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Virus Bioinformatics

First edition, 2021

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Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

Nucleic acids research, 2014-01, Vol.42 (Database issue), p.D396-D400

2014

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TargetSpy: a supervised machine learning approach for microRNA target prediction

BMC bioinformatics, 2010-05, Vol.11 (1), p.292-292, Article 292

2010

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PROSO II – a new method for protein solubility prediction

The FEBS journal, 2012-06, Vol.279 (12), p.2192-2200

2012

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Author Correction: Edgetic perturbation signatures represent known and novel cancer biomarkers

Scientific reports, 2021-02, Vol.11 (1), p.3582-3, Article 3582

2021

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Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies

BMC genomics, 2024-06, Vol.25 (1), p.1-15, Article 619

2024

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Inter-chromosomal contact networks provide insights into Mammalian chromatin organization

PloS one, 2015-05, Vol.10 (5), p.e0126125-e0126125

2015

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Protein abundance profiling of the Escherichia coli cytosol

BMC genomics, 2008-02, Vol.9 (1), p.102-102

2008

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Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites

PloS one, 2016-06, Vol.11 (6), p.e0157896-e0157896

2016

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Edgetic perturbation signatures represent known and novel cancer biomarkers

Scientific reports, 2020-03, Vol.10 (1), p.4350, Article 4350

2020

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Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning

Computational and structural biotechnology journal, 2021-01, Vol.19, p.1512-1530

2021

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Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure

PloS one, 2019-07, Vol.14 (7), p.e0219452-e0219452

2019

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Genetic Spectrum of Idiopathic Restrictive Cardiomyopathy Uncovered by Next-Generation Sequencing

PloS one, 2016-09, Vol.11 (9), p.e0163362-e0163362

2016

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Genome‐wide analysis of somatic copy number alterations and chromosomal breakages in osteosarcoma

International journal of cancer, 2017-08, Vol.141 (4), p.816-828

2017

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AllesTM: predicting multiple structural features of transmembrane proteins

BMC bioinformatics, 2020-06, Vol.21 (1), p.1-242, Article 242

2020

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Influenza A Virus Infection Reactivates Human Endogenous Retroviruses Associated with Modulation of Antiviral Immunity

Viruses, 2022-07, Vol.14 (7), p.1591

2022

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Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation

PLoS computational biology, 2018-02, Vol.14 (2), p.e1005987-e1005987

2018

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Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors

Frontiers in genetics, 2019-11, Vol.10, p.1141-1141

2019

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Computational Approaches for Investigating Disease-causing Mutations in Membrane Proteins: Database Development, Analysis and Prediction

Current topics in medicinal chemistry, 2022-01, Vol.22 (21), p.1766-1775

2022

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SCOTCH: subtype A coreceptor tropism classification in HIV-1

Bioinformatics, 2018-08, Vol.34 (15), p.2575-2580

2018

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The MIPS mammalian protein–protein interaction database

Bioinformatics, 2005-03, Vol.21 (6), p.832-834

2005

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HDVdb: A Comprehensive Hepatitis D Virus Database

Viruses, 2020-05, Vol.12 (5), p.538

2020

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Analysis of micro-rearrangements in 25 eukaryotic species pairs by SyntenyMapper

PloS one, 2014-11, Vol.9 (11), p.e112341-e112341

2014

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Proline codon pair selection determines ribosome pausing strength and translation efficiency in bacteria

Communications biology, 2021-05, Vol.4 (1), p.589-589, Article 589

2021

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Phosphorylation variation during the cell cycle scales with structural propensities of proteins

PLoS computational biology, 2013-01, Vol.9 (1), p.e1002842-e1002842

2013

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Virus Bioinformatics

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

TargetSpy: a supervised machine learning approach for microRNA target prediction

PROSO II – a new method for protein solubility prediction

Author Correction: Edgetic perturbation signatures represent known and novel cancer biomarkers

Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies

Inter-chromosomal contact networks provide insights into Mammalian chromatin organization

Protein abundance profiling of the Escherichia coli cytosol

Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites

Edgetic perturbation signatures represent known and novel cancer biomarkers

Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning

Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure

Genetic Spectrum of Idiopathic Restrictive Cardiomyopathy Uncovered by Next-Generation Sequencing

Genome‐wide analysis of somatic copy number alterations and chromosomal breakages in osteosarcoma

AllesTM: predicting multiple structural features of transmembrane proteins

Influenza A Virus Infection Reactivates Human Endogenous Retroviruses Associated with Modulation of Antiviral Immunity

Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation

Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors

Computational Approaches for Investigating Disease-causing Mutations in Membrane Proteins: Database Development, Analysis and Prediction

SCOTCH: subtype A coreceptor tropism classification in HIV-1

The MIPS mammalian protein–protein interaction database

HDVdb: A Comprehensive Hepatitis D Virus Database

Analysis of micro-rearrangements in 25 eukaryotic species pairs by SyntenyMapper

Proline codon pair selection determines ribosome pausing strength and translation efficiency in bacteria

Phosphorylation variation during the cell cycle scales with structural propensities of proteins

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