Detecting coevolving amino acid sites using Bayesian mutational mapping. - Matthew W. Dimmic; Melissa J. Hubisz; Carlos D. Bustamante; Rasmus Nielsen (ISMB (Supplement of Bioinformatics), 2005)

Session Introduction: Inferring SNP Function Using Evolutionary, Structural and Computational Methods. - Matthew W. Dimmic; Shamil R. Sunyaev; Carlos D. Bustamante (Pacific Symposium on Biocomputing, 2005)

Improving the Fitness of High-Dimensional Biomechanical Models via Data-Driven Stochastic Exploration. - Veronica J. Santos; Carlos D. Bustamante; Francisco J. Valero Cuevas (IEEE Trans. Biomed. Eng., 2009)

ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. - Mark H. Wright; Chih-Wei Tung; Keyan Zhao; Andy Reynolds; Susan McCouch; Carlos D. Bustamante (Bioinform., 2010)

SnIPRE: Selection Inference Using a Poisson Random Effects Model. - Kirsten E. Eilertson; James G. Booth; Carlos D. Bustamante (PLoS Comput. Biol., 2012)

PATH-SCAN: A Reporting Tool for Identifying Clinically Actionable Variants. - Roxana Daneshjou; Zachary Zappala; Kimberly R. Kukurba; Sean M. Boyle; Kelly E. Ormond; Teri E. Klein; Michael Snyder 001; Carlos D. Bustamante; Russ B. Altman; Stephen B. Montgomery (Pacific Symposium on Biocomputing, 2014)

Imputation-based Assessment of Next Generation Rare Exome Variant Arrays. - Alicia R. Martin; Gerard Tse; Carlos D. Bustamante; Eimear E. Kenny (Pacific Symposium on Biocomputing, 2014)

Efficient analysis of large datasets and sex bias with ADMIXTURE. - Suyash S. Shringarpure; Carlos D. Bustamante; Kenneth Lange; David H. Alexander (BMC Bioinform., 2016)

FIRE: functional inference of genetic variants that regulate gene expression. - Nilah M. Ioannidis; Joe R. Davis; Marianne K. DeGorter; Nicholas B. Larson; Shannon K. McDonnell; Amy J. French; Alexis J. Battle; Trevor J. Hastie; Stephen N. Thibodeau; Stephen B. Montgomery; Carlos D. Bustamante; Weiva Sieh; et al. (Bioinform., 2017)

Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks. - Jean Louis Raisaro; Florian Tramèr; Zhanglong Ji; Diyue Bu; Yongan Zhao; W. Knox Carey; David D. Lloyd; Heidi Sofia; Dixie Baker; Paul Flicek; Suyash S. Shringarpure; Carlos D. Bustamante; et al. (J. Am. Medical Informatics Assoc., 2017)

Network Enhancement: a general method to denoise weighted biological networks. - Bo Wang 044; Armin Pourshafeie; Marinka Zitnik; Junjie Zhu; Carlos D. Bustamante; Serafim Batzoglou; Jure Leskovec (CoRR, 2018)

DeepTag: inferring all-cause diagnoses from clinical notes in under-resourced medical domain. - Allen Nie; Ashley Zehnder; Rodney López Page; Arturo L. Pineda; Manuel A. Rivas; Carlos D. Bustamante; James Zou 001 (CoRR, 2018)

DeepTag: inferring diagnoses from veterinary clinical notes. - Allen Nie; Ashley Zehnder; Rodney López Page; Yuhui Zhang; Arturo López Pineda; Manuel A. Rivas; Carlos D. Bustamante; James Zou 001 (npj Digit. Medicine, 2018)

Class-Conditional VAE-GAN for Local-Ancestry Simulation. - Daniel Mas Montserrat; Carlos D. Bustamante; Alexander G. Ioannidis (CoRR, 2019)

Lai-Net: Local-Ancestry Inference with Neural Networks. - Daniel Mas Montserrat; Carlos D. Bustamante; Alexander G. Ioannidis (ICASSP, 2020)

LitGen: Genetic Literature Recommendation Guided by Human Explanations. - Allen Nie; Arturo L. Pineda; Matt W. Wright; Hannah Wand; Bryan Wulf; Helio A. Costa; Ronak Y. Patel; Carlos D. Bustamante; James Zou 001 (PSB, 2020)

Discovering prescription patterns in pediatric acute-onset neuropsychiatric syndrome patients. - Arturo López Pineda; Armin Pourshafeie; Alexander G. Ioannidis; Collin McCloskey Leibold; Avis L. Chan; Carlos D. Bustamante; Jennifer Frankovich; Genevieve L. Wojcik (J. Biomed. Informatics, 2021)

Archetypal Analysis for population genetics. - Julia Gimbernat-Mayol; Albert Dominguez Mantes; Carlos D. Bustamante; Daniel Mas Montserrat; Alexander G. Ioannidis (PLoS Comput. Biol., 2022)

Neural ADMIXTURE for rapid genomic clustering. - Albert Dominguez Mantes; Daniel Mas Montserrat; Carlos D. Bustamante; Xavier Giró-i-Nieto; Alexander G. Ioannidis (Nat. Comput. Sci., 2023)