Search Results - "Miller, Martin L."

Emerging landscape of oncogenic signatures across human cancers by Ciriello, Giovanni, Miller, Martin L, Aksoy, Bülent Arman, Senbabaoglu, Yasin, Schultz, Nikolaus, Sander, Chris

“…Chris Sander and colleagues have extracted significant functional events from 12 tumor types. Tumors can be classified as being driven largely by either…”
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Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer by Rizvi, Naiyer A., Hellmann, Matthew D., Snyder, Alexandra, Kvistborg, Pia, Makarov, Vladimir, Havel, Jonathan J., Lee, William, Yuan, Jianda, Wong, Phillip, Ho, Teresa S., Miller, Martin L., Rekhtman, Natasha, Moreira, Andre L., Ibrahim, Fawzia, Bruggeman, Cameron, Gasmi, Billel, Zappasodi, Roberta, Maeda, Yuka, Sander, Chris, Garon, Edward B., Merghoub, Taha, Wolchok, Jedd D., Schumacher, Ton N., Chan, Timothy A.

“…Immune checkpoint inhibitors, which unleash a patient's own T cells to kill tumors, are revolutionizing cancer treatment. To unravel the genomic determinants…”
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Mitochondrial DNA copy number variation across human cancers by Reznik, Ed, Miller, Martin L, Şenbabaoğlu, Yasin, Riaz, Nadeem, Sarungbam, Judy, Tickoo, Satish K, Al-Ahmadie, Hikmat A, Lee, William, Seshan, Venkatraman E, Hakimi, A Ari, Sander, Chris

“…Mutations, deletions, and changes in copy number of mitochondrial DNA (mtDNA), are observed throughout cancers. Here, we survey mtDNA copy number variation…”
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Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis by Olsen, Jesper V, Vermeulen, Michiel, Santamaria, Anna, Kumar, Chanchal, Miller, Martin L, Jensen, Lars J, Gnad, Florian, Cox, Jürgen, Jensen, Thomas S, Nigg, Erich A, Brunak, Søren, Mann, Matthias

“…Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle…”
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Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs by Leslie, Christina S, Marks, Debora S, Khan, Aly A, Betel, Doron, Miller, Martin L, Sander, Chris

“…Transfection of siRNAs and miRNAs into cells has been observed to generate unexpected effects in the form of gene upregulation. By statistically analyzing…”
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Perturbation biology: inferring signaling networks in cellular systems by Molinelli, Evan J, Korkut, Anil, Wang, Weiqing, Miller, Martin L, Gauthier, Nicholas P, Jing, Xiaohong, Kaushik, Poorvi, He, Qin, Mills, Gordon, Solit, David B, Pratilas, Christine A, Weigt, Martin, Braunstein, Alfredo, Pagnani, Andrea, Zecchina, Riccardo, Sander, Chris

“…We present a powerful experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be…”
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Mutational Analysis Identifies Therapeutic Biomarkers in Inflammatory Bowel Disease-Associated Colorectal Cancers by Din, Shahida, Wong, Kim, Mueller, Mike F, Oniscu, Anca, Hewinson, James, Black, Catherine J, Miller, Martin L, Jiménez-Sánchez, Alejandro, Rabbie, Roy, Rashid, Mamunar, Satsangi, Jack, Adams, David J, Arends, Mark J

“…Inflammatory bowel disease-associated colorectal cancers (IBD-CRC) are associated with a higher mortality than sporadic colorectal cancers. The poorly defined…”
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Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases by Rabbie, Roy, Ansari-Pour, Naser, Cast, Oliver, Lau, Doreen, Scott, Francis, Welsh, Sarah J., Parkinson, Christine, Khoja, Leila, Moore, Luiza, Tullett, Mark, Wong, Kim, Ferreira, Ingrid, Gómez, Julia M. Martínez, Levesque, Mitchell, Gallagher, Ferdia A., Jiménez-Sánchez, Alejandro, Riva, Laura, Miller, Martin L., Allinson, Kieren, Campbell, Peter J., Corrie, Pippa, Wedge, David C., Adams, David J.

“…Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient…”
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Integrin-α10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma by Okada, Tomoyo, Lee, Ann Y, Qin, Li-Xuan, Agaram, Narasimhan, Mimae, Takahiro, Shen, Yawei, O'Connor, Rachael, López-Lago, Miguel A, Craig, Amanda, Miller, Martin L, Agius, Phaedra, Molinelli, Evan, Socci, Nicholas D, Crago, Aimee M, Shima, Fumi, Sander, Chris, Singer, Samuel

“…Myxofibrosarcoma is a common mesenchymal malignancy with complex genomics and heterogeneous clinical outcomes. Through gene-expression profiling of 64 primary…”
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Spatial normalization of reverse phase protein array data by Kaushik, Poorvi, Molinelli, Evan J, Miller, Martin L, Wang, Weiqing, Korkut, Anil, Liu, Wenbin, Ju, Zhenlin, Lu, Yiling, Mills, Gordon, Sander, Chris

“…Reverse phase protein arrays (RPPA) are an efficient, high-throughput, cost-effective method for the quantification of specific proteins in complex biological…”
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Copy number aberrations drive kinase rewiring, leading to genetic vulnerabilities in cancer by Memon, Danish, Gill, Michael B., Papachristou, Evangelia K., Ochoa, David, D’Santos, Clive S., Miller, Martin L., Beltrao, Pedro

“…Somatic DNA copy number variations (CNVs) are prevalent in cancer and can drive cancer progression, albeit with often uncharacterized roles in altering cell…”
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Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets by Miller, Martin L, Molinelli, Evan J, Nair, Jayasree S, Sheikh, Tahir, Samy, Rita, Jing, Xiaohong, He, Qin, Korkut, Anil, Crago, Aimee M, Singer, Samuel, Schwartz, Gary K, Sander, Chris

“…Dedifferentiated liposarcoma (DDLS) is a rare but aggressive cancer with high recurrence and low response rates to targeted therapies. Increasing treatment…”
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Kinase-specific prediction of protein phosphorylation sites by Miller, Martin L, Blom, Nikolaj

“…As extensive mass spectrometry-based mapping of the phosphoproteome progresses, computational analysis of phosphorylation-dependent signaling becomes…”
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The SH2 Domain Interaction Landscape by Tinti, Michele, Kiemer, Lars, Costa, Stefano, Miller, Martin L., Sacco, Francesca, Olsen, Jesper V., Carducci, Martina, Paoluzi, Serena, Langone, Francesca, Workman, Christopher T., Blom, Nikolaj, Machida, Kazuya, Thompson, Christopher M., Schutkowski, Mike, Brunak, Søren, Mann, Matthias, Mayer, Bruce J., Castagnoli, Luisa, Cesareni, Gianni

“…Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct…”
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Comprehensive Benchmarking and Integration of Tumor Microenvironment Cell Estimation Methods by Jiménez-Sánchez, Alejandro, Cast, Oliver, Miller, Martin L

“…Various computational approaches have been developed for estimating the relative abundance of different cell types in the tumor microenvironment (TME) using…”
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Ovarian tumors orchestrate distinct cellular compositions by Bou-Tayeh, Berna, Miller, Martin L

“…The determinants of T cell infiltration in tumors remain largely unknown. In a recent issue of Cancer Cell, Hornburg et al. use single-cell RNA sequencing to…”
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Lack of detectable neoantigen depletion signals in the untreated cancer genome by Van den Eynden, Jimmy, Jiménez-Sánchez, Alejandro, Miller, Martin L., Larsson, Erik

“…Somatic mutations can result in the formation of neoantigens, immunogenic peptides that are presented on the tumor cell surface by HLA molecules. These…”
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Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient by Jiménez-Sánchez, Alejandro, Memon, Danish, Pourpe, Stephane, Veeraraghavan, Harini, Li, Yanyun, Vargas, Hebert Alberto, Gill, Michael B., Park, Kay J., Zivanovic, Oliver, Konner, Jason, Ricca, Jacob, Zamarin, Dmitriy, Walther, Tyler, Aghajanian, Carol, Wolchok, Jedd D., Sala, Evis, Merghoub, Taha, Snyder, Alexandra, Miller, Martin L.

“…We present an exceptional case of a patient with high-grade serous ovarian cancer, treated with multiple chemotherapy regimens, who exhibited regression of…”
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KinomeXplorer: an integrated platform for kinome biology studies by Horn, Heiko, Schoof, Erwin M, Kim, Jinho, Robin, Xavier, Miller, Martin L, Diella, Francesca, Palma, Anita, Cesareni, Gianni, Jensen, Lars Juhl, Linding, Rune

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UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma by Wolf, Yochai, Bartok, Osnat, Patkar, Sushant, Eli, Gitit Bar, Cohen, Sapir, Litchfield, Kevin, Levy, Ronen, Jiménez-Sánchez, Alejandro, Trabish, Sophie, Lee, Joo Sang, Karathia, Hiren, Barnea, Eilon, Day, Chi-Ping, Cinnamon, Einat, Stein, Ilan, Solomon, Adam, Bitton, Lital, Pérez-Guijarro, Eva, Dubovik, Tania, Shen-Orr, Shai S., Miller, Martin L., Merlino, Glenn, Levin, Yishai, Pikarsky, Eli, Eisenbach, Lea, Admon, Arie, Swanton, Charles, Ruppin, Eytan, Samuels, Yardena

“…Although clonal neo-antigen burden is associated with improved response to immune therapy, the functional basis for this remains unclear. Here we study this…”
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