(Q30381459)

15 November 2017

Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. (English)

1 reference

15 November 2017

0 references

Alejandro Ochoa

1

0 references

John D. Storey

object named as

John D Storey

series ordinal

2

0 references

author name string

Manuel Llinás

series ordinal

3

1 reference

PMC publication ID

4648515

15 November 2017

Mona Singh

series ordinal

4

1 reference

15 November 2017

17 November 2015

1 reference

PLOS Computational Biology

15 November 2017

1 reference

15 November 2017

11

1 reference

15 November 2017

11

1 reference

15 November 2017

e1004509

1 reference

Creative Commons Attribution 4.0 International

15 November 2017

start time

17 November 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Transmembrane helix: simple or complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

The Pfam protein families database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Reorganizing the protein space at the Universal Protein Resource (UniProt)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Accelerated Profile HMM Searches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

False Discovery Rate Control With Groups

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Using context to improve protein domain identification

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

The construction and use of log-odds substitution scores for multiple sequence alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

A fast and automated solution for accurately resolving protein domain architectures.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

The evolutionary history of protein domains viewed by species phylogeny

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

SMART 6: recent updates and new developments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

A unified approach to false discovery rate estimation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Predicting protein function from domain content

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

A probabilistic model of local sequence alignment that simplifies statistical significance estimation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Posterior error probabilities and false discovery rates: two sides of the same coin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Prioritized subset analysis: improving power in genome-wide association studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Protein homology detection by HMM-HMM comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Statistical significance for genomewide studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Domain combinations in archaeal, eubacterial and eukaryotic proteomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Gene ontology: tool for the unification of biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Profile hidden Markov models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Pfam: a comprehensive database of protein domain families based on seed alignments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Scoring hidden Markov models.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Hidden Markov models in computational biology. Applications to protein modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Non-globular domains in protein sequences: automated segmentation using complexity measures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Identification of common molecular subsequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

A general method applicable to the search for similarities in the amino acid sequence of two proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Rapid and sensitive protein similarity searches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

Basic local alignment search tool

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4648515

A direct approach to false discovery rates

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

The positive false discovery rate: a Bayesian interpretation and the q -value

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

Calibrating E-values for hidden Markov models using reverse-sequence null models

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

The evolution and structure prediction of coiled coils across all genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

Paircoil2: improved prediction of coiled coils from sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

Empirical Bayes Analysis of a Microarray Experiment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004509

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26575353

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004509

1 reference

journals/ploscb/OchoaSLS15

15 November 2017

1 reference

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

4648515

15 November 2017

PubMed publication ID

26575353

1 reference

PMC publication ID

4648515