spillR: Spillover Compensation in Mass Cytometry Data
M. Guazzini, A. Reisach, S. Weichwald, C. Seiler
This preprint is not yet peer-reviewed
bioRxiv
Simple Sorting Criteria Help Find the Causal Order in Additive Noise Models
A. Reisach, M. Tami, C. Seiler, A. Chambaz, and S. Weichwald
To appear at 36th Conference on Neural Information Processing Systems (NeurIPS)
New Orleans, LA, US, December 2023
arXiv
Conformal Regression in Calorie Prediction for Team Jumbo-Visma
K. van Kuijk, M. Dirksen, C. Seiler
12th Symposium on Conformal and Probabilistic Prediction with Applications (COPA)
Limassol, Cyprus, PMLR, Volume 204, Pages 5–15, September 2023
pdf
Beware of the Simulated DAG! Causal Discovery Benchmarks May Be Easy To Game
A. Reisach, C. Seiler, and S. Weichwald
34th 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This preprint is not yet peer-reviewed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
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
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
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
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
Positive Curvature and Hamiltonian Monte Carlo
C. Seiler, S. Rubinstein-Salzedo, and S. Holmes
27th 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
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
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
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
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
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
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
Displacement Vector Field Regularization for Modelling of Soft Tissue Deformations
C. Seiler
MSc Thesis, University of Bern, June 2008
pdf