Publications

Classifiers: 
DS = (biomedical) data science / applied statistics
EPI = mathematical epidemiology / infectious disease modeling
GRN = gene regulatory (Boolean) networks
MB = general mathematical biology
* = lead/shared lead and/or corresponding author
 

2026

• [DS] C Pasin, P Rusert, D Schmidt, M Schanz, B Pedenko, N Friedrich, P Szwedziak, C Niklaus, MM Kaufmann, M Schwarzmüller, IA, Abela, K Kusejko, C Kadelka, M Sickmann, J Weber, H Ebner, M Huber, A Manrique, MC Hesselman, M Mafu, O Zagordi, J Bergadà-Pijuan, DL Braun, A Rauch, A Calmy, M Cavassini, M Stöckle, P Schmid, J Nemeth, E Bernasconi, G Effantin, PL Moore, W Weissenhorn, HF Günthard, RD Kouyos, A Trkola, the Swiss HIV Cohort Study. "Multi-specificity is a common trait of HIV-1 broad neutralizing capacity"
   
• [GRN*] VSN Bavisetty, M Wheeler, C Kadelka. "Attractors are less stable than their basins: Canalization creates a coherence gap in gene regulatory networks" bioRxiv (preprint)
   
• [GRN*] C Kadelka. "On the number of non-degenerate canalizing Boolean functions" arXiv (preprint)
   
• [GRN*] C Kadelka. "Canalization as a stabilizing principle of gene regulatory networks: a discrete dynamical systems perspective" npj Systems Biology and Applications
   
• [GRN*] C Kadelka, B Coberly. "BoolForge: random generation and analysis of Boolean functions and networks in Python" arXiv (preprint)
   
• [GRN] P Harlapur, R Jagadeesan, AS Ribeiro, C Kadelka, MK Jolly. "Hierarchical organization in sparse gene regulatory networks shapes structural coherence and emergent regulatory coordination" bioRxiv (preprint)
   
• [MB] DKM Arachchi, R Parshad, C Kadelka. "A discrete stage-structured model for the Trojan Y-chromosome strategy" arXiv (preprint)

2025

• [DS] A Phan, P Joshi, C Kadelka, I Friedberg. "A longitudinal analysis of function annotations of the human proteome reveals consistently high biases" Database: The Journal of Biological Databases and Curation
   
• [DS] M Zeeb, K Kusejko, S Hartnack, C Pasin, IA Abela, P Rusert, T Liechti, C Kadelka, J Notter, A Eichenberger, M Hoffmann, HH Hirsch, A Calmy, M Cavassini, ND Labhardt, E Bernasconi, HF Günthard, RD Kouyos, A Trkola, J Nemeth, the Swiss HIV Cohort Study. "Infection with Mycobacterium tuberculosis alters the antibody response to HIV-1" PLOS Pathogens
   
• [EPI*] MS Mahmud, S Eshun, B Espinoza, C Kadelka. "Adaptive human behavior and delays in information availability autonomously modulate epidemic waves" PNAS Nexus
   
• [GRN*] C Kadelka, K Hari. "Critical assessment of the ability of Boolean threshold models to describe gene regulatory network dynamics" PNAS Nexus
   
• [GRN] D Murrugarra, A Veliz-Cuba, E Dimitrova, C Kadelka, M Wheeler, R Laubenbacher. "Modular control of biological networks" Bulletin of Mathematical Biology
   
• [GRN*] VSN Bavisetty, M Wheeler, R Laubenbacher, C Kadelka. "Upper bound for the stability of Boolean networks" Physical Review E
   
• [MB] B Vibishan, P Jain, V Sharma, K Hari, C Kadelka, JT George, MK Jolly. "Impacts of competition and phenotypic plasticity on the viability of adaptive therapy" Mathematical Biosciences
   
• [MB*] T Byer, T Hatfield, C Kadelka. "A mathematical model informs optimal fungicide use against Sclerotinia stem rot to maximize profits in soybean production" Bulletin of Mathematical Biology [free pdf]

2024

• [DS & GRN*] C Kadelka, T Butrie, E Hilton, J Kinseth, A Schmidt, H Serdarevic. "A meta-analysis of Boolean network models reveals design principles of gene regulatory networks" Science Advances. See also:
  • Boolean Gene Regulatory Networks
  • New research guides mathematical model-building for gene regulatory networks
     
• [EPI*] G Gonzalez-Parra, MS Mahmud, C Kadelka. "Learning from the COVID-19 pandemic: a systematic review of mathematical vaccine prioritization models" Infectious Disease Modelling
   
• [EPI*] V Srivastava, D Sarkar, C Kadelka. "­­­­Model-informed optimal allocation of limited resources to mitigate infectious disease outbreaks in societies at war" Journal of the Royal Society Interface
   
• [GRN*] C Kadelka, D Murrugarra. "Canalization reduces the nonlinearity of regulation in biological networks" npj Systems Biology and Applications 
   
• [GRN*] M Wheeler, C Kadelka, A Veliz-Cuba, D Murrugarra, R Laubenbacher. "Modular construction of Boolean networks" Physica D: Nonlinear Phenomena [free pdf]
   
• [OTHER] H Shaban, C Kadelka, S Clark, N Delchier. "­­­­Diffusion and chemical degradation of vitamin B6 in chickpeas (Cicer arietinum L.) during hydrothermal treatments: a kinetic approach" Foods
   

2023

• [DS*] X Jia, A Phan, C Kadelka. "Concise functional enrichment of ranked gene lists" bioRxiv (preprint)
   
• [DS] K Borchardt, C Kadelka, L Schulte, A Toth. "An ecological networks approach reveals restored native vegetation benefits wild bees in agroecosystems" Biological Conservation
   
• [EPI*] C Kadelka. "Projecting social contact matrices to populations stratified by binary attributes with known homophily" Mathematical Biosciences and Engineering
   
• [GRN*] C Kadelka, B Keilty, R Laubenbacher. "Collectively canalizing Boolean functions" Advances in Applied Mathematics [free pdf]
   
• [GRN*] C Kadelka, M Wheeler, A Veliz-Cuba, D Murrugarra, R Laubenbacher, "Modularity of biological systems: a link between structure and function" Journal of the Royal Society Interface 
   
• [GRN] K Chandrasekhar, C Kadelka, R Laubenbacher, D Murrugarra. "Stability of linear Boolean networks" Physica D: Nonlinear Phenomena
   

• [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" LWT - Food Science and Technology

   

2022 

• [EPI*] C Kadelka, R Islam, A McCombs, J Alston, N Morton. "Ethnic homophily affects vaccine prioritization strategies" Journal of Theoretical Biology (free pdf "Ethnic homophily affects vaccine prioritization strategies": medRxiv) See also:
  • ISU News: Researchers recommend future pandemic responses account for ethnicity, social factors
     

• [GRN] E Dimitrova, B Stigler, C Kadelka, D Murrugarra. "Revealing the canalizing structure of Boolean functions: Algorithms and applications" Automatica

   

2021

• [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: US vaccine rollout was close to optimal at reducing deaths and infections, according to a model comparing 17.5 million alternative approaches
  • Futurity: Comparing 17.5 million options shows CDC got COVID vaccine rollout right
  • The Atlantic: What America Lost by Delaying the Vaccine Rollout
  • Healthline: Which COVID-19 Vaccine Is Best for You in 2025?
     
• [EPI*] C Kadelka, A McCombs. "Effect of clustering and correlation of belief systems on COVID-19 and general infectious disease outbreaks" PLOS One
   

• [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

   

2020

• [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: COVID-19 model compares effectiveness of vaccine and mitigation strategies
  • Iowa Public Radio: Math expert at ISU looks for better way to track COVID

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
   
• [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 
   
• [OTHER] I Abela, C Kadelka, A Trkola. “Correlates of broadly neutralizing antibody development.” Current Opinion in HIV and AIDS
   

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*] 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
   
• [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
   
• [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. See also:
  • Newsweek: HIV Vaccine: Special Antibodies That Neutralize Virus Could Hold the Key
     
• [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

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