BOL: Related items

Senior Bioinformatics Scientist at Elucidata

Tue, 27 Nov 2018 04:05:57 -0600

Key Responsibilities
- Process and analyse metabolomic, transcriptional, genomics, proteomics
and any other kind of biological data.
- Interpret the data in the context of relevant biological literature to generate
actionable insights.
- Communicate the findings from data and literature to biologists and use the
biological insights to derive next steps/analyses.
- Communicate work through blogs, meet-ups, research papers, posters, etc.
- Identify, troubleshoot, and implement improvements to existing pipelines
and algorithms.
- Identify and implement new tools and pipelines to use for different types of
biological data.
- Work in a multi-disciplinary team with biologists, data scientists and data
analysts.
- Help with any other requirements (from database design to generating
prototypes for the product team).

Requirements
- 3-5 years of relevant bioinformatics experience such as public data mining,
processing, analysing and visualising omics data, etc.
- Ph.D., Masters or Bachelors in Bioinformatics, Biotechnology,
Computational Biology, or related field.
- Understanding of molecular biology and biochemistry.
- Comfort and experience with biological research and data.
- Proficient in a programming language used for bioinformatics such as R or
python.
- Excellent communication skills.
- Ability to summarise and simplify complex analyses for a non-technical
audience.
- Strong analytical skills, curiosity and a knack to solve difficult problems.
- Work well in multi-disciplinary teams with people of vastly different
backgrounds.
- Demonstrated success in collaboration and independent work.

More at https://angel.co/elucidata/jobs/460104-senior-bioinformatics-scientist

GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.

Jit — Fri, 05 Feb 2021 21:22:24 -0600

GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.

https://www.biorxiv.org/content/biorxiv/early/2021/02/01/2021.01.29.428779.full.pdf

Address of the bookmark: https://github.com/nadegeguiglielmoni/GraphUnzip

BINC Exam merged with DBT- BET JRF Exam

Jit — Thu, 21 Feb 2019 09:37:36 -0600

Another breaking news received has been received from the Department of biotechnology – DBT. As per a notification released by DBT, Bioinformatics National Certification (BINC) Exam conducted once per year by DBT has been now merged with DBT- BET JRF Exam.

Also, Bioinformatics Industrial Training Program (BIITP) is merged with the HRD Biotechnology Industrial Training Programme (BITP).

While this comes as a surprise for a lot of participants. We believe this is a good attempt to unify and create a national benchmark for talent. And we appreciate this endeavor from Department of biotechnology.

However, such last-minute announcements can create confusion. Thus candidates are advised to go through the complete notification DBT-BET JRF 2019 via the link below.If you have any kind of doubts, you must contact DBT JRF or Biotecnika for any kind of help & assistance.

Attention:-Bioinformatics Programs (BINC and BIITP)

1. Bioinformatics National Certification (BINC) has been merged with DBT-Junior
Research Fellow (BET Exam)

2. Bioinformatics Industrial Training Program (BIITP) is merged with HRDBiotechnology Industrial Training Programme (BITP).

Students of Bioinformatics, who are interested to apply for Fellowship or Industrial
Training may keep track of the advertisement of DBT-JRF (BET Exam) and BITP
of DBT.

More at http://www.bcil.nic.in/files/Attention_Bioinformatics_Programs_(BINC_and_BIITP).pdf

LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data

Neel — Wed, 23 Jun 2021 07:54:53 -0500

LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

https://academic.oup.com/ve/article/7/1/veab042/6248116

Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116

Bioinformatics web development course

Jit — Wed, 06 Nov 2019 20:42:48 -0600

This web development course, targeted at Biology and Bioinformatics students, aims at teaching from scratch all the skills needed to setup a fully working Linux web server and to develop and deploy web applications for Bioinformatics.

No previous programming knowledge is assumed. By following this tutorial you will learn the fundamental concepts of programming by using scripting languages: variables, types, arrays, cycles, conditional statements, functions, objects, regular expressions, files reading and manipulation et-cetera.

Address of the bookmark: http://www.cellbiol.com/bioinformatics_web_development/introduction/

Spades tutorial PDF

Abhimanyu Singh — Tue, 01 Feb 2022 04:56:43 -0600

SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole-genome sequencing and metagenomic datasets.

The Clark Lab

Fri, 07 Feb 2020 13:57:24 -0600

Study the process of Adaptive Evolution, during which species adopt novel traits to overcome challenges. We retrace the evolutionary histories of genomic elements to determine the changes underlying adaptation and to discover previously unknown genetic networks. These discoveries have already led to advances in human health, species conservation, and molecular biology.

More at http://clark.genetics.utah.edu/

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

LEGE — Wed, 08 May 2024 07:32:45 -0500

ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953547/

Address of the bookmark: https://github.com/dengzac/contig-extender

MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction

Abhi — Mon, 08 Apr 2024 06:19:52 -0500

MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Address of the bookmark: https://github.com/Argonum-Clever2/mike

Bioinformatics Scientist/Research Software Engineer at University of Dundee Dundee, United Kingdom

Wed, 26 Aug 2020 10:31:25 -0500

We are recruiting for an exceptional individual to join us as a computational scientist, bioinformatician, or (research) software engineer with an interest in interactive data analysis platforms for biology and medicine within our Jalview (www.jalview.org) research software engineering team.

More at https://www.jobs.dundee.ac.uk/fe/tpl_uod01.asp?s=4A515F4E5A565B1A&jobid=104342,2382988671&key=147934117&c=99413415238921&pagestamp=sesxbbuyifokdsfygf

Last date: 30th August 2020

Informal enquiries about this position may be made to Prof. Geoff Barton (gjbarton@dundee.ac.uk) or Dr Jim Procter (jprocter@dundee.ac.uk). To find out more about Jalview research software engineering team please visit www.jalview.org and www.compbio.dundee.ac.uk