Network Analysis of Global Influenza Spread. - Joseph Chan; Antony Holmes; Raul Rabadan (PLoS Comput. Biol., 2010)

Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis. - Santiago Vilar; Rave Harpaz; Herbert S. Chase; Stefano Costanzi; Raul Rabadan; Carol Friedman (J. Am. Medical Informatics Assoc., 2011)

Drug-drug interaction through molecular structure similarity analysis. - Santiago Vilar; Rave Harpaz; Eugenio Uriarte; Lourdes Santana; Raul Rabadan; Carol Friedman (J. Am. Medical Informatics Assoc., 2012)

MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples. - Vladimir Trifonov; Laura Pasqualucci; Riccardo Dalla Favera; Raul Rabadan (BMC Syst. Biol., 2013)

SAVI: a statistical algorithm for variant frequency identification. - Vladimir Trifonov; Laura Pasqualucci; Enrico Tiacci; Brunangelo Falini; Raul Rabadan (BMC Syst. Biol., 2013)

Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis. - Kevin J. Emmett; Raul Rabadan (Brain Informatics and Health, 2014)

Moduli Spaces of Phylogenetic Trees Describing Tumor Evolutionary Patterns. - Sakellarios Zairis; Hossein Khiabanian; Andrew J. Blumberg; Raul Rabadan (Brain Informatics and Health, 2014)

Darwin, Lamarck, or Baldwin: Applying Evolutionary Algorithms to Machine Learning Techniques. - Andreas Holzinger; David Blanchard; Marcus D. Bloice; Katharina Holzinger; Vasile Palade; Raul Rabadan (WI-IAT (1), 2014)

Data-driven discovery of seasonally linked diseases from an Electronic Health Records system. - Rachel D. Melamed; Hossein Khiabanian; Raul Rabadan (BMC Bioinform., 2014)

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. - Francesco Abate; Sakellarios Zairis; Elisa Ficarra; Andrea Acquaviva; Chris H. Wiggins 001; Veronique Frattini; Anna Lasorella; Antonio Iavarone; Giorgio Inghirami; Raul Rabadan (BMC Syst. Biol., 2014)

Darwin or Lamarck? Future Challenges in Evolutionary Algorithms for Knowledge Discovery and Data Mining. - Katharina Holzinger; Vasile Palade; Raul Rabadan; Andreas Holzinger (Interactive Knowledge Discovery and Data Mining in Biomedical Informatics, 2014)

Quantifying Reticulation in Phylogenetic Complexes Using Homology. - Kevin J. Emmett; Raul Rabadan (BICT, 2015)

Multiscale Topology of Chromatin Folding. - Kevin J. Emmett; Benjamin Schweinhart; Raul Rabadan (BICT, 2015)

A Fast Semi-Automatic Segmentation Tool for Processing Brain Tumor Images. - Andrew X. Chen; Raúl Rabadán (BIRS-IMLKE, 2015)

A Theory of Taxonomy. - Guido D'Amico; Raul Rabadan; Matthew Kleban (CoRR, 2016)

Inference of Ancestral Recombination Graphs through Topological Data Analysis. - Pablo G. Cámara; Arnold J. Levine; Raúl Rabadán (PLoS Comput. Biol., 2016)

Black Box FDR. - Wesley Tansey; Yixin Wang 002; David M. Blei; Raul Rabadan (ICML, 2018)

Topological Data Analysis of Single-cell Hi-C Contact Maps. - Mathieu Carrière; Raul Rabadan (CoRR, 2018)

Longitudinal molecular trajectories of diffuse glioma in adults. - Floris P. Barthel; Kevin C. Johnson; Frederick S. Varn; Anzhela D. Moskalik; Georgette Tanner; Emre Kocakavuk; Kevin J. Anderson; Olajide Abiola; Kenneth D. Aldape; Kristin D. Alfaro; Donat Alpar; Samirkumar B. Amin; et al. (Nat., 2019)

arcasHLA: high-resolution HLA typing from RNAseq. - Rose Orenbuch; Ioan Filip; Devon Comito; Jeffrey Shaman; Itsik Pe'er; Raul Rabadan (Bioinform., 2020)

MREC: a fast and versatile framework for aligning and matching point clouds with applications to single cell molecular data. - Andrew J. Blumberg; Mathieu Carrière; Michael A. Mandell; Raul Rabadan; Soledad Villar (CoRR, 2020)

A Random Matrix Theory Approach to Denoise Single-Cell Data. - Luis C. Aparicio; Mykola Bordyuh; Andrew J. Blumberg; Raul Rabadan (Patterns, 2020)

Quantifying Genetic Innovation: Mathematical Foundations for the Topological Study of Reticulate Evolution. - Michael Lesnick; Raúl Rabadán; Daniel I. S. Rosenbloom (SIAM J. Appl. Algebra Geom., 2020)

Topology identifies emerging adaptive mutations in SARS-CoV-2. - Michael Bleher; Lukas Hahn; Juan Ángel Patino-Galindo; Mathieu Carrière; Ulrich Bauer; Raul Rabadan; Andreas Ott (CoRR, 2021)

Persistent homology based characterization of the breast cancer immune microenvironment: a feasibility study. - Andrew Aukerman; Mathieu Carrière; Chao Chen 012; Kevin Gardner; Raúl Rabadán; Rami Vanguri (J. Comput. Geom., 2021)

The Holdout Randomization Test for Feature Selection in Black Box Models. - Wesley Tansey; Victor Veitch; Haoran Zhang; Raul Rabadan; David M. Blei (J. Comput. Graph. Stat., 2022)

Disentangling Interpretable Factors with Supervised Independent Subspace Principal Component Analysis. - Jiayu Su; David A. Knowles; Raúl Rabadán (NeurIPS, 2024)