Search Results - "Shahrokh Esfahani, Mohammad"

An experimental design framework for Markovian gene regulatory networks under stationary control policy by Dehghannasiri, Roozbeh, Shahrokh Esfahani, Mohammad, Dougherty, Edward R

“…A fundamental problem for translational genomics is to find optimal therapies based on gene regulatory intervention. Dynamic intervention involves a control…”
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Classifier design given an uncertainty class of feature distributions via regularized maximum likelihood and the incorporation of biological pathway knowledge in steady-state phenotype classification by Shahrokh Esfahani, Mohammad, Knight, Jason, Zollanvari, Amin, Yoon, Byung-Jun, Dougherty, Edward R.

“…Contemporary high-throughput technologies provide measurements of very large numbers of variables but often with very small sample sizes. This paper proposes…”
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Effect of separate sampling on classification accuracy by Shahrokh Esfahani, Mohammad, Dougherty, Edward R

“…Measurements are commonly taken from two phenotypes to build a classifier, where the number of data points from each class is predetermined, not random. In…”
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Evaluating upfront high-dose consolidation after R-CHOP for follicular lymphoma by clinical and genetic risk models by Alig, Stefan, Jurinovic, Vindi, Shahrokh Esfahani, Mohammad, Haebe, Sarah, Passerini, Verena, Hellmuth, Johannes C., Gaitzsch, Erik, Keay, William, Tahiri, Natyra, Zoellner, Anna, Rosenwald, Andreas, Klapper, Wolfram, Stein, Harald, Feller, Alfred, Ott, German, Staiger, Annette M., Horn, Heike, Hansmann, Martin L., Pott, Christiane, Unterhalt, Michael, Schmidt, Christian, Dreyling, Martin, Alizadeh, Ash A., Hiddemann, Wolfgang, Hoster, Eva, Weigert, Oliver

“…High-dose therapy and autologous stem cell transplantation (HDT/ASCT) is an effective salvage treatment for eligible patients with follicular lymphoma (FL) and…”
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Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma by Kurtz, David M, Scherer, Florian, Jin, Michael C, Soo, Joanne, Craig, Alexander F M, Esfahani, Mohammad Shahrokh, Chabon, Jacob J, Stehr, Henning, Liu, Chih Long, Tibshirani, Robert, Maeda, Lauren S, Gupta, Neel K, Khodadoust, Michael S, Advani, Ranjana H, Levy, Ronald, Newman, Aaron M, Dührsen, Ulrich, Hüttmann, Andreas, Meignan, Michel, Casasnovas, René-Olivier, Westin, Jason R, Roschewski, Mark, Wilson, Wyndham H, Gaidano, Gianluca, Rossi, Davide, Diehn, Maximilian, Alizadeh, Ash A

“…Outcomes for patients with diffuse large B-cell lymphoma remain heterogeneous, with existing methods failing to consistently predict treatment failure. We…”
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Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling by Chaudhuri, Aadel A, Chabon, Jacob J, Lovejoy, Alexander F, Newman, Aaron M, Stehr, Henning, Azad, Tej D, Khodadoust, Michael S, Esfahani, Mohammad Shahrokh, Liu, Chih Long, Zhou, Li, Scherer, Florian, Kurtz, David M, Say, Carmen, Carter, Justin N, Merriott, David J, Dudley, Jonathan C, Binkley, Michael S, Modlin, Leslie, Padda, Sukhmani K, Gensheimer, Michael F, West, Robert B, Shrager, Joseph B, Neal, Joel W, Wakelee, Heather A, Loo, Jr, Billy W, Alizadeh, Ash A, Diehn, Maximilian

“…Identifying molecular residual disease (MRD) after treatment of localized lung cancer could facilitate early intervention and personalization of adjuvant…”
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Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors by Boluki, Shahin, Esfahani, Mohammad Shahrokh, Qian, Xiaoning, Dougherty, Edward R

“…Phenotypic classification is problematic because small samples are ubiquitous; and, for these, use of prior knowledge is critical. If knowledge concerning the…”
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Constructing Pathway-Based Priors within a Gaussian Mixture Model for Bayesian Regression and Classification by Boluki, Shahin, Esfahani, Mohammad Shahrokh, Qian, Xiaoning, Dougherty, Edward R.

“…Gene-expression-based classification and regression are major concerns in translational genomics. If the feature-label distribution is known, then an optimal…”
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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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Determinants of resistance to engineered T cell therapies targeting CD19 in large B cell lymphomas by Sworder, Brian J., Kurtz, David M., Alig, Stefan K., Frank, Matthew J., Shukla, Navika, Garofalo, Andrea, Macaulay, Charles W., Shahrokh Esfahani, Mohammad, Olsen, Mari N., Hamilton, James, Hosoya, Hitomi, Hamilton, Mark, Spiegel, Jay Y., Baird, John H., Sugio, Takeshi, Carleton, Mia, Craig, Alexander F.M., Younes, Sheren F., Sahaf, Bita, Sheybani, Natasha D., Schroers-Martin, Joseph G., Liu, Chih Long, Oak, Jean S., Jin, Michael C., Beygi, Sara, Hüttmann, Andreas, Hanoun, Christine, Dührsen, Ulrich, Westin, Jason R., Khodadoust, Michael S., Natkunam, Yasodha, Majzner, Robbie G., Mackall, Crystal L., Diehn, Maximilian, Miklos, David B., Alizadeh, Ash A.

“…Most relapsed/refractory large B cell lymphoma (r/rLBCL) patients receiving anti-CD19 chimeric antigen receptor (CAR19) T cells relapse. To characterize…”
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Short Diagnosis-to-Treatment Interval Is Associated With Higher Circulating Tumor DNA Levels in Diffuse Large B-Cell Lymphoma by Alig, Stefan, Macaulay, Charles W, Kurtz, David M, Dührsen, Ulrich, Hüttmann, Andreas, Schmitz, Christine, Jin, Michael C, Sworder, Brian J, Garofalo, Andrea, Shahrokh Esfahani, Mohammad, Nabet, Barzin Y, Soo, Joanne, Scherer, Florian, Craig, Alexander F M, Casasnovas, Olivier, Westin, Jason R, Gaidano, Gianluca, Rossi, Davide, Roschewski, Mark, Wilson, Wyndham H, Meignan, Michel, Diehn, Maximilian, Alizadeh, Ash A

“…Patients with Diffuse Large B-cell Lymphoma (DLBCL) in need of immediate therapy are largely under-represented in clinical trials. The diagnosis-to-treatment…”
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Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling by Alig, Stefan K., Shahrokh Esfahani, Mohammad, Garofalo, Andrea, Li, Michael Yu, Rossi, Cédric, Flerlage, Tim, Flerlage, Jamie E., Adams, Ragini, Binkley, Michael S., Shukla, Navika, Jin, Michael C., Olsen, Mari, Telenius, Adèle, Mutter, Jurik A., Schroers-Martin, Joseph G., Sworder, Brian J., Rai, Shinya, King, Daniel A., Schultz, Andre, Bögeholz, Jan, Su, Shengqin, Kathuria, Karan R., Liu, Chih Long, Kang, Xiaoman, Strohband, Maya J., Langfitt, Deanna, Pobre-Piza, Kristine Faye, Surman, Sherri, Tian, Feng, Spina, Valeria, Tousseyn, Thomas, Buedts, Lieselot, Hoppe, Richard, Natkunam, Yasodha, Fornecker, Luc-Matthieu, Castellino, Sharon M., Advani, Ranjana, Rossi, Davide, Lynch, Ryan, Ghesquières, Hervé, Casasnovas, Olivier, Kurtz, David M., Marks, Lianna J., Link, Michael P., André, Marc, Vandenberghe, Peter, Steidl, Christian, Diehn, Maximilian, Alizadeh, Ash A.

“…The scarcity of malignant Hodgkin and Reed–Sternberg cells hampers tissue-based comprehensive genomic profiling of classic Hodgkin lymphoma (cHL). By contrast,…”
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Intrinsically Bayesian Robust Kalman Filter: An Innovation Process Approach by Dehghannasiri, Roozbeh, Esfahani, Mohammad Shahrokh, Dougherty, Edward R.

“…In many contemporary engineering problems, model uncertainty is inherent because accurate system identification is virtually impossible owing to system…”
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Optimal Bayesian Kalman Filtering With Prior Update by Dehghannasiri, Roozbeh, Esfahani, Mohammad Shahrokh, Xiaoning Qian, Dougherty, Edward R.

“…In many practical filter design problems, the exact statistical information of the underlying random processes is not available. One robust filtering approach…”
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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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Discrete optimal Bayesian classification with error-conditioned sequential sampling by Broumand, Ariana, Esfahani, Mohammad Shahrokh, Yoon, Byung-Jun, Dougherty, Edward R.

“…When in possession of prior knowledge concerning the feature-label distribution, in particular, when it is known that the feature-label distribution belongs to…”
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Longitudinal Noninvasive Surveillance & Fragmentomic Characterization of Follicular Lymphoma by Schroers-Martin, Joseph, Mutter, Jurik A, Shahrokh Esfahani, Mohammad, Scherer, Florian, Soo, Joanne, Alig, Stefan K., Kurtz, David M., Sugio, Takeshi, Rossi, Cédric, Tessoulin, Benoit, Olsen, Mari, Liu, Chih Long, Diehn, Maximilian, Alizadeh, Ash A.

“…Introduction While cell-free DNA (cfDNA) plays an increasingly defined role in aggressive lymphomas, its characteristics in indolent lymphomas are less…”
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Accurate Detection of Clinically Actionable Copy Number Variants in Diverse Hematological Neoplasms By Routine Targeted Sequencing: A Comparative Performance Study by Palomino Mosquera, Alicia, Hosoya, Hitomi, Jin, Michael C., Shahrokh Esfahani, Mohammad, Schroers-Martin, Joseph, Sworder, Brian, Liu, Chih Long, Spiteri, Elizabeth, Natkunam, Yasodha, Zehnder, James L, Stehr, Henning, Kurtz, David M., Alizadeh, Ash A.

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An Integrated Multimodal Framework for Noninvasive TCL Disease Detection and Monitoring by Sugio, Takeshi, Shukla, Navika, Khodadoust, Michael S, Nesselbush, Monica, Kato, Koji, Alig, Stefan K., Boegeholz, Jan, Schroers-Martin, Joseph, Shahrokh Esfahani, Mohammad, Mutter, Jurik A., Garofalo, Andrea, Jun, Soyeong, Hamilton, Mark P., Rossi, Cédric, Olsen, Mari, Liu, Chih Long, Akashi, Koichi, Diehn, Maximilian, Alizadeh, Ash A.

“…Background: Early noninvasive identification of therapeutic responses could help accelerate the development of more effective therapies for T-cell lymphoma…”
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Distinct Circulating Genomic Features of Classical Hodgkin Lymphoma of Older Adults by Rossi, Cédric, Boegeholz, Jan, Alig, Stefan K., Garofalo, Andrea, Shahrokh Esfahani, Mohammad, Schroers-Martin, Joseph, Olsen, Mari, Kang, Xiaoman, Kurtz, David M., Sugio, Takeshi, Hamilton, Mark P., Andre, Marc, Casasnovas, Rene-Olivier, Fornecker, Luc Matthieu, Diehn, Maximilian, Ghesquieres, Herve, Alizadeh, Ash A.

“…Introduction: Despite significant progress in curing younger patients with classical Hodgkin lymphoma (cHL), older patients continue to have substantially…”
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