Research

Google Scholar

2024

  • spillR: Spillover Compensation in Mass Cytometry Data
    M. Guazzini, A. Reisach, S. Weichwald, and C. Seiler
    Bioinformatics, 2024
    open access, R package

  • Multipotent Adult Progenitor Cells Prevent Functional Impairment and Improve Development in Inflammation Driven Detriment of Preterm Ovine Lungs
    S. Neuen, D. Ophelders, H. Widowski, M. Hütten, T. Brokken, C. van Gorp, P. Nikkels, C. Severens-Rijvers, M. Sthijns, C. van Blitterswijk, F. Troost, V. LaPointe, S. Jolani, C. Seiler, J. Pillow, T. Delhaas, N. Reynaert, and T. Wolfs
    Regenerative Therapy, Volume 27, Pages 207–217, December 2024
    open access

  • NKp30 and NKG2D Contribute to Natural Killer Recognition of HIV-Infected Cells
    N. Zhao, R. Pi, Ruoxi, D. Nguyen, T. Ranganath, C. Seiler, S. Holmes, A. Marson, and C. Blish
    preprint

2023

  • Simple Sorting Criteria Help Find the Causal Order in Additive Noise Models
    A. Reisach, M. Tami, C. Seiler, A. Chambaz, and S. Weichwald
    37th Conference on Neural Information Processing Systems (NeurIPS)
    New Orleans, LA, US, Pages 785–807, December 2023
    pdf

  • Conformal Regression in Calorie Prediction for Team Jumbo-Visma
    K. van Kuijk, M. Dirksen, and C. Seiler
    12th Symposium on Conformal and Probabilistic Prediction with Applications (COPA)
    Limassol, Cyprus, PMLR, Volume 204, Pages 5–15, September 2023
    pdf

2021

  • Beware of the Simulated DAG! Causal Discovery Benchmarks May Be Easy to Game
    A. Reisach, C. Seiler, and S. Weichwald
    35th Conference on Neural Information Processing Systems (NeurIPS)
    Virtual-only, Pages 27772–27784, December 2021
    pdf

  • Spatial Patterns of Dental Disease in Patients with Low Salivary Flow
    D. Proctor, C. Seiler, A. Burns, S. Walker, T. Jung, J. Weng, S. Sastiel, Y. Rajendran, Y. Kapila, M. Millman, G. Armitage, P. Loomer, S. Holmes, M. Ryder, and D. Relman
    This preprint is not yet peer-reviewed
    medRxiv

  • CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments
    C. Seiler, A.-M. Ferreira, L. Kronstad, L. Simpson, M. Le Gars, E. Vendrame, C. Blish, and S. Holmes
    BMC Bioinformatics, Volume 22, Article 137, Pages 1–14, March 2021
    open access, R package

2020

  • Natural Killer Cell Phenotype is Altered in HIV-Exposed Seronegative Women
    N. Zhao, E. Vendrame, A.-M. Ferreira, C. Seiler, T. Ranganath, M. Alary, A.-C. Labbé, F. Guédou, J. Poudrier, S. Holmes, M. Roger, and C. Blish
    PLOS ONE, Volume 15, Issue 9, Pages 1–17, September 2020
    open access

  • Characterization of the Impact of Daclizumab Beta on Circulating Natural Killer Cells by Mass Cytometry
    T. Ranganath, L. Simpson, A.-M. Ferreira, C. Seiler, E. Vendrame, N. Zhao, J. Fontenot, S. Holmes, and C. Blish
    Frontiers in Immunology, Volume 11, Article 714, Pages 1–13, April 2020
    open access

  • Influenza-Induced Interferon Lambda Response Is Associated with Longer Time to Delivery Among Pregnant Kenyan Women
    C. Seiler, N. Bayless, R. Vergara, J. Pintye, J. Kinuthia, L. Osborn, D. Matemo, B. Richardson, G. John-Stewart, S. Holmes, and C. Blish
    Frontiers in Immunology, Volume 11, Article 452, Pages 1–10, March 2020
    open access

  • TIGIT is Upregulated by HIV-1 Infection and Marks a Highly Functional Adaptive and Mature Subset of Natural Killer Cells
    E. Vendrame, C. Seiler, T. Ranganath, N. Zhao, R. Vergara, M. Alary, AC. Labbé, F. Guédou, J. Poudrier, S. Holmes, M. Roger, and C. Blish
    AIDS, Volume 34, Issue 6, Pages 801–813, May 2020
    bioRxiv, journal

2019

  • Pregnancy-Induced Alterations in NK Cell Phenotype and Function
    M. Le Gars, C. Seiler, A. Kay N. Bayless, E. Starosvetsky, L. Moore, S. Shen-Orr, N. Aziz, P. Khatri, C. Dekker, G. Swan, M. Davis, S. Holmes, and C. Blish
    Frontiers in Immunology, Volume 10, Article 2469, Pages 1–13, October 2019
    open access

  • Uncertainty Quantification in Multivariate Mixed Models for Mass Cytometry Data
    C. Seiler, L. Kronstad, L. Simpson, M. Le Gars, E. Vendrame, C. Blish, and S. Holmes
    This preprint is not yet peer-reviewed
    arXiv, posters, talk, R package

  • CCD38 contributes to human natural killer cell responses through a role in immune synapse formation
    M. Le Gars, C. Seiler, A. Kay, N. Bayless, E. Sola, E. Starosvetsky, L. Moore, S. Shen-Orr, N. Aziz, P. Khatri, C. Dekker, G. Swan, M. Davis, S. Holmes, Catherine A. Blish
    This preprint is not yet peer-reviewed
    bioRxiv

2018

  • Differential Induction of IFN-α and Modulation of CD112 and CD54 Expression Govern the Magnitude of NK Cell IFN-γ Response to Influenza A Viruses
    L. Kronstad, C. Seiler, R. Vergara, S. Holmes, and C. Blish
    The Journal of Immunology, Volume 201, Issue 7, Pages 2117–2131, October 2018
    bioRxiv, journal, github, open access

  • Multi-Table Differential Correlation Analysis of Neuroanatomical and Cognitive Interactions in Turner Syndrome
    C. Seiler, T. Green, D. Hong, L. Chromik, L. Huffman, S. Holmes, and A.L. Reiss
    Neuroinformatics, Volume 16, Issue 1, Pages 81–93, January 2018
    pdf, view, journal, open access, R package

2017

  • Multivariate Heteroscedasticity Models for Functional Brain Connectivity
    C. Seiler and S. Holmes
    Frontiers in Neuroscience, Volume 11, Article 696, Pages 1–11, December 2017
    open access, R package

  • Bayesian Statistics in Computational Anatomy
    C. Seiler
    Statistical Shape and Deformation Analysis: Methods, Implementations & Applications (G. Zheng, S. Li, and G. Székely, eds.), Chapter 8, Academic Press, Pages 193–214, March 2017
    pdf, journal, C++ code

2015

  • Curvature and Concentration of Hamiltonian Monte Carlo in High Dimensions
    S. Holmes, S. Rubinstein-Salzedo, and C. Seiler
    This preprint is not yet peer-reviewed
    arXiv, R package

2014

  • Positive Curvature and Hamiltonian Monte Carlo
    C. Seiler, S. Rubinstein-Salzedo, and S. Holmes
    28th Conference on Neural Information Processing Systems (NIPS now NeurIPS)
    Montreal, Canada, Pages 586–594, December 2014
    pdf, poster, R package

  • Image-based vs. Mesh-based Statistical Appearance Model of the Human Femur: Implications for Finite Element Simulations
    S. Bonaretti, C. Seiler, C. Boichon, M. Reyes, and P. Büchler
    Medical Engineering and Physics, Volume 36, Issue 12, Pages 1626–1635, December 2014
    pdf, journal

  • Time-Lapse Microscopy and Classification of 2D Human Mesenchymal Stem Cells Based on Cell Shape Picks Up Myogenic from Osteogenic and Adipogenic Differentiation
    C. Seiler, A. Gazdhar, M. Reyes, L.M. Benneker, T. Geiser, K.A. Siebenrock, and B. Gantenbein-Ritter
    Journal of Tissue Engineering and Regenerative Medicine, Volume 8, Issue 9, Pages 737–746, September 2014
    pdf, journal, Matlab and R code

  • Discussion of “Geodesic Monte Carlo on Embedded Manifolds”
    P. Diaconis, C. Seiler, and S. Holmes
    Scandinavian Journal of Statistics, Volume 41, Issue 1, Pages 3–7, March 2014
    pdf, journal

2013

  • Spatio-Temporal Dimension Reduction of Cardiac Motion for Group-Wise Analysis and Statistical Testing
    K. McLeod, C. Seiler, M. Sermesant, and X. Pennec
    16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)
    Nagoya, Japan, LNCS, Volume 8150, Part II, Pages 501–508, September 2013
    pdf

  • Random Spatial Structure of Geometric Deformations and Bayesian Nonparametrics
    C. Seiler, X. Pennec, and S. Holmes
    1st International Conference on Geometric Science of Information (GSI)
    Paris, France, LNCS, Volume 8085, Part III, Pages 120–127, August 2013
    pdf, talk (youtube), discussion (youtube), C++ code

  • Validity of an Automatic Measure Protocol in Distal Femur for Allograft Selection from a Three-Dimensional Virtual Bone Bank System
    L. Ritacco, C. Seiler, G. Farfalli, L. Nolte, M. Reyes, D. Muscolo, and L. Tinao
    Cell and Tissue Banking, Volume 14, Issue 2, Pages 213–220, June 2013
    pdf, journal

  • Regional Analysis of Left Ventricle Function using a Cardiac-Specific Polyaffine Motion Model
    K. McLeod, C. Seiler, Nicolas Toussaint, M. Sermesant, and X. Pennec
    7th International Conference on Functional Imaging and Modeling of the Heart (FIMH)
    London, UK, LNCS, Volume 7945, Pages 483–490, June 2013
    pdf

2012

  • Capturing the Multiscale Anatomical Shape Variability with Polyaffine Transformation Trees
    C. Seiler, X. Pennec, and M. Reyes
    Medical Image Analysis, Volume 16, Issue 7, Pages 1371–1384, October 2012
    pdf, journal, C++ code

  • Simultaneous Multiscale Polyaffine Registration by Incorporating Deformation Statistics
    C. Seiler, X. Pennec, and M. Reyes
    15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)
    Nice, France, LNCS, Volume 7511, Part II, Pages 130–137, October 2012
    pdf, journal

  • Population-Based Design of Mandibular Plates Based on Bone Quality and Morphology
    H. Bousleiman, C. Seiler, T. Iizuka, L. Nolte, and M. Reyes
    15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)
    Nice, France, LNCS, Volume 7510, Part I, Pages 66–73, October 2012
    pdf, journal

  • A Near-Incompressible Poly-Affine Motion Model for Cardiac Function Analysis
    K. McLeod, C. Seiler, A. Prakosa, M. Sermesant, and X. Pennec
    STATCOM Workshop, MICCAI, Nice, France, October 2012
    pdf

  • Statistical Model Based Shape Prediction from a Combination of Direct Observations and Various Surrogates: Application to Orthopaedic Research
    R. Blanc, C. Seiler, G. Székely, L. Nolte, and M. Reyes
    Medical Image Analysis, Volume 16, Issue 6, Pages 1156–1166, August 2012
    pdf, journal

2011

  • Geometry-Aware Multiscale Image Registration Via OBBTree-Based Polyaffine Log-Demons
    C. Seiler, X. Pennec, and M. Reyes
    14th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)
    Toronto, Canada, LNCS, Volume 6892, Part II, Pages 631–638, September 2011
    Young Scientist Award
    (Top 5 out of the majority of 819 papers written by PhD students and postdocs)
    Student Travel Award and Oral Podium Presentation
    pdf, journal, C++ code

  • Mesh-based vs. Image-based Statistical Model of Appearance of the Human Femur: A Preliminary Comparison Study for the Creation of Finite Element Meshes
    S. Bonaretti, C. Seiler, C. Boichon, P. Büchler, and M. Reyes
    MeshMed Workshop, MICCAI, Toronto, Canada, September 2011
    pdf

  • Femur Specific Polyaffine Model to Regularize the Log-domain Demons Registration
    C. Seiler, X. Pennec, L. Ritacco, and M. Reyes
    SPIE Medical Imaging, Orlando, USA, February 2011
    pdf, journal

2010

  • Atlas-Based Segmentation of Brain Tumor Images Using a Markov Random Field-Based Tumor Growth Model and Non-Rigid Registration
    S. Bauer, C. Seiler, T. Bardyn, P. Büchler, and M. Reyes
    32nd International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
    Buenos Aires, Argentina, Pages 4080–4083, September 2010
    pdf, journal

  • Parametric Regression of 3D Medical Images Through the Exploration of Non-Parametric Regression Models
    C. Seiler, X. Pennec, and M. Reyes
    7th IEEE International Symposium on Biomedical Imaging (ISBI)
    Rotterdam, The Netherlands, Pages 452–455, April 2010
    pdf, journal

  • Combined Statistical Model of Bone Shape and Mechanical Properties for Bone and Implant Modeling
    S. Bonaretti, M. Kistler, C. Seiler, M. Reyes, and P. Büchler
    9th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering (CMBBE)
    Valencia, Spain, February 2010
    pdf

2009

  • Conditional Variability of Statistical Shape Models Based on Surrogate Variables
    R. Blanc, M. Reyes, C. Seiler, and G. Székely
    12th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)
    London, UK, LNCS, Volume 5762, Part II, Pages 84–91, September 2009
    pdf, journal

  • Hierarchical Markov Random Fields Applied to Model Soft Tissue Deformations on Graphics Hardware
    C. Seiler, P. Büchler, L.-P. Nolte, R. Paulsen, and M. Reyes
    Recent Advances in the 3D Physiological Human (N. Magnenat-Thalmann, J.J. Zhang, and D.D. Feng, eds.), Chapter 9, Springer London, Pages 133–148, July 2009
    pdf, journal, C++ code

Theses

  1. Trees on Geometrical Deformations to Model the Statistical Variability of Organs in Medical Images
    C. Seiler
    PhD Thesis, University of Nice Sophia Antipolis and University of Bern, September 2012
    pdf

  2. Displacement Vector Field Regularization for Modelling of Soft Tissue Deformations
    C. Seiler
    MSc Thesis, University of Bern, June 2008
    pdf