Address of the bookmark: http://www.weizmann.ac.il/Biological_Regulation/IgorUlitsky/PLAR

Novel diagnostic platform for detection of Osteoarthritis

I invite applications from highly motivated individuals to join my laboratory as a PhD student in Systems Biology at the University of Calgary McCaig Institute for Bone and Joint Health. This project is aimed at characterizing the networks of physical (protein-protein) interactions underlying inflammatory processes in patients with Osteoarthritis and how this differs from patients with Rheumatoid Arthritis and normal individuals. This work will eventually lead to the development of a novel diagnostic platform for the non-invasive and accurate detection of early Osteoarthritis. The selected candidate will use state-of-the-art computational methodologies to systematically analyze proteomic data, and develop /implement new algorithms to identify protein and functional interaction networks from high throughput experimental data. The individual will also benefit by working closely with experts at the UofC and UofA through an AIHS Alberta Osteoarthritis Team Grant which includes experts from all pillars of health research. The candidate will also be supported to attend bioinformatics workshops and conferences to advance and disseminate their research.
Qualifications: The ideal candidate will have a Master’s degree in Computational Biology, Bioinformatics, or equivalent with strong background knowledge of the Biological Sciences, Biochemistry, and Microbiology. The individual should additionally have experience in handling high-throughput data sets as well as programming skills. The candidate will be registered as a PhD student in Dr. Krawetz’s laboratory, located in the new state-of-the-art Health Research Innovation Centre at the UofC. The individual will have strong verbal and written skills and the ability to work efficiently in a team environment.

In addition to the outstanding research opportunities available in this setting, students also enjoy the many cultural and sporting amenities provided in the city of Calgary, and can take advantage of the unparalleled skiing and hiking in the Rocky Mountains that are less than an hour away.

Candidates must be academically competitive and will be expected to apply for external funding. The stipend is $25,000/yr. For outstanding PhD students, internal top-up award opportunities are available on a competitive basis. If interested in joining the lab, please contact Dr. Krawetz directly at rkrawetz@ucalgary.ca and provide the following information:

- Short cover letter explaining your interest in the lab
- Resume
- Scanned copy of transcript or listing of course grades
- Names and contact information for two individuals who will be willing to provide letters of reference

- Development of computational methods to investigate the interplay between epigenetic and genetic layers and their role in tumor progression, by integrating genomic, epigenomic and transcriptional data. PI: Mattia Pelizzola (http://tiny.cc/comEpi)
- Epigenome and transcriptome analysis in mouse models of Hepatocellular Carcinoma. PI: Bruno Amati - Small and long non-coding RNAs in cancer stem cells. PI: Francesco Nicassio

All projects will benefit from the availability of both in-house and publicly available next-generation sequencing datasets. Familiarity with Linux environment, programming skills (especially in R) and a background in either computational biology, or physics/engineering/math will be advantageous.

Deadline for the application January 6th, to apply: http://genomics.iit.it/resources.html

Start date: March 1st, 2014

Duration: 1+2 years

Contact Person (Referent): Mattia Pelizzola

Ref. E-Mail: mattia.pelizzola@iit.it

Tel: 0039-02-94375058
Group Web Page: http://genomics.iit.it

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

Address of the bookmark: https://github.com/HuffordLab/GenomeQC

The course topics will include theoretical and practical aspects in:
- Genomes comparisons,
- Evolutionary analyses (orthologs, paralogs and ancestral genomes
inference),
- RNAseq and Next Generation Sequencing (including algorithms, methods
and sequence mapping tools, data analyses and applications).

The course programme will be centred on theoretical presentations
followed by practical sessions. Practical sessions in a Linux
environment will involve Unix shell and Perl scripting. Participants
are assumed to be familiar with this environment.

A series of lectures delivered by prominent scientists on recent hot
topics in genome (Viruses, Prokaryotes, Eukaryotes) studies will be
included in the programme and future research perspectives will be
highlighted.

The topics that will be included in the course programme are similar
to those included in previously organized courses:http://www.pasteur.fr/~tekaia/BGA_courses.html

The course is aimed at motivated Ph.D students and Post-Doctoral
Researchers in Academic Institutions, with background in Mathematics,
Statistics, Biology or Computer Science and who are involved in
Bioinformatics and Genomes studies.

Selection of participants will be based on their background, running
research projects and on expressed motivations.
Selected students will have free accommodation and meals and are
expected to contribute with 200 euros and to pay for their travel
expenses.
All participants (students and invited speakers) will stay in the same
hotel.

Detailed indications are available on the course web site: http://events.embo.org/14-comparative-genomics/index.html

Candidates are advised to complete carefully the application form,
together with an abstract of at least one of their running projects, a
"one-page CV" and a personal Identity Picture (Photo).

The application deadline is March 14, 2014.

The organizers:
Menelaos Manoussakis, Hellenic Pasteur Institute, Athens, Greece.
Evdokia Karagouni, Hellenic Pasteur Institute, Athens - Greece.
Evie Melanitou, Institut Pasteur Paris - France.
Fredj Tekaia ( Institut Pasteur Paris France)
URL: http://www.pasteur.fr/~tekaia/BGA_courses.html

Date: 5 – 17 May, 2014.
More at http://events.embo.org/14-comparative-genomics/index.html
will take place in the ,

What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a high throughput program dealing with lower quality data. Examples include low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data, retrieving low-copy nuclear genes from medium coverage (5x nucDNA) genome skimming.

License: GNU General Public License

Citation:

• Cai, Liming, Hongrui Zhang, and Charles C. Davis. 2022. PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome‐skimming data. Applications in Plant Sciences 10(3): 1–9. https://doi.org/10.1002/aps3.11475

Address of the bookmark: https://github.com/lmcai/PhyloHerb/

Reference

http://www.sciencedaily.com/releases/2013/12/131204132018.htm

1. Earth BioGenome Project (EBP) - A global effort to sequence and annotate roughly 1.5 million known eukaryotic species and create a comprehensive reference library of Earth's biodiversity.
2. Vertebrate Genomes Project (VGP) - Focuses on producing high-quality reference genomes for vertebrate species, providing a major foundation for the wider Tree of Life.
3. Darwin Tree of Life - A UK and Ireland initiative aiming to sequence approximately 70,000 species, creating a detailed genomic map of regional biodiversity.
4. African BioGenome Project (AfricaBP) - A pan-African initiative focused on sequencing Africa's biodiversity while strengthening genomics and bioinformatics capacity across the continent.
5. European Reference Genome Atlas (ERGA) - A European effort to generate high-quality reference genomes for Europe's biodiversity and connect national sequencing efforts.
6. Canada BioGenome Project - Building reference genomes for Canadian biodiversity, supporting conservation, research and the study of ecosystems.
7. California Conservation Genomics Project - Uses genomics to understand and protect California's biodiversity and help inform conservation decisions.
8. Bat1K - An ambitious global effort to sequence the genomes of all known bat species, helping scientists study their evolution, longevity, immunity and unique biology.
9. Bird 10,000 (B10K) - A global project aiming to create genome resources covering the world's bird diversity and reconstruct avian evolutionary history.
10. Global Invertebrate Genomics Alliance (GIGA) - Builds genomic resources for the enormous and genetically diverse world of invertebrates.
11. GenomeIndia - India's national human-genome initiative, designed to capture the country's extraordinary population diversity and create a reference resource for Indian genomics.
12. All of Us Research Program - A US national research program combining genomic information with health and lifestyle data at population scale.
13. 1+ Million Genomes / Genome of Europe - A European effort to enable secure, cross-border use of genomic and health data and develop genome-scale resources involving more than one million people.
14. Korea National Integrated Bio Big Data Project - South Korea's large-scale national effort combining genomic and health information from a very large population cohort.
15. Saudi Genome Program - A national genomics initiative focused on genetic diseases, population genomics and precision medicine in Saudi Arabia.
16. Australian Genomics / Genomics Health Futures Mission - Australia's growing investment in genomic medicine, rare disease research and population-scale health genomics.

.NET Bio

http://blogs.msdn.com/b/msr_er/archive/2011/10/18/microsoft-biology-foundation-evolves-into-new-toolkit-net-bio.aspx

A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists.

AMPHORA ("AutoMated Phylogenomic infeRence Application")

http://wolbachia.biology.virginia.edu/WuLab/Software.html

Metagenomics analysis software

Anduril

http://www.anduril.org/anduril/site/

Component-based workflow framework for data analysis

Armadillo workflow platform

Tool for designing and executing phylogenetic workflows

AutoDock

http://autodock.scripps.edu/

suite of automated docking tools

Biochemical Algorithms Library (BALL)

http://www.ball-project.org/

C++ library and framework for molecular modeling and visualization designed for rapid prototyping

Bio4j

http://bio4j.com/

Bio4j is a bioinformatics platform and graph based database built around most data available in UniProt KB(Swiss-Prot + TrEMBL), Gene Ontology (GO), UniRef (50,90,100), RefSeq, NCBI taxonomy, and Expasy Enzyme DB

Bioclipse

www.bioclipse.net

Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).

Bioconductor

http://www.bioconductor.org/

R (programming language) language toolkit

Bioinformatics Learning Tutorial (BLT)

http://sourceforge.net/projects/biotutorial/

Educational interactive tutorials and 3D animations for Replication, Transcription, and Translation

BioHaskell

http://biohaskell.org/

Haskell (programming language)

BioJava

http://biojava.org/wiki/Main_Page

Java (programming language)

BioMOBY

http://biomoby.org/

registry of web services

BioPerl

http://www.bioperl.org/wiki/Main_Page

Perl language toolkit

BioPHP

http://www.biophp.org/

PHP language toolkit

Biopython

http://biopython.org/wiki/Main_Page

Python language toolkit

BioRails

https://github.com/biorails

a data management system designed to support researchers in drug discovery

BioRuby

http://bioruby.org/

Ruby language toolkit

BioSmalltalk

https://code.google.com/p/biosmalltalk/

Smalltalk language toolkit

BioUno

http://www.biouno.org/

BioUno is a project that applies Continuous Integration tools and techniques in Bioinformatics. It uses Jenkins and its plug-in API to create biology workflows and manage computer clusters.

caCORE

ontologic representation environment

caArray

https://cabig-stage.nci.nih.gov/community/tools/caArray

ontologic representation environment

EMBOSS

http://emboss.sourceforge.net/

Suite of packages for sequencing, searching, etc.

Gaggle

https://www.gaggle.net/

A framework for interoperability between systems biology software

Galaxy

http://galaxyproject.org/

Scientific workflow and data integration system

GenePattern

http://www.broadinstitute.org/cancer/software/genepattern/

Scientific workflow system that provides access to more than 150 genomic analysis tools

GeWorkbench

http://wiki.c2b2.columbia.edu/workbench/index.php/Home

Genomic data integration platform

GMOD

http://www.gmod.org/wiki/Main_Page

Toolkit for addressing many common challenges at biological databases.

GeneProf

http://www.geneprof.org/GeneProf/

A web-based, bioinformatics software suite for the analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq.

GeneTalk

http://www.gene-talk.de/

Tool for filtering sequence variants in VCF files. Network for scientists and clinicians for expertise and knowledge exchange. Database of annotations aboute sequence variants with clinically relevant information.

GenGIS

http://kiwi.cs.dal.ca/GenGIS/Main_Page

Application that allows users to combine digital map data with information about biological sequences collected from the environment.

GenomeSpace

http://www.genomespace.org/

Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools

GENtle

http://directory.fsf.org/wiki/GENtle

An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files

Integrated Genome Browser

http://bioviz.org/igb/

Java-based desktop genome browser

Integrative Genomics Viewer (IGV)

http://www.broadinstitute.org/igv/

High-performance desktop tool for interactive visual exploration of diverse genomic data

IntAct

http://www.ebi.ac.uk/intact/

molecular interaction database

InterMine

http://intermine.github.io/intermine.org/

Extensive data warehouse system for the analysis and integration of biological datasets

Java Treeview

http://jtreeview.sourceforge.net/

microarray data viewer

LabKey Server

http://labkey.com/

platform for integrating, analyzing and sharing data

OpenClinica

https://www.openclinica.com/

software for capturing and managing data in clinical trials

PromKappa

http://xbioinformatics.wordpress.com/tag/promkappa/

PromKappa (Promoter analysis by Kappa) software program used for promoter pattern generation and promoter analysis.

MeV: Multi-Experiment Viewer

http://www.tm4.org/mev.html

a desktop application for the analysis, visualization and data-mining of large-scale genomic data

PathVisio

http://www.pathvisio.org/

a desktop software for drawing, analysis and visualization of biological pathways

REDCRAFT

software for determining tertiary protein structure given assigned Residual Dipolar Coupling data

SAM Tools

Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments

Staden Package

Sequence assembly, editing and analysis, primarily consisting of gap4, gap5 and spin.

STAMP

Software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results.

supraHex

An open-source R/Bioconductor package for omics data analysis using a supra-hexagonal map

Taverna workbench

Tool for designing and executing workflows

TGAC Browser

Genome Browser, visualisation solutions for big data in the genomic era

T-REX WebServer

Bioinformatics and phylogenetics webserver (NJ, PhyML, RAxML, MAFFT, MUSCLE, Newick viewer, Horizontal gene transfer detection, Reticulograms, Substitution models)

UGENE

integrated bioinformatics tools

Visomics

bioinformatics tools for omics data

Genome Analysis Toolkit 1.0 (GATK 1.0)

a software package to analyse next-generation resequencing data

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400