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3. Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Author

Bassani, Sissy, Chrast, Jacqueline, Ambrosini, Giovanna, Voisin, Norine, Schütz, Frédéric, Brusco, Alfredo, Sirchia, Fabio, Turban, Lydia, Schubert, Susanna, Abou Jamra, Rami, Schlump, Jan-Ulrich, DeMille, Desiree, Bayrak-Toydemir, Pinar, Nelson, Gary Rex, Wong, Kristen Nicole, Duncan, Laura, Mosera, Mackenzie, Gilissen, Christian, Vissers, Lisenka E. L. M., Pfundt, Rolph, Kersseboom, Rogier, Yttervik, Hilde, Hansen, Geir Åsmund Myge, Smeland, Marie Falkenberg, Butler, Kameryn M., Lyons, Michael J., Carvalho, Claudia M. B., Zhang, Chaofan, Lupski, James R., Potocki, Lorraine, Flores-Gallegos, Leticia, Morales-Toquero, Rodrigo, Petit, Florence, Yalcin, Binnaz, Tuttle, Annabelle, Elloumi, Houda Zghal, McCormick, Lane, Kukolich, Mary, Klaas, Oliver, Horvath, Judit, Scala, Marcello, Iacomino, Michele, Operto, Francesca, Zara, Federico, Writzl, Karin, Maver, Aleš, Haanpää, Maria K., Pohjola, Pia, Arikka, Harri, Kievit, Anneke J. A., Calandrini, Camilla, Iseli, Christian, Guex, Nicolas, and Reymond, Alexandre

Published
2024
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5. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Author

Wells, Daniel K, van Buuren, Marit M, Dang, Kristen K, Hubbard-Lucey, Vanessa M, Sheehan, Kathleen CF, Campbell, Katie M, Lamb, Andrew, Ward, Jeffrey P, Sidney, John, Blazquez, Ana B, Rech, Andrew J, Zaretsky, Jesse M, Comin-Anduix, Begonya, Ng, Alphonsus HC, Chour, William, Yu, Thomas V, Rizvi, Hira, Chen, Jia M, Manning, Patrice, Steiner, Gabriela M, Doan, Xengie C, Alliance, The Tumor Neoantigen Selection, Khan, Aly A, Lugade, Amit, Lazic, Ana M Mijalkovic, Frentzen, Angela A Elizabeth, Tadmor, Arbel D, Sasson, Ariella S, Rao, Arjun A, Pei, Baikang, Schrörs, Barbara, Berent-Maoz, Beata, Carreno, Beatriz M, Song, Bin, Peters, Bjoern, Li, Bo, Higgs, Brandon W, Stevenson, Brian J, Iseli, Christian, Miller, Christopher A, Morehouse, Christopher A, Melief, Cornelis JM, Puig-Saus, Cristina, van Beek, Daphne, Balli, David, Gfeller, David, Haussler, David, Jäger, Dirk, Cortes, Eduardo, Esaulova, Ekaterina, Sherafat, Elham, Arcila, Francisco, Bartha, Gabor, Liu, Geng, Coukos, George, Richard, Guilhem, Chang, Han, Si, Han, Zörnig, Inka, Xenarios, Ioannis, Mandoiu, Ion, Kooi, Irsan, Conway, James P, Kessler, Jan H, Greenbaum, Jason A, Perera, Jason F, Harris, Jason, Hundal, Jasreet, Shelton, Jennifer M, Wang, Jianmin, Wang, Jiaqian, Greshock, Joel, Blake, Jonathon, Szustakowski, Joseph, Kodysh, Julia, Forman, Juliet, Wei, Lei, Lee, Leo J, Fanchi, Lorenzo F, Slagter, Maarten, Lang, Maren, Mueller, Markus, Lower, Martin, Vormehr, Mathias, Artyomov, Maxim N, Kuziora, Michael, Princiotta, Michael, Bassani-Sternberg, Michal, Macabali, Mignonette, Kojicic, Milica R, Yang, Naibo, Raicevic, Nevena M Ilic, Guex, Nicolas, Robine, Nicolas, Halama, Niels, Skundric, Nikola M, Milicevic, Ognjen S, Gellert, Pascal, Jongeneel, Patrick, and Charoentong, Pornpimol

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Immunology, Cancer, Vaccine Related, Genetics, Immunization, Good Health and Well Being, Alleles, Antigen Presentation, Antigens, Neoplasm, Cohort Studies, Epitopes, Humans, Neoplasms, Peptides, Programmed Cell Death 1 Receptor, Reproducibility of Results, Tumor Neoantigen Selection Alliance, TESLA, epitope, immunogenicity, immunogenomics, immunotherapy, neoantigen, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community.

Published
2020

7. Biomathematical enzyme kinetics model of prebiotic autocatalytic RNA networks: degenerating parasite-specific hyperparasite catalysts confer parasite resistance and herald the birth of molecular immunity.

Author

Pirovino, Magnus, Iseli, Christian, Curran, Joseph A., and Conrad, Bernard

Subjects
*ENZYME kinetics, *CHEMICAL reactions, *ARMS race, *ERROR rates, *AUTOCATALYSIS
Abstract

Catalysis and specifically autocatalysis are the quintessential building blocks of life. Yet, although autocatalytic networks are necessary, they are not sufficient for the emergence of life-like properties, such as replication and adaptation. The ultimate and potentially fatal threat faced by molecular replicators is parasitism; if the polymerase error rate exceeds a critical threshold, even the fittest molecular species will disappear. Here we have developed an autocatalytic RNA early life mathematical network model based on enzyme kinetics, specifically the steady-state approximation. We confirm previous models showing that these second-order autocatalytic cycles are sustainable, provided there is a sufficient nucleotide pool. However, molecular parasites become untenable unless they sequentially degenerate to hyperparasites (i.e. parasites of parasites). Parasite resistance–a parasite-specific host response decreasing parasite fitness–is acquired gradually, and eventually involves an increased binding affinity of hyperparasites for parasites. Our model is supported at three levels; firstly, ribozyme polymerases display Michaelis-Menten saturation kinetics and comply with the steady-state approximation. Secondly, ribozyme polymerases are capable of sustainable auto-amplification and of surmounting the fatal error threshold. Thirdly, with growing sequence divergence of host and parasite catalysts, the probability of self-binding is expected to increase and the trend towards cross-reactivity to diminish. Our model predicts that primordial host-RNA populations evolved via an arms race towards a host-parasite-hyperparasite catalyst trio that conferred parasite resistance within an RNA replicator niche. While molecular parasites have traditionally been viewed as a nuisance, our model argues for their integration into the host habitat rather than their separation. It adds another mechanism–with biochemical precision–by which parasitism can be tamed and offers an attractive explanation for the universal coexistence of catalyst trios within prokaryotes and the virosphere, heralding the birth of a primitive molecular immunity. Author summary: The quintessential components of life comprise a potent mixture of naturally occurring, but improbable chemical reactions (catalysis), and the arrangement of such accelerated chemical reactions into closed loops (autocatalytic sets). This is required but is not sufficient for such networks to self-propagate (amplification of the information carrier = host polymerization) and adapt (Darwinian evolution). As soon as self-propagation is attained, the next hurdle is parasitism. This typically involves shorter molecules (the products of replicative errors) that hitchhike the replicative potential of the host. They will invariably outcompete the regular amplification process, unless a solution is found. We have addressed this problem using a new model based on the mathematics of catalysis. It confirms previous studies demonstrating that autocatalytic sets become self-sustaining, assuming that a sufficient pool of molecular building blocks is available. However, molecular parasitism is pervasive and potentially fatal for both host and parasite. In our model, we allow these parasites to degenerate in a controlled fashion, giving rise to parasites of parasites (hyperparasites). As long as these hyperparasites acquire binding specificity for parasites, an attenuation of parasitism is observed. These parasite-hyperparasite cycles stabilize the host cycle, explaining why they are conserved, and why they are the likely reason behind the observation that all cellular hosts are associated with parasites (e.g. bacteria) and hyperparasites (e.g. viruses) across all kingdoms of life. Moreover, it provides a novel solution to the usually intractable problem of parasitism. [ABSTRACT FROM AUTHOR]

Published
2025
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9. Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING

Author

Bruand, Marine, Barras, David, Mina, Marco, Ghisoni, Eleonora, Morotti, Matteo, Lanitis, Evripidis, Fahr, Noémie, Desbuisson, Mathieu, Grimm, Alizée, Zhang, Hualing, Chong, Chloe, Dagher, Julien, Chee, Sora, Tsianou, Theodora, Dorier, Julien, Stevenson, Brian J., Iseli, Christian, Ronet, Catherine, Bobisse, Sara, Genolet, Raphael, Walton, Josephine, Bassani-Sternberg, Michal, Kandalaft, Lana E., Ren, Bing, McNeish, Iain, Swisher, Elizabeth, Harari, Alexandre, Delorenzi, Mauro, Ciriello, Giovanni, Irving, Melita, Rusakiewicz, Sylvie, Foukas, Periklis G., Martinon, Fabio, Dangaj Laniti, Denarda, and Coukos, George

Published
2021
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11. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Author

Khan, Aly A., Lugade, Amit, Lazic, Ana M. Mijalkovic, Frentzen, Angela A. Elizabeth, Tadmor, Arbel D., Sasson, Ariella S., Rao, Arjun A., Pei, Baikang, Schrörs, Barbara, Berent-Maoz, Beata, Carreno, Beatriz M., Song, Bin, Peters, Bjoern, Li, Bo, Higgs, Brandon W., Stevenson, Brian J., Iseli, Christian, Miller, Christopher A., Morehouse, Christopher A., Melief, Cornelis J.M., Puig-Saus, Cristina, van Beek, Daphne, Balli, David, Gfeller, David, Haussler, David, Jäger, Dirk, Cortes, Eduardo, Esaulova, Ekaterina, Sherafat, Elham, Arcila, Francisco, Bartha, Gabor, Liu, Geng, Coukos, George, Richard, Guilhem, Chang, Han, Si, Han, Zörnig, Inka, Xenarios, Ioannis, Mandoiu, Ion, Kooi, Irsan, Conway, James P., Kessler, Jan H., Greenbaum, Jason A., Perera, Jason F., Harris, Jason, Hundal, Jasreet, Shelton, Jennifer M., Wang, Jianmin, Wang, Jiaqian, Greshock, Joel, Blake, Jonathon, Szustakowski, Joseph, Kodysh, Julia, Forman, Juliet, Wei, Lei, Lee, Leo J., Fanchi, Lorenzo F., Slagter, Maarten, Lang, Maren, Mueller, Markus, Lower, Martin, Vormehr, Mathias, Artyomov, Maxim N., Kuziora, Michael, Princiotta, Michael, Bassani-Sternberg, Michal, Macabali, Mignonette, Kojicic, Milica R., Yang, Naibo, Raicevic, Nevena M. Ilic, Guex, Nicolas, Robine, Nicolas, Halama, Niels, Skundric, Nikola M., Milicevic, Ognjen S., Gellert, Pascal, Jongeneel, Patrick, Charoentong, Pornpimol, Srivastava, Pramod K., Tanden, Prateek, Shah, Priyanka, Hu, Qiang, Gupta, Ravi, Chen, Richard, Petit, Robert, Ziman, Robert, Hilker, Rolf, Shukla, Sachet A., Al Seesi, Sahar, Boyle, Sean M., Qiu, Si, Sarkizova, Siranush, Salama, Sofie, Liu, Song, Wu, Song, Sridhar, Sriram, Ketelaars, Steven L.C., Jhunjhunwala, Suchit, Shcheglova, Tatiana, Schuepbach, Thierry, Creasy, Todd H., Josipovic, Veliborka, Kovacevic, Vladimir B., Fu, Weixuan, Krebber, Willem-Jan, Hsu, Yi-Hsiang, Sebastian, Yinong, Yalcin, Zeynep Kosaloglu, Huang, Zhiqin, Wells, Daniel K., van Buuren, Marit M., Dang, Kristen K., Hubbard-Lucey, Vanessa M., Sheehan, Kathleen C.F., Campbell, Katie M., Lamb, Andrew, Ward, Jeffrey P., Sidney, John, Blazquez, Ana B., Rech, Andrew J., Zaretsky, Jesse M., Comin-Anduix, Begonya, Ng, Alphonsus H.C., Chour, William, Yu, Thomas V., Rizvi, Hira, Chen, Jia M., Manning, Patrice, Steiner, Gabriela M., Doan, Xengie C., Merghoub, Taha, Guinney, Justin, Kolom, Adam, Selinsky, Cheryl, Ribas, Antoni, Hellmann, Matthew D., Hacohen, Nir, Sette, Alessandro, Heath, James R., Bhardwaj, Nina, Ramsdell, Fred, Schreiber, Robert D., Schumacher, Ton N., Kvistborg, Pia, and Defranoux, Nadine A.

Published
2020
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14. Repairing a deleterious domestication variant in a floral regulator of tomato by base editing

Author

Glaus, Anna N., primary, Brechet, Marion, additional, Lebeigle, Ludivine, additional, Iwaszkiewicz, Justyna, additional, Ambrosini, Giovanna, additional, Julca, Irene, additional, Zhang, Jing, additional, Roberts, Robyn, additional, Iseli, Christian, additional, Guex, Nicolas, additional, Jiménez-Gómez, José, additional, Glover, Natasha, additional, Martin, Gregory B., additional, Strickler, Susan, additional, and Soyk, Sebastian, additional

Published
2024
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16. Variant-specific pathophysiological mechanisms ofAFF3differently influence transcriptome profiles

Author

Bassani, Sissy, primary, Chrast, Jacqueline, additional, Ambrosini, Giovanna, additional, Voisin, Norine, additional, Schütz, Frédéric, additional, Brusco, Alfredo, additional, Sirchia, Fabio, additional, Turban, Lydia, additional, Schubert, Susanna, additional, Jamra, Rami Abou, additional, Schlump, Jan-Ulrich, additional, DeMille, Desiree, additional, Bayrak-Toydemir, Pinar, additional, Nelson, Gary Rex, additional, Wong, Kristen Nicole, additional, Duncan, Laura, additional, Mosera, Mackenzie, additional, Gilissen, Christian, additional, Vissers, Lisenka E.L.M., additional, Pfundt, Rolph, additional, Kersseboom, Rogier, additional, Yttervik, Hilde, additional, Hansen, Geir Åsmund Myge, additional, Smeland, Marie Falkenberg, additional, Butler, Kameryn M., additional, Lyons, Michael J., additional, Carvalho, Claudia M.B., additional, Zhang, Chaofan, additional, Lupski, James R., additional, Potocki, Lorraine, additional, Flores-Gallegos, Leticia, additional, Morales-Toquero, Rodrigo, additional, Petit, Florence, additional, Yalcin, Binnaz, additional, Tuttle, Annabelle, additional, Elloumi, Houda Zghal, additional, Mccormick, Lane, additional, Kukolich, Mary, additional, Klaas, Oliver, additional, Horvath, Judit, additional, Scala, Marcello, additional, Iacomino, Michele, additional, Operto, Francesca, additional, Zara, Federico, additional, Writzl, Karin, additional, Maver, Ales, additional, Haanpää, Maria K., additional, Pohjola, Pia, additional, Arikka, Harri, additional, Iseli, Christian, additional, Guex, Nicolas, additional, and Reymond, Alexandre, additional

Published
2024
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20. Genomic Data Clustering on FPGAs for Compression

Author

Petraglio, Enrico, Wertenbroek, Rick, Capitao, Flavio, Guex, Nicolas, Iseli, Christian, Thoma, Yann, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Wong, Stephan, editor, Beck, Antonio Carlos, editor, Bertels, Koen, editor, and Carro, Luigi, editor

Published
2017
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22. The Generation and Utilization of a Cancer-Oriented Representation of the Human Transcriptome by Using Expressed Sequence Tags

Author

Brentani, Helena, Caballero, Otávia L., Camargo, Anamaria A., da Silva, Aline M., da Silva,, Wilson Araújo, Neto, Emmanuel Dias, Grivet, Marco, Gruber, Arthur, Hide, Winston, Iseli, Christian, Jongeneel, C. Victor, Kelso, Janet, Nagai, Maria Aparecida, Osorio, Elisson C., Riggins, Gregory J., de Souza, Sandro, Stevenson, Brian J., Strausberg, Robert L., Tajara, Eloiza H., and Verjovski-Almeida, Sergio

Published
2003

24. Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data

Author

Grigoriadis, Anita, Mackay, Alan, Reis-Filho, Jorge S, Steele, Dawn, Iseli, Christian, Stevenson, Brian J, Jongeneel, C Victor, Valgeirsson, Haukur, Fenwick, Kerry, Iravani, Marjan, Leao, Maria, Simpson, Andrew JG, Strausberg, Robert L, Jat, Parmjit S, Ashworth, Alan, Neville, A Munro, and O'Hare, Michael J

Subjects
Cancer, Genetics, Human Genome, Biotechnology, Breast Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, 2.1 Biological and endogenous factors, Aetiology, Biomarkers, Tumor, Breast, Breast Neoplasms, Cell Adhesion Molecules, Cells, Cultured, Epithelial Cells, Female, Gene Expression Profiling, Humans, Oligonucleotide Array Sequence Analysis, Prognosis, Transcription, Genetic, Tumor Cells, Cultured, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

IntroductionDiverse microarray and sequencing technologies have been widely used to characterise the molecular changes in malignant epithelial cells in breast cancers. Such gene expression studies to identify markers and targets in tumour cells are, however, compromised by the cellular heterogeneity of solid breast tumours and by the lack of appropriate counterparts representing normal breast epithelial cells.MethodsMalignant neoplastic epithelial cells from primary breast cancers and luminal and myoepithelial cells isolated from normal human breast tissue were isolated by immunomagnetic separation methods. Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using massively parallel signature sequencing (MPSS) and four different genome wide microarray platforms. Functional related transcripts of the differential tumour epithelial transcriptome were used for gene set enrichment analysis to identify enrichment of luminal and myoepithelial type genes. Clinical pathological validation of a small number of genes was performed on tissue microarrays.ResultsMPSS identified 6,553 differentially expressed genes between the pool of normal luminal cells and that of primary tumours substantially enriched for epithelial cells, of which 98% were represented and 60% were confirmed by microarray profiling. Significant expression level changes between these two samples detected only by microarray technology were shown by 4,149 transcripts, resulting in a combined differential tumour epithelial transcriptome of 8,051 genes. Microarray gene signatures identified a comprehensive list of 907 and 955 transcripts whose expression differed between luminal epithelial cells and myoepithelial cells, respectively. Functional annotation and gene set enrichment analysis highlighted a group of genes related to skeletal development that were associated with the myoepithelial/basal cells and upregulated in the tumour sample. One of the most highly overexpressed genes in this category, that encoding periostin, was analysed immunohistochemically on breast cancer tissue microarrays and its expression in neoplastic cells correlated with poor outcome in a cohort of poor prognosis estrogen receptor-positive tumours.ConclusionUsing highly enriched cell populations in combination with multiplatform gene expression profiling studies, a comprehensive analysis of molecular changes between the normal and malignant breast tissue was established. This study provides a basis for the identification of novel and potentially important targets for diagnosis, prognosis and therapy in breast cancer.

Published
2006

26. Epigenetic silencing of selected hypothalamic neuropeptides in narcolepsy with cataplexy

Author

Seifinejad, Ali, Ramosaj, Mergim, Shan, Ling, Li, Sha, Possovre, Marie-Laure, Pfister, Corinne, Fronczek, Rolf, Garrett-Sinha, Lee A, Frieser, David, Honda, Makoto, Arribat, Yoan, Grepper, Dogan, Amati, Francesca, Picot, Marie, Agnoletto, Andrea, Iseli, Christian, Chartrel, Nicolas, Liblau, Roland, Lammers, Gert J, Vassalli, Anne, Tafti, Mehdi, Seifinejad, Ali, Ramosaj, Mergim, Shan, Ling, Li, Sha, Possovre, Marie-Laure, Pfister, Corinne, Fronczek, Rolf, Garrett-Sinha, Lee A, Frieser, David, Honda, Makoto, Arribat, Yoan, Grepper, Dogan, Amati, Francesca, Picot, Marie, Agnoletto, Andrea, Iseli, Christian, Chartrel, Nicolas, Liblau, Roland, Lammers, Gert J, Vassalli, Anne, and Tafti, Mehdi

Abstract

Narcolepsy with cataplexy is a sleep disorder caused by deficiency in the hypothalamic neuropeptide hypocretin/orexin (HCRT), unanimously believed to result from autoimmune destruction of hypocretin-producing neurons. HCRT deficiency can also occur in secondary forms of narcolepsy and be only temporary, suggesting it can occur without irreversible neuronal loss. The recent discovery that narcolepsy patients also show loss of hypothalamic (corticotropin-releasing hormone) CRH-producing neurons suggests that other mechanisms than cell-specific autoimmune attack, are involved. Here, we identify the HCRT cell-colocalized neuropeptide QRFP as the best marker of HCRT neurons. We show that if HCRT neurons are ablated in mice, in addition to Hcrt, Qrfp transcript is also lost in the lateral hypothalamus, while in mice where only the Hcrt gene is inactivated Qrfp is unchanged. Similarly, postmortem hypothalamic tissues of narcolepsy patients show preserved QRFP expression, suggesting the neurons are present but fail to actively produce HCRT. We show that the promoter of the HCRT gene of patients exhibits hypermethylation at a methylation-sensitive and evolutionary-conserved PAX5:ETS1 transcription factor-binding site, suggesting the gene is subject to transcriptional silencing. We show also that in addition to HCRT, CRH and Dynorphin (PDYN) gene promoters, exhibit hypermethylation in the hypothalamus of patients. Altogether, we propose that HCRT, PDYN, and CRH are epigenetically silenced by a hypothalamic assault (inflammation) in narcolepsy patients, without concurrent cell death. Since methylation is reversible, our findings open the prospect of reversing or curing narcolepsy.

Published
2023

29. Epigenetic silencing of selected hypothalamic neuropeptides in narcolepsy with cataplexy

Author

Seifinejad, Ali, primary, Ramosaj, Mergim, additional, Shan, Ling, additional, Li, Sha, additional, Possovre, Marie-Laure, additional, Pfister, Corinne, additional, Fronczek, Rolf, additional, Garrett-Sinha, Lee A., additional, Frieser, David, additional, Honda, Makoto, additional, Arribat, Yoan, additional, Grepper, Dogan, additional, Amati, Francesca, additional, Picot, Marie, additional, Agnoletto, Andrea, additional, Iseli, Christian, additional, Chartrel, Nicolas, additional, Liblau, Roland, additional, Lammers, Gert J., additional, Vassalli, Anne, additional, and Tafti, Mehdi, additional

Published
2023
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31. Low number of fixed somatic mutations in a long-lived oak tree

Author

Schmid-Siegert, Emanuel, Sarkar, Namrata, Iseli, Christian, Calderon, Sandra, Gouhier-Darimont, Caroline, Chrast, Jacqueline, Cattaneo, Pietro, Schütz, Frédéric, Farinelli, Laurent, Pagni, Marco, Schneider, Michel, Voumard, Jérémie, Jaboyedoff, Michel, Fankhauser, Christian, Hardtke, Christian S., Keller, Laurent, Pannell, John R., Reymond, Alexandre, Robinson-Rechavi, Marc, Xenarios, Ioannis, and Reymond, Philippe

Published
2017
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34. Essential role of Cp190 in physical and regulatory boundary formation

Author

Kaushal, Anjali, primary, Dorier, Julien, additional, Wang, Bihan, additional, Mohana, Giriram, additional, Taschner, Michael, additional, Cousin, Pascal, additional, Waridel, Patrice, additional, Iseli, Christian, additional, Semenova, Anastasiia, additional, Restrepo, Simon, additional, Guex, Nicolas, additional, Aiden, Erez Lieberman, additional, and Gambetta, Maria Cristina, additional

Published
2022
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35. Neighbouring modifications interfere with the detection of phosphorylated alpha-synuclein at Serine 129: Revisiting the specificity of pS129 antibodies

Author

Lashuel, Hilal A., primary, Mahul-Mellier, Anne-Laure, additional, Novello, Salvatore, additional, Hegde, Ramanath Narayana, additional, Jasiqi, Yllza, additional, Altay, Melek Firat, additional, Donzelli, Sonia, additional, DeGuire, Sean M., additional, Burai, Ritwik, additional, Magalhães, Pedro, additional, Chiki, Anass, additional, Ricci, Jonathan, additional, Boussouf, Manel, additional, Sadek, Ahmed, additional, Stoops, Erik, additional, Iseli, Christian, additional, and Guex, Nicolas, additional

Published
2022
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36. Virtually Real: Aesthetics and perception of virtual spaces in film

Author

Iseli, Christian, Gerber, Thomas, Huber, Valentin, Schaerer, Michael, and Loertscher, Miriam

Subjects
Virtual Production, Digital Realism, Production Aesthetics, Visual Effects
Abstract

Due to the rapid pace of digitalization, Virtual Production (VP) in film is gaining importance. With this gamified production process, live-action and computer graphics can be combined in real-time while filming on set. This paper focuses on an interdisciplinary research project that investigates the effects of VP on visual aesthetics, on the changing workflows of filmmakers and actors, and on the percep-tion of a cinema audience. To systematically compare conventional filmmaking with new virtual forms of production, two short feature films were shot both conventionally (in real loca-tions) and virtually (in the digitally scanned versions of these locations). The filmmakers aspired to keep all parameters of the production the same so that wherever possible, the only differences would be in terms of spatial representation. The process of VP included shooting with green-screen and pre-visualization based on real time image rendering in moderate quality. The high-resolution variants, however, were still processed in post-production. The methodology comprised a combination of qualitative, practice-based research and quantitative, empirical ap-proaches, in the tradition of mixed methods. As VP continues to develop, green-screens are being replaced by large arrays of LED-displays, as in, for example, The Mandalorian. The present study shows that in the first phase of VP, in which green-screen procedures are still predominant, com-position artifacts occur mainly in the context of moderate production resources and are still measurable in terms of image quality., + ID: 584533 + PeerReviewed

Published
2022
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39. Virtually Real

Author

Iseli, Christian, primary, Loertscher, Miriam Laura, additional, and Thomas, Gerber, additional

Published
2022
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41. Unexpected post‐glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles

Author

Machado, Ana Paula, primary, Cumer, Tristan, additional, Iseli, Christian, additional, Beaudoing, Emmanuel, additional, Ducrest, Anne‐Lyse, additional, Dupasquier, Melanie, additional, Guex, Nicolas, additional, Dichmann, Klaus, additional, Lourenço, Rui, additional, Lusby, John, additional, Martens, Hans‐Dieter, additional, Prévost, Laure, additional, Ramsden, David, additional, Roulin, Alexandre, additional, and Goudet, Jérôme, additional

Published
2021
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42. Narcolepsy with cataplexy is caused by epigenetic silencing of hypocretin neurons

Author

Seifinejad, Ali, primary, Neiteler, Almar, additional, Li, Sha, additional, Pfister, Corinne, additional, Fronczek, Rolf, additional, Shan, Ling, additional, Garrett-Sinha, Lee A., additional, Frieser, David, additional, Honda, Makoto, additional, Arribat, Yoan, additional, Grepper, Dogan, additional, Amati, Francesca, additional, Picot, Marie, additional, Iseli, Christian, additional, Chartrel, Nicolas, additional, Lammers, Gert J., additional, Liblau, Roland, additional, Vassalli, Anne, additional, and Tafti, Mehdi, additional

Published
2021
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45. Blood virosphere in febrile Tanzanian children

Author

Cordey, Samuel, primary, Laubscher, Florian, additional, Hartley, Mary-Anne, additional, Junier, Thomas, additional, Keitel, Kristina, additional, Docquier, Mylène, additional, Guex, Nicolas, additional, Iseli, Christian, additional, Vieille, Gael, additional, Le Mercier, Philippe, additional, Gleizes, Anne, additional, Samaka, Josephine, additional, Mlaganile, Tarsis, additional, Kagoro, Frank, additional, Masimba, John, additional, Said, Zamzam, additional, Temba, Hosiana, additional, Elbanna, Gasser H., additional, Tapparel, Caroline, additional, Zanella, Marie-Celine, additional, Xenarios, Ioannis, additional, Fellay, Jacques, additional, D’Acremont, Valérie, additional, and Kaiser, Laurent, additional

Published
2021
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47. Blood Virosphere in Febrile Tanzanian Children

Author

Cordey, Samuel, primary, Laubscher, Florian, additional, Hartley, Mary-Anne, additional, Junier, Thomas, additional, Keitel, Kristina, additional, Docquier, Mylène, additional, Guex, Nicolas, additional, Iseli, Christian, additional, Vieille, Gael, additional, Mercier, Philippe Le, additional, Gleizes, Anne, additional, Samaka, Josephine, additional, Mlaganile, Tarsis, additional, Kagoro, Frank, additional, Masimba, John, additional, Said, Zamzam, additional, Temba, Hosiana, additional, Tapparel, Caroline, additional, Zanella, Marie-Celine, additional, Xenarios, Ioannis, additional, Fellay, Jacques, additional, D’Acremont, Valérie, additional, and Kaiser, Laurent, additional

Published
2020
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50. Unexpected post‐glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles.

Author

Machado, Ana Paula, Cumer, Tristan, Iseli, Christian, Beaudoing, Emmanuel, Ducrest, Anne‐Lyse, Dupasquier, Melanie, Guex, Nicolas, Dichmann, Klaus, Lourenço, Rui, Lusby, John, Martens, Hans‐Dieter, Prévost, Laure, Ramsden, David, Roulin, Alexandre, and Goudet, Jérôme

Subjects
BARN owl, COLONIZATION (Ecology), ISLANDS, SUBMERGED lands, WHOLE genome sequencing
Abstract

The climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the north. Like most organisms, barn owls are assumed to have colonized the British Isles by crossing over Doggerland, a land bridge that connected Britain to northern Europe. However, while they are dark rufous in northern Europe, barn owls in the British Isles are conspicuously white, a contrast that could suggest selective forces are at play on the islands. Yet, our analysis of known candidate genes involved in coloration found no signature of selection. Instead, using whole genome sequences and species distribution modelling, we found that owls colonised the British Isles soon after the last glaciation, directly from a white coloured refugium in the Iberian Peninsula, before colonising northern Europe. They would have followed a hitherto unknown post‐glacial colonization route to the Isles over a westwards path of suitable habitat in now submerged land in the Bay of Biscay, thus not crossing Doggerland. As such, they inherited the white colour of their Iberian founders and maintained it through low gene flow with the mainland that prevents the import of rufous alleles. Thus, we contend that neutral processes probably explain this contrasting white colour compared to continental owls. With the barn owl being a top predator, we expect future research will show this unanticipated route was used by other species from its paleo community. [ABSTRACT FROM AUTHOR]

Published
2022
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