PubRank

Alfonso Valencia

Author PubWeight™ 463.73‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 75.09
2 International network of cancer genome projects. Nature 2010 20.35
3 GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2012 19.19
4 IntAct: an open source molecular interaction database. Nucleic Acids Res 2004 15.02
5 Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics 2005 14.50
6 Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011 13.18
7 Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet 2011 6.43
8 A gene network for navigating the literature. Nat Genet 2004 6.43
9 Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol 2008 6.38
10 Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics 2005 6.02
11 Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A 2003 4.88
12 Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol 2008 4.36
13 Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A 2012 4.26
14 The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A 2007 3.93
15 Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 2005 3.85
16 Text-mining and information-retrieval services for molecular biology. Genome Biol 2005 3.54
17 Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol 2008 3.54
18 BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol 2012 3.24
19 Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet 2012 3.08
20 The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics 2011 3.03
21 An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform 2010 3.01
22 Introducing meta-services for biomedical information extraction. Genome Biol 2008 2.78
23 Emerging methods in protein co-evolution. Nat Rev Genet 2013 2.72
24 BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford) 2013 2.69
25 Evaluation of annotation strategies using an entire genome sequence. Bioinformatics 2003 2.66
26 iHOP web services. Nucleic Acids Res 2007 2.65
27 EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res 2003 2.50
28 Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nat Genet 2013 2.44
29 Predicting reliable regions in protein alignments from sequence profiles. J Mol Biol 2003 2.42
30 Automatic methods for predicting functionally important residues. J Mol Biol 2003 2.39
31 Text mining for the biocuration workflow. Database (Oxford) 2012 2.37
32 Overview of the BioCreative III Workshop. BMC Bioinformatics 2011 2.31
33 On the organization of bioinformatics core services in biology-based research institutes. Bioinformatics 2011 2.29
34 Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins 2005 2.27
35 The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol 2010 2.18
36 A text-mining perspective on the requirements for electronically annotated abstracts. FEBS Lett 2008 2.10
37 Identification of amino acid residues crucial for chemokine receptor dimerization. Nat Immunol 2004 2.09
38 In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 2002 2.05
39 Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Res 2012 2.04
40 POTRA: a conserved domain in the FtsQ family and a class of beta-barrel outer membrane proteins. Trends Biochem Sci 2003 2.02
41 Assessment of predictions submitted for the CASP7 function prediction category. Proteins 2007 1.98
42 Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome. Am J Hum Genet 2010 1.97
43 EnrichNet: network-based gene set enrichment analysis. Bioinformatics 2012 1.92
44 Text mining for biology--the way forward: opinions from leading scientists. Genome Biol 2008 1.91
45 firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res 2007 1.91
46 Text-mining approaches in molecular biology and biomedicine. Drug Discov Today 2005 1.91
47 Clustering of proximal sequence space for the identification of protein families. Bioinformatics 2002 1.87
48 The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genome Res 2009 1.87
49 Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform 2008 1.80
50 Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002 1.74
51 High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci U S A 2008 1.72
52 MARVEL: a conserved domain involved in membrane apposition events. Trends Biochem Sci 2002 1.71
53 Text mining for metabolic pathways, signaling cascades, and protein networks. Sci STKE 2005 1.71
54 Filamin-A regulates actin-dependent clustering of HIV receptors. Nat Cell Biol 2007 1.71
55 Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci U S A 2010 1.71
56 Analysis of biological processes and diseases using text mining approaches. Methods Mol Biol 2010 1.70
57 p23 and HSP20/alpha-crystallin proteins define a conserved sequence domain present in other eukaryotic protein families. FEBS Lett 2002 1.66
58 BRICHOS: a conserved domain in proteins associated with dementia, respiratory distress and cancer. Trends Biochem Sci 2002 1.66
59 Protein co-evolution, co-adaptation and interactions. EMBO J 2008 1.65
60 Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods 2013 1.64
61 Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery. J Mol Biol 2005 1.63
62 Life cycles of successful genes. Trends Genet 2003 1.61
63 A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinformatics 2005 1.59
64 Information extraction in molecular biology. Brief Bioinform 2002 1.57
65 Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome Res 2013 1.51
66 The Ras protein superfamily: evolutionary tree and role of conserved amino acids. J Cell Biol 2012 1.50
67 Progress and challenges in predicting protein-protein interaction sites. Brief Bioinform 2009 1.44
68 firestar--advances in the prediction of functionally important residues. Nucleic Acids Res 2011 1.43
69 The small GTP-binding protein, Rhes, regulates signal transduction from G protein-coupled receptors. Oncogene 2004 1.42
70 Assessment of intramolecular contact predictions for CASP7. Proteins 2007 1.40
71 CASP6 assessment of contact prediction. Proteins 2005 1.39
72 The success (or not) of HUGO nomenclature. Genome Biol 2006 1.37
73 Defining functional distances over gene ontology. BMC Bioinformatics 2008 1.33
74 The three-dimensional structure of an eukaryotic glutamine synthetase: functional implications of its oligomeric structure. J Struct Biol 2006 1.31
75 Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol 2011 1.30
76 No paradox, no progress: inverse cancer comorbidity in people with other complex diseases. Lancet Oncol 2011 1.30
77 Extraction of human kinase mutations from literature, databases and genotyping studies. BMC Bioinformatics 2009 1.28
78 Sequence-based feature prediction and annotation of proteins. Genome Biol 2009 1.28
79 Automatic annotation of protein function based on family identification. Proteins 2003 1.27
80 Text mining and protein annotations: the construction and use of protein description sentences. Genome Inform 2006 1.26
81 BioCreative-2012 virtual issue. Database (Oxford) 2012 1.26
82 Determination and validation of principal gene products. Bioinformatics 2007 1.25
83 Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. Hum Mutat 2011 1.25
84 TopoGSA: network topological gene set analysis. Bioinformatics 2010 1.24
85 How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database (Oxford) 2012 1.23
86 APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res 2012 1.21
87 Early bioinformatics: the birth of a discipline--a personal view. Bioinformatics 2003 1.20
88 Towards a detailed atlas of protein-protein interactions. Curr Opin Struct Biol 2013 1.19
89 Automatic classification of protein functions from the literature. Comp Funct Genomics 2003 1.18
90 CARGO: a web portal to integrate customized biological information. Nucleic Acids Res 2007 1.18
91 Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biol 2008 1.17
92 Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA. Proteins 2003 1.17
93 Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One 2012 1.16
94 MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinformatics 2012 1.16
95 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. Psychother Psychosom 2014 1.15
96 Phylogeny-independent detection of functional residues. Bioinformatics 2006 1.13
97 Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. J Biotechnol 2002 1.13
98 Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Mol Biol Evol 2012 1.12
99 Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinformatics 2010 1.12
100 The organization of the microbial biodegradation network from a systems-biology perspective. EMBO Rep 2003 1.11
101 The environmental fate of organic pollutants through the global microbial metabolism. Mol Syst Biol 2007 1.11
102 Gas1 is related to the glial cell-derived neurotrophic factor family receptors alpha and regulates Ret signaling. J Biol Chem 2006 1.11
103 Domain definition and target classification for CASP6. Proteins 2005 1.06
104 TreeDet: a web server to explore sequence space. Nucleic Acids Res 2006 1.05
105 EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Res 2008 1.05
106 SQUARE--determining reliable regions in sequence alignments. Bioinformatics 2004 1.04
107 Creating reference datasets for systems biology applications using text mining. Ann N Y Acad Sci 2009 1.04
108 Predicted residue-residue contacts can help the scoring of 3D models. Proteins 2010 1.03
109 MetaRouter: bioinformatics for bioremediation. Nucleic Acids Res 2005 1.03
110 ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res 2012 1.03
111 Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment. Clin Cancer Res 2014 1.02
112 RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. Bioinformatics 2013 1.00
113 PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Res 2009 1.00
114 ACRATA: a novel electron transfer domain associated to apoptosis and cancer. BMC Cancer 2004 1.00
115 Identification of conserved amino acid residues in rat liver carnitine palmitoyltransferase I critical for malonyl-CoA inhibition. Mutation of methionine 593 abolishes malonyl-CoA inhibition. J Biol Chem 2002 0.99
116 Modular organization in the reductive evolution of protein-protein interaction networks. Genome Biol 2007 0.99
117 Scoring docking models with evolutionary information. Proteins 2005 0.98
118 Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis. J Mol Evol 2002 0.97
119 Mutated genes, pathways and processes in tumours. EMBO Rep 2010 0.97
120 Beta-propellers: associated functions and their role in human diseases. Curr Med Chem 2003 0.97
121 Structural model of a malonyl-CoA-binding site of carnitine octanoyltransferase and carnitine palmitoyltransferase I: mutational analysis of a malonyl-CoA affinity domain. J Biol Chem 2002 0.96
122 Novel domain combinations in proteins encoded by chimeric transcripts. Bioinformatics 2012 0.96
123 Co-evolution and co-adaptation in protein networks. FEBS Lett 2008 0.96
124 Protein interaction: same network, different hubs. Trends Genet 2003 0.96
125 Bioimage informatics: a new category in Bioinformatics. Bioinformatics 2012 0.96
126 NOTCH pathway inactivation promotes bladder cancer progression. J Clin Invest 2015 0.95
127 CAFASP3 in the spotlight of EVA. Proteins 2003 0.95
128 From cancer genomes to cancer models: bridging the gaps. EMBO Rep 2009 0.95
129 Long-range epigenetic silencing associates with deregulation of Ikaros targets in colorectal cancer cells. Mol Cancer Res 2011 0.95
130 Prioritization of pathogenic mutations in the protein kinase superfamily. BMC Genomics 2012 0.95
131 SPOC: a widely distributed domain associated with cancer, apoptosis and transcription. BMC Bioinformatics 2004 0.95
132 Synthetic biology: challenges ahead. Bioinformatics 2006 0.95
133 Cancer-associated mutations are preferentially distributed in protein kinase functional sites. Proteins 2009 0.94
134 Functional interaction between the Ser/Thr kinase PKL12 and N-acetylglucosamine kinase, a prominent enzyme implicated in the salvage pathway for GlcNAc recycling. J Biol Chem 2001 0.93
135 Genome-wide analysis of Pax8 binding provides new insights into thyroid functions. BMC Genomics 2012 0.93
136 Automated alphabet reduction for protein datasets. BMC Bioinformatics 2009 0.92
137 Protein refinement: a new challenge for CASP in its 10th anniversary. Bioinformatics 2005 0.92
138 The FEBS Letters SDA corpus: a collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community. FEBS Lett 2010 0.92
139 Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b. Mol Biol Evol 2013 0.92
140 TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res 2006 0.91
141 Translational disease interpretation with molecular networks. Genome Biol 2009 0.91
142 Death inducer obliterator protein 1 in the context of DNA regulation. Sequence analyses of distant homologues point to a novel functional role. FEBS J 2005 0.90
143 CheNER: chemical named entity recognizer. Bioinformatics 2013 0.90
144 MidA is a putative methyltransferase that is required for mitochondrial complex I function. J Cell Sci 2010 0.89
145 Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions. J Mol Biol 2009 0.88
146 Automatic ontology construction from the literature. Genome Inform 2002 0.88
147 FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Res 2013 0.87
148 Are promyelocytic leukaemia protein nuclear bodies a scaffold for caspase-2 programmed cell death? Trends Biochem Sci 2007 0.87
149 Prediction of protein interaction based on similarity of phylogenetic trees. Methods Mol Biol 2008 0.87
150 An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D. BMC Bioinformatics 2009 0.87
151 Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinformatics 2008 0.86
152 Characterization of pathogenic germline mutations in human protein kinases. BMC Bioinformatics 2011 0.86
153 EVAcon: a protein contact prediction evaluation service. Nucleic Acids Res 2005 0.86
154 Structural genomics meets computational biology. Bioinformatics 2006 0.85
155 Structural model of carnitine palmitoyltransferase I based on the carnitine acetyltransferase crystal. Biochem J 2004 0.85
156 Meta, Meta(N) and cyber servers. Bioinformatics 2003 0.84
157 Late-replicating CNVs as a source of new genes. Biol Open 2013 0.84
158 The Functional Genomics Network in the evolution of biological text mining over the past decade. N Biotechnol 2012 0.83
159 Chapter 14: Cancer genome analysis. PLoS Comput Biol 2012 0.83
160 Selection of organisms for the co-evolution-based study of protein interactions. BMC Bioinformatics 2011 0.83
161 Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. Front Physiol 2012 0.83
162 JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics 2011 0.82
163 Systemic approaches to biodegradation. FEMS Microbiol Rev 2008 0.82
164 An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinformatics 2006 0.82
165 Alzheimer's disease and cancer: current epidemiological evidence for a mutual protection. Neuroepidemiology 2014 0.82
166 Ras classical effectors: new tales from in silico complexes. Trends Biochem Sci 2009 0.81
167 Bioinformatics and cancer research: building bridges for translational research. Clin Transl Oncol 2008 0.81
168 Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology. PLoS One 2012 0.81
169 Molecular and structural analysis of the panallergen profilin B cell epitopes defined by monoclonal antibodies. Int Immunol 2002 0.81
170 Mirroring co-evolving trees in the light of their topologies. Bioinformatics 2012 0.80
171 Inference of functional relations in predicted protein networks with a machine learning approach. PLoS One 2010 0.80
172 Sumoylation regulates nuclear localization of repressor DREAM. Biochim Biophys Acta 2010 0.80
173 The REGIA database (RegiaDB): status, limitations and future developments. Comp Funct Genomics 2002 0.80
174 A framework for computational and experimental methods: identifying dimerization residues in CCR chemokine receptors. Bioinformatics 2005 0.80
175 Predicting functional residues in Plasmodium falciparum plasmepsins by combining sequence and structural analysis with molecular dynamics simulations. Proteins 2008 0.79
176 wKinMut: an integrated tool for the analysis and interpretation of mutations in human protein kinases. BMC Bioinformatics 2013 0.79
177 Bioinformatics: biology by other means. Bioinformatics 2002 0.79
178 Bioinformatics in the human interactome project. Bioinformatics 2006 0.78
179 HCAD, closing the gap between breakpoints and genes. Nucleic Acids Res 2005 0.78
180 Structural (betaalpha)8 TIM barrel model of 3-hydroxy-3-methylglutaryl-coenzyme A lyase. J Biol Chem 2003 0.78
181 An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility. PLoS One 2013 0.77
182 Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005). Bioinformatics 2006 0.77
183 Do you do text? Bioinformatics 2005 0.77
184 Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res 2008 0.77
185 FragKB: structural and literature annotation resource of conserved peptide fragments and residues. PLoS One 2010 0.77
186 YAdumper: extracting and translating large information volumes from relational databases to structured flat files. Bioinformatics 2004 0.77
187 Critical assessment of information extraction systems in biology. Comp Funct Genomics 2003 0.76
188 Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions. Mol Biosyst 2012 0.76
189 Correction to "Analyzing the first drafts of the human proteome". J Proteome Res 2015 0.76
190 The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-alpha-helical bundle domain. Eur J Biochem 2003 0.76
191 ISMB 2003 Text Mining SIG Meeting Report. Comp Funct Genomics 2003 0.75
192 Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold. Protein Sci 2004 0.75
193 A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins 2013 0.75
194 Predicting Protein Relationships to Human Pathways through a Relational Learning Approach Based on Simple Sequence Features. IEEE/ACM Trans Comput Biol Bioinform 2015 0.75
195 Precision medicine needs pioneering clinical bioinformaticians. Brief Bioinform 2017 0.75
196 Late-replicating CNVs as a source of new genes. Biol Open 2014 0.75
197 Bioinformatics in structural genomics. Bioinformatics 2002 0.75
198 Involvement of intramolecular interactions in the regulation of G protein-coupled receptor kinase 2. Mol Pharmacol 2003 0.75
199 The BioLink SIG Workshop at ISMB2004. Comp Funct Genomics 2005 0.75
200 ESF Programme on 'Integrated Approaches for Functional Genomics' Workshop on 'Modelling of Molecular Networks'. Comp Funct Genomics 2003 0.75