Niko Beerenwinkel (N Beerenwinkel)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 77

Top Topics

Positive Breast Cancer

Top Venues

Nature communications

PLoS computational biology

Bioinformatics (Oxford, England)

This page only lists publications with an associated author ORCID identifier.

Publications

Monica-Andreea Baciu-Drăgan, Niko Beerenwinkel
Oncotree2vec - a method for embedding and clustering of tumor mutation trees. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Pelin Icer Baykal, Paweł Piotr Łabaj, Florian Markowetz, Lynn M Schriml, Daniel Johannes Stekhoven, Serghei Mangul, Niko Beerenwinkel
Genomic reproducibility in the bioinformatics era. Genome biology 25 (1) (2024)
Pelin Icer Baykal, Paweł Piotr Łabaj, Florian Markowetz, Lynn M Schriml, Daniel Johannes Stekhoven, Serghei Mangul, Niko Beerenwinkel
Genomic reproducibility in the bioinformatics era. Genome biology 25 (1) (2024)
Matthias Egger, Mamatha Sauermann, Tom Loosli, Stefanie Hossmann, Selma Riedo, Niko Beerenwinkel, Antoine Jaquet, Albert Minga, Jeremy L Ross, Jennifer Giandhari, Roger D Kouyos, Richard Lessells
HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre longitudinal study (DTG RESIST). medRxiv : the preprint server for health sciences (2024)
Kevin Rupp, Andreas Lösch, Yanren Linda Hu, Chenxi Nie, Rudolf Schill, Maren Klever, Simon Pfahler, Lars Grasedyck, Tilo Wettig, Niko Beerenwinkel, Rainer Spang
Modeling metastatic progression from cross-sectional cancer genomics data. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Kevin Rupp, Andreas Lösch, Yanren Linda Hu, Chenxi Nie, Rudolf Schill, Maren Klever, Simon Pfahler, Lars Grasedyck, Tilo Wettig, Niko Beerenwinkel, Rainer Spang
Modeling metastatic progression from cross-sectional cancer genomics data. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Qian Qin, Victoria Popic, Houlin Yu, Emily White, Akanksha Khorgade, Asa Shin, Kirsty Wienand, Arthur Dondi, Niko Beerenwinkel, Francisca Vazquez, Aziz M Al'Khafaji, Brian J Haas
CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution. bioRxiv : the preprint server for biology (2024)
Arthur Dondi, Nico Borgsmüller, Pedro F Ferreira, Brian J Haas, Francis Jacob, Viola A Heinzelmann-Schwarz, null null, Niko Beerenwinkel
De novo detection of somatic variants in long-read single-cell RNA sequencing data. bioRxiv : the preprint server for biology (2024)
Viktor Zaika, Meher K Prakash, Chih-Yuan Cheng, Michael Schlander, Brian M Lang, Niko Beerenwinkel, Amnon Sonnenberg, Niklas Krupka, Benjamin Misselwitz, Jan Poleszczuk
Optimal timing of a colonoscopy screening schedule depends on adenoma detection, adenoma risk, adherence to screening and the screening objective: A microsimulation study. PloS one 19 (5) (2024)
Matthias Egger, Mamatha Sauermann, Tom Loosli, Stefanie Hossmann, Selma Riedo, Niko Beerenwinkel, Antoine Jaquet, Albert Minga, Jeremy L Ross, Jennifer Giandhari, Roger D Kouyos, Richard Lessells
HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre longitudinal study (DTG RESIST). medRxiv : the preprint server for health sciences (2024)
Monica-Andreea Baciu-Drăgan, Niko Beerenwinkel
Oncotree2vec - a method for embedding and clustering of tumor mutation trees. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Arthur Dondi, Nico Borgsmüller, Pedro F Ferreira, Brian J Haas, Francis Jacob, Viola A Heinzelmann-Schwarz, null null, Niko Beerenwinkel
De novo detection of somatic variants in long-read single-cell RNA sequencing data. bioRxiv : the preprint server for biology (2024)
Pelin Icer Baykal, Paweł Piotr Łabaj, Florian Markowetz, Lynn M Schriml, Daniel Johannes Stekhoven, Serghei Mangul, Niko Beerenwinkel
Genomic reproducibility in the bioinformatics era. Genome biology 25 (1) (2024)
Viktor Zaika, Meher K Prakash, Chih-Yuan Cheng, Michael Schlander, Brian M Lang, Niko Beerenwinkel, Amnon Sonnenberg, Niklas Krupka, Benjamin Misselwitz, Jan Poleszczuk
Optimal timing of a colonoscopy screening schedule depends on adenoma detection, adenoma risk, adherence to screening and the screening objective: A microsimulation study. PloS one 19 (5) (2024)
Monica-Andreea Baciu-Drăgan, Niko Beerenwinkel
Oncotree2vec - a method for embedding and clustering of tumor mutation trees. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Kevin Rupp, Andreas Lösch, Yanren Linda Hu, Chenxi Nie, Rudolf Schill, Maren Klever, Simon Pfahler, Lars Grasedyck, Tilo Wettig, Niko Beerenwinkel, Rainer Spang
Modeling metastatic progression from cross-sectional cancer genomics data. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Qian Qin, Victoria Popic, Houlin Yu, Emily White, Akanksha Khorgade, Asa Shin, Kirsty Wienand, Arthur Dondi, Niko Beerenwinkel, Francisca Vazquez, Aziz M AlKhafaji, Brian J Haas
CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution. bioRxiv : the preprint server for biology (2024)
Oscar M Lezcano, Lara Fuhrmann, Gayatri Ramakrishnan, Niko Beerenwinkel, Martijn A Huynen, Ronald P Van Rij
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster . Virus evolution 9 (2) (2023)
Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel
Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees. Nature communications 14 (1) (2023)
Evelyn Kuhlmeier, Tatjana Chan, Cecilia Valenzuela Agüí, Barbara Willi, Aline Wolfensberger, Christian Beisel, Ivan Topolsky, Niko Beerenwinkel, Tanja Stadler, null Swiss Sars-CoV-Sequencing Consortium, Sarah Jones, Grace B Tyson, Margaret J Hosie, Katja Reitt, Julia Hüttl, Marina Luisa Meli, Regina Hofmann-Lehmann
Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 15 (1) (2023)
Evelyn Kuhlmeier, Tatjana Chan, Cecilia Valenzuela Agüí, Barbara Willi, Aline Wolfensberger, Christian Beisel, Ivan Topolsky, Niko Beerenwinkel, Tanja Stadler, null Swiss Sars-CoV-Sequencing Consortium, Sarah Jones, Grace B Tyson, Margaret J Hosie, Katja Reitt, Julia Hüttl, Marina Luisa Meli, Regina Hofmann-Lehmann
Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 15 (1) (2023)
Evelyn Kuhlmeier, Tatjana Chan, Cecilia Valenzuela Agüí, Barbara Willi, Aline Wolfensberger, Christian Beisel, Ivan Topolsky, Niko Beerenwinkel, Tanja Stadler, null Swiss Sars-CoV-Sequencing Consortium, Sarah Jones, Grace B Tyson, Margaret J Hosie, Katja Reitt, Julia Hüttl, Marina Luisa Meli, Regina Hofmann-Lehmann
Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 15 (1) (2023)
Evelyn Kuhlmeier, Tatjana Chan, Cecilia Valenzuela Agüí, Barbara Willi, Aline Wolfensberger, Christian Beisel, Ivan Topolsky, Niko Beerenwinkel, Tanja Stadler, null Swiss Sars-CoV-Sequencing Consortium, Sarah Jones, Grace B Tyson, Margaret J Hosie, Katja Reitt, Julia Hüttl, Marina Luisa Meli, Regina Hofmann-Lehmann
Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 15 (1) (2023)
Etienne Sollier, Jack Kuipers, Koichi Takahashi, Niko Beerenwinkel, Katharina Jahn
COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data. Nature communications 14 (1) (2023)
Oscar M Lezcano, Lara Fuhrmann, Gayatri Ramakrishnan, Niko Beerenwinkel, Martijn A Huynen, Ronald P Van Rij
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster . Virus evolution 9 (2) (2023)
Evelyn Kuhlmeier, Tatjana Chan, Cecilia Valenzuela Agüí, Barbara Willi, Aline Wolfensberger, Christian Beisel, Ivan Topolsky, Niko Beerenwinkel, Tanja Stadler, null Swiss Sars-CoV-Sequencing Consortium, Sarah Jones, Grace B Tyson, Margaret J Hosie, Katja Reitt, Julia Hüttl, Marina Luisa Meli, Regina Hofmann-Lehmann
Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 15 (1) (2023)
Arthur Dondi, Ulrike Lischetti, Francis Jacob, Franziska Singer, Nico Borgsmüller, Ricardo Coelho, null null, Viola Heinzelmann-Schwarz, Christian Beisel, Niko Beerenwinkel
Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer. Nature communications 14 (1) (2023)
Evelyn Kuhlmeier, Tatjana Chan, Cecilia Valenzuela Agüí, Barbara Willi, Aline Wolfensberger, Christian Beisel, Ivan Topolsky, Niko Beerenwinkel, Tanja Stadler, null Swiss Sars-CoV-Sequencing Consortium, Sarah Jones, Grace B Tyson, Margaret J Hosie, Katja Reitt, Julia Hüttl, Marina Luisa Meli, Regina Hofmann-Lehmann
Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 15 (1) (2023)
Sumana Srivatsa, Hesam Montazeri, Gaia Bianco, Mairene Coto-Llerena, Mattia Marinucci, Charlotte C K Ng, Salvatore Piscuoglio, Niko Beerenwinkel
Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nature communications 13 (1) (2022)
Sarah A Nadeau, Timothy G Vaughan, Christiane Beckmann, Ivan Topolsky, Chaoran Chen, Emma B Hodcroft, Tobias Schär, Ina Nissen, Natascha Santacroce, Elodie Burcklen, Pedro F Ferreira, Kim Philipp Jablonski, Susana Posada Céspedes, Vincenzo Capece, Sophie Seidel, Noemi Santamaria de Souza, Julia Martínez Gómez, Phil Fang Cheng, Philipp Peter Bosshard, Mitchell Paul Levesque, Verena Kufner, Stefan Schmutz, Maryam Zaheri, Michael Huber, Alexandra Trkola, Samuel Cordey, Florian Laubscher, Ana Rita Gonçalves, Sébastien Aeby, Trestan Pillonel, Damien Jacot, Claire Bertelli, Gilbert Greub, Karoline Leuzinger, Madlen Stange, Alfredo Mari, Tim Roloff, Helena Seth-Smith, Hans H Hirsch, Adrian Egli, Maurice Redondo, Olivier Kobel, Christoph Noppen, Louis du Plessis, Niko Beerenwinkel, Richard A Neher, Christian Beisel, Tanja Stadler
Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Science translational medicine (2022)
Jack Kuipers, Jochen Singer, Niko Beerenwinkel
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. Bioinformatics (Oxford, England) 38 (20) (2022)
Gaia Bianco, Mairene Coto-Llerena, John Gallon, Venkatesh Kancherla, Stephanie Taha-Mehlitz, Mattia Marinucci, Martina Konantz, Sumana Srivatsa, Hesam Montazeri, Federica Panebianco, Vijaya G Tirunagaru, Marta De Menna, Viola Paradiso, Caner Ercan, Ahmed Dahmani, Elodie Montaudon, Niko Beerenwinkel, Marianna Kruithof de Julio, Luigi M Terracciano, Claudia Lengerke, Rinath M Jeselsohn, Robert C Doebele, Francois-Clement Bidard, Elisabetta Marangoni, Charlotte C K Ng, Salvatore Piscuoglio
GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Communications biology 5 (1) (2022)
Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Pelin Icer Baykal, Zoia Comarova, Angela Lu, Yuri B Porozov, Tetyana I Vasylyeva, Joel O Wertheim, Braden T Tierney, Charles Y Chiu, Ren Sun, Aiping Wu, Malak S Abedalthagafi, Victoria M Pak, Shivashankar H Nagaraj, Adam L Smith, Pavel Skums, Bogdan Pasaniuc, Andrey Komissarov, Christopher E Mason, Eric Bortz, Philippe Lemey, Fyodor Kondrashov, Niko Beerenwinkel, Tommy Tsan-Yuk Lam, Nicholas C Wu, Alex Zelikovsky, Rob Knight, Keith A Crandall, Serghei Mangul
Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature methods 19 (4) (2022)
Katharina Jahn, David Dreifuss, Ivan Topolsky, Anina Kull, Pravin Ganesanandamoorthy, Xavier Fernandez-Cassi, Carola Bänziger, Alexander J Devaux, Elyse Stachler, Lea Caduff, Federica Cariti, Alex Tuñas Corzón, Lara Fuhrmann, Chaoran Chen, Kim Philipp Jablonski, Sarah Nadeau, Mirjam Feldkamp, Christian Beisel, Catharine Aquino, Tanja Stadler, Christoph Ort, Tamar Kohn, Timothy R Julian, Niko Beerenwinkel
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC. Nature microbiology 7 (8) (2022)
Sumana Srivatsa, Hesam Montazeri, Gaia Bianco, Mairene Coto-Llerena, Mattia Marinucci, Charlotte C K Ng, Salvatore Piscuoglio, Niko Beerenwinkel
Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nature communications 13 (1) (2022)
Gaia Bianco, Mairene Coto-Llerena, John Gallon, Venkatesh Kancherla, Stephanie Taha-Mehlitz, Mattia Marinucci, Martina Konantz, Sumana Srivatsa, Hesam Montazeri, Federica Panebianco, Vijaya G Tirunagaru, Marta De Menna, Viola Paradiso, Caner Ercan, Ahmed Dahmani, Elodie Montaudon, Niko Beerenwinkel, Marianna Kruithof de Julio, Luigi M Terracciano, Claudia Lengerke, Rinath M Jeselsohn, Robert C Doebele, Francois-Clement Bidard, Elisabetta Marangoni, Charlotte C K Ng, Salvatore Piscuoglio
Author Correction: GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Communications biology 5 (1) (2022)
Sumana Srivatsa, Hesam Montazeri, Gaia Bianco, Mairene Coto-Llerena, Mattia Marinucci, Charlotte C K Ng, Salvatore Piscuoglio, Niko Beerenwinkel
Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nature communications 13 (1) (2022)
Anne Bertolini, Michael Prummer, Mustafa Anil Tuncel, Ulrike Lischetti, María Lourdes Rosano-González, Jack Kuipers, Daniel Johannes Stekhoven, null null, Niko Beerenwinkel, Franziska Singer
scAmpi-A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. PLoS computational biology 18 (6) (2022)
David Seifert, Beda Joos, Dominique L Braun, Corinna S Oberle, Corinne D Schenkel, Herbert Kuster, Christina Grube, Jürg Böni, Sabine Yerly, Vincent Aubert, Thomas Klimkait, Huldrych F Gunthard, Niko Beerenwinkel, Karin J Metzner, null On Behalf Of The Swiss Hiv Cohort Study
Detecting Selection in the HIV-1 Genome during Sexual Transmission Events. Viruses 14 (2) (2022)
Polina Suter, Eva Dazert, Jack Kuipers, Charlotte C K Ng, Tuyana Boldanova, Michael N Hall, Markus H Heim, Niko Beerenwinkel
Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS computational biology 18 (9) (2022)
Sumana Srivatsa, Hesam Montazeri, Gaia Bianco, Mairene Coto-Llerena, Mattia Marinucci, Charlotte C K Ng, Salvatore Piscuoglio, Niko Beerenwinkel
Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nature communications 13 (1) (2022)
Susana Posada Céspedes, Gert U van Zyl, Hesam Montazeri, Jack Kuipers, Soo-Yon Rhee, Roger D Kouyos, Huldrych F Gunthard, Niko Beerenwinkel
Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS computational biology 17 (9) (2021)
Winfried Goettsch, Niko Beerenwinkel, Li Deng, Lars Dölken, Bas E Dutilh, Florian Erhard, Lars Kaderali, Max von Kleist, Roland Marquet, Jelle Matthijnssens, Shawna McCallin, Dino P McMahon, Thomas Rattei, Ronald P Van Rij, David L Robertson, Martin Schwemmle, Noam Stern-Ginossar, Manja Marz
ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses 13 (5) (2021)
Robert John Noble, Dominik Burri, Cécile Le Sueur, Jeanne Lemant, Yannick Viossat, Jakob Nikolas Kather, Niko Beerenwinkel
Spatial structure governs the mode of tumour evolution. Nature ecology & evolution 6 (2) (2021)
Kieran Elmes, Fabian Schmich, Ewa Szczurek, Jeremy L Jenkins, Niko Beerenwinkel, Alex Gavryushkin
Learning epistatic gene interactions from perturbation screens. PloS one 16 (7) (2021)
Kiyomi Morita, Feng Wang, Katharina Jahn, Tianyuan Hu, Tomoyuki Tanaka, Yuya Sasaki, Jack Kuipers, Sanam Loghavi, Sa A Wang, Yuanqing Yan, Ken Furudate, Jairo Matthews, Latasha Little, Curtis Gumbs, Jianhua Zhang, Xingzhi Song, Erika Thompson, Keyur P Patel, Carlos E Bueso-Ramos, Courtney D D DiNardo, Farhad Ravandi, Elias Jabbour, Michael Andreeff, Jorge E Cortes, Kapil Bhalla, Guillermo Garcia Manero, Hagop Kantarjian, Marina Y Konopleva, Daisuke Nakada, Nicholas Navin, Niko Beerenwinkel, P Andrew Futreal, Koichi Takahashi
Author Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics. Nature communications 12 (1) (2021)
André Franken, Bianca Behrens, Florian Reinhardt, Liwen Yang, Mahdi Rivandi, Francesco Marass, Bernadette Jaeger, Natalia Krawczyk, Jan-Philipp Cieslik, Ellen Honisch, Hannah Asperger, Emmanuelle Jeannot, Charlotte Proudhon, Niko Beerenwinkel, Natali Schölermann, Irene Esposito, Frederic Dietzel, Nikolas H Stoecklein, Dieter Niederacher, Tanja Fehm, Tanja N Fehm
Multiparametric Circulating Tumor Cell Analysis to Select Targeted Therapies for Breast Cancer Patients. Cancers 13 (23) (2021)
Hesam Montazeri, Mairene Coto-Llerena, Gaia Bianco, Ehsan Zangene, Stephanie Taha-Mehlitz, Viola Paradiso, Sumana Srivatsa, Antoine de Weck, Guglielmo Roma, Manuela Lanzafame, Martin Bolli, Niko Beerenwinkel, Markus von Flüe, Luigi M Terracciano, Salvatore Piscuoglio, Charlotte C K Ng
Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens. Nucleic acids research 49 (15) (2021)
Fabiana Lüönd, Martin Pirkl, Mizue Hisano, Vincenzo Prestigiacomo, Ravi Kr Kalathur, Niko Beerenwinkel, Gerhard Christofori
Hierarchy of TGFβ/SMAD, Hippo/YAP/TAZ, and Wnt/β-catenin signaling in melanoma phenotype switching. Life science alliance 5 (2) (2021)
Teemu Kuosmanen, Johannes Cairns, Robert John Noble, Niko Beerenwinkel, Tommi Mononen, Ville Mustonen
Drug-induced resistance evolution necessitates less aggressive treatment. PLoS computational biology 17 (9) (2021)
Jack Kuipers, Ariane L Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko Beerenwinkel
Statistical tests for intra-tumour clonal co-occurrence and exclusivity. PLoS computational biology 17 (12) (2021)
Christos Dimitrakopoulos, Sravanth Kumar Hindupur, Marco Colombi, Dritan Liko, Charlotte K Y Ng, Salvatore Piscuoglio, Jonas Behr, Ariane L Moore, Jochen Singer, Hans-Joachim Ruscheweyh, Matthias S Matter, Dirk Mossmann, Luigi M Terracciano, Michael N Hall, Niko Beerenwinkel
Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma. BMC genomics 22 (1) (2021)
Ariane L Moore, Aashil A Batavia, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch, Niko Beerenwinkel
Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma. Cancers 13 (9) (2021)
Ewa Szczurek, Tyll Krüger, Barbara Klink, Niko Beerenwinkel
A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment. PLoS computational biology 16 (10) (2020)
Kiyomi Morita, Feng Wang, Katharina Jahn, Tianyuan Hu, Tomoyuki Tanaka, Yuya Sasaki, Jack Kuipers, Sanam Loghavi, Sa A Wang, Yuanqing Yan, Ken Furudate, Jairo Matthews, Latasha Little, Curtis Gumbs, Jianhua Zhang, Xingzhi Song, Erika Thompson, Keyur P Patel, Carlos E Bueso-Ramos, Courtney D D DiNardo, Farhad Ravandi, Elias Jabbour, Michael Andreeff, Jorge E Cortes, Kapil Bhalla, Guillermo Garcia Manero, Hagop Kantarjian, Marina Y Konopleva, Daisuke Nakada, Nicholas Navin, Niko Beerenwinkel, P Andrew Futreal, Koichi Takahashi
Publisher Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics. Nature communications 11 (1) (2020)
Hesam Montazeri, Susan Little, Mozhgan Mozaffarilegha, Niko Beerenwinkel, Victor DeGruttola
Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times. Statistical applications in genetics and molecular biology (2020)
Patrick Grossmann, Simona Cristea, Niko Beerenwinkel
Clonal evolution driven by superdriver mutations. BMC evolutionary biology 20 (1) (2020)
Chenjie Wan, Nadine Tschumi, Venelin Mitov, François Blanquart, Susana Posada Céspedes, Teja Turk, Kathrin Neumann, Niko Beerenwinkel, Jasmina Bogojeska, Jacques Fellay, Volker Roth, Katharina Kusejko, Matthieu Perreau, Thomas Klimkait, Sabine Yerly, Manuel Battegay, Laura Walti, Alexandra Calmy, Pietro Vernazza, Enos Bernasconi, Matthias Cavassini, Karin J Metzner, Huldrych F Gunthard, Roger D Kouyos, null null
Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART. Nature communications 11 (1) (2020)
Kiyomi Morita, Feng Wang, Katharina Jahn, Tianyuan Hu, Tomoyuki Tanaka, Yuya Sasaki, Jack Kuipers, Sanam Loghavi, Sa A Wang, Yuanqing Yan, Ken Furudate, Jairo Matthews, Latasha Little, Curtis Gumbs, Jianhua Zhang, Xingzhi Song, Erika Thompson, Keyur P Patel, Carlos E Bueso-Ramos, Courtney D D DiNardo, Farhad Ravandi, Elias Jabbour, Michael Andreeff, Jorge E Cortes, Kapil Bhalla, Guillermo Garcia Manero, Hagop Kantarjian, Marina Y Konopleva, Daisuke Nakada, Nicholas Navin, Niko Beerenwinkel, P Andrew Futreal, Koichi Takahashi
Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics. Nature communications 11 (1) (2020)
Monica Golumbeanu, Sébastien Desfarges, Céline Hernandez, Manfredo Quadroni, Sylvie Rato, Pejman Mohammadi, Amalio Telenti, Niko Beerenwinkel, Angela Ciuffi
Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Scientific reports 9 (1) (2019)
Fabian Schmich, Jack Kuipers, Gunter Merdes, Niko Beerenwinkel
netprioR: a probabilistic model for integrative hit prioritisation of genetic screens. Statistical applications in genetics and molecular biology 18 (3) (2019)
Salem Malikic, Katharina Jahn, Jack Kuipers, S Cenk Sahinalp, Niko Beerenwinkel
Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data. Nature communications 10 (1) (2019)
Brian Matthew Lang, Niko Beerenwinkel, Benjamin Misselwitz
Editorial: the influence of genetic factors in mediating the effects of tobacco smoke in IBD-Authors' reply. Alimentary pharmacology & therapeutics 47 (2) (2019)
Nadine Tschumi, Chantal von Siebenthal, Valentina Vongrad, Teja Turk, Kathrin Neumann, Niko Beerenwinkel, Jasmina Bogojeska, Jacques Fellay, Volker Roth, Yik Lim Kok, Christian W Thorball, Alessandro Borghesi, Sonali Parbhoo, Mario Wieser, Katharina Kusejko, Matthieu Perreau, Thomas Klimkait, Sabine Yerly, Manuel Battegay, Andri Rauch, Matthias Hoffmann, Enos Bernasconi, Matthias Cavassini, Roger D Kouyos, Huldrych F Gunthard, Karin J Metzner, null null
Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nature communications 10 (1) (2019)
Jack Kuipers, Thomas Thurnherr, Giusi Moffa, Polina Suter, Jonas Behr, Ryan Goosen, Gerhard Christofori, Niko Beerenwinkel
Mutational interactions define novel cancer subgroups. Nature communications 9 (1) (2018)
Congwei Wang, Fabian Schmich, Sumana Srivatsa, Julie Weidner, Niko Beerenwinkel, Anne Spang
Correction: Context-dependent deposition and regulation of mRNAs in P-bodies. eLife 7 (2018)
Congwei Wang, Fabian Schmich, Sumana Srivatsa, Julie Weidner, Niko Beerenwinkel, Anne Spang
Context-dependent deposition and regulation of mRNAs in P-bodies. eLife 7 (2018)
Joana Torres, Remo Monti, Ariane L Moore, Makiko Seimiya, Yanrui Jiang, Niko Beerenwinkel, Christian Beisel, Jorge V Beira, Renato Paro
A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila. eLife 7 (2018)
Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
Single-cell mutation identification via phylogenetic inference. Nature communications 9 (1) (2018)
Remo Monti, Iros Barozzi, Marco Osterwalder, Elizabeth Lee, Momoe Kato, Tyler H Garvin, Ingrid Plajzer-Frick, Catherine S Pickle, Jennifer A Akiyama, Veena Afzal, Niko Beerenwinkel, Diane E Dickel, Axel Visel, Len A Pennacchio
Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS computational biology 13 (8) (2017)
Mitasha Bharadwaj, Nico Strohmeyer, Georgina P Colo, Jonne Helenius, Niko Beerenwinkel, Herbert B Schiller, Reinhard Fässler, Daniel J Müller
αV-class integrins exert dual roles on α5β1 integrins to strengthen adhesion to fibronectin. Nature communications 8 (2017)
Kee Pang Soh, Ewa Szczurek, Thomas Sakoparnig, Niko Beerenwinkel
Predicting cancer type from tumour DNA signatures. Genome medicine 9 (1) (2017)
Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz
Inferring modulators of genetic interactions with epistatic nested effects models. PLoS computational biology 13 (4) (2017)
Priyanka G Bhosale, Manishkumar Pandey, Simona Cristea, Mickey Shah, Asawari Patil, Niko Beerenwinkel, Alejandro A Schäffer, Manoj B Mahimkar
Recurring Amplification at 11q22.1-q22.2 Locus Plays an Important Role in Lymph Node Metastasis and Radioresistance in OSCC. Scientific reports 7 (1) (2017)
Kristina Crona, Alex Gavryushkin, Devin Greene, Niko Beerenwinkel
Inferring genetic interactions from comparative fitness data. eLife 6 (2017)
C Lutz, B Weder, A Hünerwadel, S Fagagnini, B Lang, Niko Beerenwinkel, J B Rossel, G Rogler, B Misselwitz, M Hausmann
Myeloid differentiation primary response gene (MyD) 88 signalling is not essential for intestinal fibrosis development. Scientific reports 7 (1) (2017)
Brian Matthew Lang, L Biedermann, W T van Haaften, C de Vallière, M Schuurmans, S Begré, J Zeitz, M Scharl, M Turina, T Greuter, P Schreiner, Henriette Heinrich, T Kuntzen, S R Vavricka, G Rogler, Niko Beerenwinkel, Benjamin Misselwitz, null null
Genetic polymorphisms associated with smoking behaviour predict the risk of surgery in patients with Crohn's disease. Alimentary pharmacology & therapeutics 47 (1) (2017)