Publications and Preprints

Statistical methodology: Empirical Bayes

1. Nikolaos Ignatiadis, Bodhisattva Sen 2024
   Empirical partially Bayes multiple testing and compound χ² decisions.
   Annals of Statistics (accepted).
   arXiv Reproduction code
2. Nikolaos Ignatiadis, Stefan Wager 2022
   Confidence Intervals for Nonparametric Empirical Bayes Analysis.
   Journal of the American Statistical Association, Theory and Methods, 117(539), 1149-1166.
   Selected as a discussion paper by the editors of JASA. The discussion took place at JSM 2022. Discussants: Noel Cressie, Subhashis Ghosal, Peter Hoff, Bradley Efron, Guido Imbens, Marianna Pensky, Dongyue Xie & Matthew Stephens. Rejoinder: N.I. & Stefan Wager.
   Journal paper arXiv Reproduction code Julia package
3. Nikolaos Ignatiadis, Sujayam Saha, Dennis L. Sun, Omkar Muralidharan 2023
   Empirical Bayes mean estimation with nonparametric errors via order statistic regression on replicated data.
   Journal of the American Statistical Association, Theory and Methods, 118(542), 987-999.
   Journal paper arXiv Reproduction code Julia package
4. Nikolaos Ignatiadis, Panagiotis Lolas 2021
   σ-Ridge: group-regularized ridge regression via empirical Bayes noise level cross-validation.
   Working paper.
   arXiv Reproduction code Julia package
5. Nikolaos Ignatiadis, Stefan Wager 2019
   Covariate-Powered Empirical Bayes Estimation.
   Advances in Neural Information Processing Systems 32 (NeurIPS 2019).
   Conference paper arXiv Poster Reproduction code Julia package

Statistical methodology: Multiple testing

1. Nikolaos Ignatiadis, Ruodu Wang, Aaditya Ramdas 2024
   Compound e-values and empirical Bayes.
   Working paper.
   arXiv
2. Daniel Xiang, Nikolaos Ignatiadis, Peter McCullagh 2024
   Interpretation of local false discovery rates under the zero assumption.
   Working paper.
   arXiv Reproduction code
3. Nikolaos Ignatiadis, Ruodu Wang, Aaditya Ramdas 2024
   E-values as unnormalized weights in multiple testing.
   Biometrika, 111(2), 417–439.
   Journal paper arXiv Reproduction code
4. Nikolaos Ignatiadis, Wolfgang Huber 2021
   Covariate powered cross-weighted multiple testing.
   Journal of the Royal Statistical Society: Series B (JRSS-B), 83(4), 720-751.
   Journal paper arXiv Reproduction code R package
5. Nikolaos Ignatiadis, Bernd Klaus, Judith Zaugg, Wolfgang Huber 2016
   Data-driven hypothesis weighting increases detection power in genome-scale multiple testing.
   Nature methods, 13(7), 577-580.
   Journal paper Reproduction code R package

Statistical methodology: Causal inference

1. Dean Eckles, Nikolaos Ignatiadis, Stefan Wager, Han Wu 2024
   Noise-Induced Randomization in Regression Discontinuity Designs.
   Biometrika (accepted).
   arXiv Reproduction code Julia package
2. Yizhe Xu, Nikolaos Ignatiadis, Erik Sverdrup, Scott Fleming, Stefan Wager, Nigam H. Shah 2023
   Treatment Heterogeneity with Survival Outcomes.
   Book chapter in: Handbook of Matching and Weighting Adjustments for Causal Inference. Edited by José R. Zubizaretta, Elizabeth A. Stuart, Dylan S. Small, and Paul R. Rosenbaum. Chapman and Hall / CRC Press.
   Book chapter arXiv Reproduction code R package

Applied Collaborations

1. Yefeng Yang, Erik van Zwet, Nikolaos Ignatiadis, Shinichi Nakagawa 2024
   A large-scale in silico replication of ecological and evolutionary studies.
   Nature ecology & evolution.
   Journal paper Reproduction code
2. Ethan Steinberg, Nikolaos Ignatiadis, Steve Yadlowsky, Yizhe Xu, Nigam H. Shah 2023
   Using public clinical trial reports to probe non-experimental causal inference methods.
   BMC Medical Research Methodology, 23, 204.
   Journal paper Reproduction code
3. Stephen Pfohl, Yizhe Xu, Agata Foryciarz, Nikolaos Ignatiadis, Julian Genkins, Nigam H. Shah 2022
   Net benefit, calibration, threshold selection, and training objectives for algorithmic fairness in healthcare.
   ACM Conference on Fairness, Accountability, and Transparency (FAccT'22).
   Conference paper arXiv Reproduction code
4. Loukia Karacosta, Benedict Anchang, Nikolaos Ignatiadis, Samuel Kimmey, Jalen Benson, Joseph Shrager, Robert Tibshirani, Sean Bendall, Sylvia K. Plevritis 2019
   Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution.
   Nature communications, 10, 5887.
   Journal paper Reproduction code Julia package
5. Ralf Beer, Konrad Herbst, Nikolaos Ignatiadis, Ilia Kats, Lorenz Adlung, Hannah Meyer, Dominik Niopek, Tania Christiansen, Fanny Georgi, Nils Kurzawa, Johanna Meichsner, Sophie Rabe, Anja Riedel, Joshua Sachs, Julia Schessner, Florian Schmidt, Philipp Walch, Katharina Niopek, Tim Heinemann, Roland Eils, Barbara Di Ventura 2014
   Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange.
   Molecular BioSystems, 10(7), 1709-1718.
   Journal paper