Search Results - "LONG LIU, Chih"

Single-nucleosome mapping of histone modifications in S. cerevisiae by Liu, Chih Long, Kaplan, Tommy, Kim, Minkyu, Buratowski, Stephen, Schreiber, Stuart L, Friedman, Nir, Rando, Oliver J

“…Covalent modification of histone proteins plays a role in virtually every process on eukaryotic DNA, from transcription to DNA repair. Many different residues…”
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Nucleic Acid-Targeting Pathways Promote Inflammation in Obesity-Related Insulin Resistance by Revelo, Xavier S., Ghazarian, Magar, Chng, Melissa Hui Yen, Luck, Helen, Kim, Justin H., Zeng, Kejing, Shi, Sally Y., Tsai, Sue, Lei, Helena, Kenkel, Justin, Liu, Chih Long, Tangsombatvisit, Stephanie, Tsui, Hubert, Sima, Corneliu, Xiao, Changting, Shen, Lei, Li, Xiaoying, Jin, Tianru, Lewis, Gary F., Woo, Minna, Utz, Paul J., Glogauer, Michael, Engleman, Edgar, Winer, Shawn, Winer, Daniel A.

“…Obesity-related inflammation of metabolic tissues, including visceral adipose tissue (VAT) and liver, are key factors in the development of insulin resistance…”
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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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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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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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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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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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Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA by Kurtz, David M., Soo, Joanne, Co Ting Keh, Lyron, Alig, Stefan, Chabon, Jacob J., Sworder, Brian J., Schultz, Andre, Jin, Michael C., Scherer, Florian, Garofalo, Andrea, Macaulay, Charles W., Hamilton, Emily G., Chen, Binbin, Olsen, Mari, Schroers-Martin, Joseph G., Craig, Alexander F. M., Moding, Everett J., Esfahani, Mohammad S., Liu, Chih Long, Dührsen, Ulrich, Hüttmann, Andreas, Casasnovas, René-Olivier, Westin, Jason R., Roschewski, Mark, Wilson, Wyndham H., Gaidano, Gianluca, Rossi, Davide, Diehn, Maximilian, Alizadeh, Ash A.

“…Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility…”
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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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Immune Inhibitory Molecules LAG-3 and PD-1 Synergistically Regulate T-cell Function to Promote Tumoral Immune Escape by WOO, Seng-Ryong, TURNIS, Meghan E, TANGSOMBATVISIT, Stephanie, GROSSO, Joseph F, NETTO, George, SMELTZER, Matthew P, CHAUX, Alcides, UTZ, Paul J, WORKMAN, Creg J, PARDOLL, Drew M, KORMAN, Alan J, DRAKE, Charles G, GOLDBERG, Monica V, VIGNALI, Dario A. A, BANKOTI, Jaishree, SELBY, Mark, NIRSCHL, Christopher J, BETTINI, Matthew L, GRAVANO, David M, VOGEL, Peter, LONG LIU, Chih

“…Inhibitory receptors on immune cells are pivotal regulators of immune escape in cancer. Among these inhibitory receptors, CTLA-4 (targeted clinically by…”
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Inferring gene expression from cell-free DNA fragmentation profiles by Esfahani, Mohammad Shahrokh, Hamilton, Emily G., Mehrmohamadi, Mahya, Nabet, Barzin Y., Alig, Stefan K., King, Daniel A., Steen, Chloé B., Macaulay, Charles W., Schultz, Andre, Nesselbush, Monica C., Soo, Joanne, Schroers-Martin, Joseph G., Chen, Binbin, Binkley, Michael S., Stehr, Henning, Chabon, Jacob J., Sworder, Brian J., Hui, Angela B-Y, Frank, Matthew J., Moding, Everett J., Liu, Chih Long, Newman, Aaron M., Isbell, James M., Rudin, Charles M., Li, Bob T., Kurtz, David M., Diehn, Maximilian, Alizadeh, Ash A.

“…Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously…”
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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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Development and validation of a T7 based linear amplification for genomic DNA by Liu, Chih Long, Schreiber, Stuart L, Bernstein, Bradley E

“…Genomic maps of transcription factor binding sites and histone modification patterns provide unique insight into the nature of gene regulatory networks and…”
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Tissue Microarrays Are an Effective Quality Assurance Tool for Diagnostic Immunohistochemistry by Hsu, Forrest D, Nielsen, Torsten O, Alkushi, Abdulmohsen, Dupuis, Bev, Huntsman, David, Liu, Chih Long, van de Rijn, Matt, Gilks, C Blake

“…There has been considerable variability in the reported results of immunohistochemical staining for some diagnostically relevant antigens. Our objectives in…”
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Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing by Kurtz, David M., Green, Michael R., Bratman, Scott V., Scherer, Florian, Liu, Chih Long, Kunder, Christian A., Takahashi, Kazuhiro, Glover, Cynthia, Keane, Colm, Kihira, Shingo, Visser, Brendan, Callahan, Jason, Kong, Katherine A., Faham, Malek, Corbelli, Karen S., Miklos, David, Advani, Ranjana H., Levy, Ronald, Hicks, Rodney J., Hertzberg, Mark, Ohgami, Robert S., Gandhi, Maher K., Diehn, Maximilian, Alizadeh, Ash A.

“…Recent studies have shown limited utility of routine surveillance imaging for diffuse large B-cell lymphoma (DLBCL) patients achieving remission. Detection of…”
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Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA by Scherer, Florian, Kurtz, David M, Newman, Aaron M, Stehr, Henning, Craig, Alexander F M, Esfahani, Mohammad Shahrokh, Lovejoy, Alexander F, Chabon, Jacob J, Klass, Daniel M, Liu, Chih Long, Zhou, Li, Glover, Cynthia, Visser, Brendan C, Poultsides, George A, Advani, Ranjana H, Maeda, Lauren S, Gupta, Neel K, Levy, Ronald, Ohgami, Robert S, Kunder, Christian A, Diehn, Maximilian, Alizadeh, Ash A

“…Patients with diffuse large B cell lymphoma (DLBCL) exhibit marked diversity in tumor behavior and outcomes, yet the identification of poor-risk groups remains…”
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Risk of Second Tumors and T-Cell Lymphoma after CAR T-Cell Therapy by Hamilton, Mark P., Sugio, Takeshi, Noordenbos, Troy, Shi, Shuyu, Bulterys, Philip L., Liu, Chih Long, Kang, Xiaoman, Olsen, Mari N., Good, Zinaida, Dahiya, Saurabh, Frank, Matthew J., Sahaf, Bita, Mackall, Crystal L., Gratzinger, Dita, Diehn, Maximilian, Alizadeh, Ash A., Miklos, David B.

“…Second tumors after CAR T-cell therapy are rare, and in one case of a secondary T-cell lymphoma, detailed analysis showed that the genetic construct that was…”
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Detection and Surveillance of Bladder Cancer Using Urine Tumor DNA by Dudley, Jonathan C, Schroers-Martin, Joseph, Lazzareschi, Daniel V, Shi, William Y, Chen, Simon B, Esfahani, Mohammad S, Trivedi, Dharati, Chabon, Jacob J, Chaudhuri, Aadel A, Stehr, Henning, Liu, Chih Long, Lim, Harumi, Costa, Helio A, Nabet, Barzin Y, Sin, Mandy L Y, Liao, Joseph C, Alizadeh, Ash A, Diehn, Maximilian

“…Current regimens for the detection and surveillance of bladder cancer are invasive and have suboptimal sensitivity. Here, we present a novel high-throughput…”
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