BOL: Related items

Two postdoc positions to study multiscale genome evolution and cephalopod gene regulation (University of Vienna, Austria)

Thu, 17 Dec 2020 11:45:16 -0600

Vienna Biocenter are seeking two postdoctoral researchers to join our team and work on the ERC funded project "METASCALE: Modes of genome evolution during major metazoan transitions". The task of both positions will be to study co-evolutionary trends within animal genomes and their association with the emergence of new gene regulation. Our group employs methods of comparative and regulatory genomics to study the regulatory impact of transitions in animal genome architecture. More recently, we have identified a major genome reorganization in the "smart" coleoid cephalopod molluscs (squid, octopus, cuttlefish) that, together with other genomic changes, potentially comprises a unique path or mode of genome evolution among animals. We are thus interested in quantifying these modes of genome evolution across all available animal genomes and to test whether their shifts are associated with the emergence of novel regulation (e.g., in cephalopods). One of our main model species is the Hawaiian bobtail squid species Euprymna scolopes. The tasks of the two candidates will be complimentary and highly collaborative with one position focusing on comparative genomics analyses across all metazoans and the other position on regulatory genomics in the squid. A solid background in in bioinformatics and comparative genomics is highly desired for the first position, whereas the second position will benefit from experience in molecular and regulatory genomics methods such as HiC, ATAC-seq, RNA-seq or single cell transcriptomics.

The postdocs will join an international group and network of researchers at the University of Vienna studying a diverse range of species and questions in molecular evolution, development, morphology and genomics. Our group is also part of the large evolVienna network of more than 50 evolutionary biology labs in Vienna, across several universities and research institutes. Our Faculty will be relocating to a new campus at the Vienna Biocenter in summer 2021 (https://biologiezentrum.univie.ac.at/en/). Vienna is a vibrant historic European capital with a high QOL. Information about postdoctoral salaries in Austria can be found on this webpage: https://www.fwf.ac.at/en/research-funding/personnel-costs/

Earliest start date will be after July 2021. Initial term of employment is for two years with the possibility of extension. Remote working, at least initially, is a possibility.

Requirements:
- PhD degree or equivalent by the start date
- Publishing record in peer-reviewed journals or evidence thereof
- At least 2 letters of support

Applications including a letter of motivation should be submitted via the Job Center to the University of Vienna (https://personalwesen.univie.ac.at/en/jobs-recruiting/job-center/,
job reference number 11615).

Application deadline: January 15th 2021.
Application link: https://univis.univie.ac.at/ebewerbung

dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements

Rahul Nayak — Sat, 02 Dec 2017 18:25:44 -0600

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

dnaPipeTE is developped by Clément Goubert, Laurent Modolo and the TREEP team of the LBBE: http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en
You can find the original publication in GBE here: https://academic.oup.com/gbe/article/7/4/1192/533768

output examples of quantification and TE landscape (relative age) produced by dnaPipeTE

Address of the bookmark: https://github.com/clemgoub/dnaPipeTE

Bioinformatics in Africa:- Part 1

BioStar — Sun, 31 Jan 2021 09:04:01 -0600

The Institut Pasteur de Côte d’Ivoire was created by the N°72511 law of July 27th, 1972 under the Presidency of his Excellency Felix Houphouët Boigny and Professor Jacques Monod, then Leading of the Pasteur institute of Paris.

The objectives of the Bioinformatics pole are:

• Encourage the access to innovations in research and the best exploitation of research data management.

• Develop the critical spirit of the researchers around their axis of research.

• Bring an active help to the improvement of the public health while having for constant worries to feed it by research and the innovation.

• Start training researchers to use bioinformatics as an indispensable tool to research.

• Encourage interdisciplinary creating a network of scientific information available to the researchers of the institute and partners

Longterm training activities:

• To integrate the bioinformatics in the training programs of academic scientists.

• Development of West Africa Centre training in bioinformatics and genome data analysis.

Shortterm training activities:

The IPCI will organize in the month of May 2007 a yearly regional course of initiation and using genome data analysis with the participation of the Centre Biotechnologique de Sfax, Tunisia (Pr Ahmed Rebaï, Department of bioinformatics).

More at https://www.pasteur.ci/

Bioinformatics in Africa: Part5 - Nigeria

BioStar — Sat, 06 Feb 2021 21:13:47 -0600

Covenant University (CU)Ota:
Covenant University (with her enriching and growing stateoftheart laboratories in the area of science and technology, arts, business and social sciences) is presently the Best University in Nigeria (Private University category), based on the recent overall rating just concluded by the Nigeria University Commission (NUC). Recently, Covenant University has initiated the establishment of a Centre for Applied Biotech, BioInformatics and Microbiology (CBBM) to be situated at the University. The institute has been designed to be a PublicPrivate Partnership for a productive synergy b/w Academia, Industry and Government. The whole concept is still evolving and more details will be release soon. As regards CBBM, a dedicated computing lab is in plan, but even our computing capacity is presently enormous. In the department of Computer and Information Sciences, we have more than 250 Pentium 4 PCs set aside for teaching and research purposes. Furthermore, we have several moderate speed PCs at the Postgraduate research lab and our engineering departments and units. Our wet lab facilities is presently minimal (basic for teaching), the Centre requirement as it touches the wetlaboratories is also set to upgrade this to basic tools expected at an international centre of learning.

University of Ibadan (UIB)Ibadan:
There has been significant increase in the number of bioinformatics activities in Nigeria (and West Africa) since 2003 when the program was initiated by the West African Biotechnology Workshops Series (WABWS, http://www.wabw.org) at the University of Ibadan, Nigeria (in collaboration with the South African National Bioinformatics Institute (SANBI, http:/www.sanbi.ac.za). Workshops that were open to scientists from all African countries have seen a very high number of applications from scientists based in West Africa. The encouraging desire to acquire cuttingedge skills to computational process data and extract useful knowledge from genome projects led to the interest of the West African Biotechnology Workshops (WABW) to develop an agenda to address the bioinformatics skills gap among scientists in West Africa. An increased commitment from agencies like NEPAD would be required in the provision of infrastructure to establish and sustain regional and national networks.

University of Ilorin (UIL)Ilorin:
The University of Ilorin was established in 1976 by the Federal Government of Nigeria. Bioinformatics activities started at the University in February 2003 with the establishment of the West African Bioinformatics Research Initiative (WABRI). However, progress has been rather slow due to inadequate funding. We are mainly engaged in Bioinformatics training at the introductory level and proteomics studies on various species of malaria parasites. Recently, we became interested in comparative genome analysis of various species of Plasmodium and the comparison of chloroquine sensitive and chloroquine resistant strains of Plasmodium falciparum. Other activities and areas of interest can be seen on our website, http://www.wabri.org, although not all our proposed interests have been fully implemented due to our level of funding.

Training:
The University of Ilorin has introduced M.Sc. and Ph.D. programmes in Computer Science (with options in Bioinformatics). The programme is based in the Department of Computer Science and emphasis is on the development of algorithms to solve problems in bioinformatics. The Covenant University offers M.Sc. and Ph.D in Computer Science with option in Bioinformatics (Computational Biology). Furthermore, through affiliated departments, the CBBM is been design to award Diploma and Degree certificates in Biotechnology.

Web sites and links: http://www.covenantuniversity.com http://www.run.edu.ng http://www.uniben.edu http://www.wabri.org http://www.wabw.org http://www.unilorin.edu.ng http://www.wabri.org http://www.asopah.org

RA Bioinformatics at Sir Ganga Ram Hospital, New Delhi

Sun, 14 Mar 2021 10:40:18 -0500

Opportunities available at Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi.

1) Senior Research Fellow under ICMR Project: M.Sc. (Life Sciences) with 2 years of experience (preferable in the field of Bioinformatics) or MBBS Degree.

2) Research Associate under ICMR Project: . Ph.D.(Life Science/Biotechnology/Bioinformatics) or equivalent degree or having 3 years of research, teaching and design and development experience after M.Tech with at least one research paper in science Citation Indexed (SCI) Journal.
Work experience in the area of Human genomics/Next Generation Sequencing data analysis/Big data genomics would be preferred.
Application link:

https://sgrh.com/joblist

Post Code: 2023, 2024

Nigerian Bioinformatics and Genomics Network (NBGN)

Tue, 31 Aug 2021 08:29:40 -0500

This is to announce the second official conference of the Nigerian Bioinformatics and Genomics Network (NBGN). October 11-13,2021 at Landmark University, Omu-Aran, Kwara State and Zoom ( conference link to be announced soon

#NBGN21

www.nbgn21conference.com

EUKulele: Taxonomic annotation of the unsung eukaryotic microbes

Shruti Paniwala — Sat, 26 Dec 2020 12:10:17 -0600

EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting the taxonomic completeness of each sample.

Address of the bookmark: https://github.com/AlexanderLabWHOI/EUKulele

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.

Linux Cheat Sheet

Jitendra Narayan — Tue, 09 Jul 2013 17:30:04 -0500

In an attempt to find a good Linux reference for bioinformatician and BOL readers, I was unsuccessful at finding a decent one on the Internet. So, we decided to make a cheat sheet for biological programmers.

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/