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List of works by Maria-Jesus Martin

A GO catalogue of human DNA-binding transcription factors

scientific article published on 28 October 2020

A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine

scientific article published on 01 June 1998

A method for determining the position and size of optimal sequence regions for phylogenetic analysis.

scientific article published in December 1995

A procedure for detecting selection in highly variable viral genomes: evidence of positive selection in antigenic regions of capsid protein VP1 of foot-and-mouth disease virus.

scientific article published in October 1998

Advances and Applications in the Quest for Orthologs

scientific article published on 01 October 2019

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

scientific article

Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets

scientific article (publication date: July 2014)

Analysis of the tryptic search space in UniProt databases.

scientific article

Annotation of biologically relevant ligands in UniProtKB using ChEBI

scientific article published on 9 December 2022

AntiFam: a tool to help identify spurious ORFs in protein annotation

scientific article published on 20 March 2012

Big data and other challenges in the quest for orthologs

scientific article

BioJS-HGV Viewer: Genetic Variation Visualizer

CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations

scientific article published on 15 September 2020

CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

scientific article published on 01 September 2021

Comparing bacterial genomes through conservation profiles.

scientific article published on 14 April 2003

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

scientific article published on 23 May 2020

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

scientific article published on 04 November 2020

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

scientific article published on 17 October 2011

DEEPScreen: High Performance Drug-Target Interaction Prediction with Convolutional Neural Networks Using 2-D Structural Compound Representations

scientific article published on 9 December 2018

DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations

scientific article published on 08 January 2020

DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

scientific article published on 14 May 2019

Dasty3, a WEB framework for DAS.

scientific article published on 28 July 2011

Design, Implementation and Updating of Knowledge Bases

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

scholarly article by Alperen Dalkiran published in September 2018

Effect of Sequence Padding on the Performance of Protein-Based Deep Learning Models

scientific article published on 20 January 2020

Effect of sequence padding on the performance of deep learning models in archaeal protein functional prediction

scientific article published on 03 September 2020

Expanding the horizons of microRNA bioinformatics

scientific article published on 05 June 2018

FAIR adoption, assessment and challenges at UniProt

scientific article published on 20 September 2019

FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences

scientific article published on 13 February 2014

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF

scientific article

Gene Ontology Consortium: going forward

scientific article (publication date: 2015)

Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data

scientific article published on 13 May 2020

GlyGen data model and processing workflow

scientific article published on 23 April 2020

GlyGen: Computational and Informatics Resources for Glycoscience

scientific article published on 01 January 2020

High-quality protein knowledge resource: SWISS-PROT and TrEMBL.

scientific article

Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses

scientific article published in January 2001

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

Improved selection of canonical proteins for reference proteomes

scientific article published in 2024

Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’s Disease Data

article

Infrastructure for the life sciences: design and implementation of the UniProt website

scientific article (publication date: 8 May 2009)

Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants.

scientific article published on 3 November 2017

MDeePred: Novel Multi-Channel protein featurization for deep learning based binding affinity prediction in drug discovery

scientific article published on 17 October 2020

Managing core resources for genomics and proteomics

scientific article

Minimizing proteome redundancy in the UniProt Knowledgebase

scientific article published on 26 December 2016

Molecular disease presentation in diabetic nephropathy.

scientific article published on August 2015

Molecular epidemiology of HIV-1 in Madrid.

scientific article published in March 1994

MyDas, an extensible Java DAS server

scientific article

Netamines A–G: seven new tricyclic guanidine alkaloids from the marine sponge Biemna laboutei

Ongoing and future developments at the Universal Protein Resource

scientific article

Open Targets: a platform for therapeutic target identification and validation

scientific article

Perspectives on tracking data reuse across biodata resources

Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining

scientific article

Primary genetic characterization of HIV-1 isolates from WHO-sponsored vaccine evaluation sites by the RNase-A mismatch method.

scientific article

ProForma: A Standard Proteoform Notation.

scientific article published on 5 February 2018

Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation

scientific article published on 09 May 2022

ProtVista: visualization of protein sequence annotations

scientific article published on 7 March 2017

Protein Sequence Databases

Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases

scientific article published on 29 November 2021

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

scientific article published in January 1997

Protein sequence database methods.

scientific article published in January 2004

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

scientific article (publication date: 2012)

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

scientific article published on 01 September 2019

Removing redundancy in SWISS-PROT and TrEMBL.

scientific article published in March 1999

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

scientific article (publication date: 2012)

Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways.

scientific article published on January 2017

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

scientific article (publication date: 2013)

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins

scientific article published on 01 January 2019

Searching and Navigating UniProt Databases

scientific article published on 19 June 2015

Searching and Navigating UniProt Databases

scientific article published in March 2023

Sequence analysis of HIV-1 vif gene in Spanish isolates.

scientific article published in February 1995

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Ten Years of Collaborative Progress in the Quest for Orthologs

scientific article published on 2 April 2021

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

scientific article published on 19 November 2019

The COMBREX project: design, methodology, and initial results

scientific article

The EBI RDF platform: linked open data for the life sciences

scientific article

The European Bioinformatics Institute's data resources.

scientific article

The GOA database: gene Ontology annotation updates for 2015

scientific article

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The IntAct database: efficient access to fine-grained molecular interaction data

scientific article published on 21 October 2021

The Proteins API: accessing key integrated protein and genome information

scientific article

The Quest for Orthologs benchmark service and consensus calls in 2020

scientific article published on 06 May 2020

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

scientific article (publication date: 2003)

The UniProt-GO Annotation database in 2011.

scientific article published on 28 November 2011

The Universal Protein Resource (UniProt)

scientific article

The Universal Protein Resource (UniProt): an expanding universe of protein information

scientific article

The cardiovascular gene annotation initiative: Impact on data analysis

scientific article published in July 2015

The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants

The impact of focused Gene Ontology curation of specific mammalian systems

scientific article

The role SWISS-PROT and TrEMBL play in the genome research environment.

scientific article

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.

scientific article published on 18 March 2014

UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants

UniProt Protein Knowledgebase

scientific article

UniProt Tools

scientific article published on 24 March 2016

UniProt and Mass Spectrometry-Based Proteomics—A 2-Way Working Relationship

scientific article published in August 2023

UniProt and Mass Spectrometry-Based Proteomics—A 2-Way Working Relationship

UniProt genomic mapping for deciphering functional effects of missense variants.

scientific article published on 3 April 2019

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

scientific article published on 07 March 2016

UniProt: the Universal Protein Knowledgebase in 2023

scientific article published on 21 November 2022

UniProt: the Universal Protein knowledgebase

scientific article from 2004

UniProtJAPI: a remote API for accessing UniProt data

scientific article

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

scientific article published on 12 May 2020

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

scientific article published in December 2020

Uniclust databases of clustered and deeply annotated protein sequences and alignments.

scientific article

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans

scientific article published on 17 January 2013

Using the Gene Ontology to Annotate Key Players in Parkinson's Disease

scientific article published on 29 January 2016

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