Beyond the E-Value: Stratified Statistics for Protein Domain Prediction

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs

(2013) Andrew J. Schork et al.   PLoS Genetics

Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum

(2012) Nicolas Terrapon et al.   BMC BIOINFORMATICS

P-value-based regulatory motif discovery using positional weight matrices

(2012) H. Hartmann et al.   GENOME RESEARCH

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

Using context to improve protein domain identification

(2011) Alejandro Ochoa et al.   BMC BIOINFORMATICS

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

A fast and automated solution for accurately resolving protein domain architectures

(2010) Corin Yeats et al.   BIOINFORMATICS

The Evolution and Structure Prediction of Coiled Coils across All Genomes

(2010) Owen J.L. Rackham et al.   JOURNAL OF MOLECULAR BIOLOGY

Simultaneous Testing of Grouped Hypotheses: Finding Needles in Multiple Haystacks

(2010) T. Tony Cai et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

False Discovery Rate Control With Groups

(2010) James X. Hu et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment

(2010) Stephen F. Altschul et al.   PLoS Computational Biology

More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology

(2010) Wing-Cheong Wong et al.   PLoS Computational Biology

Detection of new protein domains using co-occurrence: application to Plasmodium falciparum

(2009) Nicolas Terrapon et al.   BIOINFORMATICS

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

(2009) Song Yang et al.   PLoS One

Simultaneous inference: When should hypothesis testing problems be combined?

(2008) Bradley Efron   Annals of Applied Statistics

Profile Comparer: a program for scoring and aligning profile hidden Markov models

(2008) M. Madera   BIOINFORMATICS

Predicting protein function from domain content

(2008) Kristoffer Forslund et al.   BIOINFORMATICS

A unified approach to false discovery rate estimation

(2008) Korbinian Strimmer   BMC BIOINFORMATICS

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

SMART 6: recent updates and new developments

(2008) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology

Prioritized Subset Analysis: Improving Power in Genome-wide Association Studies

(2007) Chun Li et al.   HUMAN HEREDITY

Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics

(2007) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH

Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH

Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling

(2007) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH