clusterMaker: a multi-algorithm clustering plugin for Cytoscape
Morris, John H, Apeltsin, Leonard, Newman, Aaron M, Baumbach, Jan, Wittkop, Tobias, Su, Gang, Bader, Gary D, Ferrin, Thomas E
Published in BMC bioinformatics (09.11.2011)
Published in BMC bioinformatics (09.11.2011)
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Journal Article
Genetic Correction of Huntington's Disease Phenotypes in Induced Pluripotent Stem Cells
An, Mahru C., Zhang, Ningzhe, Scott, Gary, Montoro, Daniel, Wittkop, Tobias, Mooney, Sean, Melov, Simon, Ellerby, Lisa M.
Published in Cell stem cell (03.08.2012)
Published in Cell stem cell (03.08.2012)
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Journal Article
Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing
Klinger, Mark, Pepin, Francois, Wilkins, Jen, Asbury, Thomas, Wittkop, Tobias, Zheng, Jianbiao, Moorhead, Martin, Faham, Malek
Published in PloS one (28.10.2015)
Published in PloS one (28.10.2015)
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Journal Article
Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction
Li, Xinxing, Liu, Tao, Bacchiocchi, Antonella, Li, Mengxing, Cheng, Wen, Wittkop, Tobias, Mendez, Fernando L, Wang, Yingyu, Tang, Paul, Yao, Qianqian, Bosenberg, Marcus W, Sznol, Mario, Yan, Qin, Faham, Malek, Weng, Li, Halaban, Ruth, Jin, Hai, Hu, Zhiqian
Published in EMBO molecular medicine (12.09.2024)
Published in EMBO molecular medicine (12.09.2024)
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Journal Article
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing
Wittkop, Tobias, Baumbach, Jan, Lobo, Francisco P, Rahmann, Sven
Published in BMC bioinformatics (17.10.2007)
Published in BMC bioinformatics (17.10.2007)
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Journal Article
CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes
Baumbach, Jan, Brinkrolf, Karina, Wittkop, Tobias, Tauch, Andreas, Rahmann, Sven
Published in Journal of integrative bioinformatics (01.12.2006)
Published in Journal of integrative bioinformatics (01.12.2006)
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Journal Article
A large-scale evaluation of computational protein function prediction
Clark, Wyatt T, Oron, Tal Ronnen, Schnoes, Alexandra M, Wittkop, Tobias, Sokolov, Artem, Graim, Kiley, Funk, Christopher, Verspoor, Karin, Ben-Hur, Asa, Pandey, Gaurav, Yunes, Jeffrey M, Talwalkar, Ameet S, Repo, Susanna, Souza, Michael L, Piovesan, Damiano, Casadio, Rita, Wang, Zheng, Cheng, Jianlin, Fang, Hai, Gough, Julian, Koskinen, Patrik, Törönen, Petri, Nokso-Koivisto, Jussi, Holm, Liisa, Cozzetto, Domenico, Buchan, Daniel W A, Bryson, Kevin, Jones, David T, Limaye, Bhakti, Inamdar, Harshal, Datta, Avik, Manjari, Sunitha K, Joshi, Rajendra, Chitale, Meghana, Kihara, Daisuke, Lisewski, Andreas M, Erdin, Serkan, Venner, Eric, Lichtarge, Olivier, Rentzsch, Robert, Yang, Haixuan, Romero, Alfonso E, Bhat, Prajwal, Paccanaro, Alberto, Hamp, Tobias, Kaßner, Rebecca, Seemayer, Stefan, Vicedo, Esmeralda, Schaefer, Christian, Achten, Dominik, Auer, Florian, Boehm, Ariane, Braun, Tatjana, Hecht, Maximilian, Heron, Mark, Hönigschmid, Peter, Hopf, Thomas A, Kaufmann, Stefanie, Kiening, Michael, Krompass, Denis, Landerer, Cedric, Mahlich, Yannick, Roos, Manfred, Björne, Jari, Salakoski, Tapio, Wong, Andrew, Shatkay, Hagit, Gatzmann, Fanny, Sommer, Ingolf, Wass, Mark N, Sternberg, Michael J E, Škunca, Nives, Supek, Fran, Bošnjak, Matko, Panov, Panče, Džeroski, Sašo, Šmuc, Tomislav, Kourmpetis, Yiannis A I, van Dijk, Aalt D J, Braak, Cajo J F ter, Zhou, Yuanpeng, Gong, Qingtian, Dong, Xinran, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Di Camillo, Barbara, Toppo, Stefano, Lan, Liang, Djuric, Nemanja, Guo, Yuhong, Vucetic, Slobodan, Bairoch, Amos, Linial, Michal, Babbitt, Patricia C, Brenner, Steven E, Orengo, Christine, Mooney, Sean D, Friedberg, Iddo
Published in Nature methods (01.03.2013)
Published in Nature methods (01.03.2013)
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Journal Article
Ultra-short cell-free DNA fragments enhance cancer early detection in a multi-analyte blood test combining mutation, protein and fragmentomics
Wang, Fenfen, Li, Xinxing, Li, Mengxing, Liu, Wendi, Lu, Lingjia, Li, Yang, Chen, Xiaojing, Yang, Siqi, Liu, Tao, Cheng, Wen, Weng, Li, Wang, Hongyan, Lu, Dongsheng, Yao, Qianqian, Wang, Yingyu, Wu, Johnny, Wittkop, Tobias, Faham, Malek, Zhou, Huabang, Hu, Heping, Jin, Hai, Hu, Zhiqian, Ma, Ding, Cheng, Xiaodong
Published in Clinical chemistry and laboratory medicine (26.01.2024)
Published in Clinical chemistry and laboratory medicine (26.01.2024)
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Journal Article
Partitioning biological data with transitivity clustering
Baumbach, Jan, Wittkop, Tobias, Emig, Dorothea, Lange, Sita, Rahmann, Sven, Albrecht, Mario, Morris, John H, Böcker, Sebastian, Stoye, Jens
Published in Nature methods (01.06.2010)
Published in Nature methods (01.06.2010)
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Journal Article
Comprehensive cluster analysis with Transitivity Clustering
Baumbach, Jan, Wittkop, Tobias, Emig, Dorothea, Truss, Anke, Albrecht, Mario, Böcker, Sebastian
Published in Nature protocols (01.03.2011)
Published in Nature protocols (01.03.2011)
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Journal Article
Early cancer detection using multi-omic approach including epigenetic signal from ultra-small fragments
Wu, Johnny, Li, Xin-Xing, Zhou, Huabang, Liu, Wendi, Wang, Fenfen, Yao, Qianqian, Lu, Dongsheng, Lu, Huiqi, Wang, Hongyan, Wittkop, Tobias, Tang, Paul, Hu, Heping, Cheng, Xiaodong, Hu, Zhiqian, Faham, Malek, Weng, Li
Published in Journal of clinical oncology (20.05.2020)
Published in Journal of clinical oncology (20.05.2020)
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Journal Article
Abstract 938: Detection of actionable mutations in plasma cfDNA samples from patients with non-small cell lung carcinoma using a novel amplicon-based Firefly NGS assay
Wang, Lin, Weng, Li, Chen, Xiao, Li, Min, Guo, Qiaomei, Yu, Wenjun, Wittkop, Tobias, Wang, Hongyan, Fahem, Malek, Lin, Shengrong, Zhao, Grace Q., Lou, Jiatao
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
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Journal Article
Density parameter estimation for finding clusters of homologous proteins--tracing actinobacterial pathogenicity lifestyles
Röttger, Richard, Kalaghatgi, Prabhav, Sun, Peng, Soares, Siomar de Castro, Azevedo, Vasco, Wittkop, Tobias, Baumbach, Jan
Published in Bioinformatics (15.01.2013)
Published in Bioinformatics (15.01.2013)
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Journal Article
A scalable multiplex assay enabling assessment of T cell receptor specificity to hundreds of self- and pathogen-derived antigens
Klinger, Mark, Taniguchi, Ruth, Hu, Joyce, Hayes, Tim, Wittkop, Tobias, Asbury, Thomas, Moorhead, Martin, Emerson, Ryan, Sherwood, Anna, Robins, Harlan, Faham, Malek
Published in The Journal of immunology (1950) (01.05.2016)
Published in The Journal of immunology (1950) (01.05.2016)
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Journal Article
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation
Wittkop, Tobias, TerAvest, Emily, Evani, Uday S, Fleisch, K Mathew, Berman, Ari E, Powell, Corey, Shah, Nigam H, Mooney, Sean D
Published in BMC bioinformatics (14.02.2013)
Published in BMC bioinformatics (14.02.2013)
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Journal Article
Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing: e0141561
Klinger, Mark, Pepin, Francois, Wilkins, Jen, Asbury, Thomas, Wittkop, Tobias, Zheng, Jianbiao, Moorhead, Martin, Faham, Malek
Published in PloS one (01.10.2015)
Published in PloS one (01.10.2015)
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