Lista de obras - Predrag Radivojac - Dominio Público Uruguay

A bayesian approach to protein inference problem in shotgun proteomics

artículo científico publicado en 2009

A computational approach toward label-free protein quantification using predicted peptide detectability.

artículo científico publicado en 2006

A large-scale evaluation of computational protein function prediction

artículo científico publicado en 2013

A machine learning approach to predicting peptide fragmentation spectra.

artículo científico publicado en 2006

A maximum-likelihood approach to absolute protein quantification in mass spectrometry

scholarly article published 2015

A new class of metrics for learning on real-valued and structured data

artículo científico publicado en 2019

Advancement in protein inference from shotgun proteomics using peptide detectability

artículo científico publicado en 2007

Allosteric post-translational modification codes

artículo científico publicado en 2012

Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

artículo científico publicado en 2006

An examination of citation-based impact of the computational biology conferences

scientific article published on 04 February 2020

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

artículo científico publicado en 2016

An integrated approach to inferring gene-disease associations in humans

artículo científico publicado en 2008

An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors ⬇️

artículo científico publicado el 26 de julio de 2012

Analysis of AML Genes in Dysregulated Molecular Networks ⬇️

artículo científico publicado el 1 de marzo de 2009

Analysis of AML genes in dysregulated molecular networks

artículo científico publicado en 2009

Analysis of molecular recognition features (MoRFs)

artículo científico publicado en 2006

Analysis of protein function and its prediction from amino acid sequence ⬇️

artículo científico publicado el 19 de abril de 2011

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

artículo científico publicado en 2016

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

artículo científico publicado en 2019

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

scientific article published on 17 August 2019

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

scientific article published on 23 August 2019

Assessment of methods for predicting the effects of PTEN and TPMT protein variants

scientific article published on 03 July 2019

Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge

artículo científico publicado en 2019

Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016

artículo científico publicado en 2019

Automated inference of molecular mechanisms of disease from amino acid substitutions.

artículo científico publicado en 2009

Bioinformatics curriculum guidelines: toward a definition of core competencies

artículo científico publicado en 2014

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

scientific article published on 03 September 2019

COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION.

artículo científico publicado en 2017

Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions

artículo científico publicado en 2012

Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition

scientific article published on 01 May 2006

Characterization of molecular recognition features, MoRFs, and their binding partners

artículo científico publicado en 2007

Classification and knowledge discovery in protein databases.

artículo científico publicado en 2004

Classification in biological networks with hypergraphlet kernels

artículo científico publicado en 2020

Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics ⬇️

artículo científico publicado el 1 de agosto de 2010

Community-Wide Evaluation of Computational Function Prediction

artículo científico

Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity

artículo científico publicado en 2011

Computational approaches to protein inference in shotgun proteomics ⬇️

artículo científico publicado el 5 de noviembre de 2012

Computational methods for identification of functional residues in protein structures

artículo científico

DisProt: a database of protein disorder

artículo científico publicado en 2004

Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies.

artículo científico publicado en 2018

Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies

scientific article published on 01 January 2019

Estimating the class prior and posterior from noisy positives and unlabeled data ⬇️

artículo científico publicado en 2016

Evaluating purifying selection in the mitochondrial DNA of various mammalian species

artículo científico publicado en 2013

Evaluation of features for catalytic residue prediction in novel folds

artículo científico publicado en 2006

Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

artículo científico publicado en 2016

Exploiting heterogeneous sequence properties improves prediction of protein disorder.

artículo científico publicado en 2005

Extending the coverage of spectral libraries: A neighbor-based approach to predicting intensities of peptide fragmentation spectra ⬇️

artículo científico publicado el 4 de febrero de 2013

Fast and accurate identification of semi-tryptic peptides in shotgun proteomics

artículo científico publicado en 2007

From protein-disease associations to disease informatics

scientific article published on May 2008

Gain and loss of phosphorylation sites in human cancer

artículo científico publicado en 2008

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential

artículo científico publicado en 2014

Graphlet kernels for prediction of functional residues in protein structures

artículo científico publicado en 2010

HIP2: an online database of human plasma proteins from healthy individuals

artículo científico publicado en 2008

ISCB computational biology Wikipedia competition

artículo científico publicado en 2013

ISMB 2018 proceedings.

artículo científico publicado en 2018

ISMB/ECCB 2019 Proceedings

artículo científico publicado en 2019

Identification of N-terminal protein processing sites by chemical labeling mass spectrometry

scientific article published on 01 June 2019

Identification, analysis, and prediction of protein ubiquitination sites

artículo científico publicado en 2010

Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics

artículo científico publicado en 2016

Improved amino acid flexibility parameters ⬇️

artículo científico publicado el 1 de mayo de 2003

Improving sequence alignments for intrinsically disordered proteins

artículo científico publicado en 2002

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions

artículo científico publicado en 2010

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

artículo científico publicado en 2020

Influence of sequence changes and environment on intrinsically disordered proteins.

artículo científico publicado en 2009

Information-theoretic evaluation of predicted ontological annotations ⬇️

artículo científico publicado el 1 de julio de 2013

Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides

artículo científico publicado en 2014

Intrinsic disorder and functional proteomics

artículo científico publicado en 2006

Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes

artículo científico publicado en 2008

Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes

artículo científico publicado en 2006

Investigation of VUV photodissociation propensities using peptide libraries ⬇️

artículo científico publicado el 1 de diciembre de 2011

Length-dependent prediction of protein intrinsic disorder.

artículo científico publicado en 2006

Loss of post-translational modification sites in disease

artículo científico publicado en 2010

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges

artículo científico publicado en 2017

MutDB: update on development of tools for the biochemical analysis of genetic variation

artículo científico publicado en 2007

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing

artículo científico publicado en 2014

New Drosophila long-term memory genes revealed by assessing computational function prediction methods

article

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

article

New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics

scientific article published on 01 December 2020

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction ⬇️

artículo científico publicado el 22 de diciembre de 2010

On the split personality of penultimate proline

artículo científico publicado en 2014

Optimizing long intrinsic disorder predictors with protein evolutionary information

artículo científico publicado en 2005

Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability

artículo científico publicado en 2020

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome

scientific article published on 14 June 2019

Penultimate Proline in Neuropeptides

scientific article published on 29 July 2015

Physicochemical sequence characteristics that influence S-palmitoylation propensity

artículo científico publicado en 2016

Position of Proline Mediates the Reactivity of S-Palmitoylation

artículo científico publicado en 2015

Post-translational modifications induce significant yet not extreme changes to protein structure

artículo científico publicado en 2012

Precision Medicine: Improving health through high-resolution analysis of personal data

scientific article published on 01 January 2019

Predicting intrinsic disorder from amino acid sequence ⬇️

artículo científico publicado el 1 de enero de 2003

Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

artículo científico publicado en 2019

Prediction of boundaries between intrinsically ordered and disordered protein regions

scientific article published on 01 January 2003

Prediction of functional regulatory SNPs in monogenic and complex disease

scientific article published on 09 September 2011

Prediction of intrinsic disorder and its use in functional proteomics

artículo científico publicado en 2007

Protein flexibility and intrinsic disorder

artículo científico publicado en 2004

Protein function in precision medicine: deep understanding with machine learning

artículo científico publicado en 2016

Protein identification problem from a Bayesian point of view

artículo científico publicado en 2012

Proteomic evidence for in-frame and out-of-frame alternatively spliced isoforms in human and mouse

artículo científico publicado en 2015

Quantitative Measurement of Phosphoproteome Response to Osmotic Stress in Arabidopsis Based on Library-Assisted eXtracted Ion Chromatogram (LAXIC) ⬇️

artículo científico publicado el 8 de mayo de 2013

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

artículo científico publicado en 2016

Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants

artículo científico publicado en 2016

Reproductive Longevity Predicts Mutation Rates in Primates

artículo científico publicado en 2018

Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease

artículo científico publicado en 2010

Target site specificity and in vivo complexity of the mammalian arginylome

artículo científico publicado en 2018

Ten simple rules for a community computational challenge

artículo científico publicado en 2015

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals ⬇️

artículo científico publicado el 9 de junio de 2011

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

scientific article published on 19 November 2019

The Importance of Peptide Detectability for Protein Identification, Quantification, and Experiment Design in MS/MS Proteomics ⬇️

artículo científico publicado el 10 de noviembre de 2010

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease

artículo científico publicado en 2016

The automated function prediction SIG looks back at 2013 and prepares for 2014.

artículo científico publicado en 2014

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective

artículo científico publicado en 2014

The importance of intrinsic disorder for protein phosphorylation

artículo científico publicado en 2004

The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction

artículo científico publicado en 2020

The sequencing and interpretation of the genome obtained from a Serbian individual

scientific article published in PLoS ONE

The structural and functional signatures of proteins that undergo multiple events of post-translational modification

artículo científico publicado en 2014

Training the next generation of quantitative biologists in the era of big data

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments

artículo científico publicado en 2006

Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

artículo científico publicado en 2008

Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map.

artículo científico publicado en 2006

Vector quantization kernels for the classification of protein sequences and structures

artículo científico

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

artículo científico publicado en 2017

XLSearch: a Probabilistic Database Search Algorithm for Identifying Cross-Linked Peptides

artículo científico publicado en 2016

Lista de obras de Predrag Radivojac

A bayesian approach to protein inference problem in shotgun proteomics

A computational approach toward label-free protein quantification using predicted peptide detectability.

A large-scale evaluation of computational protein function prediction

A machine learning approach to predicting peptide fragmentation spectra.

A maximum-likelihood approach to absolute protein quantification in mass spectrometry

A new class of metrics for learning on real-valued and structured data

Advancement in protein inference from shotgun proteomics using peptide detectability

Allosteric post-translational modification codes

Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

An examination of citation-based impact of the computational biology conferences

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

An integrated approach to inferring gene-disease associations in humans

An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors ⬇️

Analysis of AML Genes in Dysregulated Molecular Networks ⬇️

Analysis of AML genes in dysregulated molecular networks

Analysis of molecular recognition features (MoRFs)

Analysis of protein function and its prediction from amino acid sequence ⬇️

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

Assessment of methods for predicting the effects of PTEN and TPMT protein variants

Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge

Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016

Automated inference of molecular mechanisms of disease from amino acid substitutions.

Bioinformatics curriculum guidelines: toward a definition of core competencies

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION.

Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions

Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition

Characterization of molecular recognition features, MoRFs, and their binding partners

Classification and knowledge discovery in protein databases.

Classification in biological networks with hypergraphlet kernels

Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics ⬇️

Community-Wide Evaluation of Computational Function Prediction

Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity

Computational approaches to protein inference in shotgun proteomics ⬇️

Computational methods for identification of functional residues in protein structures

DisProt: a database of protein disorder

Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies.

Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies

Estimating the class prior and posterior from noisy positives and unlabeled data ⬇️

Evaluating purifying selection in the mitochondrial DNA of various mammalian species

Evaluation of features for catalytic residue prediction in novel folds

Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

Exploiting heterogeneous sequence properties improves prediction of protein disorder.

Extending the coverage of spectral libraries: A neighbor-based approach to predicting intensities of peptide fragmentation spectra ⬇️

Fast and accurate identification of semi-tryptic peptides in shotgun proteomics

From protein-disease associations to disease informatics

Gain and loss of phosphorylation sites in human cancer

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential

Graphlet kernels for prediction of functional residues in protein structures

HIP2: an online database of human plasma proteins from healthy individuals

ISCB computational biology Wikipedia competition

ISMB 2018 proceedings.

ISMB/ECCB 2019 Proceedings

Identification of N-terminal protein processing sites by chemical labeling mass spectrometry

Identification, analysis, and prediction of protein ubiquitination sites

Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics

Improved amino acid flexibility parameters ⬇️

Improving sequence alignments for intrinsically disordered proteins

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

Influence of sequence changes and environment on intrinsically disordered proteins.

Information-theoretic evaluation of predicted ontological annotations ⬇️

Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides

Intrinsic disorder and functional proteomics

Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes

Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes

Investigation of VUV photodissociation propensities using peptide libraries ⬇️

Length-dependent prediction of protein intrinsic disorder.

Loss of post-translational modification sites in disease

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges

MutDB: update on development of tools for the biochemical analysis of genetic variation

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing

New Drosophila long-term memory genes revealed by assessing computational function prediction methods

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction ⬇️