From hype to reality: data science enabling personalized medicine von Fröhlich, Holger, Balling, Rudi, Beerenwinkel, Niko, Kohlbacher, Oliver, Kumar, Santosh, Lengauer, Thomas, Maathuis, Marloes H, Moreau, Yves, Murphy, Susan A, Przytycka, Teresa M, Rebhan, Michael, Röst, Hannes, Schuppert, Andreas, Schwab, Matthias, Spang, Rainer, Stekhoven, Daniel, Sun, Jimeng, Weber, Andreas, Ziemek, Daniel, Zupan, Blaz

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ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci von Stacey, David, Fauman, Eric B, Ziemek, Daniel, Sun, Benjamin B, Harshfield, Eric L, Wood, Angela M, Butterworth, Adam S, Suhre, Karsten, Paul, Dirk S

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Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease von Folkersen, Lasse, Fauman, Eric, Sabater-Lleal, Maria, Strawbridge, Rona J, Frånberg, Mattias, Sennblad, Bengt, Baldassarre, Damiano, Veglia, Fabrizio, Humphries, Steve E, Rauramaa, Rainer, de Faire, Ulf, Smit, Andries J, Giral, Philippe, Kurl, Sudhir, Mannarino, Elmo, Enroth, Stefan, Johansson, Åsa, Enroth, Sofia Bosdotter, Gustafsson, Stefan, Lind, Lars, Lindgren, Cecilia, Morris, Andrew P, Giedraitis, Vilmantas, Silveira, Angela, Franco-Cereceda, Anders, Tremoli, Elena, Gyllensten, Ulf, Ingelsson, Erik, Brunak, Søren, Eriksson, Per, Ziemek, Daniel, Hamsten, Anders, Mälarstig, Anders

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Early prediction of clinical response to anti-TNF treatment using multi-omics and machine learning in rheumatoid arthritis von Yoosuf, Niyaz, Maciejewski, Mateusz, Ziemek, Daniel, Jelinsky, Scott A, Folkersen, Lasse, Müller, Malin, Sahlström, Peter, Vivar, Nancy, Catrina, Anca, Berg, Louise, Klareskog, Lars, Padyukov, Leonid, Brynedal, Boel

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A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data von Kang, Tianyu, Ding, Wei, Zhang, Luoyan, Ziemek, Daniel, Zarringhalam, Kourosh

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Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes von Zarringhalam, Kourosh, Degras, David, Brockel, Christoph, Ziemek, Daniel

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Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data von Smith, Aaron M, Walsh, Jonathan R, Long, John, Davis, Craig B, Henstock, Peter, Hodge, Martin R, Maciejewski, Mateusz, Mu, Xinmeng Jasmine, Ra, Stephen, Zhao, Shanrong, Ziemek, Daniel, Fisher, Charles K

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The Genetic Landscape of Renal Complications in Type 1 Diabetes von Sandholm, Niina, Van Zuydam, Natalie, Ahlqvist, Emma, Juliusdottir, Thorhildur, Deshmukh, Harshal A, Rayner, N William, Di Camillo, Barbara, Forsblom, Carol, Fadista, Joao, Ziemek, Daniel, Salem, Rany M, Hiraki, Linda T, Pezzolesi, Marcus, Trégouët, David, Dahlström, Emma, Valo, Erkka, Oskolkov, Nikolay, Ladenvall, Claes, Marcovecchio, M Loredana, Cooper, Jason, Sambo, Francesco, Malovini, Alberto, Manfrini, Marco, McKnight, Amy Jayne, Lajer, Maria, Harjutsalo, Valma, Gordin, Daniel, Parkkonen, Maija, Tuomilehto, Jaakko, Lyssenko, Valeriya, McKeigue, Paul M, Rich, Stephen S, Brosnan, Mary Julia, Fauman, Eric, Bellazzi, Riccardo, Rossing, Peter, Hadjadj, Samy, Krolewski, Andrzej, Paterson, Andrew D, Florez, Jose C, Hirschhorn, Joel N, Maxwell, Alexander P, Dunger, David, Cobelli, Claudio, Colhoun, Helen M, Groop, Leif, McCarthy, Mark I, Groop, Per-Henrik

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The influence of HLA genetic variation on plasma protein expression von Krishna, Chirag, Chiou, Joshua, Sakaue, Saori, Kang, Joyce B., Christensen, Stephen M., Lee, Isac, Aksit, Melis Atalar, Kim, Hye In, von Schack, David, Raychaudhuri, Soumya, Ziemek, Daniel, Hu, Xinli

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HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain von Denk, Franziska, Huang, Wenlong, Sidders, Ben, Bithell, Angela, Crow, Megan, Grist, John, Sharma, Simone, Ziemek, Daniel, Rice, Andrew S.C., Buckley, Noel J., McMahon, Stephen B.

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Prediction of response of methotrexate in patients with rheumatoid arthritis using serum lipidomics von Maciejewski, Mateusz, Sands, Caroline, Nair, Nisha, Ling, Stephanie, Verstappen, Suzanne, Hyrich, Kimme, Barton, Anne, Ziemek, Daniel, Lewis, Matthew R., Plant, Darren

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Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci von Harshfield, Eric L, Fauman, Eric B, Stacey, David, Paul, Dirk S, Ziemek, Daniel, Ong, Rachel M Y, Danesh, John, Butterworth, Adam S, Rasheed, Asif, Sattar, Taniya, Zameer-Ul-Asar, Saleem, Imran, Hina, Zoubia, Ishtiaq, Unzila, Qamar, Nadeem, Mallick, Nadeem Hayat, Yaqub, Zia, Saghir, Tahir, Rizvi, Syed Nadeem Hasan, Memon, Anis, Ishaq, Mohammad, Rasheed, Syed Zahed, Memon, Fazal-Ur-Rehman, Jalal, Anjum, Abbas, Shahid, Frossard, Philippe, Saleheen, Danish, Wood, Angela M, Griffin, Julian L, Koulman, Albert

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Peripheral blood cellular dynamics of rheumatoid arthritis treatment informs about efficacy of response to disease modifying drugs von Hedman, Åsa K., Winter, Eitan, Yoosuf, Niyaz, Benita, Yair, Berg, Louise, Brynedal, Boel, Folkersen, Lasse, Klareskog, Lars, Maciejewski, Mateusz, Sirota-Madi, Alexandra, Spector, Yael, Ziemek, Daniel, Padyukov, Leonid, Shen-Orr, Shai S., Jelinsky, Scott A.

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ImmUniverse Consortium: Multi-omics integrative approach in personalized medicine for immune-mediated inflammatory diseases von Vetrano, Stefania, Bouma, Gerben, Benschop, Robert J., Birngruber, Thomas, Costanzo, Antonio, D’Haens, G. R. A. M., Frasca, Loredana, Hillenbrand, Rainer, Iversen, Lars, Johansen, Claus, Kaser, Arthur, Koenen, Hans J. P. M., Noehammer, Christa, Peyrin-Biroulet, Laurent, Raes, Jeroen, Ricotti, Leonardo, Rosenstiel, Philip, Satagopam, Venkata P., Schreiber, Stefan, Vermeire, Severine, Wollenberg, Andreas, Weidinger, Stephan, Ziemek, Daniel, Danese, Silvio

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What Is the Persistence to Methotrexate in Rheumatoid Arthritis, and Does Machine Learning Outperform Hypothesis‐Based Approaches to Its Prediction? von Westerlind, Helga, Maciejewski, Mateusz, Frisell, Thomas, Jelinsky, Scott A, Ziemek, Daniel, Askling, Johan

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Genes contributing to pain sensitivity in the normal population: an exome sequencing study von Williams, Frances M K, Scollen, Serena, Cao, Dandan, Memari, Yasin, Hyde, Craig L, Zhang, Baohong, Sidders, Benjamin, Ziemek, Daniel, Shi, Yujian, Harris, Juliette, Harrow, Ian, Dougherty, Brian, Malarstig, Anders, McEwen, Robert, Stephens, Joel C, Patel, Ketan, Menni, Cristina, Shin, So-Youn, Hodgkiss, Dylan, Surdulescu, Gabriela, He, Wen, Jin, Xin, McMahon, Stephen B, Soranzo, Nicole, John, Sally, Wang, Jun, Spector, Tim D

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Molecular signature of methotrexate response among rheumatoid arthritis patients von Brynedal, Boel, Yoosuf, Niyaz, Ulfarsdottir, Tinna Bjorg, Ziemek, Daniel, Maciejewski, Mateusz, Folkersen, Lasse, Westerlind, Helga, Müller, Malin, Sahlström, Peter, Jelinsky, Scott A, Hensvold, Aase, Padyukov, Leonid, Pomiano, Nancy Vivar, Catrina, Anca, Klareskog, Lars, Berg, Louise

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Brown fat determination and development from muscle precursor cells by novel action of bone morphogenetic protein 6 von Sharma, Ankur, Huard, Christine, Vernochet, Cecile, Ziemek, Daniel, Knowlton, Kelly M, Tyminski, Edyta, Paradis, Theresa, Zhang, Ying, Jones, Jessica E C, von Schack, David, Brown, Christopher T, Milos, Patrice M, Coyle, Anthony J, Tremblay, Frederic, Martinez, Robert V

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Silencing of enzymes involved in ceramide biosynthesis causes distinct global alterations of lipid homeostasis and gene expression[S] von Ruangsiriluk, Wanida, Grosskurth, Shaun E., Ziemek, Daniel, Kuhn, Max, des Etages, Shelley G., Francone, Omar L.

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Assessing statistical significance in causal graphs von Chindelevitch, Leonid, Loh, Po-Ru, Enayetallah, Ahmed, Berger, Bonnie, Ziemek, Daniel

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