Gene Function Prediction

Benchmarking selected computational gene network growing tools in context of virus-host interactions

Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens.

type: 
Journal Paper
journal: 
Scientific Reports, 2017 Jul 19;7(1):5805. doi: 10.1038/s41598-017-06020-6
pubmed: 
28724991
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28724991
Impact Factor: 
4.259
Date of acceptance: 
2017-06-07

Crystallographic and solution studies of NAD+- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps

Redox homeostasis is significant for the survival of pro- and eukaryotic cells and is crucial for defense against reactive oxygen species like superoxide and hydrogen peroxide. In Escherichia coli, the reduction of peroxides occurs via the redox active disulfide center of the alkyl hydroperoxide reductase C subunit (AhpC), whose reduced state becomes restored by AhpF. The 57kDa EcAhpF contains an N-terminal domain (NTD), which catalyzes the electron transfer from NADH via an FAD of the C-terminal domain into EcAhpC. The NTD is connected to the C-terminal domain via a linker.

type: 
Journal Paper
journal: 
Biochimica et Biophysica Acta 1847 (2015) Pg. 1139–1152 doi: 10.1016/j.bbabio.2015.06.011
pubmed: 
26092085
Url: 
http://www.sciencedirect.com/science/article/pii/S0005272815001218
Date of acceptance: 
2015-06-11

Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: to be or not to be exposed for enzyme access

Many protein posttranslational modifications (PTMs) are the result of an enzymatic reaction. The modifying enzyme has to recognize the substrate protein’s sequence motif containing the residue(s) to be modified; thus, the enzyme’s catalytic cleft engulfs these residue(s) and the respective sequence environment. This residue accessibility condition principally limits the range where enzymatic PTMs can occur in the protein sequence.

type: 
Journal Paper
journal: 
Proteomics, 2015, Jun 2, doi: 10.1002/pmic.201400633
pubmed: 
26038108
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/?term=26038108
Impact Factor: 
3.973
Date of acceptance: 
2015-05-29

Unix interfaces, Kleisli, bucandin structure, etc. — The heroic beginning of bioinformatics in Singapore

Remarkably, Singapore as one of today's hotspots for bioinformatics and computational biology research appeared de novo out of pioneering efforts of engaged local individuals in the early 90-s that, supported with increasing public funds from 1996 on, morphed into the present vibrant research community. This article brings to mind the pioneers, their first successes and early institutional developments.

type: 
Journal Paper
journal: 
Journal of Bioinformatics and Computational Biology, Vol. 12, Issue 3, June 2014, doi : 10.1142/S0219720014710024
pubmed: 
24969753
Url: 
http://www.worldscientific.com/doi/abs/10.1142/S0219720014710024
Date of acceptance: 
2014-03-28
Authors: 

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

Background

type: 
Journal Paper
journal: 
BMC Bioinformatics 2014, 15:66, doi:10.1186/1471-2105-15-166
Url: 
http://www.biomedcentral.com/1471-2105/15/166/abstract
Impact Factor: 
3.02
Date of acceptance: 
2014-05-27

10 Years for the Journal of Bioinformatics and Computational Biology (2003-2013) - A retrospective

The Journal of Bioinformatics and Computational Biology (JBCB) started publishing scientific articles in 2003. It has established itself as home for solid research articles in the field (~ 60 per year) that are surprisingly well cited. JBCB has an important function as alternative publishing channel in addition to other, bigger journals.

type: 
Journal Paper
journal: 
Journal of Bioinformatics and Computational Biology, Vol. 12, Issue 3, June 2014, doi : 10.1142/S0219720014710012
pubmed: 
24969752
Url: 
http://www.worldscientific.com/doi/abs/10.1142/S0219720014710012
Date of acceptance: 
2014-03-16

Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein’s omega-site and the GPI lipid anchor’s phosphoethanolamine

The transamidase subunit GAA1/GPAA1 is predicted to be the enzyme that catalyzes the attachment of the glycosylphosphatidyl (GPI) lipid anchor to the carbonyl intermediate of the substrate protein at the ω-site. Its ~300-amino acid residue lumenal domain is a M28 family metallo-peptide-synthetase with an α/β hydrolase fold, including a central 8-strand β-sheet and a single metal (most likely zinc) ion coordinated by 3 conserved polar residues. Phosphoethanolamine is used as an adaptor to make the non-peptide GPI lipid anchor look chemically similar to the N terminus of a peptide.

type: 
Journal Paper
journal: 
Cell Cycle, June 15, 2014, Vol. 13 Issue 12, Pg 1-6, doi: 10.4161/cc.28761
pubmed: 
24743167
Url: 
https://www.landesbioscience.com/journals/cc/article/28761/
Date of acceptance: 
2014-04-02

Guest Editorial for the International Conference on Genome Informatics (GIW 2013)

type: 
Journal Paper
journal: 
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Jan/Feb 2014, Vol. 11, No. 1, doi: 10.1109/TCBB.2014.2299751
Url: 
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6815736
Impact Factor: 
1.616

International Conference on Genome Informatics (GIW 2013) in Singapore: introduction to the systems biology contributions

type: 
Journal Paper
journal: 
BMC Systems Biology 2013, 7(Suppl 6):S11, doi:10.1186/1752-0509-7-S6-I1
Url: 
http://www.biomedcentral.com/1752-0509/7/S6/I1
Impact Factor: 
2.98
Research Group: 

Automatic Phylogenetic Classification of Baterial Beta-Lactamase Sequences Including Structural and Antibiotic Substrate Preference Information

Beta lactams comprise the largest and still most effective group of antibiotics, but bacteria can gain resistance through different beta lactamases that can degrade these antibiotics. We developed a user friendly tree building web server that allows users to assign beta lactamase sequences to their respective molecular classes and subclasses. Further clinically relevant information includes if the gene is typically chromosomal or transferable through plasmids as well as listing the antibiotics which the most closely related reference sequences are known to target and cause resistance against.

type: 
Journal Paper
journal: 
Journal of Bioinformatics and Computational Biology, Vol. 11, No. 6 (2013), doi : 10.1142/S0219720013430117
Url: 
http://www.worldscientific.com/doi/abs/10.1142/S0219720013430117
Date of acceptance: 
2013-10-12
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