Search Results - "Ash, A"

From patterns to patients: Advances in clinical machine learning for cancer diagnosis, prognosis, and treatment by Swanson, Kyle, Wu, Eric, Zhang, Angela, Alizadeh, Ash A., Zou, James

“…Machine learning (ML) is increasingly used in clinical oncology to diagnose cancers, predict patient outcomes, and inform treatment planning. Here, we review…”
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Simple Method for Estimating Interactions Between a Treatment and a Large Number of Covariates by Tian, Lu, Alizadeh, Ash A., Gentles, Andrew J., Tibshirani, Robert

“…We consider a setting in which we have a treatment and a potentially large number of covariates for a set of observations, and wish to model their relationship…”
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Robust enumeration of cell subsets from tissue expression profiles by Newman, Aaron M, Liu, Chih Long, Green, Michael R, Gentles, Andrew J, Feng, Weiguo, Xu, Yue, Hoang, Chuong D, Diehn, Maximilian, Alizadeh, Ash A

“…A computational method to identify cell types within a complex tissue, based on analysis of gene expression profiles, is described in this paper. We introduce…”
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Detecting Liquid Remnants of Solid Tumors: Circulating Tumor DNA Minimal Residual Disease by Moding, Everett J, Nabet, Barzin Y, Alizadeh, Ash A, Diehn, Maximilian

“…Growing evidence demonstrates that circulating tumor DNA (ctDNA) minimal residual disease (MRD) following treatment for solid tumors predicts relapse. These…”
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Profiling Tumor Infiltrating Immune Cells with CIBERSORT by Chen, Binbin, Khodadoust, Michael S, Liu, Chih Long, Newman, Aaron M, Alizadeh, Ash A

“…Tumor infiltrating leukocytes (TILs) are an integral component of the tumor microenvironment and have been found to correlate with prognosis and response to…”
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Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx by Steen, Chloé B, Liu, Chih Long, Alizadeh, Ash A, Newman, Aaron M

“…CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance and cell type-specific gene expression patterns from bulk tissue…”
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The prognostic landscape of genes and infiltrating immune cells across human cancers by Gentles, Andrew J, Newman, Aaron M, Liu, Chih Long, Bratman, Scott V, Feng, Weiguo, Kim, Dongkyoon, Nair, Viswam S, Xu, Yue, Khuong, Amanda, Hoang, Chuong D, Diehn, Maximilian, West, Robert B, Plevritis, Sylvia K, Alizadeh, Ash A

“…A searchable pan-cancer resource generated using data from nearly 18,000 human tumors reveals links between tumor infiltration by particular leukocyte subsets,…”
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Caesarean scar pregnancy by Ash, A, Smith, A, Maxwell, D

“…Caesarean scar pregnancy is one of the rarest forms of ectopic pregnancy. Little is known about its incidence and natural history. With increasing incidence of…”
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Determining cell type abundance and expression from bulk tissues with digital cytometry by Newman, Aaron M., Steen, Chloé B., Liu, Chih Long, Gentles, Andrew J., Chaudhuri, Aadel A., Scherer, Florian, Khodadoust, Michael S., Esfahani, Mohammad S., Luca, Bogdan A., Steiner, David, Diehn, Maximilian, Alizadeh, Ash A.

“…Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular heterogeneity, but it is currently impractical on large sample…”
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Predicting HLA class II antigen presentation through integrated deep learning by Chen, Binbin, Khodadoust, Michael S., Olsson, Niclas, Wagar, Lisa E., Fast, Ethan, Liu, Chih Long, Muftuoglu, Yagmur, Sworder, Brian J., Diehn, Maximilian, Levy, Ronald, Davis, Mark M., Elias, Joshua E., Altman, Russ B., Alizadeh, Ash A.

“…Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer…”
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Molecular epidemiology of Giardia and Cryptosporidium infections by Thompson, R.C.A., Ash, A.

“…Giardia and Cryptosporidium are ubiquitous enteric protozoan pathogens of vertebrates. Although recognised as the aetiological agents of disease in humans and…”
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Atlas of clinically distinct cell states and ecosystems across human solid tumors by Luca, Bogdan A., Steen, Chloé B., Matusiak, Magdalena, Azizi, Armon, Varma, Sushama, Zhu, Chunfang, Przybyl, Joanna, Espín-Pérez, Almudena, Diehn, Maximilian, Alizadeh, Ash A., van de Rijn, Matt, Gentles, Andrew J., Newman, Aaron M.

“…Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as…”
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Circulating Tumor DNA Analysis for Detection of Minimal Residual Disease After Chemoradiotherapy for Localized Esophageal Cancer by Azad, Tej D., Chaudhuri, Aadel A., Fang, Penny, Qiao, Yawei, Esfahani, Mohammad S., Chabon, Jacob J., Hamilton, Emily G., Yang, Yi D., Lovejoy, Alex, Newman, Aaron M., Kurtz, David M., Jin, Michael, Schroers-Martin, Joseph, Stehr, Henning, Liu, Chih Long, Hui, Angela Bik-Yu, Patel, Viren, Maru, Dipen, Lin, Steven H., Alizadeh, Ash A., Diehn, Maximilian

“…Biomarkers are needed to risk stratify after chemoradiotherapy for localized esophageal cancer. These could improve identification of patients at risk for…”
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The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma by Steen, Chloé B., Luca, Bogdan A., Esfahani, Mohammad S., Azizi, Armon, Sworder, Brian J., Nabet, Barzin Y., Kurtz, David M., Liu, Chih Long, Khameneh, Farnaz, Advani, Ranjana H., Natkunam, Yasodha, Myklebust, June H., Diehn, Maximilian, Gentles, Andrew J., Newman, Aaron M., Alizadeh, Ash A.

“…Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by…”
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High-throughput sequencing for noninvasive disease detection in hematologic malignancies by Scherer, Florian, Kurtz, David M., Diehn, Maximilian, Alizadeh, Ash A.

“…Noninvasive monitoring of minimal residual disease (MRD) has led to significant advances in personalized management of patients with hematologic malignancies…”
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Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation by Green, Michael R., Kihira, Shingo, Liu, Chih Long, Nair, Ramesh V., Salari, Raheleh, Gentles, Andrew J., Irish, Jonathan, Stehr, Henning, Vicente-Dueñas, Carolina, Romero-Camarero, Isabel, Sanchez-Garcia, Isidro, Plevritis, Sylvia K., Arber, Daniel A., Batzoglou, Serafim, Levy, Ronald, Alizadeh, Ash A.

“…Follicular lymphoma (FL) is incurable with conventional therapies and has a clinical course typified by multiple relapses after therapy. These tumors are…”
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Dynamic Risk Profiling Using Serial Tumor Biomarkers for Personalized Outcome Prediction by Kurtz, David M., Esfahani, Mohammad S., Scherer, Florian, Soo, Joanne, Jin, Michael C., Liu, Chih Long, Newman, Aaron M., Dührsen, Ulrich, Hüttmann, Andreas, Casasnovas, Olivier, Westin, Jason R., Ritgen, Matthais, Böttcher, Sebastian, Langerak, Anton W., Roschewski, Mark, Wilson, Wyndham H., Gaidano, Gianluca, Rossi, Davide, Bahlo, Jasmin, Hallek, Michael, Tibshirani, Robert, Diehn, Maximilian, Alizadeh, Ash A.

“…Accurate prediction of long-term outcomes remains a challenge in the care of cancer patients. Due to the difficulty of serial tumor sampling, previous…”
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Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients by Chabon, Jacob J., Simmons, Andrew D., Lovejoy, Alexander F., Esfahani, Mohammad S., Newman, Aaron M., Haringsma, Henry J., Kurtz, David M., Stehr, Henning, Scherer, Florian, Karlovich, Chris A., Harding, Thomas C., Durkin, Kathleen A., Otterson, Gregory A., Purcell, W. Thomas, Camidge, D. Ross, Goldman, Jonathan W., Sequist, Lecia V., Piotrowska, Zofia, Wakelee, Heather A., Neal, Joel W., Alizadeh, Ash A., Diehn, Maximilian

“…Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in…”
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Association of a Leukemic Stem Cell Gene Expression Signature With Clinical Outcomes in Acute Myeloid Leukemia by Gentles, Andrew J, Plevritis, Sylvia K, Majeti, Ravindra, Alizadeh, Ash A

“…CONTEXT In many cancers, specific subpopulations of cells appear to be uniquely capable of initiating and maintaining tumors. The strongest support for this…”
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ViPOR’s Venom — Rationally Targeting DLBCL with Precision by Goldstein, Jordan S., Alizadeh, Ash A.

“…Large B-cell lymphoma (LBCL) spans the gamut of aggressive lymphoid tumors with extensive biologic and clinical heterogeneity. Most patients with LBCL are…”
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