Eisenhaber F

Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723

Published date : 23 May 2019

BACKGROUND:
Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis.

type
Journal Paper
journal
BMC Genomics 2019, 20:374, doi: 10.1186/s12864-019-5762-6
Impact Factor
3.730

AllerCatPro - Prediction of protein allergenicity potential from the protein sequence

Published date : 18 Jan 2019

MOTIVATION:
Due to the risk of inducing an immediate type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens.

type
Journal Paper
journal
Bioinformatics. 2019 Jan 18. doi: 10.1093/bioinformatics/btz029
Impact Factor
5.481

The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine

Published date : 27 Nov 2018

Background
Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts.

type
Journal Paper
journal
Open Forum Infectious Diseases, Vol. 5, issue 12, 1 Dec 2018, doi: 10.1093/ofid/ofy318
Impact Factor
3.240

Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

Published date : 28 Sep 2018

The mentioning of gene names in the body of the scientific literature 1901-2017 and their fractional counting was used as a proxy to assess the level of biological function discovery. We define a literature score of one as full publication equivalent (FPE), the amount of literature necessary to achieve one publication solely dedicated to a gene. We find that less than 5000 human genes have each at least 100 FPEs in the available literature corpus.

type
Journal Paper
journal
Proteomics 2018, Sep 28, doi: 10.1002/pmic.201800093
Impact Factor
3.532

Molecular mechanism of the Escherichia coli AhpC in the function of a chaperone under heat-shock conditions

Published date : 20 Sep 2018

Peroxiredoxins (Prxs) are ubiquitous antioxidants utilizing a reactive cysteine for peroxide reduction and acting as a molecular chaperone under various stress conditions. Besides other stimulating factors, oxidative- and heat stress conditions trigger their ATP-independent chaperoning function. So far, many studies were intended to reveal the chaperoning mechanisms of the so-called sensitive Prxs of eukaryotes, which are susceptible to inactivation by over-oxidation of its reactive cysteine during H2O2 reduction.

type
Journal Paper
journal
Scientific Reports 8, No. 14151, 2018, doi: 10.1038/s41598-018-32527-7
Impact Factor
4.122

Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z

Published date : 15 May 2018

Distant homology relationships among proteins with many transmembrane regions (TMs) are difficult to detect as they are clouded by the TMs’ hydrophobic compositional bias and mutational divergence in connecting loops. In the case of several GPI lipid anchor biosynthesis pathway components, the hidden evolutionary signal can be revealed with dissectHMMER, a sequence similarity search tool focusing on fold-critical, high complexity sequence segments.

type
Journal Paper
journal
Cell Cycle, Vol 17, 2018, Issue 7, doi: 10.1080/15384101.2018.1456294
Impact Factor
3.304

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy

Published date : 11 May 2018

Background
Single Nucleotide Polymorphisms (SNPs) can influence patient outcome such as drug response and toxicity after drug intervention. The purpose of this study is to develop a systematic pathway approach to accurately and efficiently predict novel non-synonymous SNPs (nsSNPs) that could be causative to gemcitabine-based chemotherapy treatment outcome in Singaporean non-small cell lung cancer (NSCLC) patients.

type
Journal Paper
journal
BMC Cancer (2018), 18:555, doi: 10.1186/s12885-018-4471-x
Impact Factor
3.288

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins

Published date : 21 Feb 2018

Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (CP) located in a conserved sequence Pxxx(T/S)xxCP motif known as CP-loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the CP-loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure.

type
Journal Paper
journal
Free Radical Biology and Medicine, Volume 118, April 2018, Pages 59-70, doi:10.1016/j.freeradbiomed.2018.02.027
Impact Factor
5.606