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Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function

Bioinformatics, 2021-04, Vol.37 (2), p.162-170

2021

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The quest for orthologs: finding the corresponding gene across genomes

Trends in genetics, 2008-11, Vol.24 (11), p.539-551

2008

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Metric learning on expression data for gene function prediction

Bioinformatics, 2020-02, Vol.36 (4), p.1182-1190

2020

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Improving protein function prediction using protein sequence and GO-term similarities

Bioinformatics, 2019-04, Vol.35 (7), p.1116-1124

2019

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A Comparison of Global Sensitivity Analysis Methods for Explainable AI With an Application in Genomic Prediction

IEEE access, 2022, Vol.10, p.103364-103381

2022

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Bayesian Markov Random Field analysis for protein function prediction based on network data

PloS one, 2010-02, Vol.5 (2), p.e9293-e9293

2010

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Automatic Gene Function Prediction in the 2020's

Genes, 2020-10, Vol.11 (11), p.1264

2020

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Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction

PLoS computational biology, 2010-11, Vol.6 (11), p.e1001017-e1001017

2010

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High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6

The Plant journal : for cell and molecular biology, 2008-11, Vol.56 (4), p.627-637

2008

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Predicting the impact of alternative splicing on plant MADS domain protein function

PloS one, 2012-01, Vol.7 (1), p.e30524-e30524

2012

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Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data

BMC plant biology, 2011-05, Vol.11 (1), p.82-82

2011

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The genome of the stress-tolerant wild tomato species Solanum pennellii

Nature genetics, 2014-09, Vol.46 (9), p.1034-1038

2014

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Genome-Wide Computational Function Prediction of Arabidopsis Proteins by Integration of Multiple Data Sources

Plant physiology (Bethesda), 2011-01, Vol.155 (1), p.271-281

2011

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Reductive Genome Evolution in Buchnera aphidicola

Proceedings of the National Academy of Sciences - PNAS, 2003-01, Vol.100 (2), p.581-586

2003

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De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

Microbial cell factories, 2012-03, Vol.11 (1), p.36-36, Article 36

2012

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Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis

PLoS genetics, 2011-06, Vol.7 (6), p.e1002070-e1002070

2011

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Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome

BMC genomics, 2009-04, Vol.10 (1), p.154-154, Article 154

2009

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Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines

BMC bioinformatics, 2004-09, Vol.5 (1), p.133-133

2004

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The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry

PLoS genetics, 2012-11, Vol.8 (11), p.e1003088-e1003088

2012

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The Genome Sequence of Blochmannia floridanus: Comparative Analysis of Reduced Genomes

Proceedings of the National Academy of Sciences - PNAS, 2003-08, Vol.100 (16), p.9388-9393

2003

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In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

BMC genomics, 2009-04, Vol.10 (204), p.204-204, Article 204

2009

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Mutational robustness of gene regulatory networks

PloS one, 2012-01, Vol.7 (1), p.e30591-e30591

2012

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ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

Plant methods, 2011-05, Vol.7 (1), p.11-11

2011

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Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin

BMC genomics, 2015-05, Vol.16 (1), p.374-374, Article 374

2015

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PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

Nucleic acids research, 2011-07, Vol.39 (Web Server issue), p.W524-W527

2011

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Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function

The quest for orthologs: finding the corresponding gene across genomes

Metric learning on expression data for gene function prediction

Improving protein function prediction using protein sequence and GO-term similarities

A Comparison of Global Sensitivity Analysis Methods for Explainable AI With an Application in Genomic Prediction

Bayesian Markov Random Field analysis for protein function prediction based on network data

Automatic Gene Function Prediction in the 2020's

Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction

High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6

Predicting the impact of alternative splicing on plant MADS domain protein function

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data

The genome of the stress-tolerant wild tomato species Solanum pennellii

Genome-Wide Computational Function Prediction of Arabidopsis Proteins by Integration of Multiple Data Sources

Reductive Genome Evolution in Buchnera aphidicola

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome

Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry

The Genome Sequence of Blochmannia floridanus: Comparative Analysis of Reduced Genomes

In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

Mutational robustness of gene regulatory networks

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

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