Factors influencing the immune response over 15 months after SARS‐CoV‐2 infection: A longitudinal population‐wide study in the Faroe Islands von Petersen, Maria Skaalum, Pérez‐Alós, Laura, Armenteros, Jose Juan A., Hansen, Cecilie B., Fjallsbak, Jógvan Páll, Larsen, Sólrun, Hansen, Jóhanna L., Jarlhelt, Ida, Kristiansen, Marnar F., við Streym, Fríða, á Steig, Bjarni, Christiansen, Debes H., Møller, Lars F., Strøm, Marin, Andorsdóttir, Guðrið, Gaini, Shahin, Weihe, Pál, Garred, Peter

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Single-cell genomics and regulatory networks for 388 human brains von Emani, Prashant S, Liu, Jason J, Clarke, Declan, Jensen, Matthew, Warrell, Jonathan, Gupta, Chirag, Meng, Ran, Lee, Che Yu, Xu, Siwei, Dursun, Cagatay, Lou, Shaoke, Chen, Yuhang, Chu, Zhiyuan, Galeev, Timur, Hwang, Ahyeon, Li, Yunyang, Ni, Pengyu, Zhou, Xiao, Bakken, Trygve E, Bendl, Jaroslav, Bicks, Lucy, Chatterjee, Tanima, Cheng, Lijun, Cheng, Yuyan, Dai, Yi, Duan, Ziheng, Flaherty, Mary, Fullard, John F, Gancz, Michael, Garrido-Martín, Diego, Gaynor-Gillett, Sophia, Grundman, Jennifer, Hawken, Natalie, Henry, Ella, Hoffman, Gabriel E, Huang, Ao, Jiang, Yunzhe, Jin, Ting, Jorstad, Nikolas L, Kawaguchi, Riki, Khullar, Saniya, Liu, Jianyin, Liu, Junhao, Liu, Shuang, Ma, Shaojie, Margolis, Michael, Mazariegos, Samantha, Moore, Jill, Moran, Jennifer R, Nguyen, Eric, Phalke, Nishigandha, Pjanic, Milos, Pratt, Henry, Quintero, Diana, Rajagopalan, Ananya S, Riesenmy, Tiernon R, Shedd, Nicole, Shi, Manman, Spector, Megan, Terwilliger, Rosemarie, Travaglini, Kyle J, Wamsley, Brie, Wang, Gaoyuan, Xia, Yan, Xiao, Shaohua, Yang, Andrew C, Zheng, Suchen, Gandal, Michael J, Lee, Donghoon, Lein, Ed S, Roussos, Panos, Sestan, Nenad, Weng, Zhiping, White, Kevin P, Won, Hyejung, Girgenti, Matthew J, Zhang, Jing, Wang, Daifeng, Geschwind, Daniel, Gerstein, Mark

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Single-cell multi-cohort dissection of the schizophrenia transcriptome von Ruzicka, W Brad, Mohammadi, Shahin, Fullard, John F, Davila-Velderrain, Jose, Subburaju, Sivan, Tso, Daniel Reed, Hourihan, Makayla, Jiang, Shan, Lee, Hao-Chih, Bendl, Jaroslav, Voloudakis, Georgios, Haroutunian, Vahram, Hoffman, Gabriel E, Roussos, Panos, Kellis, Manolis

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Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain von Wen, Cindy, Margolis, Michael, Dai, Rujia, Zhang, Pan, Przytycki, Pawel F, Vo, Daniel D, Bhattacharya, Arjun, Matoba, Nana, Tang, Miao, Jiao, Chuan, Kim, Minsoo, Tsai, Ellen, Hoh, Celine, Aygün, Nil, Walker, Rebecca L, Chatzinakos, Christos, Clarke, Declan, Pratt, Henry, Peters, Mette A, Gerstein, Mark, Daskalakis, Nikolaos P, Weng, Zhiping, Jaffe, Andrew E, Kleinman, Joel E, Hyde, Thomas M, Weinberger, Daniel R, Bray, Nicholas J, Sestan, Nenad, Geschwind, Daniel H, Roeder, Kathryn, Gusev, Alexander, Pasaniuc, Bogdan, Stein, Jason L, Love, Michael I, Pollard, Katherine S, Liu, Chunyu, Gandal, Michael J

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A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex von Huuki-Myers, Louise A, Spangler, Abby, Eagles, Nicholas J, Montgomery, Kelsey D, Kwon, Sang Ho, Guo, Boyi, Grant-Peters, Melissa, Divecha, Heena R, Tippani, Madhavi, Sriworarat, Chaichontat, Nguyen, Annie B, Ravichandran, Prashanthi, Tran, Matthew N, Seyedian, Arta, Hyde, Thomas M, Kleinman, Joel E, Battle, Alexis, Page, Stephanie C, Ryten, Mina, Hicks, Stephanie C, Martinowich, Keri, Collado-Torres, Leonardo, Maynard, Kristen R

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Massively parallel characterization of regulatory elements in the developing human cortex von Deng, Chengyu, Whalen, Sean, Steyert, Marilyn, Ziffra, Ryan, Przytycki, Pawel F, Inoue, Fumitaka, Pereira, Daniela A, Capauto, Davide, Norton, Scott, Vaccarino, Flora M, Pollen, Alex A, Nowakowski, Tomasz J, Ahituv, Nadav, Pollard, Katherine S

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The mitochondrial multi-omic response to exercise training across rat tissues von Amar, David, Jimenez-Morales, David, Ramaker, Megan E., Raja, Archana Natarajan, Zhao, Bingqing, Marwaha, Shruti, Gaul, David A., Hershman, Steven G., Ferrasse, Alexis, Xia, Ashley, Lanza, Ian, Fernández, Facundo M., Montgomery, Stephen B., Hevener, Andrea L., Ashley, Euan A., Walsh, Martin J., Sparks, Lauren M., Rector, R. Scott, Thyfault, John, Goodpaster, Bret H., Coen, Paul M., Schenk, Simon, Lindholm, Malene E., Adkins, Joshua N., Armenteros, Jose Juan Almagro, Amper, Mary Anne S., Bae, Dam, Bamman, Marcas, Bararpour, Nasim, Barnes, Jerry, Bergman, Bryan C., Bessesen, Daniel H., Broskey, Nicholas T., Carr, Steven, Chambers, Toby L., Chavez, Clarisa, Chiu, Roxanne, Clark, Natalie, Evans, Charles R., Franczak, Edziu, Gagne, Nicole, Ge, Yongchao, Houmard, Joseph A., Huffman, Kim M., Hung, Chia-Jui, Hutchinson-Bunch, Chelsea, Ilkayeva, Olga, Jackson, Bailey E., Jankowski, Catherine M., Jin, Christopher A., Johannsen, Neil M., Keshishian, Hasmik, Kohrt, Wendy M., Kramer, Kyle S., Kraus, William E., Lester, Bridget, Li, Jun Z., Lira, Ana K., Lowe, Adam, Mani, D.R., Many, Gina M., May, Sandy, Melanson, Edward L., Moore, Samuel G., Moreau, Kerrie L., Musi, Nicolas, Nachun, Daniel, Nair, Venugopalan D., Newgard, Christopher, Nudelman, German, Piehowski, Paul D., Pincas, Hanna, Qian, Wei-Jun, Rankinen, Tuomo, Rasmussen, Blake B., Ravussin, Eric, Rooney, Jessica L., Rushing, Scott, Samdarshi, Mihir, Sanford, James A., Schauer, Irene E., Sealfon, Stuart C., Smith, Kevin S., Smith, Gregory R., Snyder, Michael, Stowe, Cynthia L., Talton, Jennifer W., Thalacker-Mercer, Anna, Trappe, Scott, Trappe, Todd A., Vasoya, Mital, Vetr, Nikolai G., Volpi, Elena, Walkup, Michael P., Wiel, Laurens, Wu, Si, Yan, Zhen, Yu, Jiye, Zaslavsky, Elena, Zhen, Jimmy

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The impact of exercise on gene regulation in association with complex trait genetics von Vetr, Nikolai G., Gay, Nicole R., Montgomery, Stephen B.

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Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures von Nair, Venugopalan D., Pincas, Hanna, Smith, Gregory R., Zaslavsky, Elena, Ge, Yongchao, Amper, Mary Anne S., Vasoya, Mital, Chikina, Maria, Sun, Yifei, Raja, Archana Natarajan, Mao, Weiguang, Gay, Nicole R., Esser, Karyn A., Smith, Kevin S., Zhao, Bingqing, Wiel, Laurens, Singh, Aditya, Lindholm, Malene E., Amar, David, Montgomery, Stephen, Snyder, Michael P., Walsh, Martin J., Sealfon, Stuart C., Adkins, Joshua N., Almagro Armenteros, Jose Juan, Ashley, Euan, Bae, Dam, Bamman, Marcas, Bararpour, Nasim, Bennett, Alexis, Bergman, Bryan C., Bessesen, Daniel H., Bodine, Sue C., Buford, Thomas W., Chambers, Toby L., Chavez, Clarisa, Cortes, Tiffany, Cutter, Gary, Espinoza, Sara, Fernández, Facundo M., Gagne, Nicole, Gaul, David A., Goodpaster, Bret H., Hung, Chia-Jui, Jackson, Bailey E., Jankowski, Catherine M., Jin, Christopher A., Kohrt, Wendy M., Kramer, Kyle S., Lester, Bridget, Lira, Ana K., May, Sandy, Marjanovic, Nada, Melanson, Edward L., Moore, Samuel G., Moreau, Kerrie L., Musi, Nicolas, Nachum, Daniel, Nudelman, German, Pahor, Marco, Patel, Darpan, Piehowski, Paul D., Qian, Wei-Jun, Rasmussen, Blake B., Rirak, Stas, Rooney, Jessica L., Sanford, James A., Savage, Evan M., Schauer, Irene E., Serra, Monica, Stowe, Cynthia L., Thalacker-Mercer, Anna, Trappe, Todd A., Trappe, Scott, Vetr, Nikolai G., Volpi, Elena, Wheeler, Matthew T., Wu, Si, Zebarjadi, Navid, Zhen, Jimmy

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Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue von Many, Gina M., Sanford, James A., Sagendorf, Tyler J., Hou, Zhenxin, Nigro, Pasquale, Whytock, Katie L., Amar, David, Caputo, Tiziana, Gay, Nicole R., Gaul, David A., Hirshman, Michael F., Jimenez-Morales, David, Lindholm, Malene E., Muehlbauer, Michael J., Vamvini, Maria, Bergman, Bryan C., Fernández, Facundo M., Goodyear, Laurie J., Hevener, Andrea L., Ortlund, Eric A., Sparks, Lauren M., Xia, Ashley, Adkins, Joshua N., Bodine, Sue C., Newgard, Christopher B., Schenk, Simon

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DeepLoc 2.0: multi-label subcellular localization prediction using protein language models von Thumuluri, Vineet, Almagro Armenteros, José Juan, Johansen, Alexander Rosenberg, Nielsen, Henrik, Winther, Ole

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DeepLoc: prediction of protein subcellular localization using deep learning von Almagro Armenteros, José Juan, Sønderby, Casper Kaae, Sønderby, Søren Kaae, Nielsen, Henrik, Winther, Ole

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SignalP 5.0 improves signal peptide predictions using deep neural networks von Almagro Armenteros, José Juan, Tsirigos, Konstantinos D., Sønderby, Casper Kaae, Petersen, Thomas Nordahl, Winther, Ole, Brunak, Søren, von Heijne, Gunnar, Nielsen, Henrik

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SignalP 6.0 predicts all five types of signal peptides using protein language models von Teufel, Felix, Almagro Armenteros, José Juan, Johansen, Alexander Rosenberg, Gíslason, Magnús Halldór, Pihl, Silas Irby, Tsirigos, Konstantinos D., Winther, Ole, Brunak, Søren, von Heijne, Gunnar, Nielsen, Henrik

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Detecting sequence signals in targeting peptides using deep learning von Almagro Armenteros, Jose Juan, Salvatore, Marco, Emanuelsson, Olof, Winther, Ole, von Heijne, Gunnar, Elofsson, Arne, Nielsen, Henrik

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DeepLoc 2.1: multi-label membrane protein type prediction using protein language models von Ødum, Marius Thrane, Teufel, Felix, Thumuluri, Vineet, Almagro Armenteros, José Juan, Johansen, Alexander Rosenberg, Winther, Ole, Nielsen, Henrik

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An introduction to deep learning on biological sequence data: examples and solutions von Jurtz, Vanessa Isabell, Johansen, Alexander Rosenberg, Nielsen, Morten, Almagro Armenteros, Jose Juan, Nielsen, Henrik, Sønderby, Casper Kaae, Winther, Ole, Sønderby, Søren Kaae

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Modeling of waning immunity after SARS-CoV-2 vaccination and influencing factors von Pérez-Alós, Laura, Armenteros, Jose Juan Almagro, Madsen, Johannes Roth, Hansen, Cecilie Bo, Jarlhelt, Ida, Hamm, Sebastian Rask, Heftdal, Line Dam, Pries-Heje, Mia Marie, Møller, Dina Leth, Fogh, Kamille, Hasselbalch, Rasmus Bo, Rosbjerg, Anne, Brunak, Søren, Sørensen, Erik, Larsen, Margit Anita Hørup, Ostrowski, Sisse Rye, Frikke-Schmidt, Ruth, Bayarri-Olmos, Rafael, Hilsted, Linda Maria, Iversen, Kasper Karmark, Bundgaard, Henning, Nielsen, Susanne Dam, Garred, Peter

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Improved metagenome binning and assembly using deep variational autoencoders von Nissen, Jakob Nybo, Johansen, Joachim, Allesøe, Rosa Lundbye, Sønderby, Casper Kaae, Armenteros, Jose Juan Almagro, Grønbech, Christopher Heje, Jensen, Lars Juhl, Nielsen, Henrik Bjørn, Petersen, Thomas Nordahl, Winther, Ole, Rasmussen, Simon

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Previous immunity shapes immune responses to SARS-CoV-2 booster vaccination and Omicron breakthrough infection risk von Pérez-Alós, Laura, Hansen, Cecilie Bo, Almagro Armenteros, Jose Juan, Madsen, Johannes Roth, Heftdal, Line Dam, Hasselbalch, Rasmus Bo, Pries-Heje, Mia Marie, Bayarri-Olmos, Rafael, Jarlhelt, Ida, Hamm, Sebastian Rask, Møller, Dina Leth, Sørensen, Erik, Ostrowski, Sisse Rye, Frikke-Schmidt, Ruth, Hilsted, Linda Maria, Bundgaard, Henning, Nielsen, Susanne Dam, Iversen, Kasper Karmark, Garred, Peter

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