Alfonso Valéncia
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Alfonso Valéncia's AcademicInfluence.com Rankings
Alfonso Valénciacomputer-science Degrees
Computer Science
#4082
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#4298
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Information Systems
#14
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#16
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Data Science
#42
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#42
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Database
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Alfonso Valénciabiology Degrees
Biology
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Bioinformatics
#61
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#62
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Computational Biology
#95
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#95
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Computer Science Biology
Alfonso Valéncia's Degrees
- PhD Bioinformatics University of California, Santa Cruz
- Masters Computer Science University of California, Santa Cruz
- Bachelors Computer Science University of California, Santa Cruz
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(Suggest an Edit or Addition)Alfonso Valéncia's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- GENCODE: The reference human genome annotation for The ENCODE Project (2012) (4009)
- An integrated encyclopedia of DNA elements in the human genome (2012) (2080)
- International network of cancer genome projects (2010) (1839)
- Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia (2011) (1488)
- A User's Guide to the Encyclopedia of DNA Elements (ENCODE) (2011) (1467)
- Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia (2011) (993)
- IntAct: an open source molecular interaction database (2004) (967)
- The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease (2016) (885)
- Correlated mutations and residue contacts in proteins (1994) (853)
- An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. (1992) (823)
- Distinct DNA methylomes of newborns and centenarians (2012) (707)
- A hierarchical unsupervised growing neural network for clustering gene expression patterns (2001) (662)
- Non-coding recurrent mutations in chronic lymphocytic leukaemia (2015) (654)
- Overview of BioCreAtIvE: critical assessment of information extraction for biology (2005) (578)
- A gene network for navigating the literature (2004) (553)
- The ras protein family: evolutionary tree and role of conserved amino acids. (1991) (551)
- Emerging methods in protein co-evolution (2013) (543)
- Correlated mutations contain information about protein-protein interaction. (1997) (535)
- Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia (2012) (534)
- Similarity of phylogenetic trees as indicator of protein-protein interaction. (2001) (517)
- Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions (1999) (511)
- Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes (2014) (507)
- Reductive genome evolution in Buchnera aphidicola (2003) (498)
- Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells (2016) (475)
- A method to predict functional residues in proteins (1995) (414)
- Computational methods for the prediction of protein interactions. (2002) (384)
- Practical limits of function prediction (2000) (374)
- The Ras protein superfamily: Evolutionary tree and role of conserved amino acids (2012) (352)
- Prediction of human protein function from post-translational modifications and localization features. (2002) (333)
- BLUEPRINT to decode the epigenetic signature written in blood (2012) (320)
- Intrinsic errors in genome annotation. (2001) (319)
- An expanded evaluation of protein function prediction methods shows an improvement in accuracy (2016) (316)
- The CHEMDNER corpus of chemicals and drugs and its annotation principles (2015) (315)
- Overview of the protein-protein interaction annotation extraction task of BioCreative II (2008) (289)
- Pathway and network analysis of cancer genomes (2015) (285)
- Prediction of protein--protein interaction sites in heterocomplexes with neural networks. (2002) (282)
- EnrichNet: network-based gene set enrichment analysis (2012) (275)
- Whole-genome fingerprint of the DNA methylome during human B cell differentiation (2015) (265)
- POTRA: a conserved domain in the FtsQ family and a class of beta-barrel outer membrane proteins. (2003) (256)
- In silico two‐hybrid system for the selection of physically interacting protein pairs (2002) (254)
- Implementing the iHOP concept for navigation of biomedical literature (2005) (253)
- Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families (1998) (249)
- Linking genes to literature: text mining, information extraction, and retrieval applications for biology (2008) (248)
- The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. (2008) (242)
- Text-mining and information-retrieval services for molecular biology (2005) (235)
- Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy (2013) (235)
- Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells (2012) (233)
- Prediction of contact maps with neural networks and correlated mutations. (2001) (230)
- Improving contact predictions by the combination of correlated mutations and other sources of sequence information. (1997) (230)
- Heteromeric amino acid transporters: biochemistry, genetics, and physiology. (2001) (227)
- The implications of alternative splicing in the ENCODE protein complement (2007) (227)
- Alternative Splicing May Not Be the Key to Proteome Complexity. (2017) (226)
- Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (2020) (220)
- Automated genome sequence analysis and annotation (1999) (219)
- EVA: continuous automatic evaluation of protein structure prediction servers (2001) (214)
- From Structure to Function (2021) (214)
- BRICHOS: a conserved domain in proteins associated with dementia, respiratory distress and cancer. (2002) (212)
- Automatic methods for predicting functionally important residues. (2003) (211)
- Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge (2008) (211)
- Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes (1997) (209)
- 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 (2015) (204)
- MARVEL: a conserved domain involved in membrane apposition events. (2002) (203)
- Correlated Mutations and Residue Contacts (1994) (196)
- EVA: evaluation of protein structure prediction servers (2003) (192)
- APPRIS: annotation of principal and alternative splice isoforms (2012) (191)
- Information Retrieval and Text Mining Technologies for Chemistry. (2017) (189)
- CHEMDNER: The drugs and chemical names extraction challenge (2015) (187)
- Identification of amino acid residues crucial for chemokine receptor dimerization (2004) (186)
- Protein co-evolution, co-adaptation and interactions (2008) (186)
- Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia (2014) (185)
- CAFASP2: The second critical assessment of fully automated structure prediction methods (2001) (178)
- Effective use of sequence correlation and conservation in fold recognition. (1999) (177)
- Filamin-A regulates actin-dependent clustering of HIV receptors (2007) (177)
- High-confidence prediction of global interactomes based on genome-wide coevolutionary networks (2008) (174)
- Text mining for the biocuration workflow (2012) (172)
- Distinct structural elements of rab5 define its functional specificity. (1994) (169)
- Overview of the BioCreative VI chemical-protein interaction Track (2017) (167)
- Progress and challenges in predicting protein-protein interaction sites (2008) (167)
- Evaluation of BioCreAtIvE assessment of task 2 (2005) (164)
- Computational approaches to identify functional genetic variants in cancer genomes (2013) (161)
- Mutations in the DnaK chaperone affecting interaction with the DnaJ cochaperone. (1998) (160)
- Text-mining approaches in molecular biology and biomedicine. (2005) (159)
- iHOP web services (2007) (158)
- Eukaryotic translation elongation factor 1γ contains a glutathione transferase domain—Study of a diverse, ancient protein super family using motif search and structural modeling (1994) (153)
- Molecular Evidence for the Inverse Comorbidity between Central Nervous System Disorders and Cancers Detected by Transcriptomic Meta-analyses (2014) (148)
- Integrated Next-Generation Sequencing and Avatar Mouse Models for Personalized Cancer Treatment (2014) (148)
- A structural biology community assessment of AlphaFold2 applications (2021) (147)
- The Frame-Based Module of the SUISEKI Information Extraction System (2002) (146)
- Rab17, a novel small GTPase, is specific for epithelial cells and is induced during cell polarization (1993) (143)
- p23 and HSP20/α‐crystallin proteins define a conserved sequence domain present in other eukaryotic protein families (2002) (141)
- Correlation between the structure and biochemical activities of FtsA, an essential cell division protein of the actin family. (1994) (139)
- Protein interactions and ligand binding: From protein subfamilies to functional specificity (2010) (136)
- Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts (2012) (130)
- An Overview of BioCreative II.5 (2010) (130)
- Early bioinformatics: the birth of a discipline - a personal view (2003) (126)
- Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome. (2010) (123)
- Assessment of predictions submitted for the CASP6 comparative modeling category (2005) (123)
- Information extraction in molecular biology (2002) (121)
- Automatic annotation of protein function. (2005) (120)
- A conserved loop in the ATPase domain of the DnaK chaperone is essential for stable binding of GrpE (1994) (118)
- Overview of the BioCreative III Workshop (2011) (118)
- Towards the prediction of protein interaction partners using physical docking (2011) (118)
- The chaperone function of DnaK requires the coupling of ATPase activity with substrate binding through residue E171. (1994) (117)
- Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx (2016) (116)
- Interoperability with Moby 1.0 - It's better than sharing your toothbrush! (2008) (114)
- Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery. (2005) (113)
- Progress in predicting inter‐residue contacts of proteins with neural networks and correlated mutations (2001) (113)
- From residue coevolution to protein conformational ensembles and functional dynamics (2015) (110)
- Text mining for biology - the way forward: opinions from leading scientists (2008) (109)
- APPRIS 2017: principal isoforms for multiple gene sets (2017) (109)
- Cloning and subcellular localization of novel rab proteins reveals polarized and cell type-specific expression. (1994) (106)
- The BLUEPRINT Data Analysis Portal. (2016) (105)
- The pseudo GTPase CENP-M drives human kinetochore assembly (2014) (105)
- firestar—prediction of functionally important residues using structural templates and alignment reliability (2007) (104)
- GeneQuiz: A Workbench for Sequence Analysis (1994) (103)
- Identification of an RNA binding region within the N-terminal third of the influenza A virus nucleoprotein (1995) (101)
- Analyzing the First Drafts of the Human Proteome (2014) (100)
- Germline Mutations in FAN1 Cause Hereditary Colorectal Cancer by Impairing DNA Repair. (2015) (100)
- Analysis of biological processes and diseases using text mining approaches. (2010) (98)
- Challenging times for bioinformatics (1995) (98)
- Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks (2005) (98)
- Towards a detailed atlas of protein-protein interactions. (2013) (97)
- The small GTP-binding protein, Rhes, regulates signal transduction from G protein-coupled receptors (2004) (97)
- The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies (2015) (96)
- Introducing meta-services for biomedical information extraction (2008) (96)
- CASP6 assessment of contact prediction (2005) (96)
- Most highly expressed protein-coding genes have a single dominant isoform. (2015) (95)
- Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. (2000) (90)
- Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types (2016) (88)
- Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications (2011) (87)
- LifeTime and improving European healthcare through cell-based interceptive medicine (2020) (87)
- NOTCH pathway inactivation promotes bladder cancer progression. (2015) (86)
- Evaluation of annotation strategies using an entire genome sequence (2003) (86)
- Mining functional information associated with expression arrays (2001) (86)
- A module of the DnaJ heat shock proteins found in malaria parasites. (1992) (84)
- Defining functional distances over Gene Ontology (2008) (84)
- Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function (2012) (83)
- The organization of the microbial biodegradation network from a systems‐biology perspective (2003) (80)
- Can Bibliographic Pointers for Known Biological Data Be Found Automatically? Protein Interactions as a Case Study (2001) (80)
- Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis (2020) (80)
- Identification of Conserved Amino Acid Residues in Rat Liver Carnitine Palmitoyltransferase I Critical for Malonyl-CoA Inhibition (2003) (78)
- A new ATP-binding fold in actin, hexokinase and Hsc70. (1993) (78)
- Assessment of intramolecular contact predictions for CASP7 (2007) (77)
- Clustering of proximal sequence space for the identification of protein families (2002) (73)
- EUCLID: automatic classification of proteins in functional classes by their database annotations (1998) (73)
- Automatic ontology construction from the literature. (2002) (73)
- Phylogeny-independent detection of functional residues (2006) (72)
- Gas1 Is Related to the Glial Cell-derived Neurotrophic Factor Family Receptors α and Regulates Ret Signaling* (2006) (71)
- MetaRouter: bioinformatics for bioremediation (2004) (71)
- Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils (2018) (71)
- Proteomics studies confirm the presence of alternative protein isoforms on a large scale (2008) (70)
- Beta-propellers: associated functions and their role in human diseases. (2003) (69)
- Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level (2015) (69)
- A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer (2017) (68)
- TopoGSA: network topological gene set analysis (2010) (68)
- Predicting reliable regions in protein alignments from sequence profiles. (2003) (67)
- Comparison of algorithms for the detection of cancer drivers at subgene resolution (2017) (67)
- Systemic approaches to biodegradation. (2009) (65)
- The three-dimensional structure of an eukaryotic glutamine synthetase: functional implications of its oligomeric structure. (2006) (64)
- Classification of protein families and detection of the determinant residues with an improved self-organizing map (1997) (64)
- Assessment of copy number variation using the Illumina Infinium 1M SNP‐array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study (2011) (64)
- Assessment of predictions submitted for the CASP7 function prediction category. (2007) (63)
- Life cycles of successful genes. (2003) (63)
- Automatic Annotation for Biological Sequences by Etraction of Keywords from MEDLINE Abstracts: Development of a Prototype System (1997) (63)
- PDBe-KB: a community-driven resource for structural and functional annotations (2019) (63)
- Most Alternative Isoforms Are Not Functionally Important. (2017) (62)
- Pathway and network analysis of more than 2500 whole cancer genomes (2018) (62)
- Genome sequences and great expectations (2000) (62)
- FireDB—a database of functionally important residues from proteins of known structure (2006) (62)
- Overview of the chemical compound and drug name recognition ( CHEMDNER ) task (2013) (62)
- GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites. (1991) (61)
- Automatic annotation of protein function based on family identification (2003) (61)
- Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity (2018) (61)
- Automated Alphabet Reduction for Protein Datasets (2009) (60)
- Sequence-based feature prediction and annotation of proteins (2009) (59)
- Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b. (2013) (59)
- Extending pathways and processes using molecular interaction networks to analyse cancer genome data (2010) (58)
- MidA is a putative methyltransferase that is required for mitochondrial complex I function (2010) (57)
- PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data (2018) (55)
- Model of the ran-RCC1 interaction using biochemical and docking experiments. (1999) (55)
- Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia (2015) (55)
- A text‐mining perspective on the requirements for electronically annotated abstracts (2008) (55)
- firestar—advances in the prediction of functionally important residues (2011) (54)
- ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data (2012) (54)
- Prediction of protein-protein interactions from evolutionary information. (2003) (53)
- Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. (2002) (53)
- BioCreative-IV virtual issue (2014) (51)
- ACRATA: a novel electron transfer domain associated to apoptosis and cancer (2004) (51)
- Co‐evolution and co‐adaptation in protein networks (2008) (50)
- The success (or not) of HUGO nomenclature (2006) (50)
- Scoring docking models with evolutionary information (2005) (49)
- Overview of the CHEMDNER patents task (2015) (49)
- Phage‐display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA (2002) (48)
- Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: a structural model of its N-terminal domain. (2002) (47)
- The structural coverage of the human proteome before and after AlphaFold (2021) (47)
- Intronic CNVs and gene expression variation in human populations (2019) (47)
- Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation (2014) (46)
- The FEBS Letters/BioCreative II.5 experiment: making biological information accessible (2010) (46)
- Long-Range Epigenetic Silencing Associates with Deregulation of Ikaros Targets in Colorectal Cancer Cells (2011) (46)
- Structural Model of a Malonyl-CoA-binding Site of Carnitine Octanoyltransferase and Carnitine Palmitoyltransferase I (2002) (44)
- Bionemo: molecular information on biodegradation metabolism (2008) (43)
- Structural model of carnitine palmitoyltransferase I based on the carnitine acetyltransferase crystal. (2004) (43)
- MyMiner: a web application for computer-assisted biocuration and text annotation (2012) (43)
- CD8+ T Cells from Human Neonates Are Biased toward an Innate Immune Response. (2016) (42)
- Genome-wide analysis of Pax8 binding provides new insights into thyroid functions (2012) (42)
- Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity (2015) (41)
- Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs. (2016) (41)
- Analysis of the Cellular Functions of Escherichia coli Operons and Their Conservation in Bacillus subtilis (2002) (41)
- RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses (2013) (40)
- The environmental fate of organic pollutants through the global microbial metabolism (2007) (40)
- Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug- gene/protein relations (2021) (40)
- Extraction of human kinase mutations from literature, databases and genotyping studies (2009) (39)
- Critical Assessment of Information Extraction Systems in Biology (2003) (38)
- Novel domain combinations in proteins encoded by chimeric transcripts (2012) (37)
- Are binding residues conserved? (1998) (37)
- Functional Classes in the Three Domains of Life (1999) (37)
- Mutated genes, pathways and processes in tumours (2010) (37)
- From cancer genomes to cancer models: bridging the gaps (2009) (37)
- Predicted residue–residue contacts can help the scoring of 3D models (2010) (36)
- LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes (2017) (36)
- Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology (1996) (36)
- Transcriptional dissection of pancreatic tumors engrafted in mice (2014) (35)
- Cancer‐associated mutations are preferentially distributed in protein kinase functional sites (2009) (35)
- How to link ontologies and protein–protein interactions to literature: text-mining approaches and the BioCreative experience (2012) (35)
- EcID. A database for the inference of functional interactions in E. coli (2008) (35)
- PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction (2009) (33)
- Computational comparisons of model genomes. (1996) (33)
- Precision medicine needs pioneering clinical bioinformaticians (2019) (33)
- ChiTaRS 2.1—an improved database of the chimeric transcripts and RNA-seq data with novel sense–antisense chimeric RNA transcripts (2014) (33)
- Association Between Germline Mutations in BRF1, a Subunit of the RNA Polymerase III Transcription Complex, and Hereditary Colorectal Cancer. (2018) (33)
- SPOC: A widely distributed domain associated with cancer, apoptosis and transcription (2004) (33)
- Identification of a Mammalian Homologue of the Fungal Tom70 Mitochondrial Precursor Protein Import Receptor as a Thyroid Mitochondrial Precursor Protein Import Receptor as a Thyroid Hormone‐Regulated Gene in Specific Brain Regions (1999) (33)
- Evaluation of chemical and gene/protein entity recognition systems at BioCreative V.5: the CEMP and GPRO patents tracks (2017) (32)
- Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone (2016) (32)
- Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions. (2009) (32)
- Challenges for Intelligent Systems in Biology (2001) (32)
- Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein–protein interfaces (2015) (32)
- Domain definition and target classification for CASP6 (2005) (32)
- Death inducer obliterator protein 1 in the context of DNA regulation (2005) (31)
- Prediction of protein interaction based on similarity of phylogenetic trees. (2008) (31)
- Combined burden and functional impact tests for cancer driver discovery using DriverPower (2020) (31)
- Protein interaction: same network, different hubs. (2003) (31)
- Bioimage informatics: a new category in Bioinformatics (2012) (31)
- TreeDet: a web server to explore sequence space (2006) (30)
- Extracting Information Automatically From Biological Literature (2001) (30)
- ChiPPI: a novel method for mapping chimeric protein–protein interactions uncovers selection principles of protein fusion events in cancer (2017) (30)
- Modular organization in the reductive evolution of protein-protein interaction networks (2007) (30)
- Determination and validation of principal gene products (2008) (29)
- The Evolutionary Fate of Alternatively Spliced Homologous Exons after Gene Duplication (2015) (29)
- CAFASP3 in the spotlight of EVA (2003) (29)
- Functional Interaction between the Ser/Thr Kinase PKL12 and N-Acetylglucosamine Kinase, a Prominent Enzyme Implicated in the Salvage Pathway for GlcNAc Recycling* (2002) (29)
- A graphical interface for correlated mutations and other protein structure prediction methods (1997) (29)
- A sentence sliding window approach to extract protein annotations from biomedical articles (2005) (29)
- Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics (2012) (28)
- Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals (2015) (28)
- TSEMA: interactive prediction of protein pairings between interacting families (2006) (28)
- Molecular and structural analysis of the panallergen profilin B cell epitopes defined by monoclonal antibodies. (2002) (27)
- SQUARE-determining reliable regions in sequence alignments (2004) (26)
- Elucidating the molecular basis of MSH2‐deficient tumors by combined germline and somatic analysis (2017) (26)
- Computational space reduction and parallelization of a new clustering approach for large groups of sequences (1998) (26)
- Search and retrieve (2002) (26)
- Sumoylation regulates nuclear localization of repressor DREAM. (2011) (26)
- Prioritization of pathogenic mutations in the protein kinase superfamily (2012) (25)
- Synthetic Biology: challenges ahead (2006) (25)
- Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function (1997) (25)
- Are promyelocytic leukaemia protein nuclear bodies a scaffold for caspase-2 programmed cell death? (2007) (25)
- Detection of significant protein coevolution (2015) (24)
- Nucleotide sequence and analysis of the centromeric region of yeast chromosome IX (1995) (24)
- Translational disease interpretation with molecular networks (2009) (24)
- The potential clinical impact of the release of two drafts of the human proteome (2015) (24)
- APPRIS WebServer and WebServices (2015) (23)
- BioCreative-2012 Virtual Issue (2012) (23)
- EVAcon: a protein contact prediction evaluation service (2005) (23)
- Predicting functional residues in Plasmodium falciparum plasmepsins by combining sequence and structural analysis with molecular dynamics simulations (2008) (23)
- Shaping of Drosophila Alcohol Dehydrogenase Through Evolution: Relationship with Enzyme Functionality (1998) (23)
- CARGO: a web portal to integrate customized biological information (2007) (23)
- Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention (2019) (23)
- Germline mutations in the spindle assembly checkpoint genes BUB1 and BUB3 are infrequent in familial colorectal cancer and polyposis (2018) (23)
- Genequiz II: Automatic Function Assignment For Genome Sequence Analysis (1996) (23)
- Enhancing the prediction of protein pairings between interacting families using orthology information (2008) (22)
- An analysis of the Sargasso Sea resource and the consequences for database composition (2006) (22)
- The Ras protein superfamily: Evolutionary tree and role of conserved amino acids (2012) (22)
- Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas (2021) (22)
- CheNER: chemical named entity recognizer (2013) (22)
- JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures (2012) (22)
- Machine Reading of Biomedical Texts about Alzheimer's Disease (2013) (21)
- Protein Refinement: A New Challenge For Casp In Its 10th Anniversary (2005) (21)
- Automatic identification of informative regions with epigenomic changes associated to hematopoiesis (2017) (20)
- Text mining and protein annotations: the construction and use of protein description sentences. (2006) (20)
- Unveiling new disease, pathway, and gene associations via multi-scale neural network (2019) (19)
- Empirical limits for template‐based protein structure prediction: the CASP5 example (2005) (19)
- A neural network approach to evaluate fold recognition results (2003) (19)
- Characterization of pathogenic germline mutations in human Protein Kinases (2011) (19)
- Chromatin Regulators as a Guide for Cancer Treatment Choice (2016) (18)
- Somatic Embryonic FGFR2 Mutations in Keratinocytic Epidermal Nevi. (2016) (18)
- FireDB: a compendium of biological and pharmacologically relevant ligands (2013) (18)
- Modern Genome Annotation: The Biosapiens Network (2008) (18)
- Late-replicating CNVs as a source of new genes (2013) (17)
- The Functional Genomics Network in the evolution of biological text mining over the past decade. (2013) (16)
- Benchmarking biomedical text mining web servers at BioCreative V.5: the technical Interoperability and Performance of annotation Servers - TIPS track (2017) (16)
- Bioinformatics in the human interactome project (2006) (16)
- A user guide for the online exploration and visualization of PCAWG data (2020) (16)
- The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge (2016) (16)
- Creating Reference Datasets for Systems Biology Applications Using Text Mining (2009) (15)
- Inference of Functional Relations in Predicted Protein Networks with a Machine Learning Approach (2010) (15)
- Structural (βα)8 TIM Barrel Model of 3-Hydroxy-3-methylglutaryl-Coenzyme A Lyase* (2003) (15)
- Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era (2020) (15)
- Bioinformatics and cancer research: building bridges for translational research (2008) (15)
- Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data? (2002) (14)
- A platform for integrating threading results with protein family analyses (1999) (14)
- Interpretation of the Consequences of Mutations in Protein Kinases: Combined Use of Bioinformatics and Text Mining (2012) (14)
- Chapter 14: Cancer Genome Analysis (2012) (14)
- Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families (1997) (14)
- Selection of organisms for the co-evolution-based study of protein interactions (2011) (14)
- An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D (2009) (13)
- A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors (2005) (13)
- The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts (2017) (12)
- Prediction of Functional Sites in Proteins by Evolutionary Methods (2004) (12)
- CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets (2017) (12)
- The shrinking human protein coding complement: are there now fewer than 20,000 genes? (2013) (12)
- Three-dimensional connectivity and chromatin environment mediate the activation efficiency of mammalian DNA replication origins (2019) (11)
- The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-alpha-helical bundle domain. (2003) (11)
- Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology (2012) (11)
- KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily (2016) (11)
- An Epistatic Interaction between the PAX8 and STK17B Genes in Papillary Thyroid Cancer Susceptibility (2013) (11)
- MIB2 variants altering NOTCH signalling result in left ventricle hypertrabeculation/non-compaction and are associated with Ménétrier-like gastropathy (2016) (11)
- Multiple Sequence Alignments as Tools for Protein Structure and Function Prediction (2003) (10)
- FUN-L: gene prioritization for RNAi screens (2015) (10)
- The BioCreative V.5 evaluation workshop: tasks, organization, sessions and topics (2017) (10)
- 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 (2010) (10)
- On the organization of bioinformatics core services in biology-based research institutes (2011) (9)
- Colorectal cancer classification based on gene expression is not associated with FOLFIRI response (2014) (9)
- Germline variation in the oxidative DNA repair genes NUDT1 and OGG1 is not associated with hereditary colorectal cancer or polyposis (2018) (9)
- Analysis working group of the International Cancer Genome Consortium (2015) (9)
- HCAD, closing the gap between breakpoints and genes (2004) (9)
- A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders (2015) (9)
- Ras classical effectors: new tales from in silico complexes. (2009) (9)
- wKinMut‐2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases (2016) (9)
- Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells (2021) (9)
- MAX mutant small-cell lung cancers exhibit impaired activities of MGA-dependent noncanonical polycomb repressive complex (2021) (8)
- DNA methylation profiling of hepatosplenic T-cell lymphoma (2018) (8)
- Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions. (2013) (8)
- OGER: OntoGene’s Entity Recogniser in the BeCalm TIPS Task (2017) (8)
- The GENCODE human gene set (2010) (8)
- Late-replicating CNVs as a source of new genes (2013) (8)
- Do you do text? (2005) (8)
- SOA-Based Integration of Text Mining Services (2009) (8)
- Bioinformatics: Biology by other means (2002) (8)
- Meta, Metan and Cyber Servers (2003) (7)
- The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions (2010) (7)
- Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine (2021) (7)
- Protein-protein interactions: analysis and prediction (2009) (7)
- Increasing the Impact of Bioinformatics (2005) (7)
- STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells (2021) (7)
- FragKB: Structural and Literature Annotation Resource of Conserved Peptide Fragments and Residues (2010) (7)
- wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases (2013) (7)
- vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer (2019) (7)
- Involvement of intramolecular interactions in the regulation of G protein-coupled receptor kinase 2. (2003) (6)
- Searching for the chromatin determinants of human hematopoiesis (2016) (6)
- Computational Methods to Predict Protein Interaction Partners (2008) (6)
- Modern Genome Annotation (2010) (6)
- Knowledge Acquisition from the Biomedical Literature (2007) (6)
- Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm (2019) (6)
- 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2011, April 6-8, 2011, Salamanca, Spain (2011) (6)
- Text mining in genomics and systems biology (2008) (6)
- Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories (2005) (5)
- Corrigendum to “Automatic Methods for Predicting Functionally Important Residues” [J. Mol. Biol. 326 (2003) 1289–1302] (2009) (5)
- Structural genomics meets computational biology (2006) (5)
- Assessment of predictions submitted for the CASP7 function prediction category (2007) (5)
- Chromatin network markers of leukemia (2020) (5)
- Bioinformatics in structural genomics - Editorial (2002) (5)
- Online resources for PCAWG data exploration, visualization, and discovery (2017) (4)
- Erratum to: The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies (2016) (4)
- iHOP Web Services Family (2010) (4)
- Mirroring co-evolving trees in the light of their topologies (2011) (4)
- Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools (2020) (4)
- Origin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus-Deinococcus group (2001) (4)
- Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005) (2006) (4)
- Structural (betaalpha)8 TIM barrel model of 3-hydroxy-3-methylglutaryl-coenzyme A lyase. (2003) (4)
- Integrating Prediction of Structure, Function, and Interactions (2008) (4)
- Gene order in Prokaryotes: conservation and implications (2004) (4)
- Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps (2005) (3)
- DrugProt corpus: Biocreative VII Track 1 - Text mining drug and chemical-protein interactions (2021) (3)
- MMR: a tool for read multi-mapper resolution (2015) (3)
- ISMB 2003 Text Mining SIG Meeting Report (2003) (3)
- On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models (2019) (3)
- Comparative analysis of neutrophil and monocyte epigenomes (2017) (3)
- Automatic Classification of Protein Functions From the Literature (2003) (3)
- The consequences of variant calling decisions in secondary analyses of cancer genomics data (2020) (3)
- Erratum to: The UBC-40 Urothelial Bladder Cancer Cell Line Index: a genomic resource for functional studies (2015) (3)
- Evolution of the Ras Superfamily of GTPases (2014) (3)
- A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms (2014) (3)
- Unveiling the molecular basis of disease co-occurrence: towards personalized comorbidity profiles (2018) (3)
- The Functional Composition of Living Machines as a Design Principle for Artificial Organisms (1995) (3)
- Assessing the Correlation between Contextual Patterns and Biological Entity Tagging (2004) (3)
- ExTRI: Extraction of transcription regulation interactions from literature (2021) (3)
- Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region (2012) (2)
- New Leadership for Bioinformatics (2004) (2)
- Annotation Process, Guidelines and Text Corpus of Small Non-Coding RNA Molecules: the MiNCor for MicroRNA Annotations (2016) (2)
- Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis (2014) (2)
- Predicting Protein Relationships to Human Pathways through a Relational Learning Approach Based on Simple Sequence Features (2014) (2)
- Computational methods for the prediction of protein interaction partners (2004) (2)
- Artemia Mitochondrial DNA (1989) (2)
- Sequence analysis Alternative splicing and co-option of transposable elements : the case of TMPO / LAP 2 a and ZNF 451 in mammals (2015) (2)
- Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology (2009) (2)
- iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology (2008) (2)
- Original article Text mining for the biocuration workflow (2012) (2)
- Introduction BIOSAPIENS: A European Network of Excellence to develop genome annotation resources (2008) (2)
- Correction to "Analyzing the first drafts of the human proteome". (2015) (2)
- A Case Study of iHOP and Other Language Processing Systems (2009) (2)
- Patient Dossier: Healthcare queries over distributed resources (2019) (2)
- 6.04 – Text Mining (2014) (2)
- A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG) (2019) (2)
- The REGIA Database (RegiaDB): Status, Limitations and Future Developments (2002) (2)
- Bioinformatic Software Developments in Spain (2010) (1)
- GTPase domains of ras p 21 oncogene protein and elongation factor (1)
- YAdumper: extracting and translating large information volumes from relational databases to structured flat files (2004) (1)
- Bioinformatics and Computational Biology at the crossroads of post-genomic technology (2002) (1)
- STAG2 loss-of-function affects short-range genomic contacts and modulates urothelial differentiation in bladder cancer cells (2020) (1)
- Abstract SY10-02: Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants (2017) (1)
- Biological Knowledge Extraction (2009) (1)
- SBARS: fast creation of dotplots for DNA sequences on different scales using GA,GC-content (2014) (1)
- Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold. (2004) (1)
- Molecular interactions: Learning from protein complexes (2006) (1)
- associated with human cancer The dynamic DNA methylomes of double-stranded DNA viruses Material Supplemental (2009) (1)
- TiFoSi: an Efficient Tool for Mechanobiology Simulations of Epithelia (2020) (1)
- Intronic CNVs cause gene expression variation in human populations (2018) (1)
- New EMBO Member's Review Protein co-evolution, co-adaptation and interactions (2008) (1)
- Correction: An Epistatic Interaction between the PAX8 and STK17B Genes in Papillary Thyroid Cancer Susceptibility (2013) (1)
- Whole-genome sequencing identifies recurrent mutations in chronic lymphocyticleukaemia (2011) (1)
- European Mathematical Genetics Meeting, Munich, Germany, 14th–15th May 2009 (2009) (1)
- XML Databases, are Ready for Bioinformatics? (2004) (1)
- Bioinformatics Analysis of Pancreas Cancer Genome in High-Throughput Genomic Technologies (2014) (1)
- High-throughput , interoperability and benchmarking of text-mining with BeCalm biomedical metaserver (2017) (1)
- The impact of European bioinformatics (2001) (1)
- Software patents in Bioinformatics (2006) (1)
- DIDO3 acts at the interface of RNAPII transcription and chromatin structure regulation (2021) (1)
- Sequence analysis of aMolluscum contagiosum virus DNA region which includes the gene encoding protein kinase 2 and other genes with unique organization (2004) (1)
- Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: A novel α+β fold (2004) (1)
- An update from the Bioinformatics Editors (2005) (0)
- The promyelocytic Leukaemia protein nuclear bodies: a proposed novel scaffold for caspase-2 activation (2007) (0)
- CORNET: a server for the prediction of residue contacts in proteins (2004) (0)
- CHEMDNER challenge overview paper with summary tables of systems performance , methods , features and used resources : • (2014) (0)
- Epigenomic and functional dynamics of human bone marrow myeloid differentiation to mature blood neutrophils (2018) (0)
- Additional file 1 Chromatin assortativity : Integrating epigenomic data and 3 D genomic structure (2016) (0)
- Protein Databases: Operations, Possibilities and Challenges (2014) (0)
- OP-CBIO181009 2518..2520 (2019) (0)
- BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications (2018) (0)
- Education Chapter 14 : Cancer Genome Analysis (2012) (0)
- The landscape of interactions between cancer polygenic risk scores and somatic alterations in cancer cells (2020) (0)
- Systems for the analyses of potential cancer target gene-lists (2006) (0)
- Intercellular Signaling in Cardiovascular Development and Disease Group, Centro Nacional de Investigaciones Cardiovasculares, (2015) (0)
- Integrated genomics and avatar mouse models for personalized cancer treatment. (2013) (0)
- Protein Interactions Extracted from Genomes and Papers (2007) (0)
- chimeric RNA transcripts Chimeras taking shape : Potential functions of proteins encoded by P < P (2012) (0)
- Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004) (2004) (0)
- ESF Programme on ‘Integrated Approaches for Functional Genomics’ Workshop on ‘Modelling of Molecular Networks’ (2003) (0)
- chimeric RNA transcripts Chimeras taking shape : Potential functions of proteins encoded by Material Supplemental (2012) (0)
- The Biodegradation Network, a New Scenario for Computational Systems Biology Research (2004) (0)
- Pitfalls of protein sequence analysis Commentary (2001) (0)
- 1 Data and Text-Mining CheNER : Chemical Named Entity Recognizer (2013) (0)
- Abstract LB-155: Epigenetic profiling of chemotherapy sensitivity (2015) (0)
- Abstract 2205: Integrated next generation sequencing and patient-derived xenografts to personalized cancer treatment. (2013) (0)
- Extracting information automatically from biological literature A presentation for the ESF workshop 'Proteomics: Focus on Protein Interactions' (2001) (0)
- Conservation of co-evolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone (2016) (0)
- The BioLink SIG workshop at ISMB2004: Conference Editorials - Special Interest Group on Text Data Mining, in association with ISMB 2004, Glasgow, UK; (2005) (0)
- Data and text mining Do you do text ? (2005) (0)
- FireDB and firestar - beyond functional annotation (2013) (0)
- Gene expression variability and the prediction of clinical outcome in Chronic Lymphocytic Leukemia (2014) (0)
- Thechaperone function ofDnaKrequires thecoupling ofATPaseactivity withsubstrate binding through residue E171 (1994) (0)
- Mining Information on Protein Function from Text (2008) (0)
- TheUBC-40UrothelialBladderCancercellline index:agenomicresourceforfunctionalstudies (2015) (0)
- Widespread population variability of intron size in evolutionary old genes: implications for gene expression variability (2017) (0)
- Epigenomic co-localization and co-evolution reveal a key role for 5hmC as a communication hub in the chromatin network of ESCs (2015) (0)
- The BioLink SIG Workshop at ISMB2004 (2005) (0)
- Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013 (2015) (0)
- Characterization of the DNA Methylome during Human B-Cell Differentiation (2014) (0)
- Early evolution of RNAbinding domains (2002) (0)
- Bioinformatics Approaches to the Detection of Protein Interaction 5.-andrade M A, Valencia a (1997) Automatic Annotation for Biological Sequences by Extraction of Keywords from Medline Abstracts. Development of a Prototype System. Ismb 5, 25-32 (0)
- Abstract LB-129: Epigenetic regulators to predict docetaxel sensitivity; a guide for treatment choice (2016) (0)
- Cell Systems Tool The BLUEPRINT Data Analysis Portal (0)
- Functional analysis and co-evolutionary model of chromatin and DNA methylation networks in embryonic stem cells (2014) (0)
- Solution structure of the Hypothetical protein mth677 from Methanothermobacter Thermautotrophicus (2004) (0)
- Prioritization of pathogenic mutations in the protein kinase superfamily (2012) (0)
- Chromatin assortativity: Integrating epigenomic data and 3D genomic structure (2016) (0)
- Genome analysis Determination and validation of principal gene products (2007) (0)
- Cell Reports Resource CD 8 + T Cells from Human Neonates Are Biased toward an Innate Immune Response (2016) (0)
- leukemia major molecular and clinical subdivision in chronic lymphocytic Transcriptome characterization by RNA sequencing identifies a Material (2014) (0)
- Integrated next-generation sequencing and patient-derived xenografts to personalized cancer treatment. (2012) (0)
- National strategy on endocrine disruptors. (1996) (0)
- Protein Function Prediction : Application of a Propositional Rules Learning System to a set of Human Protein Sequences (2003) (0)
- Abstract A22: PanDrugsDB: Identifying druggable genetic dependencies for personalized cancer therapy (2015) (0)
- Editorial (2007) (0)
- Algorithmic complexity in computational biology: basics, challenges and limitations (2018) (0)
- Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997 (1997) (0)
- Resource Epigenomic Co-localizatio n and Co-evolution Reveal a Key Role for 5 hmC as a Communication Hub in the Chromatin Network of ESCs Graphical (2016) (0)
- SIGIR 2003 workshop on text analysis and search for bioinformatics (2004) (0)
- TreeDet: analysisng protein functional specificity (2006) (0)
- ECCB2020: the 19th European Conference on Computational Biology. (2020) (0)
- Conservation of co-evolving protein interfaces bridges 1 prokaryote-eukaryote homologies in the twilight zone 2 3 4 (2016) (0)
- Alternative Splicing in the ENCODE Protein complement (2008) (0)
- PathExpand: Extending biological pathways using molecular interaction networks (2011) (0)
- Original Text mining for the biocuration workflow (2012) (0)
- Bioinformatic Analyses of the Dio Family of Proteins (2004) (0)
- Pointers to understand cancer components: developing a system knowledge portal (2006) (0)
- Functional gene groups are concentrated within chromosomes , among chromosomes and in the nuclear space of the human genome (2013) (0)
- An insight into the century timescale evolution of transposable element populations from the sequencing of the recent allotetraploid oilseed rape ( Brassica napus ) (2013) (0)
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