(Q28242198)

Jose Manuel Rodriguez

3

0 references

Alfonso Valencia

Alfonso Valencia

8

0 references

Adam Frankish

4

Adam Frankish

0 references

Mark Diekhans

5

Mark Diekhans

0 references

Iakes Ezkurdia

1

Iakes Ezkurdia

0 references

Michael L Tress

Michael L Tress

9

0 references

David Juan

David Juan

2

0 references

author name string

Jesus Vazquez

Database resources of the National Center for Biotechnology Information

7

0 references

language of work or name

English

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publication date

15 November 2014

0 references

published in

Human Molecular Genetics

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volume

23

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issue

22

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page(s)

5866-78

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cites work

1 reference

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20 March 2017

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GENCODE: the reference human genome annotation for The ENCODE Project

20 March 2017

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An integrated encyclopedia of DNA elements in the human genome

20 March 2017

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The Pfam protein families database

20 March 2017

1 reference

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A high-resolution map of human evolutionary constraint using 29 mammals

20 March 2017

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20 March 2017

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The RCSB Protein Data Bank: redesigned web site and web services

20 March 2017

1 reference

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Quantifying the mechanisms of domain gain in animal proteins

20 March 2017

1 reference

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

20 March 2017

1 reference

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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Distinguishing protein-coding and noncoding genes in the human genome

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

GENCODE: producing a reference annotation for ENCODE

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

EGASP: the human ENCODE Genome Annotation Assessment Project

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Kalign--an accurate and fast multiple sequence alignment algorithm

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Finishing the euchromatic sequence of the human genome

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Mass spectrometry-based proteomics

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

The Ensembl genome database project

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Initial sequencing and analysis of the human genome

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

The Sequence of the Human Genome

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

A phylogenomic study of human, dog, and mouse

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Locating proteins in the cell using TargetP, SignalP and related tools

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Aligning multiple genomic sequences with the threaded blockset aligner

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Andromeda: a peptide search engine integrated into the MaxQuant environment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

An algorithm for progressive multiple alignment of sequences with insertions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

A combined transmembrane topology and signal peptide prediction method

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Update on activities at the Universal Protein Resource (UniProt) in 2013

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Towards a knowledge-based Human Protein Atlas

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Late-replicating CNVs as a source of new genes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Protein synthesis rate is the predominant regulator of protein expression during differentiation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

The state of the human proteome in 2012 as viewed through PeptideAtlas

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

APPRIS: annotation of principal and alternative splice isoforms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

PASSEL: the PeptideAtlas SRMexperiment library

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

The quantitative proteome of a human cell line.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Deep proteome and transcriptome mapping of a human cancer cell line

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

firestar--advances in the prediction of functionally important residues

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Combining quantitative proteomics data processing workflows for greater sensitivity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Proteomics: a pragmatic perspective

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

The potentially deleterious functional variant flavin-containing monooxygenase 2*1 is at high frequency throughout sub-Saharan Africa

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Improving the accuracy of transmembrane protein topology prediction using evolutionary information

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Improving gene annotation using peptide mass spectrometry

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Open source system for analyzing, validating, and storing protein identification data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

HUMAN GENOME: A Low Number Wins the GeneSweep Pool

29 September 2017

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FHMG%2FDDU309

Qscore: an algorithm for evaluating SEQUEST database search results

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FHMG%2FDDU309

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FHMG%2FDDU309

Detecting amino acid sites under positive selection and purifying selection

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204768

Comprehensive Genome-Wide Proteomic Analysis of Human Placental Tissue for the Chromosome-Centric Human Proteome Project

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24939910

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A method for reducing the time required to match protein sequences with tandem mass spectra

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24939910

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/HMG/DDU309

1 reference

1341728

1341728

1 reference

1 reference

1 reference