Items where Community is "Krasnitz lab"

Paper

Tonelli, Claudia, Yordanov, Georgi N, Hao, Yuan, Deschênes, Astrid, Hinds, Juliene, Belleau, Pascal, Klingbeil, Olaf, Brosnan, Erin, Doshi, Abhishek, Park, Youngkyu, Hruban, Ralph H, Vakoc, Christopher R, Dobin, Alexander, Preall, Jonathan, Tuveson, David A (January 2024) A mucus production programme promotes classical pancreatic ductal adenocarcinoma. Gut. ISSN 0017-5749

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

Ganzel, Chezi, Sun, Zhuoxin, Baslan, Timour, Zhang, Yanming, Gönen, Mithat, Abdel-Wahab, Omar I, Racevskis, Janis, Garrett-Bakelman, Francine, Lowe, Scott W, Fernandez, Hugo F, Ketterling, Rhett, Luger, Selina M, Litzow, Mark, Lazarus, Hillard M, Rowe, Jacob M, Tallman, Martin S, Levine, Ross L, Paietta, Elisabeth (December 2022) Measurable residual disease by flow cytometry in acute myeloid leukemia is prognostic, independent of genomic profiling. Leukemia Research, 123. p. 106971. ISSN 0145-2126

Barriga, Francisco M, Tsanov, Kaloyan M, Ho, Yu-Jui, Sohail, Noor, Zhang, Amy, Baslan, Timour, Wuest, Alexandra N, Del Priore, Isabella, Meškauskaitė, Brigita, Livshits, Geulah, Alonso-Curbelo, Direna, Simon, Janelle, Chaves-Perez, Almudena, Bar-Sagi, Dafna, Iacobuzio-Donahue, Christine A, Notta, Faiyaz, Chaligne, Ronan, Sharma, Roshan, Pe'er, Dana, Lowe, Scott W (November 2022) MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis. Nature Cancer, 3 (11). pp. 1367-1385. ISSN 2662-1347

Matsukawa, Toshihiro, Yin, Mianmian, Baslan, Timour, Chung, Yang Jo, Cao, Dengchao, Bertoli, Ryan, Zhu, Yuelin J, Walker, Robert L, Freeland, Amy, Knudsen, Erik, Lowe, Scott W, Meltzer, Paul S, Aplan, Peter D (September 2022) Mcm2 hypomorph leads to acute leukemia or hematopoietic stem cell failure, dependent on genetic context. The FASEB Journal, 36 (9). e22430. ISSN 0892-6638

Baslan, Timour, Morris, John P, Zhao, Zhen, Reyes, Jose, Ho, Yu-Jui, Tsanov, Kaloyan M, Bermeo, Jonathan, Tian, Sha, Zhang, Sean, Askan, Gokce, Yavas, Aslihan, Lecomte, Nicolas, Erakky, Amanda, Varghese, Anna M, Zhang, Amy, Kendall, Jude, Ghiban, Elena, Chorbadjiev, Lubomir, Wu, Jie, Dimitrova, Nevenka, Chadalavada, Kalyani, Nanjangud, Gouri J, Bandlamudi, Chaitanya, Gong, Yixiao, Donoghue, Mark TA, Socci, Nicholas D, Krasnitz, Alex, Notta, Faiyaz, Leach, Steve D, Iacobuzio-Donahue, Christine A, Lowe, Scott W (August 2022) Ordered and deterministic cancer genome evolution after p53 loss. Nature. ISSN 0028-0836

Belleau, Pascal, Deschênes, Astrid, Tuveson, David, Krasnitz, Alexander (February 2022) Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms. BioRxiv. (Unpublished)

Paffenholz, Stella V, Salvagno, Camilla, Ho, Yu-Jui, Limjoco, Matthew, Baslan, Timour, Tian, Sha, Kulick, Amanda, de Stanchina, Elisa, Wilkinson, John E, Barriga, Francisco M, Zamarin, Dmitriy, Cubillos-Ruiz, Juan R, Leibold, Josef, Lowe, Scott W (February 2022) Senescence induction dictates response to chemo- and immunotherapy in preclinical models of ovarian cancer. Proceedings of the National Academy of Sciences of USA, 119 (5). e2117754119-e2117754119. ISSN 0027-8424

Baslan, Timour, Kovaka, Sam, Sedlazeck, Fritz J, Zhang, Yanming, Wappel, Robert, Tian, Sha, Lowe, Scott W, Goodwin, Sara, Schatz, Michael C (September 2021) High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Research. ISSN 0305-1048

Lawrence, R, Ranade, N, Sullivan, D (June 2021) Quantitative towers in finite difference calculus approximating the continuum. Quarterly Journal of Mathematics, 72 (1-2). pp. 515-545. ISSN 0033-5606

Miyabayashi, Koji, Baker, Lindsey A, Deschênes, Astrid, Traub, Benno, Caligiuri, Giuseppina, Plenker, Dennis, Alagesan, Brinda, Belleau, Pascal, Li, Siran, Kendall, Jude, Jang, Gun Ho, Kawaguchi, Risa Karakida, Somerville, Tim DD, Tiriac, Hervé, Hwang, Chang-Il, Burkhart, Richard A, Roberts, Nicholas J, Wood, Laura D, Hruban, Ralph H, Gillis, Jesse, Krasnitz, Alexander, Vakoc, Christopher R, Wigler, Michael, Notta, Faiyaz, Gallinger, Steven, Park, Youngkyu, Tuveson, David A (October 2020) Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes. Cancer Discovery, 10 (10). pp. 1566-1589. ISSN 2159-8274

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.

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

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)

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. (November 2019) Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res, 30 (1). pp. 49-61. ISSN 1088-9051 (Public Dataset)

Thorsson, Vésteinn, Gibbs, David L, Brown, Scott D, Wolf, Denise, Bortone, Dante S, Ou Yang, Tai-Hsien, Porta-Pardo, Eduard, Gao, Galen F, Plaisier, Christopher L, Eddy, James A, Ziv, Elad, Culhane, Aedin C, Paull, Evan O, Sivakumar, IK Ashok, Gentles, Andrew J, Malhotra, Raunaq, Farshidfar, Farshad, Colaprico, Antonio, Parker, Joel S, Mose, Lisle E, Vo, Nam Sy, Liu, Jianfang, Liu, Yuexin, Rader, Janet, Dhankani, Varsha, Reynolds, Sheila M, Bowlby, Reanne, Califano, Andrea, Cherniack, Andrew D, Anastassiou, Dimitris, Bedognetti, Davide, Mokrab, Younes, Newman, Aaron M, Rao, Arvind, Chen, Ken, Krasnitz, Alexander, Hu, Hai, Malta, Tathiane M, Noushmehr, Houtan, Pedamallu, Chandra Sekhar, Bullman, Susan, Ojesina, Akinyemi I, Lamb, Andrew, Zhou, Wanding, Shen, Hui, Choueiri, Toni K, Weinstein, John N, Guinney, Justin, Saltz, Joel, Holt, Robert A, Rabkin, Charles S, Cancer Genome Atlas Research Network, Lazar, Alexander J, Serody, Jonathan S, Demicco, Elizabeth G, Disis, Mary L, Vincent, Benjamin G, Shmulevich, Ilya (August 2019) The Immune Landscape of Cancer [Correction]. Immunity, 51 (2). pp. 411-412. ISSN 1074-7613

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

Boutchueng-Djidjou, M., Belleau, P., Bilodeau, N., Fortier, S., Bourassa, S., Droit, A., Elowe, S., Faure, R. L. (October 2018) A type 2 diabetes disease module with a high collective influence for Cdk2 and PTPLAD1 is localized in endosomes. PLoS One, 13 (10). e0205180. ISSN 1932-6203

Malta, T. M., Sokolov, A., Gentles, A. J., Burzykowski, T., Poisson, L., Weinstein, J., Kaminska, B., Huelsken, J., Omberg, L., Gevaert, O., Colaprico, A., Czerwinska, P., Mazurek, S., Mishra, L., Heyn, H., Krasnitz, A., Godwin, A. K., Lazar, A. J., Stuart, J. M., Hoadley, K., Laird, P. W., Noushmehr, H., Wiznerowicz, M., Canc Genome Atlas Res, Network (July 2018) Comprehensive analysis of cancer stemness. Cancer Research, 78 (13 S). LB-373. ISSN 0008-5472

Malhotra, R., Krasnitz, A., Sethi, A., Lehnert, E., Williams, E. H., Brandi, D. D. N. (July 2018) Low-cost and accurate human leukocyte antigen (HLA) class I typing of The Cancer Genome Atlas on the Seven Bridges Cancer Genomics Cloud. Cancer Research, 78 (13 S). Meeting Abstract: 2348 . ISSN 0008-5472

Tiriac, H., Belleau, P., Engle, D. D., Plenker, D., Deschenes, A., Somerville, T., Froeling, F. E. M., Burkhart, R. A., Denroche, R. E., Jang, G. H., Miyabayashi, K., Young, C. M., Patel, H., Ma, M., LaComb, J. F., Palmaira, R. L. D., Javed, A. A., Huynh, J. A., Johnson, M., Arora, K., Robine, N., Shah, M., Sanghvi, R., Goetz, A. B., Lowder, C. Y., Martello, L., Driehuis, E., Lecomte, N., Askan, G., Iacobuzio-Donahue, C. A., Clevers, H., Wood, L. D., Hruban, R. H., Thompson, E. D., Aguirre, A. J., Wolpin, B. M., Sasson, A., Kim, J., Wu, M., Bucobo, J. C., Allen, P. J., Sejpal, D. V., Nealon, W., Sullivan, J. D., Winter, J. M., Gimotty, P. A., Grem, J. L., DiMaio, D. J., Buscaglia, J. M., Grandgenett, P. M., Brody, J. R., Hollingsworth, M. A., O'Kane, G. M., Notta, F., Kim, E. J., Crawford, J. M., Devoe, C. E., Ocean, A., Wolfgang, C. L., Yu, K. H., Li, E., Vakoc, C. R., Hubert, B., Fischer, S. E., Wilson, J. M., Moffitt, R. A., Knox, J. J., Krasnitz, A., Gallinger, S., Tuveson, D. A. (May 2018) Organoid profiling identifies common responders to chemotherapy in pancreatic cancer. Cancer Discovery, 8 (9). pp. 1112-1129. ISSN 21598274 (Public Dataset)

Thorsson, V., Gibbs, D. L., Brown, S. D., Wolf, D., Bortone, D. S., Ou Yang, T. H., Porta-Pardo, E., Gao, G. F., Plaisier, C. L., Eddy, J. A., Ziv, E., Culhane, A. C., Paull, E. O., Sivakumar, I. K. A., Gentles, A. J., Malhotra, R., Farshidfar, F., Colaprico, A., Parker, J. S., Mose, L. E., Vo, N. S., Liu, J., Liu, Y., Rader, J., Dhankani, V., Reynolds, S. M., Bowlby, R., Califano, A., Cherniack, A. D., Anastassiou, D., Bedognetti, D., Rao, A., Chen, K., Krasnitz, A., Hu, H., Malta, T. M., Noushmehr, H., Pedamallu, C. S., Bullman, S., Ojesina, A. I., Lamb, A., Zhou, W., Shen, H., Choueiri, T. K., Weinstein, J. N., Guinney, J., Saltz, J., Holt, R. A., Rabkin, C. E., Lazar, A. J., Serody, J. S., Demicco, E. G., Disis, M. L., Vincent, B. G., Shmulevich, L. (April 2018) The Immune Landscape of Cancer. Immunity, 48 (4). pp. 812-830. ISSN 1074-7613

Malta, T. M., Sokolov, A., Gentles, A. J., Burzykowski, T., Poisson, L., Weinstein, J. N., Kaminska, B., Huelsken, J., Omberg, L., Gevaert, O., Colaprico, A., Czerwinska, P., Mazurek, S., Mishra, L., Heyn, H., Krasnitz, A., Godwin, A. K., Lazar, A. J., Stuart, J. M., Hoadley, K. A., Laird, P. W., Noushmehr, H., Wiznerowicz, M. (April 2018) Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell, 173 (2). 338-354.e15. ISSN 0092-8674

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

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

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

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)

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)

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

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

Kendall, J., Krasnitz, A. (July 2014) Computational methods for DNA copy-number analysis of tumors. Methods in Molecular Biology, 1176. pp. 243-59. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Rajaram, M., Zhang, J., Wang, T., Li, J., Kuscu, C., Qi, H., Kato, M., Grubor, V., Weil, R. J., Helland, A., Borrenson-Dale, A. L., Cho, K. R., Levine, D. A., Houghton, A. N., Wolchok, J. D., Myeroff, L., Markowitz, S. D., Lowe, S. W., Zhang, M., Krasnitz, A., Lucito, R., Mu, D., Powers, R. S. (June 2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, 8 (6). e66264. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Krasnitz, A., Sun, G., Andrews, P., Wigler, M. (June 2013) Target inference from collections of genomic intervals. Proceedings of the National Academy of Sciences of the United States of America, 110 (25). E2271-E2278. ISSN 0027-8424

Miething, C., Scuoppo, C., Lindqvist, L., Reyes, J., Ruse, C., Appelmann, I., Yoon, S., Krasnitz, A., Teruya-Feldstein, J., Pappin, D., Pelletier, J., Lowe, S. (October 2012) An oncogenome-based RNAi screen identifies a tumour suppressor network in B-cell lymphoma relying on the polyamine-hypusine axis. Onkologie, 35. p. 104. ISSN 0378-584X

Scuoppo, C., Miething, C., Lindqvist, L., Reyes, J., Ruse, C., Appelmann, I., Yoon, S., Krasnitz, A., Teruya-Feldstein, J., Pappin, D., Pelletier, J., Lowe, S. W. (July 2012) A tumour suppressor network relying on the polyamine-hypusine axis. Nature, 487 (7406). pp. 244-8. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Kitzing, T., Xue, W., Roessler, S., Krasnitz, A., Schultz, N., Wang, X. W., Wigler, M., Lowe, S. W. (July 2012) Cooperating Tumor Suppressor Genes on Chromosome 8p Predict Survival Outcome in Hepatocellular Carcinoma. European Journal of Cancer, 48. S139-S139. ISSN 0959-8049

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., Revill, K., Weissmueller, S., Rappaport, A. R., Simon, J., Zhang, J., Luo, W. J., Hicks, J., Zender, L., Wang, X. W., Powers, S., Wigler, M., Lowe, S. W. (May 2012) A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109 (21). pp. 8212-8217. ISSN 0027-8424

Mazurek, A., Luo, W., Krasnitz, A., Hicks, J., Powers, R. S., Stillman, B. (2012) DDX5 regulates DNA replication and is required for cell proliferation in a subset of breast cancer cells. Cancer Discovery, 2 (9). pp. 812-825. ISSN 21598274 (ISSN)

Navin, N. E., Kendall, J. T., Troge, J. E., Andrews, P., Rodgers,  L., McIndoo, J., Cook, K., Stepansky,  A., Levy, D., Esposito, D., Muthuswamy, L., Krasnitz, A., McCombie, W. R., Hicks, J. B., Wigler, M. H. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472 (7341). pp. 90-94. ISSN 00280836 (ISSN)

Schreiber, S. L., Shamji, A. F., Clemons, P. A., Hon, C., Koehler, A. N., Munoz, B., Palmer, M., Stern, A. M., Wagner, B. K., Powers, S., Lowe, S. W., Guo, X., Krasnitz, A., Sawey, E. T., Sordella, R., Stein, L. D., Trotman, L. C., Califano, A., Dalla-Favera, R., Ferrando, A., Iavarone, A., Pasqualucci, L., Silva, J., Stockwell, B. R., Hahn, W. C., Chin, L., DePinho, R. A., Boehm, J. S., Gopal, S., Huang, A., Root, D. E., Weir, B. A., Gerhard, D. S., Zenklusen, J. C., Roth, M. G., White, M. A., Minna, J. D., MacMillan, J. B., Posner, B. A. (September 2010) Towards patient-based cancer therapeutics. Nature Biotechnology, 28 (9). pp. 904-906.

Russnes, H. G., Vollan, H. K. M., Lingjærde, O. C., Krasnitz, A., Lundin, P., Naume, B., Sørlie, T., Borgen, E., Rye, I. H., Langerød, A., Chin, S. F., Teschendorff, A. E., Stephens, P. J., Månér, S., Schlichting, E., Baumbusch, L. O., Kåresen, R., Stratton, M. P., Wigler, M. H., Caldas, C., Zetterberg, A., Hicks, J. B., Børresen-Dale, A. L. (June 2010) Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Science Translational Medicine, 2 (38).

Floer, M., Wang, X., Prabhu, V., Berrozpe, G., Narayan, S., Spagna, D., Alvarez, D., Kendall, J. T., Krasnitz, A., Stepansky,  A., Hicks, J. B., Bryant, G. O., Ptashne, M. (April 2010) A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell, 141 (3). pp. 407-418.

Navin, N. E., Krasnitz, A., Rodgers, L., Cook, K., Meth, J. L., Kendall, J. T., Riggs, M., Eberling, Y., Troge, J. E., Grubor, V., Levy, D., Lundin, P., Månér, S., Zetterberg, A., Hicks, J. B., Wigler, M. H. (January 2010) Inferring tumor progression from genomic heterogeneity. Genome Research, 20 (1). pp. 68-80.

Kato, M., Kawaguchi, T., Ishikawa, S., Umeda, T., Nakamichi, R., Shapero, M. H., Jones, K. W., Nakamura, Y., Aburatani, H., Tsunoda, T. (2010) Population-genetic nature of copy number variations in the human genome. Human Molecular Genetics, 19 (5). pp. 761-773.

Harris, L. N., Parker, J., Broadwater, G., Schulz, V., Halligan, K., Geyda, K., Seidman, A., Berry, D., Winer, E., Hudis, C., Krasnitz, A., Hicks, J., Tuck, D. P., Perou, C. (December 2009) Genome-Wide Profiling of Archived Material from CALGB 9840 and 9342 for Paclitaxel (P) and Trastuzumab (T) Response Biomarkers Using Gene Expression and Copy Number Analysis. Cancer Research, 69 (24 (S3). 716S-717S. ISSN 0008-5472

Bric, A., Miething, C., Bialucha, C. U., Scuoppo, C., Zender, L., Krasnitz, A., Xuan, Z., Zuber, J., Wigler, M. H., Hicks, J. B., McCombie, W. R., Hemann, M. T., Hannon, G. J., Powers, S., Lowe, S. W. (October 2009) Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell, 16 (4). pp. 324-35. ISSN 1535-6108

Russnes, H. G., Vollan, H. K. M., Sorlie, T., Krasnitz, A., Zetterberg, A., Naume, B., Borgen, E., Nesland, J. M., Wigler, M. H., Borresen-Dale, A. L., Hicks, J. B. (March 2009) Molecular subclassification of breast carcinomas based on aCGH reveals two major groups of tumors with common genomic, transcriptomic and clinicopathological characteristics. APMIS, 117 (3). pp. 238-239. ISSN 0903-4641

Grubor, V., Krasnitz, A., Troge, J. E., Meth, J. L., Lakshmi, B., Kendall, J. T., Yamrom, B., Alex, G., Pai, D., Navin, N. E., Hufnagel, L. A., Lee, Y. H., Cook, K., Allen, S. L., Rai, K. R., Damle, R. N., Calissano, C., Chiorazzi, N., Wigler, M. H., Esposito, D. (February 2009) Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood, 113 (6). pp. 1294-1303. ISSN 0006-4971

Zender, L., Xue, W., Zuber, J., Semighini, C. P., Krasnitz, A., Ma, B., Zender, P., Kubicka, S., Luk, J. M., Schirmacher, P., McCombie, W. R., Wigler, M. H., Hicks, J. B., Hannon, G. J., Powers, S., Lowe, S. W. (November 2008) An Oncogenomics-Based In Vivo RNAi Screen Identifies Tumor Suppressors in Liver Cancer. Cell, 135 (5). pp. 852-864. ISSN 0092-8674

Xiang, B., Chatti, K., Qiu, H., Lakshmi, B., Krasnitz, A., Hicks, J. B., Yu, M., Miller, W. T., Muthuswamy, S. K. (August 2008) Brk is coamplified with ErbB2 to promote proliferation in breast cancer. Proc Natl Acad Sci U S A, 105 (34). pp. 12463-8.

Russnes, H. G., Sorlie, T., Krasnitz, A., Zetterberg, A., Naume, B., Borgen, E., Nesland, J. M., Wigler, M. H., Borresen-Dale, A. L., Hicks, J. B. (July 2008) Molecular subclassification of breast carcinomas based on aCGH, gene expression, IHC and ploidy - relevance for clinical outcome. European Journal of Cancer Supplements, 6 (9). p. 9. ISSN 1359-6349

Xue, W., Krasnitz, A., Lucito, R., Sordella, R., Van Aelst, L., Cordon-Cardo, C., Singer, S., Kuehnel, F., Wigler, M. H., Powers, S., Zender, L., Lowe, S. W. (June 2008) DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma. Genes & Development, 22 (11). pp. 1439-44. ISSN 0890-9369

Kendall, J. T., Liu, Q. A., Bakleh, A., Krasnitz, A., Nguyen, K. C. Q., Lakshmi, B., Gerald, W., Powers, S., Mu, D. (October 2007) Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer. Proc Natl Acad Sci U S A, 104 (42). pp. 16663-16668. ISSN 0027-8424 (Print)

Lucito, R., Suresh, S., Walter, K., Pandey, A., Lakshmi, B., Krasnitz, A., Sebat, J., Wigler, M. H., Klein, A. P., Brune, K., Palmisano, E., Maitra, A., Goggins, M., Hruban, R. H. (October 2007) Copy-Number Variants in Patients with a Strong Family History of Pancreatic Cancer. Cancer Biol Ther, 6 (10). pp. 1592-9. ISSN 1538-4047 (Print)

Sebat, J., Lakshmi, B., Malhotra, D., Troge, J. E., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J. T., Leotta, A., Pai, D., Zhang, R., Lee, Y. H., Hicks, J. B., Spence, S. J., Lee, A. T., Puura, K., Lehtimaki, T., Ledbetter, D., Gregersen, P. K., Bregman, J., Sutcliffe, J. S., Jobanputra, V., Chung, W., Warburton, D., King, M. C., Skuse, D., Geschwind, D. H., Gilliam, T. C., Ye, K., Wigler, M. H. (April 2007) Strong Association of De Novo Copy Number Mutations with Autism. Science, 316 (5823). pp. 445-449.

Hicks, J. B., Krasnitz, A., Lakshmi, B., Navin, N. E., Riggs, M., Leibu, E., Esposito, D., Alexander, J., Troge, J. E., Grubor, V., Yoon, S., Wigler, M. H., Ye, K., Borresen-Dale, A. L., Naume, B., Schlicting, E., Norton, L., Hagerstrom, T., Skoog, L., Auer, G., Månér, S., Lundin, P., Zetterberg, A. (December 2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Research, 16 (12). pp. 1465-79. ISSN 1088-9051

Hicks, J. B., Muthuswamy, L., Krasnitz, A., Navin, N. E., Riggs, M., Grubor, V., Esposito, D., Alexander, J., Troge, J. E., Wigler, M. H., Maner, S., Lundin, P., Zetterberg, A. (2005) High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. Cold Spring Harb Symp Quant Biol, 70. pp. 51-63. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

Conference or Workshop Item

Belleau, Pascal, Deschenes, Astrid, Tuveson, David A, Krasnitz, Alexander (2022) Accurate inference of genetic ancestry from cancer-derived data. In: American Association for Cancer Research Annual Meeting 2022, 2022 Apr 8-13, Philadelphia, PA.

Belleau, Pascal, Deschenes, Astrid, Tuveson, David A, Krasnitz, Alexander (2022) Reliable determination of genetic ancestry from cancer-derived molecular data. In: Annual Meeting of the American-Society-of-Clinical-Oncology (ASCO), JUN 03-07, 2022.

Nattestad, Maria, Ng, Karen, Goodwin, Sara, Baslan, Timour, Sedlazeck, Fritz, Gurtowski, James, Hutton, Elizabeth, Sundaravadanam, Yogi, Garvin, Tyler, Alford, Marley, Tseng, Elizabeth, Rescheneder, Philipp, Chin, Jason, Beck, Timothy, Kramer, Melissa, McPherson, John, Hicks, James, Schatz, Michael C, McCombie, William R (2016) Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research, 2016 Apr 16-20, New Orleans, LA.

Book

Krasnitz, Alexander (2018) Cancer Bioinformatics. Humana Press. ISBN 9781493988686

Video

Krasnitz, A. (November 2012) Talk from Alex Krasnitz at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)