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Paper

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

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

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

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, J., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., McPherson, J., Hicks, J., McCombie, W. R., Schatz, M. C. (August 2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res, 28 (8). pp. 1126-1135. ISSN 1088-9051

Baslan, T., Hicks, J. (August 2017) Unravelling biology and shifting paradigms in cancer with single-cell sequencing. Nat Rev Cancer, 17 (9). pp. 557-569. ISSN 1474-175x

Martelotto, L. G., Baslan, T., Kendall, J., Geyer, F. C., Burke, K. A., Spraggon, L., Piscuoglio, S., Chadalavada, K., Nanjangud, G., Ng, C. K., Moody, P., D'Italia, S., Rodgers, L., Cox, H., da Cruz Paula, A., Stepansky, A., Schizas, M., Wen, H. Y., King, T. A., Norton, L., Weigelt, B., Hicks, J. B., Reis-Filho, J. S. (March 2017) Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Nat Med, 23 (3). pp. 376-385. ISSN 1546-170X (Electronic)1078-8956 (Linking)

Piscuoglio, S., Ng, C. K., Murray, M. P., Guerini-Rocco, E., Martelotto, L. G., Geyer, F. C., Bidard, F. C., Berman, S., Fusco, N., Sakr, R. A., Eberle, C., De Mattos-Arruda, L., Macedo, G. S., Akram, M., Baslan, T., Hicks, J., King, T. A., Brogi, E., Norton, L., Weigelt, B., Hudis, C. A., Reis-Filho, J. S. (March 2016) The Genomic Landscape of Male Breast Cancers. Clin Cancer Res, 22 (16). pp. 4045-56. ISSN 1078-0432 (Electronic)1078-0432 (Linking)

Baslan, T., Kendall, J., Rodgers, L., Cox, H., Riggs, M., Stepansky, A., Troge, J., Ravi, K., Esposito, D., Lakshmi, B., Wigler, M., Navin, N., Hicks, J. (March 2016) Corrigendum: Genome-wide copy number analysis of single cells. Nat Protoc, 11 (3). p. 616. ISSN 1750-2799

Martelotto, L. G., Baslan, T., Kendall, J., Rodgers, L., Cox, H., King, T. A., Weigelt, B., Hicks, J., Reis, J. S. (February 2016) Single cell sequencing analysis of formalin-fixed paraffin-embedded ductal carcinomas in situ and invasive breast cancers reveals clonal selection in the progression from in situ to invasive disease. Cancer Research, 76 (Supple). Abstract P2-05. ISSN 0008-5472

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)

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

Piscuoglio, S., Murray, M., Ng, C. K. Y., Rocco, E. G., Martelotto, L. G., Bidard, F. C., Eberle, C. A., Fusco, N., Sakr, R. A., De Mattos-Arruda, L., Lim, R., Baslan, T., Hicks, J., King, T. A., Brogi, E., Norton, L., Weigelt, B., Hudis, C. A., Reis, J. S. (May 2015) The genomic landscape of male breast cancers. Cancer Research, 75 (9 Supp). ISSN 0008-5472

Garvin, Tyler, Aboukhalil, Robert, Kendall, Jude, Baslan, Timour, Atwal, Gurinder S, Hicks, James, Wigler, Michael, Schatz, Michael (2015) Interactive analysis and quality assessment of single-cell copy-number variations. Nature Methods, 12. pp. 1058-1060. ISSN 15487091 (ISSN)

Dago, A. E., Stepansky, A., Carlsson, A., Luttgen, M., Kendall, J., Baslan, T., Kolatkar, A., Wigler, M., Bethel, K., Gross, M. E., Hicks, J., Kuhn, P. (August 2014) Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells. PLoS One, 9 (8). e101777. ISSN 1932-6203

Baslan, T., Hicks, J. (July 2014) Single cell sequencing approaches for complex biological systems. Curr Opin Genet Dev, 26c. pp. 59-65. ISSN 0959-437x

Baslan, T., Kendall, J. T., Rodgers, L., Cox, H., Riggs, M., Stepansky, A., Troge, J. E., Ravi, K., Esposito, D., Lakshmi, B., Wigler, M., Navin, N. E., Hicks, J. B. (May 2012) Genome-wide copy number analysis of single cells. Nat Protoc, 7 (6). pp. 1024-41. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

Conference or Workshop Item

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.