Tankyrase inhibition sensitizes cells to CDK4 blockade. PLoS One, 14 (12). e0226645. ISSN 1932-6203

Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., Schatz, M. C. (December 2019) Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics, 20 (Suppl). p. 641. ISSN 1471-2105 (Public Dataset)

Gryder, B. E., Pomella, S., Sayers, C., Wu, X. S., Song, Y., Chiarella, A. M., Bagchi, S., Chou, H. C., Sinniah, R. S., Walton, A., Wen, X., Rota, R., Hathaway, N. A., Zhao, K., Chen, J., Vakoc, C. R., Shern, J. F., Stanton, B. Z., Khan, J. (December 2019) Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nat Genet, 51 (12). pp. 1714-1722. ISSN 1061-4036 (Public Dataset)

Kneissig, M., Keuper, K., de Pagter, M. S., van Roosmalen, M. J., Martin, J., Otto, H., Passerini, V., Campos Sparr, A., Renkens, I., Kropveld, F., Vasudevan, A., Sheltzer, J. M., Kloosterman, W. P., Storchova, Z. (November 2019) Micronuclei-based model system reveals functional consequences of chromothripsis in human cells. Elife, 8. e50292. ISSN 2050-084x (Public Dataset)

Caiado, F., Maia-Silva, D., Jardim, C., Schmolka, N., Carvalho, T., Reforco, C., Faria, R., Kolundzija, B., Simoes, A. E., Baubec, T., Vakoc, C. R., da Silva, M. G., Manz, M. G., Schumacher, T. N., Norell, H., Silva-Santos, B. (November 2019) Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection. Nat Commun, 10 (1). p. 4986. ISSN 2041-1723

Tarumoto, Y., Lin, S., Wang, J., Milazzo, J. P., Xu, Y., Lu, B., Yang, Z., Wei, Y., Polyanskaya, S., Wunderlich, M., Gray, N. S., Stegmaier, K., Vakoc, C. R. (November 2019) Salt-Inducible Kinase inhibition suppresses acute myeloid leukemia progression in vivo. Blood. ISSN 0006-4971

Rahmanian, S., Murad, R., Breschi, A., Zeng, W., Mackiewicz, M., Williams, B., Davis, C. A., Roberts, B., Meadows, S., Moore, D., Trout, D., Zaleski, C., Dobin, A., Sei, L. H., Drenkow, J., Scavelli, A., Gingeras, T. R., Wold, B. J., Myers, R. M., Guigo, R., Mortazavi, A. (November 2019) Dynamics of microRNA expression during mouse prenatal development. Genome Res, 29 (11). pp. 1900-1909. ISSN 1088-9051

Tam, O. H., Rozhkov, N. V., Shaw, R., Kim, D., Hubbard, I., Fennessey, S., Propp, N., Fagegaltier, D., Harris, B. T., Ostrow, L. W., Phatnani, H., Ravits, J., Dubnau, J., Gale Hammell, M. (October 2019) Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Rep, 29 (5). 1164-1177.e5.

Carter, J. A., Preall, J. B., Atwal, G. S. (October 2019) Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire. Cell Syst, 9 (5). pp. 475-482. ISSN 2405-4712 (Public Dataset)

Li, Y., Brooks, M., Yeoh-Wang, J., McCoy, R. M., Rock, T. M., Pasquino, A., Moon, C. I., Patrick, R. M., Tanurdzic, M., Ruffel, S., Widhalm, J. R., McCombie, W. R., Coruzzi, G. M. (October 2019) SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling. Plant Physiol. ISSN 0032-0889

Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., Regev, A. (October 2019) Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol, 20 (1). p. 213. ISSN 1474-7596

Lin, A., Giuliano, C. J., Palladino, A., John, K. M., Abramowicz, C., Yuan, M. L., Sausville, E. L., Lukow, D. A., Liu, L., Chait, A. R., Galluzzo, Z. C., Tucker, C., Sheltzer, J. M. (September 2019) Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. Sci Transl Med, 11 (509). ISSN 1946-6234

Li, F., Deng, Z., Zhang, L., Wu, C., Jin, Y., Hwang, I., Vladimirova, O., Xu, L., Yang, L., Lu, B., Dheekollu, J., Li, J. Y., Feng, H., Hu, J., Vakoc, C. R., Ying, H., Paik, J., Lieberman, P. M., Zheng, H. (August 2019) ATRX loss induces telomere dysfunction and necessitates induction of alternative lengthening of telomeres during human cell immortalization. Embo j, 38 (19). e96659. ISSN 0261-4189

Kneuss, E., Munafo, M., Eastwood, E. L., Deumer, U. S., Preall, J. B., Hannon, G. J., Czech, B. (August 2019) Specialization of the Drosophila nuclear export family protein Nxf3 for piRNA precursor export. Genes Dev, 33 (17-18). pp. 1208-1220. ISSN 0890-9369

Zhang, X. O., Gingeras, T. R., Weng, Z. (August 2019) Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Genome Res, 29 (9). pp. 1402-1414. ISSN 1088-9051

Ehrenhofer-Wolfer, K., Puchner, T., Schwarz, C., Rippka, J., Blaha-Ostermann, S., Strobl, U., Hormann, A., Bader, G., Kornigg, S., Zahn, S., Sommergruber, W., Schweifer, N., Zichner, T., Schlattl, A., Neumuller, R. A., Shi, J., Vakoc, C. R., Kogl, M., Petronczki, M., Kraut, N., Pearson, M. A., Wohrle, S. (August 2019) SMARCA2-deficiency confers sensitivity to targeted inhibition of SMARCA4 in esophageal squamous cell carcinoma cell lines. Sci Rep, 9 (1). p. 11661. ISSN 2045-2322

Giuliano, C. J., Lin, A., Girish, V., Sheltzer, J. M. (August 2019) Generating Single Cell–Derived Knockout Clones in Mammalian Cells with CRISPR/Cas9. Current Protocols in Molecular Biology, 128 (1). Art number e100. ISSN 19343639 (ISSN)

Carter, J. A., Preall, J. B., Grigaityte, K., Goldfless, S. J., Jeffery, E., Briggs, A. W., Vigneault, F., Atwal, G. S. (July 2019) Single T Cell Sequencing Demonstrates the Functional Role alpha beta TCR Pairing in Cell Lineage and Antigen Specificity. Frontiers in Immunology, 10. Article Number:1516. ISSN 1664-3224

Storz, J. F., Natarajan, C., Signore, A. V., Witt, C. C., McCandlish, D. M., Stoltzfus, A. (July 2019) The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function. Philos Trans R Soc Lond B Biol Sci, 374 (1777). p. 20180238. ISSN 0962-8436 (Public Dataset)

Bottcher, J., Dilworth, D., Reiser, U., Neumuller, R. A., Schleicher, M., Petronczki, M., Zeeb, M., Mischerikow, N., Allali-Hassani, A., Szewczyk, M. M., Li, F., Kennedy, S., Vedadi, M., Barsyte-Lovejoy, D., Brown, P. J., Huber, K. V. M., Rogers, C. M., Wells, C. I., Fedorov, O., Rumpel, K., Zoephel, A., Mayer, M., Wunberg, T., Bose, D., Zahn, S., Arnhof, H., Berger, H., Reiser, C., Hormann, A., Krammer, T., Corcokovic, M., Sharps, B., Winkler, S., Haring, D., Cockcroft, X. L., Fuchs, J. E., Mullauer, B., Weiss-Puxbaum, A., Gerstberger, T., Boehmelt, G., Vakoc, C. R., Arrowsmith, C. H., Pearson, M., McConnell, D. B. (July 2019) Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Nat Chem Biol, 15 (8). pp. 822-829. ISSN 1552-4450

Huang, Yi-Fei, Siepel, Adam (June 2019) Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease. Genome Research, 29 (8). pp. 1310-1321. ISSN 10889051 (ISSN)

Bell, C. C., Fennell, K. A., Chan, Y. C., Rambow, F., Yeung, M. M., Vassiliadis, D., Lara, L., Yeh, P., Martelotto, L. G., Rogiers, A., Kremer, B. E., Barbash, O., Mohammad, H. P., Johanson, T. M., Burr, M. L., Dhar, A., Karpinich, N., Tian, L., Tyler, D. S., MacPherson, L., Shi, J., Pinnawala, N., Yew Fong, C., Papenfuss, A. T., Grimmond, S. M., Dawson, S. J., Allan, R. S., Kruger, R. G., Vakoc, C. R., Goode, D. L., Naik, S. H., Gilan, O., Lam, E. Y. N., Marine, J. C., Prinjha, R. K., Dawson, M. A. (June 2019) Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia. Nat Commun, 10 (1). p. 2723. ISSN 2041-1723

Lan, X., Khandros, E., Huang, P., Peslak, S. A., Bhardwaj, S. K., Grevet, J. D., Abdulmalik, O., Wang, H., Keller, C. A., Giardine, B., Baeza, J., Duffner, E. R., El Demerdash, O., Wu, X. S., Vakoc, C. R., Garcia, B. A., Hardison, R. C., Shi, J., Blobel, G. A. (May 2019) The E3 ligase adaptor molecule SPOP regulates fetal hemoglobin levels in adult erythroid cells. Blood Adv, 3 (10). pp. 1586-1597. ISSN 2473-9529

Bharathy, N., Berlow, N. E., Wang, E., Abraham, J., Settelmeyer, T. P., Hooper, J. E., Svalina, M. N., Bajwa, Z., Goros, M. W., Hernandez, B. S., Wolff, J. E., Pal, R., Davies, A. M., Ashok, A., Bushby, D., Mancini, M., Noakes, C., Goodwin, N. C., Ordentlich, P., Keck, J., Hawkins, D. S., Rudzinski, E. R., Mansoor, A., Perkins, T. J., Vakoc, C. R., Michalek, J. E., Keller, C. (May 2019) Preclinical rationale for entinostat in embryonal rhabdomyosarcoma. Skelet Muscle, 9 (1). p. 12. ISSN 2044-5040

Kinney, J. B., McCandlish, D. M. (May 2019) Massively Parallel Assays and Quantitative Sequence-Function Relationships. Annu Rev Genomics Hum Genet. ISSN 1527-8204

Rudin, C. M., Poirier, J. T., Byers, L. A., Dive, C., Dowlati, A., George, J., Heymach, J. V., Johnson, J. E., Lehman, J. M., MacPherson, D., Massion, P. P., Minna, J. D., Oliver, T. G., Quaranta, V., Sage, J., Thomas, R. K., Vakoc, C. R., Gazdar, A. F. (March 2019) Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data. Nat Rev Cancer, 19 (5). pp. 289-297. ISSN 1474-175x

Zhang, Q., Chao, T. C., Patil, V. S., Qin, Y., Tiwari, S. K., Chiou, J., Dobin, A., Tsai, C. M., Li, Z., Dang, J., Gupta, S., Urdahl, K., Nizet, V., Gingeras, T. R., Gaulton, K. J., Rana, T. M. (March 2019) The long noncoding RNA ROCKI regulates inflammatory gene expression. Embo j, 38 (8). Article number e100041. ISSN 0261-4189

Aho, E. R., Wang, J., Gogliotti, R. D., Howard, G. C., Phan, J., Acharya, P., Macdonald, J. D., Cheng, K., Lorey, S. L., Lu, B., Wenzel, S., Foshage, A. M., Alvarado, J., Wang, F., Shaw, J. G., Zhao, B., Weissmiller, A. M., Thomas, L. R., Vakoc, C. R., Hall, M. D., Hiebert, S. W., Liu, Q., Stauffer, S. R., Fesik, S. W., Tansey, W. P. (March 2019) Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity. Cell Reports, 26 (11). 2916-2928.e13. ISSN 22111247 (ISSN)

Gulko, B., Siepel, A. (February 2019) Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nat Genet, 51 (2). pp. 335-342. ISSN 1061-4036

Stein, C. B., Genzor, P., Mitra, S., Elchert, A. R., Ipsaro, J. J., Benner, L., Sobti, S., Su, Y., Hammell, M., Joshua-Tor, L., Haase, A. D. (February 2019) Decoding the 5' nucleotide bias of PIWI-interacting RNAs. Nat Commun, 10 (1). p. 828. ISSN 2041-1723

Liu, P. H., Shah, R. B., Li, Y., Arora, A., Ung, P. M., Raman, R., Gorbatenko, A., Kozono, S., Zhou, X. Z., Brechin, V., Barbaro, J. M., Thompson, R., White, R. M., Aguirre-Ghiso, J. A., Heymach, J. V., Lu, K. P., Silva, J. M., Panageas, K. S., Schlessinger, A., Maki, R. G., Skinner, H. D., de Stanchina, E., Sidi, S. (January 2019) An IRAK1-PIN1 signalling axis drives intrinsic tumour resistance to radiation therapy. Nat Cell Biol, 21 (2). pp. 203-213. ISSN 1465-7392

Anaparthy, N., Ho, Y. J., Martelotto, L., Hammell, M., Hicks, J. (January 2019) Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harb Perspect Med, 9 (10). ISSN 2157-1422

Sun, G., Krasnitz, A. (2019) CORE: A Software Tool for Delineating Regions of Recurrent DNA Copy Number Alteration in Cancer. Methods Mol Biol, 1878. pp. 85-93. ISSN 1064-3745

Sun, G., Krasnitz, A. (2019) Statistically Supported Identification of Tumor Subtypes. Methods Mol Biol, 1878. pp. 209-216. ISSN 1064-3745

Gounder, M. M., Mahoney, M. R., Van Tine, B. A., Ravi, V., Attia, S., Deshpande, H. A., Gupta, A. A., Milhem, M. M., Conry, R. M., Movva, S., Pishvaian, M. J., Riedel, R. F., Sabagh, T., Tap, W. D., Horvat, N., Basch, E., Schwartz, L. H., Maki, R. G., Agaram, N. P., Lefkowitz, R. A., Mazaheri, Y., Yamashita, R., Wright, J. J., Dueck, A. C., Schwartz, G. K. (December 2018) Sorafenib for Advanced and Refractory Desmoid Tumors. N Engl J Med, 379 (25). pp. 2417-2428. ISSN 0028-4793

Gulko, B., Siepel, A. (December 2018) An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nat Genet, 51 (2). pp. 335-342. ISSN 1061-4036

Smith, J. C., Sheltzer, J. M. (December 2018) Systematic identification of mutations and copy number alterations associated with cancer patient prognosis. Elife, 7. ISSN 2050-084x

Ramani, R., Krumholz, K., Huang, Y. F., Siepel, A. (November 2018) PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. Bioinformatics, 35 (13). pp. 2320-2322. ISSN 1367-4803

McCombie, W. R., McPherson, J. D., Mardis, E. R. (November 2018) Next-Generation Sequencing Technologies. Cold Spring Harb Perspect Med, 9 (11). ISSN 2157-1422

Bharathy, N., Berlow, N. E., Wang, E., Abraham, J., Settelmeyer, T. P., Hooper, J. E., Svalina, M. N., Ishikawa, Y., Zientek, K., Bajwa, Z., Goros, M. W., Hernandez, B. S., Wolff, J. E., Rudek, M. A., Xu, L., Anders, N. M., Pal, R., Harrold, A. P., Davies, A. M., Ashok, A., Bushby, D., Mancini, M., Noakes, C., Goodwin, N. C., Ordentlich, P., Keck, J., Hawkins, D. S., Rudzinski, E. R., Chatterjee, B., Bachinger, H. P., Barr, F. G., Liddle, J., Garcia, B. A., Mansoor, A., Perkins, T. J., Vakoc, C. R., Michalek, J. E., Keller, C. (November 2018) The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma. Sci Signal, 11 (557). ISSN 1945-0877

Brien, G. L., Remillard, D., Shi, J., Hemming, M. L., Chabon, J., Wynne, K., Dillon, E. T., Cagney, G., Van Mierlo, G., Baltissen, M. P., Vermeulen, M., Qi, J., Frohling, S., Gray, N. S., Bradner, J. E., Vakoc, C. R., Armstrong, S. A. (November 2018) Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. Elife, 7. ISSN 2050-084x

Lu, B., Klingbeil, O., Tarumoto, Y., Somerville, T. D. D., Huang, Y. H., Wei, Y., Wai, D. C., Low, J. K. K., Milazzo, J. P., Wu, X. S., Cao, Z., Yan, X., Demerdash, O. E., Huang, G., Mackay, J. P., Kinney, J. B., Shi, J., Vakoc, C. R. (November 2018) A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. Cancer Cell, 34 (6). pp. 970-981. ISSN 1535-6108

Somerville, T. D. D., Xu, Y., Miyabayashi, K., Tiriac, H., Cleary, C. R., Maia-Silva, D., Milazzo, J. P., Tuveson, D. A., Vakoc, C. R. (November 2018) TP63-Mediated Enhancer Reprogramming Drives the Squamous Subtype of Pancreatic Ductal Adenocarcinoma. Cell Rep, 25 (7). 1741-1755.e7. ISSN 2211-1247 (Public Dataset)

Raut, C. P., Espat, N. J., Maki, R. G., Araujo, D. M., Trent, J., Williams, T. F., Purkayastha, D. D., DeMatteo, R. P. (November 2018) Efficacy and Tolerability of 5-Year Adjuvant Imatinib Treatment for Patients With Resected Intermediate- or High-Risk Primary Gastrointestinal Stromal Tumor: The PERSIST-5 Clinical Trial. JAMA Oncol, 4 (12). e184060. ISSN 2374-2437

Demicco, E. G., Wani, K., Ingram, D., Wagner, M., Maki, R. G., Rizzo, A., Meeker, A., Lazar, A. J., Wang, W. L. (November 2018) TERT Promoter Mutations in Solitary Fibrous Tumor. Histopathology, 73 (5). pp. 843-851. ISSN 0309-0167

Paoluzzi, L., Maki, R. G. (October 2018) Diagnosis, Prognosis, and Treatment of Alveolar Soft-Part Sarcoma: A Review. JAMA Oncol, 5 (2). pp. 254-260. ISSN 2374-2437

O'Neill, K., Liao, W. W., Patel, A., Hammell, M. G. (October 2018) TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma. Frontiers in Genetics, 9. Article Number: 461 . ISSN 1664-8021

Zafra, M. P., Schatoff, E. M., Katti, A., Foronda, M., Breinig, M., Schweitzer, A. Y., Simon, A., Han, T., Goswami, S., Montgomery, E., Thibado, J., Kastenhuber, E. R., Sanchez-Rivera, F. J., Shi, J., Vakoc, C. R., Lowe, S. W., Tschaharganeh, D. F., Dow, L. E. (October 2018) Optimized base editors enable efficient editing in cells, organoids and mice. Nat Biotechnol, 36 (9). pp. 888-896. ISSN 1087-0156

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Ipsaro, J. J., Shen, C., Arai, E., Xu, Y., Kinney, J. B., Joshua-Tor, L., Vakoc, C. R., Shi, J. (February 2017) Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis. PLoS One, 12 (2). e0172177. ISSN 1932-6203

Sheltzer, Jason M., Ko, Julie H., Replogle, John M., Habibe Burgos, Nicole C., Chung, Erica S., Meehl, Colleen M., Sayles, Nicole M., Passerini, Verena, Storchova, Zuzana, Amon, Angelika (February 2017) Single-chromosome Gains Commonly Function as Tumor Suppressors. Cancer Cell, 31 (2). pp. 240-255. ISSN 1535-6108 (Public Dataset)

Roe, J. S., Vakoc, C. R. (February 2017) The Essential Transcriptional Function of BRD4 in Acute Myeloid Leukemia. Cold Spring Harb Symp Quant Biol, 81. pp. 61-66. ISSN 0091-7451

Pal, D., Pertot, A., Shirole, N. H., Yao, Z., Anaparthy, N., Garvin, T., Cox, H., Chang, K., Rollins, F., Kendall, J., Edwards, L., Singh, V. A., Stone, G. C., Schatz, M. C., Hicks, J., Hannon, G., Sordella, R. (January 2017) TGF-beta reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells. Elife, 6. ISSN 2050-084X (Electronic)2050-084X (Linking)

Dukler, N., Gulko, B., Huang, Y. F., Siepel, A. (December 2016) Is a super-enhancer greater than the sum of its parts? Nat Genet, 49 (1). pp. 2-3. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Fang, H., Bergmann, E. A., Arora, K., Vacic, V., Zody, M. C., Iossifov, I., O'Rawe, J. A., Wu, Y., Jimenez Barron, L. T., Rosenbaum, J., Ronemus, M., Lee, Y. H., Wang, Z., Dikoglu, E., Jobanputra, V., Lyon, G. J., Wigler, M., Schatz, M. C., Narzisi, G. (December 2016) Indel variant analysis of short-read sequencing data with Scalpel. Nat Protoc, 11 (12). pp. 2529-2548. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

Oran, A. R., Adams, C. M., Zhang, X. Y., Gennaro, V. J., Pfeiffer, H. K., Mellert, H. S., Seidel, H. E., Mascioli, K., Kaplan, J., Gaballa, M. R., Shen, C., Rigoutsos, I., King, M. P., Cotney, J. L., Arnold, J. J., Sharma, S. D., Martinez-Outschoorn, U. E., Vakoc, C. R., Chodosh, L. A., Thompson, J. E., Bradner, J. E., Cameron, C. E., Shadel, G. S., Eischen, C. M., McMahon, S. B. (November 2016) Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget, 7 (45). pp. 72395-72414. ISSN 1949-2553 (Electronic)1949-2553 (Linking)

Dodgson, S. E., Santaguida, S., Kim, S., Sheltzer, J., Amon, A. (November 2016) The pleiotropic deubiquitinase Ubp3 confers aneuploidy tolerance. Genes Dev. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Andrews, Peter A., Iossifov, Ivan, Kendall, Jude, Marks, Steven, Muthuswamy, Lakshmi, Wang, Zihua, Levy, Dan, Wigler, Michael (September 2016) MUMdex: MUM-based structural variation detection. bioRxiv. 078261.

Diermeier, Sarah D, Chang, Kung-Chi, Freier, Susan M, Song, Junyan, El Demerdash, Osama, Krasnitz, Alexander, Rigo, Frank, Bennett, C.  Frank, Spector, David L (September 2016) Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration. Cell Reports, 17 (1). pp. 261-274. ISSN 2211-1247 (Public Dataset)

Lee, H. J., Li, C. F., Ruan, D., Powers, S., Thompson, P. A., Frohman, M. A., Chan, C. H. (September 2016) The DNA Damage Transducer RNF8 Facilitates Cancer Chemoresistance and Progression through Twist Activation. Mol Cell, 63 (6). pp. 1021-33. ISSN 1097-2765

Hohmann, A. F., Martin, L. J., Minder, J. L., Roe, J. S., Shi, J., Steurer, S., Bader, G., McConnell, D., Pearson, M., Gerstberger, T., Gottschamel, T., Thompson, D., Suzuki, Y., Koegl, M., Vakoc, C. R. (September 2016) Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition. Nat Chem Biol, 12 (9). pp. 672-9. ISSN 1552-4469 (Electronic)1552-4450 (Linking) (Public Dataset)

Chio, Iok In Christine, Jafarnejad, Seyed Mehdi, Ponz-Sarvise, Mariano, Park, Youngkyu, Rivera, Keith, Palm, Wilhelm, Wilson, John, Sangar, Vineet, Hao, Yuan, Öhlund, Daniel, Wright, Kevin, Filippini, Dea, Lee, Eun Jung, Da Silva, Brandon, Schoepfer, Christina, Wilkinson, John Erby, Buscaglia, Jonathan M, DeNicola, Gina M, Tiriac, Herve, Hammell, Molly, Crawford, Howard C, Schmidt, Edward E, Thompson, Craig B, Pappin, Darryl J, Sonenberg, Nahum, Tuveson, David A (August 2016) NRF2 Promotes Tumor Maintenance by Modulating mRNA Translation in Pancreatic Cancer. Cell, 166 (4). pp. 963-976. ISSN 0092-8674

Scott, K. L., Powers, S. (August 2016) Functionally Assessing Candidate Drivers Advances Precision Cancer Medicine. Cancer Cell, 30 (2). pp. 187-189. ISSN 1535-6108

Huang, Yu-Han, Vakoc, Christopher R (July 2016) A Biomarker Harvest from One Thousand Cancer Cell Lines. Cell, 166 (3). pp. 536-537. ISSN 0092-8674

Somerville, Tim D D., Vakoc, Christopher R (July 2016) Modeling the Epigenetic Chain Reaction Downstream of DNMT3A(R882H). Cancer Cell, 30 (1). pp. 9-10. ISSN 1535-6108

Gerhard, D. S., Clemons, P. A., Shamji, A. F., Hon, C., Wagner, B. K., Schreiber, S. L., Krasnitz, A., Sordella, R., Sander, C., Lowe, S. W., Powers, S., Smith, K., Aburi, M., Iavarone, A., Lasorella, A., Silva, J., Stockwell, B. R., Califano, A., Boehm, J. S., Vazquez, F., Weir, B. A., Hahn, W. C., Khuri, F. R., Moreno, C. S., Johns, M., Fu, H., Nikolova, O., Mendez, E., Gadi, V. K., Margolin, A. A., Grandori, C., Kemp, C. J., Warren, E. H., Riddell, S. R., McIntosh, M. W., Gevaert, O., Kuo, C. J., Ji, H. P., Dhruv, H., Finlay, D., Kiefer, J., Kim, S., Vuori, K., Berens, M. E., Hangauer, M., Boettcher, M., Weissman, J. S., Bivona, T. G., Bandyopadhyay, S., McManus, M. T., McCormick, F., Aksoy, O., Simonds, E. F., Zheng, T., Chen, J., An, Z., Balmain, A., Weiss, W. A., Chen, K., Liang, H., Scott, K. L., Mills, G. B., Posner, B. A., MacMillan, J., Minna, J., White, M., Roth, M. G., Jagu, S., Mazerik, J. (July 2016) Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Mol Cancer Res. ISSN 1557-3125 (Electronic)1541-7786 (Linking)

Pang, A., Carbini, M., Maki, R. G. (July 2016) Contemporary Therapy for Advanced Soft-Tissue Sarcomas in Adults: A Review. JAMA Oncol, 2 (7). pp. 941-7. ISSN 2374-2437

Li, J., Sordella, R., Powers, S. (June 2016) Effectors and potential targets selectively upregulated in human KRAS-mutant lung adenocarcinomas. Sci Rep, 6. p. 27891. ISSN 2045-2322 (Electronic)2045-2322 (Linking)

Zhang, Qiang, Zeng, Lei, Shen, Chen, Ju, Ying, Konuma, Tsuyoshi, Zhao, Chengcheng, Vakoc, Christopher R, Zhou, Ming-Ming (June 2016) Structural Mechanism of Transcriptional Regulator NSD3 Recognition by the ET Domain of BRD4. Structure. ISSN 0969-2126

Tasdemir, N., Banito, A., Roe, J. S., Alonso-Curbelo, D., Camiolo, M., Tschaharganeh, D. F., Huang, C. H., Aksoy, O., Bolden, J. E., Chen, C. C., Fennell, M., Thapar, V., Chicas, A., Vakoc, C. R., Lowe, S. W. (June 2016) BRD4 connects enhancer remodeling to senescence immune surveillance. Cancer Discov, 6 (6). pp. 612-629. ISSN 2159-8290 (Electronic)2159-8274 (Linking)

Wang, Z., Andrews, P., Kendall, J., Ma, B., Hakker, I., Rodgers, L., Ronemus, M., Wigler, M., Levy, D. (June 2016) SMASH, a fragmentation and sequencing method for genomic copy number analysis. Genome Res, 26 (6). pp. 844-51. ISSN 1549-5469 (Electronic)1088-9051 (Linking) (Public Dataset)

Martin, L. J., Koegl, M., Bader, G., Cockcroft, X. L., Fedorov, O., Fiegen, D., Gerstberger, T., Hofmann, M. H., Hohmann, A. F., Kessler, D., Knapp, S., Knesl, P., Kornigg, S., Muller, S., Nar, H., Rogers, C., Rumpel, K., Schaaf, O., Steurer, S., Tallant, C., Vakoc, C. R., Zeeb, M., Zoephel, A., Pearson, M., Boehmelt, G., McConnell, D. (May 2016) Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor. J Med Chem, 59 (10). pp. 4462-75. ISSN 1520-4804 (Electronic)0022-2623 (Linking)

Goodwin, S., McPherson, J. D., McCombie, W. R. (May 2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet, 17 (6). pp. 333-51. ISSN 1471-0064 (Electronic)1471-0056 (Linking)

Teng, M., Love, M. I., Davis, C. A., Djebali, S., Dobin, A., Graveley, B. R., Li, S., Mason, C. E., Olson, S., Pervouchine, D., Sloan, C. A., Wei, X., Zhan, L., Irizarry, R. A. (April 2016) A benchmark for RNA-seq quantification pipelines. Genome Biol, 17 (1). p. 74. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Bhagwat, A. S., Roe, J. S., Mok, B. Y., Hohmann, A. F., Shi, J., Vakoc, C. R. (April 2016) BET Bromodomain Inhibition Releases the Mediator Complex from Select cis-Regulatory Elements. Cell Rep, 15 (3). pp. 519-30. ISSN 2211-1247 (Electronic)

Schoffski, P., Chawla, S., Maki, R. G., Italiano, A., Gelderblom, H., Choy, E., Grignani, G., Camargo, V., Bauer, S., Rha, S. Y., Blay, J. Y., Hohenberger, P., D'Adamo, D., Guo, M., Chmielowski, B., Le Cesne, A., Demetri, G. D., Patel, S. R. (April 2016) Eribulin versus dacarbazine in previously treated patients with advanced liposarcoma or leiomyosarcoma: a randomised, open-label, multicentre, phase 3 trial. Lancet, 387 (10028). pp. 1629-37. ISSN 0140-6736

Powers, S., Pollack, R. E. (April 2016) Inducing stable reversion to achieve cancer control. Nature Reviews Cancer, 16 (4). pp. 266-270. ISSN 1474-175X

Dobin, A., Gingeras, T. R. (April 2016) Optimizing RNA-Seq Mapping with STAR. Methods Mol Biol, 1415. pp. 245-262. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Atwal, G. S., Kinney, J. B. (March 2016) Learning Quantitative Sequence–Function Relationships from Massively Parallel Experiments. Journal of Statistical Physics, 162 (5). pp. 1203-1243. ISSN 00224715

Roberts, N. J., Norris, A. L., Petersen, G. M., Bondy, M. L., Brand, R., Gallinger, S., Kurtz, R. C., Olson, S. H., Rustgi, A. K., Schwartz, A. G., Stoffel, E. M., Syngal, S., Zogopoulos, G., Ali, S. Z., Axilbund, J., Chaffee, K. G., Chen, Y. C., Cote, M. L., Childs, E. J., Douville, C., Goes, F. S., Herman, J. M., Iacobuzio-Donahue, C., Kramer, M., Makohon-Moore, A., McCombie, R. W., McMahon, K. W., Niknafs, N., Parla, J., Pirooznia, M., Potash, J. B., Rhim, A. D., Smith, A. L., Wang, Y., Wolfgang, C. L., Wood, L. D., Zandi, P. P., Goggins, M., Karchin, R., Eshleman, J. R., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., Hruban, R. H., Klein, A. P. (February 2016) Whole genome sequencing defines the genetic heterogeneity of familial pancreatic cancer. Cancer Discov, 6 (2). pp. 166-175. ISSN 2159-8290 (Electronic)2159-8274 (Linking)

Wu, S., Powers, S., Zhu, W., Hannun, Y. A. (January 2016) Substantial contribution of extrinsic risk factors to cancer development. Nature, 529 (7584). pp. 43-7. ISSN 0028-0836

Breschi, A., Djebali, S., Gillis, J., Pervouchine, D. D., Dobin, A., Davis, C. A., Gingeras, T. R., Guigo, R. (2016) Gene-specific patterns of expression variation across organs and species. Genome Biol, 17 (1). p. 151. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Shen, Chen, Ipsaro, Jonathan J, Shi, Junwei, Milazzo, Joseph P, Wang, Eric, Roe, Jae-Seok, Suzuki, Yutaka, Pappin, Darryl J, Joshua-Tor, Leemor, Vakoc, Christopher R (December 2015) NSD3-Short Is an Adaptor Protein that Couples BRD4 to the CHD8 Chromatin Remodeler. Molecular Cell, 60 (6). pp. 847-859. ISSN 1097-2765

Sanchez, Carlos G, Teixeira, Felipe Karam, Czech, Benjamin, Preall, Jonathan B, Zamparini, Andrea L, Seifert, Jessica R K., Malone, Colin D, Hannon, Gregory J, Lehmann, Ruth (December 2015) Regulation of Ribosome Biogenesis and Protein Synthesis Controls Germline Stem Cell Differentiation. Cell Stem Cell, 18 (2). pp. 276-290. ISSN 1934-5909

Bott, A. J., Peng, I. C., Fan, Y., Faubert, B., Zhao, L., Li, J., Neidler, S., Sun, Y., Jaber, N., Krokowski, D., Lu, W., Pan, J. A., Powers, S., Rabinowitz, J., Hatzoglou, M., Murphy, D. J., Jones, R., Wu, S., Girnun, G., Zong, W. X. (December 2015) Oncogenic Myc Induces Expression of Glutamine Synthetase through Promoter Demethylation. Cell Metab, 22 (6). pp. 1068-77. ISSN 1550-4131

Matthews, G. M., Mehdipour, P., Cluse, L. A., Falkenberg, K. J., Wang, E., Roth, M., Santoro, F., Vidacs, E., Stanley, K., House, C. M., Rusche, J. R., Vakoc, C. R., Zuber, J., Minucci, S., Johnstone, R. W. (November 2015) Functional-genetic dissection of HDAC dependencies in mouse lymphoid and myeloid malignancies. Blood, 126 (21). pp. 2392-2403. ISSN 1528-0020 (Electronic)0006-4971 (Linking)

Montal, E. D., Dewi, R., Bhalla, K., Ou, L., Hwang, B. J., Ropell, A. E., Gordon, C., Liu, W. J., DeBerardinis, R. J., Sudderth, J., Twaddel, W., Boros, L. G., Shroyer, K. R., Duraisamy, S., Drapkin, R., Powers, R. S., Rohde, J. M., Boxer, M. B., Wong, K. K., Girnun, G. D. (November 2015) PEPCK Coordinates the Regulation of Central Carbon Metabolism to Promote Cancer Cell Growth. Mol Cell, 60 (4). pp. 571-83. ISSN 1097-2765

Chakrabortty, S. K., Prakash, A., Nechooshtan, G., Hearn, S., Gingeras, T. R. (November 2015) Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. RNA, 21 (11). pp. 1966-1979. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M., Schatz, M. C. (November 2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking) (Public Dataset)

Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M. C., McCombie, W. R. (November 2015) Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res, 25 (11). pp. 1750-1756. ISSN 1088-9051

Jin, Y., Tam, O. H., Paniagua, E., Hammell, M. (November 2015) TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics, 31 (22). pp. 3593-3599. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

Yu, Y., Gu, J., Jin, Y., Luo, Y., Preall, J. B., Ma, J., Czech, B., Hannon, G. J. (October 2015) Panoramix enforces piRNA-dependent cotranscriptional silencing. Science, 350 (6258). pp. 339-42. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Tajima, K., Yae, T., Javaid, S., Tam, O., Comaills, V., Morris, R., Wittner, B. S., Liu, M., Engstrom, A., Takahashi, F., Black, J. C., Ramaswamy, S., Shioda, T., Hammell, M., Haber, D. A., Whetstine, J. R., Maheswaran, S. (September 2015) SETD1A modulates cell cycle progression through a miRNA network that regulates p53 target genes. Nat Commun, 6. p. 8257. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Rathert, P., Roth, M., Neumann, T., Muerdter, F., Roe, J. S., Muhar, M., Deswal, S., Cerny-Reiterer, S., Peter, B., Jude, J., Hoffmann, T., Boryn, L. M., Axelsson, E., Schweifer, N., Tontsch-Grunt, U., Dow, L. E., Gianni, D., Pearson, M., Valent, P., Stark, A., Kraut, N., Vakoc, C. R., Zuber, J. (September 2015) Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature, 525. pp. 543-547. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Dobin, A., Gingeras, T. R. (September 2015) Mapping RNA-seq Reads with STAR. Curr Protoc Bioinformatics, 51. 11.14.1-11.14.19. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Bhagwat, A. S., Vakoc, C. R. (September 2015) Targeting Transcription Factors in Cancer. Trends Cancer, 1 (1). pp. 53-65. ISSN 2405-8033 (Print)

Goh, W. S., Falciatori, I., Tam, O. H., Burgess, R., Meikar, O., Kotaja, N., Hammell, M., Hannon, G. J. (May 2015) piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev, 29 (10). pp. 1032-44. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Blank, H. M., Sheltzer, J. M., Meehl, C. M., Amon, A. (April 2015) Mitotic entry in the presence of DNA damage is a widespread property of aneuploidy in yeast. Mol Biol Cell, 26 (8). pp. 1440-51. ISSN 1939-4586 (Electronic)1059-1524 (Linking)

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