Publications

Classifiers: 
DS = (biomedical) data science / applied statistics
EPI = mathematical epidemiology / infectious disease modeling
GRN = gene regulatory (Boolean) networks
 

2023

  • [GRN] C Kadelka, B Keilty, R Laubenbacher. "Collectively canalizing Boolean functions." Advances in Applied Mathematics (free pdf: Arxiv)
     
  • [OTHER] C Renard, H Brick, J-F Maingonnat, C Kadelka, N Delchier. "­­­­Relative role of leaching and chemical degradation in the loss of water-soluble vitamins C and B9 from frozen vegetables cooked in water". Accepted in LWT - Food Science and Technology 

2022

  • [EPI] C Kadelka. "Projecting social contact matrices to populations stratified by binary attributes with known homophily" Mathematical Biosciences and Engineering
     
  • [GRN] K Chandrasekhar, C Kadelka, R Laubenbacher, D Murrugarra. "Stability of Linear Boolean Networks" Arxiv (preprint)
     
  • [EPI] C Kadelka, R Islam, A McCombs, J Alston, N Morton. "Ethnic homophily affects vaccine prioritization strategies" Journal of Theoretical Biology (free pdf: medRxiv) [see also ISU News]
     
  • [GRN] C Kadelka, R Laubenbacher, D Murrugarra, A Veliz-Cuba, M Wheeler. "Decomposition of Boolean networks: An approach to modularity of biological systems" Arxiv (preprint)
     
  • [GRN] E Dimitrova, B Stigler, C Kadelka, D Murrugarra. "Revealing the canalizing structure of Boolean functions: Algorithms and applications" Automatica

2021

  • [EPI] C Kadelka, A McCombs. "Effect of clustering and correlation of belief systems on COVID-19 and general infectious disease outbreaks" PLOS One
     
  • [DS] N Friedrich, E Stiegeler, M Glögl, T Lemmin, S Hansen, C Kadelka, Y Wu, P Ernst, L Maliqi, C Foulkes, M Morin, M Eroglu, T Liechti, B Ivan, T Reinberg, J Schaefer, U Karakus, S Ursprung, A Mann, P Rusert, R Kouyos, J Robinson, H Gunthard, A Plückthun, and A Trkola. "Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization" Nature Communications
     
  • [EPI] R Islam, T Oraby, A McCombs, MM Chowdhury, M Al-Mamun, MG Tyshenko, C Kadelka. "Evaluation of the United States COVID-19 Vaccine Allocation Strategy" PLOS One [see also The Conversation, Futurity, The Atlantic, Healthline]

2020

  • [GRN] C Kadelka, T Butrie, E Hilton, J Kinseth, H Serdarevic. "A meta-analysis of Boolean network models reveals design principles of gene regulatory networks." Arxiv (preprint) [see also project website]
     
  • [EPI] A McCombs, C Kadelka. “A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies.”  PLOS Computational Biology [see also ISU News, Iowa Public Radio]
     

  • [EPI] N Bachmann, K Kusejko, H Nguyen, SE Chaudron, C Kadelka, T Turk, J Boni, M Perreau, T Klimkait, S Yerly, M Battegay, A Rauch, A Ramette, P Vernazza, E Bernasconi, M Cavassini, HF Gunthard, RD Kouyos. “Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of HIV Transmission in MSM.” Clinical Infectious Diseases

2019

  • [DS] T Liechti, C Kadelka, DL Braun, H Kuster, J Boni, M Robbiani, HF Gunthard, A Trkola. “Widespread B cell perturbations in HIV-1 infection afflict naive and marginal zone B cells.”  Journal of Experimental Medicine

  • [OTHER] I Abela, C Kadelka, A Trkola. “Correlates of broadly neutralizing antibody development.” Current Opinion in HIV and AIDS
     
  • [DS] N Bachmann, A von Braun, N Labhardt, C Kadelka, HF Gunthard, C Sekaggya- Wiltshire, B Castelnuovo, A Kambugu, I Ringera, J Boni, S Yerly, M Perreau, T Klimkait, RD Kouyos, J Fehr, the Swiss HIV Cohort Study. “The importance of routine viral load monitoring: Higher levels of resistance at antiretroviral therapy failure in Uganda and Lesotho compared to Switzerland.” Journal of Antimicrobial Chemotherapy 

2018

  • [DS] C Kadelka, T Liechti, H Ebner, M Schanz, P Rusert, N Friedrich, E Stiegeler, DL Braun, M Huber, AU Scherrer, J Weber, T Uhr, H Kuster, B Misselwitz, M Cavassini, E Bernasoni, M Hoffmann, A Calmy, M Battegay, A Rauch, S Yerly, V Aubert, T Klimkait, J Boni, RD Kouyos, HF Gunthard, A Trkola. “Distinct, IgG1 driven antibody response landscapes demarcate individuals with broadly HIV-1 neutralizing activity.” Journal of Experimental Medicine

  • [DS & EPI] R Kouyos, P Rusert, C Kadelka, M Huber, A Marzel, H Ebner, M Schanz, T Liechti, N Friedrich, DL Braun, AU Scherrer, J Weber, T Uhr, NS Baumann, C Leemann, H Kuster, JP Chave, M Cavassini, E Bernasoni, M Hoffmann, A Calmy, M Battegay, A Rauch, S Yerly, V Aubert, T Klimkait, J Boni, KJ Metzner, HF Gunthard, A Trkola. “Tracing HIV-1 strains that imprint broadly neutralizing responses.” Nature

  • [DS] T Liechti, C Kadelka, H Ebner, N Friedrich, RD Kouyos, HF Gunthard, A Trkola. “Development of a high-throughput bead based assay system to measure HIV- 1 specific immune signatures in clinical samples.” Journal of Immunological Methods

  • [EPI] K Kusejko, C Kadelka, A Marzel, M Battegay, E Bernasoni, A Calmy, M Cavassini, M Hoffmann, J Boni, S Yerly, T Klimkait, M Perreau, A Rauch, HF Gunthard, RD Kouyos, the Swiss HIV Cohort Study. “Inferring age-assortative mixing patterns by applying phylogenetic methods on the HIV transmission tree of the Swiss HIV Cohort Study.” Virus Evolution

  • [DS] L Reh, C Magnus, C Kadelka, T Uhr, J Weber, L Morris, PL Moore, A Trkola. “Viral escape from the CAP256-VRC26 bnAb lineage is associated with slower entry kinetics and increased cell-cell transmission capacity.” PLOS Pathogens

2017

  • [GRN] C Kadelka, J Kuipers, R Laubenbacher. “The influence of canalization on the robustness of Boolean networks.” Physica D: Nonlinear Phenomena

  • [GRN] C Kadelka, Y Li, J Kuipers, JO Adeyeye, R Laubenbacher. “Multistate nested canalizing functions and their networks.” Theoretical Computer Science

  • [EPI] T Turk, N Bachmann, C Kadelka, J Boni, S Yerly, V Aubert, T Klimkait, M Battegay, E Bernasoni, A Calmy, M Cavassini, H Furrer, M Hoffmann, HF Gunthard, RD Kouyos. “Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis.” eLife

  • [DS] N Bachmann, T Turk, C Kadelka, A Marzel, M Shilaih, J Boni, V Aubert, T Klimkait, GE Leventhal, HF Gunthard, RD Kouyos. “Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup.” Retrovirology

  • [DS] D Beauparlant, P Rusert, C Magnus, C Kadelka, J Weber, T Uhr, O Zagordi, C Oberle, MJ Duenas-Decamp, P Clapham, KJ Metzner, HF Gunthard, A Trkola. “Delineating CD4 dependency of HIV-1: Adaptation to infect low level CD4 expressing target cells widens cellular tropism but severely impacts on envelope functionality.” PLOS Pathogens

2016

  • [DS] P Rusert, RD Kouyos, C Kadelka, H Ebner, M Schanz, M Huber, DL Braun, AU Scherrer, C Magnus, J Weber, T Uhr, V Cippa, CW Thorball, H Kuster, M Cavassini, E Bernasoni, M Hoffmann, A Calmy, M Battegay, A Rauch, S Yerly, V Aubert, T Klimkait, J Boni, J Fellay, R Regoes, HF Gunthard, A Trkola. “Determinants of HIV-1 broadly neutralizing antibody induction.” Nature Medicine

2013

  • [GRN] C Kadelka, D Murrugarra, R Laubenbacher. “Stabilizing gene regulatory networks through feedforward loops.” Chaos