A Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences. - Charles E. Lawrence; Stephen F. Altschul; John C. Wootton; Mark S. Boguski; Andrew F. Neuwald; Jun S. Liu (HICSS (5), 1994)

A Theory of Information with Special Application to Search Problems. - W. John Wilbur; Andrew F. Neuwald (Comput. Chem., 2000)

Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. - Andrew F. Neuwald; Jun S. Liu (BMC Bioinform., 2004)

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. - Andrew F. Neuwald (Bioinform., 2009)

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. - Andrew F. Neuwald; Christopher J. Lanczycki; Aron Marchler-Bauer (BMC Bioinform., 2012)

A Bayesian Sampler for Optimization of Protein Domain Hierarchies. - Andrew F. Neuwald (J. Comput. Biol., 2014)

Evaluating, Comparing, and Interpreting Protein Domain Hierarchies. - Andrew F. Neuwald (J. Comput. Biol., 2014)

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties. - Andrew F. Neuwald; Stephen F. Altschul (PLoS Comput. Biol., 2016)

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations. - Andrew F. Neuwald; Stephen F. Altschul (PLoS Comput. Biol., 2016)

Initial Cluster Analysis. - Stephen F. Altschul; Andrew F. Neuwald (J. Comput. Biol., 2018)

Statistical investigations of protein residue direct couplings. - Andrew F. Neuwald; Stephen F. Altschul (PLoS Comput. Biol., 2018)

Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments. - Andrew F. Neuwald; Christopher J. Lanczycki; Theresa K. Hodges; Aron Marchler-Bauer (Database J. Biol. Databases Curation, 2020)

eCOMPASS: evaluative comparison of multiple protein alignments by statistical score. - Andrew F. Neuwald; Bryan D. Kolaczkowski; Stephen F. Altschul (Bioinform., 2021)

IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. - Xu Shi; Andrew F. Neuwald; Xiao Wang 031; Tian-Li Wang; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (Bioinform., 2021)

ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach. - Xi Chen 056; Xu Shi; Andrew F. Neuwald; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (BMC Bioinform., 2021)

ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements. - Xi Chen 056; Andrew F. Neuwald; Leena Hilakivi-Clarke; Robert Clarke; Jianhua Xuan (PLoS Comput. Biol., 2021)

Reflections on the quest to obtain biological information from genomic data. - Andrew F. Neuwald (Quant. Biol., 2021)

Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data. - Xu Shi; Xiao Wang 031; Lu Jin; Leena Halakivi-Clarke; Robert Clarke; Andrew F. Neuwald; Jianhua Xuan (PLoS Comput. Biol., 2025)