Search Results - "Culhane, Aedin"

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models by Schröder, Markus S., Culhane, Aedín C., Quackenbush, John, Haibe-Kains, Benjamin

“…The survcomp package provides functions to assess and statistically compare the performance of survival/risk prediction models. It implements state-of-the-art…”
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RAP80 Targets BRCA1 to Specific Ubiquitin Structures at DNA Damage Sites by Sobhian, Bijan, Shao, Genze, Lilli, Dana R, Culhane, Aedín C, Moreau, Lisa A, Xia, Bing, Livingston, David M, Greenberg, Roger A

“…Mutations affecting the BRCT domains of the breast cancer-associated tumor suppressor BRCA1 disrupt the recruitment of this protein to DNA double-strand breaks…”
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An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence by Dhimolea, Eugen, de Matos Simoes, Ricardo, Kansara, Dhvanir, Al’Khafaji, Aziz, Bouyssou, Juliette, Weng, Xiang, Sharma, Shruti, Raja, Joseline, Awate, Pallavi, Shirasaki, Ryosuke, Tang, Huihui, Glassner, Brian J., Liu, Zhiyi, Gao, Dong, Bryan, Jordan, Bender, Samantha, Roth, Jennifer, Scheffer, Michal, Jeselsohn, Rinath, Gray, Nathanael S., Georgakoudi, Irene, Vazquez, Francisca, Tsherniak, Aviad, Chen, Yu, Welm, Alana, Duy, Cihangir, Melnick, Ari, Bartholdy, Boris, Brown, Myles, Culhane, Aedin C., Mitsiades, Constantine S.

“…Treatment-persistent residual tumors impede curative cancer therapy. To understand this cancer cell state we generated models of treatment persistence that…”
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Repeatability of published microarray gene expression analyses by Jurman, Giuseppe, Page, Grier P, Ball, Catherine A, Mehta, Tapan, Falchi, Mario, Cui, Xiangqin, Coulibaly, Issa, van Noort, Vera, Nitzberg, Michael, Ioannidis, John P A, Culhane, Aedín C, Game, Laurence, Petretto, Enrico, Furlanello, Cesare, Allison, David B, Mangion, Jon

“…Four teams of analysts attempted exact reproduction of results of 18 microarray experiments published in the journal in 2005–2006 using the data and analytical…”
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A Three-Gene Model to Robustly Identify Breast Cancer Molecular Subtypes by Haibe-Kains, Benjamin, Desmedt, Christine, Loi, Sherene, Culhane, Aedin C., Bontempi, Gianluca, Quackenbush, John, Sotiriou, Christos

“…Background Single sample predictors (SSPs) and Subtype classification models (SCMs) are gene expression-based classifiers used to identify the four primary…”
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Enter the Matrix: Factorization Uncovers Knowledge from Omics by Stein-O’Brien, Genevieve L., Arora, Raman, Culhane, Aedin C., Favorov, Alexander V., Garmire, Lana X., Greene, Casey S., Goff, Loyal A., Li, Yifeng, Ngom, Aloune, Ochs, Michael F., Xu, Yanxun, Fertig, Elana J.

“…Omics data contain signals from the molecular, physical, and kinetic inter- and intracellular interactions that control biological systems. Matrix…”
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Comparative Meta-analysis of Prognostic Gene Signatures for Late-Stage Ovarian Cancer by WALDRON, Levi, HAIBE-KAINS, Benjamin, GANZFRIED, Benjamin Frederick, HUTTENHOWER, Curtis, BIRRER, Michael, PARMIGIANI, Giovanni, CULHANE, Aedín C, RIESTER, Markus, JIE DING, WANG, Xin Victoria, AHMADIFAR, Mahnaz, TYEKUCHEVA, Svitlana, BERNAU, Christoph, RISCH, Thomas

“…Ovarian cancer is the fifth most common cause of cancer deaths in women in the United States. Numerous gene signatures of patient prognosis have been proposed,…”
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Risk Prediction for Late-Stage Ovarian Cancer by Meta-analysis of 1525 Patient Samples by RIESTER, Markus, WEI WEI, BIRRER, Michael J, WALDRON, Levi, CULHANE, Aedin C, TRIPPA, Lorenzo, OLIVA, Esther, KIM, Sung-Hoon, MICHOR, Franziska, HUTTENHOWER, Curtis, PARMIGIANI, Giovanni

“…Ovarian cancer causes more than 15000 deaths per year in the United States. The survival of patients is quite heterogeneous, and accurate prognostic tools…”
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The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer by Schwede, Matthew, Waldron, Levi, Mok, Samuel C, Wei, Wei, Basunia, Azfar, Merritt, Melissa A, Mitsiades, Constantine S, Parmigiani, Giovanni, Harrington, David P, Quackenbush, John, Birrer, Michael J, Culhane, Aedín C

“…Recent efforts to improve outcomes for high-grade serous ovarian cancer, a leading cause of cancer death in women, have focused on identifying molecular…”
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Taxonomy of breast cancer based on normal cell phenotype predicts outcome by Santagata, Sandro, Thakkar, Ankita, Ergonul, Ayse, Wang, Bin, Woo, Terri, Hu, Rong, Harrell, J Chuck, McNamara, George, Schwede, Matthew, Culhane, Aedin C, Kindelberger, David, Rodig, Scott, Richardson, Andrea, Schnitt, Stuart J, Tamimi, Rulla M, Ince, Tan A

“…Accurate classification is essential for understanding the pathophysiology of a disease and can inform therapeutic choices. For hematopoietic malignancies, a…”
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Molecular Subtypes Improve Prognostic Value of International Metastatic Renal Cell Carcinoma Database Consortium Prognostic Model by de Velasco, Guillermo, Culhane, Aedín C., Fay, André P., Hakimi, A. Ari, Voss, Martin H., Tannir, Nizar M., Tamboli, Pheroze, Appleman, Leonard J., Bellmunt, Joaquim, Kimryn Rathmell, W., Albiges, Laurence, Hsieh, James J., Heng, Daniel Y. C., Signoretti, Sabina, Choueiri, Toni K.

“…Introduction Gene‐expression signatures for prognosis have been reported in localized renal cell carcinoma (RCC). The aim of this study was to test the…”
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Pleiotropic Mechanisms Drive Endocrine Resistance in the Three-Dimensional Bone Microenvironment by Dhimolea, Eugen, de Matos Simoes, Ricardo, Kansara, Dhvanir, Weng, Xiang, Sharma, Shruti, Awate, Pallavi, Liu, Zhiyi, Gao, Dong, Mitsiades, Nicholas, Schwab, Joseph H, Chen, Yu, Jeselsohn, Rinath, Culhane, Aedín C, Brown, Myles, Georgakoudi, Irene, Mitsiades, Constantine S

“…Although hormonal therapy (HT) inhibits the growth of hormone receptor-positive (HR ) breast and prostate cancers, HT resistance frequently develops within the…”
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Confounding Effects in A Six-Gene Signature Predicting Breast Cancer Lung Metastasis by CULHANE, Aedín C, QUACKENBUSH, John

“…The majority of breast cancer deaths result from metastases rather than from direct effects of the primary tumor itself. Recently, Landemaine and colleagues…”
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Genome-scale screens identify factors regulating tumor cell responses to natural killer cells by Sheffer, Michal, Lowry, Emily, Beelen, Nicky, Borah, Minasri, Amara, Suha Naffar-Abu, Mader, Chris C., Roth, Jennifer A., Tsherniak, Aviad, Freeman, Samuel S., Dashevsky, Olga, Gandolfi, Sara, Bender, Samantha, Bryan, Jordan G., Zhu, Cong, Wang, Li, Tariq, Ifrah, Kamath, Govinda M., Simoes, Ricardo De Matos, Dhimolea, Eugen, Yu, Channing, Hu, Yiguo, Dufva, Olli, Giannakis, Marios, Syrgkanis, Vasilis, Fraenkel, Ernest, Golub, Todd, Romee, Rizwan, Mustjoki, Satu, Culhane, Aedin C., Wieten, Lotte, Mitsiades, Constantine S.

“…To systematically define molecular features in human tumor cells that determine their degree of sensitivity to human allogeneic natural killer (NK) cells, we…”
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Curated single cell multimodal landmark datasets for R/Bioconductor by Eckenrode, Kelly B, Righelli, Dario, Ramos, Marcel, Argelaguet, Ricard, Vanderaa, Christophe, Geistlinger, Ludwig, Culhane, Aedin C, Gatto, Laurent, Carey, Vincent, Morgan, Martin, Risso, Davide, Waldron, Levi

“…The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous…”
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Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data by Hsu, Lauren L., Culhane, Aedin C.

“…Integrative, single-cell analyses may provide unprecedented insights into cellular and spatial diversity of the tumor microenvironment. The sparsity, noise,…”
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Software for the Integration of Multiomics Experiments in Bioconductor by Ramos, Marcel, Schiffer, Lucas, Re, Angela, Azhar, Rimsha, Basunia, Azfar, Rodriguez, Carmen, Chan, Tiffany, Chapman, Phil, Davis, Sean R, Gomez-Cabrero, David, Culhane, Aedin C, Haibe-Kains, Benjamin, Hansen, Kasper D, Kodali, Hanish, Louis, Marie S, Mer, Arvind S, Riester, Markus, Morgan, Martin, Carey, Vince, Waldron, Levi

“…Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis…”
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GeneSigDB--a curated database of gene expression signatures by Culhane, Aedín C, Schwarzl, Thomas, Sultana, Razvan, Picard, Kermshlise C, Picard, Shaita C, Lu, Tim H, Franklin, Katherine R, French, Simon J, Papenhausen, Gerald, Correll, Mick, Quackenbush, John

“…The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are…”
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Altered Cytoplasmic-to-Nuclear Ratio of Survivin Is a Prognostic Indicator in Breast Cancer by Brennan, Donal J, Rexhepaj, Elton, O'Brien, Sallyann L, McSherry, Elaine, O'Connor, Darran P, Fagan, Ailís, Culhane, Aedín C, Higgins, Desmond G, Jirstrom, Karin, Millikan, Robert C, Landberg, Goran, Duffy, Michael J, Hewitt, Stephen M, Gallagher, William M

“…Purpose: Survivin (BIRC5) is a promising tumor biomarker. Conflicting data exist on its prognostic effect in breast cancer. These data may at least be partly…”
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Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins by Shirasaki, Ryosuke, Matthews, Geoffrey M., Gandolfi, Sara, de Matos Simoes, Ricardo, Buckley, Dennis L., Raja Vora, Joseline, Sievers, Quinlan L., Brüggenthies, Johanna B., Dashevsky, Olga, Poarch, Haley, Tang, Huihui, Bariteau, Megan A., Sheffer, Michal, Hu, Yiguo, Downey-Kopyscinski, Sondra L., Hengeveld, Paul J., Glassner, Brian J., Dhimolea, Eugen, Ott, Christopher J., Zhang, Tinghu, Kwiatkowski, Nicholas P., Laubach, Jacob P., Schlossman, Robert L., Richardson, Paul G., Culhane, Aedin C., Groen, Richard W.J., Fischer, Eric S., Vazquez, Francisca, Tsherniak, Aviad, Hahn, William C., Levy, Joan, Auclair, Daniel, Licht, Jonathan D., Keats, Jonathan J., Boise, Lawrence H., Ebert, Benjamin L., Bradner, James E., Gray, Nathanael S., Mitsiades, Constantine S.

“…Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent…”
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