Andrew F. Neuwald

19 papers Journal 18Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data.
PLoS Comput. Biol.
Xu Shi, Xiao Wang, Lu Jin, Leena Halakivi-Clarke, Robert Clarke, Andrew F. Neuwald, Jianhua Xuan
2021 J jnl
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach.
BMC Bioinform.
Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2021 J jnl
ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.
PLoS Comput. Biol.
Xi Chen, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2021 J jnl
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles.
Bioinform.
Xu Shi, Andrew F. Neuwald, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
2021 J jnl
Reflections on the quest to obtain biological information from genomic data.
Quant. Biol.
Andrew F. Neuwald
2021 J jnl
eCOMPASS: evaluative comparison of multiple protein alignments by statistical score.
Bioinform.
Andrew F. Neuwald, Bryan D. Kolaczkowski, Stephen F. Altschul
2020 J jnl
Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments.
Database J. Biol. Databases Curation
Andrew F. Neuwald, Christopher J. Lanczycki, Theresa K. Hodges, Aron Marchler-Bauer
2018 J jnl
Initial Cluster Analysis.
J. Comput. Biol.
Stephen F. Altschul, Andrew F. Neuwald
2018 J jnl
Statistical investigations of protein residue direct couplings.
PLoS Comput. Biol.
Andrew F. Neuwald, Stephen F. Altschul
2016 J jnl
Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
PLoS Comput. Biol.
Andrew F. Neuwald, Stephen F. Altschul
2016 J jnl
Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.
PLoS Comput. Biol.
Andrew F. Neuwald, Stephen F. Altschul
2014 J jnl
A Bayesian Sampler for Optimization of Protein Domain Hierarchies.
J. Comput. Biol.
Andrew F. Neuwald
2014 J jnl
Evaluating, Comparing, and Interpreting Protein Domain Hierarchies.
J. Comput. Biol.
Andrew F. Neuwald
2012 J jnl
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.
BMC Bioinform.
Andrew F. Neuwald, Christopher J. Lanczycki, Aron Marchler-Bauer
2009 J jnl
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.
Bioinform.
Andrew F. Neuwald
2009 J jnl
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.
Bioinform.
Andrew F. Neuwald
2004 J jnl
Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model.
BMC Bioinform.
Andrew F. Neuwald, Jun S. Liu
2000 J jnl
A Theory of Information with Special Application to Search Problems.
Comput. Chem.
W. John Wilbur, Andrew F. Neuwald
1994 — conf
A Gibbs Sampler for the Detection of Subtle Motifs in Multiple Sequences.
HICSS (5)
Charles E. Lawrence, Stephen F. Altschul, John C. Wootton, Mark S. Boguski, Andrew F. Neuwald, Jun S. Liu