Search Results - "CALIFANO, ANDREA"

Rewiring makes the difference by Califano, Andrea

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ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information by Lachmann, Alexander, Giorgi, Federico M, Lopez, Gonzalo, Califano, Andrea

“…The accurate reconstruction of gene regulatory networks from large scale molecular profile datasets represents one of the grand challenges of Systems Biology…”
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Functional characterization of somatic mutations in cancer using network-based inference of protein activity by Alvarez, Mariano J, Shen, Yao, Giorgi, Federico M, Lachmann, Alexander, Ding, B Belinda, Ye, B Hilda, Califano, Andrea

“…Andrea Califano, Mariano Alvarez and colleagues present an approach, VIPER, for inferring protein activity in single cancer samples based on expression of a…”
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tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma by Maute, Roy L., Schneider, Christof, Sumazin, Pavel, Holmes, Antony, Califano, Andrea, Basso, Katia, Dalla-Favera, Riccardo

“…Sequencing studies from several model systems have suggested that diverse and abundant small RNAs may be derived from tRNA, but the function of these molecules…”
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Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts by Elyada, Ela, Bolisetty, Mohan, Laise, Pasquale, Flynn, William F, Courtois, Elise T, Burkhart, Richard A, Teinor, Jonathan A, Belleau, Pascal, Biffi, Giulia, Lucito, Matthew S, Sivajothi, Santhosh, Armstrong, Todd D, Engle, Dannielle D, Yu, Kenneth H, Hao, Yuan, Wolfgang, Christopher L, Park, Youngkyu, Preall, Jonathan, Jaffee, Elizabeth M, Califano, Andrea, Robson, Paul, Tuveson, David A

“…Cancer-associated fibroblasts (CAF) are major players in the progression and drug resistance of pancreatic ductal adenocarcinoma (PDAC). CAFs constitute a…”
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Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human by Pan, Huize, Xue, Chenyi, Auerbach, Benjamin J., Fan, Jiaxin, Bashore, Alexander C., Cui, Jian, Yang, Dina Y., Trignano, Sarah B., Liu, Wen, Shi, Jianting, Ihuegbu, Chinyere O., Bush, Erin C., Worley, Jeremy, Vlahos, Lukas, Laise, Pasquale, Solomon, Robert A., Connolly, Edward S., Califano, Andrea, Sims, Peter A., Zhang, Hanrui, Li, Mingyao, Reilly, Muredach P.

“…BACKGROUND:Smooth muscle cells (SMC) play significant roles in atherosclerosis via phenotypic switching, a pathological process in which SMC dedifferentiation,…”
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Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages by Obradovic, Aleksandar, Chowdhury, Nivedita, Haake, Scott M., Ager, Casey, Wang, Vinson, Vlahos, Lukas, Guo, Xinzheng V., Aggen, David H., Rathmell, W. Kimryn, Jonasch, Eric, Johnson, Joyce E., Roth, Marc, Beckermann, Kathryn E., Rini, Brian I., McKiernan, James, Califano, Andrea, Drake, Charles G.

“…Clear cell renal carcinoma (ccRCC) is a heterogeneous disease with a variable post-surgical course. To assemble a comprehensive ccRCC tumor microenvironment…”
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Structure-based prediction of protein–protein interactions on a genome-wide scale by Zhang, Qiangfeng Cliff, Petrey, Donald, Deng, Lei, Qiang, Li, Shi, Yu, Thu, Chan Aye, Bisikirska, Brygida, Lefebvre, Celine, Accili, Domenico, Hunter, Tony, Maniatis, Tom, Califano, Andrea, Honig, Barry

“…Protein–protein interactions, essential for understanding how a cell functions, are predicted using a new method that combines protein structure with other…”
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Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations by Affo, Silvia, Nair, Ajay, Brundu, Francesco, Ravichandra, Aashreya, Bhattacharjee, Sonakshi, Matsuda, Michitaka, Chin, LiKang, Filliol, Aveline, Wen, Wen, Song, Xinhua, Decker, Aubrianna, Worley, Jeremy, Caviglia, Jorge Matias, Yu, Lexing, Yin, Deqi, Saito, Yoshinobu, Savage, Thomas, Wells, Rebecca G., Mack, Matthias, Zender, Lars, Arpaia, Nicholas, Remotti, Helen E., Rabadan, Raul, Sims, Peter, Leblond, Anne-Laure, Weber, Achim, Riener, Marc-Oliver, Stockwell, Brent R., Gaublomme, Jellert, Llovet, Josep M., Kalluri, Raghu, Michalopoulos, George K., Seki, Ekihiro, Sia, Daniela, Chen, Xin, Califano, Andrea, Schwabe, Robert F.

“…Cancer-associated fibroblasts (CAF) are a poorly characterized cell population in the context of liver cancer. Our study investigates CAF functions in…”
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Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer by Zou, Min, Toivanen, Roxanne, Mitrofanova, Antonina, Floch, Nicolas, Hayati, Sheida, Sun, Yanping, Le Magnen, Clémentine, Chester, Daniel, Mostaghel, Elahe A, Califano, Andrea, Rubin, Mark A, Shen, Michael M, Abate-Shen, Cory

“…Current treatments for castration-resistant prostate cancer (CRPC) that target androgen receptor (AR) signaling improve patient survival, yet ultimately fail…”
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An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma by Sumazin, Pavel, Yang, Xuerui, Chiu, Hua-Sheng, Chung, Wei-Jen, Iyer, Archana, Llobet-Navas, David, Rajbhandari, Presha, Bansal, Mukesh, Guarnieri, Paolo, Silva, Jose, Califano, Andrea

“…By analyzing gene expression data in glioblastoma in combination with matched microRNA profiles, we have uncovered a posttranscriptional regulation layer of…”
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Elucidating Compound Mechanism of Action by Network Perturbation Analysis by Woo, Jung Hoon, Shimoni, Yishai, Yang, Wan Seok, Subramaniam, Prem, Iyer, Archana, Nicoletti, Paola, Rodríguez Martínez, María, López, Gonzalo, Mattioli, Michela, Realubit, Ronald, Karan, Charles, Stockwell, Brent R., Bansal, Mukesh, Califano, Andrea

“…Genome-wide identification of the mechanism of action (MoA) of small-molecule compounds characterizing their targets, effectors, and activity modulators…”
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Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer by Obradovic, Aleksandar, Graves, Diana, Korrer, Michael, Wang, Yu, Roy, Sohini, Naveed, Abdullah, Xu, Yaomin, Luginbuhl, Adam, Curry, Joseph, Gibson, Michael, Idrees, Kamran, Hurley, Paula, Jiang, Peng, Liu, X Shirley, Uppaluri, Ravindra, Drake, Charles G, Califano, Andrea, Kim, Young J

“…Cancer-associated fibroblasts (CAF) have been implicated as potential mediators of checkpoint immunotherapy response. However, the extensive heterogeneity of…”
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Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state by Echeverria, Gloria V, Ge, Zhongqi, Seth, Sahil, Zhang, Xiaomei, Jeter-Jones, Sabrina, Zhou, Xinhui, Cai, Shirong, Tu, Yizheng, McCoy, Aaron, Peoples, Michael, Sun, Yuting, Qiu, Huan, Chang, Qing, Bristow, Christopher, Carugo, Alessandro, Shao, Jiansu, Ma, Xiaoyan, Harris, Angela, Mundi, Prabhjot, Lau, Rosanna, Ramamoorthy, Vandhana, Wu, Yun, Alvarez, Mariano J, Califano, Andrea, Moulder, Stacy L, Symmans, William F, Marszalek, Joseph R, Heffernan, Timothy P, Chang, Jeffrey T, Piwnica-Worms, Helen

“…Eradicating triple-negative breast cancer (TNBC) resistant to neoadjuvant chemotherapy (NACT) is a critical unmet clinical need. In this study, patient-derived…”
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The DLEU2/ miR-15a/ 16-1 Cluster Controls B Cell Proliferation and Its Deletion Leads to Chronic Lymphocytic Leukemia by Klein, Ulf, Lia, Marie, Crespo, Marta, Siegel, Rachael, Shen, Qiong, Mo, Tongwei, Ambesi-Impiombato, Alberto, Califano, Andrea, Migliazza, Anna, Bhagat, Govind, Dalla-Favera, Riccardo

“…Chronic lymphocytic leukemia (CLL) is a malignancy of B cells of unknown etiology. Deletions of the chromosomal region 13q14 are commonly associated with CLL,…”
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ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling by Yu, Jiyang, Silva, Jose, Califano, Andrea

“…Functional genomics (FG) screens, using RNAi or CRISPR technology, have become a standard tool for systematic, genome-wide loss-of-function studies for…”
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War, Sanctions, Deglobalization: Which Comes First? by Brancaccio, Emiliano, Califano, Andrea

“…We argue that the war in Ukraine and the instrument of sanctions should be framed into a long trend – from globalization and the international imbalances it…”
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NSD2 is a conserved driver of metastatic prostate cancer progression by Aytes, Alvaro, Giacobbe, Arianna, Mitrofanova, Antonina, Ruggero, Katia, Cyrta, Joanna, Arriaga, Juan, Palomero, Luis, Farran-Matas, Sonia, Rubin, Mark A., Shen, Michael M., Califano, Andrea, Abate-Shen, Cory

“…Deciphering cell-intrinsic mechanisms of metastasis progression in vivo is essential to identify novel therapeutic approaches. Here we elucidate cell-intrinsic…”
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Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer by Risom, Tyler, Langer, Ellen M., Chapman, Margaret P., Rantala, Juha, Fields, Andrew J., Boniface, Christopher, Alvarez, Mariano J., Kendsersky, Nicholas D., Pelz, Carl R., Johnson-Camacho, Katherine, Dobrolecki, Lacey E., Chin, Koei, Aswani, Anil J., Wang, Nicholas J., Califano, Andrea, Lewis, Michael T., Tomlin, Claire J., Spellman, Paul T., Adey, Andrew, Gray, Joe W., Sears, Rosalie C.

“…Intratumoral heterogeneity in cancers arises from genomic instability and epigenomic plasticity and is associated with resistance to cytotoxic and targeted…”
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Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma by Vaubel, Rachael A, Tian, Shulan, Remonde, Dioval, Schroeder, Mark A, Mladek, Ann C, Kitange, Gaspar J, Caron, Alissa, Kollmeyer, Thomas M, Grove, Rebecca, Peng, Sen, Carlson, Brett L, Ma, Daniel J, Sarkar, Gobinda, Evers, Lisa, Decker, Paul A, Yan, Huihuang, Dhruv, Harshil D, Berens, Michael E, Wang, Qianghu, Marin, Bianca M, Klee, Eric W, Califano, Andrea, LaChance, Daniel H, Eckel-Passow, Jeanette E, Verhaak, Roel G, Sulman, Erik P, Burns, Terry C, Meyer, Fredrick B, O'Neill, Brian P, Tran, Nhan L, Giannini, Caterina, Jenkins, Robert B, Parney, Ian F, Sarkaria, Jann N

“…Glioblastoma is the most frequent and lethal primary brain tumor. Development of novel therapies relies on the availability of relevant preclinical models. We…”
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