A new computational method for the detection of horizontal gene transfer events von Tsirigos, Aristotelis, Rigoutsos, Isidore

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Analysis of multipath Routing-Part I: the effect on the packet delivery ratio von Tsirigos, A., Haas, Z.J.

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A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes von Tsirigos, Aristotelis, Rigoutsos, Isidore

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Analysis of multipath routing, part 2: mitigation of the effects of frequently changing network topologies von Tsirigos, A., Haas, Z.J.

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LncRNA RP11-19E11 is an E2F1 target required for proliferation and survival of basal breast cancer von Giro-Perafita, A., Luo, L., Khodadadi-Jamayran, A., Thompson, M., Akgol Oksuz, B., Tsirigos, A., Dynlacht, B. D., Sánchez, I., Esteva, F. J.

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A reference map of potential determinants for the human serum metabolome von Bar, Noam, Korem, Tal, Weissbrod, Omer, Zeevi, David, Rothschild, Daphna, Leviatan, Sigal, Kosower, Noa, Lotan-Pompan, Maya, Weinberger, Adina, Le Roy, Caroline I., Menni, Cristina, Visconti, Alessia, Falchi, Mario, Spector, Tim D., Adamski, Jerzy, Franks, Paul W., Pedersen, Oluf, Segal, Eran

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Interleukin-17 governs hypoxic adaptation of injured epithelium von Konieczny, Piotr, Xing, Yue, Sidhu, Ikjot, Subudhi, Ipsita, Mansfield, Kody P, Hsieh, Brandon, Biancur, Douglas E, Larsen, Samantha B, Cammer, Michael, Li, Dongqing, Landén, Ning Xu, Loomis, Cynthia, Heguy, Adriana, Tikhonova, Anastasia N, Tsirigos, Aristotelis, Naik, Shruti

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Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models von Allesøe, Rosa Lundbye, Lundgaard, Agnete Troen, Hernández Medina, Ricardo, Aguayo-Orozco, Alejandro, Johansen, Joachim, Nissen, Jakob Nybo, Brorsson, Caroline, Mazzoni, Gianluca, Niu, Lili, Biel, Jorge Hernansanz, Leal Rodríguez, Cristina, Brasas, Valentas, Webel, Henry, Benros, Michael Eriksen, Pedersen, Anders Gorm, Chmura, Piotr Jaroslaw, Jacobsen, Ulrik Plesner, Mari, Andrea, Koivula, Robert, Mahajan, Anubha, Vinuela, Ana, Tajes, Juan Fernandez, Sharma, Sapna, Haid, Mark, Hong, Mun-Gwan, Musholt, Petra B., De Masi, Federico, Vogt, Josef, Pedersen, Helle Krogh, Gudmundsdottir, Valborg, Jones, Angus, Kennedy, Gwen, Bell, Jimmy, Thomas, E. Louise, Frost, Gary, Thomsen, Henrik, Hansen, Elizaveta, Hansen, Tue Haldor, Vestergaard, Henrik, Muilwijk, Mirthe, Blom, Marieke T., ‘t Hart, Leen M., Pattou, Francois, Raverdy, Violeta, Brage, Soren, Kokkola, Tarja, Heggie, Alison, McEvoy, Donna, Mourby, Miranda, Kaye, Jane, Hattersley, Andrew, McDonald, Timothy, Ridderstråle, Martin, Walker, Mark, Forgie, Ian, Giordano, Giuseppe N., Pavo, Imre, Ruetten, Hartmut, Pedersen, Oluf, Hansen, Torben, Dermitzakis, Emmanouil, Franks, Paul W., Schwenk, Jochen M., Adamski, Jerzy, McCarthy, Mark I., Pearson, Ewan, Banasik, Karina, Rasmussen, Simon, Brunak, Søren

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Machine learning and data mining frameworks for predicting drug response in cancer: An overview and a novel in silico screening process based on association rule mining von Vougas, Konstantinos, Sakellaropoulos, Theodore, Kotsinas, Athanassios, Foukas, George-Romanos P., Ntargaras, Andreas, Koinis, Filippos, Polyzos, Alexander, Myrianthopoulos, Vassilios, Zhou, Hua, Narang, Sonali, Georgoulias, Vassilis, Alexopoulos, Leonidas, Aifantis, Iannis, Townsend, Paul A., Sfikakis, Petros, Fitzgerald, Rebecca, Thanos, Dimitris, Bartek, Jiri, Petty, Russell, Tsirigos, Aristotelis, Gorgoulis, Vassilis G.

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Axon TRAP reveals learning-associated alterations in cortical axonal mRNAs in the lateral amgydala von Ostroff, Linnaea E, Santini, Emanuela, Sears, Robert, Deane, Zachary, Kanadia, Rahul N, LeDoux, Joseph E, Lhakhang, Tenzin, Tsirigos, Aristotelis, Heguy, Adriana, Klann, Eric

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Apoptotic cell–induced AhR activity is required for immunological tolerance and suppression of systemic lupus erythematosus in mice and humans von Shinde, Rahul, Hezaveh, Kebria, Halaby, Marie Jo, Kloetgen, Andreas, Chakravarthy, Ankur, da Silva Medina, Tiago, Deol, Reema, Manion, Kieran P., Baglaenko, Yuriy, Eldh, Maria, Lamorte, Sara, Wallace, Drew, Chodisetti, Sathi Babu, Ravishankar, Buvana, Liu, Haiyun, Chaudhary, Kapil, Munn, David H., Tsirigos, Aristotelis, Madaio, Michael, Gabrielsson, Susanne, Touma, Zahi, Wither, Joan, De Carvalho, Daniel D., McGaha, Tracy L.

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131 Defining cellular quiescence as a multi-drug resistance mechanism in squamous cell carcinoma von Brown, J., Yonekubo, Y., Tsirigos, A.

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Author Correction: Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models von Allesøe, Rosa Lundbye, Lundgaard, Agnete Troen, Hernández Medina, Ricardo, Aguayo-Orozco, Alejandro, Johansen, Joachim, Nissen, Jakob Nybo, Brorsson, Caroline, Mazzoni, Gianluca, Niu, Lili, Biel, Jorge Hernansanz, Leal Rodríguez, Cristina, Brasas, Valentas, Webel, Henry, Benros, Michael Eriksen, Pedersen, Anders Gorm, Chmura, Piotr Jaroslaw, Jacobsen, Ulrik Plesner, Mari, Andrea, Koivula, Robert, Mahajan, Anubha, Vinuela, Ana, Tajes, Juan Fernandez, Sharma, Sapna, Haid, Mark, Hong, Mun-Gwan, Musholt, Petra B., De Masi, Federico, Vogt, Josef, Pedersen, Helle Krogh, Gudmundsdottir, Valborg, Jones, Angus, Kennedy, Gwen, Bell, Jimmy, Thomas, E. Louise, Frost, Gary, Thomsen, Henrik, Hansen, Elizaveta, Hansen, Tue Haldor, Vestergaard, Henrik, Muilwijk, Mirthe, Blom, Marieke T., ‘t Hart, Leen M., Pattou, Francois, Raverdy, Violeta, Brage, Soren, Kokkola, Tarja, Heggie, Alison, McEvoy, Donna, Mourby, Miranda, Kaye, Jane, Hattersley, Andrew, McDonald, Timothy, Ridderstråle, Martin, Walker, Mark, Forgie, Ian, Giordano, Giuseppe N., Pavo, Imre, Ruetten, Hartmut, Pedersen, Oluf, Hansen, Torben, Dermitzakis, Emmanouil, Franks, Paul W., Schwenk, Jochen M., Adamski, Jerzy, McCarthy, Mark I., Pearson, Ewan, Banasik, Karina, Rasmussen, Simon, Brunak, Søren

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A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization von Zampetidis, Christos P., Galanos, Panagiotis, Angelopoulou, Andriani, Zhu, Yajie, Polyzou, Aikaterini, Karamitros, Timokratis, Kotsinas, Athanassios, Lagopati, Nefeli, Mourkioti, Ioanna, Mirzazadeh, Reza, Polyzos, Alexandros, Garnerone, Silvano, Mizi, Athanasia, Gusmao, Eduardo G., Sofiadis, Konstantinos, Gál, Zita, Larsen, Dorthe H., Pefani, Dafni-Eleftheria, Demaria, Marco, Tsirigos, Aristotelis, Crosetto, Nicola, Maya-Mendoza, Apolinar, Papaspyropoulos, Angelos, Evangelou, Konstantinos, Bartek, Jiri, Papantonis, Argyris, Gorgoulis, Vassilis G.

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Mapping the landscape of histomorphological cancer phenotypes using self-supervised learning on unannotated pathology slides von Claudio Quiros, Adalberto, Coudray, Nicolas, Yeaton, Anna, Yang, Xinyu, Liu, Bojing, Le, Hortense, Chiriboga, Luis, Karimkhan, Afreen, Narula, Navneet, Moore, David A., Park, Christopher Y., Pass, Harvey, Moreira, Andre L., Le Quesne, John, Tsirigos, Aristotelis, Yuan, Ke

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A Deep Learning Framework for Predicting Response to Therapy in Cancer von Sakellaropoulos, Theodore, Vougas, Konstantinos, Narang, Sonali, Koinis, Filippos, Kotsinas, Athanassios, Polyzos, Alexander, Moss, Tyler J., Piha-Paul, Sarina, Zhou, Hua, Kardala, Eleni, Damianidou, Eleni, Alexopoulos, Leonidas G., Aifantis, Iannis, Townsend, Paul A., Panayiotidis, Mihalis I., Sfikakis, Petros, Bartek, Jiri, Fitzgerald, Rebecca C., Thanos, Dimitris, Mills Shaw, Kenna R., Petty, Russell, Tsirigos, Aristotelis, Gorgoulis, Vassilis G.

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137 Decreased cytotoxic T cells, decreased cytotoxic/regulatory T-cell ratio, and decreased TCR clonality are associated with increased numbers of primary cutaneous squamous cell c... von Doudican, N., Frazzette, N., Khodadadi-Jamayran, A., Tsirigos, A., Carucci, J.

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135 Defining the T cell landscape and neoantigens via T-cell receptor sequencing and gene expression profiling in cutaneous squamous cell carcinoma von Doudican, N.A., Santana, A., Felsen, D., Khodadadi-Jamayran, A., Tsirigos, A., Carucci, J.

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P1.20-06 Mapping the Histopathological Landscape of Lung Adenocarcinoma using Self-Supervised Learning Artificial Intelligence von Quiros, A.C., Coudray, N., Yeaton, A., Yang, X., Liu, B., Chiriboga, L., Karimkhan, A., Narula, N., Moore, D., Park, C., Pass, H., Moreira, A., Le Quesne, J., Tsirigos, A., Yuan, K.

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Mosaic blastocysts diagnosed with next generation sequencing (NGS) have unique transcriptomic profiles different from those of euploid or aneuploid embryos von Maxwell, S.M., Lhakhang, T., Kramer, Y.G., Zhang, Y., Heguy, A., Tsirigos, A., Grifo, J.A., Licciardi, F.

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