BOL: Related items

EFS: an ensemble feature selection tool implemented as R-package and web-application

Jit — Tue, 28 Jan 2020 05:12:23 -0600

The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in EFS, which can be used separately or combined in an ensemble.

https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0142-8

Address of the bookmark: http://efs.heiderlab.de/

PPAI: a web server for predicting protein-aptamer interactions

Jit — Fri, 12 Jun 2020 07:26:23 -0500

PPAI can query aptamers and proteins, predict aptamers and predict protein-aptamer interactions in batch mode precisely and efficiently, which would be a novel bioinformatics tool for the research of protein-aptamer interactions. PPAI web-server is freely available at http://39.96.85.9/PPAI

Address of the bookmark: http://39.96.85.9/PPAI/

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Abhimanyu Singh — Tue, 23 May 2017 05:28:56 -0500

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7

Address of the bookmark: http://ufmg-simba.sourceforge.net/

Frontend: Perl Web framework documentation - Andrej Sali Lab

Jit — Mon, 08 Jan 2018 22:32:03 -0600

The frontend is a set of Perl classes that displays the web interface, allowing a user to upload their input files, start a job, display a list of all jobs in the system, and get back job results. The main saliwebfrontend class must be subclassed for each web service. This class is then used to display the web pages using a set of CGI scripts that are set up automatically by the build system.

Address of the bookmark: https://saliweb.readthedocs.io/en/latest/frontend.html

Vvek's Lab

Thu, 26 Sep 2013 11:11:39 -0500

Broad Area of Research: RNA biology (microRNA, lncRNA), Stem cells, Functional genomics, Epigenomics and Cancer

RNAs, especially non-coding RNAs (such as microRNA, long ncRNAs) are recently identified to be very abundant in mammalian organisms and play some key roles in gene expression regulation, gene silencing, and also implicated in disease progression, stem cell pluripotency etc. Current research activities of our lab include analysis of expression pattern of ncRNAs by microarray and next-gen sequencing data and understanding the role of miRNAs or other regulatory RNAs in various diseases, especially cancer and validation by reporter assays (renilla/luciferase) and other experimental tools.

More @ http://vvekslab.in/index.html

Nieduszynski Group

Fri, 26 Sep 2014 19:35:06 -0500

Complete, accurate replication of the genome is essential for life. All chromosomes in eukaryotic cells must be duplicated and then segregated to daughter cells to ensure genetic integrity and produce the large number of cells that make up a multicellular organism. We are using genetic, genomic and computational methods to understand how chromosome replication is regulated to ensure genome stability. By focusing on the basic biology that underpins cell growth and division we aim to provide new insights that may help our understanding of diseases such as cancer and congenital disorders.

More http://www.nieduszynski.org/index.php
http://www.path.ox.ac.uk/research/cell-biology-and-pathology/conrad-nieduszynski-group

Bioinformatician - Purdue Cancer Center

Wed, 03 Feb 2021 22:54:14 -0600

The Center for Cancer Research is an NCI-designated cancer center. The center is a catalyst for collaborative cancer research around Purdue University. In this role, the selected individual will have the opportunity to cooperate with Purdue faculty and students in performing cutting-edge research and analyses, with opportunities for professional development, and the possibility of co-authorship in faculty research publications.
Projects will be challenging, including various model organisms, and we are looking for an individual who is excited about interacting with multi-disciplinary cancer research groups and the development of new tools, techniques, and workflows. Independently perform both routine and project-specific analyses, advise faculty on the design of experiments, writing manuscripts for publication, and writing grant proposals. Interact and collaborate with bioinformatics services (i.e. Statistical Consulting Center to provide relevant services to the campus research community), where applicable. Support all of the bioinformatics activities of the Center for Cancer Research at Purdue University
Required:

Master's degree in bioinformatics, computer science, molecular biology, or related field
One year of experience in analyzing RNA-Seq data
In lieu of a degree, consideration will be given to an equivalent combination of related education and required work experience.
Understanding of molecular biology, biochemistry, and genetics
Proficiency in writing scripts using Perl, Python, Java, or equivalent languages
Proficiency in R and UNIX/LINUX
Knowledge of genomics, alignment, annotation, bioinformatics, concepts of sequence assembly
Highly motivated and detail-oriented
Ability, interest, and curiosity to learn new skills
Must possess strong communication skills to work effectively with users across disciplines
Ability to work independently and as part of a multi-disciplinary team
Strong visual, verbal, and written communication skills
Excellent time organizational skills
Preferred:

Experience writing software or building software pipelines
Experience with oncology-specific public databases including TCGA
Experience with deploying and/or running software on high-performance computational systems
Statistical and experimental design knowledge
Additional Information:

This position is contingent on the availability of funding
Purdue will not sponsor employment authorization for this position
A background check will be required for employment in this position
FLSA: Exempt (Not Eligible For Overtime)
Retirement Eligibility: Defined Contribution Waiting Period
Purdue University is an EOE/AA employer. All individuals, including minorities, women, individuals with disabilities, and veterans are encouraged to apply

More at https://careers.purdue.edu/job/West-Lafayette-Bioinformatician-Purdue-Cancer-Center-IN-47906/686617600/

PhD position in Molecular Cell Biology

Sat, 15 Feb 2020 06:09:55 -0600

https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/wissenschaftliche-r-mitarbeiter-in/phd-position-molecular-cell-biology-129604.html?suid=0ec057818886c1eceac674ca3f83943367a6cbe2

Essential experience / qualifications:
We are looking for highly motivated candidates holding a Master / Diploma in Biology, Biochemistry, Molecular Medicine or similar; solid knowledge of molecular and cell biological techniques; good English knowledge.

Applications:
Please send your application (including CV, letter of motivation, contact information of two references, and list of publication) by 13.03.2020 at the latest to:

Universitätsklinikum Erlangen
Chirurgische Klinik
Translational Research Center
Prof. Dr. rer. nat. Michael Stürzl
Schwabachanlage 12
91054 Erlangen
E-Mail: michael.stuerzl@uk-erlangen.de

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

Jit — Mon, 28 May 2018 09:41:39 -0500

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.

Address of the bookmark: https://github.com/Illumina/manta

Multiple PhD positions

Sun, 09 Feb 2020 03:10:28 -0600

14 PhD positions in the EU Horizon 2020 Marie Skłodowska-Curie Project PRECODE:
International training network which sets a joint research programme to train a new generation of leading scientists in model systems and methods for the development of new therapies for pancreatic cancer (PaCa)

http://precode-project.eu/jobs-board/#1572451761376-39d75f63-c6fb