SCHNEIDER Georg

Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins

Published date : 23 Oct 2013

The genome sequences of new viruses often contain many “orphan” or “taxon-specific” proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as “genus specific” by BLAST.

type
Journal Paper
journal
Journal of Virology, Jan 2014, Vol. 88, Issue 1, doi: 10.1128/JVI.02595-13
Impact Factor
5.076

Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects

Published date : 30 Sep 2013

BACKGROUND: Atopic dermatitis (AD) is a major inflammatory condition of the skin caused by inherited skin barrier deficiency, with mutations in the filaggrin gene predisposing to development of AD. Support for barrier deficiency initiating AD came from flaky tail mice, which have a frameshift mutation in Flg and also carry an unknown gene, matted, causing a matted hair phenotype.

OBJECTIVE: We sought to identify the matted mutant gene in mice and further define whether mutations in the human gene were associated with AD.

type
Journal Paper
journal
The Journal of Allergy and Clinical Immunology, 28 Sep 2013, doi: 10.1016/j.jaci.2013.08.046
Impact Factor
12.047

Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia

Published date : 02 May 2013

Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere.

type
Journal Paper
journal
The American Journal of Human Genetics, Vol. 92, issue 5, Pg 820-826, 2 May 2013, doi:10.1016/j.ajhg.2013.04.005

Protein Sequence-Structure-Function-Network Links Discovered with the ANNOTATOR Software Suite: Application to ELYS/Mel-28

Published date : 19 Sep 2012

While very little genomic sequence is interpretable in terms of biological mechanism directly, the chances are much better for protein-coding genes that can be translated into protein sequences. This review considers the different concepts applicable to sequence analysis and function prediction of globular and non-globular protein segments. The publicly accessible ANNOTATOR software environment integrates most of the reliable protein sequence-based function prediction methods, protein domain databases and pathway, and protein–protein interaction collections developed in academia.

type
Book/Book Chapter
journal
Computational Medicine - Tools and Challenges, 2012, pg 111-143, ISBN 978-3-7091-0946-5

Beware Of Moving Targets: Reference Proteome Content Fluctuates Substantially Over The Years

Published date : 09 Aug 2012

Reference proteomes are generated by increasingly sophisticated annotation pipelines as part of regular genome build releases; yet, the corresponding changes in reference proteomes' content are dramatic. In the history of the NCBI-curated human proteome, the total number of entries has remained roughly constant but approximately half of the proteins from the 2003 build 33 are no longer represented by entries in current releases, while about the same number of new proteins have been added (for sequence identity thresholds 50-90%).

type
Journal Paper
journal
Journal of Bioinformatics and Computational Biology, Vol. 10, No. 6 (2012), doi: 10.1142/S0219720012500205

SIFT web server: predicting effects of amino aci substitutions on proteins

Published date : 11 Jun 2012

The Sorting Intolerant from Tolerant (SIFT) algorithm predicts the effect of coding variants on protein function. It was first introduced in 2001, with a

type
Journal Paper
journal
Nucleic Acids Research, 2012, Pg 1-6

Transmembrane helix: simple or complex

Published date : 07 May 2012

Transmembrane helical segments (TMs) can be classified into two groups of so-called ‘simple’ and ‘complex’ TMs. Whereas the first group represents mere hydrophobic anchors with an overrepresentation of aliphatic hydrophobic residues that are likely attributed to convergent evolution in many cases, the complex ones embody ancestral information and tend to have structural and functional roles beyond just membrane immersion. Hence, the sequence homology concept is not applicable on simple TMs.

type
Journal Paper
journal
Nuclei Acids Research, 2012, Pg 1-6, doi:10.1093/NAR/GKS379

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

Published date : 23 Apr 2012

The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic.

type
Journal Paper
journal
Bioinformatics 2012, June 15, Vol 28, Issue 12, Pg 1645-1646

Genome-wide analysis of cell wall-related genes in Tuber melanosporum

Published date : 06 Apr 2012

A genome-wide inventory of proteins involved in cell wall synthesis and remodeling has been obtained by taking advantage of the recently released genome sequence of the ectomycorrhizal Tuber melanosporum black truffle. Genes that encode cell wall biosynthetic enzymes, enzymes involved in cell wall polysaccharide synthesis or modification, GPI-anchored proteins and other cell wall proteins were identified in the black truffle genome. As a second step, array data were validated and the symbiotic stage was chosen as the main focus.

type
Journal Paper
journal
Current Genetics 2012, doi : 1007/s00294-012-0374-6