André Kahles

According to our database, André Kahles authored at least 19 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.

Harun Mustafa, Mikhail Karasikov, Nika Mansouri-Ghiasi, Gunnar Rätsch, André Kahles

Bioinform., 2024

Probabilistic pathway-based multimodal factor analysis.

Alexander Immer, Stefan G. Stark, Francis Jacob, Ximena Bonilla, Tinu Thomas, André Kahles, Sandra Götze, Emanuela S. Milani, Bernd Wollscheid, Tumor Profiler Consortium, Gunnar Rätsch, Kjong-Van Lehmann

Bioinform., 2024

2022

RNA Instant Quality Check: Alignment-Free RNA-Degradation Detection.

Kjong-Van Lehmann, André Kahles, Magdalena Murr, Gunnar Rätsch

J. Comput. Biol., 2022

SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing.

Hana Rozhonová, Daniel Danciu, Stefan Stark, Gunnar Rätsch, André Kahles, Kjong-Van Lehmann

Bioinform., 2022

Lossless Indexing with Counting de Bruijn Graphs.

Mikhail Karasikov, Harun Mustafa, Gunnar Rätsch, André Kahles

Proceedings of the Research in Computational Molecular Biology, 2022

2021

Topology-based sparsification of graph annotations.

Daniel Danciu, Mikhail Karasikov, Harun Mustafa, André Kahles, Gunnar Rätsch

Bioinform., 2021

2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora

Nat., 2020

Genomic basis for RNA alterations in cancer.

Claudia Calabrese, Natalie R. Davidson, Deniz Demircioglu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina K. Yung, Shida Zhu, Philip Awadalla, Matthew Meyerson, B. F. Francis Ouellette, Kui Wu, Huanming Yang, Samirkumar B. Amin, Aurélien Chateigner, Isidro Cortés-Ciriano, Brian Craft, Milana Frenkel-Morgenstern, Mary Goldman, Ekta Khurana, Fabien C. Lamaze, Chang Li, Xiaobo Li, Xinyue Li, Xingmin Liu, Morten Muhlig Nielsen, Akinyemi I. Ojesina, Peter J. Park, Jakob Skou Pedersen, Bin Tean Teh, Jian Wang, Heng Xiong, Sergei Yakneen, Chen Ye, Xiuqing Zhang, Liangtao Zheng, Jingchun Zhu, Chad Creighton, Jonathan Göke, Roland F. Schwarz, Oliver Stegle, Zemin Zhang, Alvis Brazma, Gunnar Rätsch, Angela N. Brooks

Nat., 2020

AStarix: Fast and Optimal Sequence-to-Graph Alignment.

Pesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles, Gunnar Rätsch, Martin T. Vechev

Proceedings of the Research in Computational Molecular Biology, 2020

2019

Dynamic compression schemes for graph coloring.

Harun Mustafa, Ingo Schilken, Mikhail Karasikov, Carsten Eickhoff, Gunnar Rätsch, André Kahles

Bioinform., 2019

Sparse Binary Relation Representations for Genome Graph Annotation.

Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles

Proceedings of the Research in Computational Molecular Biology, 2019

2016

<i>SplAdder</i>: identification, quantification and testing of alternative splicing events from RNA-Seq data.

André Kahles, Cheng Soon Ong, Yi Zhong, Gunnar Rätsch

Bioinform., 2016

MMR: a tool for read multi-mapper resolution.

André Kahles, Jonas Behr, Gunnar Rätsch

Bioinform., 2016

2015

Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma.

Kjong-Van Lehmann, André Kahles, Cyriac Kandoth, William Lee, Nikolaus Schultz, Oliver Stegle, Gunnar Rätsch

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2014

Oqtans: a multifunctional workbench for RNA-seq data analysis.

Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch

BMC Bioinform., 2014

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch

Bioinform., 2014

2013

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.

Jonas Behr, André Kahles, Yi Zhong, Vipin T. Sreedharan, Philipp Drewe, Gunnar Rätsch

Bioinform., 2013

2011

Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data.

Sebastian J. Schultheiß, Géraldine Jean, Jonas Behr, Regina Bohnert, Philipp Drewe, Nico Görnitz, André Kahles, Pramod Mudrakarta, Vipin T. Sreedharan, Georg Zeller, Gunnar Rätsch

BMC Bioinform., 2011

Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation.

Nico Görnitz, Christian Widmer, Georg Zeller, André Kahles, Sören Sonnenburg, Gunnar Rätsch

Proceedings of the Advances in Neural Information Processing Systems 24: 25th Annual Conference on Neural Information Processing Systems 2011. Proceedings of a meeting held 12-14 December 2011, 2011