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keywords = {Animals,BAF complex,chromatin,chromatin remodeling,clonal precursor cells,DNA-Binding Proteins,epigenetics,Humans,humoral immunity,lymphoma,Lymphoma,Memory B Cells,Mice,Mutation,Nuclear Proteins,pioneer transcription factors,plasticity,precision therapy,Transcription Factors}

}

title = {{{TP53}} and {{OSBPL10}} Alterations in Diffuse Large {{B-cell}} Lymphoma: Prognostic Markers Identified via Exome Analysis of Cases with Extreme Prognosis},

shorttitle = {{{TP53}} and {{OSBPL10}} Alterations in Diffuse Large {{B-cell}} Lymphoma},

author = {Dobashi, Akito and Togashi, Yuki and Tanaka, Norio and Yokoyama, Masahiro and Tsuyama, Naoko and Baba, Satoko and Mori, Seiichi and Hatake, Kiyohiko and Yamaguchi, Toshiharu and Noda, Tetsuo and Takeuchi, Kengo},

keywords = {DNA methylation,Long non-coding RNAs,Reprogramming}

}

title = {Cathepsin {{S Alterations Induce}} a {{Tumor-Promoting Immune Microenvironment}} in {{Follicular Lymphoma}}},

author = {Bararia, Deepak and Hildebrand, Johannes A. and Stolz, Sebastian and Haebe, Sarah and Alig, Stefan and Trevisani, Christopher P. and Osorio-Barrios, Francisco and Bartoschek, Michael D. and Mentz, Michael and Pastore, Alessandro and Gaitzsch, Erik and Heide, Michael and Jurinovic, Vindi and Rautter, Katharina and Gunawardana, Jay and Sabdia, Muhammed B. and Szczepanowski, Monika and Richter, Julia and Klapper, Wolfram and Louissaint, Abner and Ludwig, Christina and Bultmann, Sebastian and Leonhardt, Heinrich and Eustermann, Sebastian and Hopfner, Karl-Peter and Hiddemann, Wolfgang and family=Bergwelt-Baildon, given=Michael, prefix=von, useprefix=true and Steidl, Christian and Kridel, Robert and Tobin, Joshua W. D. and Gandhi, Maher K. and Weinstock, David M. and Schmidt-Supprian, Marc and Sárosi, Menyhárt B. and Rudelius, Martina and Passerini, Verena and Mautner, Josef and Weigert, Oliver},

date = {2020-05-05},

keywords = {Adult,Aged,Aged 80 and over,Amyloid Precursor Protein Secretases,Apoptosis,Base Sequence,Benzodiazepinones,Cell Line Tumor,Cell Proliferation,Cyclin D1,Exons,Female,Gene Expression Profiling,Humans,Lymphoma Mantle-Cell,Male,Middle Aged,Mutation,Prognosis,Receptor Notch1,Sequence Analysis RNA,Signal Transduction,Survival Analysis,Transcriptome}

}

title = {Recurrent Somatic Mutations Affecting {{B-cell}} Receptor Signaling Pathway Genes in Follicular Lymphoma},

author = {Krysiak, Kilannin and Gomez, Felicia and White, Brian S. and Matlock, Matthew and Miller, Christopher A. and Trani, Lee and Fronick, Catrina C. and Fulton, Robert S. and Kreisel, Friederike and Cashen, Amanda F. and Carson, Kenneth R. and Berrien-Elliott, Melissa M. and Bartlett, Nancy L. and Griffith, Malachi and Griffith, Obi L. and Fehniger, Todd A.},

date = {2017-01-26},

pages = {1381--1385}

}

title = {Recurrent {{mTORC1-activating RRAGC}} Mutations in Follicular Lymphoma},

author = {Okosun, Jessica and Wolfson, Rachel L. and Wang, Jun and Araf, Shamzah and Wilkins, Lucy and Castellano, Brian M. and Escudero-Ibarz, Leire and Al Seraihi, Ahad Fahad and Richter, Julia and Bernhart, Stephan H. and Efeyan, Alejo and Iqbal, Sameena and Matthews, Janet and Clear, Andrew and Guerra-Assunção, José Afonso and Bödör, Csaba and Quentmeier, Hilmar and Mansbridge, Christopher and Johnson, Peter and Davies, Andrew and Strefford, Jonathan C. and Packham, Graham and Barrans, Sharon and Jack, Andrew and Du, Ming-Qing and Calaminici, Maria and Lister, T. Andrew and Auer, Rebecca and Montoto, Silvia and Gribben, John G. and Siebert, Reiner and Chelala, Claude and Zoncu, Roberto and Sabatini, David M. and Fitzgibbon, Jude},

date = {2016-02},

keywords = {Cell staining,Cytoplasm,Cytoplasmic staining,Metastasis,Renal cancer,Renal cell carcinoma,Small interfering RNA,Transfection}

}

title = {Genetic Lesions of the {{TRAF3}} and {{MAP3K14}} Genes in Classical {{Hodgkin}} Lymphoma},

author = {Otto, Claudia and Giefing, Maciej and Massow, Anne and Vater, Inga and Gesk, Stefan and Schlesner, Matthias and Richter, Julia and Klapper, Wolfram and Hansmann, Martin-Leo and Siebert, Reiner and Küppers, Ralf},

date = {2012-06},

pages = {55--60}

}

title = {Recurrent Mutation of the {{ID3}} Gene in {{Burkitt}} Lymphoma Identified by Integrated Genome, Exome and Transcriptome Sequencing},

author = {Richter, Julia and Schlesner, Matthias and Hoffmann, Steve and Kreuz, Markus and Leich, Ellen and Burkhardt, Birgit and Rosolowski, Maciej and Ammerpohl, Ole and Wagener, Rabea and Bernhart, Stephan H. and Lenze, Dido and Szczepanowski, Monika and Paulsen, Maren and Lipinski, Simone and Russell, Robert B. and Adam-Klages, Sabine and Apic, Gordana and Claviez, Alexander and Hasenclever, Dirk and Hovestadt, Volker and Hornig, Nadine and Korbel, Jan O. and Kube, Dieter and Langenberger, David and Lawerenz, Chris and Lisfeld, Jasmin and Meyer, Katharina and Picelli, Simone and Pischimarov, Jordan and Radlwimmer, Bernhard and Rausch, Tobias and Rohde, Marius and Schilhabel, Markus and Scholtysik, René and Spang, Rainer and Trautmann, Heiko and Zenz, Thorsten and Borkhardt, Arndt and Drexler, Hans G. and Möller, Peter and MacLeod, Roderick A. F. and Pott, Christiane and Schreiber, Stefan and Trümper, Lorenz and Loeffler, Markus and Stadler, Peter F. and Lichter, Peter and Eils, Roland and Küppers, Ralf and Hummel, Michael and Klapper, Wolfram and Rosenstiel, Philip and Rosenwald, Andreas and Brors, Benedikt and Siebert, Reiner and {ICGC MMML-Seq Project}},

date = {2012-12},

abstract = {limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.}

}

title = {Recurrent Mutations of the {{STAT6 DNA}} Binding Domain in Primary Mediastinal {{B-cell}} Lymphoma},

author = {Ritz, Olga and Guiter, Chrystelle and Castellano, Flavia and Dorsch, Karola and Melzner, Julia and Jais, Jean-Philippe and Dubois, Gwendoline and Gaulard, Philippe and Möller, Peter and Leroy, Karen},

date = {2009-08-06},

keywords = {Antibodies Monoclonal Murine-Derived,Antineoplastic Combined Chemotherapy Protocols,Humans,Lymphoma Large B-Cell Diffuse,Morinlab,Neoplasm Recurrence Local,Rituximab}

}

title = {Mutations Associated with Progression in Follicular Lymphoma Predict Inferior Outcomes at Diagnosis: {{Alliance A151303}}},

author = {Russler-Germain, David A. and Krysiak, Kilannin and Ramirez, Cody A. and Mosior, Matthew and Watkins, Marcus P. and Gomez, Felicia and Skidmore, Zachary L. and Trani, L. and Gao, F. and Geyer, Susan and Cashen, A. and Mehta-Shah, N. and Kahl, B. and Bartlett, N. and Alderuccio, J. and Lossos, I. and Ondrejka, S. and Hsi, E. and Martin, P. and Leonard, J. and Griffith, M. and Griffith, O. and Fehniger, T.},

date = {2023},

pmcid = {PMC6154734}

}

title = {Mutational Landscape of Gray Zone Lymphoma},

author = {Sarkozy, Clémentine and Hung, Stacy S. and Chavez, Elizabeth A. and Duns, Gerben and Takata, Katsuyoshi and Chong, Lauren C. and Aoki, Tomohiro and Jiang, Aixiang and Miyata-Takata, Tomoko and Telenius, Adèle and Slack, Graham W. and Molina, Thierry Jo and Ben-Neriah, Susana and Farinha, Pedro and Dartigues, Peggy and Damotte, Diane and Mottok, Anja and Salles, Gilles A. and Casasnovas, Rene-Olivier and Savage, Kerry J. and Laurent, Camille and Scott, David W. and Traverse-Glehen, Alexandra and Steidl, Christian},

date = {2021-04-01},

keywords = {Cancer genomics,DNA sequencing,Research data}

}

title = {Genomic Analyses of Flow-Sorted {{Hodgkin Reed-Sternberg}} Cells Reveal Complementary Mechanisms of Immune Evasion},

author = {Wienand, Kirsty and Chapuy, Bjoern and Stewart, Chip and Dunford, Andrew J. and Wu, David and Kim, Jaegil and Kamburov, Atanas and Wood, Timothy R. and Cader, Fathima Zumla and Ducar, Matthew D. and Thorner, Aaron R. and Nag, Anwesha and Heubeck, Alexander T. and Buonopane, Michael J. and Redd, Robert A. and Bojarczuk, Kamil and Lawton, Lee N. and Armand, Philippe and Rodig, Scott J. and Fromm, Jonathan R. and Getz, Gad and Shipp, Margaret A.},

date = {2019-12-10},