List of works by Alfonso Valencia

A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration

scientific article published on 15 January 2021

A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms.

scientific article published on 10 September 2013

A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders

A gene network for navigating the literature

scientific article

A hierarchical unsupervised growing neural network for clustering gene expression patterns

scientific article

A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer's Disease, Glioblastoma and Lung cancer

scientific article

A sentence sliding window approach to extract protein annotations from biomedical articles

scientific article

A single residue substitution causes a switch from the dual DNA binding specificity of plant transcription factor MYB.Ph3 to the animal c-MYB specificity

scientific article published on January 1997

A structural biology community assessment of AlphaFold2 applications

scientific article published in 2022

A text-mining perspective on the requirements for electronically annotated abstracts

scientific article published on 06 March 2008

ACRATA: a novel electron transfer domain associated to apoptosis and cancer

scientific article

APPRIS 2017: principal isoforms for multiple gene sets

scientific article published on 23 October 2017

APPRIS WebServer and WebServices

scientific article published on 18 May 2015

APPRIS: annotation of principal and alternative splice isoforms

scientific article

Aberrant Rab11-dependent trafficking of the neuronal glutamate transporter EAAC1 causes oxidative stress and cell death in Huntington's disease

scientific article published on March 2010

Addressing sex bias in biological databases worldwide

Alternative Splicing May Not Be the Key to Proteome Complexity

scientific article

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals

scientific article published on 2 March 2015

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

scientific article published on 10 June 2015

Alzheimer's disease and cancer: current epidemiological evidence for a mutual protection.

scientific article

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins ⬇️

scientific article (publication date: 15 August 1992)

An Overview of BioCreative II.5.

scientific article published on July 2010

An analysis of the Sargasso Sea resource and the consequences for database composition

scientific article (publication date: 19 April 2006)

An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility.

scientific article

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

scientific article

An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D.

scientific article

Analyzing the first drafts of the human proteome.

scientific article published on 16 July 2014

Anna Tramontano 1957-2017.

scientific article published in May 2017

Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies.

scientific article

Are promyelocytic leukaemia protein nuclear bodies a scaffold for caspase-2 programmed cell death?

scientific article published on 10 August 2007

Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study

scientific article published on 25 January 2011

Assessment of intramolecular contact predictions for CASP7.

scientific article

Assessment of predictions submitted for the CASP7 function prediction category.

scientific article

Association Between Germline Mutations in BRF1, a Subunit of the RNA Polymerase III Transcription Complex, and Hereditary Colorectal Cancer.

scientific article

Association of Anorexia Nervosa With Risk of Cancer: A Systematic Review and Meta-analysis

scientific article published on 05 June 2019

Automated alphabet reduction for protein datasets.

scientific article

Automatic annotation of protein function

scientific article

Automatic classification of protein functions from the literature

scientific article published on January 2003

Automatic extraction of biological information from scientific text: protein-protein interactions

scientific article

Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

Automatic identification of informative regions with epigenomic changes associated to hematopoiesis.

scientific article published on September 2017

BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications

scientific article published on 01 July 2019

BRCA1 is a novel regulator of metabolic function in skeletal muscle

scientific article published on 24 February 2014

BRICHOS: a conserved domain in proteins associated with dementia, respiratory distress and cancer

scientific article

Big data analytics for personalized medicine

scientific article published on 06 April 2019

BioC: a minimalist approach to interoperability for biomedical text processing

scientific article

BioCreative-IV virtual issue

scientific article published on 22 May 2014

Bioinformatics Analysis of Pancreas Cancer Genome in High-Throughput Genomic Technologies

Bioinformatics and Computational Biology at the crossroads of post-genomic technology

Bioinformatics and cancer research: building bridges for translational research

scientific article published on February 2008

Bionemo: molecular information on biodegradation metabolism

scientific article

CARGO: a web portal to integrate customized biological information

scientific article published on 5 May 2007

CD8+ T Cells from Human Neonates Are Biased toward an Innate Immune Response.

scientific article published in November 2016

CHEMDNER: The drugs and chemical names extraction challenge

scientific article

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets

scientific article published on 19 April 2017

COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain

publication published on 30 November 2021

Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study

scientific article

Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of observational studies

scientific article published on 04 April 2017

Chapter 14: Cancer genome analysis

scientific article

Characterization of pathogenic germline mutations in human protein kinases

scientific article

CheNER: chemical named entity recognizer.

scientific article

ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer

scientific article

ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts

scientific article

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

scientific article

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts

scientific article

Chromatin Regulators as a Guide for Cancer Treatment Choice

scientific article published on 16 May 2016

Co-evolution and co-adaptation in protein networks

scientific article published on 20 February 2008

Colorectal cancer classification based on gene expression is not associated with FOLFIRI response

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

scientific article

Comparison of algorithms for the detection of cancer drivers at subgene resolution

scientific article published on 17 July 2017

Computational approaches to identify functional genetic variants in cancer genomes

scientific article published on August 2013

Computational methods for the prediction of protein interactions

scientific article

Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone

scientific article published on 13 December 2016

Correction to "Analyzing the first drafts of the human proteome".

scientific article published on 10 March 2015

Correlated mutations and residue contacts in proteins

scientific article

Correlated mutations contain information about protein-protein interaction 1 1Edited by A. R. Fersht ⬇️

scientific article published on August 29, 1997

DNA methylation profiles and their relationship with cytogenetic status in adult acute myeloid leukemia

scientific article

DNA methylation profiling identifies candidate genes for the pathogenesis of hepatosplenic T-cell lymphoma

article

Data mining of molecular dynamics trajectories of nucleic acids

scientific article

Defining functional distances over gene ontology

scientific article

Design and methodological characteristics of studies using observational routinely collected health data for investigating the link between cancer and neurodegenerative diseases: protocol for a meta-research study

scientific article published in 2022

Detection of significant protein coevolution

scientific article

Distinct DNA methylomes of newborns and centenarians

scientific article

Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils

scientific article published on 01 September 2018

Early bioinformatics: the birth of a discipline--a personal view

scientific article

EcID. A database for the inference of functional interactions in E. coli

scientific article

Effective use of sequence correlation and conservation in fold recognition

scientific article

Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis.

scientific article published on 2 June 2017

Emerging methods in protein co-evolution

scientific article published on 05 March 2013

Enhancing the prediction of protein pairings between interacting families using orthology information

scientific article

EnrichNet: network-based gene set enrichment analysis.

scientific article

Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity

scientific article published on 18 December 2017

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

scientific article

Erratum to: The UBC-40 Urothelial Bladder Cancer Cell Line Index: a genomic resource for functional studies.

scientific article published on 30 November 2015

Erratum to: The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies

scientific article published on 25 October 2016

Evaluation of annotation strategies using an entire genome sequence

scientific article

Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge

scientific article

Evidence for transcript networks composed of chimeric RNAs in human cells

scientific article

Evolution of the Ras Superfamily of GTPases

Extending pathways and processes using molecular interaction networks to analyse cancer genome data

scientific article

Extracting information automatically from biological literature

scientific article published on January 2001

Extraction of human kinase mutations from literature, databases and genotyping studies

scientific article

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

scientific article

FUN-L: gene prioritization for RNAi screens

scientific article published on 08 February 2015

FireDB--a database of functionally important residues from proteins of known structure

scientific article

FireDB: a compendium of biological and pharmacologically relevant ligands

scientific article

FragKB: structural and literature annotation resource of conserved peptide fragments and residues

scientific article

From cancer genomes to cancer models: bridging the gaps

scientific article published on 20 March 2009

From residue coevolution to protein conformational ensembles and functional dynamics

scientific article

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

GENCODE: the reference human genome annotation for The ENCODE Project

scientific article

Gene order in Prokaryotes: conservation and implications

article

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

scientific article

Genome-wide analysis of Pax8 binding provides new insights into thyroid functions

scientific article

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

scientific article published on 26 January 2017

Germline Mutations in FAN1 Cause Hereditary Colorectal Cancer by Impairing DNA Repair.

scientific article

Germline variation in the oxidative DNA repair genes NUDT1 and OGG1 is not associated with hereditary colorectal cancer or polyposis

article

Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics

scientific article

Heteromeric amino acid transporters: biochemistry, genetics, and physiology

scientific article

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

scholarly article

Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia

scientific article

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing

scientific article

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing

scientific article

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing

scientific article published on 24 March 2016

ISMB 2003 Text Mining SIG Meeting Report

scientific article published on January 2003

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

scientific article published in June 2007

Identifying ELIXIR Core Data Resources

scientific article

Implementing the iHOP concept for navigation of biomedical literature

scientific article

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions

scientific article published on 26 October 2012

Inference of functional relations in predicted protein networks with a machine learning approach

scientific article

Information Retrieval and Text Mining Technologies for Chemistry.

scientific article

IntAct: an open source molecular interaction database

scientific article

Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment

scientific article

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity

scientific article

Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation

scientific article

International network of cancer genome projects

scientific article

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

scientific article

Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining

scientific article

Intrinsic errors in genome annotation

scientific article

Introducing meta-services for biomedical information extraction

scientific article published on September 2008

Introduction BIOSAPIENS: A European Network of Excellence to develop genome annotation resources

article

Intronic CNVs and gene expression variation in human populations

article

Intronic CNVs cause gene expression variation in human population

article

Inverse and direct cancer comorbidity in people with central nervous system disorders: a meta-analysis of cancer incidence in 577,013 participants of 50 observational studies

scientific article published on 22 January 2014

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures

scientific article

KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily

scientific article

Late-replicating CNVs as a source of new genes

scientific article published on 15 December 2013

Late-replicating CNVs as a source of new genes.

scientific article published on 15 March 2014

Life cycles of successful genes

article

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

scientific article published on 22 May 2017

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

scientific article published on September 2008

MARVEL: a conserved domain involved in membrane apposition events

scientific article

MIB2 variants altering NOTCH signalling result in left ventricle hypertrabeculation/non-compaction and are associated with Ménétrier-like gastropathy

scientific article published on 23 December 2016

Mining Information on Protein Function from Text

Modular organization in the reductive evolution of protein-protein interaction networks

scientific article published in January 2007

Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization

scientific article published on 26 June 2019

Molecular evidence for the inverse comorbidity between central nervous system disorders and cancers detected by transcriptomic meta-analyses

scientific article (publication date: February 2014)

Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome

scientific article

Most Alternative Isoforms Are Not Functionally Important.

scientific article published on 5 May 2017

Most highly expressed protein-coding genes have a single dominant isoform.

scientific article

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes

scientific article (publication date: 15 November 2014)

Multiple sequence alignments as tools for protein structure and function prediction.

scientific article

Mutated genes, pathways and processes in tumours ⬇️

scientific article published on September 17, 2010

MyMiner: a web application for computer-assisted biocuration and text annotation

scientific article published on 12 July 2012

NOTCH pathway inactivation promotes bladder cancer progression

scientific article

Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

scientific article published on 24 June 2019

No paradox, no progress: inverse cancer comorbidity in people with other complex diseases

scientific article

Non-coding recurrent mutations in chronic lymphocytic leukaemia

scientific article published in Nature

Novel domain combinations in proteins encoded by chimeric transcripts

scientific article

Overview of BioCreAtIvE: critical assessment of information extraction for biology

scientific article published in 2005

Overview of the BioCreative III Workshop

scientific article

Overview of the protein-protein interaction annotation extraction task of BioCreative II

scientific article

PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction

scientific article published on 11 June 2009

POLE and POLD1 mutations in 529 kindred with familial colorectal cancer and/or polyposis: review of reported cases and recommendations for genetic testing and surveillance

scientific article

PROTEIN INTERACTIONS EXTRACTED FROM GENOMES AND PAPERS

article published in 2007

PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data.

scientific article

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

Patient Dossier: Healthcare queries over distributed resources

scientific article published on 17 October 2019

Patient-specific Boolean models of signalling networks guide personalised treatments

scientific article published in 2022

Pitfalls of protein sequence analysis

scientific article published on August 1996

Precision medicine needs pioneering clinical bioinformaticians.

scientific article published on 25 October 2017

Predicted residue-residue contacts can help the scoring of 3D models

scientific article

Predicting Protein Relationships to Human Pathways through a Relational Learning Approach Based on Simple Sequence Features

scientific article published on July 2014

Prediction of protein-protein interactions from evolutionary information.

scientific article

Prioritization of pathogenic mutations in the protein kinase superfamily

scientific article

Progress and challenges in predicting protein-protein interaction sites

scientific article published on 03 April 2009

Protein co-evolution, co-adaptation and interactions

scientific article published on 25 September 2008

Protein interaction: same network, different hubs

scientific article published on December 2003

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

scientific article

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses

scientific article published on 28 April 2013

Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes

scientific article published in 2024

Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy.

scientific article published on 13 October 2013

Reductive genome evolution in Buchnera aphidicola

scientific article

Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis

scholarly article by Martin Krallinger et al published 2014 in Advances in Intelligent Systems and Computing

Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity disorder and their first-degree relatives: a protocol for a systematic review and meta-analysis of observational studies

scientific article published on 15 September 2017

SPOC: a widely distributed domain associated with cancer, apoptosis and transcription

scientific article

Selection of organisms for the co-evolution-based study of protein interactions

scientific article

Similarity of phylogenetic trees as indicator of protein-protein interaction.

scientific article

Somatic Embryonic FGFR2 Mutations in Keratinocytic Epidermal Nevi.

scientific article

Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces

scientific article

Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions

scientific article

Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b

scientific article published on 2 May 2013

Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.

scientific article published on 14 July 2014

Systemic approaches to biodegradation

scientific article

TSEMA: interactive prediction of protein pairings between interacting families

scientific article

Text mining for the biocuration workflow

scientific article

Text-mining and information-retrieval services for molecular biology

scientific article

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

scientific article

The BLUEPRINT Data Analysis Portal.

scientific article

The BioLink SIG Workshop at ISMB2004

scientific article published on January 2005

The CHEMDNER corpus of chemicals and drugs and its annotation principles

scientific article

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

scientific article published on 13 October 2020

The Functional Genomics Network in the evolution of biological text mining over the past decade

scientific article

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

scientific article

The REGIA database (RegiaDB): status, limitations and future developments

scientific article published on January 2002

The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies

scientific article published on 22 May 2015

The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer

scientific article published on 10 February 2009

The evolutionary fate of alternatively spliced homologous exons after gene duplication

scientific article published on 29 April 2015

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The organization of the microbial biodegradation network from a systems-biology perspective

scientific article

The potential clinical impact of the release of two drafts of the human proteome

scientific article published on 23 October 2015

The pseudo GTPase CENP-M drives human kinetochore assembly

scientific article published on 8 July 2014

The ras protein family: evolutionary tree and role of conserved amino acids

scientific article published on May 1991

The structural coverage of the human proteome before and after AlphaFold

scientific article published on 24 January 2022

The success (or not) of HUGO nomenclature

scientific article published on 15 May 2006

TopoGSA: network topological gene set analysis

scientific article

Towards a detailed atlas of protein-protein interactions

scientific article published on 26 July 2013

Towards the prediction of protein interaction partners using physical docking

scientific article

Transcriptional dissection of pancreatic tumors engrafted in mice.

scientific article

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

scientific article

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

article

Translational disease interpretation with molecular networks.

scientific article

TreeDet: a web server to explore sequence space

scientific article

Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology

scientific article

Unveiling new disease, pathway, and gene associations via multi-scale neural network

scientific article published on 06 April 2020

Whole-genome fingerprint of the DNA methylome during human B cell differentiation

scientific article

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

scientific article (publication date: 5 June 2011)

YAdumper: extracting and translating large information volumes from relational databases to structured flat files

scientific article

firestar--advances in the prediction of functionally important residues

scientific article

firestar--prediction of functionally important residues using structural templates and alignment reliability

scientific article published on 21 June 2007

iHOP web services

scientific article (publication date: July 2007)

wKinMut-2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases.

scientific article published on 7 October 2015

wKinMut: an integrated tool for the analysis and interpretation of mutations in human protein kinases

scientific article

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