Items where Community is "Cancer Genetics"

Paper

Belleau, Pascal, Deschênes, Astrid, Chambwe, Nyasha, Tuveson, David A, Krasnitz, Alexander (December 2022) Genetic ancestry inference from cancer-derived molecular data across genomic and transcriptomic platforms. Cancer Research. CAN-22. ISSN 0008-5472

Xie, Y., Cao, Z., Wong, E. W., Guan, Y., Ma, W., Zhang, J. Q., Walczak, E. G., Murphy, D., Ran, L., Sirota, I., Wang, S., Shukla, S., Gao, D., Knott, S. R., Chang, K., Leu, J., Wongvipat, J., Antonescu, C. R., Hannon, G., Chi, P., Chen, Y. (April 2018) COP1-DET1-ETS axis regulates ERK transcriptome and sensitivity to MAPK inhibitors. J Clin Invest, 128 (4). pp. 1442-1457. ISSN 0021-9738

Chen, X., Sun, Y. C., Church, G. M., Lee, J. H., Zador, A. M. (February 2018) Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Nucleic Acids Res, 46 (4). e22. ISSN 0305-1048

Fang, Han, Huang, Yi-Fei, Radhakrishnan, Aditya, Siepel, Adam, Lyon, Gholson J., Schatz, Michael C. (February 2018) Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Systems, 6 (2). pp. 180-191. ISSN 2405-4712

Giuliano, C. J., Lin, A., Smith, J. C., Palladino, A. C., Sheltzer, J. M. (February 2018) MELK expression correlates with tumor mitotic activity but is not required for cancer growth. Elife, 7. ISSN 2050-084x

Lee, J. H. (February 2018) Tracing single-cell histories. Science, 359 (6375). pp. 521-522. ISSN 0036-8075

Danko, C. G., Choate, L. A., Marks, B. A., Rice, E. J., Wang, Z., Chu, T., Martins, A. L., Dukler, N., Coonrod, S. A., Tait Wojno, E. D., Lis, J. T., Kraus, W. L., Siepel, A. (January 2018) Dynamic evolution of regulatory element ensembles in primate CD4(+) T cells. Nat Ecol Evol. pp. 1-12. ISSN 2397-334x

Kumar, V., Rosenbaum, J., Wang, Z., Forcier, T., Ronemus, M., Wigler, M., Levy, D. (January 2018) Partial bisulfite conversion for unique template sequencing. Nucleic Acids Res, 46 (2). e10. ISSN 0305-1048

Alexander, J., Kendall, J., McIndoo, J., Rodgers, L., Aboukhalil, R., Levy, D., Stepansky, A., Sun, G., Chobadjiev, L., Riggs, M., Cox, H., Hakker, I., Nowak, D. G., Laze, J., Llukani, E., Srivastava, A., Gruschow, S., Yadav, S. S., Robinson, B. D., Atwal, G., Trotman, L. C., Lepor, H., Hicks, J. B., Wigler, M., Krasnitz, A. (January 2018) Utility of single cell genomics in diagnostic evaluation of prostate cancer. Cancer Res, 78 (2). pp. 348-358. ISSN 0008-5472

Dukler, N., Booth, G. T., Huang, Y. F., Tippens, N., Waters, C. T., Danko, C. G., Lis, J. T., Siepel, A. (November 2017) Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome Res, 27 (11). pp. 1816-1829. ISSN 1088-9051

Kato, M., Vasco, D. A., Sugino, R., Narushima, D., Krasnitz, A. (September 2017) Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer. R Soc Open Sci, 4 (9). p. 171060. ISSN 2054-5703 (Print)2054-5703

Miller, J. R., Zhou, P., Mudge, J., Gurtowski, J., Lee, H., Ramaraj, T., Walenz, B. P., Liu, J., Stupar, R. M., Denny, R., Song, L., Singh, N., Maron, L. G., McCouch, S. R., McCombie, W. R., Schatz, M. C., Tiffin, P., Young, N. D., Silverstein, K. A. T. (July 2017) Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics, 18 (1). p. 541. ISSN 1471-2164

Goodwin, S., Wappel, R., McCombie, W. R. (July 2017) 1D Genome Sequencing on the Oxford Nanopore MinION. Curr Protoc Hum Genet, 94. 18.11.1-18.11.14. ISSN 1934-8258

Lee, Je H. (July 2017) De Novo Gene Expression Reconstruction in Space. Trends in Molecular Medicine, 23 (7). pp. 583-593. ISSN 1471-4914

Krasnitz, Alexander, Kendall, Jude, Alexander, Joan, Levy, Dan, Wigler, Michael (July 2017) Early Detection of Cancer in Blood Using Single-Cell Analysis: A Proposal. Trends in Molecular Medicine, 23 (7). pp. 594-603. ISSN 1471-4914

English, W. R., Lunt, S. J., Fisher, M., Lefley, D. V., Dhingra, M., Lee, Y. C., Bingham, K., Hurrell, J. E., Lyons, S. K., Kanthou, C., Tozer, G. M. (May 2017) Differential Expression of VEGFA Isoforms Regulates Metastasis and Response to Anti-VEGFA Therapy in Sarcoma. Cancer Res, 77 (10). pp. 2633-2646. ISSN 1538-7445 (Electronic)0008-5472 (Linking)

Huang, Y. F., Gulko, B., Siepel, A. (April 2017) Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet, 49 (4). pp. 618-624. ISSN 1061-4036

Lin, A., Giuliano, C. J., Sayles, N. M., Sheltzer, J. M. (March 2017) CRISPR/Cas9 mutagenesis invalidates a putative cancer dependency targeted in on-going clinical trials. Elife, 6. e24179. ISSN 2050-084x

Lee, J. H. (March 2017) Quantitative approaches for investigating the spatial context of gene expression. Wiley Interdiscip Rev Syst Biol Med, 9 (2). ISSN 1939-005X (Electronic)1939-005X (Linking)

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)

Mills, A. A. (January 2017) The Chromodomain Helicase DNA-Binding Chromatin Remodelers: Family Traits that Protect from and Promote Cancer. Cold Spring Harb Perspect Med. ISSN 2157-1422 (Electronic)2157-1422 (Linking)

Koh, S. B., Mascalchi, P., Rodriguez, E., Lin, Y., Jodrell, D. I., Richards, F. M., Lyons, S. K. (January 2017) A quantitative FastFUCCI assay defines cell cycle dynamics at a single-cell level. J Cell Sci, 130 (2). pp. 512-520. ISSN 0021-9533

Kawata, M., Taniguchi, Y., Mori, D., Yano, F., Ohba, S., Chung, U. I., Shimogori, T., Mills, A. A., Tanaka, S., Saito, T. (2017) Different regulation of limb development by p63 transcript variants. PLoS One, 12 (3). e0174122. ISSN 1932-6203

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)

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)

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

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

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)

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)

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)

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)

Asim, M., Massie, C. E., Orafidiya, F., Pertega-Gomes, N., Warren, A. Y., Esmaeili, M., Selth, L. A., Zecchini, H. I., Luko, K., Qureshi, A., Baridi, A., Menon, S., Madhu, B., Escriu, C., Lyons, S., Vowler, S. L., Zecchini, V. R., Shaw, G., Hessenkemper, W., Russell, R., Mohammed, H., Stefanos, N., Lynch, A. G., Grigorenko, E., D'Santos, C., Taylor, C., Lamb, A., Sriranjan, R., Yang, J., Stark, R., Dehm, S. M., Rennie, P. S., Carroll, J. S., Griffiths, J. R., Tavare, S., Mills, I. G., McEwan, I. J., Baniahmad, A., Tilley, W. D., Neal, D. E. (May 2016) Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target. J Natl Cancer Inst, 108 (5). ISSN 1460-2105 (Electronic)0027-8874 (Linking)

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

Liu, Y., Chen, C., Xu, Z., Scuoppo, C., Rillahan, C. D., Gao, J., Spitzer, B., Bosbach, B., Kastenhuber, E. R., Baslan, T., Ackermann, S., Cheng, L., Wang, Q., Niu, T., Schultz, N., Levine, R. L., Mills, A. A., Lowe, S. W. (March 2016) Deletions linked to TP53 loss drive cancer through p53-independent mechanisms. Nature, 531 (7595). pp. 471-475. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

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

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

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

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

Pendleton, M., Sebra, R., Pang, A. W., Ummat, A., Franzen, O., Rausch, T., Stutz, A. M., Stedman, W., Anantharaman, T., Hastie, A., Dai, H., Fritz, M. H., Cao, H., Cohain, A., Deikus, G., Durrett, R. E., Blanchard, S. C., Altman, R., Chin, C. S., Guo, Y., Paxinos, E. E., Korbel, J. O., Darnell, R. B., McCombie, W. R., Kwok, P. Y., Mason, C. E., Schadt, E. E., Bashir, A. (August 2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods, 12 (8). pp. 780-786. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Stephens, Z. D., Lee, S. Y., Faghri, F., Campbell, R. H., Zhai, C., Efron, M. J., Iyer, R., Schatz, M. C., Sinha, S., Robinson, G. E. (July 2015) Big Data: Astronomical or Genomical? PLoS Biol, 13 (7). e1002195. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

Wasik, K. A., Tam, O. H., Knott, S. R., Falciatori, I., Hammell, M., Vagin, V. V., Hannon, G. J. (June 2015) RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev, 29 (13). pp. 1403-1415. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

Wang, X., Yu, X., Zhu, W., McCombie, W. R., Antoniou, E., Powers, R. S., Davidson, N. O., Li, E., Williams, J. (June 2015) A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics, 31 (12). pp. 2040-2042. ISSN 1367-4803

Dos Santos, C. O., Dolzhenko, E., Hodges, E., Smith, A. D., Hannon, G. J. (May 2015) An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland. Cell Reports. ISSN 2211-1247

Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., Cheung, V. G., Kraus, W. L., Lis, J. T., Siepel, A. (May 2015) Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods, 12 (5). pp. 433-8. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Lyons, S. K. (May 2015) Imaging Mouse Models of Cancer. Cancer J, 21 (3). pp. 152-164. ISSN 1540-336X (Electronic)1528-9117 (Linking)

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. (May 2015) Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Research, 25 (5). pp. 714-724. ISSN 1088-9051

Teixeira, F. K., Sanchez, C. G., Hurd, T. R., Seifert, J. R., Czech, B., Preall, J. B., Hannon, G. J., Lehmann, R. (April 2015) ATP synthase promotes germ cell differentiation independent of oxidative phosphorylation. Nature Cell Biology, 17 (5). pp. 689-696. ISSN 1465-7392

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)

Wagenblast, E., Soto, M., Gutierrez-Angel, S., Hartl, C. A., Gable, A. L., Maceli, A. R., Erard, N., Williams, A. M., Kim, S. Y., Dickopf, S., Harrell, J. C., Smith, A. D., Perou, C. M., Wilkinson, J. E., Hannon, G. J., Knott, S. R. (April 2015) A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis. Nature, 520 (7547). pp. 358-362. ISSN 0028-0836

Rye, I. H., Lundin, P., Maner, S., Fjelldal, R., Naume, B., Wigler, M., Hicks, J., Borresen-Dale, A. L., Zetterberg, A., Russnes, H. G. (April 2015) Quantitative multigene FISH on breast carcinomas identifies der(1;16)(q10;p10) as an early event in luminal A tumors. Genes, Chromosomes & Cancer, 54 (4). pp. 235-48. ISSN 1045-2257

Fuda, N. J., Guertin, M. J., Sharma, S., Danko, C. G., Martins, A. L., Siepel, A., Lis, J. T. (March 2015) GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters. Plos Genetics, 11 (3). e1005108. ISSN 1553-7390

Marinov, Georgi K, Wang, Jie, Handler, Dominik, Wold, Barbara J, Weng, Zhiping, Hannon, Gregory J, Aravin, Alexei A, Zamore, Phillip D, Brennecke, Julius, Toth, Katalin Fejes (March 2015) Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified. Developmental Cell, 32 (6). pp. 765-771. ISSN 1534-5807

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Ferrante, T. C., Terry, R., Turczyk, B. M., Yang, J. L., Lee, H. S., Aach, J., Zhang, K., Church, G. M. (March 2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc, 10 (3). pp. 442-58. ISSN 1750-2799

Kirschner, K., Samarajiwa, S. A., Cairns, J. M., Menon, S., Perez-Mancera, P. A., Tomimatsu, K., Bermejo-Rodriguez, C., Ito, Y., Chandra, T., Narita, M., Lyons, S. K., Lynch, A. G., Kimura, H., Ohbayashi, T., Tavare, S., Narita, M. (March 2015) Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genet, 11 (3). e1005053. ISSN 1553-7390

Stein, P., Rozhkov, N. V., Li, F., Cardenas, F. L., Davydenk, O., Vandivier, L. E., Gregory, B. D., Hannon, G. J., Schultz, R. M. (February 2015) Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes. PLoS Genetics, 11 (2). e1005013. ISSN 1553-7390

Jayaprakash, A. D., Benson, E. K., Gone, S., Liang, R., Shim, J., Lambertini, L., Toloue, M. M., Wigler, M., Aaronson, S. A., Sachidanandam, R. (February 2015) Stable heteroplasmy at the single-cell level is facilitated by intercellular exchange of mtDNA. Nucleic Acids Research, 43 (4). pp. 2177-2187. ISSN 0305-1048

Ruiz, C., Li, J., Luttgen, M. S., Kolatkar, A., Kendall, J. T., Flores, E., Topp, Z., Samlowski, W. E., McClay, E., Bethel, K., Ferrone, S., Hicks, J., Kuhn, P. (February 2015) Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Physical biology, 12 (1). 016008. ISSN 1478-3967

Church, D. M., Schneider, V. A., Steinberg, K. M., Schatz, M. C., Quinlan, A. R., Chin, C. S., Kitts, P. A., Aken, B., Marth, G. T., Hoffman, M. M., Herrero, J., Mendoza, M. L. Z., Durbin, R., Flicek, P. (January 2015) Extending reference assembly models. Genome Biology, 16. Article no. 13. ISSN 1465-6906

Patrick, P. S., Rodrigues, T. B., Kettunen, M. I., Lyons, S. K., Neves, A. A., Brindle, K. M. (2015) Development of Timd2 as a reporter gene for MRI. Magn Reson Med. ISSN 0740-3194

Narzisi, G., Schatz, M. C. (2015) The challenge of small-scale repeats for indel discovery. Front Bioeng Biotechnol, 3. p. 8. ISSN 2296-4185

Knott, S. R., Maceli, A. R., Erard, N., Chang, K., Marran, K., Zhou, X., Gordon, A., El Demerdash, O., Wagenblast, E., Kim, S., Fellmann, C., Hannon, G. J. (December 2014) A Computational Algorithm to Predict shRNA Potency. Mol Cell, 56 (6). pp. 796-807. ISSN 1097-2765

Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., Lis, J. T. (December 2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet, 46 (12). pp. 1311-20. ISSN 1061-4036

Sun, G., Krasnitz, A. (November 2014) Significant distinct branches of hierarchical trees: a framework for statistical analysis and applications to biological data. BMC Genomics, 15. p. 1000. ISSN 1471-2164

Pratt, E. D., Stepansky, A., Hicks, J., Kirby, B. J. (November 2014) Single-cell copy number analysis of prostate cancer cells captured with geometrically enhanced differential immunocapture microdevices. Analytical Chemistry, 86 (22). pp. 11013-7. ISSN 0003-2700

Marcus, S., Lee, H., Schatz, M. C. (November 2014) SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips. Bioinformatics, 30 (24). pp. 3476-3483. ISSN 1367-4803

Levy, D., Wigler, M. (October 2014) Facilitated sequence counting and assembly by template mutagenesis. Proceedings of the National Academy of Sciences of the United States of America, 111 (43). E4632-E4637. ISSN 0027-8424

Rudalska, R., Dauch, D., Longerich, T., McJunkin, K., Wuestefeld, T., Kang, T. W., Hohmeyer, A., Pesic, M., Leibold, J., von Thun, A., Schirmacher, P., Zuber, J., Weiss, K. H., Powers, S., Malek, N.P., Eilers, M., Sipos, B., Lowe, S. W., Geffers, R., Laufer, S., Zender, L. (September 2014) In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer. Nature Medicine, 20 (10). pp. 1138-1146. ISSN 1078-8956

Deng, L., Shang, L., Bai, S., Chen, J., He, X., Trevino, R. M., Chen, S., Li, X., Meng, X., Yu, B., Wang, X., Liu, Y., McDermott, S. P., Ariazi, A. E., Ginestier, C., Ibarra, I., Ke, J., Luther, T. K., Clouthier, S. G., Xu, L., Shan, G., Song, E., Yao, H., Hannon, G. J., Weiss, S. J., Wicha, M. S., Liu, S. (September 2014) microRNA100 inhibits self-renewal of breast cancer stem-like cells and breast tumor development. Cancer Res, 74 (22). pp. 6648-6660. ISSN 0008-5472

Yang, M., Haase, A. D., Huang, F. K., Coulis, G., Rivera, K. D., Dickinson, B. C., Chang, C. J., Pappin, D. J., Neubert, T. A., Hannon, G. J., Boivin, B., Tonks, N. K. (August 2014) Dephosphorylation of Tyrosine 393 in Argonaute 2 by Protein Tyrosine Phosphatase 1B Regulates Gene Silencing in Oncogenic RAS-Induced Senescence. Mol Cell, 55 (5). pp. 782-790. ISSN 1097-2765

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