Apply now Job no: 494553
Work type: Continuing full time
Vacancy type: External Vacancy, Internal Vacancy
Categories: Academic - Teaching and Research

The Faculty of Science is launching a new and innovative branch of biological science at Macquarie University – Synthetic Biology. Synthetic biology combines engineering principles with molecular biological approaches to design and construct biological devices and systems. Recent highlights in this field include the design and synthesis of a functional bacterial genome and a yeast chromosome, and generation of synthetic bacterial cells. The rational synthesis of "designer" organisms yield important insights into how organisms work and has the potential to revolutionise biotechnological applications in areas such as bioenergy and biomanufacturing.

Find more at http://jobs.mq.edu.au/cw/en/job/494553/lecturersenior-lecturer-level-bc-in-synthetic-biology-research-fellow-level-b-in-synthetic-biology-lecturersenior-lecturer-level-bc-in-bioinformatics

Features

• Circular and linear views of genomes

• Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs

• Smooth zooming down to the sequence level

• Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)

• Save high resolution PNG maps up to 8000x8000px

• Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

Applicants are invited to send their resume and a recommendation letter to Prof. Patrick Meyer (more details at www.biosys.ulg.ac.be )

Prokka – Standalone command line tool, takes just a few minutes per genome. This is the best way to get good quality annotation in a flash, which is particularly useful if you have loads of genomes or need to annotate a pangenome or metagenome. Note however that the quality of functional information is not as good as RAST, and you will need several extra steps if you want to do functional profiling and pathway analysis of your genome(s)… which is in-built in RAST.

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

PGAP: NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume.  NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

BEACON (automated tool for Bacterial GEnome Annotation ComparisON), a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.

BlastKOLA: Assigns K numbers to the user's sequence data by BLAST searches, respectively, against a nonredundant set of KEGG GENES. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to this server and can be executed in an interactive mode. BlastKOALA is suitable for annotating fully sequenced genomes.

PAGIT: Provides a toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four tools: (i) ABACAS which classifies and orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying and correcting small errors in consensus sequences and; (iv) RATT for help annotation. The software was mainly created to analyze parasite genomes of up to about 300 Mb.

MAKER: A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).

MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.

This job will allow the intern to become more familiar with new biological and bioinformatics tools like next generation sequencing, RNA-Seq data analysis and comparative genomics.

To apply for this position, send the following documents (in PDF format) to Dr Pierre-Yves Dupont (email p.y.dupont@massey.ac.nz):

1. A short cover letter.
2. A curriculum vitae, with transcript details.
3. The names and contact details of two referees willing to provide a confidential letter of recommendation upon request.

Informal enquiries are welcome. Formal applications are due by Sunday 2nd December 2012.
Requirements:

This position requires a good understanding of genetic problems, a good command of at least one scripting language (Perl, Python...), a basic knowledge of MySQL or any relational database management system. Knowledge in biological programming libraries (BioPython, BioPerl, BioRuby...), Java, C++ or any compiled language is an asset but not required. Undergraduate or Master degree is required.
Contact Information:

Dr. Pierre-Yves Dupont
Institute of Molecular BioSciences
Massey University
Private Bag 11 222
Palmerston North 4442
NEW ZEALAND

http://massey.genomicus.com/
p.y.dupont@massey.ac.nz

Information about the Institute of Molecular BioSciences (http://imbs.massey.ac.nz/) and the Computational Biology Research Group (http://massey.genomicus.com/) is available online. For more information about the position, you can contact Dr Pierre-Yves Dupont (email p.y.dupont@massey.ac.nz).

Following are the list of tools commonly used to PPIs predictions:

Protein-Protein Interaction Sites

PPISP

A consensus neural network method for predicting protein-protein interaction sites

HOMCOS

A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures

HotPOINT

Prediction of protein interfaces using an empirical model

ISIS

Prediction of interaction hotspots from sequence

KFC server

Automated decision-tree approach to predicting protein-protein interaction hot spots

meta-PPISP

A meta server for predicting protein-protein interaction sites. meta-PPISP is built on three individual web servers: cons-PPISP, PINUP, and Promate

ODA

Identification of optimal surface patches with the lowest docking desolvation energy values

PINUP

Protein binding site prediction with an empirical scoring function

Other Sites (DNA, RNA, Metals)

CHED 

Web server for predicting soft metal binding sites in proteins

DBD-Hunter

A knowledge-based method for the prediction of DNA-protein interactions

DISPLAR

Given the structure of a protein known to bind DNA, the method predicts residues that contact DNA using neural network method

iDBPs

Predicts DNA binding proteins for proteins with known 3D structure.

PFplus

The candidate will be mainly in charge of developing research on Gene Expression/SNP Arrays data, NGS whole -exome and -transcriptome datasets and biological networks in the contexts of genetic diseases, innovative therapies and regenerative medicine. Main activities will be: (i) data analysis (short-reads mapping, genomics aberrations discovery and annotation, variants pathogenicity detection); (ii) functional/pathway enrichment analysis; (iii) biological networks analysis (artificial knockout, redundancy and lethality analysis, gene set essentiality); (iv) developing of ad-hoc software solutions/routines on clusters of CPUs and GPUs.

The correct cultural background (training in Biology / Computer Science / Statistics or a mix of the three) and a strong interest in working in high throughput data analysis will be considered at the same level of specific experience in the above-mentioned fields.

Knowledge of molecular modeling and simulation and willingness to learn one or more of these languages: python, perl, R, Java, C++, C# is a golden plus. Good knowledge of Scientific English will be positively evaluated for this position, together with good presentation and teamwork skills.

Candidates should send:
• a cover letter explaining the role they would like to undertake within the Center, even if it is not listed in this job adv, stating clearly why they would be a good fit to the proposed role, and what they would bring to the Center in terms of expertise, ideas, talent;
• a CV including a list of publications;
• List of referees.

A CV with one professional reference, details on educational background and of the biological and/or bioinformatic and/or data analysis skills and experience should be sent by email for a preliminary selection to: Tommaso Mazza t.mazza@css-mendel.it

The Mix algorithm, approach and results were published in BMC bioinformatics : http://www.biomedcentral.com/1471-2105/14/S15/S16.

Address of the bookmark: https://github.com/cbib/MIX

Adv. No. URDIP/ 6/2014

Opportunity for young Bioinformatics Professionals to make a career in the area of Intellectual Property CSIR has set up a Unit for Research and Development of Information Products (CSIR-URDIP) at Pune to work in the area of scientific informatics. One of the major focus areas of research work at CSIR-URDIP is PATENT INFORMATICS. With the increasing applications of Bioinformatics in the areas of life sciences industry such as Agriculture and Health Care (Diagnostics and Drugs), the output of research in these area is being protected by different forms of Intellectual Property rights. Realizing the importance of IP in the Bioinformatics field, Department of Biotechnology (DBT) has sanctioned a project on “Development, Facilitation and Harvesting of Bioinformatics related Intellectual Property” at CSIR-URDIP.

The project will involve application of Patent Informatics tools and techniques to Bioinformatics (including creation of patent landscapes, preparation of techno-legal reports of patentability, freedom to operate studies) to help protect IPRs and develop and conduct training programmes on IPRs related to Bioinformatics.

CSIR-URDIP invites applications from young Bioinformatics professionals to work on this emerging area which offers challenging opportunities and attractive career possibilities in future.

Position I: Research Associate

No of Positions: One

Consolidated amount Payable: Rs. 22,000/- per month + 20% HRA= Rs.26,400

Qualification: PhD in Bioinformatics. In exceptional cases, candidature of M. Tech. candidates with First class in Bioinformatics with three years of relevant work experience will also be considered.

Age Limit: 35 years. The age should not exceed the limit indicated as on a closing date of receipt of completed application form.

Upper age limit is relaxable for 5 years for SC/ST, OBC, Physically handicapped and female candidates as per CSIR/Government of India rules.

Position II: Junior Research Fellow

No of Positions: one

Consolidated amount Payable: Rs. 16,000/- + 20% HRA = 19,200

Qualification: M.Sc / BE or equivalent in Bioinformatics with minimum of 55% marks in aggregate Job requirement: Scientific literature and patent search, analysis and Report Writing

Preference: Preference will be given to candidates with knowledge of patents and or 1-2 years of experience + Knowledge of Computers (MS Excel + Word Processing)

Age Limit: 28 years. The age should not exceed the limit indicated as on a closing date of receipt of completed application form.

For details please visit our website (www.urdip.res.in/careers) for further details and apply online by 30th September, 2014.

Advertisement: http://www.urdip.res.in/download/Advt6_2014.pdf

Address of the bookmark: https://github.com/knausb/vcfR