Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently "Orphan" Viral Proteins

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

(2013) Lothar Wissler et al.   Genome Biology and Evolution

Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features

(2013) D. F. Quito-Avila et al.   JOURNAL OF GENERAL VIROLOGY

Membrane Topology and Function of Dengue Virus NS2A Protein

(2013) X. Xie et al.   JOURNAL OF VIROLOGY

Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage

(2013) Swati Kaushik et al.   PLoS One

Real Time Classification of Viruses in 12 Dimensions

(2013) Chenglong Yu et al.   PLoS One

Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses

(2013) Angelo Pavesi et al.   PLoS Computational Biology

Discriminative modelling of context-specific amino acid substitution probabilities

(2012) Christof Angermüller et al.   BIOINFORMATICS

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

(2012) Jia-Ming Chang et al.   BMC BIOINFORMATICS

Negevirus: a Proposed New Taxon of Insect-Specific Viruses with Wide Geographic Distribution

(2012) N. Vasilakis et al.   JOURNAL OF VIROLOGY

Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

(2012) C. Lauber et al.   JOURNAL OF VIROLOGY

Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

(2012) C. Lauber et al.   JOURNAL OF VIROLOGY

Transmembrane helix: simple or complex

(2012) Wing-Cheong Wong et al.   NUCLEIC ACIDS RESEARCH

ViralZone: recent updates to the virus knowledge resource

(2012) Patrick Masson et al.   NUCLEIC ACIDS RESEARCH

A Novel Virus of the Genus Cilevirus Causing Symptoms Similar to Citrus Leprosis

(2012) Avijit Roy et al.   PHYTOPATHOLOGY

Detecting Remote Sequence Homology in Disordered Proteins: Discovery of Conserved Motifs in the N-Termini of Mononegavirales phosphoproteins

(2012) David Karlin et al.   PLoS One

Paleovirology and virally derived immunity

(2012) Amr Aswad et al.   TRENDS IN ECOLOGY & EVOLUTION

Computational tools for viral metagenomics and their application in clinical research

(2012) L. Fancello et al.   VIROLOGY

Endogenous RNA viruses of plants in insect genomes

(2012) Jie Cui et al.   VIROLOGY

Experimental infection of the honeybee (Apis mellifera L.) with the chronic bee paralysis virus (CBPV): infectivity of naked CBPV RNAs

(2012) Aurore Chevin et al.   VIRUS RESEARCH

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

(2012) Eugene V. Koonin et al.   Frontiers in Cellular and Infection Microbiology

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

(2011) Wing-Cheong Wong et al.   Biology Direct

Using context to improve protein domain identification

(2011) Alejandro Ochoa et al.   BMC BIOINFORMATICS

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

(2011) Johannes Söding et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Sobemovirus RNA linked to VPg over a threonine residue

(2011) Allan Olspert et al.   FEBS LETTERS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

FFAS server: novel features and applications

(2011) L. Jaroszewski et al.   NUCLEIC ACIDS RESEARCH

MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence

(2011) Andrea Passerini et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Characterization of a Virus Infecting Citrus volkameriana with Citrus Leprosis-Like Symptoms

(2011) Michael J. Melzer et al.   PHYTOPATHOLOGY

Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia

(2011) Charles Runckel et al.   PLoS One

Paleovirology—ghosts and gifts of viruses past

(2011) Maulik R Patel et al.   Current Opinion in Virology

Classification and Determination of Possible Origins of ORFans through Analysis of Nucleocytoplasmic Large DNA Viruses

(2010) Mickaël Boyer et al.   INTERVIROLOGY

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Membrane transport proteins: surprises in structural sameness

(2010) Douglas L Theobald et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Detection of new protein domains using co-occurrence: application to Plasmodium falciparum

(2009) Nicolas Terrapon et al.   BIOINFORMATICS

Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation

(2009) C. Rancurel et al.   JOURNAL OF VIROLOGY

webPRC: the Profile Comparer for alignment-based searching of public domain databases

(2009) B. W. Brandt et al.   NUCLEIC ACIDS RESEARCH

ANNIE: integrated de novo protein sequence annotation

(2009) H. S. Ooi et al.   NUCLEIC ACIDS RESEARCH

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

More than just orphans: are taxonomically-restricted genes important in evolution?

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS

Studies on membrane topology, N-glycosylation and functionality of SARS-CoV membrane protein

(2009) Daniel Voß et al.   Virology Journal

Prediction of disordered regions in proteins based on the meta approach

(2008) T. Ishida et al.   BIOINFORMATICS

Identification and investigation of ORFans in the viral world

(2008) Yanbin Yin et al.   BMC GENOMICS

The Flavivirus Precursor Membrane-Envelope Protein Complex: Structure and Maturation

(2008) L. Li et al.   SCIENCE

Molecular characterisation and phylogenetic analysis of Chronic bee paralysis virus, a honey bee virus

(2008) Violaine Olivier et al.   VIRUS RESEARCH