BOL: Related items

Scientist Bioinformatics Positions

Thu, 30 Jan 2020 06:53:40 -0600

Bioinformatics-Multi_Omics_Integration

https://www.researchgate.net/job/939073_Senior_Scientist_Bioinformatics-Multi_Omics_Integration

Senior_Scientist_Bioinformatics-Transcriptomics_Analysis

https://www.researchgate.net/job/939075_Senior_Scientist_Bioinformatics-Transcriptomics_Analysis-Belgium_France_Switzerland_The_Netherlands

Senior Scientist Bioinformatics - Network Analytics

https://www.researchgate.net/job/939070_Senior_Scientist_Bioinformatics-Network_Analytics_Belgium_France_Switzerland_the_Netherlands

Team Leader Bioinformatics Data Sciences - Mechelen, Belgium

https://www.researchgate.net/job/938787_Team_Leader_Bioinformatics_Data_Sciences-Mechelen_Belgium

10 NGS services companies around the globe !

BioStar — Sun, 22 Nov 2020 23:56:17 -0600

The global NGS services market is expected to reach USD 13.1 billion by 2025. Here are the top 10 NGS services companies to look for –

1. Illumina, Inc. (U.S.)

Illumina, Inc. was founded in 1998 and is headquartered at San Diego, U.S. Illumina, Inc. is one of the leading players in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets. The company offers products for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments. The company serves government laboratories, genomic research centers, academics institutions as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostics laboratories and consumer genomics companies. Illumina, Inc. has its geographic presence in North America, Europe, Latin America, Asia-pacific, and others.

2. QIAGEN N.V. (Netherlands)

QIAGEN N.V. was incorporated in 1986 and is headquartered at Venlo, The Netherlands. The Company is engaged in providing Sample to Insight solutions that transform biological samples into molecular insights. QIAGEN provides its workflow to customers in molecular diagnostics, assay technologies, bioservices and automation systems. The company’s genome services are suitable for custom/tailored projects that allow access to genomic sequence information. The Company market its products in more than 100 countries across the Americas, Europe, Asia, Australia, and the Middle-East &Africa through its subsidiaries and channel partners.

3. PerkinElmer, Inc. (U.S.)

PerkinElmer, Inc. was founded in 1947 and is headquartered in Waltham, Massachusetts, the U.S. PerkinElmer, Inc. offers its products & services and solutions for the diagnostics, food, environmental, industrial, life sciences research and laboratory services markets. The company offer comprehensive genetic testing solutions that help to provide insight into the complex nature of rare and inherited diseases. Some of the subsidiaries of the company are Caliper Life Sciences, Improvision, Viacell Inc., ViaCord LLC, among many others. The company has its facilities located in Europe (France, Germany, and Belgium), U.S. and Asia (China, India, and Japan).

4. Eurofins Scientific SE (Luxembourg)

Eurofins Scientific SE was founded in 1987 and is headquartered in Luxembourg, Europe. The company offers a portfolio of over 130,000 analytical methods and more than 150 million assays performed each year to establish the safety, identity, composition, authenticity, origin, traceability, and purity of biological substances and products, as well as carry out human diagnostic services. The company has its geographic presence across 39 countries in Europe, North and South America, and Asia-Pacific.

5. GATC Biotech AG (Germany)

GATC Biotech AG was founded in 1990 and is headquartered in Constance, Germany. The company provides DNA and RNA sequencing and bioservices solutions to academics and industrial areas. It also provides next generation sequencing services including genomes, targeted (re)-sequencing, human sample sequencing, transcriptomes, metagenomes, regulomes, pre-sequencing, NGS barcode labels, and next generation sequencing technologies; and bioservices services, including bioservices tools, pipelines and workflows, compute resources, data analysis reports, and case studies. GATC Biotech AG operates as a subsidiary of Eurofins Scientific SE. It offers its products through distributors in Italy, Japan, Portugal, Spain, and the Czech Republic.

6. Macrogen, Inc. (South Korea)

Macrogen, Inc. was founded in 1997 and is headquartered in Seoul, South Korea. Macrogen, Inc. provides next generation sequencing services such as whole genome, de novo, exome, targeted, transcriptomics, metagenome, and epigenome sequencing. The company also provides a variety of services such as oligo synthesis, database construction, genome research, and bioservices analysis system consulting services. Macrogen, Inc. provides genome research services in Korea and internationally.

7. Genotypic Technology Pvt. Ltd. (India)

Genotypic Technology Pvt. Ltd. was incorporated in 1998 and is headquartered in Bangalore, India. Genotypic Technology is the first Genomics service provider in India providing Microarray, Next Generation Sequencing (NGS), Bioservices and solutions to domestic/ international pharma, biotech companies and academia. The company provides its services for protocol optimization, probe designing, array layouts, project designing, and nucleic acid analysis to in-depth analysis. Genotypic Technology has its geographic presence in North America, Europe, Asia Pacific, Middle East & Africa, and Latin America.

8. GENEWIZ, Inc. (U.S.)

GENEWIZ, Inc. was founded in 1999 and is headquartered in South Plainfield, New Jersey, the U.S.; The company is a leading provider of research service in the field of Next Generation Sequencing, Sanger DNA sequencing, sequencing of bacteria and phage, gene synthesis, DNA cloning, genomics including mutation analysis, single nucleotide polymorphism, and bioservices. GENEWIZ, Inc. has its geographic presence in U.S., China, Germany, France, Japan, and the U.K.

9. Beijing Genomics Institute (China)

Beijing Genomics Institute (BGI) is the world’s largest genomics organization and non-profit research institution that was founded in 1999 and is headquartered in Shenzhen, China. The Company provides a wide range of commercial next generation sequencing services and genetic tests for medical institutions, agricultural and environmental applications. The Company operates all across the globe through its subsidiaries, namely, BGI China (Mainland), BGI Asia Pacific, BGI Americas (North and South America) and BGI Europe (Europe and Africa).

10. SciGenom Labs Pvt. Ltd (India)

SciGenom Labs Pvt. Ltd was founded in 2010 and is headquartered in Cochin, India with offices in Chennai & Hyderabad in India, and San Francisco in the U.S. It is a Genomics R&D services company that provides genomic sequencing and NGS services to life sciences and healthcare businesses globally as well as academic and government institutions in India.

Popular mentions – MedGenome (India), DNA Link, Inc. (South Korea), Otogenetics Corporation (U.S.), Novogene Corporation (China), LGC Limited (U.K.), CD Genomics (U.S.), SeqLL, LLC (U.S.)

SAU Bioinformatics/Plant Biotech JRF Vacancy

Fri, 12 Dec 2014 21:27:12 -0600

Applications are invited for the post of Junior Research Fellow (JRF) to work on SERB, DST funded project entitled “Genome wide analysis of ascorbate oxidase multi-gene family and elucidating its role in negative regulation of stress response in rice” under the supervision of Dr. Ananda Mustafiz, Faculty of Life Sciences and Biotechnology, South Asian University.

Qualification: Highly motivated M.Sc. (Bioinformatics/ Biotechnology/ Life Sciences/ Botany/ Agriculture) students are encouraged to apply. Prior experience in Bioinformatics/Plant tissue culture work is preferable. Preferences would be given to DBT/ CSIR / UGC NET qualified students.

Application Procedure: A detailed CV indicating name, date of birth, address, contact number, e-mail address, educational qualifications, NET qualified or not, research experiences if any, should be e-mailed to This email address is being protected from spambots. You need JavaScript enabled to view it. on or before 24th December 2014.

Important Note: Only short listed candidates will be called for interview at Akbar Bhawan, Chanakyapuri, New Delhi. No TA/DA will be paid for attending the interview. SAU Selection Committee reserves the rights to relax any of the qualifications in case the candidate is found otherwise well qualified. The above- mentioned post is temporary and will be initially offered for a period of one year, which can be extended to one more year.

Advertisement: www.sau.ac.in/recruitment/vacancy.html

Common steps for reads mapping !

BioStar — Thu, 09 Mar 2023 02:48:02 -0600

Mapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis. Here are some general steps to follow for mapping reads to a genome:

Choose a read mapper: There are many read mappers available, such as BWA, Bowtie, and HISAT2. Choose a mapper that is appropriate for your type of data and research question.
Index the reference genome: Before mapping reads, the reference genome needs to be indexed. This involves creating an index of the genome sequence that allows the mapper to quickly find matches to the reads. Most mappers have their own indexing tools.
Prepare the read data: The reads should be in a format that is compatible with the mapper. Most mappers accept FASTQ or BAM files. Depending on the quality of the data, it may need to be filtered or trimmed before mapping.
Run the mapper: The mapper is run with the command-line interface or using a graphical user interface. The specific command depends on the mapper being used, but typically involves specifying the input data, reference genome, and output file format.
Evaluate the mapping results: After the mapping is complete, the results should be evaluated. This includes assessing the quality of the mapping, such as the mapping rate, the number of mapped reads, and the mapping quality score.
Post-processing: Depending on the analysis being performed, post-processing of the mapped reads may be necessary. This can include filtering reads based on quality, removing duplicate reads, and calling variants.

Overall, mapping reads to a reference genome is a complex process that requires careful consideration of the type of data, the research question, and the specific mapper being used.

Walk in interview for Research Associate, Studentship and Traineeship at BIF, NEHU, Tura Campus

Thu, 18 Dec 2014 11:02:05 -0600

BIOINFORMATICS INFRASTRUCTURE FACILITY (BIF)
Department of RDAP
North-Eastern Hil University, Tura Campus
Tura-79402, Meghalaya

Walk in interview for Research Associate, Studentship and Traineeship at BIF

Applications are invited for the Post of Research Associate, Traineeship and Studentship in the DBT sponsored Bioinformatics Infrastructure Facility (BIF) at the Bioinformatics Centre, Department of RDAP, North-Eastern Hil University, Tura Campus, Tura-79402, Meghalaya. The Posts are purely temporary and terminable at any time without prior notice or assigning any reason thereof. The person engaged, shall not be entailed for any claim implicit or explicit for permanent absorption in the University.

Research Associate- 01

Essential Qualification: M.Sc. in Bioinformatics/Biotechnology from a recognized University/ institute.

Desirable: PhD or Pursuing PhD in the relevant subject(s) or equivalent published work in reputed peer reviewed journals or Advance PG diploma in Bioinformatics courses.

Duties: Creation of database, web designing, maintenance of internet, training of students in Bioinformatics, handling and knowledge of Bioinformatics software tools and technique, conducting Bioinformatics based research and other day to day laboratory work, writing report and scientific papers.

Pay:Rs. 2,00/- + Admissible 10% HRA per month

Age: Below 35 years

Traineeship- 02

Students who have completed Masters Degree in Bioinformatics/Biotechnology or any branch of Life Sciences/Agricultural Sciences/Computer Science to cary out a project work in Bioinformatics.

Desirable: Prior Knowledge of programming languages such as C, JAVA, MySQL is preferable.

Stipend: Rs. 800/- p.m. fixed. Purely temporary for a period of six months.

Studentship: 02

Students pursuing postgraduate degree in Bioinformatics/biotechnology/Agricultural Sciences or any branch of Life Science

Desirable: Prior knowledge of bioinformatics/ programming language is preferable.

Stipend: 800/- p.m. fixed. Purely temporary for a period of six months.

Candidates must send the detailed Biodata via mail/post and bring al the relevant documents in original and one set of attested photocopies of the same at the time of interview. No TA/DA will be paid for attending the interview and candidates have to make their own arrangements.

Last date for receiving application by mail or by post: 16.02.2014

Contact Information:
Dr.B.K. Mishra
Cordinator BIF,
RDAP Department, NEHU, Tura Campus
Phone: 91-03651-23107
Fax: 91-03651-23953
E-mail: drbkm1972@yaho.co.in, birendramishra14@gmail.com

Advertisement: http://www.nehu.ac.in/Advertisements/BIF_TuraAdtvPV_171214.pdf

Nanopolis: polish a genome assembly

Rahul Nayak — Thu, 26 Jul 2018 04:51:28 -0500

Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

Quickstart

http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

Algorithms

http://simpsonlab.github.io/2017/06/30/nanopolish-v0.7.0/

Address of the bookmark: https://github.com/jts/nanopolish

Assistant Professor at GAUHATI UNIVERSITY, GUWAHATI

Tue, 16 Dec 2014 01:15:30 -0600

Advt. No.T/2014/4

Ref. No. GU/Estt/T/308(VI)/2014/6451-61

Applications are invited from the Indian citizens for five (5) teaching posts of Assistant Professor (Contractual) under various departments of Gauhati University. Details of the advertisement, other terms and conditions and the application forms are available in the University website www.gauhati.ac.in

Asstt. Professor (Contractual)

2. M.Sc. Microbiology Course in Botany

3 1.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biochemistry (1 post). (Preference will be given to candidates having experience in Biochemistry).

2.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Bioinformatics).

3.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Microbial Genetics).

As per UGC norms

Pay Band & Academic Grade Pay : (Consolidated pay) : Rs. 21,600/- per month

Application Form : Prescribe application form may download from the G.U. website www.gauhati.ac.in

Last date of receipt of filled-in application is 08.01.2015.

Advertisement: www.gauhati.ac.in/openfile.php?file=Notice1258.pdf

Long read assembly workshop !

Rahul Nayak — Thu, 04 Oct 2018 17:23:18 -0500

This is a tutorial for a workshop on long-read (PacBio) genome assembly.

It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data.

Please comment if you know any other long read addembly tutorial.

Address of the bookmark: http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/

China University of Macau PhD Position 2015 in Bioinformatics, Computer Science

Mon, 22 Dec 2014 00:12:49 -0600

The Computational Biology and Bioinformatics Group at the University of Macau is inviting applications for PhD Position. Applicants will work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems. The duration of this PhD position is 2-3 years, starting in August 2015. Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month). The applications should be submitted before March 2015.

Study Subject(s): PhD position is award in the field of Bioinformatics/Computer Science.
Course Level: Position is available for pursuing PhD degree level at the University of Macau.
Scholarship Provider: University of Macau
Scholarship can be taken at: China

Eligibility: The ideal candidate would be a master degree holder in Bioinformatics or related disciplines with knowledge in Medical sciences or Life sciences (with GPA of at least 3.0 on a 4-point scale or equivalent) . Knowledge in programming (C and C++) and Linux scripting are necessary; experience in molecular docking, molecular dynamics simulations or molecular modeling is an advantage. The candidate should be fluent in spoken and written English; preference will be given to applicants with good publication records in relevant areas.

Scholarship Open for International Students: Researchers from China can apply for this PhD position.

Scholarship Description:

The Computational Biology and Bioinformatics Group at the University of Macau is looking for a motivated PhD student in Bioinformatics or Computer Science to work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems.

Number of award(s): There is only one PhD position available.

Duration of award(s): The duration of this PhD position is 2-3 years.

What does it cover? Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month).

Selection Criteria: Not Known

Notification: Not Known

How to Apply: Send your current CV, your academic transcripts, a letter of motivation and research interests, two letters of recommendations from academic faculty to Dr. Shirley Siu at shirleysiu[at]umac.mo before March 2015.

Scholarship Application Deadline: The applications should be submitted before March 2015.

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

BioJoker — Tue, 02 Apr 2019 21:54:55 -0500

Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye