Andrew F. Neuwald

Publication Activity (10 Years)

Years Active: 1994-2021
Publications (10 Years): 10

Top Topics

Multiple Sequence Alignments

Regulatory Elements

Protein Sequences

Top Venues

PLoS Comput. Biol.

J. Comput. Biol.

Publications

Xu Shi, Andrew F. Neuwald, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. Bioinform. 37 (5) (2021)
Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach. BMC Bioinform. 22 (1) (2021)
Andrew F. Neuwald, Bryan D. Kolaczkowski, Stephen F. Altschul
eCOMPASS: evaluative comparison of multiple protein alignments by statistical score. Bioinform. 37 (20) (2021)
Andrew F. Neuwald
Reflections on the quest to obtain biological information from genomic data. Quant. Biol. 9 (3) (2021)
Xi Chen, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements. PLoS Comput. Biol. 17 (7) (2021)
Andrew F. Neuwald, Christopher J. Lanczycki, Theresa K. Hodges, Aron Marchler-Bauer
Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments. Database J. Biol. Databases Curation 2020 (2020)
Andrew F. Neuwald, Stephen F. Altschul
Statistical investigations of protein residue direct couplings. PLoS Comput. Biol. 14 (12) (2018)
Stephen F. Altschul, Andrew F. Neuwald
Initial Cluster Analysis. J. Comput. Biol. 25 (2) (2018)
Andrew F. Neuwald, Stephen F. Altschul
Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations. PLoS Comput. Biol. 12 (12) (2016)
Andrew F. Neuwald, Stephen F. Altschul
Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties. PLoS Comput. Biol. 12 (5) (2016)
Andrew F. Neuwald
A Bayesian Sampler for Optimization of Protein Domain Hierarchies. J. Comput. Biol. 21 (3) (2014)
Andrew F. Neuwald
Evaluating, Comparing, and Interpreting Protein Domain Hierarchies. J. Comput. Biol. 21 (4) (2014)
Andrew F. Neuwald, Christopher J. Lanczycki, Aron Marchler-Bauer
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. BMC Bioinform. 13 (2012)
Andrew F. Neuwald
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. Bioinform. 25 (22) (2009)
Andrew F. Neuwald
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. Bioinform. 25 (15) (2009)
Andrew F. Neuwald, Jun S. Liu
Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. BMC Bioinform. 5 (2004)
W. John Wilbur, Andrew F. Neuwald
A Theory of Information with Special Application to Search Problems. Comput. Chem. 24 (1) (2000)
Charles E. Lawrence, Stephen F. Altschul, John C. Wootton, Mark S. Boguski, Andrew F. Neuwald, Jun S. Liu
A Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences. HICSS (5) (1994)