BOL: Related items

ICGEB Bioinformatics Job

Sat, 23 Jan 2021 21:01:55 -0600

The following vacancies are available in the various ongoing bioinformatics projects at.
Translational Bioinformatics Group (https://www.icgeb.org/dinesh-gupta/), ICGEB, New Delhi, India. Shortlisted candidates will be welcomed for an on-line interview at ICGEB. Only the chosen applicants will be informed individually. Preference will be given to the applicants with experience related to Bioinformatics as well as Computational area.

Interested applicants must submit their complete, updated Curriculum Vitae, mentioning details of two references as well as various other details at – http://14.139.62.220/survey/index.php/2021/01/21/icgeb-dbt-project-vacancy/

The last date of submission of applications is January 31st, 2021.

Research Associate : PhD. Degree in Computational Biology/Bioinformatics.

Consolidated Salary: 58280/- pm (including HRA).

More at https://www.icgeb.org/project-positions-translational-bioinformatics-group/ and https://www.icgeb.org/category/vacancies/

Lecturer in Evolutionary Biology (Bioinformatics) at DEPARTMENT of ZOOLOGY | TE TARI MĀTAI KARAREHE DIVISION of SCIENCES | TE ROHE A AHIKAROA

Tue, 23 Feb 2021 02:05:15 -0600

DEPARTMENT of ZOOLOGY | TE TARI MĀTAI KARAREHE
DIVISION of SCIENCES | TE ROHE A AHIKAROA

Applications are invited for the position of Lecturer in Evolutionary Biology (Bioinformatics).

We are seeking a person with a relevant doctorate, and demonstrated potential to develop as an outstanding researcher and teacher in evolutionary bioinformatics in the Department of Zoology. The position affords an exciting opportunity for an emerging scholar to research and teach in a vibrant and diverse Department. The successful candidate will develop a transformative and collaborative research program, supporting the university's commitment to excellence in research.

Your skills and experience

A PhD with a background in analysis of high-throughput sequencing data and evolutionary biology.
Knowledge of and familiarity with a range of bioinformatics skills, concepts, and practices as they relate to the biology of animals, including genomic, transcriptomic and metabarcoding data analyses.
A strong interest, and experience, in research and teaching of bioinformatics and evolutionary genomics.
An ability to contribute to teaching and learning environments that support engagement of students and staff with bioinformatics and genomics.
Be committed to and or have established connections or track record of working with national and local bioinformaticians.
Be committed to being a productive collaborator with a track record of working collegially.
Further details

This is a confirmation-path (tenure track) position at the level of Lecturer. The successful candidate is expected to take up duties by 1 July 2021.

To see a full job description and to apply online go to: https://otago.taleo.net/careersection/2/jobdetail.ftl?job=2100342

Human Genome Meeting 2014, Geneva, Switzerland

Fri, 20 Sep 2013 12:36:44 -0500

The spectacular advances of the last few years resulted in the rapid analysis of the genome sequence of each individual. The biomedical world is now faced with the enormous challenges of assigning pathogenicity to each genomic variant, the functional analysis of the genome of each individual, and the accurate and detailed phenotypic characterization. Advances in these challenges are likely to fundamentally change the medical practice in a global scale.

This 2014 HUGO Meeting in Geneva will be a Forum for discussions on innovative approaches, and proposals to tackle the anticipated challenges.

Time : 27 April 2014 - 30 April 2014

For enquiries, please email hugo2014@mci-group.com or visit www.hugo-international.org

More at http://www.hgm2014-geneva.org/

Job offer for a postdoctoral researcher in genomics / bioinformatics (2 years)

Fri, 22 Oct 2021 04:44:33 -0500

Ongoing research in the group of Karine Van Doninck involves topics at the core of
evolutionary biology, including the evolution of sex, genome maintenance,
recombination and extreme stress resistance on different eukaryotic systems,
including rotifers, amoeba and Corbicula clams. We are employing different tools
(including experimental ecology, population genetics, phylogeny, comparative
genomics, transcriptomics, bioinformatics, molecular and cellular biology) to study
evolutionary processes at the level of populations, both experimental and natural, and
genomes.

Offer
We offer a full-time contract for two years. The contract starts between October 2021
and December 2021. The position involves no or extremely light teaching load, if the
candidate is interested. Salaries are competitive at the European level. The recruited
person will benefit from the Belgian social insurance scheme (health care, etc.) without
additional expenses.

Profile
Applicants are expected to show outstanding commitment to research and must have
obtained a PhD by the start of the position. A strong expertise in genomics is required.
More specifically, solid competences in bioinformatics (e.g. scripting pipelines) and in
genome evolution are needed. Knowledge or interest regarding recombination,
metazoan evolution, phylogenomics and population genomics is an added-value.

Application
Applications should be submitted via email to karine.van.doninck@ulb.be. The
application package should contain the following documents:
- A curriculum vitae with the complete list of publications
- A cover letter mentioning why the candidate is interested in the position
- Minimum 2 recommendation letters
Interviews: Interviews will be conducted with the selected candidates. Selected
candidates could also be invited to give a seminar to MBE ULB.
For any additional information, please contact karine.van.doninck@ulb.be

PhD positions on integrative omics and phylogenomics

Wed, 19 Oct 2022 05:11:11 -0500

Would you like to participate in an exciting interdisciplinary research project to discover the hidden chemistry of plants and its evolution using computational omics approaches? Do you enjoy collaboration and teamwork while being at the cutting edge of scientific progress? We are looking for two PhD candidates with complementary skills to pioneer new technologies to analyze, explore and leverage the diversity of plant chemistry hidden in plant genomes.

Plants represent an untapped resource of natural bioactive compounds that significantly contribute to plant resilience to pathogens, herbivores, and abiotic stresses, and may be applied for medicine or crop protection. In this project, you will design and/or apply innovative omics integration strategies for genomics, transcriptomics, and metabolomics data, to discover plant specialized metabolite biosynthetic pathways and study their evolution. You will work together with the other PhD candidate in this project, which will entail a combination of algorithm development, greenhouse experiments, integrative omics analysis, and evolutionary genomics. Extensive local and international collaboration is foreseen, including possibilities for a foreign research visit as part of your PhD project.

The research is embedded within the chairs of Bioinformatics and Biosystematics. The projects will be (co-)supervised by Dr. Marnix Medema, Dr. Justin van der Hooft, Dr. Klaas Bouwmeester and Prof. Dr. Eric Schranz.

We ask

We are looking for two enthusiastic and complementary team players with all or a subset of the following skills:

a solid academic record (MSc) in bioinformatics, biology, or biotechnology
experience in computational omics analysis and proficiency in programming (in, e.g., Python)
at least basic to intermediate statistical and mathematical skills
demonstrable experience in working with next-generation sequencing data or with greenhouse experiments with plants
affinity with plant science, metabolism and/or biosynthetic pathways
you meet all the entry requirements of the WUR PhD programme.
More information

For more information about this position, please contact Marnix Medema, Associate Professor Bioinformatics, by email (marnix.medema@wur.nl).
For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.

Bioinformatics Chat !

BioStar — Mon, 13 Mar 2023 13:20:27 -0500

The bioinformatics chat is a podcast about computational biology, bioinformatics, and next generation sequencing.

The bioinformatics chat is produced by Roman Cheplyaka and hosted by Roman and Jacob Schreiber.

Address of the bookmark: https://bioinformatics.chat/

National Training on Bioinformatics Computational Tools for Microbial Research Nov 19 to 30, 2013

Fri, 27 Sep 2013 10:49:34 -0500

Agricultural research in modern scientific arena is being represented by proper integration among various research fields of biological, chemical and physical sciences, because this field encompasses many more complexities of biology in nature. In the era of fast accumulating biological data coming out from the research on many crop plants, live stocks and microbes and the impact of changing climate, habitat and other interrelations on these biological entities, bioinformatics has come forward across the globe to solve the problems of analysis, prediction, storage, management, pattern recognition, submission, retrieval and storage of the data to find out a fruitful outcome. This area is becoming increasingly important in the context of systems biology approach where a holistic approach is required to understand the biology and chemistry of the biological entities and their behavior during environmental interactions to resolve the harmful impact of biotic or abiotic causes on crop plants, animals, fishes, livestock sector, beneficial insects as well as microbes. The National Training program on ‘Computational Tools for Microbial Research” is an initiative for the capacity building of NARS scientists/researchers in this most emerging area and fast developing area of i.e. agricultural bioinformatics.

Contact The Director, National Bureau of Agriculturally Important Microorganisms, Kusmaur, Maunath Bhanjan-275101 (U.P.); Phone: 0547-2530080, Fax: 0547-2530358, e mail: nbaimicar@gmail.com; website: www.nbaim.org.in OR

Dr. Dhananjaya P. Singh, Senior Scientist & CCPI, NABG project, NBAIM, Maunath Bhanjan, 275101; Mob.- 09415291703; e mail - dpsfarm@rediffmail.com, nabg.nbaim@gmail.com

More at http://www.nbaim.org.in/Announc.aspx?cd=36

Important Bioinformatics Tools !

BioStar — Tue, 30 Jul 2024 05:03:29 -0500

1. Ktrim: An extra-fast, accurate adapter trimmer for sequencing data. It processes FASTQ files from multiple lanes with minimal mismatching and over-trimming of adapters.

2. BWA MEM: A reliable alignment tool (particularly for mapping ALT contigs and HLA genes, which are not fully addressed in BWA-MEM2).

3. Sambamba markdup: Quickly marks or removes duplicate reads using Picard's criteria.

4. ichorCNA: Estimates the tumor DNA fraction in cell-free DNA from ultra-low-pass whole genome sequencing (0.1x coverage) based on copy number alterations (CNA).

5. Fragle: A deep learning method for quantifying ctDNA levels from cell-free DNA fragmentomic profiles. It detects TF as low as ~1% ctDNA and works with targeted genomic panel sequencing data.

6. AlfredQC: A quality control tool for high-throughput sequencing data. It assesses metrics like read quality scores, GC content, and duplication rates, visualized through detailed plots and summary statistics.

7. Mosdepth: A fast tool for calculating sequencing coverage depth, offering a quicker alternative to samtools/sambamba depth by processing BAM and CRAM files.

8. Bedtools: A versatile toolkit for genomics, enabling operations like intersect, merge, count, and shuffle on genomic intervals across formats such as BAM, BED, GFF/GTF, and VCF.

9. Datamash: A command-line tool for basic numeric, textual, and statistical operations on input data streams. It supports operations such as grouping, sorting, transposing, and performing arithmetic calculations on tabular data.

10. gwf.app: A pragmatic alternative to Snakemake. Developed at Aarhus University, this flexible, generic workflow tool builds and runs large scientific workflows.

EMBL Postdoc position in Bacterial Gene Gain Loss

Thu, 20 Aug 2015 14:09:21 -0500

A post-doctoral fellowship is available in the research groups of Nick Goldman (EBI) and John Welch (Genetics Department, Cambridge University) under the EMBL-EBI / Cambridge Computational Biomedical Postdoctoral Fellowship scheme.

The project is on bacterial gene gain and loss and emerging pathogenicity, and is described in full here: https://www.ebi.ac.uk/research/postdocs/ebpods/projects/goldman-welch-2015 . The EMBL-EBI / Cambridge Computational Biomedical Postdoctoral (“EBPOD”)

The closing date for applications is 3 September 2015. Nick Goldman EMBL-European Bioinformatics Institute Nick Goldman

More at https://www.ebi.ac.uk/research/postdocs/ebpods/projects/goldman-welch-2015

Bioinformatics Lecture Notes

LEGE — Tue, 01 Oct 2024 03:45:26 -0500

Study Resources for

ECM3413 - Bioinformatics

Contents

General Information

Lecture Slides

Past Exam Paper

Continuous Assessments

	This module runs in Semester 2.
	It is taught by Dr Ed Keedwell (Module Coordinator)
	Module Descriptor: ECM3413
	Lecture Times: Tuesday 5pm, 171\| Thursday, 171
	Workshop Times: Wednesday 11am Blue Room (Weeks 29,33 &40)
	Assessment: 2 CAs each worth 15% \| 1 Examination worth 70%

	PPT\|PDF\| Lecture 1 - Introduction to Bioinformatics (& Biology)
	PPT\|PDF\| Lecture 2 - Genome Sequences: from fragments to sequences
	PPT\|PDF\| Lecture 3 - Sequence Alignment 1
	PPT\|PDF\| Lecture 4 - Global Pairwise Sequence Alignment
	PPT\|PDF\| Lecture 5 - Local Pairwise Sequence Alignment (Smith-Waterman & BLAST)
	DOC\| Workshop 1 - Using BLAST and other Bioinformatics Databases
	PPT\|PDF\| Lecture 6 - Multiple Sequence Alignment
	PPT\|PDF\| Lecture 7 - BLAST (in more detail) & FASTA
	PPT\|PDF\| Lecture 8 - Sequence Alignment Conclusion & Other Sequence Analyses
	PPT\|PDF\| Lecture 9 - Markov Chains and Intro to Hidden Markov Models
	PPT\|PDF\| Lecture 10 - Hidden Markov Models
	PPT\|PDF\| Lecture 11 - Classification in Bioinformatics
	DOC\|Workshop 2 - Using See5
	Workshop Data - Part 1 - adult.names \| adult.data \| adult.test, Part 3 - wdbc.names\| wdbc.data
	PPT\|PDF\| Lecture 12 - Gene Expression Data
	PPT\|PDF\| Lecture 13 - Decision Trees and Gene Expression Classification
	PPT\|PDF\| Lecture 14 - Other Methods for Gene Expression Classification
	PPT\|PDF\| Lecture 15 - Gene Regulation
	PPT\|PDF\| Lecture 16 - Neural Networks in Gene Expression Analysis
	PPT\|PDF\| Lecture 17 - Genome Analysis
	PPT\|PDF\| Lecture 18 - Conclusion/Revision Lecture

	PDF\| CA1 - Manual Sequence Alignment
	PDF\|Promoter.names\|Promoter.data\|ML.names\|ML.data\| CA2 - Data Mining in Bioinformatics

	Lesk, A.M., (2002) Introduction to Bioinformatics, Oxford University Press
	Higgs, P.G., (2005) Bioinformatics and Molecular Evolution, Blackwell Publishing

	Baldi, P., Brunak, S., (2001) Bioinformatics: The Machine Learning Approach, MIT Press
	Keedwell, E., Narayanan, A., (2005) Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics Problems, Wiley