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6. Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

Author

Jahn, Katharina, Dreifuss, David, Topolsky, Ivan, Kull, Anina, Ganesanandamoorthy, Pravin, Fernandez-Cassi, Xavier, Bänziger, Carola, Devaux, Alexander J., Stachler, Elyse, Caduff, Lea, Cariti, Federica, Corzón, Alex Tuñas, Fuhrmann, Lara, Chen, Chaoran, Jablonski, Kim Philipp, Nadeau, Sarah, Feldkamp, Mirjam, Beisel, Christian, Aquino, Catharine, Stadler, Tanja, Ort, Christoph, Kohn, Tamar, Julian, Timothy R., and Beerenwinkel, Niko

Published
2022
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7. One ‘Stop Smoking’ to Take Away, Please! A Preliminary Evaluation of an AAT Mobile App

Author

Eiler, Tanja Joan, Forneberg, Tobias, Grünewald, Armin, Machulska, Alla, Klucken, Tim, Jahn, Katharina, Niehaves, Björn, Gethmann, Carl Friedrich, Brück, Rainer, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Pietka, Ewa, editor, Badura, Pawel, editor, Kawa, Jacek, editor, and Wieclawek, Wojciech, editor

Published
2021
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8. Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland

Author

Chen, Chaoran, Nadeau, Sarah Ann, Topolsky, Ivan, Manceau, Marc, Huisman, Jana S., Jablonski, Kim Philipp, Fuhrmann, Lara, Dreifuss, David, Jahn, Katharina, Beckmann, Christiane, Redondo, Maurice, Noppen, Christoph, Risch, Lorenz, Risch, Martin, Wohlwend, Nadia, Kas, Sinem, Bodmer, Thomas, Roloff, Tim, Stange, Madlen, Egli, Adrian, Eckerle, Isabella, Kaiser, Laurent, Denes, Rebecca, Feldkamp, Mirjam, Nissen, Ina, Santacroce, Natascha, Burcklen, Elodie, Aquino, Catharine, de Gouvea, Andreia Cabral, Moccia, Maria Domenica, Grüter, Simon, Sykes, Timothy, Opitz, Lennart, White, Griffin, Neff, Laura, Popovic, Doris, Patrignani, Andrea, Tracy, Jay, Schlapbach, Ralph, Dermitzakis, Emmanouil T., Harshman, Keith, Xenarios, Ioannis, Pegeot, Henri, Cerutti, Lorenzo, Penet, Deborah, Blin, Anthony, Elies, Melyssa, Althaus, Christian L., Beisel, Christian, Beerenwinkel, Niko, Ackermann, Martin, and Stadler, Tanja

Published
2021
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9. Establishing standardized immune phenotyping of metastatic melanoma by digital pathology

Author

Sobottka, Bettina, Nowak, Marta, Frei, Anja Laura, Haberecker, Martina, Merki, Samuel, Levesque, Mitchell P., Dummer, Reinhard, Moch, Holger, Koelzer, Viktor Hendrik, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baumhoer, Daniel, Beck-Schimmer, Beatrice, Beerenwinkel, Niko, Beisel, Christian, Bernasconi, Lara, Bertolini, Anne, Bodenmiller, Bernd, Bonilla, Ximena, Casanova, Ruben, Chevrier, Stéphane, Chicherova, Natalia, D'Costa, Maya, Danenberg, Esther, Davidson, Natalie, Drăganmoch, Monica-Andreea, Engler, Stefanie, Erkens, Martin, Eschbach, Katja, Esposito, Cinzia, Fedier, André, Ferreira, Pedro, Ficek, Joanna, Frey, Bruno, Goetze, Sandra, Grob, Linda, Gut, Gabriele, Günther, Detlef, Haeuptle, Pirmin, Heinzelmann-Schwarz, Viola, Herter, Sylvia, Holtackers, Rene, Huesser, Tamara, Irmisch, Anja, Jacob, Francis, Jacobs, Andrea, Jaeger, Tim M., Jahn, Katharina, James, Alva R., Jermann, Philip M., Kahles, André, Kahraman, Abdullah, Kuebler, Werner, Kuipers, Jack, Kunze, Christian P., Kurzeder, Christian, Lehmann, Kjong-Van, Lugert, Sebastian, Maass, Gerd, Manz, Markus G., Markolin, Philipp, Mena, Julien, Menzel, Ulrike, Metzler, Julian M., Miglino, Nicola, Milani, Emanuela S., Muenst, Simone, Murri, Riccardo, Ng, Charlotte K.Y., Nicolet, Stefan, Pedrioli, Patrick G.A., Pelkmans, Lucas, Piscuoglio, Salvatore, Prummer, Michael, Ritter, Mathilde, Rommel, Christian, Rosano-González, María L., Rätsch, Gunnar, Santacroce, Natascha, del Castillo, Jacobo Sarabia, Schlenker, Ramona, Schwalie, Petra C., Schwan, Severin, Schär, Tobias, Senti, Gabriela, Singer, Franziska, Sivapatham, Sujana, Snijder, Berend, Sreedharan, Vipin T., Stark, Stefan, Stekhoven, Daniel J., Theocharides, Alexandre P.A., Thomas, Tinu M., Tolnay, Markus, Tosevski, Vinko, Toussaint, Nora C., Tuncel, Mustafa A., Tusup, Marina, Van Drogen, Audrey, Vetter, Marcus, Vlajnic, Tatjana, Weber, Sandra, Weber, Walter P., Wegmann, Rebekka, Weller, Michael, Wendt, Fabian, Wey, Norbert, Wicki, Andreas, Wildschut, Mattheus HE, Wollscheid, Bernd, Yu, Shuqing, Ziegler, Johanna, Zimmermann, Marc, Zoche, Martin, and Zuend, Gregor

Published
2021
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10. Designing Self-presence in Immersive Virtual Reality to Improve Cognitive Performance—A Research Proposal

Author

Jahn, Katharina, Kordyaka, Bastian, Ressing, Caroline, Roeding, Kristina, Niehaves, Bjoern, Spagnoletti, Paolo, Series Editor, De Marco, Marco, Series Editor, Pouloudi, Nancy, Series Editor, Te'eni, Dov, Series Editor, vom Brocke, Jan, Series Editor, Winter, Robert, Series Editor, Baskerville, Richard, Series Editor, Davis, Fred D., editor, Riedl, René, editor, Léger, Pierre-Majorique, editor, Randolph, Adriane, editor, and Fischer, Thomas, editor

Published
2020
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14. A Preliminary Evaluation of Transferring the Approach Avoidance Task into Virtual Reality

Author

Eiler, Tanja Joan, Grünewald, Armin, Machulska, Alla, Klucken, Tim, Jahn, Katharina, Niehaves, Björn, Gethmann, Carl Friedrich, Brück, Rainer, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Pietka, Ewa, editor, Badura, Pawel, editor, Kawa, Jacek, editor, and Wieclawek, Wojciech, editor

Published
2019
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17. Swipe up to smoke less cigarettes! Introducing a mobile Approach-Avoidance Task Application to fight Smoking

Author

Eiler Tanja Joan, Haßler Benjamin, Grünewald Armin, Machulska Alla, Klucken Tim, Jahn Katharina, Niehaves Björn, Gethmann Carl Friedrich, and Brück Rainer

Subjects
addiction, approach-avoidance task, aat, approach bias, cognitive bias, cognitive bias modification, cbm, dual process model, mobile applications, smoking, therapy, usability, Medicine
Abstract

Automatic tendencies to approach addictionrelated stimuli have been linked to the development and maintenance of harmful drug use behavior. Recent studies have shown that these automatic approaches can be directly addressed and modified by cognitive bias modification (CBM). However, the training and treatment effects are rather small and compliance could be impaired by time-consuming, multiple laboratory training sessions. Here we present a mobile variant of the Approach-Avoidance Task (app-AAT), which is evaluated by a feasibility study. The app-AAT is designed to improve the efficiency of CBM training by allowing smokers to access the training at any time, and by offering the option to track consumed cigarettes. Our first run with eight participants showed that the app was rated very positively with 4.2 out of 5 points (engagement: 3.7, functionality: 4.5, aesthetics: 4.4) by using the german Mobile App Rating Scale (MARS-G).

Published
2020
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19. Author Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics

Author

Morita, Kiyomi, Wang, Feng, Jahn, Katharina, Hu, Tianyuan, Tanaka, Tomoyuki, Sasaki, Yuya, Kuipers, Jack, Loghavi, Sanam, Wang, Sa A., Yan, Yuanqing, Furudate, Ken, Matthews, Jairo, Little, Latasha, Gumbs, Curtis, Zhang, Jianhua, Song, Xingzhi, Thompson, Erika, Patel, Keyur P., Bueso-Ramos, Carlos E., DiNardo, Courtney D., Ravandi, Farhad, Jabbour, Elias, Andreeff, Michael, Cortes, Jorge, Bhalla, Kapil, Garcia-Manero, Guillermo, Kantarjian, Hagop, Konopleva, Marina, Nakada, Daisuke, Navin, Nicholas, Beerenwinkel, Niko, Futreal, P. Andrew, and Takahashi, Koichi

Published
2021
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20. 1.1 Datenkultur

Author

Teille, Karl, primary, Baidinger, Denise, additional, Jahn, Katharina, additional, Waschke, Thomas, additional, Wust, Christoph, additional, Zebuhr, Yulika, additional, and Hofmann, Klaus Markus, additional

Published
2021
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21. Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity

Author

Majeti, Ravi, primary, Schwede, Matthew, additional, Jahn, Katharina, additional, Kuipers, Jack, additional, Miles, Linde, additional, Bowman, Robert, additional, Robinson, Troy, additional, Furudate, Ken, additional, Uryu, Hidetaka, additional, Tanaka, Tomoyuki, additional, Sasaki, Yuya, additional, Ediriwickrema, Asiri, additional, Benard, Brooks, additional, Gentles, Andrew, additional, Levine, Ross, additional, Beerenwinkel, Niko, additional, and Takahashi, Koichi, additional

Published
2023
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24. Ex vivo and in vitro culture models of human osteoblast-like cells and the effects of TGFbeta3 and serum-free culture

Author

Jahn, Katharina

Subjects
616.7
Abstract

The loss of viable osteocytes in the elderly is a critical issue upon the development of osteoporosis. Previous work in our group suggested a positive osteocyte survival effect by TGFβ3 supplemented to a serum containing medium during long-term ex vivo culture of human cancellous bone explants. In this study, no beneficial effect by TGFβ3 addition to serum-free cultured ex vivo osteocytes was observed. Therefore, the effect of TGFβ3 on osteocyte survival was further investigated in vitro. The most commonly used culture model for osteoblast-lineage cells is 2D/monolayer culture. However, monolayer culture only resembles the in vivo situation of osteoblast-lineage cells in bone to a limited extent, omitting the extensive 3D cell-to-cell and cell-to-matrix interconnectivity. In order find a more relevant culture model to be used for in vitro investigations of osteoblast biology this study evaluated a variety of cell culture systems. In all systems evaluated, the effect of TGFβ3 was strongly dependent upon the presence of serum. Only in the presence of serum did TGFβ3 increase osteocyte survival both ex vivo and in vitro. These investigations, also, led to the generation of different 3D in vitro culture models. Within a multilayer and pellet culture model for human primary osteoblasts, a reduction of initial proliferation in combination with a more rapid cell differentiation in comparison to monolayer culture was identified. Such 3D culture models are of great benefit compared to the existing in vitro osteoblast monolayer culture as they create more active/mature osteoblasts or potentially early osteocytes in a shorter time course. This study showed, firstly TGFβ3 is an in vitro survival factor for osteocytes, if cultured in the presence of serum, and secondly the choice of 3D culture models for osteoblast-lineage cells should be intended more frequently to properly evaluate cellular reactions prior to conducting animal studies.

Published
2010

25. Eleven grand challenges in single-cell data science

Author

Lähnemann, David, Köster, Johannes, Szczurek, Ewa, McCarthy, Davis J., Hicks, Stephanie C., Robinson, Mark D., Vallejos, Catalina A., Campbell, Kieran R., Beerenwinkel, Niko, Mahfouz, Ahmed, Pinello, Luca, Skums, Pavel, Stamatakis, Alexandros, Attolini, Camille Stephan-Otto, Aparicio, Samuel, Baaijens, Jasmijn, Balvert, Marleen, Barbanson, Buys de, Cappuccio, Antonio, Corleone, Giacomo, Dutilh, Bas E., Florescu, Maria, Guryev, Victor, Holmer, Rens, Jahn, Katharina, Lobo, Thamar Jessurun, Keizer, Emma M., Khatri, Indu, Kielbasa, Szymon M., Korbel, Jan O., Kozlov, Alexey M., Kuo, Tzu-Hao, Lelieveldt, Boudewijn P.F., Mandoiu, Ion I., Marioni, John C., Marschall, Tobias, Mölder, Felix, Niknejad, Amir, Rączkowska, Alicja, Reinders, Marcel, Ridder, Jeroen de, Saliba, Antoine-Emmanuel, Somarakis, Antonios, Stegle, Oliver, Theis, Fabian J., Yang, Huan, Zelikovsky, Alex, McHardy, Alice C., Raphael, Benjamin J., Shah, Sohrab P., and Schönhuth, Alexander

Published
2020
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26. Publisher Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics

Author

Morita, Kiyomi, Wang, Feng, Jahn, Katharina, Hu, Tianyuan, Tanaka, Tomoyuki, Sasaki, Yuya, Kuipers, Jack, Loghavi, Sanam, Wang, Sa A., Yan, Yuanqing, Furudate, Ken, Matthews, Jairo, Little, Latasha, Gumbs, Curtis, Zhang, Jianhua, Song, Xingzhi, Thompson, Erika, Patel, Keyur P., Bueso-Ramos, Carlos E., DiNardo, Courtney D., Ravandi, Farhad, Jabbour, Elias, Andreeff, Michael, Cortes, Jorge, Bhalla, Kapil, Garcia-Manero, Guillermo, Kantarjian, Hagop, Konopleva, Marina, Nakada, Daisuke, Navin, Nicholas, Beerenwinkel, Niko, Futreal, P. Andrew, and Takahashi, Koichi

Published
2020
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27. Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics

Author

Morita, Kiyomi, Wang, Feng, Jahn, Katharina, Hu, Tianyuan, Tanaka, Tomoyuki, Sasaki, Yuya, Kuipers, Jack, Loghavi, Sanam, Wang, Sa A., Yan, Yuanqing, Furudate, Ken, Matthews, Jairo, Little, Latasha, Gumbs, Curtis, Zhang, Jianhua, Song, Xingzhi, Thompson, Erika, Patel, Keyur P., Bueso-Ramos, Carlos E., DiNardo, Courtney D., Ravandi, Farhad, Jabbour, Elias, Andreeff, Michael, Cortes, Jorge, Bhalla, Kapil, Garcia-Manero, Guillermo, Kantarjian, Hagop, Konopleva, Marina, Nakada, Daisuke, Navin, Nicholas, Beerenwinkel, Niko, Futreal, P. Andrew, and Takahashi, Koichi

Published
2020
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32. Microbe-host interplay in atopic dermatitis and psoriasis

Author

Fyhrquist, Nanna, Muirhead, Gareth, Prast-Nielsen, Stefanie, Jeanmougin, Marine, Olah, Peter, Skoog, Tiina, Jules-Clement, Gerome, Feld, Micha, Barrientos-Somarribas, Mauricio, Sinkko, Hanna, van den Bogaard, Ellen H., Zeeuwen, Patrick L.J.M., Rikken, Gijs, Schalkwijk, Joost, Niehues, Hanna, Däubener, Walter, Eller, Silvia Kathrin, Alexander, Helen, Pennino, Davide, Suomela, Sari, Tessas, Ioannis, Lybeck, Emilia, Baran, Anna M., Darban, Hamid, Gangwar, Roopesh Singh, Gerstel, Ulrich, Jahn, Katharina, Karisola, Piia, Yan, Lee, Hansmann, Britta, Katayama, Shintaro, Meller, Stephan, Bylesjö, Max, Hupé, Philippe, Levi-Schaffer, Francesca, Greco, Dario, Ranki, Annamari, Schröder, Jens M., Barker, Jonathan, Kere, Juha, Tsoka, Sophia, Lauerma, Antti, Soumelis, Vassili, Nestle, Frank O., Homey, Bernhard, Andersson, Björn, and Alenius, Harri

Published
2019
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35. Abstract A49: Characterizing the order of mutation acquisition in acute myeloid leukemia using large-scale single-cell sequencing

Author

Schwede, Matthew, primary, Jahn, Katharina, additional, Miles, Linde A, additional, Bowman, Robert L, additional, Kuipers, Jack, additional, Robinson, Troy M, additional, Ediriwickrema, Asiri, additional, Gentles, Andrew J, additional, Levine, Ross, additional, Beerenwinkel, Niko, additional, Takahashi, Koichi, additional, and Majeti, Ravindra, additional

Published
2023
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36. NaturalWalk: An Anatomy-based Synthesizer for Human Walking Motions

Author

Technische Universität Chemnitz, Salamah, Samer, Brunnett, Guido, Bräuer, Sabrina, Uhlmann, Tom, Rehren, Oliver, Jahn, Katharina, Milani, Thomas L., Rey, Günter Daniel, Technische Universität Chemnitz, Salamah, Samer, Brunnett, Guido, Bräuer, Sabrina, Uhlmann, Tom, Rehren, Oliver, Jahn, Katharina, Milani, Thomas L., and Rey, Günter Daniel

Abstract

We present a novel data-driven approach for synthesizing human gait motions with individual style characteristics and natural appearance. Our approach is based on the concept of a motion signature that captures the essential characteristic of an individual walking motion. For each joint angle our motion model consists of a shape template and feature functions that describe the variation of that shape with the stride length. For the synthesis of a walking motion, the feature functions are evaluated for a desired stride length. Then the templates are adapted to match the computed features and used as progressions for the joint angles of the skeleton. We demonstrate our data driven approach using motion data captured from 12 individuals. We report on an experiment showing that the synthesized motions have a natural appearance and maintain the individual style.:1. Introduction 2. Related Work 3. Preliminaries 3.1 Mathematics of motion 3.2 Walking motions 4. Data acquisition and analysis 5. Shape templates and feature functions 5.1 Definition of template functions 5.2 Continuous representation of template functions 5.3 Building the feature functions 6. Motion Generation 6.1 Adaption of template functions 6.2 Computing the poses 7 Experimental Results 7.1 Numerical Evaluation 7.2 User Study Acknowledgment References

Published
2023

37. NaturalWalk: An Anatomy-based Synthesizer for Human Walking Motions

Author

Salamah, Samer, Brunnett, Guido, Bräuer, Sabrina, Uhlmann, Tom, Rehren, Oliver, Jahn, Katharina, Milani, Thomas L., Rey, Günter Daniel, and Technische Universität Chemnitz

Subjects
Motion capturing, Walking motion synthesis, Individual motion characteristics, Template-based motion synthesis, Motion perception, ddc:000, Motion capturing, Walking
Abstract

We present a novel data-driven approach for synthesizing human gait motions with individual style characteristics and natural appearance. Our approach is based on the concept of a motion signature that captures the essential characteristic of an individual walking motion. For each joint angle our motion model consists of a shape template and feature functions that describe the variation of that shape with the stride length. For the synthesis of a walking motion, the feature functions are evaluated for a desired stride length. Then the templates are adapted to match the computed features and used as progressions for the joint angles of the skeleton. We demonstrate our data driven approach using motion data captured from 12 individuals. We report on an experiment showing that the synthesized motions have a natural appearance and maintain the individual style.:1. Introduction 2. Related Work 3. Preliminaries 3.1 Mathematics of motion 3.2 Walking motions 4. Data acquisition and analysis 5. Shape templates and feature functions 5.1 Definition of template functions 5.2 Continuous representation of template functions 5.3 Building the feature functions 6. Motion Generation 6.1 Adaption of template functions 6.2 Computing the poses 7 Experimental Results 7.1 Numerical Evaluation 7.2 User Study Acknowledgment References

Published
2023

39. The Potential of Family-Free Genome Comparison

Author

Braga, Marília D. V., Chauve, Cedric, Doerr, Daniel, Jahn, Katharina, Stoye, Jens, Thévenin, Annelyse, Wittler, Roland, Dress, Andreas, Series editor, Linial, Michal, Series editor, Troyanskaya, Olga, Series editor, Vingron, Martin, Series editor, Chauve, Cedric, editor, El-Mabrouk, Nadia, editor, and Tannier, Eric, editor

Published
2013
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40. Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences

Author

Jahn, Katharina, 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, and Tannier, Eric, editor

Published
2010
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41. Swiftly Computing Center Strings

Author

Hufsky, Franziska, Kuchenbecker, Léon, Jahn, Katharina, Stoye, Jens, Böcker, Sebastian, 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Moulton, Vincent, editor, and Singh, Mona, editor

Published
2010
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42. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Author

Denoeud, France, Carretero-Paulet, Lorenzo, Dereeper, Alexis, Droc, Gaëtan, Guyot, Romain, Pietrella, Marco, Zheng, Chunfang, Alberti, Adriana, Anthony, François, Aprea, Giuseppe, Aury, Jean-Marc, Bento, Pascal, Bernard, Maria, Bocs, Stéphanie, Campa, Claudine, Cenci, Alberto, Combes, Marie-Christine, Crouzillat, Dominique, Da Silva, Corinne, Daddiego, Loretta, De Bellis, Fabien, Dussert, Stéphane, Garsmeur, Olivier, Gayraud, Thomas, Guignon, Valentin, Jahn, Katharina, Jamilloux, Véronique, Joët, Thierry, Labadie, Karine, Lan, Tianying, Leclercq, Julie, Lepelley, Maud, Leroy, Thierry, Li, Lei-Ting, Librado, Pablo, Lopez, Loredana, Muñoz, Adriana, Noel, Benjamin, Pallavicini, Alberto, Perrotta, Gaetano, Poncet, Valérie, Pot, David, Rigoreau, Michel, Rouard, Mathieu, Rozas, Julio, Tranchant-Dubreuil, Christine, VanBuren, Robert, Zhang, Qiong, Andrade, Alan C., Argout, Xavier, Bertrand, Benoît, de Kochko, Alexandre, Graziosi, Giorgio, Henry, Robert J, Ming, Ray, Nagai, Chifumi, Rounsley, Steve, Sankoff, David, Giuliano, Giovanni, Albert, Victor A., Wincker, Patrick, and Lashermes, Philippe

Published
2014

43. Computation of Median Gene Clusters

Author

Böcker, Sebastian, Jahn, Katharina, Mixtacki, Julia, Stoye, Jens, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Vingron, Martin, editor, and Wong, Limsoon, editor

Published
2008
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44. Joint copy number and mutation phylogeny reconstruction from single-cell amplicon sequencing data

Author

Sollier, Etienne, Kuipers, Jack, Takahashi, Koichi, Beerenwinkel, Niko, and Jahn, Katharina

Abstract

Reconstructing the history of somatic DNA alterations that occurred in a tumour can help understand its evolution and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, existing phylogenetic methods for scDNAseq data are designed either for point mutations or for large copy number variations, but not for both types of events simultaneously. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of mutations and copy number alterations from targeted scDNAseq data. We evaluate COMPASS on simulated data and show that it outperforms existing methods. We apply COMPASS to a large cohort of 123 patients with acute myeloid leukemia (AML) and detect copy number alterations, including subclonal ones, which are in agreement with and extend current knowledge of AML development. We further used bulk sequencing and SNP array data to orthogonally validate our findings., bioRxiv

Published
2022

45. Learning with gamified information systems

Author

Jahn, Katharina

Subjects
Acceptance, Motivation, 330 Wirtschaft, Approach bias, Virtual bodies, Individualization, Uncanny valley, Roboter, Lernen, Virtuelle Realit��t, Gamification
Abstract

Gamification is increasingly used in both private and work life domains. Whereas research on gamification has shown that gamification can have a positive impact on motivational and performance-related outcomes, some contradictory findings suggest that the specific design and implementation of gamification as well as the contexts in which gamification takes place play a crucial role for the specific effects on learning-related outcomes. Moreover, it is still unclear which specific gamification design elements are effective, how they can be combined, and how the implementation of specific gamification design elements might affect learning-related outcomes. Against this background, this thesis investigates the effects of gamification and the contexts in which gamification may take place using both quantitative and qualitative methods. The results show that individualized gamification design elements can positively affect motivational and performance-related outcomes. Additionally, the specific learning opportunities of the contexts in which gamification is implemented should be considered in the design of suitable gamification design elements., Gamification wird zunehmend sowohl im privaten als auch im beruflichen Bereich eingesetzt. W��hrend die Forschung zu Gamification gezeigt hat, dass Gamification sich positiv auf motivations- und leistungsbezogene Ergebnisse auswirken kann, deuten einige widerspr��chliche Ergebnisse darauf hin, dass die spezifische Gestaltung und Umsetzung von Gamification sowie die Kontexte, in denen Gamification stattfindet, eine entscheidende Rolle f��r die spezifischen Auswirkungen auf lernbezogene Ergebnisse spielen. Dar��ber hinaus ist nach wie vor unklar, welche spezifischen Gamificationdesignelemente wirksam sind, wie sie kombiniert werden k��nnen und wie sich die Implementierung spezifischer Gamificationdesignelemente auf die Lernergebnisse auswirken kann. Vor diesem Hintergrund werden in dieser Arbeit die Wirkungen von Gamification und die Kontexte, in denen Gamification stattfinden kann, mit quantitativen und qualitativen Methoden untersucht. Die Ergebnisse zeigen, dass sich individualisierte Gamificationdesignelemente positiv auf motivationale und leistungsbezogene Ergebnisse auswirken k��nnen. Dar��ber hinaus sollten die spezifischen Lernm��glichkeiten der Kontexte, in denen Gamification eingesetzt wird, bei der Gestaltung geeigneter Gamificationdesignelemente ber��cksichtigt werden.

Published
2022
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46. Emotional Capabilities of Conversational Agents: A Review

Author

Jahn, Katharina, Rehren, Oliver, Schneider, Sascha, Ohler, Peter, and Rey, Günter Daniel

Subjects
emotional capabilities, anthropomorphism, conversational agents, uncanny valley
Abstract

Proceedings of the 12th Media Psychology Conference 2021 (MediaPsych 2021) : September 8 10, 2021 RWTH Aachen University, Aachen, Germany / Astrid Rosenthal-von der P��tten, Malte Elson, Stefan Schiffer (editors) 12th Media Psychology Conference, MediaPsych 2021, Aachen, Germany, 8 Sep 2021 - 10 Sep 2021; Aachen : RWTH Aachen University 26-30 (2022)., Published by RWTH Aachen University, Aachen

Published
2022
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47. Creating an anthropomorphism questionnaire - A multidimensional approach

Author

Rehren, Oliver, Jahn, Katharina, Schneider, Sascha, Forner, Lisa, Rey, Günter Daniel, and Ohler, Peter

Subjects
questionnaire, anthropomorphism, dehumanization, method, human-robotic-interaction, human-computer-interaction
Abstract

Proceedings of the 12th Media Psychology Conference 2021 (MediaPsych 2021) : September 8 10, 2021 RWTH Aachen University, Aachen, Germany / Astrid Rosenthal-von der P��tten, Malte Elson, Stefan Schiffer (editors) 12th Media Psychology Conference, MediaPsych 2021, Aachen, Germany, 8 Sep 2021 - 10 Sep 2021; Aachen : RWTH Aachen University 111-113 (2022)., Published by RWTH Aachen University, Aachen

Published
2022
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49. Statistical tests for intra-tumour clonal co-occurrence and exclusivity

Author

Kuipers, Jack, primary, Moore, Ariane L., additional, Jahn, Katharina, additional, Schraml, Peter, additional, Wang, Feng, additional, Morita, Kiyomi, additional, Futreal, P. Andrew, additional, Takahashi, Koichi, additional, Beisel, Christian, additional, Moch, Holger, additional, and Beerenwinkel, Niko, additional

Published
2021
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50. Detection and surveillance of SARS-CoV-2 genomic variants in wastewater

Author

Jahn, Katharina, Dreifuss, David, Topolsky, Ivan, Kull, Anina, Ganesanandamoorthy, Pravin, Fernandez-Cassi, Xavier, Bänziger, Carola, Devaux, Alexander J., Stachler, Elyse, Caduff, Lea, Cariti, Federica, Corzón, Alex Tuñas, Fuhrmann, Lara, Chen, Chaoran, Jablonski, Kim Philipp, Nadeau, Sarah Ann, Feldkamp, Mirjam, Beisel, Christian, Aquino, Catharine, Stadler, Tanja, Ort, Christoph, Kohn, Tamar, Julian, Timothy R., and Beerenwinkel, Niko

Abstract

The emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to assess circulating viral lineages in the community. We performed genomic sequencing of 122 wastewater samples from three locations in Switzerland to analyze the B.1.1.7, B.1.351, and P.1 variants of SARS-CoV-2 on a population level. We called variant-specific signature mutations and monitored variant prevalence in the local population over time. To enable early detection of emerging variants, we developed a bioinformatics tool that uses read pairs carrying multiple signature mutations as a robust indicator of low-frequency variants. We further devised a statistical approach to estimate the transmission fitness advantage, a key epidemiological parameter indicating the speed at which a variant spreads through the population, and compared the wastewater-based findings to those derived from clinical samples. We found that the local outbreak of the B.1.1.7 variant in two Swiss cities was observable in wastewater up to 8 days before its first detection in clinical samples. We detected a high prevalence of the B.1.1.7 variant in an alpine ski resort popular among British tourists in December 2020, a time when the variant was still very rare in Switzerland. We found no evidence of local spread of the B.1.351 and P.1 variants at the monitored locations until the end of the study (mid February) which is consistent with clinical samples. Estimation of local variant prevalence performs equally well or better for wastewater samples as for a much larger number of clinical samples. We found that the transmission fitness advantage of B.1.1.7, i.e. the relative change of its reproductive number, can be estimated earlier and based on substantially fewer wastewater samples as compared to using clinical samples. Our results show that genomic sequencing of wastewater samples can detect, monitor, and evaluate genetic variants of SARS-CoV-2 on a population level. Our methodology provides a blueprint for rapid, unbiased, and cost-efficient genomic surveillance of SARS-CoV-2 variants., medRxiv

Published
2021

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